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Sticky Revision:

Revision 26379  Directory Listing
Modified Wed Sep 20 13:24:41 2017 UTC (5 days, 1 hour ago) by jcfr
ENH: Update VTKv7 backporting ClickAndDrag support for ChartXY

Thanks: Davide Punzo <punzodavide@hotmail.it>

List of changes:

$ git shortlog 021f76a..57d826c --no-merges
Davide Punzo (1):
      ENH: Backport ClickAndDrag support for ChartXY

Revision 26375  Directory Listing
Modified Wed Sep 20 07:21:42 2017 UTC (5 days, 7 hours ago) by jcfr
ENH: Update VTKv8 to include vtkChart improvements

See #770

Thanks: Davide Punzo <punzodavide@hotmail.it>

List of changes:

$ git shortlog 7be26ab..92d2539 --no-merges
Ben Boeckel (5):
      clang-tidy: fix override issues
      DICOMParser: use override
      netcdfcpp: use override
      vtkGDALRasterReader: remove unnecessary method
      netcdfcpp: add a missing override keyword

Cory Quammen (3):
      Style: eliminate space between function name and open paren
      Add on-the-fly triangulation on non-triangle cells
      Update STL writer test to reflect non-triangle polygon support

David E. DeMarle (6):
      fix a performance warning
      add the regression test data files
      fix some comp performance warnings from dashboards and some style
      fix ospray save to larger than screen resolution
      fix a style warning from a misc dashboard
      move away from singleton and add serialization of materials

David Gobbi (5):
      Add VTK_SIZEHINT for the wrappers.
      Add SIZEHINT to vtkCellArray
      Split PyVTKMutableObject according to type.
      Wrap pass-by-reference for pointers.
      Rename "vtk.mutable()" to "vtk.reference()".

Davide Punzo (1):
      ENH: Adding Click and Drag Action in ChartXY

Jean-Christophe Fillion-Robin (1):
      COMP: libproj4: Fix CMP0022 warning

Jim Eliot (1):
      Fix reflection filter for VTK_WEDGE, issue #17116

Joachim Pouderoux (1):
      When no input points, transform the error message in a debug one

Ken Martin (7):
      fix test for 32bit IdType builds
      camera was modifying a transforms matrix directly
      read xbuffer was not always handling the framebuffer
      improve the capabilities of the openvr panel
      fix for GetOrientation on scaled matrices
      speed up a few of the slower tests
      fix a couple methods missing an override

Mathieu Westphal (1):
      Test Polyhedron 4 valgrind fix

Max Smolens (1):
      COMP: WIP: Fix inconsistent-missing-override warning

Robert Maynard (1):
      Add support for VTK-m 2D Structured Grids.

Sankhesh Jhaveri (3):
      SEG-Y: Switch between source, CDP and custom bytes for XY coordinates
      Revert "Flip the Z-order of seg-y data scalars"
      Add find_package call to module export code

Sean McBride (4):
      Made a method take a const param, other misc cleanup
      Fixed undefined signed int overflow in hash function
      Fixed undefined ptr overflow
      Improved a few public API comments after working with them

Shawn Waldon (10):
      Add VTKm submodule
      VTKm within VTK configures and builds
      Change install location to avoid clobbering system VTKm headers
      Add vtkm submodule is initialized sanity check
      vtkm should put its dlls in the bin dir like the other 3rd party libs
      Make SetupForDevelopment.sh initialize the VTKm submodule
      windows: Add compile option for AcceleratorsVTKm to avoid obj sizelimits
      Fix vtkm module so ParaView's CMake code accepts it
      vtkm: add dependency on vtkglew for the OpenGL interop
      Place the vtkm_cont.dll in VTK's bin folder

Steve Pieper (1):
      BUG: WIP: fix vtkPickingManager interaction with widgets

Taylor Braun-Jones (1):
      vtkDebugLeaks: Fix platform inconsistencies in the way leaks are reported

kvankooten (1):
      OptiX Integration into VTK

Revision 26374  Directory Listing
Modified Tue Sep 19 15:27:45 2017 UTC (5 days, 23 hours ago) by lassoan
BUG: Updated CTK to latest version

Fixes DICOM database widget issue when there are multiple widgets

(https://github.com/commontk/CTK/pull/748)

Revision 26359  Directory Listing
Modified Fri Sep 8 17:14:07 2017 UTC (2 weeks, 2 days ago) by jcfr
BUG: Update VTKv8 to include fixes

Name of Slicer/VTK fork branch: slicer-v8.1.0-2017-09-08-6a35cf0

In addition to including all recent VTKv8 improvements, this commit also
re-applies patch kitware/VTK@5937390 (a number of cleanups to the VBO code)
and and now includes the associated fixes:
- kitware/VTK@269549b (fix a couple more places where data arrays were modified)
- kitware/VTK@51a76fb (Add missing Modified calls to vtkImagePlaneWidget)
- kitware/VTK@fcd0dbd (Fix updating of tcoords in ImageSliceMapper.)


Patches specific to Slicer/VTK fork available in branch
slicer-v8.1.0-2017-09-08-6a35cf0 and re-applied:

$ git shortlog 6a35cf0..7be26ab --no-merges
Jean-Christophe Fillion-Robin (1):
      COMP: libproj4: Fix CMP0022 warning

Max Smolens (1):
      COMP: WIP: Fix inconsistent-missing-override warning

Steve Pieper (1):
      BUG: WIP: fix vtkPickingManager interaction with widgets



Update to VTKv8:

$ git shortlog 5c81aa9..6a35cf0 --no-merges
Bill Lorensen (1):
      ENH: Bump PoissonRecontruction version

Cory Quammen (2):
      Remove commented out defines
      Fix deprecation of MapColorScalarsThroughLookupTable methods

David E. DeMarle (8):
      comp fixes as required by visual studio 2015 compiler
      revert the performance warning patch to fix comp
      fix a crash with spatial stratisfy point masking
      Connect advanced materials to an implementation in OSPRay's path tracer
      handle the case of material from field data arrays
      fix comp warnings detected by visual studio
      remove useless code
      make function arguments const since it is safe and wise to do so

David Gobbi (2):
      Fix updating of tcoords in ImageSliceMapper.
      Add missing Modified calls to vtkImagePlaneWidget

Ken Martin (4):
      update handling of scalar material mode
      fix bug with single arrays that should auto shift scale
      deprecate scalar material mode
      fix a couple more places where data arrays were modified

Mathieu Westphal (3):
      Adding a test for a previously fixed polyhedron segfault
      Updating gl2ps Third Party so Interface are synchronized with upstream
      Redesign the PlotLine and PlotPoint BadPoint algorithm

Michal Habera (1):
      Fix performance warning

Sankhesh Jhaveri (1):
      Flip the Z-order of seg-y data scalars

Sean McBride (1):
      Some minor updates to SimpleCocoaVTK example

Utkarsh Ayachit (3):
      Fix potential segfault in distructor.
      Fixup formatting.
      Update to use `nullptr`.

Will Schroeder (1):
      vtkExtractSurface initializes point values.

Revision 26348  Directory Listing
Modified Tue Sep 5 15:11:31 2017 UTC (2 weeks, 5 days ago) by jcfr
COMP: Update VTKv7 and VTKv8 to fix libproj4 configuration warning

VTKv8 updates:

$ git shortlog ed6b44e..5c81aa9 --no-merges
Jean-Christophe Fillion-Robin (1):
      COMP: libproj4: Fix CMP0022 warning

VTKv7 updates:

$ git shortlog a024cef..021f76a --no-merges
Jean-Christophe Fillion-Robin (1):
      COMP: libproj4: Fix CMP0022 warning

Revision 26347  Directory Listing
Modified Tue Sep 5 14:58:54 2017 UTC (2 weeks, 6 days ago) by jcfr
COMP: Update DCMTK to fix configuration warning

$ git shortlog 08dcbcd..53f8545 --no-merges
Jean-Christophe Fillion-Robin (2):
      STYLE: dcmtkPrepare: Remove unneeded setting of CMP0003 to NEW
      STYLE: dcmtkPrepare: Fix warning by conditionally setting CMP0005 to OLD

This commit fixes the following warning:

```
CMake Deprecation Warning at CMake/dcmtkPrepare.cmake:230 (CMAKE_POLICY):
  The OLD behavior for policy CMP0005 will be removed from a future version
  of CMake.

  The cmake-policies(7) manual explains that the OLD behaviors of all
  policies are deprecated and that a policy should be set to OLD only under
  specific short-term circumstances.  Projects should be ported to the NEW
  behavior and not rely on setting a policy to OLD.
Call Stack (most recent call first):
  CMakeLists.txt:17 (INCLUDE)
```

Revision 26342  Directory Listing
Modified Tue Sep 5 08:34:10 2017 UTC (2 weeks, 6 days ago) by jcfr
BUG: Update VTKv8 to fix regression preventing proper resize of viewers

See https://gitlab.kitware.com/vtk/vtk/merge_requests/3184

Revision 26340  Directory Listing
Modified Tue Sep 5 05:22:51 2017 UTC (2 weeks, 6 days ago) by jcfr
ENH: Update SimpleITK external project passing CMAKE_CXX_* for C++11 support

Revision 26339  Directory Listing
Modified Tue Sep 5 05:02:22 2017 UTC (2 weeks, 6 days ago) by jcfr
ENH: Update SimpleITK and requires CMake >= 3.8.2 to enable C+11 support

$ git shortlog 6433028..534787d --no-merges
Bradley Lowekamp (112):
      Don't use ITK_MODULES_ENABLED for complete list of install ITK modules
      Bumping version for 1.1 development
      Adding links with sha512 hash for 1.0.0 python wheels and source
      Revert "Don't use ITK_MODULES_ENABLED for complete list of install ITK modules"
      Update the SimpleITK_DIR version to the current SimpleITK version
      Add Python script used to generate download plots
      Update Superbuild SWIG version to 3.0.12
      Update PCRE version to 8.40
      Set default ITK modules configuration as override-able variables
      Remove unneeded Python development configuration passed to ITK project
      Update superbuild ITK version to 4.12 release candidate 1
      Update ITK modules in json files
      Update old return Self with new macro
      Remove conditional to add variables to propagation list
      Update the ITK_DIR path version number
      Always use CMake FindLua
      Find PythonInterp before PythonLibs
      Make the release branch also continuous
      Update ITK superbuild version to 4.12rc2
      Update IsoContourDistanceImageFilter parameter type
      Add correct alternative baseline image
      Fix ImageIO for 4d images, from variable rename
      Add wrapping of the RoundImageFilter
      Add run-time library path when packaging R
      Add CMake variable for language project for library output path
      Fix path created for output of 4D images in test
      Fix appending patch release version to R version string
      Append to R version number the post version or dev version
      Use a fix seed for the 1+1 evolution optimizer registration test
      Adding wrapping and testing for UnsharpMaskImageFilter
      Add test label for language
      Using scikit-ci-addons for cmake install and junit conversion
      BUG: Disable gtest using pthreads on mingw
      Update ITK version to past v4.12rc3 tag
      Adding converted FAQ page to reStructuredText
      Add FAQ to TOC
      Fixing code-block and table syntax warnings and errors
      Add explicit check for BSpline Order in Landmark initializer
      Update ITK superbuild version to 4.12.0 release
      Add MetaDataDictionaryArrayUpdate parameter to ImageSeriesReader
      Adding wrapped call backs for MetaDataDictionaryArray access
      Only set the meta data dictionary array call back if data is updated
      Delete member functionals before referenced filter is deleted
      Enable ITK remote modules to be enables in Superbuild
      Fix typeo in warning message
      Adding converted Getting Started page to reStructuredText
      Adding Getting Started to TOC and contents to same page
      Cleaned up Getting Started
      Updating rst link to return to external wiki or rst faq
      Fix out of bound array access in Image4D.ExtractImageFilter test
      Propagate CMAKE_THREAD_LIBS_INIT through superbuild
      Address comparison warning in test
      Moving Sphinx documentation root to the root of the repository
      Adding example into Sphix documents.
      Fixing spelling mistakes in documentation and comments
      Grammar fix
      Fix a couple more spelling errors
      To disable pthreads with MinGW, the variable must be set in the cache.
      Usage of setupegg.py has been replaced with setup.py
      Adding matrix of build status and ReadTheDocs badges to Readme
      Indexing current examples in the Sphinx Documentation
      Address warning in FAQ about missing black line
      Use Rscript instead of the R executable
      Add command line arguments to Rscript to remove local options
      Update JSON with latest ITK Doxygen
      Add a ImageCompare::extractSlice method
      Support sitkCompareDriver for MD5 and RMS image compare
      Only use the extracted slice if the image sizes don't match.
      Use sitkCompareDriver for example via CMake macro arguments
      Remove usage of itkTestDriver for testsing
      Correct title for Demons Registration 2
      Splitting GettingStarted page into Installation and Building
      Move detailed Python virtualenv recommendation to FAQ
      Follow contention of page prefix on reference
      Move Enthought distribution information to FAQ
      Fixing link from source to binary installation
      Additional clarification and simplification for wheel installation
      Remove overview from copy and paste
      Update SWIG docstring from SimpleITK generated Doxygen
      Address white space issues on commit hook
      Only support uint8 pixel types for N4 mask
      Only warn when the source version is not available.
      Fix logic for warning about missing repository version.
      Add missing compiler options to the Registration library
      Fix directory from which setup.py is called from during compilation
      BUG: remove package_data hack for overloading build_ext
      Update setup.py keywords and description
      Correct imports from distutils and setuptools
      Fix alignment of code for style
      Update the requirements for manually building SimpleITK
      Minor updates to documentation on building with superbuild
      Minor fixes to manual building documentation
      Set full path to the Python SimpleITK library used in setup.py
      Raise TypeError with unsupported numpy dtype
      Use native path for R_LIBS
      Check if template keyword can be used for disambiguation in TypeList
      Fix template disambiguate test for our specific case
      Set full path to the Python SimpleITK library used in setup.py
      Reduce the tolerance for a LandmarkBasedTransformInitializer test
      Bumping version 1.0.1 for patch release
      Propagate CMake variables related to compiler standard  and extension
      Enable CMP0067, and warn if needed and not available
      Use CMakePushCheckState
      Remove hashing of try_compile is favor of CMake standard behavior
      Use try_compiles COMPILE_DEFINITIONS argument over CMAKE_FLAGS
      Use CMP0025 new policy for Lua compilation
      Just specify the binary direction for try_compiles
      Add ITK_GIT_TAG and ITK_GIT_REPOSITORY variables for Superbuild
      Use CMake if ( <variable> ) format in LanguageOptions
      Set ITK package install path to be version free
      Remove out dated comment
      Fix ITK Superbuild install path to include "lib" directory

Dave Chen (7):
      Fixed doxy2swig.py to handle multiple See issue
      Get the HOME env var for app search path
      Also search for 'ImageJ'
      Throw Exeception with ImageJ/Fiji not found.
      Handle differing ImageJ front ends
      Clean up #defines a bit
      Fixed C Preprocessor errors.

David T. Chen (3):
      Print the Show command line when an error occurs.
      On Win32 Add User's home & desktop to search path
      Catch error of null ImageJ application

Ghislain Antony Vaillant (4):
      Fix spelling errors
      More idiomatic setuptools import
      More idiomatic setuptools import
      Correct project name for Ruby wrapping

Kasper Marstal (1):
      BUG: SITK_4D_IMAGES is a preprocessor directive, not a CMake option, and should not be renamed to SimpleITK_4D_IMAGES

Richard Beare (2):
      Typemap "ret" to attach C finalizer to Image and Transform objects.
      Add no-multiarch flag to R installation command

Sasank Chilamkurthy (1):
      Updated document with proper rst formatting

Ziv Yaniv (16):
      Updating example to use new series reader interface.
      Adding the example in R.
      Adding the overview prose for this example.
      Fixed wrong link and some markup.
      Adding documentation to the DICOM related examples.
      Responding to review comments.
      BUG: Use of floor division instead of regular division.
      Replaced the use of regular division with floor division.
      Fixed bug in direction cosine writing.
      Adding text to the Demons registration documentation files.
      Paragraphs reflowed using hard line breaks instead of a single line.
      Updating the documentation of the FilterProgressReporting example.
      Change markup in java example to be consistent with other examples.
      Update the ImageSeriesReader documentation.
      Fixed text and undid removal of a \sa reference.
      Updating registration documentation.

Revision 26338  Directory Listing
Modified Tue Sep 5 04:04:17 2017 UTC (2 weeks, 6 days ago) by jcfr
COMP: Fix NUMPY patch steps

This commit fixes a regression introduced in previous commit.

Revision 26337  Directory Listing
Modified Tue Sep 5 02:39:46 2017 UTC (2 weeks, 6 days ago) by jcfr
BUG: Patch NUMPY to ignore warning "invalid value encountered in power"

See https://discourse.slicer.org/t/runtime-warning-on-startup-in-numpy/757/10

Fixes https://issues.slicer.org/view.php?id=4419

Thanks to the use of "SlicerPatch" module, patch are applies selectively:

```
[ 93%] Performing patch step for 'NUMPY'
-- Applying 'numpy-01-system_info-fix-clang.patch' - skipping (already applied)
-- Applying 'numpy-02-fcompiler-optional-revert-4a3fd1f.patch' - skipping (already applied)
-- Applying 'numpy-03-core-getlimits-ignore-warnings.patch' - done
```

Revision 26336  Directory Listing
Modified Tue Sep 5 02:39:45 2017 UTC (2 weeks, 6 days ago) by jcfr
ENH: Introduce SlicerPatch.cmake allowing to apply patch only once

Revision 26335  Directory Listing
Modified Tue Sep 5 02:39:43 2017 UTC (2 weeks, 6 days ago) by jcfr
ENH: Update NUMPY external project to apply patches using patch executable

Revision 26334  Directory Listing
Modified Mon Sep 4 20:52:20 2017 UTC (2 weeks, 6 days ago) by jcfr
ENH: Use copy of upstream FindPatch module

This commit integrates the latest version of FindPatch module
from https://gitlab.kitware.com/cmake/cmake/merge_requests/1184

It also updates the version of the python build system where the same
change was applied:

$ git shortlog b9ae615..cc93717 --no-merges
Jean-Christophe Fillion-Robin (1):
      ApplyPatches: Use copy of upstream FindPatch.cmake

Revision 26326  Directory Listing
Modified Thu Aug 31 22:32:18 2017 UTC (3 weeks, 3 days ago) by jcfr
ENH: Update VTK8 and EMSegment

This commit updates VTK8 to include improvements related to OpenVR
support where SDL is not a dependency anymore. Thanks to Jean-Baptiste Vimort <jb.vimort@kitware.com>
and Ken Martin <ken.martin@kitware.com> for their help moving this forward.

For a complete list of VTK improvements, see below.

List of EMSegment changes:

r17138: COMP: Fix VTK8 python wrapping adding missing include dirs

List of VTK8 changes:

$ git shortlog  af1c37..a8e3680 --no-merges
Aashish Chaudhary (11):
      Fixed various compile time errors
      Fixed port missing error
      Made RDV as the default option for visualization
      Renamed to how its referred in the code
      Renamed to how its referred in the code
      Copy data during build time
      Created readme
      Fixed 2D visualization of segy
      Added vtk header to source code
      Commented out debug messages for now
      Added license

Allison Vacanti (3):
      Update VTK-m code for Result object refactor.
      Fix some unused template warnings.
      Handle empty datasets gracefully.

Alvaro Sanchez (7):
      Added support for XYSampling with depth-peeling on.
      Added support for texture-streaming with masks on.
      Added TestGPURayCastTextureStreamingMask.
      Extended vtkOpenGLRenderPass API to track the number of DrawBuffers activated.
      Added support for XYSampling with depth-peeling on.
      Extended vtkOpenGLRenderPass API to track the number of DrawBuffers activated.
      Matched depth tolerance value to that one of vtkDepthPeelingPass.

Andrew Bauer (7):
      Adding in edge uses cases for vtkLine::DistanceToLine() method.
      Adding option to vtkCellSizeFilter to sum cell sizes over the dataset.
      Updating the 'Do: test' options to remove --oneshot.
      Fixing issues with 3D cells.
      Cleaning up warnings for shadowed member variables.
      Fixing shadowed variable compiler warning
      Fixing shadowed variable compiler warnings

Aron Helser (3):
      vtkDataEncoder: fix 'ENCODING_NONE' option so it works.
      vtkWebApplication: match ParaView, change to LastStillRenderToMTime
      Lights: clear transform when switching types. Fix typos.

Ben Boeckel (1):
      vtkModuleMacros: remove VS7 workaround

Brad King (4):
      Fix -Wimplicit-fallthrough warnings on GCC 7
      Improve VTK_FALLTHROUGH portability
      QVTKWidget: Fix compilation with Qt 5
      vtkTextureObject: Add missing 'break' statements in switch cases

Cory Quammen (7):
      Rebuild representations when the RenderWindow is updated
      Minor typo cleanup
      Update baselines for TestPickingManagerWidgets
      Minor fixes to documentation to please Sphinx
      Reduce VTK module output during CMake configuration
      Set number of samples to 0 if 1 is requested
      Augment vtkTexture to color directly by more scalar types

Dan Lipsa (4):
      BUG: Various fixes to the 2D reader
      Fix the ordering of scalars.
      Replace ObjectIdMap trick for two way mapping.
      Rename TestObjetId to TestObjectIdMap.

David E. DeMarle (7):
      miscellaneous cleanup for merge readiness
      tweaks for ospray lights
      Revert "miscellaneous cleanup for merge readiness"
      Revert "Full revision and extension of support for hypertreegrid objects and filters"
      Hook up vtk's ConeAngle to ospray's SpotLight.
      workaroung a bug in scene lights
      Increment version to VTK 8.0.1

David Gobbi (21):
      Fix lex helper get_macro_arguments const cast.
      Remove C casts from generated wrapper code.
      Change NULL to nullptr in generated wrapper code.
      Fix indentation of comments after nullptr.
      Add more nullptr modernizations to wrapper code.
      Eliminate a few C-style const casts.
      Improve token regurgitation.
      Fix the parsing of function attributes.
      Add "using" to attributes.
      Add parsing of 'vtk::expects()' attributes.
      Regenerate the wrapper parser.
      Add precondition checks to python wrappers.
      Add a test for VTK_EXPECTS.
      Inherit precondition contracts from superclass.
      Add VTK_EXPECTS checks to the array classes.
      Update the vtkDICOM remote module to 0.8.5.
      Fix comparison of types for overrides.
      Add EXPECTS() checks for IdList, CellArray.
      Chain wrapper header file dependency.
      Hide the wrapper hint macros from Doxygen.
      17112: Wrapper fix for New() that returns singleton

Jean-Baptiste VIMORT (1):
      ENH: Modification of the OpenVR class

Jean-Christophe Fillion-Robin (1):
      vtkWrapHierarchy: Use response file to fix windows build in large project

Joachim Pouderoux (2):
      Fix a small bug in vtkBoundingBox::Inflate method
      Fix vtkDataSetSurfaceFilter for 1D structured and rectilinear grids.

KWSys Upstream (1):
      KWSys 2017-08-04 (9322de7a)

Ken Martin (29):
      overhaul the OpenVR support
      removed some shadowed ivars in executives
      remove extra calls that did nothing and fix some leaks
      missed two calls of UnBind for LIC
      fix shadowed ivar in OpenGLGlyph3DMapper
      forward Modified to points data as it does set methods
      start deprecating AAFrames FDFrames and SubFrames
      fix a compiler warning on MenuRepresentation
      VTK_LEGACY does not work with the set get macros
      some fixes and improvements for OpenVR
      fix a couple more spots that were missing modified calls
      fix two compailer warnings
      a number of cleanups to the VBO code
      The AnimationTime ivar was shadowed in AnimationScene
      AxisActor shadowed the Bounds ivar from Prop3D
      fix comiler warning on string to numeric
      add an option for float color buffers
      fix shadowed ivars issues
      class shadowed an ivar it should not have
      fix for mtl files that have a utf8 BOM header
      remove the android test until someone fixes it
      polaraxesactor was shadowing bounds ivar
      remove case of copied ivar that should not be there
      rmeoved shadowed ivar, clearly a copy paste issue
      rename shadowed ivar to avoid confusion
      add the ability to specify point output precision
      unused template compiler warnings
      allow the user to set the helper window for openvr
      another try at silencing the template warnings

Mathieu Westphal (2):
      Add support for selecting component/magnitude with PointGaussian array
      Fix DataArray Finite Range Information Key

Max Smolens (3):
      Fix memory leaks in vtkOpenGLRenderer::DonePick()
      Fix QVTKOpenGLWidget rendering with disabled interactor
      COMP: WIP: Fix inconsistent-missing-override warning

Michal Habera (2):
      Add FiniteElementFunction to xdmf->vtk layer
      Bump new XDMF version

Pavel Pokutnev (1):
      BUG: Return nullptr instead of call to abort().

Philippe P. Pébaÿ (1):
      Full revision and extension of support for hypertreegrid objects and filters

Robert Maynard (1):
      Add doxygen comments to all VTK-m filters.

Sankhesh Jhaveri (26):
      Fix char format warnings
      Fix memory leaks
      Fix camera view and position for viewing seismic profile
      Moved VTKSeismic files to IO/SegY
      Moved files to VTK specific locations
      Fixed IOUtils according to VTK convention
      Re-organize and format the vtkIOSegY module per VTK conventions
      Fix warnings on macOS for Seg-Y reader
      Added test for 2D SegY reader
      Remove unused main file from vtkIOSegY
      Fix test to map scalars
      Another test for vtkSegY2DReader
      Pruned code for better readability
      Fix the vtkIOSegY header test
      Baselines for new tests
      Code to read IBM 370 floating point data from Seg-Y files
      Improve SegY reader tests and add new baselines
      Add missing include header for SegY module
      Exclude private implementations from wrapped bindings
      Fix button widget when used with multiple viewports
      Bring back the button widget test
      New test for button widget with multiple viewports
      Fix slider widget with multiple viewports
      Unmap Xlib window when it is finalized without terminating app
      Test for slider widget with multiple viewports
      Change wget to curl in source tarball script

Scott Wittenburg (1):
      Update some baselines

Sean McBride (5):
      Fixed various -Wcast-qual warnings
      Fixed a bunch more -Wcast-qual clang warnings
      Fixed last of -Wcast-qual warnings
      Fixed/suppressed various new warnings from cppcheck 1.80
      Suppress many -Wunused-template warnings

Sebastien Jourdain (1):
      Expend Java Wrapping README

Shawn Waldon (2):
      Change return type of GetOperandNumber to avoid overflow
      Prefer signed char to plain char when reading TIFF files

Steve Pieper (1):
      BUG: WIP: fix vtkPickingManager interaction with widgets

Steven Hahn (2):
      Minimize duplicate code in vtkDataArrayPrivate
      Remove second information object in vtkDataArray.

Sujin Philip (1):
      Update vtkmExternalFaces

T.J. Corona (2):
      vtkVolumeOfRevolutionFilter: offset location by number of points.
      vtkTriangle: use boolean AND instead of multiplying bools.

Utkarsh Ayachit (3):
      Use doxgen codeblock markers.
      Cleanup `StereoUpdate` method.
      Make vtkPythonInterpreter use vtkOutputWindow.

Will Schroeder (7):
      Specify the maximum number of buckets/bins
      Cell divisions computed in vtkBoundingBox
      Adjusted tests to reflect changes to static locators
      Normalize weights; take into account dimension reduction
      Ensure that number of bin divisions always >1
      Clean up based on feedback
      Use better binning initialization

jiac5 (4):
      First submission to GITHUB
      2D seismic visualization in 3D space
      Update code
      Make Segy2DReader derived from vtkPolyDataAlgorithm

Revision 26312  Directory Listing
Modified Mon Aug 28 19:41:50 2017 UTC (3 weeks, 6 days ago) by lassoan
ENH: Update to latest CTK for DICOM import speed improvement

DICOM indexing is about 10x faster (tested on Windows, with Qt4).

Revision 26307  Directory Listing
Modified Sat Aug 26 02:59:35 2017 UTC (4 weeks, 2 days ago) by jcfr
COMP: Update CTKAppLauncherLib to fix finding of Qt4 in extensions

$ git shortlog 5aa21a3..e4923af --no-merges
Jean-Christophe Fillion-Robin (1):
      COMP: Do not use COMPONENTS when finding Qt in config file

Revision 26305  Directory Listing
Modified Fri Aug 25 17:49:33 2017 UTC (4 weeks, 2 days ago) by jcfr
COMP: Update ITK and CTK to fix remaining extension packaging issues

This commit improves on r26301 (COMP: Fix extension packaging setting
CMAKE_MACOSX_RPATH to 0)

Related discussions:
* https://discourse.slicer.org/t/interpreting-cdash-reporting-extension-is-packaged-despite-build-errors/856
* https://discourse.slicer.org/t/extension-build-failure-on-mac-due-to-error-copying-files/935

ITK changes:

$ git shortlog 4c38b95..c390a4e --no-merges
Jean-Christophe Fillion-Robin (1):
      COMP: Update MINC to set MACOSX_RPATH property based on CMAKE_MACOSX_RPATH

CTK changes:

git shortlog 6c5a63f..4f55362 --no-merges
Jean-Christophe Fillion-Robin (1):
      COMP: Ensure CMAKE_MACOSX_RPATH is passed to CTK inner-build

Revision 26304  Directory Listing
Modified Thu Aug 24 22:39:19 2017 UTC (4 weeks, 3 days ago) by jcfr
ENH: Abort configuration early if patch executable is not found

This commit adds the FindPatch CMake module. Corresponding merge
request adding the functionality into upstream CMake is:
https://gitlab.kitware.com/cmake/cmake/merge_requests/1184

See #4411

Revision 26302  Directory Listing
Modified Thu Aug 24 19:47:11 2017 UTC (4 weeks, 3 days ago) by jcfr
COMP: Update python-cmake-buildsystem to find patch.exe in user directory

See #4411

$ git shortlog 849e596..b9ae615 --no-merges
Jean-Christophe Fillion-Robin (1):
      ApplyPatches: Fix finding of patch.exe if installed in user folder

Revision 26301  Directory Listing
Modified Thu Aug 24 18:40:34 2017 UTC (4 weeks, 3 days ago) by jcfr
COMP: Fix extension packaging setting CMAKE_MACOSX_RPATH to 0

Following the update of the minimum required version of CMake to 3.5,
the policy CMP0042 started to default to NEW leading to CMAKE_MACOSX_RPATH
being initialized to 1 by default.

This had the side-effect of including "@rpath/..." into libraries
installed during the packaing on macOS and prior the fixup script had
a chance to recursively collect, copy and update (aka fixup) the libraries.

This commit also updates the external projects removing patches explicitly
setting CMP0042 to OLD (e.g ITK). Instead, the variable CMAKE_MACOSX_RPATH
is passed to all of them.

A merge request has also been submitted to ITK. See http://review.source.kitware.com/#/c/22581/

Related Slicer commits:
* r25180 (BUG: Extension packaging: Ensure @rpath is not applied at build time)

Related discussions:
* https://discourse.slicer.org/t/interpreting-cdash-reporting-extension-is-packaged-despite-build-errors/856
* https://discourse.slicer.org/t/extension-build-failure-on-mac-due-to-error-copying-files/935


This commit fixes error like this one:

```
[...]
Error copying file "@rpath/libITKFactoryRegistration.dylib" to "/.../SwissSkullStripper-build/_CPack_Packages/Darwin/TGZ/26298-macosx-amd64-SwissSkullStripper-git17391c3-2017-05-16/Slicer.app/Contents/lib/Slicer-4.7/libITKFactoryRegistration.dylib".
warning: target '/.../SwissSkullStripper-build/_CPack_Packages/Darwin/TGZ/26298-macosx-amd64-SwissSkullStripper-git17391c3-2017-05-16/Slicer.app/Contents/lib/Slicer-4.7/libITKFactoryRegistration.dylib' does not exist...
/usr/bin/otool: can't open file: /.../SwissSkullStripper-build/_CPack_Packages/Darwin/TGZ/26298-macosx-amd64-SwissSkullStripper-git17391c3-2017-05-16/Slicer.app/Contents/lib/Slicer-4.7/libITKFactoryRegistration.dylib (No such file or directory)
otool: can't open file: /.../SwissSkullStripper-build/_CPack_Packages/Darwin/TGZ/26298-macosx-amd64-SwissSkullStripper-git17391c3-2017-05-16/Slicer.app/Contents/lib/Slicer-4.7/libITKFactoryRegistration.dylib (No such file or directory)
install_name_tool: can't open file: /.../SwissSkullStripper-build/_CPack_Packages/Darwin/TGZ/26298-macosx-amd64-SwissSkullStripper-git17391c3-2017-05-16/Slicer.app/Contents/lib/Slicer-4.7/libITKFactoryRegistration.dylib (No such file or directory)
[...]
```

Revision 26300  Directory Listing
Modified Thu Aug 24 18:40:30 2017 UTC (4 weeks, 3 days ago) by jcfr
ENH: Update CTK to include DICOM import speedup and python wrapping updates

See https://discourse.slicer.org/t/slicer-dicom-import-performance/922

$ git shortlog 1f3eba2..6c5a63f --no-merges
Andras Lasso (1):
      ENH: Improve caching of DICOM tags fixing begin/end transaction queries

Csaba Pinter (2):
      ENH: Python wrapping of ctkBooleanMapper
      ENH: Added currentUserDataAsString property to ctkComboBox

Jean-Christophe Fillion-Robin (11):
      COMP: Update run_opengl.sh to gracefully ignore "Driver btrfs" error on CircleCI
      ENH: Update test docker images to use thewtex/opengl:debian
      ENH: Fix "build.sh" to allow exection from any directory
      ENH: Update "build/run/test" shell script to use fail early
      BUG: Fix Qt5 continuous integration
      COMP: Initialize and propagate CMAKE_MACOSX_RPATH to external projects
      ENH: Update ctkDICOMIndexer to report indexing time in seconds
      ENH: Speed up ctkDICOMBrowser removing processEvents call
      BUG: ctkDICOMDatabase: Update TagCache initialization to fix startup error
      BUG: ctkDICOMDatabase: Fix "not positioned on a valid record" error
      STYLE: ctkDICOMDatabase: Remove unused variable warnings

Revision 26296  Directory Listing
Modified Mon Aug 21 21:05:45 2017 UTC (4 weeks, 6 days ago) by jcfr
COMP: Update CTKAppLauncherLib to fix extension build error on macOS

This commit fixes error like this one:

```
make[8]: *** No rule to make target `/Users/kitware/Dashboards/Support/qt-everywhere-opensource-build-4.8.7/lib/libQtUiTools.a/QtUiTools',
needed by `lib/Slicer-4.7/qt-loadable-modules/libqSlicerDicomRtImportExportSubjectHierarchyPlugins.dylib'.
Stop
```

and ensures that Qt libraries are handled similarly when building both
Slicer and Slicer extensions.

It addresses a regression introduced in r26217 (ENH: Update CTKAppLauncherLib
adding support for Qt5) where CTKAppLauncherLibConfig was explicitly
setting QT_USE_IMPORTED_TARGETS to 1 when using Qt4.

Root cause:

Since on MacOSX not all modules are available as "framework" (e.g libQtUiTools.a),
the assumption made in "FindQt4.cmake" is not always valid and systematically
setting the imported libraries location to framework location is incorrect.

See https://gitlab.kitware.com/cmake/cmake/issues/17195


Changes:

$ git shortlog 685dd47..5aa21a3 --no-merges
Jean-Christophe Fillion-Robin (1):
      CTKAppLauncherLibConfig: Do not force use of Qt4 imported targets

Revision 26282  Directory Listing
Modified Wed Aug 16 14:33:07 2017 UTC (5 weeks, 5 days ago) by jcfr
BUG: Update CTK to fix ctkMessageBox layout with Qt >= 5.2

$ git shortlog cfbb46a..1f3eba2 --no-merges
Jean-Christophe Fillion-Robin (1):
      BUG: ctkMessageBox: Fix layout setting checkbox with Qt >= 5.2

Revision 26275  Directory Listing
Modified Wed Aug 16 04:19:15 2017 UTC (5 weeks, 5 days ago) by jcfr
COMP: Update VTKv8 to fix VS2015 build and avoid max path length issues

$ git shortlog 73a4bb8..af1c37b --no-merges
Jean-Christophe Fillion-Robin (1):
      COMP: vtkWrapHierarchy: Use response file to fix windows build in large project

Revision 26274  Directory Listing
Modified Tue Aug 15 16:03:33 2017 UTC (5 weeks, 5 days ago) by jcfr
ENH: Update DCMTK to include fixes for DCMQI

See https://github.com/QIICR/dcmqi/pull/287

Suggested-by: Andriy Fedorov <fedorov@bwh.harvard.edu>

$ git shortlog c9ccd45..08dcbcd --no-merges
Jan Schlamelcher (2):
      Updated version information for 3.6.2+ development.
      Fixed test 'ofstd_limits' failing when using Clang.

Joerg Riesmeier (17):
      Fixed issue with min/max() macros (Visual Studio).
      Updated data dictionary for DICOM 2017c.
      Added comment on new optional attribute.
      Updated code definitions for DICOM 2017c.
      Updated Context Group classes for DICOM 2017c.
      Moved ANNOUNCE file to "docs" subfolder.
      Added support for multiple finding sites (DCMSR).
      Fixed typo in comment.
      Added full support for Patient Radiation Dose SR.
      Added two SRT codes needed for TID 1501 and 300.
      Factored out error conditions for TID 14xx/15xx.
      Created new class for TID 1419 (Measurement).
      Added missing "check" parameter.
      Use constant/macro for number of list entries.
      Added support for TID 1501 and 300 (Measurement).
      Added mode for order of content items significant.
      Add extra content items to extensible templates.

Marco Eichelberg (3):
      Fixed infinite loop of dcmdata unit test on NetBSD.
      Enforcing max line width in preformatted man pages.
      Now generating preformatted man pages as pure ASCII.

Max Smolens (1):
      Fix configure error on Linux with DCMTK_ENABLE_CXX11 enabled

Revision 26273  Directory Listing
Modified Mon Aug 14 22:27:18 2017 UTC (5 weeks, 6 days ago) by jcfr
ENH: Update VTK8 to fix memory leak in OpenGL2/vtkOpenGLRenderer

$ git shortlog 1bd5876..73a4bb8 --no-merges
Max Smolens (1):
      Fix memory leaks in vtkOpenGLRenderer::DonePick()

Revision 26251  Directory Listing
Modified Mon Aug 14 02:07:21 2017 UTC (6 weeks ago) by jcfr
ENH: Add preliminary support for Qt5

Support configuration using either Qt4 or Qt5

Based on preliminary work from Steve Pieper <pieper@bwh.harvard.edu>

* vtkSlicerConfigure: Introduced Slicer_HAVE_QT5 and Slicer_HAVE_WEBKIT_SUPPORT.
  This was needed to workaround limitation of "moc" compiler preventing it
  from expanding macro like "QT_VERSION_CHECK.

* Explicitly set QT_PLUGINS_DIR and QT_BINARY_DIR variables when using Qt5

* Update extension build system to propagate Qt version

Tested with Qt 5.7 and Qt 5.9 on Ubuntu

Remaining tasks:
* Port extension manager
* Update install/packaging rules to support Qt5
* SlicerStyle (based on CommonStyle) is disabled (see Main.cxx). Application crashes on Linux.
* Fix runtime errors:
 * libpng warning: iCCP: known incorrect sRGB profile
 * QPixmap::grabWidget is deprecated, use QWidget::grab() instead

Co-authored-by: Hina Shah <hina.shah@kitware.com>
Co-authored-by: Max Smolens <max.smolens@kitware.com>

COMP adding qt5 variables for extension testing

COMP Adding Qt5 build and plugin cmake variables

From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

Revision 26250  Directory Listing
Modified Mon Aug 14 02:06:37 2017 UTC (6 weeks ago) by jcfr
ENH: Enable C++11 for external projects and extensions

From: Max Smolens <max.smolens@kitware.com>

Revision 26245  Directory Listing
Modified Mon Aug 14 02:05:10 2017 UTC (6 weeks ago) by jcfr
ENH: Update VTK project name to VTKv8

From: Max Smolens <max.smolens@kitware.com>

Revision 26244  Directory Listing
Modified Mon Aug 14 02:05:08 2017 UTC (6 weeks ago) by jcfr
ENH: Update to VTK 8.0.0

A Slicer_VTK_VERSION_MAJOR option is added to allow building with VTK7 or VTK8.
The option should be set to 7 or 8 and defaults to 8.

The VTK8 branch includes VTK 8.0.0 plus a Slicer-specific fix for
picking. Other Slicer-specific fixes, both for VTK8/Qt5 support and
older patches, have been merged upstream.

When building with VTK8, now generate VTK wrapping hierarchy files as required
by VTK.

From: Max Smolens <max.smolens@kitware.com>

Revision 26240  Directory Listing
Modified Fri Aug 11 16:59:41 2017 UTC (6 weeks, 2 days ago) by jcfr
COMP: Add support for OpenSSL when compiling with Visual Studio 2015

The OpenSSL packages available on packages.kitware.com are
compiled using the following script:

  https://gist.github.com/jcfr/6030240

From: Max Smolens <max.smolens@kitware.com>

Revision 26238  Directory Listing
Modified Fri Aug 11 15:54:26 2017 UTC (6 weeks, 2 days ago) by jcfr
COMP: Update qRestAPI: Attempt to fix build error

This commit is an attempt to fix the following build error
reported when building Slicer on Windows 10 against Qt 4.8
with Slicer_USE_PYTHONQT_WITH_OPENSSL set to OFF.

```
C:\SAB\S4NR\qRestAPI\qRestAPI.cpp(82): error C2653: 'QSslSocket' : is not a class or namespace name
```

Changes:

$ git shortlog 26bdea0..14580c3 --no-merges
Max Smolens (1):
      COMP: Fix misspelled definition

Revision 26226  Directory Listing
Modified Fri Aug 11 00:10:19 2017 UTC (6 weeks, 3 days ago) by jcfr
COMP: Update ParameterSerializer: Fix 'inconsistent-missing-override' warnings

This commit fixes warning reported when building with C++11 support enabled
and VTK8.

$ git shortlog fd28362..70e95f1 --no-merges
Hina Shah (1):
      COMP Add ITK_OVERRIDE to overridden functions

Revision 26224  Directory Listing
Modified Fri Aug 11 00:01:04 2017 UTC (6 weeks, 3 days ago) by jcfr
ENH: Update CTK to add support for Qt5

$ git shortlog 87dc559..cfbb46a --no-merges
Adam Rankin (2):
      COMP: Setting CMP0020 to NEW
      Correcting reference to policy version

Jean-Christophe Fillion-Robin (12):
      ENH: Improve Qt5 CMake configuration supporting passing of Qt5_DIR
      COMP: designer plugin: Fix deprecated use of headers in Qt5
      COMP: VisualizationVTKWidgetsPythonQt: Fix build with CTK_USE_CHARTS disabled
      ENH: CLI/Frontend/QtWekKit: Preliminary work toward supporting WebEngine in Qt5
      ENH: Re-add Qt5 CMake configuration support passing CMAKE_PREFIX_PATH
      COMP: cmake: Include CTK_Qt5_DIR and CTK_CMAKE_PREFIX_PATH to CTKConfig and UseCTK
      ENH: PythonQt: Use "patched-8" version if building against Qt5
      COMP: qt4/qt5: Work-around lacking of macro expansion by moc checking HAVE_QT5
      COMP: Fix deprecated use of "QPixmap::grabWidget" in Qt5
      BUG: PythonManager: Fix testPythonAttributeValues
      COMP: ctkLayoutManagerTest1: Fix unused variable warning
      COMP: Fix deprecated interface warning when building designer plugin with Qt5

Max Smolens (31):
      ENH: CI: Set CTK_ENABLE_Widgets
      ENH: CI: Indicate failure when tests fail
      ENH: CI: Disable MIT_SHM X11 extension
      BUG: Fix ctkLanguageComboBoxTest issues
      BUG: Fix ctkDoubleSpinBox memory corruption
      BUG: Fix ctkAbstractFactoryTest1 intermittent failure
      BUG: Update ctkScreenshotDialogTest1
      ENH: Add testing utility to compare images with a threshold
      ENH: ctkCrosshairLabelTest2: Allow for small differences from baseline images
      ENH: Fix ctkErrorLogQtMessageHandlerWithThreadsTest1 with Qt5
      ENH: Rename testing utility function
      ENH: Wrap grabWidget()
      BUG: Fix VTK widget test errors with OpenGL2 backend
      ENH: WIP: Prefer QVTKOpenGLWidget
      ENH: Update tests for compatibility with QVTKOpenGLWidget
      ENH: Export CTK_USE_QVTKOPENGLWIDGET definition
      ENH: Disable multisampling to fix volume rendering
      ENH: Fix ctkMenuComboBox behavior in Qt5
      COMP: Fix deprecated header check in Qt5
      ENH: Update ctkSettingsPanel tests for Qt5
      ENH: Make ctkSettingsTest1 more robust
      ENH: Make ctkCrosshairLabelTest2 more robust
      ENH: Make ctkWidgetsUtilsTestGrabWidget more robust
      ENH: Fix grabbing widgets on certain Qt versions
      COMP: Fix enumeration value not handled warning
      COMP: Fix deprecation warning
      BUG: Fix ctkColorDialog crash on Mac with Qt5
      COMP: Fix inconsistent-missing-override warnings
      COMP: Fix deprecated-declarations warnings
      COMP: Fix enumeration value not handled warning
      ENH: Immediately render VTK in QVTKOpenGLWidget after resize

Steve Pieper (1):
      COMP: Scripting/Python/Core: Fix building of ctkAbstractPythonManager in Qt5

Revision 26217  Directory Listing
Modified Tue Aug 8 03:17:28 2017 UTC (6 weeks, 6 days ago) by jcfr
ENH: Update CTKAppLauncherLib adding support for Qt5

$ git shortlog 5b592f1..685dd47 --no-merges
Jean-Christophe Fillion-Robin (1):
      Add support for Qt5

Max Smolens (2):
      COMP: Fix Qt4 required components
      COMP: Use proper Qt4 component capitalization

Revision 26206  Directory Listing
Modified Fri Aug 4 20:36:17 2017 UTC (7 weeks, 2 days ago) by jcfr
COMP: Update LibArchive to fix MacOSX build using older compiler. See #4407

commit slicer/LibArchive@e8a11f4
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Fri Aug 4 16:26:43 2017 -0400

    slicer: Disable LHA support

    Note: Tests have not been updated.

    Apparently the assumption in the code that all versions of clang will
    have __builtin_bswap16 is not true for the version of clang on the
    factory.

    See https://issues.slicer.org/view.php?id=4407

    On the Slicer factory, we currently use an older llvm-3.1 compiler.
    See https://www.slicer.org/wiki/Documentation/Nightly/Developers/Factory#Software
    and http://slicer-devel-archive.65872.n3.nabble.com/MacOSX-factory-build-Transitioning-from-hybrid-quot-llvm-g-quot-to-quot-clang-quot-Update-to-Qt-4-8-6-tt4032198.html#a4032199

    After we transition the Slicer build to a newer version macOS, we will
    be able to use the unmodified LibArchive sources.

    Suggested-by: Steve Pieper <pieper@bwh.harvard.edu>

Revision 26204  Directory Listing
Modified Fri Aug 4 20:02:34 2017 UTC (7 weeks, 2 days ago) by jcfr
COMP: Update DCMTK to fix Linux build error with DCMTK_ENABLE_CXX11 enabled

$ git shortlog e4df357..c9ccd45 --no-merges
Max Smolens (1):
      Fix configure error on Linux with DCMTK_ENABLE_CXX11 enabled

Revision 26198  Directory Listing
Modified Thu Aug 3 21:43:51 2017 UTC (7 weeks, 3 days ago) by jcfr
ENH: Update qRestAPI project to include Qt5 support

$ git shortlog d1b07cc..26bdea0 --no-merges
Max Smolens (1):
      Fix compiling with Qt5 without OpenSSL

Thanks: Hina Shah <hina.shah@kitware.com>
Thanks: Max Smolens <max.smolens@kitware.com>

Revision 26191  Directory Listing
Modified Thu Aug 3 04:08:57 2017 UTC (7 weeks, 4 days ago) by jcfr
COMP: Fix race condition when building python package. See #4394

commit Slicer/setuptools@057883d
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Wed Aug 2 10:53:05 2017 -0400

    Improve support for support parallel build

    The previous attempt implemented in Slicer/setuptools@057883d2bea6fc didn't scale as expected and
    triggered errors like the one reported below.

    This commit remove the use of file lock and instead force the install
    to use the backward compatibility mode.

    See https://issues.slicer.org/view.php?id=4394


    ```
    File "/path/to/Slicer-superbuild/python-install/lib/python2.7/site-packages/setuptools-35.0.1.post20170718-py2.7.egg/setuptools/command/easy_install.py", line 1595, in save
    self.lockfile.release()
    File "/path/to/Slicer-superbuild/python-install/lib/python2.7/site-packages/setuptools-35.0.1.post20170718-py2.7.egg/setuptools/command/lockfile/linklockfile.py", line 59, in release
    raise NotMyLock("%s is locked, but not by me" % self.path)
    setuptools.command.lockfile.NotMyLock: /path/to/Slicer-superbuild/python-install/lib/python2.7/site-packages/easy-install.pth is locked, but not by me
    ```

Co-authored-by: Steve Pieper <pieper@bwh.harvard.edu>
Co-authored-by: Andriy Fedorov <fedorov@bwh.harvard.edu>

From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

Revision 26189  Directory Listing
Modified Thu Aug 3 04:08:53 2017 UTC (7 weeks, 4 days ago) by jcfr
COMP: Update python-cmake-buildsystem to support python 2.7 build with VS2015

$ git shortlog python-cmake-buildsystem/python-cmake-buildsystem@ec32acc..python-cmake-buildsystem849e596 --no-merges
Jean-Christophe Fillion-Robin (2):
      Fix download of python source using "https" URL
      Fix python 2.7.15 vs2015 build and introduce patch management system

Matt McCormick (2):
      Support version detection for Git version of CPython
      Note that CMake 2.7.13 is supported in the version check.

Max Smolens (1):
      Fix applying patches when external source is provided


Thanks: Adam Rankin <arankin@robarts.ca>
Thanks: Dzenan Zukic <dzenan.zukic@kitware.com>
Thanks: Franklin King <franklin.king@queensu.ca>
Thanks: Matt McCormick <matt.mccormick@kitware.com>
Thanks: Max Smolens <max.smolens@kitware.com>

From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

Revision 26188  Directory Listing
Modified Thu Aug 3 04:08:51 2017 UTC (7 weeks, 4 days ago) by jcfr
COMP: Update libarchive version

Previously we used a Slicer-specific fork of libarchive
with a few patches, but this got behind the main line
of development and eventually would not build on gcc-6.

This patch switches us to the most recently release of the
upstream repo.

From: Steve Pieper <pieper@isomics.com>

Revision 26179  Directory Listing
Modified Thu Jul 27 02:40:33 2017 UTC (8 weeks, 4 days ago) by lassoan
BUG: Updated to latest CTK - Python console fixes

Contains fixes for recent regressions in Python console:
1. Removed extra blank lines from Python console output. Fixes #731.
2. Fixed invalid command line when string is printed while editing command.

Revision 26175  Directory Listing
Modified Wed Jul 26 02:02:27 2017 UTC (2 months ago) by jcfr
COMP: Update python project to avoid forcing value of CMAKE_CFG_INTDIR

This commit updates python external project to avoid forcing the value
of CMAKE_CFG_INTDIR (deprecated since kitware/cmake@1b9d15c). Instead it
explicitly sets the BUILD_COMMAND.

Suggested-by: Adam Rankin <adam.rankin@gmail.com>
Tested-by: Andras Lasso <lasso@queensu.ca>

Revision 26174  Directory Listing
Modified Wed Jul 26 02:02:25 2017 UTC (2 months ago) by jcfr
COMP: Update bzip external project to fix windows debug build. See #4398

This commit updates bzip2 project and install the project to ensure it
can be found independently of the build configuration.

The current approach is similar to what is done for zlib:

* It ensures bzip2 is built with a configuration
  matching the one of the main build (this potentially ensures that
  code from other libraries can link against it)

* It prevents mix of Debug and Release C runtime libraries ensuring the
  the python bzip2 module is *NOT* builtin.

Suggested-by: Andras Lasso <lasso@queensu.ca>
Thanks: Adam Rankin <adam.rankin@gmail.com>

Revision 26167  Directory Listing
Modified Sun Jul 23 01:03:25 2017 UTC (2 months ago) by lassoan
ENH: Updated to latest CTK - DICOM metadata dialog improvements

Includes:

ENH: Added Copy metadata button to DICOM metadata widget
Added "Copy metadata" button (next to "Copy path" button) in the DICOM metadata browser (ctkDICOMObjectListWidget) to copy all metadata to the clipboard.
It is useful for collecting information from users when they reporting DICOM loading errors.

ENH: Added filtering and multi-file export to DICOM metadata dialog
To further improve ability to collect DICOM metadata information from users, the following features were added to the DICOM metadata window:
- free-text search in tag, name, vale fields
- export of filtered results (useful for easily excluding patient identifiable information)
- exporting of tags in all files in the files list (useful for example for getting image position information that requires all values), it works combined with filtering
- expand/collapse of all branches
- show total number of files and 1-based file index
- resize column widths to content by default

ENH: Added option to filter displayed metadata items by regexp

Regular expressions can be now used to filter any number of tags. Useful for remote assistance: user receives a regular expression
from the developer that lists all the relevant tags and only those.

For example: this filter lists 3 specific tags:

  regexp:0008,1030|0020,0010|0020,0011

[0008,1030]	StudyDescription	p4	LO	2
[0020,0010]	StudyID		SH	0
[0020,0011]	SeriesNumber	500	IS	4

ENH: Added method to get/set filter expression

Revision 26164  Directory Listing
Modified Fri Jul 21 21:41:19 2017 UTC (2 months ago) by jcfr
ENH: Update Numpy from 1.9.2 to 1.13.1

[ci skip]

Co-authored-by: Franklin King <franklin.king@queensu.ca>
Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

From: Adam Rankin <adam.rankin@gmail.com>

Revision 26163  Directory Listing
Modified Fri Jul 21 21:06:09 2017 UTC (2 months ago) by jcfr
ENH: Enable python bz2 module adding bzlib2 dependency

The bzip2 library is statically built and linked into the corresponding
python module.

Suggested-by: Michael Hardisty <m.hardisty@utoronto.ca>

Revision 26159  Directory Listing
Modified Thu Jul 20 17:11:53 2017 UTC (2 months ago) by jcfr
ENH: Update DCMTK to 3.6.2

$ git shortlog d8ed091..DCMTK-3.6.2
Jan Schlamelcher (43):
      Fixed CMake check for <png.h> resp. <libpng/png.h>.
      Removed dead code from dcmnet.
      Hid some Visual Studio warnings regarding libxml.
      Moved config/arith.cc to config/tests/arith.cc
      Added configuration options for STL and C++11.
      Fixed segmentation fault in DcmDataDictionary.
      Enhanced recently introduced STL configuration tests.
      Fixed some code relying on C++11 features.
      Updated copyright notice in recently modified file.
      Fixed wrong paths to 'config' dir in CMake scripts.
      Added association negotiation profiles to dcmqrscp.
      Added attribute matching functions to DcmElement etc.
      Fixed combined date time range matching.
      Refactored dcmwlm's attribute matching implementation.
      Added a partial workaround for DCMTK bug #758.
      Added a workaround for a bug in x87 FPUs/GCC.
      Removed broken attributes from dcmqrdb.
      Fixed using wrong build type for configuration test.
      Several fixes for the SunPro compiler (Solaris).
      Fixed configuration test errors.
      Workaround for SunPro C vs. C++ inconsistencies.
      Fixed wrong syntax in previous commit.
      Many workarounds for SunPro.
      Fixed compiler errors on Visual Studio with OpenSSL.
      Fixed compiling with Oracle Developer Studio (SunPro).
      Fixed unexpected iconv behavior on FreeBSD.
      Fixed wrong usage of alignas.
      Silenced output of FIND_PACKAGE(ICU).
      Added a workaround for C++11 compiling errors.
      Added DCMTK_ENABLE_LFS for choosing LFS type (CMake).
      Workaround for strange LFS implementation on Windows.
      Small fixes for a previous commit.
      More fixes for SunPro.
      Added a workaround for inconsistent LFS API under QNX.
      Removed no longer required section from COPYRIGHT.
      Removed several macros from config/docs/macros.txt.
      Added support for suppressing C4307 on Visual Studio.
      Made including third-party libraries version agnostic.
      Updated ANNOUNCE and INSTALL for DCMTK release 3.6.2.
      Updated Makefile dependencies.
      Updated version information for DCMTK release 3.6.2.
      Updated man pages for DCMTK release 3.6.2.
      Created CHANGES.362 for DCMTK release 3.6.2.

Joerg Riesmeier (29):
      Removed unused local variable.
      Fixed inconsistent documentation in man page.
      Fixed documentation and other minor issues.
      Fixed issue with Simplified Adult Echo SR.
      Added unsigned suffix to large decimal constants.
      Fixed various stylistic issues.
      Fixed typo and rewrapped new text paragraphs.
      Changed the way XMLLIBS is set (Autoconf).
      Minor changes for supporting QNX 6.5.
      Added explicit type cast to keep QNX 6.5 quiet.
      Fixed issue with configure test on QNX 6.5.
      Updated Makefile dependencies.
      Updated data dictionary for DICOM 2017b.
      Added definition of new Storage SOP Class UIDs.
      Support new SOP Classes by networking tools.
      Added support for new "SR" and "PR" SOP Classes.
      Initial support for "Patient Radiation Dose SR".
      Added definition of new Presentation States.
      Added new Storage SOP Classes to comment sections.
      Updated latest tested CMake version.
      Enhanced documentation of gotoNamedChildNode().
      Added new method gotoNamedNodeInSubTree().
      Removed 2nd parameter from gotoNamedChildNode().
      Link MATHLIBS to all test programs.
      Moved MATHLIBS to LOCALLIBS.
      Removed useless target "tclabutil" from Makefile.
      Minor fixes in Makefile.
      Fixed typo in Coding Scheme Description.
      Updated copyright date.

Marco Eichelberg (4):
      Removed unused variables.
      Converting large attributes to UN in explicit VR.
      Fixed handling of EINTR in networkDataAvailable().
      Removed support for HAVE_GUSI_H (MacOS classic).

Michael Onken (28):
      Fixed write transfer syntax and support Deflated.
      Suppress error message for missing segm. types.
      Fixed check for transcoding, added documentation.
      First check number of components before value.
      Added OB/OW-related comparison operators.
      Log write errors to error logger.
      Fixed compiler warning on integer casting.
      Fixed wrong copy of SOP class in role selection.
      Made parameter const.
      Fixed possible role selection config. problem.
      Removed dcmStrictRoleSelection config. switch.
      Enhanced role selection documentation.
      Better parameter name and documentation.
      Allow search for role in SCU presentation contexts.
      Added role selection tests.
      Removed leftovers from dcmStrictRoleSelection.
      Fixed doubled space in log output.
      Fixed error message.
      Fixed ASCII art in comment.
      Opt. accept Default role if SCP role expected.
      Test recently introduced role selection option.
      Fixed ASCII art in test.
      Added missing space.
      Fixed typos.
      Removed unused variable.
      Require CMake > 2.8.3. Extended DCMTKConfig.cmake.
      Moved TRY_COMPILE to where it is first needed.
      Export new LFS CMake flag to DCMTKConfig.cmake.

Nikolas Goldhammer (3):
      Replaced 'errno' with OFStandard::getLast*ErrorCode().
      Partially refactored 'errno' usage within dcmnet.
      Fixed OFerror_code's unit test not working on OpenBSD.

Sebastian Grallert (12):
      Enhanced dcm2json application documentation.
      Added an argument conflict check for dcm2json.
      Enhanced value length information in DcmVR.
      Added some Attributes to DcmItem::checkAndUpdateVR().
      Added config test for the feenableexcept function.
      Several fixes for Solaris support.
      Fixed compiling on Solaris.
      Several fixes for NetBSD support.
      Fixed compiling error on Android.
      Added missing compiler flags for NetBSD (Autoconf).
      Modified compiler Flags for Solaris (CMake).
      Fixed configuration test errors on Visual Studio.

Thorben Hasenpusch (2):
      Added feature test files for STL and C++11 support.
      Renamed several HAVE_ macros for better consistency.

Revision 26158  Directory Listing
Modified Thu Jul 20 01:47:27 2017 UTC (2 months ago) by lassoan
ENH: Updated to latest CTK

Contains:

ENH: Added Copy metadata button to DICOM metadata widget

Added "Copy metadata" button (next to "Copy path" button) in the DICOM metadata browser (ctkDICOMObjectListWidget) to copy all metadata to the clipboard.
It is useful for collecting information from users when they reporting DICOM loading errors.
Also added tooltip for the existing, very useful, but hard-to-discover feature: if user clicks on a tag then its definition is displayed at http://dicomlookup.com.

STYLE: Fix CircleCI link

The CDash project for CTK seems retired. Clicking the test results link should
navigate to CircleCI. Additionally, update the build status icon to 'shield'
style, which includes the word 'circleci'.

Revision 26155  Directory Listing
Modified Tue Jul 18 17:32:13 2017 UTC (2 months, 1 week ago) by jcfr
ENH: Update CTK: Improve Python console completion, improve CTK build system

$ git shortlog commontk/CTK@9e6df18..commontk/CTK@3d30e4d --no-merges
Jean-Christophe Fillion-Robin (4):
      ENH: ctkConsole: Extend API adding cursorPosition, cursorColumn and cursorLine
      ENH: ctkConsole: Restore positions after building the completion model
      ENH: ctkConsole: Improve updateCommandBuffer to limit content of text
      ENH: PythonManagerTest: Add testPythonAttributeValues

Marco Nolden (2):
      Use CMAKE_CXX_STANDARD setting for inner CTK build and sub-projects
      COMP: fix build errors if DCMTK is configured to use STL

Max Smolens (1):
      BUG: Fix build when CMAKE_CXX_STANDARD is not set

Mayeul Chassagnard (15):
      ENH: Add test for ctkAbstractPythonManager::pythonAttributes()
      ENH: ctkAbstractPythonManager: pythonAttributes can instantiate class and return instance members
      ENH: ctkConsole: Display output message under command line during autocompletion
      ENH: ctkConsole: Restrict cursor to command_line's end rather than document's end
      BUG: ctkConsole: Ensure autocompleter is updated or hidden when moving left
      ENH: ctkConsole: Prevent autocomplete from interfering with the message area
      BUG: ctkConsole: Allow to replace if cursor at the beginning of the interactive area
      BUG: ctkConsole: Backspace working in every case in the PythonConsole
      BUG: ctkConsole: Fix autocomplete during insertion
      STYLE: ctkConsole: Fix indent
      ENH: ctkAbstractPythonManager: Update autocompletion to support callable with arguments
      BUG: ctkConsole: Fix delete/BackSpace when cursor = commandEnd/InteractivePosition
      ENH: ctkConsole: Support completion within multi-line statement
      BUG: ctkConsole: Do not modify selected text color if outside interactive area
      ENH: ctkConsole: Support 2 different method to InsertCompletion

Revision 26153  Directory Listing
Modified Sat Jul 15 12:57:56 2017 UTC (2 months, 1 week ago) by lassoan
ENH: Updated OpenIGTLink to latest master

Fixes socket close issue:
https://github.com/openigtlink/OpenIGTLink/issues/133

Revision 26137  Directory Listing
Modified Mon Jun 26 15:29:23 2017 UTC (2 months, 4 weeks ago) by jcfr
ENH: Updating SEM to integrate more explicitly named functions

- New Slicer Execution model version in Slicer (see Slicer/SlicerExecutionModel#91):

  $ git shortlog Slicer/SlicerExecutionModel@61bb14d..Slicer/SlicerExecutionModel@1d3e9a2 --no-merges
  Jean-Baptiste Vimort (2):
      STYLE: Renaming of the 'defaultValue' parameter's attribute to 'Value'
      ENH: Depreciation of the old functions

- Replace the use of deprecated functions with the new ones

- Deprecate the GetParameterDefault method: the GetParameterValue method
  should be used instead

Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

Reviewed-by: Johan Andruejol <johan.andruejol@kitware.com>
Reviewed-by: Steve Pieper <pieper@bwh.harvard.edu>

From: Jean-Baptiste VIMORT <jb.vimort@kitware.com>

Revision 26127  Directory Listing
Modified Fri Jun 23 00:27:41 2017 UTC (3 months ago) by pieper
BUG: move to ITK with fixed DCMTK orientation reading

In Slicer/ITK for now, moving towards ITK proper

http://review.source.kitware.com/#/c/22458/

From: Steve Pieper <pieper@isomics.com>

Revision 26107  Directory Listing
Modified Thu Jun 22 16:08:29 2017 UTC (3 months ago) by lassoan
BUG: Fixed warping of markup fiducial labels

Warping of markup fiducial labels was caused by using perspective projection in overlay renderer's camera. See details in commontk/CTK#720.

By switching to parallel projection, default scaling of widgets have to be adjusted, and all other renderers should also use parallel projection to make point placing for widgets invariant to the renderer that is picked.

Revision 26089  Directory Listing
Modified Wed Jun 14 14:46:22 2017 UTC (3 months, 1 week ago) by jcfr
COMP: Update CTK to fix build issue with CMake 3.9.0-rc2.

Build error was introduced by "cmIfCommand: Reject duplicate else() and misplaced
elseif()" (https://gitlab.kitware.com/cmake/cmake/merge_requests/594)

See #4380

$ git shortlog 7129bb0..06ac6eb --no-merges
Samuel John (1):
      BUG: BuildSystem: Remove duplicated else in ctkMacroSetupQt.cmake

Reported-by: Dzenan Zukic <dzenan.zukic@kitware.com>

Revision 26086  Directory Listing
Modified Tue Jun 13 17:11:48 2017 UTC (3 months, 1 week ago) by jcfr
COMP: Update python build system to fix build issue with CMake 3.9.0-rc2.

Build error was introduced by "cmIfCommand: Reject duplicate else() and misplaced
elseif()" (https://gitlab.kitware.com/cmake/cmake/merge_requests/594)


Fixes #4380

$ git shortlog d0f4719..ec32acc --no-merges
Jean-Christophe Fillion-Robin (1):
      cmake/UnitTests: Remove duplicated else

Reported-by: Dzenan Zukic <dzenan.zukic@kitware.com>
Co-authored-by: Andras Lasso <lasso@queensu.ca>

Revision 26069  Directory Listing
Modified Fri Jun 2 15:19:13 2017 UTC (3 months, 3 weeks ago) by jcfr
ENH: BuildSystem: Update DCMTK repo to support source download behind proxy

See https://discourse.slicer.org/t/slicer-compile-behind-proxy-clone-into-dcmtk-through-http/423

Revision 26055  Directory Listing
Modified Mon May 29 20:42:52 2017 UTC (3 months, 3 weeks ago) by jcfr
ENH: cmake: Check package availability when building against system python

This commit implements the check looking for required python modules
when building against system version of python.

For example, assuming that all required packages are installed in
a python virtual environment named "slicer":

$ cmake -DQT_QMAKE_EXECUTABLE:FILEPATH=/path/to/bin/qmake \
  -DCMAKE_BUILD_TYPE:STRING=Release \
  -DSlicer_USE_SYSTEM_python:BOOL=1 \
  ../Slicer

would output text like this one:

[...]
-- SuperBuild -         python-pyparsing => Requires python[INCLUDED],
-- SuperBuild -         python-pyparsing[OK] (SYSTEM)
-- PYPARSING_PATH: /home/jcfr/.virtualenvs/slicer/local/lib/python2.7/site-packages
-- PYPARSING_VERSION: 2.2.0
-- SuperBuild -       python-packaging[OK] (SYSTEM)
-- PACKAGING_PATH: /home/jcfr/.virtualenvs/slicer/local/lib/python2.7/site-packages/packaging
-- PACKAGING_VERSION: 16.8
-- SuperBuild -       python-six => Requires python[INCLUDED],
-- SuperBuild -       python-six[OK] (SYSTEM)
-- SIX_PATH: /home/jcfr/.virtualenvs/slicer/local/lib/python2.7/site-packages
-- SIX_VERSION: 1.10.0
[...]

Revision 26042  Directory Listing
Modified Thu May 25 05:06:47 2017 UTC (4 months ago) by jcfr
ENH: Add support for reading launcher setting using CTKAppLauncherLib

This commit introduces a dependency to the statically linked
library CTKAppLauncherLib

This library also used internally by the regular Slicer launcher allows
to read the launcher main settings and its associated revision specific
settings listing extensions paths.

Since on all platforms, environment variables are now consistently read
from settings files, this commit removes:

(1) the duplicated code path settings variables from the application
using methods like:
* qSlicerCoreApplicationPrivate::setPythonEnvironmentVariables()
* qSlicerCoreApplicationPrivate::setTclEnvironmentVariables()
* qSlicerCoreApplicationPrivate::discoverITKFactoriesDirectory()
* qSlicerCorePythonManager::pythonPaths()

(2) the application settings "Python/AdditionalPythonPaths" originally
introduced in r20852 (BUG: Ensure extension python paths are set on MacOSX)
to workaround the fact launcher settings were not used on MacOSX.

Finally, this commit also ensures that PYTHONPATH associated with thirdparty
libraries bundled in extension are considered on MacOSX. See Radiomics/SlicerRadiomics#18

[ci skip]

Revision 26024  Directory Listing
Modified Thu May 18 15:51:13 2017 UTC (4 months, 1 week ago) by jcfr
STYLE: BuildSystem: Update SimpleITK external proj to use recommended opts (2)

Suggested-by: Bradley Lowekamp <blowekamp@mail.nih.gov>

Revision 26023  Directory Listing
Modified Thu May 18 15:24:40 2017 UTC (4 months, 1 week ago) by jcfr
STYLE: BuildSystem: Update SimpleITK external proj to use recommended options

Revision 26017  Directory Listing
Modified Wed May 17 08:00:31 2017 UTC (4 months, 1 week ago) by jcfr
COMP: Update ITKv4 to fix MINC build error using redhat devtoolset 2

This commit updates ITK and fix an error reported when building
Slicer using redhat toolset 2 on CircleCI.

Details:

8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---
commit Slicer/ITK@3cc1a24
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Wed May 17 03:52:36 2017 -0400

    COMP: libminc: Define _GNU_SOURCE to enable C99 extension during introspection

    This commit addresses failure to detect "round" function on
    compiler like g++ 4.8.2 provided by redhat devtoolset 2 [1].

    More specifically, since the macro __USE_ISOC99 wasn't defined, function
    "round" declared in "mathcalls.h" (itself included from "math.h") wasn't
    found during introspection.

    Defining _GNU_SOURCE allows to enable c99. See features.h for more details.

    Error fixed by this commit is the following:

    /path/to/ITKv4/Modules/ThirdParty/MINC/src/libminc/libsrc2/hyper.c:64:1: error: redefinition of ‘round’
     round(double x)
     ^

    and it is reproducible using docker-centos-build [2].

    CMake macro was adapated from python-cmake-buildsystem [3]

    [1] https://access.redhat.com/documentation/en-US/Red_Hat_Developer_Toolset/2/html/2.0_Release_Notes/DTS2.0_Release.html
    [2] https://github.com/thewtex/docker-centos-build
    [3] https://github.com/python-cmake-buildsystem/python-cmake-buildsystem/blob/d0f47193837db6ad9e08bc99617276d4a24687c3/cmake/ConfigureChecks.cmake#L415
8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---

Revision 26011  Directory Listing
Modified Mon May 15 15:46:24 2017 UTC (4 months, 1 week ago) by jcfr
ENH: Add support for MINC image IO

Issue #4085

This enables MINC Image IO via ITK. This currently supports MINC version 2
(HDF5-based).

Reviewed-by: Andriy Fedorov <fedorov@bwh.harvard.edu>
Reviewed-by: Andras Lasso <lasso@queensu.ca>
Reviewed-by: Johan Andruejol <johan.andruejol@kitware.com>
Reviewed-by: Gabriel A. Devenyi <gdevenyi@gmail.com>
Reviewed-by: Vladimir S. FONOV <vladimir.fonov@gmail.com>

Tested-by: Andras Lasso <lasso@queensu.ca>
Tested-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

From: Matt McCormick <matt.mccormick@kitware.com>

Revision 26010  Directory Listing
Modified Mon May 15 14:44:24 2017 UTC (4 months, 1 week ago) by jcfr
ENH: Update SimpleITK (Support for debug build)

Fixes #3816

Tested-by: Andras Lasso <lasso@queensu.ca>

$ git shortlog v1.0rc1..6433028
Bradley Lowekamp (171):
      Update CircleCi CMake version to 2.7.2
      Add CMake variable CMAKE_DL_LIBS to list for superbuild propagation
      Adding initially configured Sphinx documentation
      Add logo, title and under development note
      disable imgmath due to compatibility issues with readthedocs
      Merge topic 'AddInitialSphinxDocumentation'
      Use constant reference for FileName
      Merge topic 'IOFileNameByReference'
      Merge topic 'AddCMAKE_DL_LIBToSuperbuildPropagation'
      Merge topic 'UpdateCircleCiCMakeVersion'
      Replace 0 magic number with defined constant for WallClock
      Use namespace qualification for sitkWallClock
      Add RandomSeed header to wrap sitkWallClock enum
      Use sitkWallClock enum in test and examples
      Silence CMake message for CSharp targets
      Update ITK 4.11 along release branch
      Merge topic 'UpdateITK4.11-release'
      Merge topic 'SilenceCSharpTargets'
      Add clamping to optimizer's GetCurrentIteration method
      Use target definition over directory includes
      Remove required flags and replace with compile options property
      Adding CMake macro to migrate cache variable from SITK to SimpleITK
      Add missing library target to compile definitions
      Remove SITK_EXPRESS_INSTANTIATEDPIXELS option
      Migrate CMake options from SITK_ prefix to SimpleITK_
      Migrate SITK_FORBID_DOWNLOADS option to SimpleITK_FORBID_DOWNLOADS
      Migrate option to SimpleITK_USE_VIRTUALENV from SITK prefix
      Migrate to SimpleITK_LUA_BUILD_EXECUTABLE CMake option
      Migrate to SimpleITK_GIT_PROTOCOL
      Migrate SITK_ prefix for LUA_EXECUTABLE to SimpleITK_ prefix
      Change internal variable to prefered SimpleITK_PYTHON project prefix
      Prefer SimpleITK over SIMPLEITK for CMake variables
      Merge topic 'AddressMSVCConversionWarning'
      Correct logic for running C++11 requirement
      Merge topic 'RemoveFontFromDoxygen'
      Merge topic 'UseCMakeTargetProperties'
      Merge topic 'DeprecateSITKCMakeOptionPrefix'
      Add missing EXPORTS define to BasicFilters1 library
      Merge topic 'UseCMakeTargetProperties'
      Organize json scipts into a directory
      Adding script to update json files with ITK module names
      Adding itk_module field to json files
      Separate BasicFilter library creation into function
      Add generated cxx file to list with ITK module names
      Create BasicFilter libraries corresponding to ITK modules
      Remove manual BasicFilters1 library
      Rename library by removing BasicFilters form ITK modular libraries.
      Update JSONValidate.py path for doxygen cmake code
      Include CMake legacy module when used
      Fix typeo in argument name for restoring LUA_EXECUTABLE cache variable
      Add required virutalenv version for producing wheels
      Add CMake option for --plat-name for distutils
      Merge topic 'DeprecateSITKCMakeOptionPrefix'
      Merge topic 'FixLuaExecutableCacheArgument'
      Merge topic 'UseITKModuleForLibraries'
      Merge topic 'RemoveDoubleBackticksForDoxygen'
      Adding comment to CMake function for building basic filter libraries
      Correct ITK Module some transform initializes belong to
      Fix basic filter source list to always remove modular sources
      Set target properties for using ITK modules instead of including use file
      Reduce the set of ITK modules required to build SimpleITK
      Do not process JSON filter if ITK modules is not enabled.
      Merge topic 'AddPythonPlatNameOption'
      Remove bad loop over ITK modules passed to sitk_target_use_itk
      Add library directories if needed when using an ITK module
      Use local variables for json file path
      Delete CMake all variables from cache for list of generated source
      Do not add examples as tests unless BUILD_TESTING is enabled
      Cast enum to uint32 to avoid signed integer conversion warning
      Add clamping to all optimizer's GetCurrentIteration wrapping
      Add CMake option for --plat-name for distutils
      Merge branch 'release'
      Up required Swig version to 3 in find_package command
      Merge topic 'UseEnumConstantForWallClockSentinel'
      Merge topic 'RefactorExampleIntoExampleDirectories'
      Merge topic 'AddressMSVCConversionWarning'
      Merge topic 'UseITKModulesToEnableLibraries'
      Merge topic 'RequireSwig3'
      Add error exception for pep425 wheel construction
      Merge topic 'gdcmSeriesFileNames'
      Update ITK Superbuild version along ITK 4.11 release
      Use CTest script to drive CircleCI builds
      Prefer CircleCI environment variables over repository specifics
      Merge topic 'UpdateITKOn4.11Release'
      Merge topic 'AddErrorExcpetionForPEP425Warning'
      Merge topic 'CircleCiUseCTest'
      Only install numpy into virtualenv when testing is enabled
      Fix correct syntax for CMake configuration variable substitution
      Set SITK_UNDEFINED_SYMBOLS_ALLOWED in language projects
      CircleCI builds on next branch should be the Continuous model
      Correct ctest to ingore pep425 error not warning
      Binary files were accidentally added and not md5 hash file
      Merge topic 'dicomTagsSpaceBug'
      Merge topic 'CMakeUndefVarName'
      Merge topic 'SetUndefinedSymbolsForLanguageProjects'
      Merge topic 'CircleCINextBuildAreContinuous'
      Merge topic 'FixBaselineBinaryAdded'
      Merge topic 'NumpyOnlyForTesting'
      Merge topic 'AddErrorExcpetionForPEP425Warning'
      Merge topic 'UpdateResampleDocumentation'
      Update CircleCI yaml to use ctest build flags
      Use CMake variable to execute cmake command
      Merge topic 'UpdateCircleCIWithCTestBuildFlags'
      Merge topic 'FixCMakeEchoCommand'
      Add sha512 hash data link files generated ContentLinkSynchronization
      Adding script to synchronize md5 and sha512 data link hashes
      Fix path to in source ExternalData with Superbuild
      Add Kitware's Girder as alternate download site for SHA512 data
      Fix the Doxygen mark up for the HashImageFilter
      Fix setting ITK Doxygen tag in configuration file
      Adding updated ExternalData module with support for multiple hashes
      Updating filter converge with ITK 4.11 release
      Merge topic 'FixHashFilterDocumentation'
      Merge topic 'bugExhaustiveOptimizer'
      Merge topic 'UpdateFilterConverage'
      Merge topic 'FixITKDoxygenTags'
      Add optional old_name to sitk_legacy_naming macro
      Rename Superbuild CMake variable to SimpleITK_USE_SYSTEM_*
      Remove code for old ITK_WRAPPING option.
      Merge topic 'AddSHA512ExternalDataSupport'
      Tweaks to R Documentation downloads
      Remove debugging message
      Merge topic 'FixSeeNodeIndentation'
      Merge topic 'RegeneratePythonDocstrings'
      Merge topic 'RDocFromMidas'
      Merge topic 'AddSHA512ExternalDataSupport'
      Rename git default variable to exclude from Superbuild propagation
      Merge topic 'UpdateSuperbuildUseSytemVariableNames'
      Merge topic 'RenameSimpleITKGitDefaultVar'
      Backport ExternalData.cmake for CMake version 3.0
      Define RETURN_SELF macro to void when wrapping with SWIG
      Fix missing occurrence of rename CMake variable
      Only add version suffix and properties to libraries.
      Remove AnaconaBuild script
      Merge topic 'AddSHA512ExternalDataSupport'
      Merge topic 'RenameSimpleITKGitDefaultVar'
      Merge topic 'RemoveAnacondaBuildScript'
      Add exception for trying to write DICOM with ImageSeriesWriter
      Correct the CMake DATA syntax for using a series
      Must use a ImageSeriesReader to read a DICOM series
      Add Dockerfiles and script to build manylinux complaint wheels
      Merge topic 'AddPythonManyliunxDockerScripts'
      Merge topic 'OnlyVersionLibraries'
      Merge topic 'RDocEquationFixes'
      Merge topic 'AddExceptionForWritingDICOMWithSeriesWriter'
      Merge topic 'dicomWrite'
      Merge topic 'RDocUpdateWarningsFixed'
      Merge topic 'DisableWrappedReturnSelf'
      Update setup.py classifiers
      Merge topic 'UpdatePythonAndJavaDocs'
      Merge topic 'UpdateSetup.pyClassifiers'
      Add variable options to manylinux docker builds
      Merge topic 'UpdateManyLinuxScripts'
      Fix the SimpleITK install directory used for superbuild SimpleITK Examples
      Use the install directory for include interface
      Merge branch 'FixSimpleITKVersionExampleSuperbuild-for-release' into release
      Merge branch 'FixIncludeInstallInterface-for-release' into release
      Use find_package for install and build path for build for ITK
      Pass ITK_DIR to the Examples Superbuild
      Updating Superbuild ITK version along release toward 4.11.1
      Merge branch 'FixITKTargetsPathInConfig-for-release' into release
      Relax tolerance for DiscreteGaussianImageFilter_short test
      Merge branch 'RelaxShortDiscreteGaussianTestTolerance-for-release' into release
      Relax tolerance on MagnitudeAndPhaseToComplex from i686 results
      Release tolerance for LandmarkBasedInitialization for i686
      Update to 4.11.1 tagged release
      Use exact reported version for required ITK version.
      Merge branch 'FixSimpleITKConfigITKVersion-for-release' into release
      Merge branch 'AdjustToleraceFori686Debug-for-release' into release
      Merge branch 'UpdateITK4.11.1-for-release' into release
      ENH: Support building debug SimpleITK against release Python

Dave Chen (4):
      Removed font from Doxygen
      Fix the indentation of See nodes in the docs
      PythonDocstrings.i regenerated to update docs
      Update PythonDocstring.i and JavaDoc.i

David T. Chen (2):
      Removed double backticks for Doxygen
      BUG: Check for undefined varName variable

Richard Beare (3):
      Support for downloading archive of R documentation from midas
      Improved support for converting equations for R
      update R documentation md5

Ziv Yaniv (8):
      BUG: removed the loadPrivateTags parameter from GetGDCMSeriesFileNames.
      Improved documentation for GetGDCMSeriesFileNames.
      BUG: Comparison of image type tag (0008|0008) was incorrect.
      Corrected spelling mistake and added details for Resample functions.
      BUG: Wrong metric value returned from Exhaustive optimizer.
      Adding support for writing DICOM series.
      Example moved to new directory structure and added test.
      Adding forward declaration for smart pointer.

From: Bradley Lowekamp <blowekamp@mail.nih.gov>

Revision 26008  Directory Listing
Modified Tue May 9 22:19:29 2017 UTC (4 months, 2 weeks ago) by jcfr
ENH: Update ITK to 4.12.0rc1

$ git shortlog 1619816..9c91cb6 --no-merges
Ben Boeckel (1):
      ENH: Add a script to help update third-party sources

Brad King (5):
      ENH: Update KWIML import script for new upstream URL
      ENH: Teach update-third-party.bash to add a Change-Id
      ENH: Port KWSys update script to update-third-party.bash
      ENH: KWSys: Filter out unused attributes during import
      ENH: KWSys: Apply attribute changes made upstream

Bradley Lowekamp (19):
      COMP: Enable hidden visibility property with NIFTI static libraries
      COMP: Enable hidden visibility property with GIFTI static libraries
      BUG: Correct variable name used to check CXX version
      BUG: Correct variable name used to check CXX version
      COMP: Enable hidden visibility property with NIFTI static libraries
      COMP: Enable hidden visibility property with GIFTI static libraries
      BUG: Initialize ConvergenceValue in constructor
      BUG: Initialize ConvergenceValue in constructor
      ENH: Update CircleCi script to download latest binary tar-ball
      BUG: Use CMAKE_DL_LIBS instead of explict "dl" library
      COMP: Fix CircleCI ITK data download file name
      ENH: Update CircleCI yaml file
      BUG: Apply changes from MetaIO upstream to remove static variables
      ENH: Update SWIG version to 3.0.12
      ENH: Update PCRE version to 8.40
      ENH: Add OrientedBoudingBox attributes to ShapeLabelMap
      COMP: Use std::abs over vnl_math_abs
      BUG: Initialize image data to 0
      ENH: Fix clearing build tree error

David T. Chen (1):
      BUG: Fixed quote style

Dženan Zukić (3):
      STYLE: Simplify code by using TestingMacros
      BUG: fixing wrong check for argument count
      ENH: Add Strain as a remote module

Floris Berendsen (2):
      COMP: Added missing png_get_uint_31 name mangling
      COMP: Added missing png_get_uint_31 name mangling

Francois Budin (58):
      STYLE: Typo corrections in itk*TopHatImageFilter.h
      ENH: Prefer std::atomic over compiler specific implementation
      BUG: Addresses 'ordered comparison between pointer and zero' error (clang-4)
      BUG: Addresses InDoxygenGroup Test with Python 3.6 failures
      BUG: BSplineScatteredDataPointSetToImageFilter output image is not generated
      BUG: itk::RGBPixel<unsigned short> needs to be wrapped for itkTIFFImageIO
      BUG: Usage of std::atomic was incorrectly used in itk::Detail::AtomicOps
      ENH: Exposing functions to set real and imaginary part of complex numbers
      BUG: ITK_OVERRIDE  keyword for non-overriden funtion
      BUG: 'typename' cannot be used outside of template declaration
      BUG: Missing ITK_OVERRIDE
      BUG: ITK_OVERRIDE  keyword for non-overriden funtion
      BUG: ITK_OVERRIDE  keyword for non-overriden funtion
      BUG: ITK_OVERRIDE  keyword for non-overriden funtion
      BUG: Missing ITK_OVERRIDE
      ENH: Improving usability in IPython
      ENH: Update BridgeNumPy to most recent version (2017.02.24)
      BUG: 3523 Even padding most value representations with space instead of '\0'
      BUG: Remove extra space in chronometer command
      DOC: Make it more explicit that 'push' authorization is not for everybody
      BUG: 3523 Even padding most value representations with space instead of '\0'
      BUG: 3519 KernelTransform WMatrix initialization
      BUG: KWSys symbols should not be exported with WINDOWS_EXPORT_ALL_SYMBOLS
      COMP: Do not expose functions to set real and img part of complex numbers
      BUG: KWSys symbols should not be exported with WINDOWS_EXPORT_ALL_SYMBOLS
      BUG: 3519 KernelTransform WMatrix initialization
      DOC: Typo in itkNumberToString.h
      BUG: Attribute names cannot start with a digit
      BUG: Do not define deprecated function if ITK_LEGACY_REMOVE is selected
      BUG: Wrap EllipseSpatialObject std::list in Python
      ENH: Wrap itkN4BiasFieldCorrectionImageFilter in Python
      BUG: itkStatisticsAlgorithmTest throwing exception on VS2015Update3 and VS2017
      ENH: Skip generating export headers if module does not contain a target
      BUG: Wrapping of itkHessianToObjectnessMeasureImageFilter moved out of Review
      ENH: Update BridgeNumPy to most recent version (2017.03.27)
      BUG: Wrapping of itkHessianToObjectnessMeasureImageFilter moved out of Review
      BUG: Wrap EllipseSpatialObject std::list in Python
      ENH: Improving usability in IPython
      BUG: Attribute names cannot start with a digit
      BUG: Do not export GDCM and Expat symbols with WINDOWS_EXPORT_ALL_SYMBOLS
      BUG: Do not export all symbols from third party libraries on Windows
      ENH: Allows to call ImageFileWriter in Python with Input=Filter
      BUG: Certain third party libraries need to export their symbols on Windows
      BUG: Test if 'issubclass' only if 'isclass' is True
      ENH: Add Python convenience function to read images
      BUG: 3475 AccumulateImageFilter not setting direction cosines of output image
      DOC: Removing typos in itkExtractImageFilter comments
      BUG: ProjectionImageFilter did not copy direction cosine information to output
      BUG: Test if 'issubclass' only if 'isclass' is True
      BUG: 3475 AccumulateImageFilter not setting direction cosines of output image
      BUG: Do not export GDCM and Expat symbols with WINDOWS_EXPORT_ALL_SYMBOLS
      BUG: Do not export all symbols from third party libraries on Windows
      BUG: Certain third party libraries need to export their symbols on Windows
      BUG: ProjectionImageFilter did not copy direction cosine information to output
      ENH: Update BridgeNumPy (2016.04.28) and update itkExtras.py accordingly
      BUG: Template type based input function parameter needs to be deterministic
      ENH: Bump CMakeLists.txt version to 4.11.1
      BUG: Problems due to ComputeOrientedBoundingBox in itkShapeLabelMapFilter

Jean-Baptiste VIMORT (1):
      PERF: Improvement of the itkHistogram class in order to make it faster

Jean-Christophe Fillion-Robin (3):
      ENH: Introduce ITK_WRAP_PYTHON_LEGACY to exclude older Python package layout
      BUG: ITKPython: Do not install *.mdx files required only at generation time
      COMP: Fix Slicer MacOSX extension packaging setting CMP0042 policy to OLD

Johan Andruejol (1):
      ENH: Add wrapping for PathToImageFilter

Jon Haitz Legarreta (131):
      ENH: Improve the itkFileListVideoIO coverage.
      STYLE: Improve the BSplineScatteredDataPointSetToImageFilter style,
      ENH: Improve the itkBSplineScatteredDataPointSetToImageFilter coverage.
      ENH: Add missing ivars in function PrintSelf.
      STYLE: Improve ImageNoise filters' style.
      STYLE: Improve the ImageNoise filters tests' style.
      STYLE: Improve ITKImageSources module filters' style.
      STYLE: Improve the itkLinearInterpolateImageFunction style.
      ENH: Improve the itkLabelOverlapMeasuresImageFilter coverage.
      STYLE: Improve itkAdaptiveHistogramEqualizationImageFilter style.
      ENH: Improve itkAdaptiveHistogramEqualizationImageFilter coverage.
      STYLE: Improve itkKappaStatisticImageToImageMetric style.
      ENH: Improve the itkKappaStatisticImageToImageMetric coverage.
      STYLE: Improve itkBinaryGrindPeakImageFilter style.
      STYLE: Improve the itkCannyEdgeDetectionImageFilter style.
      ENH: Improve itkCannyEdgeDetectionImageFilter coverage.
      ENH: Improve itkBarrier class coverage.
      STYLE: Improve itkFlipImageFilterStyle.
      STYLE: Improve itkSpatialObjectToPointSetFilter style.
      STYLE: Improve itkStretchIntensityImageFilter style.
      ENH: Print all ivars for itkStretchIntensityImageFilter.
      ENH: Improve itkPhysicalPointImageSource class coverage.
      ENH: Add missing ivars to LabelMapMaskImageFilter PrintSelf.
      ENH: Improve itkRealTimeClock coverage.
      STYLE: Improve the itkRealTimeClock style.
      ENH: Improve itkBsplineDecompositionImageFilter coverage.
      ENH: Improve itkTestingStretchIntensityImageFilter coverage.
      STYLE: Improve itkPathToChainCodePathFilter style.
      ENH: Add a Get method for itkPathToChainCodePathFilter ivar.
      ENH: Add specific testing macro for boolean members.
      STYLE: Improve itkLabelMapMaskImageFilter style.
      STYLE: Improve BSplineDecompositionImageFilter style.
      ENH: Finish itkAdaptiveHistogramEqualizationImageFilter PrintSelf.
      COMP: Fix ImageGrid tests compiler warnings.
      ENH: Finish BSplineDecompositionImageFilter PrintSelf.
      BUG: Fix Uninitialized Memory errors reported by Valgrind.
      ENH: Improve itkLabelMapMaskImageFilter coverage.
      ENH: Improve itkBinaryGrindPeakImageFilter coverage.
      ENH: Improve itkPathToChainCodePathFilter coverage.
      ENH: Move LabelMap module test baselines.
      ENH: Move BinaryMathMorphology test baselines out of review.
      ENH: Move ImageFusion test baselines out of review.
      ENH: Improve itkAutoCropLabelMapFilter tests.
      ENH: Improve itkSpatialObjectToPointSetFilter coverage.
      ENH: Move ImageLabel test baselines out of Review.
      ENH: Move ImageGrid test baselines out of review.
      STYLE: Improve itkGaussianSpatialFunction class' style.
      ENH: Improve the ITKPath module classes coverage.
      BUG: Fix BSplineDecompositionImageFilter Valgrind defects.
      STYLE: Improve itkColorTable style.
      ENH: Improve itkHoughTransform2DLinesImageFilter coverage.
      ENH: Improve itkHoughTransform2DCirclesImageFilter coverage.
      BUG: Address uninitialized variable defects.
      STYLE: Improve itk::HistogramThresholdImageFilter style.
      DOC: Fix a typo in the term "threshold".
      STYLE: Imporve itkContourSpatialObjectPoint style.
      ENH: Print all HoughTransform2DLinesImageFilter ivars.
      STYLE: Fix type in Optimizersv4 and Metricsv4 modules.
      ENH: Add PhiLattice regression baseline.
      ENH: Print all itkVoronoiDiagram2DGenerator ivars.
      ENH: Improve itkColorTable coverage.
      ENH: Improve the itk::GradientDescentOptimizerv4 style.
      ENH: Improve the itkImageSources module's filters' coverage.
      ENH: Add PhiLattice regression baseline.
      ENH: Add a new test for itk::ContourSpatialObjectPoint.
      BUG: Fix bug in itkContourSpatialObjectPointTest test.
      STYLE: Improve the itkGaussianSpatialFunctionTest style.
      ENH: Improve itkVotingBinaryHoleFillingImageFilter coverage.
      BUG: Fix precision issues in itkGaborKernelFunctionTest.
      BUG: Relax tolerance in itkGaborKernelFunctionTest.
      DOC: Fix minor typo in itkHistogramThresholdImageFilter doc.
      ENH: Print all ivars in GradientDescentOptimizer base classes.
      STYLE: Improve TIFFImageIO tests.
      ENH: Add Get methods for itk::BSplineDecompositionImageFilter ivars.
      BUG: Fix TimeProbes name in itkLargeTIFFImageWriteReadTest.
      BUG: Fix memory leaks in BMP and PNG tests.
      COMP: Fix signed/unsigned mismatch warning.
      COMP: Fix signed/unsigned mismatch warning.
      BUG: Fix Superclass for ITKThresholding calculators.
      BUG: Make the number of filters be an integer.
      ENH: Honor the itkBooleanMacro for boolean class members.
      ENH: Improve the Watershed module code coverage.
      COMP: Fix double to unsigned int cast warning.
      ENH: Improve coverage for MorphologicalWatersheds filters.
      STYLE: Improve the Denoising module style.
      BUG: Fix the itkPatchBasedDenoisingImageFilter RTTI Superclass name.
      COMP: Fix unsigned char from double conversion warning.
      ENH: Improve itkWatershedMiniPipelineProgressCommand coverage.
      ENH: Improve the itkRegionalMin/Max filters member print types.
      ENH: Improve the itkMorphologicalWatershedFromMarkers coverage.
      ENH: Improve the itkIsolatedWatershedImageFilter coverage.
      STYLE: Improve the Denoisinig module style.
      STYLE: Improve the FEMRegistration module files style.
      DOC: Fix itkOrientImageFilter UseImageDirection method doc typo.
      STYLE: Improve the ITKThresholding module classes style.
      BUG: Fix itkIsolatedWatershedImageFilterTest valgrind errors.
      STYLE: Improve the itkApproximateSignedDistanceMapImageFilter style.
      ENH: Improve Denoising module filters' coverage.
      ENH: Improve the FEMRegistration module coverage.
      STYLE: Improve the itkDisplacementFieldTransform class style.
      STYLE: Limit itkFlipImageFilter methods' loops variables' scope.
      ENH: Improve itkFlipImageFilter coverage.
      COMP: Fix itkPhysicsBasedNonRigidRegistrationMethodTest cast warning.
      STYLE: Improve the HessianToObjectnessMeasureImageFilter style.
      ENH: Improve coverage for HessianToObjectnessMeasureImageFilter.
      ENH: Improve DiscreteGaussianImage operators review classes' coverage.
      ENH: Add test for itk::ConicShellInteriorExteriorSpatialFunction.
      ENH: Print all itkHoughTransform2DCirclesImageFilter ivars.
      ENH: Improve coverage for itk::DisplacementFieldTransform.
      STYLE: Make itkPatchBasedDenoisingBaseImageFilter ivars private.
      STYLE: Improve the itkRobustAutomaticThreshold classes style.
      COMP: Fix itkDisplacementFieldTransformTest compiler warning.
      STYLE: Improve the itkGridForwardWarpImageFilter style.
      ENH: Improve coverage for itkGridForwardWarpImageFilter.
      ENH: Improve coverage for itkRobustAutomaticThreshold classes.
      ENH: Remove duplicate test files in Review.
      DOC: Fix itkDivideByConstantImageFilter doc error.
      STYLE: Improve exception message.
      STYLE: Improve ImageIntensity module image arithm op tests' style.
      STYLE: Improve HConc/Conv HMaxima/HMinima image filters' style.
      ENH: Improve the HConc/HConv HMaxima/HMinima filters' coverage.
      ENH: Improve DiscreteGaussianImage operators review classes' coverage.
      ENH: Change the URL for the PCA remote module repo.
      STYLE: Make flow control variables have a local scope.
      ENH: Add examples and doc build flag support for external modules.
      DOC: Remove wrong group tag for itk::QuadEdgeMeshExtendedTraits.
      BUG: Fix itk::FastMarchingImageFilter RTTI superclass name.
      STYLE: Improve the itk::NodePair class style.
      STYLE: Use the ITK_MANUAL_INSTANTIATION macro consistently.
      STYLE: Delete FastMarching module classes methods consistently.
      DOC: Fix typo in the "implementation" word across the code.

Jon Haitz Legarreta Gorroño (2):
      STYLE: Improve itkWarpHarmonicEnergyCalculator style.
      DOC: Add a notice to let users know about related implementations.

KWIML Upstream (1):
      KWIML 2017-02-27 (aa3a7733)

KWSys Upstream (3):
      KWSys 2016-11-21 (cb55cf5a)
      KWSys 2017-03-28 (34999b6a)
      KWSys 2017-04-20 (8785f84f)

Matthew McCormick (40):
      COMP: Add missing headers in OpenCVImageBridge
      COMP: Use double for gradient calculations in MinMaxCurvatureFlow
      ENH: Bump ITK version to 4.12.0.
      COMP: Add VCL support for GCC 7
      COMP: Define ITK_FALLTHROUGH for GCC 7
      COMP: Add missing ITK_FALLTHROUGH in TiffImageIO
      COMP: Avoid -Warray-bounds in FixedArray with GCC 7
      COMP: Add ProcessObject include in itkLevelSetBase.hxx
      ENH: Exclude Kitware Robot from third party update commit messages
      BUG: Address tab completion with IPython >= 5.0.0
      BUG: Do not use terminal_progress with the Jupyter Notebook
      ENH: Enable BridgeNumPy with Python wrapping
      COMP: Do not require numeric_traits::has_infinity
      BUG: Fix passing _NO_TR1 definition with VS9 and Python
      BUG: Do not tests that require NumPy when it is not available
      ENH: Build Python wrapping with hidden visibility
      ENH: Move morphological watersheds out of ITKReview
      BUG: Do not upload top level folder in ArchiveTestingDataOnGirder.py
      BUG: Remove unused content links from PNG test additions
      ENH: Add .sha512 content links for IO pallette test data
      BUG: Add missing export macros for SpatialObject forward declarations
      BUG: Always wrap basic type RGBUC
      COMP: Do not add Visual Studio numeric_traits workarounds with MinGWPy
      COMP: Increase gold linker requirement to GCC 4.9.0
      COMP: Detect Windows with _WIN32 in socket++/fork.cpp
      BUG: Revert "BUG: Include installed modules in ITK_MODULES_ENABLED"
      BUG: Set ${itk-module}_ENABLE_SHARED in ITKModuleExternal
      BUG: PolyLineParametricPath must be loaded before PathToImageFilter
      COMP: Address Python 2.7 Windows _hypot build errors
      COMP: Undefine Py_hash_t when wrapping VtkGlue
      ENH: Update BridgeNumPy to most recent version (2017.03.05)
      BUG: Improve itkTemplate New compatibility with Python 3
      ENH: Bump CastXML to 2017-04-18
      STYLE: Remove empty or erroreous comments in ImageToImageFilter
      ENH: Use itk.imread and itk.imwrite as standard function names
      BUG: Correct size specification in ImportImageFilter::SetImportPointer
      BUG: Improve large file support in MetaIO
      ENH: Wrap itk::IdentifierType for ScalarToRGBColormapImageFilter
      BUG: LevelSetNeighborhoodExtractor uses spacing
      BUG: Fix PCRE 8.40 download URL

MetaIO Maintainers (1):
      MetaIO 2017-04-08 (dead6687)

Olivier Commowick (1):
      BUG: Correct ITK eigen system (was producing NaN or different values than VNL)

Pablo Hernandez-Cerdan (4):
      ENH: Add SetReferenceImage to GenerateImageSource.
      ENH: Change the metadata of all outputs in GenerateImageSource.
      BUG: Fix Normalization kernel step of ConvolutionImageFilter.
      BUG: Remove call to Superclass::GenerateOutputInformation.

Richard Beare (1):
      DOC: PrincipleComponent flag incorrectly reported by PrintSelf

Sam Horvath (1):
      PERF: reduce memory usage of itkImagePCAShapeModelEstimator

Samuel Gerber (2):
      DOC: Added description to itkLBFGSOptimizerv4.h
      DOC: LBFGSOptimizer doc update

Shusil Dangi (2):
      ENH: Ignores MacOS .DS_Store file
      ENH: Wrap NormalVariateGenerator in the Statistics Module

Simon Rit (2):
      BUG: memory leak in ITK_USE_THREADPOOL
      BUG: Join threads when using thread pool (ITK_USE_THREADPOOL)

Taylor Braun-Jones (1):
      COMP: Only include the headers for required OpenCV modules (fixup)

VXL Maintainers (2):
      VNL 2017-02-01 (ae6eff5e)
      VNL 2017-02-08 (ae8eef13)

Vladimir S. FONOV (3):
      MINC 2017-04-28 (3d79acf3)
      MINC 2017-05-01 (4caf8f4c)
      MINC 2017-05-05 (cc682b52)

Yann Le Poul (4):
      ENH: improvement of palette image support for PNG TIFF and BMP.
      STYLE: Misleading IsReadAsScalarPlusPalette Printing string
      STYLE: ReadAsScalarPlusPalette info already printed in itkImageIOBase
      BUG: ExpandRGBPalette used instead of IsReadAsScalarPlusPalette

Revision 26007  Directory Listing
Modified Sat May 6 19:01:05 2017 UTC (4 months, 2 weeks ago) by jcfr
COMP: Update CTK and fix warnings

$ git shortlog a63253f..7129bb0 --no-merges
Jean-Christophe Fillion-Robin (2):
      Update QtTesting to fix overload warnings
      COMP: ctkErrorLogFDMessageHandler: Fix "unused-result" warning

Revision 25986  Directory Listing
Modified Fri Apr 28 18:27:37 2017 UTC (4 months, 4 weeks ago) by jcfr
COMP: Update python-cmake-buildsystem to address NUMPY build issue

This commit fixes a regression introduced in r25955 (ENH: Update
python-cmake-buildsystem version) and python-cmake-buildsystem/python-cmake-buildsystem@9cce62e

See #4366

Update details:

$ git shortlog 30b0d56..d0f4719 --no-merges
Isaiah Norton (1):
      Fix broken python2.7 config location


Thanks: Isaiah Norton <inorton@bwh.harvard.edu>

Revision 25979  Directory Listing
Modified Thu Apr 27 16:10:43 2017 UTC (4 months, 4 weeks ago) by fedorov
ENH: update DCMTK to d8ed091

This update is needed to address a bug that prevented proper handling of character
set while importing attributes into DICOM Segmentation object. This was a critical
bug for the dcmqi library, and in turn for QuantitativeReporting extension. See
detailed discussion at https://github.com/QIICR/dcmqi/issues/233.

$ git shortlog DCMTK-3.6.1_20161102..d8ed091 --no-merges
Jan Schlamelcher (82):
      Enhanced C++11 compliance of OFvariant.
      Added macros for controlling compiler diagnostics.
      Suppressed some unnecessary warnings.
      Adjusted a previous commit for older GCC versions.
      Added some missing files to the install steps.
      Added compiler version checks to ofdiag.h etc.
      Suppressed an inappropriate Visual Studio warning.
      Added support for additional compiler diagnostics.
      Several fixes for OFnumeric_limits.
      Suppressed silly Visual Studio warnings in OFvariant.
      Suppressed warnings in OFThread's unit test.
      Fixed an OFnumeric_limits problem regarding C++11.
      Refactored character set conversion classes.
      Several fixes regarding character set conversion.
      Fixed a comment in OFCharacterEncoding.
      Fixed dcm2json when compiling as shared libraries.
      Fixed oflog character set conversion defines.
      Added magic word and version checks to dcmqrdb.
      Added additional information to DcmVR.
      Refactored DcmCharString based classes using DcmVR.
      Added DcmSpecificCharacterSet state checking methods.
      Fixed: ST is also affected by specific character set.
      Refactored dcmqrdb element list to use new/delete.
      Added Specific Character Set to the dcmqrdb index.
      Minor fixes in code comments of yesterdays commits.
      Added missing comment header to several unit tests.
      Added comparison operators for OFDateTime.
      Added string to number helper functions.
      Refactored string to date and time conversion.
      Introduced DcmAttributeMatching.
      Added character set conversion support to dcmqrdb.
      Fixed date time parsing regarding time zones.
      Moved dcmqrdb's trimString() function to OFStandard.
      Added support for additional Matching Keys.
      Added support for Issuer of Patient ID to dcmqrdb.
      Fixed Q/R matching on failed character set conversion.
      Workaround for clang non-type template argument issue.
      Fixed wrong value range check in extractDigits().
      Fixed Visual Studio linker problem with DLLs.
      Fixed digits10 not being a compile time constant.
      Documented dcmqrdb's new character set features.
      Fixed formatting errors in dcmqrscp's man page.
      Updated Makefile dependencies.
      Updated man pages for new development snapshot.
      Updated DCMTK_ABI_VERSION for new development snapshot.
      Updated CHANGES.361 for new development snapshot.
      Fixed dcmqrdb falsely retrying response conversion.
      Fixed previous commit.
      Fixed dcmqrdb falsely retrying response conversion.
      Fixed previous commit.
      Fixed CMake unit tests when BUILD_APPS was disabled.
      Fixed installing manpages with CMake.
      Fixed previous commit support for old CMake versions.
      Fixed inspecting fundamental arithmetic types.
      Fixed build date definition problem regarding Xcode.
      Modified config to prefer CMake's own FindXXX modules.
      Fixed incorrect usage of FindICU.cmake.
      Replaced OFauto_ptr with OFunique_ptr.
      Updated Makefile dependencies.
      Fixed problems regarding Windows include magic.
      Enhanced the way <windows.h> is included.
      Fixed misleading commit introduced by copy and paste.
      Added dcmpstat and dcmwlm test applications to CMake.
      Refactored DSRListOfItems::EmptyItem.
      Suppressed an inappropriate Visual Studio warning.
      Fixed linking some dcmsr unit tests with MSVC.
      Added test-exhaustive target for CMake.
      Added configure tests for some reentrant functions.
      Refactored low level network API usage.
      Added double quotes around paths in CMake files.
      Added CMake config tests for int64_t and uint64_t.
      Modified CMake configuration regarding MinGW.
      Added config tests for including libc.h and math.h.
      Fixed CTest failing tests that did not compile.
      Fixed a mistake in the code generating arith.h.
      Refactored cross compiling support with MinGW/Wine.
      Fixed and refactored cross compiling for Android.
      Fixed and refactored running the unit tests via CTest.
      Refactored getMACAddress() and its use.
      Fixed a misplaced dllexport/dllimport declaration.
      Workaround for Clang regarding OFerror_category.
      Added some CMake config tests and removed a macro.

Joerg Riesmeier (169):
      Added support for InstanceCreatorUID to readXML().
      Added support for missing "ReportType" values.
      Removed check on arrays being not a null pointer.
      Made "ReportType" optional in XML Schema.
      Made getNumberOfVerifyingObservers() const.
      Added new method hasVerifyingObservers().
      Renamed empty() methods to isEmpty().
      Various Doxygen-related fixes to documentation.
      Enabled Doxygen's WARN_NO_PARAMDOC option.
      Fixed Doxygen-related issues in the documentation.
      Added missing documentation for return values.
      Fixed code value for "Pulse Sequence Name" (CP-1578).
      Added four Color Palette SOP Instances (CP-1584).
      Added support for recently approved CPs.
      Added initial support for Supplement 195.
      Added support for CP-1584 to data dictionary.
      Added support for new UID from Supplement 169.
      Added "Simplified Adult Echo SR" to known types.
      Use macro _LIBICONV_VERSION instead of variable.
      Added support for new SR IOD from Supplement 169.
      Replaced non-ASCII characters.
      Replaced tab characters by spaces.
      Fixed wrong identation with tab characters.
      Replaced non-ASCII character in comment header.
      Added note/warning on size of class instance.
      Fixed wrong reference to conventonal JPEG format.
      Fixed warning re. overloaded virtual function.
      Re-added tab characters removed by last commit.
      Rebuilt Makefile dependencies.
      Fixed issue with option "--display-overlay 0".
      Removed additional library dependencies.
      Updated data dictionary for DICOM 2016e.
      Updated code definitions for DICOM 2016e.
      Now use code constant CODE_DCM_PulseSequenceName.
      Added comments on transfer syntax name changes.
      Updated Context Group classes for DICOM 2016e.
      Updated "dcmrt" classes based on DICOM 2016e.
      Check return value of fgets() to avoid warnings.
      Check return value of write() to avoid warning.
      Replaced boolean modes in convertCharacterSet().
      Added missing API documentation for Doxygen.
      Added tests for "new" Chinese characters sets.
      Added missing character sets to XML Schema.
      Added "Simplified Adult Echo SR" to ReportType.
      Added missing API documentation (Doxygen).
      Limit number of entries in optimization LUT.
      Added (missing) comments.
      Changed the way an unused parameter is treated.
      Fixed various documentation issues.
      Updated note on character set conversion options.
      Fixed source code formatting (where appropriate).
      Renamed isAvailable() and getVersionString().
      Added missing period at the end of descriptions.
      Fixed wrong check on GLIBC macro.
      Added comments on ICU conversions flags.
      Avoid compiler warning on unused parameter.
      Various minor fixes to new "dcm2json" tool.
      Further fixes to source code formatting.
      Removed unused configure variable/definition.
      Fixed incomplete renaming of command line options.
      Added a section on the rendering limitations.
      Let git ignore recently introduced dcm2json tool.
      Added Manpage of recently introduced dcm2json tool.
      Removed "dcmwlm/wwwapps" from ".gitignore".
      Added another character set test (for ISO-IR 58).
      Updated documentation regarding HT delimiter.
      Fixed issue with wrong detection of delimiters.
      Added another character set test (for ISO-IR 149).
      Removed DCMTK's implementation of tempnam().
      Do not set TCP send and receive buffer length.
      Updated latest tested CMake version.
      Fixed warnings reported by VisualStudio 2015.
      Replaced binary ("&") by boolean ("&&") AND.
      Fixed maximum number of bytes to read from stdin.
      Do not disable Nagle algorithm by default.
      Do not pass simple const parameters by reference.
      Simplified output of default option values.
      Minor corrections to documentation/comments.
      Added #warning on DONT_DISABLE_NAGLE_ALGORITHM.
      Made send() and recv() timeout configurable.
      Added new option --socket-timeout to storescu/scp.
      Fixed typos in API documentation.
      Added missing header include (without OpenSSL).
      Removed unused variable from writeJsonOpener().
      Included missing standard header "assert".
      Enhanced comments on charset to library mapping.
      Disable exception throwing in destructor.
      Replaced remaining tabs by spaces.
      Minor cleanup in dump output of TLS connections.
      Added missing brackets to "if( || )" statement.
      Pass value of correct type to "size" parameter.
      Changed type for index/number of sequence items.
      Added explicit typecast to function parameter.
      Removed obsolete macro (Windows 95 workaround).
      Removed gethostbyname from compatibility header.
      Added support for recently approved CP-1619.
      Made sure that a value is loaded before modified.
      Minor fixes for reasons of consistency.
      Use DCM_MaxReadLength as the default value.
      Removed useless "option block" for single option.
      Updated credits with regard to the Debian package.
      Removed obsolete command line options.
      Fixed bug introduced with last commit (crash).
      Fixed description of option --prefer-mpeg4-bd.
      Shortened description of MPEG xfer options.
      Added further support for Supplement 195 (HEVC).
      Check returned status of chooseRepresentation().
      Fixed typo in command line option check.
      Added support for unkown VR "??" in dump file.
      Fixed wrong indentation of new options.
      Fixed wrong name of Storage SOP Class.
      Added new sample association negotiation profile.
      Fixes for non-patient DICOM Storage Objects.
      Further fixes regarding non-patient objects.
      Cleanup of comments (retired DICOM SOP Classes).
      Further enhanced support for non-patient objects.
      Allow for sending non-patient DICOM objects.
      Fixed name numberOfAllDcmStorageSOPClassUIDs.
      Added two missing SOP Classes to modality table.
      Fixed crash while processing an invalid DICOMDIR.
      Enhanced logging in case of error.
      Various documentation fixes to newDicomElement().
      Updated copyright date after previous commit.
      Added trailing "." after first sentence (Doxygen).
      Added parentheses around boolean operations.
      Fixed typo, tab character and trailing space.
      Removed documentation of macro STRICT_COMPARE.
      Updated documentation of getOFDateTimeFromString().
      Updated documentation of getOFTimeFromString().
      Further fixes to API documentation.
      Added "Issuer of Patient ID" to documentation.
      Removed outdated comment on DB_FindAttr struct.
      Moved dcm2json tool to the top (alphabetic order).
      Fixed output of network debug information.
      Manual fixes to data dictionary (DICOM 2017a).
      Added comment on "specific character set" options.
      Removed redundant "TransferSyntax" suffix.
      Fixed wrong comment on private GE transfer syntax.
      Updated code definitions for "SRT".
      Updated the code meaning of a "UCUM" code.
      Fixed copyright date.
      Removed trailing spaces.
      Re-added call of endOptionBlock().
      Updated data dictionary for DICOM 2017a.
      Updated code definitions for DICOM 2017a.
      Updated "dcmrt" classes based on DICOM 2017a.
      Fixed indentation and removed trailing spaces.
      Added standard comments to new CMake files.
      Fixed warning reported by gcc 4.8.5 (Linux).
      Fixed warnings reported by gcc with "-Wshadow".
      Removed unused variable "checkAllStrings".
      Fixed warnings on unused parameters.
      Enhanced logging of interface class DSRDocument.
      Replaced spaces by tabs in comment header.
      Documented that --write-ow is now the default.
      Updated Manpage after --write-us has been added.
      Documented new default value of --data-files-path.
      Removed trailing spaces added by last commit.
      Fixed issue reading XML template identification.
      Fixed minor issues in manpage.
      Enhanced XSD definition of "DecimalString".
      Enhanced XSD definition of "UniqueIdentifier".
      Fixed timezone issue with setISOFormattedTime().
      Fixed API documentation of newDicomElement().
      Separated test for dcmGenerateUniqueIdentifier().
      Disabled check of VR for unsupported charsets.
      Added missing object file to Makefile (Autoconf).
      Fixed non-ASCII character (German umlaut).
      Updated latest tested CMake version.

Marco Eichelberg (58):
      Updated dcmsign to correctly compile with OpenSSL 1.1.0.
      Updated dcmtls and dcmpstat to compile with OpenSSL 1.1.0.
      Added code for handling VOI LUT Sequences with OB/OW VR.
      Added code for handling VOI LUT Sequences with OB/OW VR.
      Fixed minor formatting issues.
      Removed unnecessary call to getBaseTag().
      JPEG encoder now writes SOF1 marker in 8-bit ext sequential TS.
      Fixed empty pixel data bug in DcmPixelData::write().
      JPEG decoder now decompresses incomplete bitstreams.
      Improved 8/12/16 bit JPEG code consistency.
      Added legal remark concerning HP's JPEG-LS patents.
      movescu now returns non-zero if c-move was unsuccessful.
      Documented new movescu return codes in man page.
      Fixed signed/unsigned comparison in dcmqrdb module.
      Minor change needed to compile on Cygwin 2.6.0.
      Increased buffer sizes to avoid buffer overflows.
      Use fseek() instead of rewind() on Win32/Cygwin.
      Fixed integer underflow condition.
      Fixed DJDecoderRegistration::registerCodecs().
      Fixed minor integer over/undeflows reported by clang.
      Length check for DICOM implementation version name.
      Fixed responding aetitle in ASC_dumpParameters().
      Delete partially received DICOM objects after error.
      Replaced unlink() with OFStandard::deleteFile().
      Added partial support for GE private transfer syntax.
      Added support for GE private transfer syntax.
      Added support for writing GE private transfer syntax.
      Fixed warnings reported by VS 2017.
      Fixed linker warnings reported by VS 2017.
      OFMutex on Win32 now based on cricital sections.
      Updated macro documentation.
      Parser can now be stopped before a certain tag.
      Updated API documentation.
      Fixed bug introduced with commit f58cfe9.
      JPEG/JPEG-LS padding now uses extended EOI marker.
      Minor API change in dcmjpls.
      Fixed policy CMP0017 warning in CMake 3.7.2.
      Fixed warnings reported by VS 2017 x64.
      Fixed warnings reported by VS 2017 x64.
      Fixed warnings reported by VS 2017 x64.
      Fixed warnings reported by VS 2017 x64.
      Fixed DLL compilation of libcharls.
      Fixed bug in dcmsign certification validation code.
      Changed wlmscpfs default data path to current dir.
      dcmquant now by default generates OW LUT data.
      Fixed server socket options on WIN32.
      Explicitly include <winsock2.h> on Windows.
      DCMTK now uses SOCKET data type on Windows.
      Added timeout handler to DUL FSM state 5.
      Fixed conversion of OF/OD to OB in big endian.
      Updated COPYRIGHT file.
      Now setting LossyImageCompression when decompressing.
      Prevent infinite loop in DUL_AbortAssociation.
      Socket handle now always passed as 64-bit on Win32.
      getMacAddress() on Windows now uses GetAdaptersInfo.
      Fixed private tag issue with dump2dcm and xml2dcm.
      Updated Makefile.
      Updated CREDITS.

Michael Onken (36):
      Renamed min() to min2() (macro name clash).
      Avoid warning regarding hidden virtual method.
      Fixed installation of DCMTKConfigVersion.cmake.
      Better SCP timeouts, test, cleanups and more docs.
      Fixed various documentation issues.
      Avoid warnings about shadowed names.
      Fixed warnings about overloaded virtual functions.
      Fixed warning about unused parameter.
      Print conn. timeout to TRACE instead DEBUG level.
      Avoid another variable shadow warning.
      Fixed (harmless) shadowed variable
      Fixed potential NULL pointer and implicit casts.
      Added hints that memory has to be freed by caller.
      Added missing documentation.
      Fixed User Identification Negotiation ack message.
      Fixed minor documnetation issue.
      Fixed minor documentation issue.
      Report error in case of wrong Pixel Data encoding.
      Fixed parameter type, and docs.
      Fixed dcumentation one more time.
      Moved latest post-read checks to DcmDataset.
      Fixed crash in debug mode (const pointer misuse).
      Remove unused files from build system.
      Rebuilt dependencies.
      Hide public element constructors setting length.
      Fixed missing assignment from last commit.
      Added error message when writing sequences.
      Fixed wrong buffer size for sprintf.
      Allow private tags creation in newDicomElement().
      Fixed module name in documentation.
      Added support for final text CP-1619.
      Fix backslash quoting for Windows --fork mode.
      Check override keys in img2dcm library code.
      Warn if patient name may lead to broken dir name.
      Take over charset on import. Minor changes.
      Ensure SPS/RP Description/Code is never empty.

Nikolas Goldhammer (2):
      Fixed OFStandard::atof() not handling "NaN".
      Introduced OFerror_code and related functionalities.

OFFIS DICOM Team (1):
      Fixed typo in method name and API docs.

Sebastian Grallert (10):
      Fixed suppressing overflow warnings with Clang.
      Added support for the DICOM JSON Model (part 18 F).
      Added MPEG-4 transfer syntax options to several apps.
      Removed unused command line parameters from dcm2json.
      Fixed and enhanced documentation of JSON functions.
      Added command line options for HEVC/H.265.
      Small fix for HEVC/H.265 commit.
      Again, a small fix for HEVC/H.265 commit.
      Added unique section labels in DCMTK man pages.
      Fixed the encoding section in dcm2json man page.

Thorben Hasenpusch (1):
      Fixed OFSemaphore for macOS.

Revision 25978  Directory Listing
Modified Wed Apr 26 18:33:02 2017 UTC (4 months, 4 weeks ago) by jcfr
ENH: Update ExternalProjectDependency based on commontk/Artichoke@0fff214

This commit fixes a configure error introduced in r25929 (ENH: Update
ExternalProjectDependency based on commontk/Artichoke@5ee3d50) by ensuring
USES_TERMINAL_* option are not used with CMake 3.3.2.

Also Update CTK to integrate a similar update:

$ git shortlog commontk/CTK@185e6e3..commontk/CTK@a63253f --no-merges
Jean-Christophe Fillion-Robin (1):
      Update ExternalProjectDependency based on commontk/Artichoke@0fff214

Reported-by: Bill Lorensen <bill.lorensen@gmail.com>

Revision 25970  Directory Listing
Modified Wed Apr 26 01:30:37 2017 UTC (5 months ago) by lassoan
BUG: Update to latest CTK to fix test errors

The new CTK version contains this fix for multi-value arguments handling in launcher.
When a multi-value argument was passed to the command-line parser, all subsequent parameters were considered part of the argument.
This lead to ignoring --python-script argument when --additional-module-paths argument was specified before.

The patch fixes these Slicer test errors:
* py_nomainwindow_SlicerTestingExitFailureTest
* py_nomainwindow_SlicerUnitTestWithErrorsTest
* py_SlicerTestingExitFailureTest).

Revision 25966  Directory Listing
Modified Tue Apr 25 23:33:16 2017 UTC (5 months ago) by jcfr
BUG: python-setuptools: Remove leftover lock file when starting build.

If build is interrupted before a lock is released, the associated lock file
needs to be explicitly removed to avoid following build from waiting
indefinitely.

Revision 25957  Directory Listing
Modified Tue Apr 25 03:58:17 2017 UTC (5 months ago) by jcfr
ENH: Install wheel and pip python packages

These packages will enable use of pip to install python dependencies.

Revision 25956  Directory Listing
Modified Tue Apr 25 03:58:15 2017 UTC (5 months ago) by jcfr
ENH: Update from Python 2.7.11 to 2.7.13

Revision 25955  Directory Listing
Modified Tue Apr 25 03:58:14 2017 UTC (5 months ago) by jcfr
ENH: Update python-cmake-buildsystem version

$ git shortlog 39ccab0..30b0d56 --no-merges
David Brooks (2):
      Correctly name the installed include and library configuration directories.
      Set PLATFORM_TRIPLET as per Python's `configure` script.

Jean-Christophe Fillion-Robin (9):
      ConfigureChecks: Add support for system not expecting "libutil" (e.g VxWorks)
      ConfigureChecks: Ensure LIBUTIL_LIBRARIES is set after first configure
      circleci: simplify load/pull/save of docker images using scikit-ci-addons
      extension_ctypes: Fix compilation on linux-x86
      circleci: Use dockcross scripts
      cmake: Change version built by default from 2.7.12 to 3.5.2
      circleci: Enable parallel build using circleci-matrix
      circleci: Speed-up build using system python
      Add support for Python 2.7.13

Jérémy Viau-Trudel (1):
      change default python version on readme.md

Marcel Metz (1):
      Replace remaining instances of BUILD_{SHARED,STATIC} control variable

Martin Oberhuber (2):
      ConfigureChecks: libutil is now optional. See #163
      ConfigureChecks: VxWorks:  Disable _XOPEN_SOURCE due to "sys/select.h" failing

Revision 25954  Directory Listing
Modified Tue Apr 25 03:58:12 2017 UTC (5 months ago) by jcfr
ENH: Support execution of python binaries using SlicerPython launcher env

Running the python executable (or any binaries installed by python) using
SlicerPython launcher environment will now resolve to the correct binary.

For example, here are after/before results associated with a linux Slicer
build tree.

After:

$ eval $(SlicerPython --launcher-show-set-environment-commands)
$ which python
/path/to/python-install/bin/python

Before:

$ eval $(SlicerPython --launcher-show-set-environment-commands)
$ which python
/usr/bin/python

Note that within a Slicer package, python executable is currently
renamed to "python-real". See r23057 (BUG: Rename installed python
executable to account for case-insistive system) for the rational.

Background:

The python project built by Slicer is installed in
/path/to/Slicer-SuperBuild/python-install, in addition to the python executable,
a launcher named "SlicerPython" is also configured and set as PYTHON_EXECUTABLE
CMake variable to ensure build step relying on python built by Slicer resolve
to the expected environment.

Revision 25950  Directory Listing
Modified Tue Apr 25 03:58:06 2017 UTC (5 months ago) by jcfr
ENH: Allow extension to check Slicer_USE_SYSTEM_python

This commit adds support for explicitly associating Slicer_USE_SYSTEM_*
variables with a label of the same name so that they are automatically
added to SlicerConfig.

This will allow to easily build Slicer extension against a system python
where extension python dependencies are already available.

Revision 25948  Directory Listing
Modified Tue Apr 25 03:58:02 2017 UTC (5 months ago) by jcfr
ENH: Improve generation of extension AdditionalLauncherSettings.ini

This commit updates the CMake module SlicerBlockAdditionalLauncherSettings
so that it reuses the function "ctkAppLauncherListToQtSettingsArray"

To allow the CMake function "ctkAppLauncherListToQtSettingsArray" to be
usable from the extension build system, "CTKAPPLAUNCHER_DIR" is added to
SlicerConfig by specifying the "FIND_PACKAGE" label.

Note that the "FIND_PACKAGE" label is used to automatically configure
the associated variables in "CMake/SlicerGenerateSlicerConfig.cmake"

Revision 25947  Directory Listing
Modified Tue Apr 25 03:58:00 2017 UTC (5 months ago) by jcfr
ENH: Introduce PYTHON_STDLIB_SUBDIR and PYTHON_SITE_PACKAGES_SUBDIR CMake vars

This commit :

 (1) avoids duplicated code paths by setting these two variables only
     in External_python.cmake,

 (2) prepares the transition to python 3 by removing most of the
     to hard-coded "python2.7" strings

 (3) adds the variables to SlicerConfig to facilitate the packaging
     of python packages within Slicer extensions.

Revision 25946  Directory Listing
Modified Tue Apr 25 03:57:56 2017 UTC (5 months ago) by jcfr
ENH: Update to setuptools v35.0.1

This commit updates to the latest version of setuptools and removes the now
unneeded patch for distutils.msvc9compiler. Indeed, latest version of
setuptools now properly patch distutils so that it works well with most
version of visual studio.

This commit also explicitly introduces the direct and indirect setuptools
dependencies:
* python-appdirs
* python-packaging
* python-pyparsing
* python-six

Note that setuptools is first bootstrapped, this is required to ensure
setuptools is installed properly with the file setuptools-X.Y.Z-py2.7.egg/EGG-INFO/entry_points.txt
available.

Revision 25929  Directory Listing
Modified Fri Apr 14 22:24:36 2017 UTC (5 months, 1 week ago) by jcfr
ENH: Update ExternalProjectDependency based on commontk/Artichoke@5ee3d50

This commit improves the support for Ninja generator by ensuring the
option USES_TERMINAL_* options are set to give Ninja access to the
terminal when the CMake version supports it.

See https://cmake.org/cmake/help/v3.4/module/ExternalProject.html

Also Update CTK to integrate a similar update:

$ git shortlog 19fc678..b8587e5 --no-merges
Jean-Christophe Fillion-Robin (2):
      Update ExternalProjectDependency based on commontk/Artichoke@5ee3d50
      ENH: ExternalProjecDependency: Re-apply commontk/CTK@6cc426b

Revision 25903  Directory Listing
Modified Tue Apr 4 05:14:08 2017 UTC (5 months, 3 weeks ago) by lassoan
ENH: Updated to latest CTK

Improves formatting of collapsible text in ctkFittedTextBrowser.

Revision 25893  Directory Listing
Modified Thu Mar 30 18:18:59 2017 UTC (5 months, 3 weeks ago) by pieper
BUG: update CTK with dicom fix

Exceptions thrown from ctk could cause spurious
errors, for example when checking for extensions.
This fix causes CTK to always return a usable
result to no error checking is needed in slicer.

https://github.com/commontk/CTK/issues/706

From: Steve Pieper <pieper@isomics.com>

Revision 25886  Directory Listing
Modified Tue Mar 28 21:27:51 2017 UTC (5 months, 4 weeks ago) by lassoan
ENH: Updated CTK to latest version

Contains ctkFittedTextBrowser API improvements for collapsible text display.

Revision 25868  Directory Listing
Modified Fri Mar 24 01:53:22 2017 UTC (6 months ago) by lassoan
ENH: Updated to latest CTK version

New feature: ctkFittedTextBrowser has a collapsible option now. It allows showing a single-line message with a 'More...' link that the user can click to see the full message.

Revision 25847  Directory Listing
Modified Mon Mar 20 16:58:37 2017 UTC (6 months ago) by jcfr
ENH: Add external project step allowing to keep track of project version.

This commit adds a module named "ExternalProjectGenerateProjectDescription"
providing a convenient function allowing to add a step generating
a project description file containing the name of the project and
its version.

For each project instrumented with this function, a file named
"version-<projectnmame>.txt" is generated in ${CMAKE_BINARY_DIR}.

Revision 25846  Directory Listing
Modified Mon Mar 20 15:07:14 2017 UTC (6 months ago) by jcfr
ENH: Support configuration of external project GIT tag and repository

For any given project checkout using Git, setting cache or environment
variables of the form:

  Slicer_<proj>_GIT_REPOSITORY
  Slicer_<proj>_GIT_TAG

allows to override the default values set within each External_* files.

Fixes #4148

Co-authored-by: "T.J. Corona" <tj.corona@kitware.com>

Revision 25843  Directory Listing
Modified Fri Mar 17 02:44:09 2017 UTC (6 months, 1 week ago) by jcfr
COMP: Update JsonCpp to fix GCC 6 build error. See #4268

See http://slicer-devel.65872.n3.nabble.com/Slicer-gcc-6-tt4038282.html
and http://na-mic.org/Mantis/view.php?id=4268

$ git shortlog f4afa75..73b8e17 --no-merges
Gregory C. Sharp (1):
      COMP: Update json_(reader|writer).cpp to fix gcc6 build error

Revision 25842  Directory Listing
Modified Thu Mar 16 03:01:11 2017 UTC (6 months, 1 week ago) by jcfr
BUG: Update qRestAPI to fix regression causing extension installation failure

$ git shortlog 9d3cfb6..d1b07cc --no-merges
Jean-Christophe Fillion-Robin (1):
      qMidasAPI: synchronousQuery: Fix regression and ensure query is sent

Reported-by: Andriy Fedorov <fedorov@bwh.harvard.edu>

Revision 25841  Directory Listing
Modified Tue Mar 14 22:49:02 2017 UTC (6 months, 1 week ago) by jcfr
ENH: Update OpenIGTLink (Misc. fixes)

$ git shortlog 96233c8..ba56464 --no-merges
Jean-Christophe Fillion-Robin (2):
      igtlMessageBase: Fix -Wsign-compare warning
      igtlTrajectoryMessage: Fix -Wunused-parameter warning

Longquan Chen (6):
      EHN: protocal file added in the library to synchonrize the source and protocol
      BUG: The example network should be updated regarding the new meta data format
      BUG: NDArray bug, private member called by child class
      EHN: the same message won't repack its contents multiple times, as its m_bodyispack flag is set to true. SetDeviceName() function reset the m_bodyIsPacked flag. So the same message is able to repack its content
      EHN: float value comparison error fixed
      BUG: unpack byte order error is fixed

Revision 25840  Directory Listing
Modified Tue Mar 14 22:49:00 2017 UTC (6 months, 1 week ago) by jcfr
ENH: Update qRestAPI (Adds Qt5 support, Fix misc issues)

$ git shortlog 5a81c92..9d3cfb6 --no-merges
Andreas Fetzer (16):
      Added support for sending HEAD request
      Moved deletion of qRestResult outside the if/else in order to prevent leakage.
      head request is now asynchronous.
      Removed unused parameter, adapted documentation
      Started to fix file upload
      Remove duplicate connections.     These ones are already created in the upload and download functions
      Refactored upload function analogous to download
      Removed unused slot
      Emitting signal if upload is finished
      Removed debug message
      Pass rawheaders again
      Added proper error handling in case the file could not be read.     Also deleted input in case of an error.
      Set parent for QFile in case of upload or download is called to assure that the     file is always deleted.
      Removed unnecessary uploadFinished signal
      Added possibility to set a http network proxy
      Use correct indent

Jean-Christophe Fillion-Robin (1):
      Fix unused variable warnings

Miklos Espak (4):
      Exporting qRestAPI_LIBRARY_DIRS for use by client code
      No data is not regarded as error in XNAT queries
      XNAT specific code removed
      Return 0 if result has already been taken

Sascha Zelzer (16):
      Added error reporting to qRestAPI.
      Don't take result object before calling waitForDone().
      Fixed inverted logic for returning true on success.
      Clean-up query results.
      Added error code for authentication errors.
      Fixed wrong error code assignment.
      Properly convert Qt network error codes to string.
      Only parse the response if no network error occurred.
      Added raw headers from the http response to qRestResult.
      Create result objects based on a string id using the Qt meta type system.
      Removed the "result" methods which instantiate objects.
      Removed template method declarations for already removed implementations.
      Deleting the QNetworkManager instance too early may lead to crashes.
      Restore Qt 4.6.2 compatibility.
      Added Qt5 compatibility.
      The Result map can be empty on connection errors. Check that.

Revision 25821  Directory Listing
Modified Sun Mar 12 19:44:26 2017 UTC (6 months, 2 weeks ago) by jcfr
BUG: Update CTK to allow ctkMacroWrapPythonQt working with absolute paths

$ git shortlog a6738bd..18019ae --no-merges
Jean-Christophe Fillion-Robin (1):
      BUG: ctkMacroWrapPythonQt: Fix handling of absolute input file paths

Reported-by: Alexis Girault <alexis.girault@kitware.com>

Revision 25820  Directory Listing
Modified Sun Mar 12 19:44:24 2017 UTC (6 months, 2 weeks ago) by jcfr
COMP: Update SlicerExecutionModel to include warning fixes

git shortlog 62d0121..61bb14d --no-merges
Jean-Christophe Fillion-Robin (9):
      STYLE: GenerateCLPTest: Update print_command_as_string to display working dir
      BUG: Fix GenerateCLP tests when JsonCpp and Serializer support are ON
      STYLE: GenerateCLP tests: Consistently use GenerateCLP_TEST_PROJECT macros
      ENH: ci: Run tests against ITK v4.10.1
      ENH: ci: Speedup testing caching docker images using scikit-ci-addons
      STYLE: circle: Update indent to facilitate reading of configuration file
      ENH: Add test building and running test with Serializer and JsonCpp ON
      COMP: GenerateCLP: Fix -Wunused-variable warning
      COMP: GenerateCLP: Fix -Wshadow warning

Stephen Aylward (1):
      BUG: ModuleDescription: Param LibraryLoader shadows this->LibraryLoader

Revision 25819  Directory Listing
Modified Sun Mar 12 19:44:22 2017 UTC (6 months, 2 weeks ago) by jcfr
COMP: Update CTK to fix unused variable warning

$ git shortlog 3b68bff..a6738bd --no-merges
Jean-Christophe Fillion-Robin (1):
      COMP: ctkVTKDataSetArrayComboBox: Fix unused variable warnings

Revision 25739  Directory Listing
Modified Wed Mar 1 18:59:46 2017 UTC (6 months, 3 weeks ago) by lassoan
ENH: Updated to latest CTK

* ENH: Implemented justified style for flow layout

It allows variable sized items (so that they use the space optimally) and nice visual alignment at the same time
(all rows have the same width).

Revision 25728  Directory Listing
Modified Fri Feb 24 22:20:13 2017 UTC (6 months, 4 weeks ago) by jcfr
ENH: Update CTK to include ctkFittedTextBrowser fix

git shortlog fc0b1b7..443dc27 --no-merges
Andras Lasso (1):
      BUG: Fixed ctkFittedTextBrowser height computation for wide content

Jean-Christophe Fillion-Robin (6):
      circleci: Rename image "ctk-test:opengl" into "ctk-test:opengl-qt4"
      circleci/Dockerfile-qt4: Speed up package install and optimize image size
      circleci: Add support for testing Qt5 build
      DICOM/Widgets: Fix "unused-but-set-variable" warning
      XNAT/Core: Fix warnings
      XNAT/Core: Fix unused warning in ctkXnatObject::fetchResources

Julien Finet (2):
      Increment QtTesting version
      Fix compilation with Qt < 5.1.1

Stephen R. Aylward (1):
      BUG: Missing vtkRenderingFreeType library option

Revision 25727  Directory Listing
Modified Fri Feb 24 22:11:35 2017 UTC (6 months, 4 weeks ago) by jcfr
BUG: Update ITK to fix building of SlicerPathology extension

Reported-by: Andriy Fedorov <fedorov@bwh.harvard.edu>

// -------------------------------------
commit Slicer/ITK@1619816
Author: Matt McCormick <matt.mccormick@kitware.com>
Date:   Mon Jan 23 13:47:32 2017 -0500

    COMP: Add missing headers in OpenCVImageBridge

    These are required when building the ITKExamples Superbuild.
// -------------------------------------

Revision 25726  Directory Listing
Modified Fri Feb 24 16:53:43 2017 UTC (7 months ago) by jcfr
BUG: Update ITK to fix ITKExternalMod/SlicerExt additional config (ITK-3529)

commit Slicer/ITK@3f7ce93
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Fri Feb 24 11:46:58 2017 -0500

    Revert "BUG: Include installed modules in ITK_MODULES_ENABLED"

    References:
        * https://issues.itk.org/jira/browse/ITK-3529
        * https://github.com/Slicer/Slicer/pull/674

    This reverts commit InsightSoftwareConsortium/ITK@4f8b60f

Revision 25722  Directory Listing
Modified Thu Feb 23 20:55:29 2017 UTC (7 months ago) by jcfr
BUG: Update ITK to fix ITKExternalMod and Slicer Extensions build (ITK-3529)

commit Slicer/ITK@0e5b94c
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Thu Feb 23 15:48:07 2017 -0500

    Revert "BUG: Binary include directory added only if enabled shared"

    References:
    * https://issues.itk.org/jira/browse/ITK-3529
    * https://github.com/Slicer/Slicer/pull/674

    This reverts commit InsightSoftwareConsortium/ITK@ea392a8

Revision 25719  Directory Listing
Modified Thu Feb 23 02:49:03 2017 UTC (7 months ago) by jcfr
ENH: Update ITK to v4.11.0 and SimpleITK to v1.0rc1

Tested-by: Andriy Fedorov <fedorov@bwh.harvard.edu>
Tested-by: Bradley Lowekamp <blowekamp@mail.nih.gov>
Tested-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Tested-by: Steve Pieper <pieper@bwh.harvard.edu>

Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

// ----------------------------------------------------------------------------
ITK changes:

git shortlog bd54ba1..71e441d --no-merges
Bill Lorensen (1):
      ENH: Bump WikiExamples version

Bradley Lowekamp (36):
      BUG: Enable VirtualDomain and FixedTransform in RegMethv4
      ENH: Adding initial CircleCi configuration file
      COMP: Fix float to unsigned integer conversion warnings
      BUG: Include installed modules in ITK_MODULES_ENABLED
      COMP: Address CMake error that ITKGPUCommon is not in export
      COMP: Address wrong library types with VS and shared libraries
      BUG: Ensure CreateImageIO is concurrent thread safe
      ENH: Mark HDF5 CMake options as internal
      COMP: Add template export declaration for ParametricPath
      COMP: Correct TEMPLATE_EXPLICIT definition in Path module
      ENH: Factor out common code in the TrasformFactoryBase registration
      ENH: Add CMake variable for max transform dimension, defaults 4
      ENH: Create CMake module to check for private RTTI compatibility
      ENH: Improving setting of default ITK_TEMPATE_VISIBILITY_DEFAULT
      COMP: Correct ifndef value to allow user defined ITK_TEMPLATE_EXPORT
      BUG: Add explicit instantiate for ObjectToObjectOptimizerBase
      COMP: Use add_definitions for CMake 2.8.9 compatibility
      COMP: Add warning suppression for distcc warning
      ENH: Explicitly instantiate the optimizer base over float
      BUG: Use IsLinear to check if transform is "affine"
      ENH: Remove unneeded includes of random iterator header
      ENH: Improve thread-safety for Generator, and unique New sequence
      ENH: Do not use global random generator
      BUG: Update v3 registration metrics to use local seed
      ENH: Prefer setting local seed over global in tests.
      ENH: Update SWIG to latest 3.0.11 release
      BUG: relax testing parameters for v3 translation registration
      BUG: Restore baseline for debug registration
      BUG: Remove unused SimpleImageRegistrationTest baselines
      ENH: Expose GetNextSeed method in MersenneTwiseter Generator
      BUG: Add option for fixed seed or wall clock seed for sampling
      BUG: Use metric random seed in v3 examples
      BUG: Prefer setting seed at algorithm in "v4" tests.
      BUG: Add itk prefix to TIFF files in binary directory.
      BUG: Remove ITK_DISALLOW_COPY_AND_ASSIGN as Doxygen private
      BUG: First IterationEvent is at CurrentIteration==0

Caspar Goch (2):
      BUG: Use printable type for RGBA pixel ostream for ITK-3501
      STYLE: Remove extra space for ITK-3501

Davis Vigneault (1):
      ENH: Add remote module DVMeshNoise

Dženan Zukić (5):
      ENH: updating version of AnisotropicDiffusionLBR
      ENH: adding UnsharpMaskingImageFilter
      COMP: explicitly cast to output type
      BUG: double call to update would cause empty output image
      ENH: Updating RLEImage remote module. Change-log:

Francois Budin (26):
      BUG: Supported extensions by PNG IO were not added in constructor.
      DOC: Documentation in itkRBGAPixel and itkRGBPixel was incorrect.
      ENH: Update SCIFIO to lastest (2016.12.01)
      ENH: FixedPointInverseDisplacementField moved to InsightSoftwareConsortium
      COMP: Remove compilation warnings
      ENH: Improved support of ccache and distcc
      BUG: GPUImage regression due to API change.
      ENH: Update Bridge Numpy (2016.12.05)
      ENH: Update VariationalRegistration to remove warnings during compilation
      ENH: FindPythonLibs does not support both debug and release python libraries
      ENH: Update VariationalRegistration
      BUG: Missing ITK_TEMPLATE_EXPORT in forward declaration of itk::ImageBase
      BUG: Missing ITK_TEMPLATE_EXPORT in itkOptimizerParametersHelper
      BUG: Missing ITK_TEMPLATE_EXPORT in templated class
      BUG: Remove linkage warnings on MacOS
      BUG: HDF5 CMake installation directory variable had not been updated
      BUG: Missing include header in AnisotropicDiffusionBLR remote module hxx files
      COMP: Silencing unused variable warning in itkTimeStamp
      STYLE: Improve style checking by using module ITKKWStyleOverwrite.txt
      COMP: OS*Barrier functions are deprecated on MacOS 10.12
      ENH: Update BridgeNumPy to latest version on 2017.01.08 to address ITK-3511
      BUG: Extra \$ in doxygen comment
      BUG: Binary include directory added only if enabled shared
      ENH: Update SCIFIO to latest revision (2017.01.17)
      ENH: Update SCIFIO to lastest commit (01.21.2017)
      BUG: Alpha value created when converted image to RGBA is not always 1

Hans Johnson (3):
      ENH: Provide mechanism for enhanced NIFTI support
      BUG: Use NIFTI sform/qform conventions correctly
      ENH: Remove ambiguity about sform/qform

Hastings Greer (1):
      BUG: Add test demonstrating Python global timestamp issue

Jean-Christophe Fillion-Robin (1):
      COMP: Fix Slicer MacOSX extension packaging setting CMP0042 policy to OLD

Jon Haitz Legarreta (54):
      ENH: Get internal ImageIO via a const macro.
      ENH: Improve Boolean Algebra ImageFilters coverage.
      STYLE: Improve the EuclideanDistancePointMetric style.
      ENH: Improve itkSigmoidImageFilter coverage.
      STYLE: Improve itkCropImageFilter style.
      ENH: Improve itkCropImageFilter coverage.
      ENH: Improve RGBToLuminanceImageFilter and Adaptor coverage.
      ENH: Improve itkRescaleIntensityImageFilter coverage.
      ENH: Improve the itkMatrixSelectionImageFilter coverage.
      ENH: Improve itkTanImageFilter and Adaptor coverage.
      ENH: Increase itkSqrtImageFilter and Adaptor coverage.
      ENH: Increase itkTernaryOperatorImageFilter coverage.
      ENH: Increase itkSymmetricEigenAnalysisImageFilter coverage.
      STYLE: Improve itkScalarImagekmeansImageFilter style.
      STYLE: Conform to TEST_SET_GET_VALUE definition.
      BUG: Fix uninitialized variable due to dynamic analysis defect.
      BUG: Fix uninitialized variable defect reported by valgrind.
      ENH: Improve the itkPointSetToPointSetRegistrationTest.
      ENH: Improve the itkPointSetToImageRegistrationTest.
      ENH: Increas BinaryMagnitudeImageFilter coverage.
      STYLE: Remove test name from std output.
      ENH: Increase MagnitudeImageFilter coverage.
      BUG: Fix uninitialized variable defect reported by valgrind.
      BUG: Fix Superclass name in RTTI.
      STYLE: Improve itkFrustumSpatialFunction style.
      STYLE: Improve the itkConicShellInteriorExteriorSpatialFunction style.
      BUG: Fix Superclass template argument list.
      STYLE: Improve the itkTorusInteriorExteriorSpatialFunction style.
      STYLE: Improve the itkCheckerBoardImageFilter class style.
      ENH: Improve the itk::LabelVotingImageFilter coverage.
      ENH: Improve itkCheckerBoardImageFilter coverage.
      STYLE: Improve itk::LabelVotingImageFilter style.
      STYLE: Improve the itkHoughTransform2DCirclesImageFilter style.
      ENH: Add test for itk::FrustumSpatialFunction class.
      ENH: Improve itkConnectedThresholdImageFilter coverage.
      STYLE: Improve itkConnectedThresholdImageFilter style.
      BUG: Fix FrustumSpatialFunction internal precision conversion.
      COMP: Fix implicit conversion warning.
      STYLE: Improve itkThresholdImageFilter style.
      ENH: Add test for itk::TorusInteriorExteriorSpatialFunction.
      BUG: Fix Superclass template argument list.
      ENH: Improve itkUnsharpMaskingImageFilter implementation.
      ENH: Improve the itkUnsharpMaskingImageFilter coverage.
      ENH: Fix UnsharpMaskingImageFilter test inconsistencies.
      BUG: Add missing itkTypeMacro.
      DOC: Document the member variables.
      BUG: Fix the itkImageSource RTTI class name,
      DOC: Document itkLabelOverlapMeasuresImageFilter methods.
      STYLE: Improve itkLabelImageGaussianInterpolateImageFunction style.
      ENH: Finish itkGaussianInterpolateImageFunction PrintSelf.
      STYLE: Improve itkLabelOverlapMeasurementImageFilter style.
      DOC: Fix ITKImageNoise filters' doc TeX errors.
      BUG: Fix uninitialized variables in itkGaussianInterpolateImageFunction.
      BUG: Fix RTTI Superclass name in itkLabelMapMaskImageFilter.

KWSys Robot (3):
      KWSys 2016-11-08 (2b3e2b1c)
      KWSys 2016-11-09 (18c65411)
      KWSys 2016-11-21 (cb55cf5a)

Matthew McCormick (21):
      ENH: Wrap VectorImage with complex real pixel types
      ENH: Bump PerformanceBenchmarking to 2016-11-07
      BUG: Do not assume zero Index in ReinitializeLevelSetImageFilter
      ENH: Create itk_module_add_library macro
      BUG: Update computeCodeCoverageLocally.sh for KWStyle addition
      COMP: Install a newer version of CMake on CircleCI
      ENH: Use GitHub Pages as the first ExternalData resource
      ENH: Add tests to demonstrate OSX dynamic_cast failure
      BUG: Use random seed with for MersenneTwisterRandomVariateGenerator.
      BUG: Enable program global timestamp
      BUG: Set random number seed in Mattes metric test
      BUG: Notify builder that ITK_DYNAMIC_LOADING is required with wrapping
      BUG: Define ITK_DYNAMIC_LOADING before ITK_WRAP_PYTHON
      BUG: Set random number seed mutual information metric tests
      BUG: Wrap std::vector< itk.Point >
      BUG: Fix wrapping of LandmarkBasedTransformInitializer
      BUG: Rename UnsharpMaskingImageFilter to UnsharpMaskImageFilter
      DOC: Add Dženan Zukić to .mailmap
      BUG: Remove invalid ImageRegistration4Test.png.sha512
      BUG: Fix cat/echo in ContentLinkSynchronization.sh
      ENH: Add missing SHA512 content links

Max Smolens (1):
      DOC: Fix itkUnsharpMaskImageFilter documentation typos

Mayeul Chassagnard (6):
      ENH: Update add_library TO itk_module_add_library
      COMP: Set Policy CMP0023 target_link_libraries for Modules/ThirdParty/VNLI...
      BUG: Add ITK_TEMPLATE_EXPORT to template classes
      BUG: Fix errors linked to dyn_cast merge
      BUG: Restore old ITKModule_TEMPLATE_EXPORT specification for classes
      BUG: dash3win7 dashboard build error unresolved external symbol

Richard Beare (1):
      BUG: Fix precision issues with poly-line FlatStructuring element

Simon Rit (1):
      BUG: ITK-based software was crasing when thread creation failed

Stephen Aylward (1):
      BUG: Target file for modules moved to subdir Targets.

Taylor Braun-Jones (1):
      COMP: Only include the headers for required OpenCV modules

// ----------------------------------------------------------------------------
SimpleITK changes:

$ git shortlog aeada7a..v1.0rc1 --no-merges
Bradley Lowekamp (135):
      Update to development version of ITK 4.11
      Remove duplication of transform being registered
      Move ExpandTemplate code generator to separate directory
      Moving template components under expand directory
      Separate the json4lua module into separate file
      Updating ITK along 4.11 development
      Adding Transform IO tests to verify BSpline order
      Add new baseline images for BSpline registration tests
      Use the list of ITK modules as required components for ITK find
      Mark integers as unsigned to avoid comparison warnings.
      Add Colormap option to LabelMapToRGB filter.
      ENH: adding methods and tests for Virtual image
      Remove extraneous print statements.
      Adding registration test with multi-levels and virtual image
      Use correct triple slash doxygen mark up for enum
      Adding documentation for EstimateLearningRate enum
      Adding check for virtual domain parameters
      Update ITK along master branch
      Use shared libraries on CircleCi to reduce memory required for linkage
      Set the displacement field interpolator for inverse too
      address signed to unsigned integer comparison warning
      Update Superbuild ITK version
      Fix the CMake type for visibility preset variables
      Adding test for concurrent file reading
      Update python virtualenv to 15.1.0
      Update tests to not use the "no_return_image" value.
      Use void return type when no_return_image is set to true.
      Adding lua JSONQuery script to get a json field
      Pass ExternalData_OBJECT_STORES to SimpleITK sub-project
      Correct version of virtualenv currently used
      Fix another signed to unsigned comparison warning
      Only use USES_TERMINAL when cmake is of sufficient version
      Only use TERMINAL feature with supported CMake version
      Use CMAKE_<LANG>_COMPILER_LAUNCHER in superbuild propagation variables
      Adding warning for CMAKE_CXX_COMPILER_ARG1 usage.
      Update example to use Enum over Value types for pixel Ids
      Update tests to use Enum over pixel Value Type
      Remove legacy CastImageFilter set output pixel id by value
      Fix Java enum does not not used construction, but value
      Updating Java example to use PixelID enum over value
      Improve error checking for memoryView creation
      Only return a memoryview for a bufferobject, rename internal method
      Reduce duplicate code in GetArray methods
      Fix unsuported Xdoclint option being used
      Fix incorrect variable used to detect if javadoc support Xdoclint option
      Update Documentation of get array methods.
      Fix detection of javadoc doclint option
      Add "sitk_" prefix to functions
      Use CMake method to set SITK_UNDEFINED_SYMBOLS_ALLOWED
      Address CMP0054 warning with "unused" string/variable
      Remove writable view option
      Due to change to use memoryview object Python 2.7 is now required
      Correct Java std::vector wrapping to rename push_back to add
      Enable NLM's midas server as download
      Update to SWIG 3.0.11
      Update SWIG version string
      Updating ITK Superbuild to 4.11 release candidate.
      Disable building of KWStyle with ITK
      Update Parameter Estimator test for ITK change
      Fix output pixel type for TransformToDisplacementFieldFilter
      Update ITK Superbuild version to 4.11rc2
      Adding missing connection for optimizer scales measurement.
      Adding test for scales callback for optimizers
      Adding OnePlusOneOptimizer to registration framework
      Update ITK superbuild version
      Adding change in header order.
      No longer return Self in Transform::AddTransform
      Separate legacy Python packaging into a separate file
      Fix path of SimpleITK documents files with language build
      Pass SKBUILD to ExternalProjects
      Using seed parameter for 1+1 optimizer
      Update to the SimpleITK 4.11.0 release!
      Remove options to compile ITK Wrapping along side SimpleITK
      Add seed parameter for registration point set generation
      Address signed to unsigned comparison warning
      Add missing time header for Visual Studio
      The next release of SimpleITK will be 1.0
      Fix failure to pass CMake visibility options to ITK
      Address new ITK template visibility feature
      Correct DYNAMIC_LOOKUP_* cache type to STRING
      Explicitly make pimple classes hidden
      Explicitly make typelist meta-programming structures hidden
      Propagate ITKV3_COMPATIBILITY to the ITK sub-build
      Add advanced CMake variable to determine default value of WRAP_*
      Update GoogleTest to 1.8.0 release
      Update FindGTest to latest CMake version
      Update GTest usage to use targets instead of CMake variables
      Correct local FindGTest to use system include file.
      Only use Threads target when it exists.
      Fallback to variable based library for link dependency on threads
      Only download GTest in Superbuild
      We require a recent version of Swig 3
      Add support for GTEST_ROOT as source directory.
      Fix checking if a variable is defined before adding to cache
      Remove SwigWin version from path
      Change to target_include_directories
      Rely on exported properties instead if SimpleITK Use file
      Remove stdint.h utility header
      Use target based include directories for languages
      Extract gtest_add_tests macro into separate file
      Update CircleCi
      Update the superbuild ITK version along the 4.11 release branch
      Correct CircleCi to use shared libraries
      Enable Python wrapping
      Adding libpython-dev for Python.h
      Move using Google Test as subdirectory
      Add casting to GetCurrentIteration in registration
      Adding Github pages as an external data download repository.
      Adding SimpleITK libraries to runtime path for Python testing
      Disable stripping post build step if CMAKE_STRIP is empty
      Install numpy for CircleCI via pip
      Explicitly add bigobj for MSVC in standalone languages
      Update ITK version to include valgrind defect patch
      Remove unused superbuild definition and MSVC bigobj flag
      Add test to verify randomness for seeds being set
      Update along ITK 4.11+ release branch
      Ran SwigDocUpdate.sh to update Java and Python Swig docstring files
      Improve Optimizer_ScalesEstimator test
      Revert "Remove stdint.h utility header"
      Remove direct include of stdint.h
      Add stdint alternative as public target include directory
      Compile the Explicit library with default visibility
      Move two example for multiple languages into the same directory
      Consolidate DicomSeriesReader examples into single directory
      Consolidate FilterProgressReporting examples
      Refactoring Demons and Method2 registration example directory
      Consolidate BSpline and Displacement registration examples
      Remove Java example subdirectory
      Removing Lua example subdirectory
      Move DicomImagePrintTags examples to one directory
      FIXUP.......
      Moving Python registration related examples to separate directories
      Adding cmake file for N4 Example
      Adding missing CMakeLists.txt files for example subdirectories
      Only add test property when language is enabled.

Dave Chen (2):
      Enforce SITK_FORBID_DOWNLOADS
      Updated JSON files

David T. Chen (4):
      Added some error handling to JSONQuery.lua
      Initial checkin of GenerateDoc.py
      Removed all groovy usage
      Delete GenerateDocumentation.groovy

Ghislain Antony Vaillant (1):
      Derive default package dir from library dir.

Hyun Jae Kang (2):
      ENH: Add new functionality to NumPy bridge methods for array views
      Copy Numpy Array test to test arrayview option

Jean-Christophe Fillion-Robin (4):
      ENH: Update external project to display build output with Ninja generator
      ENH: Update custom command to display build output with Ninja generator
      Adding .ExternalSource to gitignore
      targetLinkLibrariesWithDynamicLookup: Backport module from scikit-build

Richard Beare (2):
      Propogate C++ exceptions into R.
      Added a missing typemap for vectors of strings

Ziv Yaniv (4):
      Adding a test for R Translation Transform GetOffset method.
      Adding test for Composite transform AddTransform method.
      Adding test for returning vector of strings.
      Updated the documentation for the ReadImage procedural interfaces.

From: Bradley Lowekamp <blowekamp@mail.nih.gov>

Revision 25706  Directory Listing
Modified Mon Feb 13 21:14:55 2017 UTC (7 months, 1 week ago) by lassoan
ENH: Added Python library for CouchDB connection

CouchDB is a NoSQL database that provides document-based data storage (http://couchdb.apache.org/). It complements Slicer's file-based and SQLite-based data storage solutions.

Couchdb-python is a small native Python client library that makes database access very convenient:
https://github.com/djc/couchdb-python

This commits adds this small Python package to the Slicer installation package, similarly to
python-async python-chardet python-gitdb python-GitPython python-nose python-pydicom python-PyGithub python-smmap.

Revision 25703  Directory Listing
Modified Sat Feb 11 03:00:41 2017 UTC (7 months, 1 week ago) by lassoan
BUG: Updated OpenIGTLink to fix command handling

Fixes OpenIGTLink Remote module command handling (ISSUE 4341)

Revision 25700  Directory Listing
Modified Wed Feb 8 20:49:28 2017 UTC (7 months, 2 weeks ago) by lassoan
ENH: OpenIGTLinkIF is capable of processing RGB image

Revision 25652  Directory Listing
Modified Tue Jan 24 02:40:46 2017 UTC (8 months ago) by jcfr
ENH: Upgrade the OpenIGTLink library to version 3.0.

OpenIGTLinkIF:

$ git shortlog f3ebcbd..f0d539c --no-merges
leo chan (1):
      EHN: use of version3 OpenIGTLink

OpenIGTLink:

$ git shortlog 323b8c0..4e8a359 --no-merges
Adam Rankin (37):
      ENH: Implementation of command message in OpenIGTLink.     Added CMake implementation for v3 flag.
      ENH: Implementation of command message in OpenIGTLink.     Added CMake implementation for v3 flag.
      Adding missing files
      Correcting the default version numbers for a number of messages that should have version 2 by default.
      Removing unnecessary base classes and restoring defaults to version 1. Setting command message to version 3 to ensure header requirements.
      Adding target export for project inclusion
      Merging in all v3 functionality (#10)
      Renaming content functions to better match actual behavior and meaning
      Fixing build errors in Examples
      When the buffer is initialized, only 58 bytes are allocated
      Fixing gtest build for VS2012 (#13)
      COMP: Correcting allocation of buffer
      Adding CreateHeaderMessage to hide memory allocation details
      Undoing incorrect memory allocation fix
      Protocol2 enable build (#14)
      Bug fixes (#15)
      Enhancing exported targets to add include_directories to the properties
      Adding root level binary dir to include dirs
      Bug fixes (#16)
      Adding protection to multiple pack calls
      Adding /MP definition for targets under MSVC
      Changing return type of Get function from int to bool
      Igtlink fixes (#18)
      Add igtlTestConfig.h.in to switch between gtest and dummy gtest. (#19)
      Ensuring m_Content is properly initialized regardless of OpenIGTLink_PROTOCOL_VERSION
      merge a pick up commit
      Adding root level binary dir to include dirs
      Pick up the versin3 independent commits to the version2
      Restoring proper configuration of CMake target.
      Updating IGSIO to by synced with upstream (#21)
      Fixing v3 build
      EHN: Merge V3 fixing from IGSIO     Fixing v3 build
      Adding type enumerating the IANA encoding types for programmer-friendly usage
      Adding type enumerating the IANA encoding types for programmer-friendly usage
      Improving meta data element accessors
      Adding necessary include for linux compilers
      ENH: Making the command name field 128 bytes instead of 32

Andras Lasso (1):
      COMP: Fixed build error on VS2013 (std::min not found)

Junichi Tokuda (20):
      Fixed compile errors for Linux, and for gtest option (#12)
      Fix compile error for USE_GTEST=OFF.
      Fix return value warnings in igtlTestConfig.h.in.
      ENH: Add SetupForDevelopment.sh. The scripts and configuration files are delived from VTK.
      ENH: Rename Git setup file name.
      STYLE: Fix hooks and upstream URL setting for git.
      ENH: Add files for git hooks.
      ENH: Add .gitattributes
      STYLE: Move SetupGitAliases.sh. Change git configuration for release.
      STYLE: Remove VTK-specific line from .gitattributes.
      ENH: Add link to instruction page.
      ENH: Add SetupForDevelopment.sh. The scripts and configuration files are delived from VTK.
      ENH: Rename Git setup file name.
      STYLE: Fix hooks and upstream URL setting for git.
      ENH: Add files for git hooks.
      ENH: Add .gitattributes
      STYLE: Move SetupGitAliases.sh. Change git configuration for release.
      STYLE: Remove VTK-specific line from .gitattributes.
      ENH: Add link to instruction page.
      Move members related to headerversion3 in igtlMessageBase.h

Longquan Chen (24):
      only for triggerig the Travis Build
      The char type is set to unsigned char, so the data can be imported into c++ project
      deleting wrongly commited files
      unsigned char type for cxx test
      Google test is added to support a more professonal unit test
      Google test is now included in the MessageBase Test
      added google test library
      delete unnecessary lines in CmakeLists file
      the config cmake file is added
      added googletest library for the Linux system
      Package path is set
      MessageBaseTest Updated
      google test is super built
      resolve the warning from EXPECT_EQ(int, enum)
      serverSocket test improved
      ImageMessage2 and BindMessage Tests added
      EHN: hook_chain added for local pre-commit-msg, commit-msg and prepare-commit-msg
      EHN: hook_chain added for local pre-commit-msg, commit-msg and prepare-commit-msg
      Test marco fixed with IANA_ENCODING_TYPE
      Version Number corrected
      Query message added
      igtl_command_header_size corrected, test added
      EHN: configure the test for version2 build
      EHN: Added Version2 test for Windows CI build

VASST Build Machine (1):
      Adding headers for Xcode projects

adamrankin (1):
      Adding different RTS, STT and STP message types to factory

arankin (1):
      Enabling c++11 build on Linux

leo chan (3):
      EHN: 1. the CI server account changed, using openigtlink's own accout 2. Google test code server shifted github
      EHN: 1. the CI server account changed, using openigtlink's own accout 2. Google test code server shifted github
      EHN:Stop message added for the poly data

leochan (2):
      googletest is configured independent of different platform
      name is corrected

leochan2009 (95):
      message output deleted
      1. gmock added     2. ImageMessage Test added
      gmock test of the server socket is added
      -gmock test of the ServerSocket is added
      -contructor is protected, so an overloaded constructor is created for testing purpose
      Test improved for linux and MacOs systems
      more tests added
      Tests for these two classes extended
      Socket test is added, the send and receive functions are tested
      Added test for client socket
      ServerSocketTest added using ImageMessage2 class
      Three more tests are added
      files wrongly commited
      the duplication bug fixed
      evert "Merge pull request #1 from leochan2009/0004167-SetSendBlocking-code-Duplication"
      Duplication Bug fixed
      LabelMetaMessageTest added
      ImageMegaMessageTest and NDArrayMessageTest added
      PolyDataMessage and PointMessage tests added
      Test program Location problem fixed
      igtlUnit index incremented after one assignment
      Tests for SensorMessage, StatusMessage,StringMessage,TrackingDataMessage,TrajectoryMessage,TransformMessage added
      import filename is corrected now
      imported file names are corrected now
      Coding style: include file order improved
      first working version of Condition variable test
      BindMessage Test added
      ImageMessage2 modification for unpack purpose
      1, Float point comparison added, 2 ImageMessage2Test modified
      CapabilityMessageTest, ColorTableMessageTest, BindMesageTest, ConditionalVariableTest modified, so the code quality is improved
      Tests were refined, so that the pack and unpack tests are exact as the send and receive from socket
      nanosecond to fraction conversion is now corrected mapped
      the reserved byte is initialized to zero, otherwize this byte will be set by the sytem, sometimes not zero.     Initialization will prevent unpredictable crc in the header
      ENH: File permissions #84, file permission corrected
      1. m_content is moved outside of the #if directive, 2, test marco naming bug fixed
      appveyor server for Windows Build
      before-build script added to create visual studio project files
      delete the chocolatey install
      swich the visual studio from 2015 to 2013, due to the cmake installation problem
      clone mistake fixed
      return value need to be set for windows build
      1. Windows build improved, 2.The typeof() function is not a standard c library, so igtlTestConfig.h file was adapted for window.
      line break added
      Cmake install not needed
      build command corrected
      build command corrected
      1. windows test config,2 After build test added for windows
      Windows test platform set to visual studio 2015
      before-build script added to create visual studio project files
      delete the chocolatey install
      swich the visual studio from 2015 to 2013, due to the cmake installation problem
      clone mistake fixed
      return value need to be set for windows build
      1. Windows build improved, 2.The typeof() function is not a standard c library, so igtlTestConfig.h file was adapted for window.
      line break added
      Cmake install not needed
      build command corrected
      build command corrected
      1. windows test config,2 After build test added for windows
      Windows test platform set to visual studio 2015
      TestConfig type error fixed
      PositionMessagetest added
      correct positionMessageTest version added
      deactivate the socket tests, which is currently error prone for CI
      target_include_directories is no available in older cmake version. use include_directories instead
      web link is added to the windows build
      ENH: Testing are now removed from the library build, it is an independent project and built by the CI server
      ENH: Testing are now modified for version3
      BUG:Bind message bug fixed
      EHN: 1 Travis build for linux fixed,2. test for linux fixed, string.h file need to be included, 3. Cmake version set to 2.9 due to the target_include-directories command
      EHN: 1. use cmake 2.4 for project building, sub projects are set to 2.9, 2. Deactive the statusmessage test
      EHN: To get rid of the warning under the linux clang environment
      EHN: Testconfiguration.h modified for visual 2013,2012
      EHN: Fixed some error in testing
      EHN: Fixed some error in testing
      ENH: Testing are now removed from the library build, it is an independent project and built by the CI server
      EHN: 1 Travis build for linux fixed,2. test for linux fixed, string.h file need to be included, 3. Cmake version set to 2.9 due to the target_include-directories command
      EHN: 1. use cmake 2.4 for project building, sub projects are set to 2.9, 2. Deactive the statusmessage test
      EHN: To get rid of the warning under the linux clang environment
      EHN: Testconfiguration.h modified for visual 2013,2012
      EHN: Fixed some error in testing
      EHN: Fixed some error in testing
      BUG: Fix some merge error, mainly the confict with the verison3 development
      add build for local branch
      EHN: Status icon set to the correct link
      EHN: Tests are enabled in the library build
      EHN: 1. Google Test is integrated, 2. Enable CTest option in the building of the OpenIGTLink library
      This is a combination of 3 commits.     The first commit's message is:     EHN: 1. Google Test is integrated, 2. Enable CTest option in the building of the OpenIGTLink library
      EHN: Tests are enabled in the library build
      EHN: 1. Google Test is integrated, 2. Enable CTest option in the building of the OpenIGTLink library
      This is a combination of 2 commits.     The first commit's message is:
      EHN: 1. Multithread for win32 platform fixed. 2. More test platform a…
      EHN: 1. Multithread for win32 platform fixed. 2. More test platform a…
      ISSUE 99: openigtlink include directory added to the projec using the library
      ISSUE 99: openigtlink include directory added to the projec using the library

tpaetz (1):
      replaced angle brackets by quotation marks (this is the way including is done for all other messages)

From: Junichi Tokuda <tokuda@bwh.harvard.edu>

Revision 25644  Directory Listing
Modified Fri Jan 20 04:18:47 2017 UTC (8 months ago) by lassoan
ENH: Use RapidJSON instead of JsonCPP in Terminologies module logic

RapidJSON is magnitudes faster than JsonCPP (https://github.com/miloyip/nativejson-benchmark).
This is important, because when terminologies (rather large json documents) are parsed/searched/modified then each operation may take hundreds of milliseconds
with JsonCPP. Multiple calls easily accumulate to user-perceivable delays (magnitude of seconds). By keep using JsonCPP we would constantly have to
optimize number of logic calls to make sure only json access is minimized. Also, JsonCPP was unbearably slow in debug mode in Windows (simple operations took
tens of seconds).

To minimize development time and optimize speed we switch to RapidJSON instead. RapidJSON's advantages compared to jsoncpp (https://github.com/miloyip/nativejson-benchmark):
* Magnitudes faster, also, its API facilitates writing efficient application code
* CMake-ified
* Header-only (no need to install DLLs, ...)
* More conform to json standard
* Library is much smaller (31k vs 243k)

Revision 25643  Directory Listing
Modified Thu Jan 19 20:30:43 2017 UTC (8 months ago) by johan.andruejol
COMP: Update smmap to 2.0.1

After the update of GitPython in r25526, the smmap required version for
pythond-gdb changed to >=2.0.0.

Revision 25631  Directory Listing
Modified Fri Jan 6 02:02:33 2017 UTC (8 months, 2 weeks ago) by jcfr
BUG: Update ITK to fix linux packaging of itkhdf5_cpp library

This patch addresses the issue reported in [1], [2] and [3] by
updating ITK to include InsightSoftwareConsortium/ITK@2a07831 and
by installing the ITK component "cpplibraries" to ensure hdf5_cpp
get packaged in Slicer.

Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

[1] http://www.na-mic.org/Bug/view.php?id=4301
[2] http://www.na-mic.org/Bug/view.php?id=4302
[3] https://issues.itk.org/jira/browse/ITK-3504

From: Francois Budin <francois.budin@gmail.com>

Revision 25612  Directory Listing
Modified Thu Dec 15 02:40:35 2016 UTC (9 months, 1 week ago) by jcfr
ENH: Update CTK to include ctkSettings python wrapping improvements

$ git shortlog 9743ee2..fc0b1b7 --no-merges
Andras Lasso (1):
      ENH: Improved python wrapping for ctkSettings

Nicolas Vuaille (1):
      Fixes warnings

Revision 25608  Directory Listing
Modified Tue Dec 13 14:52:07 2016 UTC (9 months, 1 week ago) by jcfr
STYLE: External_python-pydicom: Remove unused patch code

This commit removes code obsoleted by previous commit.

From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

Revision 25607  Directory Listing
Modified Tue Dec 13 14:52:06 2016 UTC (9 months, 1 week ago) by jcfr
ENH: Update pydicom from 0.9.8 to 0.9.9

The main reason is that 0.9.8 fails to load files that have special characters in their name.

0.9.9 doesn't need patching of setup.py anymore (in 0.9.8, first 3 lines of setup.py had to be removed to avoid loading some old dependencies).

From: Andras Lasso <lasso@queensu.ca>

Revision 25606  Directory Listing
Modified Mon Dec 12 14:46:17 2016 UTC (9 months, 1 week ago) by jcfr
ENH: Update CTK to include fix for multiple view display in layouts

$ git shortlog d2b30cd..9743ee2 --no-merges
Amir Kalali (2):
      Add a DICOM database query to retrieve SOPInstanceUIDs via a SeriesInstanceUID
      Renamed 'sopsForSeries' to 'instancesForSeries' to be more consistent with     other methods

Andras Lasso (1):
      BUG: Fixed multiple view display in layouts

Jean-Christophe Fillion-Robin (1):
      ENH: Update to DCMTK-3.6.1_20161102

Revision 25548  Directory Listing
Modified Fri Nov 18 06:34:04 2016 UTC (10 months, 1 week ago) by jcfr
STYLE: External_SlicerExecutionModel: Simplify enabling of Param Serializer

Revision 25547  Directory Listing
Modified Fri Nov 18 06:34:02 2016 UTC (10 months, 1 week ago) by jcfr
ENH: Use ExternalData_OBJECT_STORES from environment as default

As a side note, a merge request updating CMake ExternalData module
has also been pushed. But has pointed out by the CMake core team, doing
so would prevent CMake from detecting an environment changes.
See https://gitlab.kitware.com/cmake/cmake/merge_requests/255#note_199077

Suggested-by: Bradley Lowekamp <blowekamp@mail.nih.gov>

Revision 25537  Directory Listing
Modified Tue Nov 15 15:13:32 2016 UTC (10 months, 1 week ago) by jcfr
ENH: Update python-cmake-buildsystem

This the first step toward the support of Python 3

$ git shortlog b012e1e..39ccab0 --no-merges
David Brooks (3):
      Allow a Python build to be part of a larger CMake project.
      Make it easier to specify the version of Python to build.
      Update the default Python to 2.7.12.

Isaiah Norton (1):
      pyconfig: guard '_LARGEFILE_SOURCE' to reduce warnings

Jean-Christophe Fillion-Robin (99):
      Do not install test scripts if BUILD_TESTING is OFF. Fixes #110
      Update travis and appveyor settings to specify major/minor/patch versions.
      Fix setting of HAVE_LCHMOD
      Reorganize libpython sources
      Add "generate_graminit" target
      Add "generate_python_ast_h" and "generate_python_ast_c" targets
      Add "generate_opcode_h" target
      Sort test list alphabetically
      Fix execution of "test_doctest"
      libpython: Remove redundant settings of POSITION_INDEPENDENT_CODE property
      Set minimum required version of OpenSSL to 0.9.7
      Fix "test_gdb" configuring and installing "python-gdb.py"
      Fix test_asdl_parser
      Add option WITH_COMPUTED_GOTOS for Python >= 2.7.11
      Update "add_python_extension" function adding "ALWAYS_BUILTIN" option.
      bdist_wininst: Fix configuration error due to not found ZLIB_LIBRARIES
      extensions/CMakeLists.txt: Add comments
      Add /Zm200 microsoft compiler flag
      add_python_extension: Re-organize code to call target_link_libraries once.
      Ensure extension include directories are associated with only one extension
      Fix "test_asdl_parser" on windows
      Add USE_BUILTIN_ZLIB option. Fixes #14
      add_python_extension: Add support for NO_INSTALL option.
      Add support for building Python 3.5.1
      python3: Fix tests like "test_loads_recursion" failing on windows
      python3: Fix "test_no_comdat_folding" disabling COMDAT folding.
      python3: Add support for _decimal extension
      python3: Fix build of _scproxy
      python3: Support building xxlimited extension
      python3: Build "python3dll" and fix msvc "xxlimited" link issue.
      python3: Add target to run "Argument Clinic"
      python3: Associate ABIFLAGS with shared/static libraries
      python3: Export and install libpython3-shared
      python3: Build libpython3-shared on unix
      appveyor: Disable Debug configuration
      appveyor: Associate python "3.5.1" with "Visual Studio 12 2013" generator
      python3: Fix MaxOSX build
      python3: Fix HAVE_READV and HAVE_WRITEV configuration check on MacOSX
      python3: Fix windows error when building 32-bit by excluding vcdiv64.asm
      python3: Associate correct architecture with python3stub.lib
      python3: Fix windows build of _decimal extension
      python3: Fix build of decimal extension
      Add configure check for HAVE_UCS4_TCL
      python2: Support setting Py_UNICODE_SIZE. Fixes #106
      Install LICENSE file. Fixes #29
      Install man pages. Fixes #30
      Generate and install grammar tables. Fixes #28
      Add configure check for MACOSX_DEPLOYMENT_TARGET.
      extension_ctypes: Simplify code introducing ctypes_COMMON_SOURCES var
      extension_ctypes: Support MacOSX build. Fixes #18
      Fix configure check HAVE_READLINE_READLINE_H on MacOSX
      python3: Do not include system processor when setting SOABI on MacOSX
      python3: Fix name of crypt extension
      Cache results of CMake checks
      Use CMake module "CheckTypeSize" and remove custom "CheckTypeExists"
      libpython-static: Use CMAKE_DL_LIBS instead to initialize CMAKE_DL_LIBS
      Add WITH_STATIC_DEPENDENCIES option (available only on Unix)
      Add INSTALL_DEVELOPMENT option
      Add INSTALL_MANUAL option
      Add INSTALL_TEST option
      Support system where libutil and libm are builtin the standard library
      Support building with HAVE_LIBDL set to False
      Build threadmodule only if WITH_THREAD is ON
      Associate "semaphore.c" with multiprocessing module only if it applies
      decimal: Display selected libmpdec_config
      python2: Add option to build threadmodule
      Exclude targets not relevant when cross compiling
      libmpdec_config: Add note for possible tweak
      circle: Add initial configuration
      circle: Cache docker images
      Associate cross-compiling emulator with custom commands & targets and tests
      Fix compilation of getpath.c crosscompiling using MinGW
      extension_datetime: Fix reference to MSVC_BUILTIN
      extensions: Generalize the built-in of Windows extensions to all compilers
      extension_ctypes: Fix indent
      Add BUILD_LIBPYTHON_SHARED option, deprecate BUILD_SHARED and BUILD_STATIC
      Consistently set LIBPYTHON_VERSION checking for WIN32 instead of MSVC
      bdist_wininst: Do not build by default if crosscompiling.
      config-mingw: Create copy of "PC/pyconfig.h"
      config-mingw: Replace "tab" with "2 spaces"
      config-mingw: Remove WINCE related config
      config-mingw: Remove support for older version of Visual Studio
      config-mingw: Remove support for Borland, egcs/gnu-win32 and lcc-win32 compiler
      config-mingw: Remove support for Intel compiler
      config-mingw: Add (i686|x86_64)-w64-mingw32 toolchain support from MXE
      fficonfig: Add test to set HAVE_MMAP_FILE
      fficonfig: Fix HAVE_AS_CFI_PSEUDO_OP test
      fficonfig: Update package metadata and fix typos
      fficonfig: Add missing SIZEOF_SIZE_T define
      fficonfig: Add test placeholders for new options introduced in libffi >= 3.0.13
      fficonfig: Add HAVE_AS_ASCII_PSEUDO_OP test
      fficonfig: Add HAVE_AS_STRING_PSEUDO_OP test
      fficonfig: Ensure HAVE_RO_EH_FRAME value is configured
      python3: Fix setting of WITH_HASH_ALGORITHM option properties
      sqlite3: Always expect the library and headers top be on the system
      circle: Fix build renaming all image references
      CMakeLists: Tweak "unknown python version" error message text
      gitignore: Ignore python source archives
      README: Minor tweaks

Jonathan White (2):
      Set target properties only if decimal/readline extensions are builtin.
      Fixed error in naming of dbm and gdbm modules when compiling for Python 3.x

Marcel Metz (1):
      Remove arguments from else and end* block termination commands

Matt McCormick (5):
      Add Python 2.7.12 MD5
      ci: Add Python 2.7.12 support
      test_coding and test_pep263 renamed to test_source_coding in 2.7.12
      test_pep293 rename to test_string in Python 2.7.12
      circle: Use dockcross images

Max Smolens (1):
      Support Python 3.5.2

Tony Narlock (7):
      Fix #132 libffi directory on FreeBSD 11-CURRENT
      Prevent BSD systems from being tagged as Linux
      ConfigureChecks: Correct HAVE_SYS_SYS_DOMAIN_H include check
      makefile-variables: Remove obsolete OTHER_LIBTOOL_OPT
      Rename fficonfig.h to fficonfig.h.in and configure it during configuration
      pyconfig.h: Add missing test for SETPGRP_HAVE_ARG
      Configure fficonfig.h using system introspection. See #135

bamboo (1):
      README: Fix typo.

Revision 25535  Directory Listing
Modified Mon Nov 14 20:05:37 2016 UTC (10 months, 1 week ago) by jcfr
COMP: Update ITK: include workaround for recent MacOSX/XCode Debug build error

This commit fixes error discussed here:

 http://slicer-devel.65872.n3.nabble.com/can-t-build-Slicer-SimpleITK-link-error-tt4037626.html


It update the Sllicer/ITK fork integrating the following workaround:

commit Slicer/ITK@cb4946d
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Mon Nov 14 15:00:39 2016 -0500

    BUG: Fix MacOSX build error occruing with newer version of XCode

    // Waiting these two patches are integrated into upstream ITK, we use
    // static_cast for both Release and Debug:
    //
    // * WIP: Add SafeDownCast to LightObject classes
    //   http://review.source.kitware.com/#/c/21499/
    //
    // * ENH: Add tests to demonstrate OSX dynamic_cast failure
    //   http://review.source.kitware.com/#/c/21755/
    //
    // Details reported here: https://issues.itk.org/jira/browse/ITK-3490
    //

Revision 25534  Directory Listing
Modified Mon Nov 14 16:31:24 2016 UTC (10 months, 1 week ago) by lassoan
BUG: Attempt to fix Windows build error due to distutils warning

This reverts commit 1b7867f8b9663940a5be618d3160de8461312341. Revert "BUG: fix Windows build error by reverting to GitPython 2.0.9" - it did not help.

Add CMake error exception instead to make sure that this warning is not treated as an error.

Revision 25533  Directory Listing
Modified Sun Nov 13 12:28:52 2016 UTC (10 months, 1 week ago) by lassoan
BUG: fix Windows build error by reverting to GitPython 2.0.9

Attempt to fix this build warning (that interpreted as a build error on Windows):

  C:\D\N\Slicer-0-build\python-install\Lib\distutils\dist.py:267: UserWarning: Unknown distribution option: 'test_requirements'

It seems that GitPython latest version (2.1.0, released 21 days ago) requires higher pip version (6.0) that we have in Slicer's Python distribution:
https://github.com/gitpython-developers/GitPython/commit/4486bcbbf49ad0eacf2d8229fb0e7e3432f440d9

We can go back to previous GitPython version (2.0.9, released 28 days ago) that does not contain this high pip requirement yet.

Revision 25526  Directory Listing
Modified Sat Nov 12 07:59:38 2016 UTC (10 months, 1 week ago) by jcfr
ENH: Update python-[GitPython|PyGithub|chardet|gitdb|smmap] projects

GitPython : 0.3.2.RC1 -> 2.1.0
PyGithub .: 1.23.0    -> 1.29
chardet ..: 2.2.1     -> 2.3.0
gitdb ....: 0.5.4     -> 2.0.0  (Note that async is not needed anymore)
smmap ....: 0.8.2     -> 0.9.0

Revision 25525  Directory Listing
Modified Sat Nov 12 07:59:35 2016 UTC (10 months, 1 week ago) by jcfr
STYLE: SyperBuild/python-chardet: Remove unneeded dependencies

async and smmap are not required by chardet and were most likely introduced
by copy/paste error

Revision 25524  Directory Listing
Modified Sat Nov 12 00:58:32 2016 UTC (10 months, 1 week ago) by jcfr
ENH: Update SimpleITK to 0.11.0.dev110, Swig 3.0.10 and PCRE 8.38

SimpleITK changes reported below:

$ git shortlog  ee2a30c..aeada7a --no-merges
Bradley Lowekamp (246):
      Adding script to run doxyall for generate SWIG .i files
      Adding script to update JSON with ITK doxygen
      Moving documentation generations scripts to separate directory
      Adding common variable/config file for scripts
      Generalizing script to generate Swig .i documentation files
      Adding README for the GenerateDocs directory
      Adding overview of the documentation process
      COMP: Adress Ununsed typenames in Common
      Update to ITK 4.9 release tag
      BUG: Do not link against specific Python version on OS X
      Add CMake option to build eggs
      Move Python virtualenv to Superbuild
      Prefer the use of distutils over setuptools
      Use virtualenv's setuptools and wheel, remove ez_setup
      Correctly add superbuild dependency on virtualenv
      Add find package for Python virtualenv
      Tweak virtualenv creation options
      Adding JSON validation on precommit and during code generation
      Correct JSON syntax errors detected by validation
      Adding missing needed changes for JSON validation.
      Adding initial description for MultiLableSTAPLEImageFilter
      In Python use open over file
      Improving order and utilizing default magic values for "unset" state.
      Adding test to verify that the input and output buffers are different
      Removing procedural methods for filters with not image output.
      Add Python support for Get/SetPixel for tuple arguments
      Adding support for CMake STRINGS property to superbuild variables.
      Fixing unused typedef reported by clang
      Updating virtualenv version to 15.0.1
      Use PYTHON_EXECUTABLE to call virtualenv
      Rename PYTHON_VIRTUALENV_EXECUTABLE to SCRIPT
      Fix TemplateComponent active member parameter name
      try_compile test for allowing undefined symbols in shared libraries
      Improve flag hashing with C++11 try_compiles
      Use localized cmake list variable for paths.
      Don't link to language libraries on linux
      Check for name of current project in stead of related variable
      Split FORBID_DOWNLOADS cmake flag into separate file
      Move Strip option and function to separate file
      Remove WRAP_PYTHON conditional in Python sub-directory for dist
      Move Java variables to sub-directory
      Moving CSharp Java dependencies to individual file generations step.
      Moved location of org_itk_simple_jar target.
      Make wrapped languages independent projects.
      Moved location of CMake sitk_target_link_libraries_with_dynamic_lookup
      Moved location of CMake sitk_target_link_libraries_with_dynamic_lookup
      Update name of CMake file for linking with dynamic lookup
      Explicitly use required ITK modules
      Update Superbuild download URLs to use https
      Update upload data script to use https
      Replace sitkExtra with now TargetLink CMake module in top-level
      Rename some CMake file with sitkPrefix
      Rename UseSWIGLocal to sitkUseSWIG
      Update ITK Superbuild version along release towards 4.9.1
      Adding ConfusionMatrix measurement
      Fix the path of setupegg.py used for packaging
      Make R's DESCRIPTION file configured
      Remove unneeded LOCATION property of SimpleITKR library
      Move md5 data files into R packaging directory
      Remove empty R library check
      Remove message statement with debug information.
      Restore using hash in variable name
      Remove unneeded include of DynamicLookup cmake module
      Remove checking for warning flags at the Superbuild level
      Check if C++11 is require at the Superbuild level.
      Update ITK to v4.9.1 release tag
      Fix CMP0042 Warning in try compile
      Splitting the Wrapping directory into separate language directories
      Correct typeo ImageSeriesWriter's Doxygen reference to procedural method
      Renaming file with sitk prefix
      Replace '=' in CMake variable name
      Fix "dist/dist" path for output of whl and eggs
      Only add Example tests when testing is enabled
      Restore missing dist target
      Enable Python wheels over eggs by default
      Adding Powell optimizer to registration
      BUG: Remove implicit deep copy in ImportImageFilter
      Documenting SetDisplacementField method "steals" the image
      Fix typo in IntegerLabelPixelIDTypeList type
      Updating Swig git version
      BUG: Adding missing return value to SetOptimizerAsPowell
      Update Superbuild ITK version to 4.10rc1
      Fix Euler3D test top support 4 fixed parameters
      Use exception in sitkSTLToITKDirection macro
      BUG: Adjust itk.org ExternalData URL.
      Fix number of expected Euler3D fixed parameters
      Update ITK Superbuild version toward ITK v4.10
      Fix CMake CMP0042 in TargetLinkLibrariesWithDynamicLookup
      Suppress libraries as being required for wrapped languages
      CMake recently add LUA_MATH_LIBRARY as an additional variable
      Require python 2.6 for running JSON validation script
      Updating Superbuild ITK version to 4.10 rc 2
      Do not require Python libs if weak linking is going to be used
      Use current binary directory for Python packaging working directory
      Update ITK Superbuild version along RC
      Adding SimpleITK version components to Config file
      Adding correct version variables to CPack
      Fix setup.py using hash with empty string
      Updating ITK Superbuild version to 4.10
      Reuse ImageIO from reading initial information
      Adding option to read DICOM private tags
      Adding Set/Get testing for LoadPrivateTags
      Adding example to print DICOM tags after reading file
      Updating to SWIG 3.0.9 release
      Add R tests for new features with SWIG
      Fix setting using git vs https protocol for ITK superbuild
      Fix PEP 440 compliance with "+" for local identifier
      Address CMP0058 issue with configure time generated files
      Fix Output path for GTEST library with Ninja
      Address narrowing conversion warnings
      Updating Superbuild version of virtualenv to 15.0.2
      Removing unused typedef of Self causing SWIG warnings
      Better suppress self warnings from SWIG
      Restore missing warnings flags to compilation
      Removing usage of return self from tests
      Remove usage or return self define from testing utility.
      Remove Self typedef in PyCommand
      Move hidden required MSVC flags to common required flags file.
      Adding flags for mingw to create big object files
      Adding missing SWIG dependency on SimpleITK_Common.i
      Move language specific Swig into language files
      Replacing Self return declarations with macro
      Remove unneeded private copy operators in Command classes
      Defining self return value
      Adding Doxygen macro for the return by self value.
      Adding option for no_size_check to named inputs
      Reducing check to expect from assert
      Changing to Named inputs for NormalizedCorrelation filter.
      Updating Masked FFT Normalized Correlation with named inputs
      Don't check size of Moving images
      Updating SimpleITK JSON from ITK doxygen
      Updating Java and Python swig documentation files
      Updating ITK version along 4.10 release branch
      Update testing functions with properties and generator expressions
      Moving Java test to global namespace
      Fix bug of missing JAR_FILE variable
      Remove C++ based driver for languages tests
      Add support for generated CSharp files with full paths
      Removing TestHarness support with language tests
      Add Expand template generation for language tests
      Restore multiple tests for language generated tests.
      Correct language test names to use "." over "[ ]".
      Adding missing new line after end of function.
      Updating ITK tag with a couple more patches with 4.10 release
      Adding link type specification to SimpleITK libraries
      Remove dead CMake code
      Add CMAKE_LINKER to propagate from Superbuild
      Create Python SimpleITK library in wrapping directory
      Override default output paths for language wrapping
      Updating Swig superbuild version to 3.0.10
      CMake version 3 is now required
      Install generated headers and ".i" files in generation function
      Remove wrapping projects dependency on SimpleITK binary directory.
      Corrected installation of headers
      Address CMP0058 issue with generate CSharp files
      Updating ITK superbuild version along 4.10 release
      Prepend SimpleITK CMake module directory to search path
      Only set POSITION_INDEPENDENT_CODE flag if not already set
      Remove unused cmake macro
      Remove SKIP_BUILD_RPATH property for SimpleITK libraries.
      Disable build RPATHs for wrapped languages.
      Remove visibility flags in superbuild for CMAKE property defaults
      Always build ITK with hidden visibility with static libraries
      Enable CMP0042 and CMP0063 to New
      Remove Segmentation examples as separate project
      Don't use per-configuration output directory for Python library.
      Move DataFinder implementation to cxx file.
      Added missing library dependencies in Testing.
      Adding missing library linkage to SimpleITKExplicit
      Default the visibility of SimpleITK libraries to hidden
      Adding Image methods to set meta-data and erase a key
      Use generator expression for itkTestDriver
      Print command when Expand generation fails for ctest generation
      Minimize headers included in SimpleITKTestHarness.h
      Updating ITK Superbuild version to just before 4.10.1 release
      Replace sitkTransformCompareDriver with sitkCompareDriver
      Remove creation for MetaDataDictionary array in ImageSeriesReader
      Explict Library only needs default visibility with shared libraries
      Correct CMake module path for independent language projects
      Updating ITK Superbuild version to include CMP0063 fix for vxl
      Fix MSVC double to float conversion warnings
      Adding wrapper for std::unique_ptr as nsstd::auto_ptr
      Renaming std::auto_ptr to nsstd::auto_ptr
      Adding alias for nsstd namespace in testing
      Update the Swig docs from generation scripts
      Update to use python from future for py3 compatibility
      Fix disabling using virtualenv from superbuild
      Fix missing arguments when setting CMake CACHE variable
      Enable policies to be set in sitkProjectLanguageCommon
      Add check for alias template to use unique_ptr
      Prefer C++11 over tr1
      Explicitly add GTest libraries to avoid pthread linking issue.
      Append LUA test ENVIRONMENT instead of overwriting in
      Fix incorrect logic for dist target dependency on virtualenv
      Correct PYTHONPATH when not using virtualenv
      Add missing language file extensions to example glob
      Only conditionally add ITK tag dependency
      Bumping version 0.11.0 for development
      Update the SimpleITK version the Super Examples use.
      Include Fiji in Show documentation
      Adding SimpleITK 0.10.0 wheels to the Python Downloads page
      Fixing Download page list to include a space
      Fix dependency for InsightDoxygen.tag
      Update ExternalProjects to use variable for URL
      Use CMake ExternalData module to download ExternalProject source
      Use ExternalData download for lua source
      Prefer ExternalProject_Add_StepDependencies for project dependencies on data
      Adding circle.yml for continuous integration with CircleCi
      Don't implicitly set SimpleITK version variable via CMake find_project
      Adding comment documentation to Config version change
      Replacing 0.10.0 manylinux wheels with build 1.
      Move compilation to dependencies for CircleCi
      Reducing number of compilations per container
      Reducing number of compilations on node 0
      explicitly required ITK components for BasicFilters libraries
      Fix R language link in readme
      Adding CircleCi badge for master branch.
      Enable shared libraries for CircleCi build
      Use git mirror for cached ITK repository
      Remove errant code it GTest external project file.
      Do not cache ITK git repository use github
      Use SEMICOLON generator expression in arg list
      Remove double underscore in header guards from ITK headers
      Fix namespace for auto_ptr
      Add missing argument to gtest_add_test
      Adding tests for Image::GetNumberOfPixels
      Correct tests for Image::EraseMetaData
      Adding examples of using R with dicom files
      Remove CircleCI rsync and distributed testing
      Ignore non-code branches
      Adding SSH multiplexing to prevent change host ID warnings distcc
      Separate R Array functions into separate file
      Fix command line argument error handing.
      Add basic JavaRegistration example
      Adding CSharp port of ImageRegistration1 example
      Use UNINITIALIZED CMake variable type when undefined.
      Use named inputs for LabelMapOverlayImageFilter
      Remove generated warning from committed files
      Add missing parameter for scaling  input
      Add uint8_t support for dim_vec test parameter for lua and ruby
      Adding SetColormap parameter to Label colormap based filters.
      Fix incorrect Java array type for uint8_t
      BUG: Fix missing sitkSourceVersionVars.cmake file from archives
      COMP: Include iostream before R
      Do not warn about python version when python not found
      Only use exact if python interpreter has been found

Dave Chen (4):
      Build a loadable Lua module
      Added return values for sitkShowTest
      Fix ITK TAGS_DEPENDS bug
      Simplified the show command

David T. Chen (23):
      Remove Clang warnings when building Lua
      COMP: CLang Warning Remediation
      COMP: Macros to suppress clang warnings
      COMP: Removed anonymous namespace
      ENH: Added debugging message option to Show
      New image tests for Java
      Added BigIntegerFix class
      Fix for CMake's semicolon issue on Windows
      Reverting deleted line
      Check for cmake version
      Fixed the timeout value for Show on Windows
      Refactored semi-colon hack
      Remove old python virtualenv on rebuild
      Updated Lua examples to load SimpleITK module
      Save LUA_EXECUTABLE cmake variable
      Old CMake Uppercase Expression Fix
      Updated filter.csv
      Update the SimpleDerivative.lua example
      Set SITK_NOSHOW env var for Lua tests
      Added Lua sub-directory
      Added SimpleDerivative example test.
      Updated filter.csv
      Initial checkin of .travis.yml

Gabriel A. Devenyi (1):
      Pass ITK module options into Superbuild

Hans Johnson (6):
      DOC: s/treaded/treated/g spelling fix
      COMP: Use Self typedef
      COMP: Typedef not used, so not tested.
      ENH: Add ignore for CLion editior temp files
      Document how to Use SimpleITK from C++ need operators
      ENH: Add GetNumberOfPixels to Images

Kasper Marstal (2):
      BUG: Fix Java 1.8 javadoc linting breaking the java build
      BUG: Fix JoinSeriesImageFilter GoogleTest should be fixture

Matt McCormick (2):
      DOC: Update itk.org URL's for HTTPS support.
      DOC: Correct issue tracker URL to https://issues.itk.org

Paolo Zaffino (1):
      ENH: add SITK_GIT_PROTOCOL to enable user selection of the protocol

Richard Beare (16):
      Support for more indexing operations.
      SimpleITK methods returning void are returning NULL when called     from R, and the NULL gets printed, which is annoying.
      Missing tests of PixelType enumeration
      A nicer way of dealing with the PixelIDValue enumeration.
      R documentation from doxygen.
      Support for building swig from a git repository.
      R vectors of images
      R documentation for procedural interface.
      Single functions for pixel access
      Advances in bracket operator/slicing
      Correct R doc linking.
      Improvements to Rd file generation
      Remove extra new lines generated in Python and Java Swig Docs file.
      Move Rdefines and Rversions outside the extern C.
      Void returns from method calls.
      Disable pthreads in GTest

Ziv Yaniv (6):
      Adding test for BSplineTransformInitializer.
      Separated the BSplineTransformInitializer test in two.
      Adding test for meta data dictionary.
      Adding example illustrating changes in DICOM tags.
      Updated readme to reflect current state of SimpleITK.
      Added missing curly brace in Cmakelists file.

Revision 25508  Directory Listing
Modified Mon Nov 7 21:08:53 2016 UTC (10 months, 2 weeks ago) by jcfr
ENH: Update ITK. Fixes #4290

This commit addresses issue #4290 avoiding the "already registered
transform" warning from being reported.

$ git shortlog 9071eea..883ecb4 --no-merges
Bill Lorensen (1):
      ENH: Bump WikiExamples remote module version

Bradley Lowekamp (2):
      BUG: Use BSpline Order 3 for 2D in transform factory.
      ENH: Add spline order to BSplineTransform's string id

Francois Budin (6):
      ENH: Update SCIFIO to latest version on 10/25/2016
      BUG: Swig and PCRE do not support space in installation paths
      BUG: exit() call from within piped commands was not exiting the script
      BUG: Typo in folder creation command
      ENH: Only display message for transform registered multiple times in debug
      ENH: Image spacing must be positive

Gilles Filippini (1):
      BUG: Use NATIVE_HBOOL for encoding HDF5 types.

Jon Haitz Legarreta (32):
      ENH: Improve itk::VectorRescaleIntensityImageFilter coverage.
      STYLE: Improve the itkVectorRescaleIntensityImageFilter style.
      ENH: Print missing ivar in filter PrintSelf method.
      ENH: Improve itkComplexToImaginaryFilter coverage.
      ENH: Improve itkComplexToPhaseImageFilter coverage.
      ENH: Improve itkComplexToModulusImageFilter coverage.
      ENH: Improve itkComplexToRealImageFilter coverage.
      ENH: Improve itkVectorResampleImageFilter coverage.
      ENH: Add GetTransform method.
      ENH: Improve itkConstrainedValueAdditionImageFilter coverage.
      ENH: Improve itkModulusImageFilter coverage.
      ENH: Improve itkLog10ImageFilter coverage.
      ENH: Imporve itkMagnitudeAndPhaseToComplexImageFilter coverage.
      ENH: Improve itkLogImageFilter coverage.
      ENH: Improve itkInvertIntensityImageFilter coverage.
      STYLE: Improve itkInvertIntensityImageFilter style.
      DOC: Add missing doc to itkInvertIntensityImageFilter.
      STYLE: Improve itkIntensityWindowingImageFilter style.
      STYLE: Use initialization lists.
      ENH: Improve itkIntensityWindowingImageFilter coverage.
      ENH: Improve itkNaryMaximumImageFilter coverage.
      COMP: Fix std::precision type casting warning.
      ENH: Improve itkPointSetToPointSetRegistrationMethod coverage.
      STYLE: Improve the itkPointSetToPointSetImageRegistrationMethod style.
      ENH: Remove SmartPointers being explicitly initialized to null.
      STYLE: Improve the itkPointSetToImageRegistrationMethod style.
      ENH: Improve itkPointSetToImageRegistration coverage.
      STYLE: Change the name of the itkPointSetToImageRegistrationMethod test.
      STYLE: Improve itkVectorResampleImageFilter style.
      STYLE: Improve the itkAntiAliasBinaryImageFilter style.
      ENH: Improve trigonometric function filters' coverage.
      STYLE: Remove test names from std::out messages.

KWSys Robot (2):
      KWSys 2016-10-23 (b630d2f5)
      KWSys 2016-11-03 (37306a1c)

Matthew McCormick (11):
      BUG: Use SpacePrecisionType in TileImageFilter
      ENH: Run .sha512, .md5 simultaneous modification pre-commit check
      BUG: Correct CastXML Windows binary
      BUG: Support non-zero Index in LevelSetNeighborhoodExtractor
      ENH: Add ArchiveTestingDataOnGirder.py
      BUG: Correct AtanRegularizationHeavisideStepFunction derivative
      ENH: Add Utilities/Maintenance/ContentLinkSynchronization.sh
      BUG: Remove extra HessianToObjectness content links
      ENH: Wrap SpatialFunction float types with ITK_WRAP_float
      BUG: Bump PerformanceBenchmarking to 2016-11-04
      BUG: itk_python_expression_add_test too many quotes.

Taylor Braun-Jones (2):
      COMP: Fix truncation from double to float warning
      DOC: Fix incorrect itkFactorylessNewMacro documentation

Revision 25499  Directory Listing
Modified Thu Nov 3 14:46:57 2016 UTC (10 months, 3 weeks ago) by jcfr
ENH: Update to DCMTK-3.6.1_20161102

Suggested-by: Andriy Fedorov <fedorov@bwh.harvard.edu>
Tested-by: Christian Herz <christianherz1985@gmail.com>

$ git shortlog efe1a17..DCMTK-3.6.1_20161102 --no-merges
Jan Schlamelcher (11):
      Fixed wrong usage of checkStringValue() in dcmpmap.
      Several fixes for dcmpstat.
      Fixed 32 vs. 64 bit problem in dcmqrdb.
      Fixed using third party libraries with MinGW.
      Fixed a problem with a previous commit.
      Added OFvariant implementation for C++11.
      Added API documentation for OFvariant etc.
      Updated Makefile dependencies.
      Updated man pages for new development snapshot.
      Updated DCMTK_ABI_VERSION for new development snapshot.
      Updated CHANGES.361 for new development snapshot.

Joerg Riesmeier (3):
      Made clear that options +/-Uo require +Ug.
      Output debug messages when updating attributes.
      Added readXML mode that accepts empty/missing UID.

Revision 25493  Directory Listing
Modified Tue Nov 1 13:36:31 2016 UTC (10 months, 3 weeks ago) by bpaniagua
ENH: Update SlicerExecutionModel version

git shortlog 983d211..62d0121 --no-merges
Jean-Christophe Fillion-Robin (3):
      gitignore: Add CMakeLists.txt.user
      docker: Associate build-time metadata with the image
      README: Add docker badges

Johan Andruejol (1):
      ENH: GenerateCLP: Include jsoncpp include dirs in UseGenerateCLP.cmake.in

Stephen Aylward (1):
      WARN: Rename isPresent variables to avoid hidden local variable

Revision 25482  Directory Listing
Modified Fri Oct 28 01:33:38 2016 UTC (10 months, 4 weeks ago) by jcfr
ENH: Updating DCMTK to 3.6.1_2016.10.12

Diff for DCMTK:
https://github.com/InsightSoftwareConsortium/DCMTK/compare/271f1e9731cfb29d9451b484ff50a39e32e2c90a...efe1a177eac040b6d41aae0db7714cd970e12bc5

A new version of ITK is required to compile Slicer with DCMTK updated:
https://github.com/Slicer/ITK/compare/16df9b689856cd4a8dd22a2cef92f5ee7222da0c...1168eba261e6a3c71c0372cc4cd833dd2d8fd693

A new version of CTK is required:
https://github.com/commontk/CTK/compare/afe8505a8286a701900fca1c97a4ad8876bbbe1a...d2b30cd1d525bd7f3856503373760921ea82dfde

A new version of BRAINSTools is required:
https://github.com/BRAINSia/BRAINSTools/compare/47dc8e66860be2bb074d17de18129978cb1ca93a...a5cfa21addf98d86da72f216d93e08913fa396d7

From: Francois Budin <francois.budin@gmail.com>

Revision 25465  Directory Listing
Modified Thu Oct 20 15:47:11 2016 UTC (11 months ago) by jcfr
BUG: Fix JsonCpp packaging on Linux. Fixes #4281

$ git shortlog 0.10.6..f4afa75 --no-merges
Jean-Christophe Fillion-Robin (1):
      Revert "0001-multiarch-path-support.patch"

Revision 25461  Directory Listing
Modified Thu Oct 20 01:15:43 2016 UTC (11 months ago) by lassoan
ENH: Updated CTK

SHA-1: afe8505a8286a701900fca1c97a4ad8876bbbe1a

* Merge pull request #674 from lassoan/checkable-combobox-python

ENH: Make ctkCheckableComboBox methods Python-wrapped

Revision 25420  Directory Listing
Modified Sat Oct 8 23:10:21 2016 UTC (11 months, 2 weeks ago) by jcfr
BUG: Update CTK to include vtkLightBoxRendererManager fix.

It fixes problem discussed in [1] and is related to Slicer issue 4251

[1] https://app.assembla.com/spaces/slicerrt/tickets/823-segmentation-disappears-after-deselecting-volume-in-slice-view/details

commit commontk/CTK@6b40e56
Author: Andras Lasso <lasso@queensu.ca>
Date:   Sat Oct 8 12:13:59 2016 -0400

    ENH: Preserve actor order in vtkLightBoxRendererManager

    The order of how 2D actors are added to the renderer greatly
    influences the rendering result. Therefore, for consistent
    rendering results actor ordering in slice viewer has to be preserved
    when just changing the input image data.

    Old behavior: When input to slice viewer was set to NULL (no image
    is selected for display), the image actor was removed from the
    renderer. When an image was selected again, the image actor was
    added again. This changed the actor order.

    Implemented fix: Modified the behavior to only hide the image actor
    when input is set to NULL. This way when image input is later set to
    non-NULL, the image actor does not get promoted to the top of the
    actor list (but keeps its original position).

Revision 25417  Directory Listing
Modified Thu Oct 6 19:43:01 2016 UTC (11 months, 2 weeks ago) by johan.andruejol
BUG: Fix windows packaging with Slicer_BUILD_PARAMETERSERIALIZER_SUPPORT

The packaging was broken in r25346 as the packaging relies on the
JsonCpp_DIR variable.
No label is given to this superbuild variable as projects that want to
depend explicitly on JsonCpp should rely on the JsonCpp_INCLUDE_DIR and
JsonCpp_LIBRARY variables.

Revision 25410  Directory Listing
Modified Tue Oct 4 18:00:39 2016 UTC (11 months, 3 weeks ago) by jcfr
ENH: Update CTK: Add python, library factory and ctkVTKRenderView improvements

$  git shortlog --no-merges e15af4d..4e85deb
Andras Lasso (3):
      ENH: Make executeString and executeFile invokable from Python
      ENH: Added test for ctkAbstractPythonManager::executeString wrapping
      ENH: Allow automatic view rotation by less than 1 degree

Caspar Goch (1):
      XnatTreeModel: Make sure last is at least first when inserting rows

Isaiah Norton (1):
      LibraryFactory: allow setting LoadHints for sym resolution

From: Andras Lasso <lasso@queensu.ca>

Revision 25395  Directory Listing
Modified Mon Sep 26 13:24:50 2016 UTC (11 months, 4 weeks ago) by msmolens
BUG: Update VTK to include 2D actor ordering fix for OpenGL2 backend

Update VTK to include 2D actor ordering fix for OpenGL2 backend. The
relevant merge commit is:
https://github.com/Kitware/VTK/commit/8c39dc64c101a7f23ec9e664be7797244dfdde95

Fixes http://www.na-mic.org/Bug/view.php?id=4251

$ git shortlog 5f83a54..3b13ad9f --no-merges
Alvaro Sanchez (6):
      Added vtkValuePass::FLOATING_POINT for point data.
      Made vtkFBO2 derive from vtkFBOBase.
      vtkValuePass::FLOATING_POINT handles viewport size changes.
      vtkValuePass::FLOATING_POINT supports cell data.
      Fixed broken tests and updated documentation.
      Sets the correct input in UseInvertibleColorFor.

Andrew Bauer (4):
      Making vtkPointSetCellIterator have same point data type as the vtkPointSet.
      Reducing output amount from vtkTemporalStatistics filter.
      Making CellIterators have same point data type as the input data set.
      Making DataSetCellIterators have proper point data type.

Armin Wehrfritz (1):
      IO/Xdmf3: Handle Polyhedron cells in unstructured grids with mixed topology

Ben Boeckel (10):
      vtkPResampleFilter: initialize UseInputBounds
      GetMTime: fix some missed mtime type changes
      vtkOSPRayPass: just use const char* up front
      vtkOSPRayPass: avoid variable length stack arrays
      vtkOSPRayPass: avoid needless memory gymnastics
      vtkOSPRayRendererNode: make M_PI available on Windows
      vtkOSPRayRendererNode: include <algorithm> for std::min/max
      vtkOSPRayRendererNode: fix brace initializers
      vtkOSPRayVolumeMapperNode: remove needless parameter
      vtkPointAccumulator: remove unused file

Berk Geveci (1):
      Added test for the FLUENT reader.

Bill Lorensen (2):
      COMP: vtkModelMetaData memory leaks
      COMP: vtkModelMetaData memory leaks

Carson Brownlee (5):
      Adding in OSPRay Volume Rendering Paths
      Reparent OSPVolumeMapper and improve layering
      crash fix
      removing depth buffer realloc.  Adding back conditional composite
      adding ospray init env arg

Chet Nieter (1):
      Clarified documentation of JacobiN method in vtkMath.

Cory Quammen (6):
      16834: Fix warnings in vtkWebGLExporter
      Added test for reading polyhedron from Xdmf file
      Fix dependency that really only needs to be a test dependency
      Removed unneeded private dependencies for IOSQL module
      Added scale factor for distance representation
      Invert the effect of the scale factor

Dan Lipsa (10):
      BUG: n lines of text include (n-1) interline spaces.
      ENH: Add vtkTextProperty::UseTightBoundingBox to center a label to anchor.
      BUG: Ascent, descent are positions from the baseline.
      BUG: Use of double LineSpacing results in one pixel off errors.
      Use NormalizedDisplay as for displaying the text.
      Shift quad position with one pixel to fix multiLineText test.
      BUG: lastPos = firstPos + size - 1.
      Baselines for text labels fixes.
      Additional baselines for text label fixes.
      Additional baseline for text label fixes.

Dave DeMarle (3):
      Fix bug exposed by update test.
      fix compilation warnings
      fix header test

David C. Lonie (6):
      Fix typo in vtkMPIImageReader.
      Add an FXAA implementation.
      Add a vtkFXAAOptions class for storing FXAA config.
      Add vtkOpenGLRenderTimer.
      Exclude vtkOpenGLRenderTimer from wrapping.
      Add FXAA to vtkSynchronizedRenderers.

David DeMarle (17):
      break core's dependence on ospray and begin to flesh out standalone
      miscellaneous fixes and cleanup and flesh out standalone ospvolmap
      attempt to cache ospray state for speed
      A workaround at least that fixes the leak
      misc cleanup and fix ospray layers
      improve benchmark and tests
      bring in Carson's scale fix, fix cell arrays, add the update test
      Fix standalone mapper test.
      remove tests that wont work and add one that should
      update test to allow VTKs own cpu vol renderer
      Protect against a case where volume updates and properties do not.
      upload baseline images
      fix unused var comp warnings
      protect against no input to prevent crash
      Fix new vtk style check
      new baselines for ospray latest
      update comments

David Gobbi (14):
      Simplify template macros in vtkPythonArgs
      Simplify extern template declaration
      16842: Fix reslice SplitMode, Stencil incompatibility
      Simplify extern template declarations for arrays
      Add extern template decls for vtkArrayIterator
      Update the vtkDICOM remote module to 0.7.9.
      Add vtkImageConnectivityFilter
      Update the vtkDICOM remote module to 0.7.10.
      Fix memory leak in TestImageConnectivityFilter
      Use pass-by-reference for assignment operator
      Export the vtkCocoaGLView interface
      Remove double underscore from include guards
      Fix a few doxygen specials for the wrappers
      Check for NaN when using a log scale with vtkLookupTable

Haocheng Liu (5):
      VTk Bug16140: Add one-point line&triangle check for vtkPolyData
      VTK Bug #16736: Add large data support&test for vtkMPIImageReader
      Rewrite all public&private dependency in module.cmake file
      VTK Bug15270: Correct empty condition for vtkGlyph3DMapper
      Fix Wrapping/Tcl => Rendering/Tk dependency direction

Joachim Pouderoux (1):
      Fix QuadRotationalExtrusionFilter bug.

Joseph G. Hennessey (1):
      update the update script

Karsten Tausche (3):
      Pass all available attribute information in vtkAssignAttribute
      Test new vtkAssignAttribute behavior
      Fix cppcheck warning in TestAssignAttribute

Ken Martin (10):
      some tweaks and fixes for VR
      fix incorrect incrment of gl_PrimitiveIDOffset
      fix glyph mapper bounds with composite polydata
      work on better resource management for OpenGL
      Rework the CompositePolyDataMapper2
      Fix a array bounds error and iffy pick
      fix missing newline at end of file
      Try to make the cppcheck happy
      fix an issue with release graphics resources
      fix an OpenGL2 issue impacting slicer and add test

Louis Bergmann (1):
      Added Volume Constraint to QuadricDecimation

Michael Fogleman (7):
      Support parallel project in OSPRay
      add TestOSPRayOrthographic
      Allow selecting scivis vs pathtracer for OSPRay
      Doxygen comments and other cleanup
      Add TestOSPRayRendererType; add 't' command for OSPRay tests
      Add some more kd tree tests
      Add more kd tree tests

Robert Maynard (2):
      Correct inconsistent-missing-override warnings in DataModel.
      VTK_USE_GCC_VISIBILITY has been replaced with CXX_VISIBILITY_PRESET property

Roman Grothausmann (9):
      neighbouring voxel values in vtkDiscreteMarchingCubes
      added documentation of ComputeNeighbours
      ComputeNeighbours now off by default
      renamed ComputeNeighbours to ComputeAdjacentScalars
      renamed newNeighbours to newPointScalars
      taking TestDiscreteMarchingCubes.py as base for *AdjacentScalars.py
      changes needed for successful test with ComputeAdjacentScalarsOn
      changes to test result of ComputeAdjacentScalarsOn
      documentation update

Sankhesh Jhaveri (4):
      [Volume] Support per component light parameters
      [Volume] Added tests for per component light parameters
      Added test baseline
      Fix rendering external configure issues introduced by 6e113ad4

Shawn Waldon (3):
      Use override/final/=delete anytime the compiler supports them
      Add a filter that groups a time series into a multiblock dataset
      gl2ps: add version check for USE_SYSTEM_GL2PS

Steven Hahn (2):
      Improve rendering performance when multiple cell types are present.
      When possible, use direct array access to speed up call to IsCellVisible.

Sujin Philip (1):
      Add vtkExtractTimeSteps filter and test

T.J. Corona (5):
      Turn off anti-aliasing in quadraticIntersection test.
      Update vtkQuadraticWedge documentation to better define point ordering.
      Update vtkPentagonalPrism doc to explicitly state restriction of convexity.
      In vtkGenericCell, add method to expose representative cell.
      Modify vtkHoudiniPolyDataWriter array dispatch to mirror vtkTemplateMacro.

Tiff Upstream (2):
      tiff 2016-09-07 (ecb008f9)
      tiff 2016-09-19 (50a32f50)

Utkarsh Ayachit (5):
      Fix #15909. Avoid double-free to static member.
      Fix #16833. Fix type conversion warning.
      Fix vtkCell3D::GetFacePoints implementations.
      Add support for composite datasets to vtkExtractTemporalFieldData.
      Fix leak in TestExtractTimeSteps.

Will Schroeder (5):
      Added Wendland quintic kernel; unit and plot tests
      Added test
      Better test image thanks Cory
      Move vtkPointCloud remote to Filters/Points
      Point cloud integration issues

XDMF Upstream (1):
      xdmf3 2016-08-24 (fb210b8c)

Revision 25392  Directory Listing
Modified Sat Sep 24 19:59:25 2016 UTC (12 months ago) by jcfr
ENH: Enable the ITKVtkGlue module

This is useful functionality that should be made available to extension
developers.

From: Matt McCormick <matt.mccormick@kitware.com>

Revision 25351  Directory Listing
Modified Mon Sep 12 22:37:47 2016 UTC (12 months, 1 week ago) by johan.andruejol
COMP: Fix windows compilation with Slicer_BUILD_PARAMETERSERIALIZER_SUPPORT

The JsonCpp_LIBRARY needs to be passed to SlicerExecutionModel as a
CMAKE_ARGS because it contains the result of the ${CMAKE_CFG_INTDIR}
variable that needs to be evaluated.
To clarify and for future improvements, the EXTERNAL_PROJECT_OPTIONAL_ARGS
variable was renamed EXTERNAL_PROJECT_OPTIONAL_CMAKE_CACHE_ARGS and the
EXTERNAL_PROJECT_OPTIONAL_CMAKE_ARGS was created.

Revision 25346  Directory Listing
Modified Fri Sep 9 22:02:32 2016 UTC (12 months, 2 weeks ago) by johan.andruejol
ENH: Standardize how JsonCpp config is managed

For consistency the JsonCpp variables passed to the projects were changed
to JsonCpp_INCLUDE_DIR and JsonCpp_LIBRARY.

JsonCpp_DIR should be used for project providing a Config module.

$ git shortlog 983d2112e..8692b09b6 --no-merges
Johan Andruejol (2):
      ENH: Uniformize the use of JsonCpp with VTK
      BUG: Fix GenerateCLP_FORWARD_PATHS_[BUILD/INSTALL] variable

Co-Authored: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

Revision 25337  Directory Listing
Modified Thu Sep 8 20:09:24 2016 UTC (12 months, 2 weeks ago) by johan.andruejol
ENH: Add ParameterSerializer Support

With the paramater serializer support, one can now serialize and
deserialize CLIs with the command line. The python test
CLISerializationTest is added to make sure it works as expected.

Revision 25336  Directory Listing
Modified Thu Sep 8 20:09:14 2016 UTC (12 months, 2 weeks ago) by johan.andruejol
ENH: Add optionnal support for JsonCpp

This allows Slicer to build JsonCpp. This is part of the integration of the
parameter serializer effort.
By default, the JsonCpp support is disabled.

Revision 25335  Directory Listing
Modified Thu Sep 8 20:09:05 2016 UTC (12 months, 2 weeks ago) by johan.andruejol
COMP: Update SlicerExecutionModel to be able to build JsonCpp

$ git shortlog --no-merges 26a62a0b..9a74e80a
Jean-Christophe Fillion-Robin (7):
      STYLE: CMakeLists: Consistently requires version 2.8.6
      STYLE: CMakeLists: Simplify code removing unneeded setting of CMP0016 to NEW
      STYLE: CMakeLists: Simplify code removing unneeded setting of CMP0017
      STYLE: CMakeLists: Simplify buildsystem using FindThreads module
      STYLE: CMakeLists: Remove obsolete option ModuleDescriptionParser_USE_PYTHON
      STYLE: CMakeLists: Finding of threading library is not needed anymore
      JsonSerializationUtilities: Remove unused method

Johan Andruejol (10):
      ENH: Improve JsonCpp support for SlicerExecutionModel
      ENH: Add JsonCpp path to the GenerateCLP launcher
      ENH: Do not pass the JsonCpp_DIR to the testing directly
      ENH: Allow CLI to deserialize without the required arguments
      ENH: Improve support for empty arrays
      ENH: ParameterSerializer: Use the longflag in priority
      ENH: ParameterSerializer: Fix multiple parameters handling for deserialization
      STYLE: GenerateCLP: Factorize out the CMakeLists of the testing CLIs
      ENH: ParameterSerializer: Improve escaping of the JSONModuleDescription
      ENH: GenerateCLP: Force GenerateCLPLauncher rebuild on GenerateCLP change

Revision 25332  Directory Listing
Modified Thu Sep 8 16:22:52 2016 UTC (12 months, 2 weeks ago) by msmolens
ENH: Update VTK to include GPU volume rendering fixes with OpenGL2 backend

Update VTK to include GPU volume rendering fixes with the OpenGL2 backend.
Additionally, the earlier fixes to the OpenGL backend in Slicer's VTK branch are
now in upstream VTK.

The original problem seen when rendering a labelmap volume is described in the
following bug report: http://www.na-mic.org/Bug/view.php?id=2165
The relevant merge commit is:
https://github.com/Kitware/VTK/commit/519720a596f732ae96fc52cb4cbb6f9183bc1e01

An additional problem rendering the dataset referenced in that bug report is
also fixed. The relevant merge commit is:
https://github.com/Kitware/VTK/commit/6d4ea59fc09eb646b6f18dcd0f785f093c97a046

$ git shortlog 0f8ed32..6d4ea59 --no-merges
Adam Updegrove (5):
      Replaced the current Intersection filter with one with bug fixes
      spaces after commas
      Braces indented and underscores in header removed
      Added another test for intersection
      Added new baseline for IntersectionPolyDataFilter3 test

Alvaro Sanchez (11):
      Added a test for the case of a camera inside a rigid-transformed volume.
      Fixes issue with the camera being inside a rigid-transformed volume.
      Fixes ProjectedTetrahedraMapper when rendering off-screen.
      Removed TempMatrix2 member and certain unecessary checks.
      Added a mode to adjust sampling distance to input spacing.
      Applying cellToPoint transformation to the ray step vector.
      Fixes int overflow in ComputeScalarRange.
      Added a method in RGBTable to check whether certain tex size is supported.
      Fixed gl color scale issue.
      Added texture width checks in opacity and gradientOpacity tables.
      Adjusted LargeColorTf test to add coverage for scale/bias patch.

Andreas Schniertshauer (2):
      Test: newline added for gitlab build bot test.
      Fix: ResolveCoincidentVertices jumpDistance y was wrong.

Andrew Bauer (7):
      Improving documentation to avoid using non-preferred method
      Fixing signed/unsigned compiler warning messages in WindBladeReader
      Fixing vtkParticleTracerBase::SetStartTime() doc
      Fixing null pointer dereferencing.
      Fixing particle tracing issue with non-zero start time
      Fixing  xml unstructured grid reader to properly read in polyhedra.
      Increasing maximum MPI message size

Andrew E Slaughter (2):
      Fixes bug introduced in 235bd27a5a72.
      Proposed fix for handling Exodus files that lack time

Ben Boeckel (10):
      FindTBB: use foreach (IN LISTS)
      FindTBB: empty out end*() commands
      FindTBB: remove variable deref in if() commands
      FindTBB: fix typo in comments
      vtkweb: import vtkWebCore properly
      vtkDataSetAttributes: make FieldList ctor/assignment private
      ThirdParty: mention that tiff has been imported
      vtkweb: skip importing the *Python modules
      vtkMatplotlibMathTextUtilities: remove unused variable
      issues: update issue URL references

Berk Geveci (5):
      Fixed how vtkPolyDataNormals handles strips.
      Fixed warnings.
      Added algorithms to mask NaNs.
      Improved ghost point support in vtkDataSetSurfaceFilter.
      Attempting to fix compiler error on Mac with Clang.

Bill Lorensen (4):
      BUG: QuadraticPyramid::IntersectWithLine fails
      BUG: Uninitialized variable
      STYLE: VTK style conformance
      ENH: Introduce vtkMTimeType

Brad King (8):
      vtkXMLDataElement: Add missing `long` overloads for some APIs
      Parallel/Core: Drop unnecessary VTK_USE_64BIT_IDS conditional blocks
      IO: Overload database BindParameter methods on `long long` directly
      IO/Xdmf2: Explicitly convert vtkIdType to corresponding Xdmf integer type
      IO/NetCDF: Fix NetCDF API selection for vtkIdType
      vtkWrapTcl: Select vtkIdType printf format based on implementation type
      vtkMersenneTwister: Work around NULL conversion error on VS 2010
      README: Update Issue Tracker link to new location

Chris Harris (1):
      Guard against using incorrect thread state

Chuck Atkins (6):
      HDF5: Fix external HDF5 to sync with upstream cmake
      HDF5: Fix external HDF5 to sync with upstream cmake
      Xdmf2: Add missing CMake checks for MPI when parallel HDF5 is used
      Xdmf2: Fix HDF5 include var used in parallel check
      Xdmf2: Add missing CMake checks for MPI when parallel HDF5 is used
      Xdmf2: Fix HDF5 include var used in parallel check

Cory Quammen (9):
      Code changes per my review
      STYLE: Indentation and spaces pass
      Set the Alt key state in vtkRenderWindowInteractor
      Documentation: Added instructions for verifying data upload
      Documentation: Correct old reference from Gerrit to GitLab
      Revert "ENH: Do not link against libpython when possible"
      Replace baseline that appeared to be anti-aliased
      Make some member functions virtual
      Move implementation of member function to device

Dan Lipsa (2):
      BUG #15968: Add missing freetype symbols
      BUG #16091: vtkXMLStructuredDataWriter aborted if writing to a string

Dave DeMarle (1):
      fix potential crash

David C. Lonie (52):
      Fix some non-linear cell contour implementations.
      Remove static var from RenderUtilities.
      Clarify vtkDataArrayAccessor prefered methods.
      Add vtkDataArray::UNITS_LABEL for annotating arrays with units info.
      Print key types in vtkInformationKeyLookup::PrintSelf.
      Support reading/writing array information in legacy IO.
      Add std::string setters to string information keys.
      Support reading/writing array information in VTK's XML IO.
      Add docs for legacy IO information serialization format.
      Style fixup for information keys in legacy IO.
      Add docs for XML IO information serialization format.
      Add option to disable array metadata in vtkDataWriter.
      Fix typo in vtkMolecule.
      Overload graph copy methods in vtkMolecule.
      Add vtkMolecule::GetBondList().
      Mark bond list as dirty when copying a vtkMolecule.
      Add support for reading/writing vtkMolecules in IO/Legacy.
      Initial support for 64-bit labels in vtkOpenFOAMReader.
      Fix bug in openfoam's main Read method.
      Remove hacky template override from vtkOpenFOAMReader.
      Fix bug in OpenFOAM's ReadBinaryList.
      Pass new option to openFOAM sub-readers.
      Fix issues in OpenFOAM reader update.
      Compare depths with a tolerance in the dual depth peeler.
      Add Depth stage to polydata fragment shaders.
      Use vtkTemplateTypeMacro for vtkBuffer.
      Add array explicit instantiation declarations for all platforms.
      Fixup depth peeling test.
      Add hidden line removal support.
      Remove early returns in vtkDualDepthPeelingPass for osx.
      Fix array size bug in vtkDepthSortPolyData.
      Add vtkTimerLog dump method that computes relative percentages.
      Clean up vtkMolecule::Initialize().
      Add support for vtkGraph/vtkMolecule in vtkPOutlineFilter.
      Add unit cell lattices to vtkMolecule.
      Add simple unit cell rendering to vtkMoleculeMapper.
      Add lattice information to the legacy molecule readers/writers.
      Add custom radius support for vtkMoleculeMapper.
      Add PV color bar support for vtkMoleculeMapper.
      Add VASPAnimationReader to read NPT_Z_ANIMATE.out files.
      Add VASPTessellationReader for NPT_Z_TESSELLATE.out files.
      Extend vtkCellIterator::GetNumberOfFaces for non-polyhedra.
      Add vtkCountFaces filter.
      Allow vtkMoleculeMapper's color array to be changed.
      Update PDB+Shadows+DOF+SSAA test.
      Update baselines.
      Make internal dependency private for Domains/Chemistry -> vtksys.
      Update new VASP readers for file format changes.
      Add filter to count cell vertices.
      Fix bug in vtkBlueObeliskDataParser.
      Move the BODR (periodic table) data into a private header.
      Fix compilation error on MingW.

David DeMarle (1):
      revert a change that broke 2D handling in at least one case

David Gobbi (15):
      Also indent closing brace for K&R braces.
      Simplifications for vtk_reindent_code.py
      Add a test for vtkLandmarkTransform
      Use vtkImagePointDataIterator in vtkImageReslice
      Use logical and in reslice nearest-neighbor path.
      Consistently specify interpolator invalid clip extent
      Optimize the reslice nearest neighbor interpolation
      Do a sanity check on the extent for the iterator
      Remove all PrintRevisions references from wrappers
      16806: Fix vtkImageActor translucency check
      Add ForceOpaque and ForceTranslucent to vtkImageActor
      Add cmake check for minimum supported Python version
      Fix cmake check for minimum supported Python version
      Add extern template decls for vtkPythonArgs::Array
      Add VTK_USE_EXTERN_TEMPLATE in vtkConfigure.h

Dhanannjay 'Djay' Deo (3):
      vtktiff: remove old import
      script to update tiff from upstream
      FIX: new location of tiffio.h

Diy2 Upstream (1):
      diy2 2016-08-08 (2976fdb3)

Dmitry Kuznetsov (1):
      Fixed "atom" reader for PDB format

D┼╛enan Zuki─ç (1):
      Form labels are no longer clipped

Eloi Gaudry (1):
      Add missing Frame() call on the renderWindow

Haocheng Liu (1):
      Bug #16089: Fix vtkmaskPoints multi-process missing condition

Hastings Greer (1):
      Fix Test for Python Invoke Event

Joachim Pouderoux (1):
      Introduce cube map creation from raw images.

John Tourtellott (1):
      Rebase vtkGDALRasterReader to Paraview 5.1.0 branch

Joseph G. Hennessey (7):
      fix ComputeOffAxisProjectionFrustum eyeseparation and near and far planes.
      fix ComputeOffAxisProjectionFrustum eyeseparation and near and far planes.
      new baseline images for vtkcamerafix changes
      added new reference file for external data repository
      fix incorrect addition of data
      removed incorrectly commited files
      add new baseline files

Julien Finet (1):
      GPU raycast volume rendering now supports textures larger than 1024

Karsten Tausche (1):
      Cleanup RemoveArray implementations in vtkFieldData and vtkDataSetAttributes

Ken Martin (20):
      suppress header test issues
      remove unused typedef which caused a warning
      fix cell coloring of degenerate polygons
      try fixing cxx11 warning
      fix cxx11 warning
      fix a few warnings that have crept in
      fixed issue introduced with recent shift scale changes
      fix an error when turnign on wide lines with surface_edges CPD
      fix a release graphics resource issue with LIC
      fix issues with textured followers
      Support multiple textures and texture blend modes
      add support for multiple texture coordinates
      fix an issue where the cell textures were not updating
      lic enable and disable was nto working properly
      try something for bigmac issue
      Add support for OpenVR and Oculus to VTK
      modified the cell normal code to not require float textures
      opengles does not use glew to ifdef glew code
      some performance improvements for the OpenGL2 shader
      move the sphere and stick mappers from Chem to OpenGL2/CMakeLists

Marcus D. Hanwell (1):
      Added the binary include directory for the config

Mathieu Westphal (7):
      Fix vtkProgressBarRepresentation memory overstep
      Fixing PnrReader cast warning
      Correcting Frame in TextActor
      Adding a Resize option in ChartMatrix and Use it in ScatterPlot
      Add module include directories before all other include directories
      Modified according to David G's recommendation
      Fix a shadow global warning in XOpenGLRenderWindow

Max Smolens (6):
      vtkOpenGLGPUVolumeRayCastMapper: use existing function to find next power of 2
      vtkOpenGLGPUVolumeRayCastMapper: remove unnecessary NULL check before delete
      vtkOpenGLGPUVolumeRayCastMapper: handle when table size increases
      Add test for GPU volume rendering with a large color transfer function.
      Fix formatting of VTK_DELETE_FUNCTION
      Consider whether volume transform preserves orientation

Menno Deij - van Rijswijk (2):
      forward the parser error and error observer to the actual readers
      added duplicate and collapsed triangle checks to vtkPolygonBuilder with tests

Michael Fogleman (1):
      Fix: Use transformed light positions in OSPRay

Michka Popoff (1):
      ENH: Do not link against libpython when possible

Mikhail Pukhlikov (3):
      fix: clang 3.5+ static cast to object from NULL is not allowed
      fix: reinterpret_cast from 'nullptr_t' is not allowed
      Window from X.h is long and there should be no need for cast

Nathan Fabian (3):
      Ensures the file is initialized through the first pass.
      Adds additional null checks around flattened names.
      Changed 0 to NULL

Orion Poplawski (2):
      Support gcc versions up to 9.X
      Support gcc versions up to 9.X

Robert Maynard (22):
      Explicitly state that we don't want compiler extensions enabled.
      Correct signed to unsigned warnings in DualDepthPeelingPass
      Prefer CXX_VISIBILITY_PRESET over add_compiler_export_flags.
      Namespace VTK's GenerateExportHeader as it differs from CMake's
      Enable CMP0063 as it is needed to properly build in kit mode
      Update which third party projects use the update.sh framework
      Correct a signed to unsigned warning in vtkTIFFReader
      Resolve unused-private-field found by RogueResearch7.
      Update FindPackageHandleStandardArgs to upstream CMake.
      FindPackageHandleStandardArgs now can be used with pre CMake 3.0
      All Common classes now mark PrintSelf method's with VTK_OVERRIDE.
      Resolve missing override warnings from NewInstance method.
      vtkAbstractArray children now use VTK_OVERRIDE on all applicable methods.
      Classes that override GetMTime now markup the method properly.
      vtkInformation* classes now use VTK_OVERRIDE.
      vtkRandomSequence* classes now use VTK_OVERRIDE.
      vtkLookupTable now use VTK_OVERRIDE
      vtkCommand derived classes now use VTK_OVERRIDE.
      vtkOutputWindow derived classes now use VTK_OVERRIDE.
      vtkRungeKutta classes now uses VTK_OVERRIDE.
      Add missing VTK_OVERRIDE to some Common kit classes
      vtkAbstractTransform derived classes now use VTK_OVERRIDE.

Sankhesh Jhaveri (13):
      Fix crash in exodus writer when writing datasets
      Fix spell error for interaction style on IOS
      Fix orientation marker viewport coordinates
      Fixed the orientation marker widget test for viewport changes
      Cleaned up commented code
      Make sure context is current before releasing graphics resources
      Fix OpenGL issues with polydata mapper when removing props
      Added test for removing volume from non-current context
      Test releasing polydata mapper resources from non-current context
      Fix unused parameter warnings in new tests
      Do not shade for max and min intensity blend modes
      Test cases for shading with intensity projections
      Fix issues with TestRemoveVolumeNonCurrentContext

Sean McBride (45):
      Use new enum names from macOS 10.12 SDK
      Use a more cannonical way to ignore a variable
      Uniformize Visual Studio snprintf workarounds
      Added VTK_DELETE_FUNCTION wrapper for =delete
      Uniformize some operator= declarations
      include vtkConfigure.h in files that will need it
      Applied VTK_DELETE_FUNCTION for operator=
      Applied VTK_DELETE_FUNCTION to many constructors
      Applied VTK_DELETE_FUNCTION to last few places
      Applied VTK_DELETE_FUNCTION after manual search
      Removed extra whitespace before VTK_DELETE_FUNCTION
      Fixed HeaderTesting.py to work with VTK_DELETE_FUNCTION
      Workaround strange ASan stack buffer overrun error
      Fix typo in URL in docs
      Disable HDF5 nonsense under thread sanitizer
      Hoist _snprintf hack up to vtkConfigure.h
      Fixed/suppressed various cppcheck warnings
      Added new vtkTypeBool typedef to bridge from int to bool
      Convert some int to vtkTypeBool
      Removed unused 'concave' field from struct
      Added a few missing VTK_DELETE_FUNCTION
      Remove redundant ivar to fix cppcheck warnings
      Removed last of leftover vtkstd crud
      Use VTK_DELETE_FUNCTION to silence VS2015 warning
      Used clang-tidy's "modernize-use-override" to add some C++11 overrides
      Workaround strange ASan stack buffer overrun error
      Add more VTK_DELETE_FUNCTION decorations
      Add XcodeΓÇÖs xcuserdata folder to .gitignore
      Adding missing va_end found by cppcheck
      Copy ivar when copying object to fix cppcheck warning
      Apply VTK_DELETE_FUNCTION to vtkFieldNode
      Fixed cppcheck warning about dead branch
      Very trivial misc improvements
      Fixed memory leaks in error paths
      Replaced more virtual with VTK_OVERRIDE
      Actually wrap old methods in VTK_LEGACY_REMOVE
      Find/replace PrintSelf to use VTK_OVERRIDE
      Added more VTK_OVERRIDE specifications
      Prevent possible null dereference
      Suppress a cppcheck warning about std::string
      Fix/suppress warnings from 10.12 beta SDK
      Fixed new cppcheck 1.75 warnings about pass by reference
      Fix/suppress more cppcheck warnings
      Use new 10.12 constant name (NSEventTypeFlagsChanged)
      Fix/suppress cppcheck warnings; remove dead code

Sebastien Jourdain (6):
      Fix VTK/Java JOGL
      Add ArcticViewer data generator modules
      Remove JavaScript from VTK Web
      Improve ImagePushBinaryWebSocketServerProtocol
      Break multiple context 'with' statement for python 2.6
      Allow BinaryStream to invalidate image cache

Seun Odutola (1):
      slight perfomance improvement to vtkImageBlend

Shawn Waldon (7):
      Make sure the selected face updates
      Update the documentation on vtkCellArray::ReplaceCell
      Add new baseline for TestDepthImageToPointCloud
      Use size_type rather than casting to vtkIdType
      Make the python version required for vtkweb a configure time check
      vtkHardwareSelector: initialize PropColorValue
      Update python version logic similar to !1873

Sujin Philip (9):
      Fix vtkPolyLine::GenerateSlidingNormals fail cases
      Fix vtkTubeFilter fail on zero-length segments
      Disable Diy2 warnings
      Probe filter return valid result for no source
      Fix Diy dashboard warning
      Fix vtkPolyLine.cxx scanbuild warning
      Add ResampleWithDataSet filters
      Fix TestPResampleWithDataSet Partition types test
      vtkResampleWithDataSet pass input arrays

T.J. Corona (31):
      vtkChartXY: Add an option to auto rescale axis range for log plots.
      in vtkLine, Assign parametric return values for colinear lines.
      Fix bugs in vtkMath, vtkLine, and add test for vtkLine static methods.
      vtkChartXY: Add an option to auto rescale axis range for log plots.
      Raise legacy ASCII writer precision to match that of XML writer.
      Fix vtkDataSetAttributes::InterpolatePoint() for nearest neighbor interp.
      Condense vtkDataSetAttributes::GetCopy<Attribute> to a single method.
      In vtkDataSetAttributes, promote warning to error in SetCopyAttribute().
      Add support for writing vtkPolyData to Houdini .geo files.
      In vtkPointDataToCellData, add support for categorical point data.
      In vtkHoudiniPolyDataWriter, do not delete subclass Component copy ctor.
      Add Mersenne Twister pseudorandom number generator to VTK.
      Fix documentation error in vtkCellIterator.
      In vtkCellIterator, provide a fast lookup for cell dimension.
      In TestMersenneTwister, add explicit cast to quiet Windows machines.
      In vtkHoudiniPolyDataWriter, quiet assignment operator warnings.
      Condense static vtkPolygon methods and add Convex check for vtkPolygon.
      Add Convex check for vtkPolyhedron.
      Support for vtkPolygon::IsConvex() to handle colinear & degenerate points.
      In vtkPolyhedron, edit comments to avoid wrng C4125 in Tcl-gen code.
      Add vtkUnstructuredGridQuadricDecimation.
      Fixes to style and documentation in vtkPolygon.
      Quell vtkUnstructuredGridQuadricDecimation warnings.
      Add vtkVolumeOfRevolutionFilter to VTK.
      Add vtkBinCellDataFilter to VTK.
      Add cell loc. to vtkBinCellDataFilter; add rand. seq. to vtkPointSource.
      Add vtkLinearToQuadraticCellsFilter.
      In vtkHoudiniPolyDataWriter, avoid using `this` in constructor init. list.
      Add another baseline for TestLinearToQuadraticCellsFilter.
      Add vtkDataSetRegionSurfaceFilter to VTK.
      Fix vtkOpenGLPolyDataMapper::GetNumberOfTextures()

Tiff Upstream (3):
      tiff 2016-07-11 (fb8cca2c)
      tiff 2016-07-13 (e6e45b2f)
      tiff 2016-08-03 (a4c0c70d)

Tim Thirion (4):
      Add NULL checks to LIC2D setters
      Ensure composite polydata mapper has correct MTime
      Only write visible actors to .pov files
      Add option to embed LLVM bitcode when crosscompiling for iOS

Utkarsh Ayachit (14):
      Style fixes for vtkPDBReader.
      Adding a test for PDB reader.
      Create correct OSMesa context.
      Add support for on and off screen Mesa in same build.
      BUG #16777: Pass cell data in vtkTessellatorFilter.
      Support requesting > 1 ghost levels.
      Enable customization of find_package().
      Cleanup QT5.
      GatherV(vtkDataObject*) now handles NULL correctly.
      Adding include for `strnlen`.
      Remove use of strnlen.
      Added simpler Gather(vtkDataObject*) method.
      Add commit log guidelines
      Fix order of representations in a view.

Waldir Pimenta (8):
      vtkXMLDataReader doc: add link, rephrase; clarifies that this is VTK-specific
      vtkXMLParser: fix grammar in doc of InitializeParser/ParseChunk/CleanupParse
      vtkXMLReader doc: add link to the 'VTK XML Formats' wiki page
      vtkMath: don't use x/y/z as argument names to avoid ambiguity
      vtkSTLWriter: harmonize whitespace within parenthesis
      adjust documentation per code review comments
      // ,SECTION --> // .SECTION, & other fixes to commas in code and docs
      link documentation of vtkArcSource and vtkEllipseArcSource

Will Schroeder (12):
      Fixed overrrun issue former MR 1120
      Eliminate last advance operation on each voxel row
      Removed ASan buffer overrun
      Corrected memory leaks due to scalar tree; added new test
      New test image
      New filter to convert depth image to point cloud
      Working through recent VTK_DELETE_FUNCTION changes
      Working around MergePieces bug
      New filter to adaptively subdivide triangle mesh
      New regression test image
      New filter visualizes point connectivity
      Add guidelines for merge request logs.

XDMF Upstream (3):
      xdmf3 2016-07-12 (86113671)
      xdmf3 2016-07-13 (e8e454cf)
      xdmf3 2016-08-03 (6e4cb06a)

Revision 25314  Directory Listing
Modified Fri Aug 26 13:32:33 2016 UTC (12 months, 4 weeks ago) by jcfr
COMP: Fix download of pydicom using valid URL

This commit re-enables download of pydicom. It started to fail either because
the package has been explicitly removed from googlecode or because google
is shutting down the system as explained in [1]. Either way, download should
now be fixed.

[1] https://google-opensource.blogspot.com/2015/03/farewell-to-google-code.html

Revision 25292  Directory Listing
Modified Tue Aug 16 18:20:30 2016 UTC (13 months, 1 week ago) by jcfr
COMP: Update CTK to fix ctkDICOMObjectModel windows build error

$ git shortlog 335e386..e15af4d --no-merges
Jean-Christophe Fillion-Robin (1):
      Fix ctkDICOMObjectModel windows build error

Revision 25289  Directory Listing
Modified Mon Aug 15 21:28:24 2016 UTC (13 months, 1 week ago) by jcfr
ENH: Update CTK to include ctkPythonConsole fixes - Fixes #1227

This commit integrates the following changes:

$ git shortlog 5b7dc1a..335e386 --no-merges
Christopher Mullins (4):
      ENH: ctkPytonConsole: Move cursor between parentheses if parameters detected
      ENH: ctkPythonConsole: Enable cursorOffset on multiline statements
      ENH: ctkPythonConsole: Offset cursor for function in user-defined classes
      ENH: ctkPythonConsole: Ignores "self" parameter

Johan Andruejol (1):
      Allow user to set/reset the range in ctkVTKHistogram

Marco Nolden (3):
      Update to DCMTK-3.6.1_20150924 in superbuild
      Remove DCMTK 3.6.0 compatibility cruft
      Fix some Qt5 component issues

Mayeul Chassagnard (1):
      ENH: Improve ctkAbstractPythonManager tests

mayeul (6):
      ENH: Add Continous Integration Support
      ENH: Improve Continuous Integration Support with graphical display
      STYLE: Add icon passed/failed in README linked to CDash
      ENH: Add test examples and switch to debug mode
      ENH: Add Site and Build Name for CDash
      ENH: ctkBackTraceTest should be run only in Debug Mode

mpkh (1):
      get rid of "_FORTIFY_SOURCE redefined" build warnings

Revision 25269  Directory Listing
Modified Wed Aug 10 13:25:24 2016 UTC (13 months, 2 weeks ago) by msmolens
COMP: Support building in RelWithDebInfo configuration on Windows

This commit fixes build errors when building in the RelWithDebInfo configuration
on Windows. Previously, projects that use OpenSSL_DIR would fail to find the
OpenSSL headers because only 'Debug' and 'Release' directories--not
'RelWithDebInfo'--are provided by the precompiled OpenSSL binaries.

An example error is:

    10>C:\S\R\Python-2.7.11\Modules\_hashopenssl.c(39): fatal error C1083: Cannot open include file: 'openssl/evp.h': No such file or directory

Fixes http://www.na-mic.org/Mantis/view.php?id=4058.

Revision 25259  Directory Listing
Modified Tue Aug 2 22:42:56 2016 UTC (13 months, 3 weeks ago) by msmolens
COMP: bump DCMTK version to 3.6.1_20160630

From: Isaiah Norton <inorton@bwh.harvard.edu>

Revision 25242  Directory Listing
Modified Wed Jul 20 14:40:35 2016 UTC (14 months ago) by msmolens
ENH: Update VTK to include vtkSeedWidget enhancement

    $ git shortlog 8f2ca63..0f8ed32
    Andras Lasso (1):
	  ENH: Allow selection of seed points using vtkSeedWidget

Revision 25219  Directory Listing
Modified Fri Jul 8 17:53:25 2016 UTC (14 months, 2 weeks ago) by msmolens
ENH: Update to VTK 7

$ git shortlog f08b7db..b824d94 --no-merges
Aashish Chaudhary (111):
      Some more style fixes
      Initial pass on supporting render to texture for volume rendering
      Writing computed depth values to a second color attachment
      Export alpha channel and single component depth texture
      Use unsigned char data type for image data
      Removed debug code
      Moved render to texture API to base class
      Fixed failing test
      Use first non-transparent fragment pos for depth buffer
      Wrapped long lines
      Fixed global variable declaration
      Do not write depth value if we need to skip a fragment
      Update textures and buffers appropriately in case of resize
      Fixed uninitialized values
      Fixed ReleaseGraphicsResources not getting called for offscreen window
      Compute min and max texture extents a cell centers
      Updated baselines
      Use cell flag to compute texture coordinates
      Fixed bad texture coordinates when dealing with negative spacing
      Fixed style issues
      Fixed bad first sample along the ray and added notes
      Silence texture internal format related messages
      Fixed volume rendering in parallel mode for IR > 1
      Fixed matrix data sent to the shader
      Fixed logic for reduction factor
      Initialize variables to reasonable defaults
      Fixed some more compiler warnings
      Added ability to query maximum texture size (1D/2D/3D)
      1D textures are not supported on ES
      Silenced compiler warning
      Made static methods for querying textures size
      Optimizing the code a bit
      Fixed gradient computation and shading for multiple components
      Added test for independent two component gradient computation
      Fixed various issues with gradient opacity
      Added missing baseline
      Fixed undefined variable
      Updated test and baselines to avoid aliasing artifacts
      Fixed style issues
      Fix bad normals for clipping planes
      Updated test to appropriately place the clip plane
      Silenced compiler warning
      May have solved the bands show up when performing clipping
      Optimized code by taking computation out of loops
      Fixed styling
      Fixed minor logic issue with when to terminate the trace
      Fixed clipping for oblique view angles
      Turn off jittering
      Fixed edge conditions with clipping
      Added API to turn on/off jittering
      Fixed typo which resulted in test failure
      Fixed volume rendering not working for cell data
      Added ability to query maximum texture size (1D/2D/3D)
      1D textures are not supported on ES
      Silenced compiler warning
      Made static methods for querying textures size
      Optimizing the code a bit
      Fixed gradient computation and shading for multiple components
      Added test for independent two component gradient computation
      Fixed various issues with gradient opacity
      Added missing baseline
      Fixed undefined variable
      Updated test and baselines to avoid aliasing artifacts
      Fixed style issues
      Fix bad normals for clipping planes
      Updated test to appropriately place the clip plane
      Silenced compiler warning
      May have solved the bands show up when performing clipping
      Optimized code by taking computation out of loops
      Fixed styling
      Fixed minor logic issue with when to terminate the trace
      Fixed clipping for oblique view angles
      Turn off jittering
      Fixed edge conditions with clipping
      Added API to turn on/off jittering
      Fixed typo which resulted in test failure
      Fixed volume rendering not working for cell data
      Fixed wrong index being used.
      Updated to use proj47 or higher
      Do not create objects every render frame
      Support external installation of FFMPEG
      Must have modules are avformat and avcodec
      Adding support for volume rendering for optimization
      Fixed order and style of header includes
      Further cleanup the code
      Fixed failing test
      Fixed shadow declaration
      Removed unnecessary call to attach and detach attachments
      Added check again null contour value object
      Undo bind buffer objects as well
      Fixed user-transform resulted in incorrect renderering
      Fixed test name in the documentation
      Fixed failing test on Mac
      New test is valid only for OpenGL2 backend
      Fixed incorrect order of multiplication
      Fixed styling
      Reduced threshold to 20
      Fixed arguments passed to the renderbuffer storage
      Fixed styling
      Fixed user-transform resulted in incorrect renderering
      Fixed test name in the documentation
      Fixed failing test on Mac
      New test is valid only for OpenGL2 backend
      Fixed incorrect order of multiplication
      Fixed styling
      Reduced threshold to 20
      Fixed arguments passed to the renderbuffer storage
      Fixed styling
      Fixed incorrect clip planes when using user transform
      Silence compiler warning
      Fixed wrong math used to compute the z value

Alex Tsui (2):
      Port PyQt4 QVTKRenderWindowInteractor to PyQt5.
      Add qt5 module

Alexis Girault (2):
      Fix bug 15787 : empty vtkCornerAnnotation text renders incorrectly
      issue #13348: Call ConfigureEvent on QEvent::Resize in QVTKInteractorAdapter

Alvaro Sanchez (11):
      Added VolumePicking test.
      vtkHardwareSelector renders VolumetricGeometry.
      Fixed volume picking test. Disabled depth mask in raycast mapper.
      RayCast mapper renders voxel Id during element selection.
      Fix value array component selection.
      Fix value-pass's scalar range initialization.
      Fixes culling in GPURayCast.
      Changed out-of-bounding-box ray termination.
      Added test for volume clipping intermixed with polyData.
      Added depth-composite checks to clipping sections.
      Fixes missing variable when using vtkLightKit with gradient opacity tf.

Andreas Buykx (3):
      Fix for VTK bug #15793, #15794.
      Added new test
      Fix for issue #15907 + new python test

Andrew Bauer (22):
      Adding ability to clear particle path cache for previous time steps.
      vtkXMLPMultiBlockDataWriter now writes out dataset block names.
      Adding in a check for a null pointer before accessing the pointer.
      Particle path improvements intended for in situ processing.
      Improving comments about particle tracer data structures.
      Fixing parallel stream tracer integration time and forward value integrators.
      Fix issue if there aren't arrays in both time steps.
      Making vtkGradientFilter more efficient.
      Fix vtkStructuredGridAppend problem detected by ASan.
      Updating changes to vtkCellDerivatives for v7.1.
      Initializing the object when SupportsOpenGL() is called.
      Moving the SupportsOpenGL call to parent class to avoid code duplication.
      Improving finding libGLdispatch.so.0 for EGL
      Fixing Intel compile error.
      Fixing compiler warnings
      Fix for point sprites for NVIDIA EGL 358 libs.
      Properly reading in polyhedra in parallel XML unstructured grid reader.
      fix XML writer segfault
      Fix for vtkIOParallelXMLPython-MPI-testParallelMultiBlockWriter test.
      Fixing parallel XML multiblock writer
      Adding tools for efficient file system introspection.
      Fixing cppcheck warning and general cleanup

Andrew E Slaughter (2):
      Fixes bug introduced in 235bd27a5a72.
      Proposed fix for handling Exodus files that lack time

Andrew Maclean (9):
      Fixing tests for Python3.
      A fix to enable this script to work with Py3k.
      A fix to enable this script to work with Py3k.
      Converting python examples so they also run on Py3k.
      Eliminate tests causing errors.
      Fixing fatal error C1017 in VC12 when TBB and Python are enabled.
      Remove a deprecated function from vtkParametricRandomHills.
      std::auto_ptr is marked deprecated in C++11/14 and will be removed in C++17.
      std::unique_ptr has a swap function.

Aniqah Mair (1):
      Fix warning macro typos

Antonella Cascitelli (7):
      Expose scissor parameters in vtkCamera
      Fixed some minor issues
      Expose scissor for OpenGL2 backend
      Fixed scissor if it is disabled
      Fixed multiple include
      Fixed scissor if it is disabled for OPENGL backend
      Changed the formatting of if/else

Armin Wehrfritz (1):
      Minor enhancement in vtkUnstructuredGrid.cxx

Ashray Malhotra (6):
      Added RGB to YIQ conversion filter
      Made variable local, clarified max variable name
      Adding YIQ to RGB conversion filter
      Removed YIQ to RGB filter from this branch
      Corrected different repo versions, added anonymous namespace
      Added test code, still to add external data png verification file

Ben Boeckel (132):
      libxml2: fix snprintf workaround
      vtktiff: look for search.h
      vtkhdf5: don't expect timezone with VS2015
      git-gitlab-push: add source_branch to the "create an MR" url
      vtkEnSightReader: refactor a call
      hdf5: detect %I64d specifier
      hdf5: fix long long format detection
      msvc2015: fix narrowing warnings
      vtkFreeTypeTools: use vtkIdType for cache ids
      vtkWin32OpenGLRenderWindow: fix some whitespace
      docs: add documentation on gitlab release flow
      QVTKWidget2: add a method for creating a suitable GLformat
      QVTKWidget2: request OpenGL 3.2 context with OpenGL2
      OpenGL2: replace VTKGL2 define
      GUISupportQtOpenGL: add a test for QVTKWidget2
      QVTKWidget2: add mouseEvent signal
      vtkWin32OpenGLRenderWindow: static_cast to BYTE
      python3: add support in IOGeoJSON and IOParallelXML tests
      TestDataArrayAPI: remove unreachable code
      TestDataArrayAPI: use Finish macro to exit the function
      python3: add support in IOGeoJSON and IOParallelXML tests
      vtkInformationObjectBaseKey: plug a memory leak
      msvc2015: _set_output_format is gone
      vtkOpenGLPolyDataMapper: warn about broken gl_PrimitiveID once
      vtkFreeTypeTools: support VTK_USE_64BIT_IDS=OFF
      vtkFreeTypeTools: support VTK_USE_64BIT_IDS=OFF
      twisted: remove pyc files
      gitignore: exclude Python build artifacts
      TestQVTKWidget2: link QtOpenGL in Qt4
      FindMPI: search the HPC MPI registry path
      GUISupportQt: update for 5.5 deprecation warnings
      vtkDirectory: support PGI and glibc dirent type mismatch
      vtkjsoncpp: remove old import
      Documentation: document Do: test
      vtkFixedPointVolumeRayCastCompositeShadeHelper: use 4
      vtkVolumeRayCastIsosurfaceFunction: use a temp variable
      vtkVolumeRayCastIsosurfaceFunction: use static_cast
      vtkPolynomialSolversUnivariate: fix comment
      vtkImageAccumulate: return 0 on error
      vtkImageAccumulate: handle errors in the actual algorithm
      headers: remove RCS replacement tags
      vtkModuleMacros: allow skipping header installation
      vtkRIBExporter: use snprintf
      RenderingCore: don't write to /tmp
      headers: conform to the CheckGuard HeaderTest
      HeaderTesting: check header guards
      HeaderTest: fix copy ctor and assignment operators
      HeaderTest: fix up some include warnings
      HeaderTest: add some missing vtkTypeMacros
      QtWebKit: require explicit enable
      TestWin32OpenGLRenderWindow: use a short timeout
      HeaderTest: fix header guards
      vtkhdf5: let CMake determine the executable path
      RenderingOpenGL: fix test name
      vtkOpenGLGPUVolumeRayCastMapper: remove BOM
      FindMPI: fix rogue curly brace
      vtkBuildPath: use the configuration in the filepath
      TestNumpyInterface: accept some numerical error in the test
      testing: catch "ERROR:" strings in the output
      TestNumpyInterface: fix comparison checks
      vtkQtSQLDatabase: clamp the port to a valid port range
      thirdparty: add infrastructure for updating third party packages
      jsoncpp: add script to update jsoncpp
      jsoncpp: use variable expansion rather than dirname
      jsoncpp: integrate into vtk
      vtkGeoJSONReader: update for deprecated methods
      vtkGeoJSONReader: omitEndingLineFeed has been removed
      vtkGDALRasterReader: add NumberOfPoints method
      vtkMergeFields, vtkSplitField: use strncpy
      vtkWebGLExporter: use vtkActor* as the key
      vtkWebGLExporter: use size_t as storage for pointers
      ThirdParty: use the subtree option to git
      vtkWebGLExporter: bump the pointer down a level
      vtkWrap{Java,Tcl}: fail if there is no class to wrap
      ThirdParty: remove -v to rmdir
      ThirdParty: ignore commit hooks when committing
      vtkWebGLObject: use size_t for renderer id type
      warnings: ignore std::exception inheritence warning
      ThirdParty: always use a subtree option for merging
      zlib: remove old import
      zlib: add update script
      PyVTKObject: own the classname memory
      PyVTKObject: shorten the lifetime of the `s` object
      PyVTKObject: add .c_str()
      PyVTKObject: own the classname memory
      PyVTKObject: shorten the lifetime of the `s` object
      PyVTKObject: add .c_str()
      java: bump default target to 1.6
      vtkJavaMemoryManagerImpl: parameterize Constructor for inspection
      java: ignore bootstrap class path warning
      Documentation: add docs for making a release
      vtkTrivialConsumer: add a trivial consumer class
      vtkStreamer: deprecate the class hierarchy
      Revert "ThirdParty: always use a subtree option for merging"
      vtkTrivialConsumer: add test for coverage
      TestMetaData: fix header comment
      Documentation: update vtk-superbuild docs
      Documentation: add notes for VTK7 builds
      Documentation: Windows and Linux should build Python
      ios: fix newline-at-end-of-file
      docs: add documentation for third party changes
      Documentation: add Chuck as a release maintainer
      Documentation: all platforms enable python
      Documentation: 10.7 is the target SDK/version
      Documentation: mention when exiting build trees are OK
      Documentation: clarify source tarball instructions
      Documentation: the source tarball script needs wget
      Documentation: clarify upload directory naming
      Documentation: fix rsync destination
      Documentation: document the semantic diff variables
      Documentation: fix shell markup
      Documentation: update that semanticdiff outputs to stdout
      Merge branch 'upstream-zlib' into update-zlib
      Maintenance: add Chuck to the CC list for release emails
      Documentation: mention old release branches
      ThirdParty: remove empty directories as well
      Documentation: mention backport strategies
      ThirdParty: read attributes from the worktree
      Documentation: document that annotated tags are used
      Python: overwrite ${vtk-module}.py modules which are in kits
      Python: import the kit module the same as module.py.in
      vtkCompilerExtras: detect GCC6
      vtkCompilerExtras: remove unnecessary variable deref
      vtkCompilerExtras: remove ARGS argument
      examples: check for _WIN32, not WIN32
      windows: check for _WIN32, not WIN32
      testing: simplify Intel compiler ID check
      Documentation: mention the -i and -e shorthand flags
      ThirdParty: support 2.9.0's new merge restrictions
      TestIncrementalOctreePointLocator: use braces
      vtkWebGLDataSet: use braces
      vtkWindBladeReader: use unsigned for the block size

Bengt Rosenberger (1):
      Fixed data rounding issue for int data

Berk Geveci (14):
      Source was not setting the right key. Fixed.
      Fixed unitialized memory access bug.
      Preparation to deprecate vtkStreamer and subclasses.
      Refactored and update the way algorithms are updated.
      Minor tweak to signature to improve const correctness.
      Fixed compile error due to recent API change.
      Enabled and fixed parallel examples.
      Disabled deprecation warning.
      Added pragma to disable warning.
      IO/Xdmf3/Testing: Updated VToXLoop.py to new API.
      Removed unnecessary shallow copy.
      RK45 was setting delTActual wrong. Fixed.
      The wrong MTime was being checked in vtkPointSet::FindCell. Fixed.
      Improved a few parallel rendering tests.

Betsy McPhail (1):
      Make sure scalars exist before using them

Bill Lorensen (47):
      STYLE: Replace vtksys_stl and vtksys_ios:: with std::
      ENH: UnitTest for vtkPlanesIntersection
      ENH: UnitTest for SimpleScalarTree
      ENH: Test vtkSphere::ComputeBoundingSphere
      ENH: Unit tests for ImplicitVolume/ImplicitDataSet
      COMP: Infinite loop compiling TestDataArrayAPI
      ENH: Bump vtkDICOM version
      COMP: Member template function use on Mac
      BUG: SetDPI() Unitialized Memory Read
      ENH: STLWriter now handles triangle strips
      vtkFixedWidthTextReader: expose internal vtkTable errors
      vtkXMLReader: expose internal error APIs
      vtkGenericCell: improve error message
      vtkQuadraticEdge: remove broken Derivatives implementation
      vtkTable: improve error message
      UnitTestCells: skip vtkQuadraticEdge Derivatives testing
      UnitTestFunctionParser: remove testing for log()
      TestTextureGlyph: use the proper data path
      TestImagePlaneWidget: use the proper data path
      TestMapperLUT: use the proper data path
      resampledTexture: fix off-by-one
      TestPolyDataPieces: fix off-by-one
      TestFixedWidthTextReader: use std:: explicitly
      TestImageDataLIC2D: use std:: explicitly
      DistributedDataRenderPass: only render if extensions are supported
      TestBlurAndSobelPasses: convert to vtkSmartPointer
      TestSobelGradientMagnitudePass: convert to vtkSmartPointer
      Testing: catch and check error messages
      Testing: output when FBOs are not supported
      ENH: Unit test for MergeFilter
      ENH: Unit tests for MaskPoints and PMaskPoints
      COMP: NIFTI Coverity buffer not null terminated
      COMP: Coverity infinite loop
      COMP: Memory leak in TestSortFieldData
      COMP: Fix recent coverity defects
      ENH: Add the VTK wiki examples as a remote module
      BUG: ImagePlaneWidget TextureVisibility
      ENH: Improved process for remote module fetching
      ENH: Change default TEST_LABELS for module
      BUG: OpenGLPolyDataMapper2D regression
      ENH: Bump WikiExamples
      ENH: Unit test for kernels
      ENH: Bump the WikiExamples to April 19, 2016 version
      ENH: Increase coverage for point kernels
      ENH: Improve coverage of vtkGenericGeometryFilter
      ENH: Improve coverage of DataSetSurfaceFilter
      ENH: Restore TestXMLCInterface

Boonthanome Nouanesengsy (1):
      Updated vtkPUnstructuredGridGhostCellsGenerator

Boris Nagaev (1):
      Fix CMake error if in directory with ++ in name.

Brad King (52):
      Revert "Remove forward boosts declarations"
      IO/GeoJSON: Fix -Wsign-compare warnings
      ENH: Remove use of include <vtksys/stl/*> and vtksys_stl::*
      ENH: Remove use of include <vtksys/ios/*> and vtksys_ios::*
      Remove use of KWSys String.hxx header
      Remove use of KWSys auto_ptr
      Remove use of KWSys cstddef compatiblilty header
      Include <sstream> header via angle brackets
      Add a vtkTemplate2Macro to dispatch to two template arguments at once
      COMP: Remove break after return in TestTemplateMacro
      vtkModuleMacros: Fix regression in header installation
      CMake/FindMPI: Drop unnecessary and incorrect use of GetPrerequisites
      Drop stream operator `long long` compatibility layer
      Drop old C++ stream EOF workarounds
      Drop unused VTK_NO_ANSI_STRING_STREAM configuration value
      Drop VTK_TEMPLATE_SPECIALIZE compatibility macro
      Drop support for lack of explicit template instantiation
      Drop unused checks for ancient C++ standard library versions
      Drop unused CMake/vtkTestBoolType.cxx source file
      Drop condtions for lack of `unsigned __int64` to `double` conversion
      GUISupport/Qt: Port QTestApp.cxx to Qt 5.5
      Drop unused memorized try_run result
      vtkFiltersStatisticsGnuR: Simplify availability of uintptr_t
      EncodeString: Compile independently from other VTK modules
      ParseOGLExt: Compile independently from other VTK modules
      Drop support for compilers with `__int64` as the only 64-bit int
      Drop support for compilers without `long long`
      EncodeString: Never build a launcher for this executable
      Defer vtkType*Array implementation selection to preprocessor
      ThirdParty: Teach update script to store upstream hash in commit message
      ThirdParty: Teach update script to find upstream hash in commit message
      ThirdParty: Improve update script default merge message behavior
      Add a script to import KWSys updates
      Add script to import KWIML library source code
      Add `vtkkwiml` module to provide external KWIML library
      vtkCommonCore: Use KWIML for type information at preprocessing time
      Drop detection of type size information for VTK at CMake time
      ThirdParty: Optionally add a `git shortlog` to upstream snapshot commits
      vtkfreetype: Use KWIML for integer sizes
      Configure KWSys import script to add a `git shortlog`
      ENH: Drop KWSys FundamentalType component
      Wrapping: Pass module name to vtk_wrap_hierarchy
      Wrapping: De-duplicate vtk_wrap_hierarchy argument file name
      Wrapping: Re-order wrapping parser flag construction
      Wrapping: Get preprocessor flags from CMake generator
      vtkCompositeSurfaceLICMapper: Add missing member initializers
      Drop unused `KWSYS_CHAR_IS_SIGNED` check result
      Fix vtkTestingGL2PS module to work in Testing/External build
      ThirdParty: Add license notice to `update-common.sh`
      vtkFFMPEGWriter: Use avformat_write_header return value
      vtkFFMPEGWriter: Fix build with libavcodec57
      vtkGDALVectorReader: Update to GDAL 2.1

Burlen Loring (1):
      modernize depth sorting code

Casey Goodlett (5):
      Workaround problematic motion events
      Remove logging statements
      Fix macro redefinition errors
      Fix test compilation
      Fix test using depth sort constants

Chiranjib Sur (1):
      make functions WriteArrayFooter, WriteArrayInline and WriteInlineData virtual

Chuck Atkins (2):
      Python: stub out python GIL calls if no thread support
      HDF5: Update the CMake FindHDF5 module to upstream CMake

Chun-Ming Chen (4):
      Add vtkImageProbeFilter for efficient probing into an vtkImageData
      Ensure the point really falls in the cell and prevent extrapolation.
      Replace raw C array by std::vector for weights. Remove unused codes.
      Fix C++ style

Cory Quammen (35):
      Fix crash where vtkColorTransferFunction has 0 nodes
      Specified that 'Do: merge' must be in the trailing lines
      Documentation: fixed up wording on 'Do:' commands
      Add newline at end of file
      Re-enabled parallel XML reader/writer test
      Added test for STL reader
      Changed warning macro into debug macro
      Fixes for Python 3
      Change misleading documentation
      BUG: Fix determination of scalar association
      Move lookup table opacity check from actor
      ENH: Computation of string bounds accounting for justification
      BUG 15797: Fix text property ID computation
      ENH: Added some useful member functions to vtkRect<T>
      BUG 12531: Fixed problem with AutoOrient
      Added option to display range labels
      Silence warnings about possibly uninitialized values
      Added test baseline and fixed some minor issues in the code
      Warn only once about Apple bug
      Fixed output point arrays problem with vtkContourFilter
      BUG 15903: Fix race condition in setting special colors in table
      Added warning about when BuildSpecialColors() must be called
      Fix case where number of colors is zero
      Report when depth peeling was used
      Activate proper texture unit prior to binding texture
      Added LabelOffset member variable
      Modified test to exercise setting of LabelOffset
      vtkProbeFilter now sets active attributes when passing point and cell arrays
      Added another valid OpenGL version string
      Added test for vtkTextActor picking
      Fix picking with 2D actors
      Add some checks before attempting to add attribute arrays
      Re-enable some chart tests when OpenGL2 backend is available
      Added more alternate baselines for TestScalarsToColors
      Fix use of integral abs function with float types

Dan Lipsa (27):
      BUG: vtkBiDimensionalRepresentation::PrintSelf does not generate an error.
      BUG: vthb file has the wrong directory.
      BUG #15654: Saving a wavelet as TIFF loops.
      BUG #15662: vtkAppendPolyData does not remove UPDATE_EXTENT
      BUG #15397: vtkPProbeFilter crash when geometry dataset is distributed.
      COMP: Add logic to selectively use OpenGL or OSMesa.
      BUG: OSMESA configuration flags can cause link errors.
      ENH: Add option to offscreen render through EGL.
      BUG: Point Sprites don't work with EGL/OpenGL driver 4.5.0 NVIDIA 355.11
      New baseline for TestLabeledGeoView2D for EGL and 4.5.0 NVIDIA 355.11
      BUG: Use EGLNativeWindowType for Window to fix Android compilation.
      BUG: The EGL Window was reinitialized on resize.
      BUG 15704: Fix crash with invalid CGNF file.
      BUG: GetCellGhostArray does string comparison if CellGhostArray is NULL.
      Cache function value in local variable.
      ENH: Add text chunk read/write to PNG reader/writer
      Update script for ThirdPary/libproj4
      Remove all proj4 files to start fresh.
      Fix Geovis tests. Projections numbers changed in proj 4.9.2
      BUG #1777: lambert test creates mangled up image
      BUG: push_back may cause pointers to become invalid
      Clean up proj4
      Update GDALVectorReader to GDAL 2.0.2
      vtkGDALVectorReader: Fix unhandled switch cases warning.
      Query EGL error on vtkEGLRenderWindow::MakeCurrent
      BUG #16744: Resources are not removed for a renderer removed from the window.
      BUG #16744: Resources are not removed for a renderer removed from the window.

Dave DeMarle (9):
      fixup regression test baseline image
      fix a bug where leftover color state would break value painter
      fix valgrind issue with the test itself
      Increment version to VTK 7.0.0
      mark master branch with anticipated next release number 7.1.0
      fix a cmake warning for users of VTK
      expand docs regarding binaries
      Allow backend agnostic render passes.
      include correct header to avoid compilation error on some machines

David C. Lonie (186):
      Add SkipDistance to vtkLabeledContourMapper.
      Use vtkDataArrayTemplate as the vtkTypeMacro Superclass in subclasses.
      Add vtkDataTypesCompare to compare data type tags.
      Add vtkDataArray::Insert[Next]Tuple6(...) methods.
      Clarify documentation for vtkDataArray::WriteVoidPointer
      Add vtkTypeTraits<...>::Name().
      Add a test for the vtkDataArray API.
      Update new test to round interpolation results.
      Add support for printf-style label formatting to vtkAxis.
      Silence warning.
      Preserve extent ranges when extracting unsampled VOIs.
      Restore the UPDATE_EXTENT after cutting subextents.
      Reflect API change in the optional FreeType benchmark.
      Remove the sampleRate arg in some ExtractGridHelper API.
      Add convenience API to vtkRect.
      Add copy constructors to vtkVector.
      Add missing information to vtkTransform2D docs.
      Add various missing API/docs to Context2D classes.
      Honor StencilCapable in vtkCocoaRenderWindow.
      Remove unneeded check in vtkCamera.
      Update how MVP matrix is computed in labeled contour mapper.
      Add vtkPropItem, to embed any vtkProp in a Context2D scene.
      Add vtkContextArea.
      Add vtkPlotItem/vtkContextArea tests.
      Remove Rendering/FreeType/vtkFreeTypeUtilities.
      Remove the ftgl third party module.
      Rerun the back buffer test if front buffer test fails.
      Return early from vtkImageData::Crop when image is empty.
      Don't attempt to ::Crop invalid datasets.
      Fix MTime bug in vtkTextMapper.
      Fix memory leak in vtkFreeTypeTools.
      Fix GL2PS export for vtkLabeledContourMapper.
      Fix class name in wrapping hints.
      More hints file cleanup.
      Update MPAS reader to handle non-double arrays.
      Remove 100 attribute array limit from MPAS reader.
      Relax restrictions on valid MPAS field data.
      Add Dimension API to vtkMPASReader.
      Dashboard fixes.
      Allow MPAS vertical dimension to be customizable.
      Restore VerticalLevel support and add generic array loading.
      Remove dead debugging code.
      Clear variable arrays when refetching info.
      Remove unused variables and unimplemented methods.
      Defer updates until an update request is received.
      Remove special vertexMask parsing in MPAS reader.
      Allow the vertical dimension to not be specified for MPAS.
      Validate dimensions for standard variables against the spec.
      Fix various compiler warnings.
      Fix planar-multilevel MPAS grids.
      Add xtime string to MPASReader's field data.
      Fix build error due to vtkStdString implicit conversion.
      Validate input indices in InterpolateTuple.
      Fix invalid array accesses in generic filters.
      Fix out-of-range array access in HyperOctreeContour.
      Use serial ExtractVOI implementations when we're not subsampling.
      Fix mathtext regex for single-character expressions.
      Notify when using the VTK modified netcdf API.
      Reset helper to use piece extents in serial ExtractVOI impls.
      Fix warning in header test.
      Split GL2PSExporter into an abstract base and OpenGL override.
      Add OpenGL2 module for vtkGL2PSExporter.
      Clean up GL2PS testing infrastructure.
      Patch GL2PS to work with new backend.
      Bind glBindBufferBase in glew.c.
      Enable GL2PS for OpenGL2.
      Enable GL2PS export for OpenGL2 Context2D rendering.
      Support GL2PS export of text classes.
      Fix FreeTypeTextMapper tests.
      Enable background rasterization for OpenGL2 GL2PS.
      Add test for GL2PS scalar bar export.
      Move non-raster GL2PS tests to OpenGL backend only.
      Enable linestippling for GL2PS on OpenGL2 Context2D.
      Clean-up debugging output.
      Update GL2PS to latest SVN.
      Add GL2PS_NO_OPENGL_CONTEXT option to gl2ps.
      Stablize qsort call in GL2PS.
      Update GL2PS baselines from dashboards.
      Fix gl2ps header install rules.
      Add new baselines due to MathText font differences.
      Disable GL2PS on Android/IOS.
      Enable wrapping for ExportOpenGL[2] modules.
      Disable vtkTransformFeedback on ES 2.0.
      Remove glGetBufferSubData (not available in ES 3.0).
      Re-exclude the helper impl from wrapping.
      Bind glMapBufferBase for glew on apple.
      Use specified array to splatter volumes in vtkCheckerboardSplatter.
      Use valid pointer in vtkLookupTable::BuildSpecialColors.
      Initialize vtkSpanSpace::Resolution.
      Fix/suppress issues uncovered by coverity.
      ScalarType->ValueType and ScalarReturnType->ReferenceType.
      Simplify vtkGenericDataArrayMacros.
      Ensure all vtkDataArrayTemplate API is in the new classes.
      Replace vtkDataArrayTemplate with vtkAoSDataArrayTemplate.
      Add AoS/SoA arrays to the data array template test.
      Increase MaxId in InsertNextValue when capacity hasn't changed.
      Add vtkArrayIterator for vtkAoSDataArrayTemplate.
      Add TestGenericDataArrayAPI.
      Cover all vtkAbstractArray methods in TestDataArrayAPI.
      Add raw array access method to SoA arrays (GetComponentArrayPointer).
      Fix compiler warnings.
      Optionally set MaxId when setting SoA arrays.
      Add ArrayDispatch implementations.
      Refactor vtkDataArrayIteratorMacro usages to use vtkArrayDispatch.
      API: Insert Typed/Mapped DataArrays into new array hierarchy.
      Move GDAHelper implementations to vtkDataArray.
      Compiler warning/error cleanup.
      Add vtkTemplateTypeMacro, deprecate vtkTypeTemplate.
      Fix TestDataArrayIterators
      Restore DLL interface for vtkAoSDataArrayTemplate.
      Prevent unhandled exception in HeaderTesting.py.
      Fix MSVC problem.
      Add vtkArrayDownCast system.
      Use vtkArrayDownCast in vtkArrayDispatch.
      Add export macro to template definition.
      Break TestDataArrayAPI into several smaller tests.
      Ensure that DataArrayAPI tests pass regardless of dispatch.
      const ReferenceType --> ConstReferenceType.
      Clean up lingering references to vtkDataArrayTemplate.
      Ensure safe access to long long, add __int64 support.
      Compile SoA array instantiations into Common/Core.
      Update header guards to new style (__CLASS --> CLASS_h).
      InterpolateTuple now rounds bits: Update baselines.
      Remove TestDataSetAttributes.
      Add fallback implementation for AppendPolyData when dispatch fails.
      Triage PSLAC reader problems.
      Prevent GCC 5.1.1 loop unrolling warning.
      Remove TestGenericDataArray.
      Fix HasStandardMemoryLayout impls.
      Mass rename AoS/SoA --> AOS/SOA.
      Add new SetVoidArray overload.
      Forward vtkDataArrayTemplate to vtkAOSDataArrayTemplate (legacy only).
      Remove __int64 cases, assume 'long long' is available.
      Refactor data array APIs.
      Add compiler detection, VTK_ASSUME.
      Add vtkDataArrayAccessor.
      Add vtkDataArray::ShallowCopy(vtkDataArray*).
      Update documentation for array classes, clean up template classes.
      Only use vtkArrayIterators for non-vtkDataArrays in vtkDSA.
      Move vtkPeriodicDataArray to inherit vtkGenericDataArray.
      Install and document the vtkBuffer header.
      Restore vtkAOSDataArrayTemplate deprecated API for compat.
      Documentation updates.
      Use custom min/max in DataArray::GetRange on MSVC 2015.
      Compute increments for current array in FlyingEdges.
      DeepCopy the array name for vtkAbstractArray.
      Initialize worker's ivar.
      Generalize the cell extraction logic in vtkExtractSGridHelper.
      Generalize the cell extraction logic in vtkExtractSGridHelper.
      Move includes out of anon namespace.
      Add missing 'inline' statements.
      Wrap vtk3DSImporter globals in a namespace.
      Ensure that stdc headers are included in HDF5 builds.
      Add a depth peeling test.
      Flesh out support for ObjectBaseVector information keys.
      Fixup vtkShaderProgram::Substitute.
      Cache uniform locations in ShaderProgram.
      Move chemistry GLSL FS vertex implementation.
      Add vtkDualDepthPeelingPass.
      Add depth peeling benchmark.
      Mark array dispatch cmake options as advanced.
      Move fullscreen quad rendering template into OGLRenderUtilities.
      Check for (3.2 context || ARB_texture_float) when picking a peeler.
      Check for uniforms/attributes before setting them.
      Update DualDepthPeelingPass to remove varying/uniform hack.
      Fix dual depth peeling on ES.
      Modify DDP occlusion queries for OGL ES 3.0.
      Free timer query with other graphics resources.
      ifdef out unsupported GL method for ES 2/3.
      Reduce dispatches in vtkDataArray.
      Remove unneeded header from vtkGenericDataArray.
      Fix typo in array dispatch documentation.
      Work around MSVC linker issues.
      Disable dual depth peeling on mesa master.
      Work around min/max macros on MSVC.
      Allow NULL inputs to array FastDownCast methods.
      Replace SafeDownCast calls on arrays with vtkArrayDownCast.
      Add missing return statement to NULL check.
      Disable dual depth peeling for llvmpipe/SWR mesa drivers.
      Support multi-stage render passes in point gaussian mapper.
      Copy attribute array information in vtkAppendFilter.
      Add vtkInformationKeyLookup to find information keys by name.
      Rename LabeledContourMapper::BuildTime to avoid shadowing superclass.
      Add VTK_USE_LEGACY_DEPTH_PEELING env var handling.
      Correct DualDepthPeeling for RGBA targets.
      Ignore nested lists following scalar data in openFOAM lists.

David DeMarle (22):
      Add a systematic approach to traversing VTK's renderables
      Add a new rendering backend that draws via the OSPRay ray tracer
      polish the tests
      Flesh out ospray rendering and scene graph
      rename Ospray to OSPRay
      fix initial cmake config
      cleanup some dashboard issues
      update our XDMF3 import to the new update script mechanism
      prepare for updates xdmf3
      change release doc to encourage signed tags
      fix a segfault with volumes in the scene
      redraw when implicit scaling function changes
      correct for excessive whiteness
      fix for recently renamed enum
      allow use of ospray from its build or install tree
      adjust for ospray 0.10's new specular
      silence dashboard warnings and update baselines for 0.10.0
      default to not using ambient occlusion and avoid speckles
      remove xml2's deprecated reference() function
      remove instead of comment
      make xdmf3 test respect lack of hdf5 files
      update update script for xdmf3 latest

David Gobbi (194):
      Create a PyTypeObject for each wrapped vtk class.
      Fix deprecated python type check in TestSubClass.
      Update PyVTKSpecialObject to match changes with PyVTKObject.
      Declare wrapped type structs as "static".
      Remove unnecessary casts for PyDict_SetItemString.
      Change wrappers to require python 2.5 or later.
      Guard against sprintf overflow in PyVTKObject_Repr.
      The type PY_LONG_LONG is always defined for python >= 2.2.
      Fix typo SUPRESS -> SUPPRESS in macro.
      Remove old "char *" casts from Python wrappers.
      Add __dict__ attribute to python-wrapped objects.
      Do type checking with type objects, not strings.
      Update the PyVTKTemplate type object.
      Add the module to the tp_name member of every type.
      Simplify type check for overload resolution.
      Make python enum type objects static.
      Simplify PyVTKClass struct by removing vtk_mangle.
      Add missing parameter types to docstrings.
      Add py3k compatibility macros for type objects.
      Remove vestigial "module" arg from python init.
      Provide py3k module initialization.
      Add the new py3k buffer interface.
      Fix PyVTKTemplate dict compatibility methods.
      Make vtk/__init__.py compatible with py3k.
      Python API compatibility for py3k.
      Patch CommonCore python tests for py3k.
      Fix numpy_interface compatibility with py3k.
      Fix a few simple py3k syntax errors.
      Fix some converted python print statements.
      Add include guard to vtkPythonCompatibility.h
      Fix typo PYTHON_VERSION_HEX to PY_VERSION_HEX
      Add a python function to check buffer equivalence.
      Add a few other minor py3k test fixes.
      Fix remaining py3k issues with vtk.tk module.
      Fix non-ascii quotes in two header files.
      Make vtkVariantStrictWeakOrder(a,b) work with Py3k.
      For Py3k, return bytes for non-utf8 C++ strings.
      Add tests for encoded strings in python.
      The Py3K wrapping broke init args for subclasses.
      Update the wrapper documentation for Python 3.
      Add Py3k support for QVTKRenderWindowInteractor.py.
      Update wxVTKRenderWindowInteractor.py for Py3k.
      Remove BTX with extra comments from headers.
      Fix warning when compiling with Python 3.5.
      Consolidate the qt4 and qt5 python interactor widgets.
      Remove the vtk.qt5 module (use vtk.qt instead).
      Help FindPythonLibs.cmake find Py3k on OS X.
      FindPythonLibs Py3k fixes from cmake master.
      Remove methods that were never implemented.
      Ensure that stream operator parameter is const.
      Ensure that entries in hierarchy file are unique.
      Wrap many more classes with python.
      Fix classes that broke the "rule of three"
      Schwarz counter idiom for vtkFreeTypeTools
      Add a missing vtkPPixelTransfer export macro.
      Special wrapping for abstract classes.
      Exclude ParallelLIC classes from wrapping.
      Export friend function in ParallelLIC.
      Add a code indentation utility to VTK.
      Do not change indent after "=".
      Add a regex to recognize case (and other) labels.
      Use raw string regexps.
      Print exception and exit on read error.
      Only write out files that have changed.
      Fix for Python 3.5 compilation on Linux, Win32.
      Convert the PythonInterpreter module for Python 3.
      Remove Python version from vtkPythonConfigure.h.
      Relative import is required for installed VTK.
      Ignore more typedefs for anonymous structs.
      Relax restrictions on location of headers.
      Ignore the __restrict and __restrict__ keywords.
      Don't add private headers to module-Headers.cmake
      Revert WARNING to FATAL_ERROR in vtkWrapPython.
      Exclude private headers from the hierarchy files.
      Fix a copy/paste error in vtkPythonInterpreter.
      Fix evaluation of char literals with escape codes.
      Add evaluation of unicode char literals.
      Add C++14 header support to wrappers.
      Add newline at end of file to silence warning.
      Silence clang warning about unnecessary "break;"
      Fix SetSource documentation for vtkProbeFilter.
      Update the vtkDICOM remote module tag.
      Consolidate vtkImageStencilData code, fix bugs.
      Fix interaction bug in OpenGL2 vtkImageSlice/ResliceMapper.
      The vtkImageResliceMapper was needlessly recomputing.
      The assertIs() test is not available in Python 2.6.
      Remove the toupper macro defined by Python.h.
      Use all FindClosestPoint signatures from superclass.
      Remove comma at end of enum (clang warning).
      Add missing EOL to last line in file.
      Update the vtkDICOM remote module to v0.7.1.
      Fix bug for parsing backslash in string literal.
      Add the update.sh for third-party libpng.
      Move some comments so they become visible to doxygen.
      Remove the legacy BTX/ETX markers.
      Mark legacy methods as "legacy".
      Rename Element parameter to element.
      Eliminate C-style casts from vtkMatrix4x4.
      Clean up wrapper custom commands.
      Remove warning about deprecated method usage.
      Synchronize vtkMatrix3x3 with vtkMatrix4x4.
      Remove AGL.framework from OS X OPENGL_LIBRARIES.
      Change deprecation warning to "VTK 7.0".
      Fix off-by-one memory write for wrapper -D args.
      zlib: remove zlib1.rc from the list of used files.
      Add preliminary doxygen comment handling for wrappers.
      Read all doxygen comments from headers.
      Apply doxygen class docs to python wrapping.
      Remove some doxygen commands when formatting comments.
      Combine vtk_wrap_python and vtk_wrap_python3.
      BUG 15914: Fix corrupt image from vtkImageResliceMapper
      Bug 15934: vtkMetaImageWriter incorrect voxel spacing and origin
      Make wrappers guess type of NULL as nullptr_t.
      Add a vtkImagePointIterator class.
      Simplify vtkImageStencilIterator.
      Add filter to convert image data to points.
      Allow const pointer for Set method of vector keys.
      Fix wrapping pointer parameters with default value 0.
      State restrictions for vtkClipClosedSurface.
      Fix a memory overrun in vtkImageStencilIterator.
      Test vtkImageStencilIterator with various extents.
      Put back the cxx file for vtkImageStencilIterator.
      Fix a memory overrun in vtkImagePointDataIterator.
      Handle default values for array parameters in python.
      Add a test for default args in python wrappers.
      Use a custom functor in vtkImageDifference.
      Rewrite vtkThreadedImageAlgorithm::SplitExtent().
      Add SetSplitMode to vtkThreadedImageAlgorithm.
      Fix vtkVolumeRayCastSpaceLeapingImageFilter split.
      Join adjacent extents before execution.
      Set number of pieces based on the data size.
      Change the SplitPath instead of overriding SplitExtent.
      Add PrepareImageData to be called from RequestData.
      Add ThreadedImageAlgorithm::MinimumPieceSize.
      Test the SplitExtent method.
      Enable SMP by default only if backend is not Sequential.
      Remove an obsolete comment from README_WRAP.
      15647 Fix bug with wrapping PyObject args in Python.
      Convert README_WRAP into markdown format.
      Small clarification to pointer wrapping for Python.
      Python uses WRAP_EXCLUDE_PYTHON, not WRAP_EXCLUDE.
      Fix vtkLoadPythonTkWidgets error with Python 2.
      15998: Fix mismatched new/free in vtkOpenGLImageSliceMapper.
      Update the vtkDICOM remote module to v0.7.4.
      Fix incorrect spelling of hexadecimal.
      15995: Implement C++ templates as Python modules.
      Fix a vtkDICOMImageReader crash for empty SliceLocation.
      16002: Fix incorrect math in vtkQuaternion
      Move re-indentation utility to the Maintenance dir.
      If a SetInterpolator() is used, then clamp the results.
      Fix cppcheck warning "index used before limits check"
      Remove the default from vtkAlgorithm::UpdateExtent().
      Set DesiredBytesPerPiece to 64KiB based on benchmarks.
      Use minimum number of splits for vtkImageResize.
      Set minimum piece size to 16x1x1 for threading.
      Do not join adjacent pieces before executing.
      Remove redundant type check.
      Remove obsolete WholeExtent check.
      Deprecate vtkAbstractImageInterpolator::GetWholeExtent.
      Bump the remote vtkDICOM hash to v0.7.5.
      Fix vtkDICOM header test failure.
      Add a benchmarking program for some important image filters.
      Use atan2() for angle in vtkTransform::GetOrientationWXYZ().
      Switch Tk cursor3D tests to vtkFixedPointVolumeRayCastMapper.
      Allow variables to be initialized with constructor args.
      Fix a crash that can occur in ImageBenchmark.
      Smooth the trackpad scrolling interaction for Qt.
      Bump the remote vtkDICOM hash to v0.7.6.
      Only provide window/level interaction with pickable image.
      Allow the user to set the image to interact with.
      Update the vtkDICOM remote module to v0.7.7.
      Fix the way that MINC IO handles null-termination.
      Make PrintImageHeader use "double" for image-min, image-max.
      Centralize array-to-string conversion in vtkMINCImageAttributes.
      BUG 16101: Freeze in vtkCellPicker for vtkVolume pick.
      BUG 16054: Reduce chance of mistaken swig pointer string.
      16130: Fix inconsistency in vtkImageSliceCollection.
      Add preprocessor macros for each wrapper language.
      Replace __WRAP__ with more descriptive __VTK_WRAP__.
      Update the vtkDICOM remote module to v0.7.8.
      Add attribute parsing for wrapper hints
      Add missing attribute-specifier-seq to parser grammar
      Fail if an unrecognized wrapper hint attribute found.
      Regenerate vtkParse.tab.c from vtkParse.y.
      Use VTK_NEWINSTANCE hint for factory methods
      Wrap the vtkArrayIteratorTemplate in Python
      Add test for vtkArrayIteratorTemplate wrapping
      Mark NewIterator as a NEW_INSTANCE method
      Use RAII instead of new/delete for wrapper temp array
      Call reindent() until no further changes occur
      Add '--test' option to vtk_reindent_code.py
      Fix flow control keyword check in reindent script
      Add more comments to the reindent script
      Fix more tricky indentation issues for macros, labels.

David K├╝gler (1):
      Correct the automatic paths produced for windows_path.bat and unix_path.sh.

David Thompson (3):
      Handle OBJ-file materials without textures.
      Add a regression test and baseline image.
      Shift and scale VBO when precision requires it.

Dhanannjay 'Djay' Deo (7):
      ADD: New Microscopy domain and vtkOpenSlideReader
      ENH: Find openslide on fedora
      ENH: Working tests for Update
      FIX: Header errors and data alignment
      ADD: CanReadFile implementation with tests
      FIX: Image streaming
      ADD: Readme

Dhanannjay Deo (1):
      FIX: for openslide v3.4.0-1 in ubuntu

Diy2 Upstream (3):
      diy2 2016-01-22 (8c89e567)
      diy2 2016-01-22 (8c89e567)
      diy2 2016-03-29 (4169b469)

D┼╛enan Zuki─ç (2):
      COMP: making Qt WebKit optional
      vtkGenericDataArray: Clarify reference to local `detail` namespace

Edson Tadeu M. Manoel (1):
      Fix vtkSTLReader bug with ASCII STL files containing multiple patches.

Elvis Stansvik (3):
      Fix mouse wheel zooming in PyQt interactor
      Support wheel events in vtkInteractorStyleUser
      Consider QVTK* headers in WhatModulesVTK.py

Fabian Wenzel (7):
      Fixes QTVTKRenderWindowInteractor for python3
      QVTKRenderWindowInteractor derived from QGLWidget
      Configurable base class for QVTKRenderWindowInteractor
      Conditional import for QGLWidget, if needed
      Combination of VTK_USE_X and VTK_USE_OSMESA possible
      Re-added VTK_OPENGL_HAS_OSMESA (needed for ParaView buildbot); fixed typos
      Added more flags for using OpenGL libraries

Greg Schussman (1):
      Add keysyms to QVTKRenderWindowInteractor.py.

Gregory Lee (1):
      Fix errors related to missing PyInt_AsLong and PyString_AsString on Python 3

Hans Johnson (1):
      COMP: VTK and ITK H5 build program collision

Haocheng LIU (1):
      Fix bugs&typo in VTK Example folder

Haocheng Liu (1):
      Bug #16737: Change BlockSize type to prevent overflow

Hastings Greer (4):
      Allow pyvtkObjects to have InvokeEvent called on them with calldata
      Add test coverage for invoking events
      Make vtkCollection implement iterable in the python wrapping
      fix reference count for python wrapper of collection iterator

Jamil Appa (1):
      VTK: Fixed XML problem when writing grids with VTK_POLYHEDRON cell types

Jatin Parekh (9):
      Updated as per VTK convention
      Formatted using VTK style
      API corrected
      Improving API
      API corrected
      GeometryCollection added
      Correct extractLineString
      Correcting reader for concave polygons
      Style changes

Jean Favre (8):
      New reader for Chemical data using the new vtkMolecule/vtkAtom objects
      cleaned up unused vars
      replace vector.data() with &vector[0] for MSVC90 compatibility
      reworked scanning the first two header lines to care for an empty second line
      style changes for variable declaration
      removed shadow var and clean up the scanning of atoms
      add python test to check # of atoms, bonds and timesteps of nanowire data
      Adding the missing data for the MoleculeXYZ python test

Jean-Christophe Fillion-Robin (3):
      Fix error preventing GPU volume rendering from working on MacOSX
      STYLE: vtkPythonUtil: Simplify code reusing vtkPythonUtilCreateIfNeeded
      BUG: vtkPythonUtil: Check if vtkPythonMap is valid

Joachim Pouderoux (32):
      Fix crash in vtkPolygon::ParametrizePolygon for invalid polygons.
      linking: default to not making warnings fatal errors
      Fix non numerical array writing crash and fix support for Quad9
      Fix a bad index issue that make constrained delaunay2d crash
      Prevent DataSetSurfaceFilter to merge points of quadratic meshes.
      Set CMake policy CMP0054 to new to avoid warning with MSVC var/string
      Introduce a new filter to compute ghost cells of unstructured grids.
      Deprecate vtkPUGGhostDataGenerator and vtkPUGConnectivity.
      Fix tests and module compilation for legacy removed classes.
      Make sure the glyphs are update when a property changed.
      Fix AppendFilter so it copies Abstract arrays too.
      Fix a bad index issue that make constrained delaunay2d crash
      Fix a bug with vtkDelaunay2D.
      Fix a bug with vtkDelaunay2D.
      Fix PExodusIIWriter called without GlobalMPController.
      Fix still LogoWidget image when used with OpenGLv2 backend
      Clear current cell/point selection arrays in RequestInformation
      Fix PUnstructuredGridGhostCellsGenerator so it does not modify input
      Add hints for Center and Axis getters of ImplicitCylinderRepresentation
      Fix crash of the WindowToImageFilter when specifying a Viewport.
      Revert previous change which clear selected arrays at each ReqInfo
      Enhance the ghost cells generator filter.
      OpenGLRenderWindow function to switch to offscreen buffers.
      Fix against build error with OpenGL ES 2.0
      Fix RenderToImage test so it passes with (old) unsupported hardware.
      Fix the AdjustWindowRectForBorders function so correct window size is computed
      Add modifier to translate center of the cylinder along the cylinder axis.
      Use GL time query to probe mapper rendering time.
      Introduce vtkFinitePlaneWidget and its representation.
      QuadRotationalExtrusionFilter output must have input structure.
      Fix the functional bag plot extraction filter.
      Add a new option to draw a frame (border) around the text actor.

Johan Andruejol (3):
      Remove forward boosts declarations
      Correct the orientation marker widget behavior inside a viewport
      Minor fix in TestOrientationMarkerWidget2.cxx

John Tourtellott (24):
      improving formatting style
      isXYZ checks completed
      style fixes
      Add string-input mode to vtkGeoJSONReader
      Fix logic to read single Feature as well as FeatureCollection objects
      Add "feature-id" data array to polydata produced by vtkGeoJSONReader
      Update GeoJSON reader to specify property data to be stored with polydata
      Parse feature properties input (GeoJSON) and apply to output (vtkPolyData)
      Add vtkGeoJSONProperty class to simplify logic a bit.
      Rename "defaultValue" --> "typeAndDefaultValue" to be more precise.
      Pass Json::Value by reference & const where appropriate
      Add option to generate polygon outline, and make triangulation optional
      Fix sundries memory leaks
      Use double precision for point coordinates
      Update GeoJSON reader classes to compile in VTK
      Update vtkGeoJSONReader to satisfy vtk header requirements
      Add test for reader (uses python bindings)
      Simplify code by removing vtkGeoJSONProperty.h file
      Add option to vtkGeoJSONReader to store serialized "properties" node
      Change GeoJSON reader to parse LineString features into vtkPolyLine instances
      Only apply NoDataValue when it is set in the input image
      Add test for vtkGDALRasterReader with image using color palette
      Add code to read images with index data & color palette
      Add annotations to lookup table, needed for display, and update test

Jorge Pérez (1):
      Add pvtk to the install rule if(vtkParallelMPI_ENABLED)

Joshua Kollat (1):
      Ensure vtkAxisActor labels are scaled similarly when using TextActor3D mode

JsonCpp Upstream (2):
      jsoncpp: update to for/vtk
      jsoncpp 2015-10-01 (eb1ddde0)

Julien Finet (1):
      Enable GPU Raycast volume mapper for recent NVIDIA drivers on Mac OS X

KWIML Upstream (1):
      KWIML 2015-12-09 (43f9f8d0)

KWSys Robot (4):
      KWSys 2015-07-10 (c9336bcf)
      KWSys 2015-07-30 (f63febb7)
      KWSys 2015-08-24 (cdaf522c)
      KWSys 2015-08-28 (dc3fdd7f)

KWSys Upstream (5):
      KWSys 2015-08-28 (dc3fdd7f)
      KWSys 2015-12-09 (cdcf4c47)
      KWSys 2015-12-14 (c1149ef6)
      KWSys 2016-03-07 (1c544330)
      KWSys 2016-06-30 (96f06c8e)

Karsten Tausche (4):
      pass field data arrays instead of the field data itself in vtkPolyDataNormals
      Add CMake switch to omit the Qt plugin when building GUISupportQt
      Let the pipeline pass field data in vtkPolyDataNormals
      copy lighting attribute in vtkProperty::DeepCopy

Ken Martin (224):
      Add basic support for shadows
      Bunch of cleanup and reorg
      Some bug fixes
      Fix a recent regression with 2d actor
      Fix issue with thick lines
      Fix use of GL_DRAW_BUFFER on es
      Some minor cleanups for release
      Fix edge drawing with cell data
      Keep old method as the old backend requires it
      Improve the capabilities of the vtkPointGaussianMapper
      Add ability to adjust the table size
      Fix an issue where we were abusing the glsl spec a bit
      Cleanup comments
      Fix for CPDM2 with wide lines
      Some more features and some cleanup reorg.
      Fix shadowed var
      A fix for a couple issues with multiblock field data OpenGL2
      Restore the prior blend func and use the piecewise func range
      Two new tests compliments of Cory
      Fix for changes in diffuse color not showing up
      a number of ios and driod fixes
      Incorporate patched from casey
      A few more fixes and cleanup
      Add PBO support into ES 3 builds and fix a warning
      Fix issue with polygon offset being left on
      Add an ability for user code to modify the default VTK shaders
      Add a missing newline
      Fix compile issue
      Add ability to override the shader template as well
      Add a mechanism where shader uniforms can be updates
      Fix some fbconfig issues on X
      Fix an issue with wide edges not showing up properly
      Fixes related to surface with edges
      Keep track of what shader uniforms were being used in the shader
      Try to shut up warning
      Warning fix for win32
      Suppress warning in system file
      Better assert for test
      Add method to set the triangle scale
      Fix some issues with release graphics resources that PV exposed
      Add eye dome lighting into VTK
      Fix for systems that only configure once
      Remove cocoa use of deprecated OpenGL code
      Fix comment to match the code now defaulting to OpenGL2
      Fix Rendering/LIC module file
      Remove debug stack printing code
      Fix missing cmake code for OpenGL with LIC
      Mark gl2ps as being part of the OpenGL backend
      Fix a couple leaks in the compositeLICMapper
      Fix two issues exposed by a failing test in PV
      Remove internal header file
      Clean up and fix for other platforms
      Changed the wrong version of the file
      Make sure edge flags use the generic path
      Add in vector include for ivar
      Fix error message when there are no unmasked points
      Fix compiler warning
      Try a fix for osx 10.6
      Fix for opengl es edl lighting
      A depth peeling fix when compositing
      Another attempt to get osx 10.6 to compile
      Try to fix boundary check error on OSX
      Extend the timeout allowed for this test
      Another tweck for OSX 10.6
      Add freetype support into android verison of vtk
      A fix for picking combined with depth peeling
      Fix a compiler warning on hythloth
      update ios support to include ios9
      Fix vtkPSurfaceLICComposite_CompFS GLSL code.
      Another picking fix and mtime issue
      Add android vr example and fixes to support it
      Fixes for samsung with linear interp
      remove dubugging statement and unneeded line
      Fix for CompositePolydata with mixed normals/tcoords
      some interaction fixes and cleanup mostly for android
      Add support for more than 16 million cells with hardware selector
      With indexed string data we never shoudl use textures
      Fix for glyph3d picking
      Update multitouch support to be more general and robust
      Fix a couple issues with lic
      Windows fixes for multitouch changes
      Add a super smapling AA pass
      Some cleanups to make the shader a bit simpler
      A fix for picking combined with depth peeling
      Another picking fix and mtime issue
      Add a Depth of field pass to VTK
      A bit of a fix to handle frameworks better
      add some opengl debugging info when a test fails
      Fix for compiler warning in OBJ test
      add missing file for ios
      fix reportcapabilities in Cocoa
      Improve the shadow maps in VTK
      Release a tunit that was not being released
      Better support for no rendering
      Cleanup a python test and some cmake code
      fix a compile error
      Fix for selectionId being set when not needed
      Add implementation for two functions
      Fix compiler warning
      Updated to have better python test code
      Add a missing header maybe
      Allow a user to override the default opacity computed value.
      Make a cool molecule rendering
      Fix for initial config case with no backend specified
      Improve rendering shadows and DOF
      Fix accidental commit of one test
      Fix for the balloonRep when using textures in OpenGL2
      ome minor updates for mobile
      Fix a few issues related to compositepolydata picking
      Move offending opengl calls inside ifdef
      Fix copy of mapper input to helpers
      Suppress another qt warning
      Modified times were not passed to the helper
      Update docs on how to build ios android examples
      Update the VBOPLY test to check against the valid image
      Return value needs to be inverted ad valid image
      Remove some classes that were not completely converted
      Update coincident geomtry support
      Fix header file
      Update the documentation a bit
      Add in mapper specific offsets
      Update valid image/test to not use multisampling
      Add a valid image that was sqeeking by earlier
      Bah  this adds the valid image
      Update test to not resize
      Start working on better checking for OpenGL2 support
      Update Cocoas check for OpenGL support
      Try to cleanup the release graphcis resources some
      Update SupportsOpenGL for X Windows
      Fix handling of failed pixel formats
      Improve testing for OpenGL support
      Try using pbuffer as drawable for checking openGL support
      Update the orientedContourWidget coincident support
      Make the rebuilding of VBO and IBO very conservative_vbo_ibo_rebuild
      Minor variable redec warning
      Remove lingering debugging code
      Provide better rendering backend support
      add an enum for none backend
      Changeup how I am doing the enum to be cleaner IMO
      bah dumb enums  switch to const char *
      Fix case where the backend has already been defined
      get a 3.2 context from OS mesa using new funcs
      try something to see if it fixes a pv issue
      fix so that it only frees the display when it created it
      update for newer versions of iOS
      better testing for opengl support
      try a different approach
      Try to make the OpenGLSupport process better
      New Win32 approach to SupportsOpenGL
      Capture warning and error macro output
      Update point picking algorithm
      Add in support for line stipple in 2d charts
      Implement SetZbufferData for OpenGL2
      Free up memory in the point gaussian
      Add a test to help track the apple PrimId bug
      Fix some coverity issues
      try to shut up that warning for json
      Start being more specific with the apple bug
      fix issue with backface combined with edges
      More fixes for issues reported by coverity
      Improvements to the pts reader
      update for newer versions of iOS
      a few more memory leak coverity fixes etc
      trying somethign else
      Fix a memory leak in the old OpenGL1 offscreen code
      add a test on android to make sure it runs
      add another catch for a ctest note
      add a point fill pass to help render point clouds
      Add new system to apple bug working
      Supress warning on master buildbot
      cleanup and expose some options for ios android
      freetype was not compiling on ios
      reduce opengl2 module dependencies
      make the opengl2 module required for the backend
      fix up how the compile tools are build for android ios
      add missing include to fix compiler error
      Fix an issue with image lic resulting in blank images
      add getNumberOfPieces to XML Reader, fix progress
      ios improvements and new example
      improve opengl context version handling
      remove glFlush calls
      ios improvements and new example
      fix for missing define on OpenGL ES2
      remove old MFC code and update vtkMFCWindow
      do not produce error message during abort
      revert non win32 code back
      try for more recent opengl versions first
      better and tighter options for clipping range
      implement the always on top option for Contour
      adding a missing mapper
      tcl test as well
      super small bug in opengl version query
      fix for props that have no bounds with EDL
      updated to avoid constraint warning
      make OSX use the generic superclass SupportsOpenGL
      try getting a 3.1 or 3.0 context
      fix progress reporting on writing XMLMultiBlockDataSets
      added in Intel HD Graphics 2000
      safer way to delete directories for ios build
      handle spaces in the paths by escaping the quotes
      fix parallel file access
      add another system for the apple amd fix
      depth peeling with multisampling not supported
      wait for resize to happen on xwindows
      try to be a little more future proof with apple fix
      use atoi as stoi is not supported everywhere
      suppress external warning on ogr code
      pass clipping planes for imageslicemapper
      need valid image for old OpenGL1 microsoft opengl
      make the point fill pass also write depth
      update incorrect valid image for ospray_valid_window
      fix cpp check warning for ambiguous precidence
      had incorrect name for valid image
      Code had an extra call to get the pick path
      Revert "Re-added VTK_OPENGL_HAS_OSMESA (needed for ParaView buildbot); fixed typos"
      Revert "Combination of VTK_USE_X and VTK_USE_OSMESA possible"
      vtkObjectFactory: add hook where extra init code can be added
      vtkPlaneWidget: fix zero movement issues
      take another pass at the LIC mapper
      fix renderbuffer isSupported method
      make some methods virtual
      ibo creation was not setting Index to zero when no cells
      add window size options to timing test
      add opengl gpu image processing support

Kenneth Moreland (1):
      Handle invalid time slices in netCDF/CF files

Libpng Upstream (3):
      Remove old vtkpng, replace with upstream 1.0.65.
      png: update to for/vtk
      png 2015-12-07 (63adbb10)

Louis Amore (1):
      Bugfix: colors of webGL export for polydata:

Marcus D. Hanwell (3):
      Wrap vtkAtom and vtkBond in Python
      Added a simple test to verify wrapped vtkMolecule
      Added vtkAtom and vtkBond back to wrap exclude

Martin Genet (3):
      Adding Green-Lagrange strain in cell derivatives
      vtkCellDerivatives nows returns tensor components in row
      removing vtkTensor

Martyn Gigg (2):
      Protect matplotlib Python calls with GIL.
      Protect Python calls with Py_Initialized in cleanup.

Mathieu Westphal (35):
      Allow the use of any kind of dataset as an input to periodicFilter
      Fixing bug with plot matrix view when clicking rapidly
      Fix bug with the screenshot of the parallel chart view
      Switchin tensor coordinates XZ and YZ with ensight tensor
      Adding test for ensight tensor inversion
      Applying GIL PYTHON patch
      correction thx to bboeckel && jpouderoux
      Fixing bug from 68c3cc53e47c30e7ef8a74fa2b40ced0f234834c with test inversion
      Initializing class members to avoid warnings
      Fixing bug from 5b6e9c49 with test inversion
      Adding a NoRelease Option to GilEnsrurer and use it
      Correcting NO_PYTHON_THREAD in PYTHON_FULL_THREADSAFE
      WebGLExporter warning fix
      Comments + style
      Correcting invalid use of GilEnsurer
      Displaying border on top of logo so it is not hidden
      Virtualizing LogoRepresentation Method
      Removing incorrect inline
      Marked image as dirty when set use cache to false
      Force Time Filter
      Scalar bar features
      Adding missing baseline
      Adding an vtkEllipseArcSource
      ScalarBar Missing Baseline
      Adding missing FinitePlane baseline
      PolxarAxisFeatures:
      Style, syntax and indents
      Adding default to switch to remove warnings and explicit falltrough
      Adding Center Cursor
      Fix parallel nhdr reader
      SphereRepresentation CenterCursor bounds fix
      Adding a vtkProgressBarRepresentation and Widget
      Improving Initial Value Problem Solver
      Copy field data in each block of a distributed data filter
      Correcting Border Representation MTime

Max Smolens (22):
      Fix HAVE_ROUND-related build warnings in Visual Studio 2013
      Fix HAVE_ROUND-related build warnings in Visual Studio 2013
      Fix vtkCaptionActor2D not scaling text
      Fix vtkViewport gradient background documentation error
      Fix rendering gradient background with vtkRenderLargeImage
      vtkInteractorStyleRubberBand2D/3D: Fix documentation typos
      vtkWin32OpenGLRenderWindow: fix setting window size for offscreen rendering
      vtkWin32OpenGLRenderWindow: fix GetScreenSize() while rendering offscreen
      Use vtkOpenGLExtensionManager to get GL driver information
      python: Add wrapping of kits when VTK_ENABLE_KITS is ON
      python: Update wrapping tool to support multiple hierarchy and hint files
      python: Add adapter modules when VTK_ENABLE_KITS is ON
      Change picking manager to not own objects associated with pickers
      vtkLegendScaleActor: add Modified() call after updating points
      Fix vtkAxisActor2D documentation error
      vtkTextMapper: fix rendering of empty string
      Update baselines for new vtkFreeTypeTools/vtkTextMapper empty string behavior
      Update baselines for new vtkFreeTypeTools/vtkTextMapper empty string behavior
      Handle case when textDims are NULL
      Add #include for offsetof() macro in generated Python wrappers
      Fix multiple definitions of vtkInteractionCallback
      Fix variable names in vtkImplicitCylinderWidget test

Menno Deij - van Rijswijk (15):
      Reverted vtkXMLPolyDataWriter.cxx to use the 'old' WriteCellsAppended method
      Removed a spurious white line
      added support for reading Coordinate{XYZ} as coordinates
      added tecplot table reader with test
      converted exceptions to vtkErrorMacro with return value of 0 on error
      updated module.cmake according to best practices
      fixed style issues with braces and indentation
      Updated the dependency list.
      Re-order warning eliminated.
      improved the polyhedron contour using tolerances dependent on the data range
      added test for improved polyhedral contouring
      added correct parentheses to value tolerance calculation
      added a second test (TestPolyhedron3)
      Minor changes to get rid of -Wunused and -Wformat compiler warnings
      from 'char ** argv' to 'char *argv[]' to prevent link error on Windows

MetaIO Upstream (4):
      metaio: update to master
      metaio: update to master
      metaio: update to master
      metaio 2015-11-23 (4c85a18e)

Mickael Philit (3):
      Fix UPDATE_EXTENT information to append multiple vtkStructuredGrids
      Prevent out of bounds access of CellData arrays
      Use this->SampleRate instead of sampleRate to benefit from optimization

Mikael Brudfors (1):
      Improvements to vtkImplicitPolyData

Nathan Fabian (30):
      Protects against empty name strings in the Info.
      Protects against side/node set strings without ID: characteristic.
      Reader transfers enough meta information in empties to robustly write.
      Replaced string contigency with regular type set
      Removes the Variant row entirely.
      Removed vtkVariantArray from the AssessFunctor.
      Fixes tests for passing.
      Removes strings entirely when dealing with numeric types.
      Replaced string contigency with regular type set
      Removes the Variant row entirely.
      Removed vtkVariantArray from the AssessFunctor.
      Fixes tests for passing.
      Removes strings entirely when dealing with numeric types.
      Compatibility with latest master branch
      Specialized integers apart from doubles.
      Converted to a class for simplicity
      Multiple components supported (needs testing)
      Workaround to make parallel work.
      Addressing compile errors.
      Addresses review criticisms.
      Addresses compile errors.
      Addresses build warnings
      Addresses more compiler errors.
      Addresses review
      Check for the global arrays by name if not set.
      Corrects the indexing for sets between Reader and Writer
      Corrected the block names for all blocks.
      Resolves failed test in Reader and warnings in Writer.
      Proper fix to the weird memory overwriting issue.
      Removed debug comment

Nico Schl├╢mer (1):
      use enum for FlyModes in vtkCubeAxesActor2D.h

Niels Dekker (1):
      COMP: A fix for MSVC warning D9025: overriding '/W1' with '/w'

Ondrej Semmler (2):
      Fix calculation of radius of sphere.
      Fix Cory Quammen note

Ortosoft Marcin Adamczyk (1):
      Fix for bug 15830

Patrick Reynolds (1):
      BUG: Add include needed by NDK for android build.

Perl Regex (1):
      Remove all BTX and ETX markers from VTK headers

Proj Upstream (5):
      libproj4 2016-02-12 (59bbf704)
      libproj4 2016-02-17 (e73c8885)
      libproj4 2016-03-01 (0da95fe9)
      libproj4 2016-03-08 (41bdf053)
      libproj4 2016-05-13 (4b728422)

Robert Maynard (10):
      Allow vtkGeoJSONProperty to be used by other libraries.
      Fix a memory leak when reading each coordinate from a json file.
      Add in support for writing JsonValues to vtkOStreamWrapper.
      Remove usage of VLA's as they aren't supported by C++.
      Get ThreadedSynchronizedTemplates3D to work with more than 4GB.
      Allow explicit binding of vtkOpenGLBufferObject without uploading.
      Remove unreachable code paths in ScaledBoxWidget2
      Prefer CXX_VISIBILITY_PRESET over add_compiler_export_flags.
      Namespace VTK's GenerateExportHeader as it differs from CMake's
      Enable CMP0063 as it is needed to properly build in kit mode

Robert O'Bara (2):
      ENH: Adding a reader for PTS Files
      ENH: Adding new line option to PTS Reader

Sankhesh Jhaveri (49):
      Initial changes to get FBO working in GPU mapper
      Allocate texture objects before attaching to FBO
      Activate and deactivate texture objects
      Removed volume module dependency on LIC module
      Make vtkPixelTransfer available to a broader range of modules
      Added API to export depth and color textures as images
      Added test for new API to export textures
      Pass the output image by reference for the mapper to dump to
      Baselines for new tests
      COMP: Use vtkOpenGL.cmake for vtkRenderingExternal module
      Reduce size of dataset processed by TestFlyingEdges3D
      Contour labels precision
      Fix leaking texture object in volume mapper
      Fix MFC examples link errors
      Fix GLUT test compile failure
      Fix test compile error due to wrong function signature
      Added test for dependent components with gradient opacity
      Gradient opacity related modifications to the shader
      Use the first component transfer functions for dependent comps
      Modify test to provide more gradients
      Added test for four dependent comps with gradient opacity
      Fix issues with volume rendering for dependent component data
      Improve documentation for IndependentComponents
      Use the right component for updating transfer function tables
      Fix test to change the second component values
      Fix private method signatures
      Change variable to a more context friendly name
      Change test to use differing values for two components
      Change the depth texture to be 32 bit
      Support all types of texture to image conversion
      Remove debugging code
      Update tests for 32 bit depth map
      Use full depth range for lookup table for test cases
      Added property to clamp depth values to back face
      Remove unnecessary depth buffer attachment for RenderToTexture
      Added superclass API for depth image type
      Use depth image scalar type for render to texture mode
      Revert "Remove unnecessary depth buffer attachment for RenderToTexture"
      Clear to a transparent white background in RenderToImage mode
      Warning message about the use RenderToImage mode
      Update the baselines for depth render to image tests
      Fix color buffer clear color for RenderToImage mode
      Avoid using the same cache variable for different passes
      Fix volume mapper issue with depth pass mode
      Release graphics resources for depth pass mode
      Cache a vtkPolyDataMapper instance for contouring in depth pass mode
      Fix Step5 tutorial compile error
      Fix missing dependencies in infovis examples
      Fix module loading for Infovis examples

Schuyler Kylstra (1):
      ENH: refs #14978 - Added virtual method to return vtkSelection pointer

Scott Wittenburg (6):
      Prevent empty splat shader string from crashing application.
      Fix a couple minor issues with this mapper.
      Loader can now insert your app html template within the app body.
      Fixed missing null check on app template attribute of loader script.
      Always respect provided close method, do not call window.close()
      When pwf range is much smaller than array range, vtk crashes.

Sean McBride (110):
      Update SimpleCocoaVTK Xcode project to work with VTK 6.3
      Purge support for OS X 10.5 and Carbon
      Removed support for GCC 4.1; >= 4.2 now required
      Added checks for minimum required compiler versions
      Add cppcheck warning suppression file
      Fixed cppcheck null deref warning
      Remove nop assignment warned by cppcheck
      Fixed cppcheck warning about array bounds
      fixed cppcheck warning about <= with unsigned
      Remove unused struct definition warned by cppcheck
      Removed workarounds for old MIPS, SGI, HP, and DEC compilers
      Added back newline at eof removed in 4398c9ca
      Added another missing newline at eof
      Fixed another pesky newline warning
      Fixed bug #2025 by forcing NSApplicationActivationPolicyRegular
      Tweaked minimum clang versions; added minimum requirements notes
      Fixed memory/file leaks of various kinds
      Fixed scanf format string mismatch
      Made ΓÇ£infiniteΓÇ¥ while loop more clear
      Fixed out-of-bounds array access
      Remove dead stores
      Removed useless comparison
      Added an apparent omission of a counter increment
      Fixed apparent mistake in error checking, where no errors actually caught
      Cleanup after evaluating cppcheck false positive
      Updated cppcheck suppressions for version 1.71
      Fixed potential null dereference warned by cppcheck
      Suppress cppcheck warnings with assert
      Fixed a bunch of clang-tidy misc-macro-parentheses warnings
      Introduced additional clamping method to vtkMath
      Replace cube root macro with function.
      Catch by reference
      Fix compile error with non-fully compliant C++11 environments
      Clarified comments in vtkMatrix4x4.h
      Fix warning about unused variable in catch
      Actually mark as deprecated a method merely commented as deprecated
      Fixed leaks in error branches, found by cppcheck
      Exhumed dead branch by no longer ignoring ForwardEvent() return value
      Fixed incorrect use of temporary memory, favour std::string over C string
      Replace obsolete asctime() with ctime()
      Misc cppcheck fixes, update cppcheck suppressions
      Remove totally unused variables
      catch by reference, warned by cppcheck
      Moved conditionally unused vars into their #ifΓÇÖs, warned by cppcheck
      Removed redundant logic warned by cppcheck
      Fixed cppcheck warnings about possible null deref
      Change param from int[3] to int[2]
      Add another exception for AMD Radeon 5770 for ΓÇÿapple bugΓÇÖ
      Use real snprintf (not _snprintf) with >= VS2015
      Fixed new clang 3.9 -Wexpansion-to-defined warning
      Rename #includes to C++ style
      Change some vtk includes from <> to ΓÇ£ΓÇ¥
      Fixed minor leaks found by cppcheck
      Fixed unused variable warnings that workaround old VS warning
      Removed unused variables, found by cppcheck
      Update cppcheck suppressions
      Suppress cppcheck null deref warning with assert
      Properly document vtkPlanes::GetPlane behaviour, remove dead code
      Fixed buffer overrun by rewriting Decode() method to be safer
      Hack HDF5 to build under ASan & UBSan
      Fix cppcheck leak warnings
      Update cppcheck suppressions
      Fixed cast/alignment warning by cppcheck
      Fixed misc cppcheck warnings:
      Fixed SimpleCocoaVTK example to work with git master (7.1)
      Suppress the last cppcheck dashboard warning
      Fixed ΓÇÿclarifyCalculationΓÇÖ cppcheck warnings
      Fixed many 'redundantAssignment' cppcheck warnings
      Fixed most ΓÇÿpassedByValueΓÇÖ cppcheck warnings
      Misc cleanup looking at cppcheck issues
      Fixed incorrect method signatures in 7.1 change notes
      Fixed most clang -Wcomma warnings
      Restore C89 support after fixing cppcheck warning
      Suppress last -Wcomma warning since itΓÇÖs a reasonable usage
      DonΓÇÖt use double-underscore in header guard
      Adjust cppcheck suppressions
      Document other cases Apple+AMD bug
      Cleanup/correct workaround for old OS X 10.6 bug
      Removed dead code, since 08d7b9fe (September 2014)
      Fixed various OS X-related comment spelling
      Mention bug number in logged output
      Add .DS_Store to .gitignore file
      Remove >= 10.6 check, since thatΓÇÖs VTKΓÇÖs minimum nowadays
      Fixed regression from da150781, correct OS X deployment check
      Fixed mixup of deployment vs SDK check
      Increase VTK OS X minimum check from 10.6.0 to 10.6.8
      fixed HDF + UBSan hack to work with old clang
      Fix build error with old clangs without UBSan
      Removed OS X specific avoidance of realloc()
      Replace unsafe C string functions with safer varieties
      Increase size of filename related buffer
      Minor improvements to type matching, style, etc.
      Compensate for recent changes to vtkDataArray
      Remove redundant logic
      Updated cppcheck suppressions
      Removed unused var found by cppcheck
      Fixed null deref found by cppcheck
      Fixed all cppcheck operatorEq warnings
      Fixed cppcheck unsignedLessThanZero warning
      Fixed cppcheck knownConditionTrueFalse warnings
      Fixed return type of various comparison operators from int to bool
      Removed pointless asserts
      Code review of vtkDebugLeaks, misc minor improvements
      Minor comment updates to vtkClipPolyData.h
      Mark some vtkObjectBase API overrides with C++11 'override' keyword
      Fixed a bunch of cppcheck format string warnings
      Fixed cppcheck null deref warning
      Update cppcheck suppressions
      Manual search & destroy of (B|E)TX
      Purged dead branch

Sebastien Jourdain (4):
      Add binary WebSocket endpoint for pushing images to Web clients
      Remove unused import that was creating circular dependency
      VTKWeb update to allow server side notification to client
      Fix OSX compilation with Java Wrapping

Shawn Waldon (8):
      Remove use of nullptr
      MRCReader: assume file is little endian unless marked othewise
      vtkChartXY: add option to disable mouse wheel zooming
      Add detection of c++11 compiler support
      Exclude compiler detection header from wrapping
      Define target before setting target_compile_features
      Update C++11 support to remove target_compile_features
      vtkweb: use dict instead of list to avoid error on reconnection

Simon ESNEAULT (2):
      Add missing call to ReleaseGraphicsResources
      Restore glBlend state after changing it

Steven Hahn (5):
      Get dimensions from a visible cell.
      Reduce time spent calculating a vtkImplicitFunction.
      Add user option to select a shared/static system JsonCpp library.
      Ensure HDF5_HL is found if available.
      VTK_USE_CXX11_FEATURES now enables C++11 compiler flags.

Sujin Philip (32):
      Improve performance of vtkCellIterator.
      Fix implicit inheritance type compiler warning
      Fix vtkSMPThreadLocal API
      Combine vtkProbeFilter and vtkImageProbeFilter
      Add Tests for vtkProbeFilter
      Fix vtkProbeFilter and vtkCompositeDataProbeFilter
      Add vtkResampleToImage Filter
      Fix vtkProbeFilter UPDATE_EXTENT handling
      Add thirdpart library diy2
      Add vtkPResampleToImage Filter
      Suppress diy2 warnings
      Make diy2 installable with VTK
      Fix Diy2 include logic
      Add a way to check for SMP back-end type
      Remove the Kaapi and Simple backends
      Fix ResampleToImage Filters
      Use Generic Arrays in ResampleToImage filter
      Fix Composite Datasets handling in ResampleToImage
      Fix sampling issues
      Fix tolerance usage in vtkProbeFilter
      Fix BuildFieldList in vtkCompositeDataProbeFilter
      Instantiate rotated arrays in AngularPeriodicFilter
      vtkPResampleToImage use Swap-Reduce decomposition
      Update TestPResampleToImage
      Refactor vtkResampleToImage filters
      Add test for CompositeDataSet handling
      Fix SynchronizedTemplatesCutter3D use of vtkIdType
      Improve Point Serialization in vtkPResampleToImage
      Fix vtkPolyData Reset
      Fix Implicit plane widget
      Fix implicit cylinder widget
      Update implicit plane/cylinder representations fix

T.J. Corona (44):
      Prevent str.begin() from being dereferenced if str is empty.
      Removed double delete in vtkXdmfWriter destructor.
      XML data reader now throws an error when reading arrays with duplicate names.
      Force a lookup table reset after vtkAbstractArray::Reset()
      Added a means to prevent private headers from being installed.
      Changing vtkTriangle::TriangleArea() to use parallelogram method.
      Fixed Doxygen latex errors.
      Including vtk3DS.h into the install
      Added unary plus and fixed scientific notation bug in vtkFunctionParser
      Modify vtkDecimatePolylineFilter to accommodate multiple polylines.
      vtkPeriodicDataArray can now return an iterator.
      vtkVolumeRayCastMapper now scales SampleDistance by ScalarOpacityUnitDistance.
      vtkPolydata without holes now pass their polygons through vtkFillHolesFilter.
      Latex newline symbols are no longer at the end of a comment.
      vtkFunctionParser: added support for capital 'E' in scientific notation.
      Suppressing signed/unsigned comparison warning in vtkDecimatePolylineFilter.
      Correct bounds and integer width computation in vtkPlotHistogram2D.
      In vtkGlyphSource2D::CreateDash, only add points if dash is filled.
      Correct and augment the behavior of vtkPolygonBuilder
      Pass cell data through vtkCurvatures filter.
      vtkDataArrayTemplate: Add a safe method to change an element with vtkVariant.
      Extend vtkPolygonBuilder to return multiple disjoint polygons, if present.
      Fix vtkTableBasedClipDataSet to handle 2-dimensional data in XZ and YZ.
      Remove SMP parallel processing examples.
      Fix vtkNewickTreeReader to read trees of type (A,B,C)D;
      Removing unused parameter name in vtkGPUVolumeRayCastMapper.
      Make closest point optional in vtkLine methods.
      Propagate safe variant setting through children of vtkAbstractArray.
      Fix IntersectWithLine methods for vtkQuadraticWedge and vtkQuadraticTetra.
      Add another baseline image for quadraticIntersection test.
      Rescale quadraticIntersection test images.
      In vtkPolygonBuilder, restrict triangle vertex traversal to counterclockwise.
      Setting up third party submodule script for MetaIO
      Deprecating vtkVolumeRaycastMapper and vtkVolumeTextureMapper2D/3D.
      In vtkOpenGLGlyph3DMapper, use color values from actor.
      Enable vtkTableBasedClipDataSet to generate clipped output.
      Enable/disable clipping planes in vtkOpenGLGlyph3DMapper
      Fix memory leak in vtkMath::SolveLeastSquares.
      Fix a bug in vtkExodusIIReader when # of timesteps equals one.
      Recover tests that were deprecated by commit 7d31157b.
      Create a fallback for writing vtkDataArrays to XML.
      Create a test array and test case for XML writer dispatch fallback.
      Clean up character array in test.
      vtkPeriodicDataArray: fix vector range computation.

Tim Meehan (2):
      Added some new parametric functions
      Added a test for the new parametric functions

Tim Thirion (5):
      Add a lighting map pass for OpenGL2 backend
      Add value rendering pass
      Use global scalar range in value pass
      Fix incorrect string compare in vtkValuePass
      Support composite datasets in value pass renders

Timo Oster (1):
      Add ability to append vtkRectilinearGrid

Tokishiro Karasawa (4):
      Fix occasional failure of testing if a point is in or out of a triangle
      Add a test for FindTriangle
      Modify the CMakeLists
      Fix occasional failure of testing if a point is in or out of a triangle

Tomas Janak (1):
      Fix misleading documentation of vtkCellQuality

Tristan Coulange (1):
      Add new Execute method in Glyph3D

Utkarsh Ayachit (76):
      Add support to read ALE fluid groups information.
      Fix VS2008 build issues with std::abs(__int64).
      Fix incorrect error when testing is disabled.
      Xdmf3 was failing to build when using system HDF5.
      BUG #14291: Fix segfault when RemoveGhostCells was off.
      Support passing vtkPoints to PointSet::SetPoints.
      Link against MPI Cxx libraries, if available.
      BUG #15746: Fixes issues with Merge Points in vtkAppendFilter.
      Exclude generated WebGLExporter classes from Python wrapping.
      Exclude generated WebGLExporter classes from Python wrapping.
      Fix leaks in vtkCompositedSynchronizedRenderers.
      Fix const-cast warnings in vtkPythonInteractiveInterpreter.
      Fix segfault when mapper is re-updated.
      BUG #15763: Avoid modifying camera when it hasn't changed.
      Fix VS2013 build issues.
      Fix VS2013 build issues.
      BUG #15632: Fix exodus performance issue with spatial files.
      Fix "same expression in both branches of ternary operator".
      BUG #15874: Fix texture blending to discard transparent pixels.
      Cleanup Cmake logic for VTK_EGL_DEVICE_INDEX.
      Fix build issue when VTK_ENABLE_KITS is ON.
      Avoid making invalid bounds valid.
      Marking several advanced variables as 'advanced'.
      Add DataModel to StandAlone group.
      Remove unused attributes.
      Refactor piece iteration for XMLP writers.
      Skip writing empty pieces.
      Reuse functions from vtksys::SystemTools.
      Handle empty directories (regression introduced by 69c6f7e48).
      Extend doxyfile to add support for processing markdown files.
      Revert "BUG #15874: Fix texture blending to discard transparent pixels."
      Revert "BUG #15874: Fix texture blending to discard transparent pixels."
      Minor clean to abstract API in vtkDataArray.
      Working on vtkAgnosticArray infrastructure.
      Simplifying allocation infrastructure.
      Adding a notion of tuple-iterator.
      Minor cleanups
      Implementing virtual API in vtkAgnosticArray (using vtkAgnosticArrayHelpers).
      Added mechanism to support const arrays.
      Make iterator type a template param (again).
      Implementing most of vtkDataArray API for vtkAgnosticArray.
      Rename as vtkGenericDataArray and vtkSoADataArrayTemplate.
      Ensure SetNumberOfTuples doesn't force a shrink only grow.
      Correct MaxId usage.
      Fix friendship declaration
      Working on adding vtkAoSDataArrayTemplate.
      Memory alloc fixes.
      Fixes to vtkAoSDataArrayTemplate.
      Moving macros to a separate file.
      Adding vtkBuffer.
      Update vtkAoSDataArrayTemplate to use vtkBuffer.
      Refactoring to remove iterators.
      PERF: Don't call DataChanged in SetValue/SetComponentValue.
      Update vtkDataSetAttributes to support GenericArrays.
      Use correct stat() function on Windows.
      Fix build issues with static builds + Python + kits
      Minor fixes to vtkSPHInterpolator.
      Misc. fixes to vtkArrayListTemplate.
      vtkSPHInterpolator was loosing derivative arrays.
      Fixed leaks in vtkArrayListTemplate.
      Making vtkPLYWriter handle RGBA color arrays.
      Modernize vtkFunctionParser.
      Perf improvements to vtkArrayCalculator.
      Cleaning up leaks in vtkModelMetadata.
      Avoid duplication in vtkXMLDataSetWriter and vtkXMLCompositeDataWriter.
      BUG 15492: Don't write empty datasets.
      Revert "Added more flags for using OpenGL libraries"
      Fix length of arrays when running in parallel.
      Plot3D: support records with multiple sub-records.
      Validate whole extent specified on vtkRTAnalyticSource.
      Fix issue exporting cell-data colors for composite datasets.
      Fix Q_WS_* usage for Qt5.
      Remove Apple warning messages in non-debug builds.
      Fix issue introduced by aa3330f4
      PointGaussianMapper: Support colors via material properties.
      QVTKWidget: add ability to defer render in paintEvent

Victor Lamoine (3):
      Add JoinContiguousSegments option to vtkStripper
      Implement JoinContiguousSegments option in vtkStripper
      Add test for vtkStripper

Vincent Chen (2):
      Add option to use vtkSMPTools for vtkThreadedImageAlgorithm.
      Add thread-local storage to SMP image filters.

Vladimir Chalupecky (3):
      vtkAVSucdReader: fix to read ASCII input correctly
      vtkAVSucdReader: add C++ tests and test ASCII data with noncontiguous IDs
      vtkAVSucdReader: add alternative baseline images

W Alan Scott (2):
      Performance improvements to vtkRTAnalyticSource.
      BUG #15399: Improve performance for exodus modeshapes.

Waldir Pimenta (20):
      fix "not" --> "nor"
      fix documentation: "not" --> "nor"
      typo: "an sheared" --> "a sheared"
      sync doc to code: UseNormalAndRadius --> UseNormalAndAngle
      improve documentation of vtkArcSource
      fix bug in vtkArcSource: default polar vector and normal vector were swapped
      Add note for github users on CONTRIBUTING.md / simplify link code
      replace broken link in QVTKWidget.cxx with a working one
      doc fix: UNSIGNED_CHAR --> VTK_UNSIGNED_CHAR
      vtkImageMapper3D: add missing space in error message
      vtkXML(Reader|Writer): remove unnecessary semicolons
      vtkXML(Reader|Writer): minor whitespace tweaks
      vtkXMLReader: fix documentation of ReadFromInputString
      fix typo: Kochenek --> Kochanek
      fix typo in vtkParametricSpline: 'quaranteed' --> 'guaranteed'
      various documentation fixes (rewording, typo-fixing, punctuation, formatting)
      several whitespace fixes (including style harmonization within each file)
      fix class references in vtkDataObject's documentation
      limit comments to ASCII characters, to prevent encoding issues
      wrap function signatures longer than 80 characters

Will Schroeder (114):
      Cleaned up header docs, refined keypress callbacks
      Threaded and templated elevation filters
      Cleaned up shadowed template parameter
      Removed leftover performance testing code
      Added new widget: vtkImplicitCylinderWidget
      Cleaned up callbacks
      Cleaned up test image
      Added alternate regression test image
      All working before SMP conversion
      First incarnation of Flying Edges
      Cleaned up warnings
      Added vtkSMPTools integration to thread algorithm
      Experimenting with grain size
      Refactored code and thread over slices
      Fixed skipping non-intersecting slices.
      Used 200grit to polish the code (bugs fixes)
      Rebased; tweaked tests
      Refining tests and test images
      Fixed UpdateExtent processing
      Added new scalar tree (span space) and fixed.
      Removed warnings
      Added proper memory management of added scalars
      Fixing memory leak
      Forgot to commit a file to remove memory leaks
      Threaded and templated vector dot and vector norm
      Cleaned up ambiguous operation order warning
      Improved documentation
      Working around SMPTools copy constructor bug
      Threaded span-space build
      Accelerated vtkSpanSpace with parallel sort
      Need to include appropriate files for std::sort
      Added Sort method with comparison parameter
      Use viewport coordinate system
      Fixed 2D handle rendering in multiple viewports
      Renderer needed to perform coordinate transformation
      Corrected constrained handle representation behvaior
      Initial working snapshot
      Removed initialization warning
      Successfully running in parallel
      Reduced test size since dashboard machines choked
      Cleaned up some numerical sensitivity; added test
      Resolved x-edge parallel plane cuts
      Documentation tweaks
      Resolved merge conflict
      New valid regression test image
      Handle multiple contour values properly
      Added new class vtkStaticPointLocator
      Addressed dashboard warnings
      Additional dashboard warnings
      Tweaked documentation
      Replaced qsort with std::sort
      New class to create links from points to cells
      Fully fleshed out and working; 2.5x faster
      Cleaned dashboard warnings
      Separated templated code; created wrappable class
      Performance related refactoring
      Tested and working
      Fixed memory leak
      Dealing with memory leak issues
      Encapsulated helper class in anonymous namespace
      Adapted back to multibuild workflow
      Dashboard warnings
      Documentation polish
      Fixed interpolation for precise hits
      Threaded and implemented power parameter
      Modernized vtkSortDataArray, threaded the sort
      Remote module for point cloud processing
      Extended static point locator API to support querying buckets for points
      Addressing remote repository access
      Created generalized point interpolation filter
      Compiler warnings
      Compiler warnings
      Added new class for oriented gaussian distributions
      Preparation for reorganization
      Created new Filters/Points module
      Refactored kernel API to support different basis
      Test cleanup
      New class generates data from implicit function
      Proper pipeline behavior
      Cleaned up documentation
      Pass input attribute data to output
      Renamed filter for consistency
      New regression test images
      Regression test image
      Work around test failure due to OpenGL2 not running on some machines
      Accelerated and thread-capable attribute data processing
      Fixed test timeout
      Now interpolating point attribute data on request
      Flying edges plane cutter interpolates attributes
      Working around dumb compilers
      New 2D point interpolator; API for weighted interp
      Dashboard warnings
      Dashboard warnings
      Dashboard warnings
      Added a quintic SPH kernel and SPH interpolator
      Dashboard warnings and errors
      Dashboard warnings
      Dashboard issues
      Dashboard issues wrt fmin()
      Replaced fmin() with std::min()
      Handle interpolation kernels with large radius
      Remove excluded array from output
      Algorithm implementation is correct
      Dashboard warnings
      Added cubic and quartic SPH kernels
      Promote integral arrays to real type if requested
      Dashboard warnings
      Dashboard warnings
      Minor style issues
      Addressing dashboard issues
      New test data for SPH interpolation
      EllipsoidalGaussian working, normalize kernels opt
      Dashboard warnings
      Support cutoff mass/density arrays; 2D kernels

XDMF Upstream (3):
      xdmf3 2016-04-07 (0c08b3ea)
      xdmf3 2016-04-08 (75c5916b)
      xdmf3 2016-06-16 (cdb48e8e)

Xabi Riobe (22):
      Support more PLY texture coordinates syntax.
      Add unit test
      Add return value check in the unit test.
      Do not retain the windows events if they are not treated
      Set the CS_DBLCLKS  flag to receive double-click notifications
      Fix issue with polygon offset being left on
      A depth peeling fix when compositing
      Write vertex texture coordinates with vtkPLYWriter
      Write comments in ply header
      Avoid use of STL list in header, and remove unnecessary array copy
      Add unit test for vtkPLYWriter
      Do not retain the windows events if they are not treated
      Add missing include for OSX and Linux
      Multiple includes restriction
      Missing include for TCL
      Remove the extra Render performed by the interactor on WM_PAINT.
      Use memory pointers to reduce vtkSmoothPolyDataFilter computation time
      Reduce vtkPolyDataConnectivityFilter computation time
      Make the code easier to read
      Optimization by using direct memory pointers
      Fix the documentation for vtkImageData::GetDimensions
      Return the MouseWheel event as a pending event in Win32 RenderWindow

Yumin Yuan (2):
      Use visible blocks to compute bounds in CompositePolyDataMapper2
      Update baselines for CompositePolyDataMapper2 tests

Zlib Upstream (6):
      zlib: update to for/vtk
      zlib 2015-11-18 (0abb295c)
      zlib 2015-12-09 (acc12639)
      zlib 2015-12-14 (751703ae)
      zlib 2016-01-08 (5a2db714)
      zlib 2016-01-20 (bfc811e0)

peter karasev (9):
      write test showing catastrophic fail with QT5+Win32, make fix(es).
      update shader program checks
      update rendering code; locally all the tests are passing
      Merge branch 'master' of gitlab.kitware.com:vtk/vtk into vtkOBJImporter-robustify-and-cleanup
      update shader program checks
      update rendering code; locally all the tests are passing
      fix for annotation rendering test
      remove incorrect error popup (QT5 + local build + OpenGL 4.x)
      STY: fix vtkErrorMacro and linelength

Revision 25207  Directory Listing
Modified Wed Jul 6 05:30:16 2016 UTC (14 months, 2 weeks ago) by jcfr
ENH: Update SlicerExecutionModel

$ git shortlog 419bed3..26a62a0 --no-merges
Hans Johnson (1):
      BUG: find_package(ITK ...) clobbered existing

ivmartel (2):
      Made implicit conversion explicit (size_t to int).
      Using static_cast instead of direct cast.

Revision 25203  Directory Listing
Modified Mon Jul 4 15:57:33 2016 UTC (14 months, 3 weeks ago) by jcfr
BUG: Ignore user site python packages.

This commit will fix error like the one reported below where PYTHONPATH
was prepended with system locations because it found packages in user
home folder.

List of folders that will NOT be prepended after env. variable "PYTHONNOUSERSITE"
is set to 1 are documented here:

  https://docs.python.org/2/library/site.html#site.USER_SITE

Error:

  File "setup.py", line 19, in <module>
    exec(init_file.read(), command_ns)
  File "<string>", line 11, in <module>
  File "/home/lucas/Projects/Slicer/Slicer-superbuild/python-setuptools/setuptools/__init__.py", line 12, in <module>
    from setuptools.extension import Extension
  File "/home/lucas/Projects/Slicer/Slicer-superbuild/python-setuptools/setuptools/extension.py", line 7, in <module>
    from setuptools.dist import _get_unpatched
  File "/home/lucas/Projects/Slicer/Slicer-superbuild/python-setuptools/setuptools/dist.py", line 16, in <module>
    from setuptools.depends import Require
  File "/home/lucas/Projects/Slicer/Slicer-superbuild/python-setuptools/setuptools/depends.py", line 6, in <module>
    from setuptools import compat
  File "/home/lucas/Projects/Slicer/Slicer-superbuild/python-setuptools/setuptools/compat.py", line 19, in <module>
    import httplib
  File "/usr/lib/python2.7/httplib.py", line 71, in <module>
    import socket
  File "/usr/lib/python2.7/socket.py", line 68, in <module>
    from _ssl import \
ImportError: cannot import name RAND_egd


Co-authored-by: Lucas Gandel <lucas.gandel@kitware.com>

Revision 25198  Directory Listing
Modified Fri Jun 17 21:00:17 2016 UTC (15 months, 1 week ago) by jcfr
ENH: Update ITK to include newer version of ITK-Minimal-Path remote module

$ git shortlog 7db7b60..16df9b6 --no-merges

Sumedha Singla (1):
      ENH: Updated the git tag for the ITK-Minimal-Path external module.

From: Sumedha Singla <sumedha.singla@kitware.com>

Revision 25177  Directory Listing
Modified Thu Jun 9 18:50:18 2016 UTC (15 months, 2 weeks ago) by jcfr
BUG: Update VTK: Support InvokeEvent with param from python. Fixes #4181

Currently it only supports strings, floats and ints.

Infrastructure to support vtkObjects is also in place, but cherry-picking
the wrapping infrastructure patches to support it are too involved
to be reliably done.

Doing the following is now expected to work:

  paramNode = slicer.vtkMRMLScriptedModuleNode()
  paramNode.InvokeEvent(vtk.vtkCommand.ModifiedEvent, 4)

$ git shortlog 4b9957b..f08b7db --no-merges
Hastings Greer (1):
      Allow pyvtkObjects to have InvokeEvent called on them with calldata


Thanks: Hastings Greer <hastings.greer@kitware.com>
Thanks: David Gobbi <david.gobbi@gmail.com>

Revision 25160  Directory Listing
Modified Fri Jun 3 20:57:02 2016 UTC (15 months, 3 weeks ago) by jcfr
ENH: Update VTK to handle default values for array parameters in python

Without this commit, one must specify parameters like (,int array[3]=0) when
the method is called from python.

$ git shortlog 1c30cb0..4b9957b --no-merges
David Gobbi (2):
      Fix wrapping pointer parameters with default value 0.
      Handle default values for array parameters in python.

From: Francois Budin <francois.budin@gmail.com>

Revision 25157  Directory Listing
Modified Fri Jun 3 06:11:49 2016 UTC (15 months, 3 weeks ago) by jcfr
ENH: Update CTK to include ctkAxesWidget support for setting AxesLabels

$ git shortlog --no-merges adc88bf..5b7dc1a
Davide Punzo (1):
      ENH: ctkWidgetAxes: Add setter for AxisLabels

Revision 25109  Directory Listing
Modified Mon May 23 06:13:48 2016 UTC (16 months ago) by jcfr
ENH: Update VTK to include vtkPythonUtil tweak

This change prevents crashes observed while investigating the impact of
python module loading on the startup time.

Merge request has been submitted upstream.
See https://gitlab.kitware.com/vtk/vtk/merge_requests/1515

$ git shortlog fe92273..1c30cb0 --no-merges
Jean-Christophe Fillion-Robin (1):
      BUG: vtkPythonUtil: Check if vtkPythonMap is valid

Revision 25108  Directory Listing
Modified Mon May 23 06:13:47 2016 UTC (16 months ago) by jcfr
ENH: Update CTK

$ git shortlog a479422..adc88bf --no-merges
Jean-Christophe Fillion-Robin (2):
      ENH: Update PythonQt
      BUG: ctkAbstractPythonManager: Handle case when PythonQt is not initialized

Revision 25098  Directory Listing
Modified Fri May 20 23:46:56 2016 UTC (16 months ago) by jcfr
ENH: Update ITK

$ git shortlog 8ac0d60..7db7b60 --no-merges
Bradley Lowekamp (1):
      ENH: Use ITK_USE_64BITS_IDS for windows 64 by default

Davis Vigneault (1):
      BUG: Improve error checking and testing for ConnectedRegionsMesh

Hyun Jae Kang (2):
      BUG: Address the issue of "Missing Delete" within SwapZeroCornerToIRP.
      COMP: Fixed Mac OSX wrapping configuration warning

Jean-Christophe Fillion-Robin (1):
      COMP: Fix Slicer MacOSX extension packaging setting CMP0042 policy to OLD

Matthew McCormick (7):
      BUG: Fix Python wrapping on Windows when ITK_USE_64BIT_IDS is ON.
      BUG: The ImageFileReader internal pipeline methods should be protected.
      BUG: Use new VNL include directory variables.
      COMP: Add missing NeighborhoodAccessor methods to PhasedArray3D image.
      BUG: Adjust itk.org ExternalData URL.
      COMP: Do not use target_include_directories with CMake 2.8.11.2.
      BUG: Address missing shared_ptr for VS9

Michka Popoff (1):
      ENH: Use https URL for OS X castxml binary (for consistency)

Ziv Yaniv (1):
      BUG: Interpretation of the Euler angles ZYX or ZXY was not exported.

Revision 25079  Directory Listing
Modified Wed May 18 23:36:00 2016 UTC (16 months, 1 week ago) by jcfr
PERF: Improve startup time delaying execution of shared and executable CLIs

This commit reduces startup time by ~50% (8.6s -> 5.5s). Detailed startup
time stats reported below.

[ci skip]

More specifically, it updates the loadable and executable CLI factories
so that (1) the XML file is directly loaded from disk if it exists along
side the executable or library and (2) the execution of the executable or
"entry point" for shared library is delayed until needed.

For CLI executable, change consists simply in reading the XML file if it
exists and postpone the execution until it is needed.

For CLI shared library, the ModuleDescription object API has been updated.
It now allows the association of a callback in charge of loading the
library and resolving symbols. The callback is automatically called
when "GetTarget()" method is called and no target has already been set.

Note that the XML file is now copied (and installed if it applies) along
side the CLI executable. There are currently no option to avoid the new
behavior, if it reveals problematic, we could revisit and introduce
an option for "SEMMacroBuildCLI" macro.

Detailed startup time stats without this change are reported in
precedent commit (ENH: Add convenience script to measure the application
startup time).

Detailed startup time stats after this change:

 - Obtained on Ubuntu 15.10, 64GB/M.2 PCIe NVMe SSD/Quad Core 3.80GHz.
 - For a release build

Slicer --no-splash --exit-after-startup
5.537 seconds

Slicer --no-splash --exit-after-startup --disable-builtin-cli-modules
5.438 seconds

Slicer --no-splash --exit-after-startup --disable-builtin-loadable-modules
2.863 seconds

Slicer --no-splash --exit-after-startup --disable-builtin-scripted-loadable-modules
3.925 seconds

Slicer --no-splash --exit-after-startup --disable-builtin-cli-modules --disable-builtin-scripted-loadable-modules
3.973 seconds

Slicer --no-splash --exit-after-startup --disable-modules
1.761 seconds

Slicer --no-splash --exit-after-startup --disable-python
3.094 seconds

Slicer --no-splash --exit-after-startup --disable-python --disable-builtin-cli-modules
3.054 seconds

Slicer --no-splash --exit-after-startup --disable-python --disable-builtin-loadable-modules
0.972 seconds

Slicer --no-splash --exit-after-startup --disable-python --disable-builtin-scripted-loadable-modules
3.135 seconds

Slicer --no-splash --exit-after-startup --disable-python --disable-builtin-cli-modules --disable-builtin-scripted-loadable-modules
3.085 seconds

Slicer --no-splash --exit-after-startup --disable-python --disable-modules
0.924 seconds

SlicerExecutionModel changes:

$ git shortlog b2c78c7..1b2a454 --no-merges
Jean-Christophe Fillion-Robin (9):
      STYLE: ModuleDescription: Move definition to cxx file
      STYLE: Remove obsolete ModuleFactory class
      STYLE: ModuleDescription: Remove unused Alternative Type/Target/Location
      STYLE: Remove obsolete BinaryFileDescriptor support
      STYLE: ModuleDescriptionParser: Add separator comment, small tweaks
      STYLE: Add ModuleDescriptionTesting Macros and Utilities files
      STYLE: ModuleDescription: Add TestDefaults
      ENH: ModuleDescription: Add support for lazily setting the target
      ENH: Update SEMMacroBuildCLI to copy (and optionally install) the XML file

Revision 25068  Directory Listing
Modified Wed May 18 04:55:05 2016 UTC (16 months, 1 week ago) by jcfr
BUG: Update CTK to fix reporting of modified settings. Fixes #4192

Other highlights includes:
* Support Qt 5.6 compilation
* Extend python wrapping ctkVTKChartView and ctkVTKScalarsToColorsView

$ git shortlog caaf2c8..a479422 --no-merges
Andreas Fetzer (12):
      Added additional documentation and also added missing session timeout timer     restarts.
      Renamed session time out related variables and signals/slots
      Changed xsiType style.
      Don't add ctkXnatResourceFolder into ctkXnatScan hierarchy
      Fix linker error on linux
      Added possibility to set network proxy for the XNAT connection
      Removed accidental linebreak
      Quick-fix for incomplete data display
      Updated qRestAPI revision
      Adding the xsiType=xnat:resource query parameter leads to     error 422: Unprocessable entity
      Changed query key from xsiType to xsi:type
      Fixed build error for MSVS 2012

Aurélien Labrosse (1):
      Updated splash screen handler management

Daniel Knorr (6):
      Inserted parameter to the httpGet that the subjects and experiments have more attributes to show in applications.
      Added static member variables for each item of the parameter string.     Added getter and setter for attributes also.
      Added some specific attributes for an experiment.
      Added a timer which keeps count of the session timeout.     This timer emits two signals: sessionTimedOut and sessionAboutToBeTimedOut.
      Removed clear numbers - added times from session cookie
      Changed signal that the session times out always in one minute.     Variable for time that the session times out soon renamed.

Dmitry Mikhirev (1):
      fix build on platforms where qreal is not equivalent of double

Eric Heim (2):
      upgraded PythonQt.cmake to use PythonQt3 in the superbuild with Qt5 and 4
      Changed name of variable to set the Qt version in PythonQt to match present naming convention

Heather (2):
      fix Core linking: FreeBSD does not have a libdl
      Add /usr/local/include for FreeBSD (QtOpengl)

Jean-Christophe Fillion-Robin (18):
      Remove unused/non-implemented VisualizationXIP library
      CTKCore: Generalize test checking if dl library is available.
      CTKCore: Fix typo introduced in commontk/CTK@f8b31c3
      COMP: ctkMacroBuildLibWrapper: Improve configuration status messages
      ENH: Extend wrapping ctkVTKChartView and ctkVTKScalarsToColorsView
      Add ctkCoreTestingUtilities module
      Add ctkCoreTestingMacros module
      Simplify ctkSettingsPanelTest1 using ctkCoreTestingMacros
      Extend ctkTesting(Utilities|Macro) to support QStringList
      ctkSettingsPanelTest1: Add "QStringList" test case
      ctkSettingsPanelTest1: Test return value of "changedSettings()"
      Extend ctkTesting(Utilities|Macro) to support QVariant
      ctkSettingsPanelTest1: Explicitly compare QVariant
      ctkSettingsPanelTest1: Improve readability splitting test in smaller functions
      ctkSettingsPanelTest1: Check settings after reloading from file
      ctkSettingsPanel: Add setter/getter for PropertyType::PreviousValue
      ctkSettingsPanel: Fix changedSettings() for empty QStringList
      ctkSettingsPanel: Ensure "settingChanged" signal is emitted only if needed.

Jerome (5):
      Added double click support for patients and studies table
      Add an accessor to the internal QTableView
      Add an accessor to the three managed tables
      Add missing ending empty line
      Update table views when deleting patient

Julien Finet (1):
      Support Qt 5.6 compilation

Tobias Doerffel (1):
      ctkCheckableComboBox: implemented missing method checkableModelHelper()

Revision 25055  Directory Listing
Modified Sun May 8 02:15:06 2016 UTC (16 months, 2 weeks ago) by jcfr
ENH: Update ITK

$ git shortlog ce3e47d..8ac0d60 --no-merges
Bradley Lowekamp (1):
      ENH: Enable run-time dependency on Python library

Jean-Christophe Fillion-Robin (1):
      COMP: Fix Slicer MacOSX extension packaging setting CMP0042 policy to OLD

Matthew McCormick (1):
      BUG: Use CastXML built against LLVM with LLVM_ENABLE_TERMINFO OFF.

Revision 25045  Directory Listing
Modified Fri May 6 05:17:46 2016 UTC (16 months, 2 weeks ago) by jcfr
ENH: Update ITK

$ git shortlog 9fa8f63..ce3e47d --no-merges
Dženan Zukić (1):
      ENH: CovariantVector's Normalize returns the norm.

Francois Budin (3):
      BUG: Wrapping intermediate files were not automatically updated
      ENH: Reduce number of dependencies for XML files generated for wrapping
      BUG: GCC is limited when calling overloaded base class functions

Hans Johnson (1):
      ENH: Merge GDCM release branch

Jean-Christophe Fillion-Robin (1):
      COMP: Fix Slicer MacOSX extension packaging setting CMP0042 policy to OLD

Jon Haitz Legarreta (2):
      ENH: Improve itkVersion class code coverage.
      ENH: Perform class name checks in test macro

Manuel Grizonnet (1):
      COMP: add ITKCommon_EXPORT to fix link issues with external applications

Matthew McCormick (10):
      COMP: Update CastXML to support Visual Studio 2015 Update 2.
      COMP: Do not set wrapping library visibility with static builds.
      COMP: Update CastXML to support Visual Studio 2015 Update 2.
      COMP: Broaden the KWStyle warning exception.
      COMP: Update KWStyle version.
      BUG: Do not use the same output file in N4BiasField Test 2,3.
      COMP: Expand EXERCISE_BASIC_OBJECT_METHODS for other GCC versions.
      ENH: Update Cuberille Remote to 2015-05-01.
      ENH: Enable registration of the IOOpenSlide module through CMake.
      ENH: Update itk.org URL's for HTTPS support.

Pablo Hernandez-Cerdan (1):
      COMP: Fix warn in FFTW about delete [].

Sean McBride (2):
      COMP: Hack HDF5 to build under ASan & UBSan
      COMP: fixed clang -Wdeprecated-writable-strings warning

VXL Maintainers (1):
      VNL 2016-04-26 (6b168535)

Vladimir S. FONOV (1):
      MINC 2016-01-30 (783bca38)

Revision 25027  Directory Listing
Modified Mon Apr 25 00:06:22 2016 UTC (17 months ago) by jcfr
ENH: Update SlicerExecutionModel version

$ git shortlog 112076b..b2c78c7 --no-merges
Hans Johnson (5):
      COMP: KWSYS removed support for pre-C++98 in 2015
      ENH: Exceptions should be caught by reference
      STYLE: Prefere initialization to assignment
      STYLE: Remove unused function WriteLines
      STYLE: Remove unused variable 'elements'

Revision 25026  Directory Listing
Modified Mon Apr 25 00:06:20 2016 UTC (17 months ago) by jcfr
ENH: Update ITK version

$ git shortlog 84ba36b..9fa8f63 --no-merges
Andrey Fedorov (2):
      BUG: Add missing itk_expat_mangle.h install target
      BUG: fix typo in file name

Bill Lorensen (5):
      ENH: Bump wiki examples version, new remote module process
      ENH: Bump wiki examples version, new remote module process
      STYLE: SuperClass should be Superclass
      COMP: Resolve clang linkage issue
      BUG: Valgrind detected an invalid read

Bradley Lowekamp (18):
      ENH: Update Insight Journal handle links to https
      ENH: Adding const qualifier to results
      BUG: Adding missing const qualifier for GetConfusionMatrix method
      BUG: Use Set/GetMacros, fix const correctness and PrintSelf.
      ENH: added inlined Zero and one values for integer NumericTraits
      ENH: Use constexpr for floating point NumericTraits
      ENH: Make NumericTraits functions constexpr for intrinsic
      BUG: Add definition of static constexpr NumericTrait members
      BUG: Declared static constexpr members need to be defined as constexpr
      ENH: ITK_CONSTEXPR_FUNC implies inline
      BUG: Addressing VS10 and VS11 NumericTraits linkage issue
      BUG: Use LargestPossible region for BSpline domain
      BUG: Remove errant file
      COMP: Address warning about this usage in initializer list
      ENH: Prefer ZeroValue function over variable
      STYLE: Use consistent path for try_compiles binary directory
      BUG: Don't use "=" in cmake variable name
      ENH: Test address of NumericTraits One and Zero constexpr

Davis Vigneault (2):
      ENH: Add Ternary Operator Image Filter
      STYLE: Prefer static cast

Francois Budin (3):
      PERF: Simplify itkTemplate New() input type identification.
      ENH: Avoid template type specification for image reader in Python wrapping
      BUG: Missing IOPixelType strings in ImageIOBase

GCC-XML Upstream (1):
      ENH: pygccxml v1.7.3 (reduced)

Hans Johnson (23):
      COMP: Provide VXL backward compatible includes
      COMP: ITK requires legacy methods
      ENH: Need propagate ITK_LIBRARY_PROPERTIES
      ENH: Added UpdateFromUpstream.sh for VNL
      ENH: Manual copy from vxl/master
      STYLE: vnl_math_[min|max] -> std::[min|max]
      STYLE: Text files should end with a newline
      COMP: Prefer C++11 constexpr when possible
      COMP: Prefer C++11 constexpr when possible
      ENH: Simplify std:: math function definitions
      COMP: Error in constexpr usage
      COMP: Add const to previous const variables
      COMP: SizeValueType can has different definition for itkArray
      ENH: Added utility for modernizing vcl_ to std::
      ENH: Reference vnl_math.h constants directly
      ENH: Avoid using vnl_math_ functions
      COMP: Missing symbol for itkStaticConstMacro
      COMP: Function override missing in BioCell
      ENH: Convert vcl_ to std::
      BUG: Windows vcl_snprintf failures addressed
      COMP: Disabmiguate function calls to SetData
      ENH: Provided static code API for external applications
      COMP: Remove possible type conversion warnings

Hyun Jae Kang (9):
      COMP: Fixed the compiler error of ITK on Mingw-w64
      COMP: Temporarily suppress the warning messages of data-conversion on VS14
      COMP: Put back the disappeared option of "BUILD EXAMPLES".
      BUG: Fix segmentation faults on mingw-W64 x86_64.
      BUG: Fix the failed test of itkCastImageFilterTest on mingw-w64 compiler.
      COMP: Fixed the cmake configuration for ITK_WRAP_DOC
      COMP: Fixed the warning messages on VS14.
      COMP: Add a missing head file at itkNumericTraitsStdVector.h
      COMP: Fix the wraning message of data-conversion

Jean-Christophe Fillion-Robin (2):
      STYLE: UseITK: Document static registration of ITK IO factories. See #3393
      COMP: Fix Slicer MacOSX extension packaging setting CMP0042 policy to OLD

Jon Haitz Legarreta (5):
      COMP: Delete unused variable compiler warning.
      ENH: Refactored itkBioCellTest
      ENH: Exercise non-tested itk::Math methods.
      ENH: Improve MersenneTwister class and test.
      ENH: Improve itkFEMLoadPoint coverage.

KWSys Robot (1):
      KWSys 2016-03-09 (36d8666f)

Lucas Gandel (6):
      ENH: Add TubeTK as a remote module
      COMP: Fix external module testing
      COMP: Fix git protocol setup
      ENH: Update TubeTK remote module
      ENH: Conditionally add testing for External Modules
      BUG: Fix call to std::max() with different variable types

Matthew McCormick (43):
      BUG: Update MIDAS url for https in archive testing data script.
      STYLE: Use PixelType and ImageType in Python tests.
      ENH: Avoid template type specification in Python wrapping.
      COMP: Do not use has_key in itkTemplate New.
      DOC: Emphasize that push access is not required to contribute patches.
      ENH: Download SWIG and PCRE from midas3.kitware.com.
      COMP: Ignore build warning from KWStyle's boost.
      BUG: Remove Azure ExternalData resource.
      BUG: ExternalData downloads from midas3.kitware.com only supports https.
      BUG: slicer.kitware.com/midas3/ ExternalData will not support http.
      ENH: Update the VNL README-ITK.txt subtree commit revision.
      BUG: Mark VXL internal CMake variables as advanced.
      BUG: Run itk_module_target on itknetlib.
      DOC: Direct patches for VXL upstream to the GitHub repository.
      BUG: Run itk_module_target on itknetlib.
      COMP: Account for removal of vcl_* from upstream VXL.
      COMP: Remove itkTypeMacro from BioCellHelper.
      COMP: Convert itkBioCellTest arguments from double to int.
      COMP: Turn off BUILD_DOCUMENTATION for VNL.
      BUG: Install VXL config files to backwards-compatible locations.
      ENH: Remove vcl_complex from the wrapping.
      BUG: Install vnl_export.h and vnl_algo_export.h to previous locations.
      BUG: midas3.kitware.com only supports the https protocol.
      BUG: ImageIOBase SetDimensions should take SizeValueType.
      ENH: Add wrapping for ImagePCAShapeModelEstimator.
      COMP: Do not specify COMPONENTS with find_package(VTK.
      DOC: Fix FFTW warning grammar.
      COMP: Build against system HDF5 1.8.16.
      ENH: Set a default CMAKE_BUILD_TYPE when building a module externally
      COMP: Make initial HDF5 discovery of 1.8.16 quiet.
      ENH: Use hidden symbol visibility for the CPython extension modules.
      ENH: Turn on CMAKE_POSITION_INDEPENDENT_CODE by default.
      BUG: FEMLoadPoint uninitialized value in the constructor.
      BUG: Fix wrapping of complex types in VNL.
      ENH: Bump CMakeLists.txt version 4.9.1.
      COMP: Address ITKCommon Python submodule order.
      BUG: Extend ExternalData_TIMEOUT_ABSOLUTE to 900 seconds.
      BUG: Do not run KWStyle Git config on a release tarball.
      COMP: Ambiguous RGBPixel access in CustomColormapFunction.
      BUG: Prevent division by zero in PhasedArray3DSpecialCoordinatesImage.
      BUG: Initialize azimuth and elevation to pi/2 in PhasedArray3D.
      BUG: Increase MaskLabel backwards compatibility in N4 bias correction.
      ENH: Deprecate MaskLabel in N4BiasFieldCorrectionImageFilter.

Michka Popoff (8):
      ENH: Wrap RayCastInterpolateImageFunction
      ENH: Wrap RayCastInterpolateImageFunction
      COMP: Remove debug output after vcl_complex removal from wrapping
      ENH: Consolidate .idx file generation with swig .i generation.
      ENH: Update UpdatepygccxmlFromUpstream.sh script
      COMP: Set CastXML path and name for pygccxml 1.7.3
      COMP: Fix RayCastInterpolateImageFunction wrapping for image dim 2
      ENH: Use argparse instead of optparse in igenerator.py

Nick Tustison (1):
      ENH:  Making the mask usage consistent with ITK.

Sean McBride (6):
      BUG: Fixed off-by-1 error found by ASan
      COMP: Fixed clang -Wcomma warning
      COMP: Introduce ITK_FALLTHROUGH, to suppress switch fall through warnings
      COMP: Fixed -Wwritable-strings warnings
      COMP: Fixed remaining -Wcomma warnings
      ENH: switch gdcm to release branch, not release-2-4

Sumedha Singla (1):
      BUG: Fixed the test itkHDF5ImageIOTest

VXL Maintainers (8):
      VNL 2015-11-22 (ea1d60fb)
      VNL 2016-03-02 (cb31149e)
      VNL 2016-03-13 (ae34f0fc)
      VNL 2016-03-15 (751698ab)
      VNL 2016-03-19 (df10fefa)
      VNL 2016-03-25 (f0040231)
      VNL 2016-03-30 (88f50849)
      VNL 2016-04-22 (0ed18124)

Vladimir S. FONOV (1):
      MINC 2016-02-24 (8632513e)

Revision 25009  Directory Listing
Modified Thu Apr 14 13:35:57 2016 UTC (17 months, 1 week ago) by pieper
BUG:two bugs are fixed, SetSendBlock and IGTLUnitAppend

From: leochan2009 <leochan2009@hotmail.com>

Revision 25004  Directory Listing
Modified Mon Apr 11 20:14:00 2016 UTC (17 months, 2 weeks ago) by jcfr
ENH: Hide symbols in the CLI modules.

Update SlicerExecutionModule to incorporate
Slicer/SlicerExecutionModel@8d607ff93a3be76274d9cedfb9f1148a6cdb6968
which hides non-CLI symbols so only ModuleEntryPoint, etc. are available in
the CLI shared libraries.

This results in the following `lib/Slicer-4.5/cli-modules` size improvements,
Slicer start-up time improvements, and reduction in
GradientAnisotropicDiffusionLib symbols:

```
                     MinSizeRel: no hidden | MinSizeRel: hidden | Release: no hidden | Release: hidden
                     ---------------------------------------------------------------------------------
size (MB)             104                     89                   119                 107
start-up time (sec)   20.2                    16.2                 20.0                18.7
example cli symbols   2593                    328                  2342                322
```

From: Matt McCormick <matt.mccormick@kitware.com>

Revision 24993  Directory Listing
Modified Wed Mar 30 23:31:24 2016 UTC (17 months, 3 weeks ago) by jcfr
ENH: Update DCMTK to include patch avoiding unneeded recompilation.

$ git shortlog --no-merges 0b5b174..023b8de
Jean-Christophe Fillion-Robin (1):
      CMake: Avoid unneeded recompilation improving generation of 'arith.h'

Revision 24992  Directory Listing
Modified Wed Mar 30 18:22:09 2016 UTC (17 months, 3 weeks ago) by jcfr
COMP: Update SlicerExecutionModel to allow reuse of PATH/DESTINATION vars.

This commit sets variable in the current scope to allow other external
project to depends on their values.

Revision 24947  Directory Listing
Modified Thu Feb 25 06:30:18 2016 UTC (19 months ago) by jcfr
BUG: Fix the ITK Python install site-packages location.

From: Matt McCormick <matt.mccormick@kitware.com>

Revision 24942  Directory Listing
Modified Tue Feb 23 03:23:59 2016 UTC (19 months ago) by jcfr
ENH: Update DCMTK

This updates DCMTK to the latest snapshot DCMTK-3.6.1_20160216

Note that the two patches that were applied to the previous update of
DCMTK hash here https://github.com/commontk/DCMTK/commits/patched-DCMTK-3.6.1_20150924
are no longer needed, as they were integrated into the DCMTK master.
Therefore, the repo is checked out from the official DCMTK source.
I tested that Slicer compiles with this change on Mac OS X
(Yosemite 10.10.5, LLVM version 7.0.0), and that no test failures related
to DCMTK are introduced (I looked at the individual failures, and there
is nothing to indicate these are due to DCMTK update):

Total Test time (real) = 7071.30 sec

The following tests FAILED:
     51 - vtkMRMLNonlinearTransformNodeTest1 (Failed)
    101 - vtkObserverManagerTest1 (Failed)
    475 - ModelToLabelMapTest (Failed)
    477 - N4ITKBiasFieldCorrectionTest (Failed)
    572 - py_RSNAVisTutorial (Timeout)
    601 - vtkMRMLFiberBundleNodeTest1 (Failed)
    609 - DiffusionWeightedVolumeMaskingTest (Failed)
Errors while running CTest

From: Andrey Fedorov <fedorov@bwh.harvard.edu>

Revision 24933  Directory Listing
Modified Thu Feb 18 00:06:07 2016 UTC (19 months, 1 week ago) by jcfr
COMP: Support toggling of Slicer_BUILD_ITKPython option.

By systematically setting the option "ITK_WRAP_PYTHON" based on the value
of "Slicer_BUILD_ITKPython", ITK Python wrapping will effectively be
enabled or disabled.

Revision 24932  Directory Listing
Modified Thu Feb 18 00:06:05 2016 UTC (19 months, 1 week ago) by jcfr
ENH: Update ITK version

$ git shortlog b61e91d..84ba36b --no-merges

Alvaro Sanchez (1):
      STYLE: moved itkKappaSigmaThresholdImageFilter/Calculator from Nonunit/Review

Bill Hoffman (2):
      COMP: fix shared build on Windows when Review is on.
      COMP: work around for VS 2015 optimizer bug causing test failures.

Bill Lorensen (1):
      ENH: Bump version for style fixups.

Bradley Lowekamp (1):
      BUG: Compilation problem with GCC 4.1 and explicit instantiation

Davis Vigneault (2):
      ENH: Update itkFileTools to allow std::string arguments.
      ENH: Add Floored and Truncated Modulus to VNL

GDCM Upstream (1):
      GDCM 2015-09-02 (1efe9e28)

Hans Johnson (3):
      COMP: Static analysis warning
      COMP: Incorrect delete found by static analysis
      PERF:  Avoid temporary std:vector copying.

Hyun Jae Kang (16):
      COMP: Fixed the compiler error of ITKCommon2TestDriver on OSX 10.6
      BUG: Fixed the runtime crash of VideoSourceTest on OSX 10.6
      BUG: Fixed the runtime crash of itkTimeProbeTest2
      BUG: Fixed the runtime crash of ITKFastMarchingTestDriver's tests on OSX 10.6
      BUG: Fixed the runtime crash of ITKReviewTestDriver on OSX 10.6
      COMP: Fixed the data conversion warning messages of itkResourceProbe
      BUG: Fixed the runtime crash of itkLabelOverlapMeasuresImageFilterTest
      BUG: Fixed the runtime crash of ITKStatisticsTestDriver tests on OSX 10.6
      BUG: Fixed the runtime crash of itkMRIBiasFieldCorrectionFilterTest
      BUG: Fixed the runtime crash of itkBinaryShapeOpeningImageFilterTest1
      BUG: Fixed the runtime crash of vnl_test_complex on OSX 10.6
      BUG: Fixed the runtime crash of vnl_test_numeric_traits
      BUG: Fixed the runtime crash of test_pow_log on OSX 10.6
      BUG: Exclude a test code of ITKLabelMapTestDriver on OSX 10.6
      BUG: Fixed the failed test case of itkSTLThreadTest on OS X 10.8
      COMP: Update KWStyle to utilize the latest boost library

Jean-Christophe Fillion-Robin (4):
      COMP: ITKExternalModule: Support building module without test directory.
      STYLE: Facilitate maintenance of CastXML generator refactoring CMakeLists
      COMP: Allow use of multiple "ITK external modules" in the same project.
      COMP: Fix Slicer MacOSX extension packaging setting CMP0042 policy to OLD

Lucas Gandel (3):
      ENH: Implement GetNumberOfParameter() in ImageToSpatialObjectMetric
      COMP: Enable wrapping of multiple "ITK external modules" in the same project
      COMP: Fix CASTXML_EXECUTABLE value for multiple external module

Matthew McCormick (18):
      ENH: Add TwoProjectionRegistration Remote Module.
      ENH: Allow ITKVideoBridgeOpenCV to be built externally.
      COMP: Add export specification for itk::ResourceProbe.
      ENH: Do not force shared libraries when wrapping.
      BUG: BUILD_TESTING should be not advanced.
      ENH: Bump ITK version to 4.10.0.
      DOC: Correct ITKImageNoise description spelling.
      ENH: Wrap FFTNormalizedCorrelationImageFilter.
      BUG: Remove Azure ExternalData resource.
      BUG: ExternalData downloads from midas3.kitware.com only supports https.
      BUG: Update ExternalData resource.
      BUG: slicer.kitware.com/midas3/ ExternalData will not support http.
      ENH: Add ITK_CUSTOM_LIBRARY_SUFFIX variable.
      ENH: Wrap PipelineMonitorImageFilter.
      ENH: Wrap std::vector< itk::ImageRegion >.
      BUG: Fix wrapping build with DEFAULT_MODULES OFF.
      ENH: Add RGB pixel support to ImageToVTKImageFilter.
      ENH: Add RGB and vector pixel type wrapping for ImageToVTKImageFilter.

Michka Popoff (3):
      ENH: Use importlib for python 3.4 instead of imp
      ENH: Update to Swig 3.0.8
      ENH: Update PCRE to version 8.38

Nick Tustison (1):
      ENH:  Add fixed/moving masking in reg. methods.

Sean McBride (10):
      COMP: Made script OS X compatible
      COMP: mark GDCM GetSeriesHelper() method as deprecated
      BUG: update script to fetch GDCM from its release-2-4 branch instead of master
      DOC: Updated comment to reflect new GDCM version
      COMP: Fixed recently introduced build error with deprecated GDCM method
      BUG: Fixed invalid memory access found by ASan
      COMP: Fixed clang warning about macro expansion giving defined
      COMP: Fixed minor dashboards warnings and typos.
      COMP: Fixed a bunch of clang -Wunreachable-code-break warnings
      COMP: fixed some dashboard warnings (dead code, false positive)

Shawn Waldon (1):
      STYLE: move itkGaussianDerivativeOperator

Sujin Philip (1):
      STYLE: Move itkBox* Filters

Sumedha Singla (2):
      ENH: Issue: ITK#3363 Replaced assignment in SetParameters function.
      ENH: Remove unnecessary const_cast

Vladimir S. FONOV (1):
      MINC 2015-12-17 (dcb93a5f)

Revision 24920  Directory Listing
Modified Wed Feb 10 02:57:59 2016 UTC (19 months, 2 weeks ago) by jcfr
ENH: Update OpenIGTLink project and module to activate connection error log.

OpenIGTLink updates:

$ git shortlog 849b434..daa957a --no-merges
Adam Rankin (2):
      ENH: Reducing Slicer log spam by only outputting a connection failed message if requested
      ENH: Changing error log output default to true to preserve current behaviour

Andras Lasso (1):
      ENH: Removed duplicate code in SetPolyDataInfo

Junichi Tokuda (6):
      STYLE: Fix indent style.
      BUG: Correct order of vertex on a polygon.
      Add .travis.yml
      ENH: Update .travis.yml to test for Mac OS X.
      ENH: Update README to include build instruction.
      STYLE: Shorten README.md.

Matt Clarkson (4):
      #48: Add SetTimeInNanoseconds and GetTimeStampInNanoseconds to igtl::TimeStamp
      #48: Formatting for readability
      #56: Added Factory class for non-query message types
      #56: Add include for use on Scientific Linux gcc 4.4.7

unknown (2):
      BUG: Fix allocation error for BindMessage     Add padding for name table section size.     #63
      BUG: empty polydata causes exception. #74

OpenIGTLinkIG updates:

$ git shortlog 480e5cf..9271ec5 --no-merges
Adam Rankin (1):
      ENH: Adding UI and MRML property to enable toggling of error log spam when IGT server is unavailable

Andras Lasso (1):
      ENH: Removed TRANSFORM_NODE_MATRIX_COPY_REQUIRED ifdefs

From: Junichi Tokuda <tokuda@bwh.harvard.edu>

Revision 24912  Directory Listing
Modified Sat Jan 30 06:26:50 2016 UTC (19 months, 3 weeks ago) by jcfr
COMP: Fix build error fixing regression in SimpleITK installation

This commit fixes a regression introduced in previous commit. It turns
that SimpleITK install has been updated in SimpleITK/SimpleITK@2fc59f9
(Moving Python Wrapping to sub-directory).

This commit fixes the following error:

-- SimpleITK: SimpleITK_WORKING_DIR: /path/to/SimpleITK-build/SimpleITK-build/Wrapping
-- SimpleITK: /path/to/python-install/bin/SlicerPython;PythonPackage/setup.py;install
-- SimpleITK: Errors detected - See below.

/path/to/python-install/bin/python: can't open file 'PythonPackage/setup.py': [Errno 2] No such file or directory

Revision 24911  Directory Listing
Modified Sat Jan 30 02:57:17 2016 UTC (19 months, 3 weeks ago) by jcfr
COMP: Update to ITK and SimpleITK to include fix for itkStaticConstMacro.

This is an attempt to address SimpleITK build error on MacOSX El Capitan
similar to the the following one:

//------------
In file included from /path/to/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_c_vector.h:26:
/path/to/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:388:41: error: declaration of constexpr static data member 'zero' requires an initializer
  static VNL_EXPORT VCL_CONSTEXPR float zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0F);
//------------

More details here: http://slicer-devel.65872.n3.nabble.com/El-Capitan-SimpleITK-build-errors-td4036108.html

Reported-by: Christian Herz <christian.herz@mevis.fraunhofer.de>



List of associated ITK changes:

$ git shortlog 615607f..b61e91d --no-merges
Dzenan Zukic (1):
      COMP: fix itkStaticAssert warnings with clang++

Hans Johnson (1):
      COMP: Incomplete solution for operators corrected

Jean-Christophe Fillion-Robin (1):
      COMP: Fix Slicer MacOSX extension packaging setting CMP0042 policy to OLD

Jon Haitz Legarreta (1):
      BUG: Fix OpenCVBridge bug for two-byte images.

Lucas Gandel (2):
      BUG: Change CMAKE_SOURCE_DIR to CMAKE_CURRENT_SOURCE_DIR
      BUG: Fix multiple external modules wrapping

Martin Michlmayr (1):
      COMP: fixed error "Dunno about this gcc" for gcc 6

Matthew McCormick (12):
      DOC: Update WikiExamples to 2016-10-20
      BUG: BUILD_TESTING should be not advanced.
      COMP: Use enum in itkStaticConstMacro for old GCC.
      BUG: Correct FlatStructuringElement wrapping location.
      BUG: Correct itkStaticConstMacro GCC version comparison operator.
      BUG: Improve GCC detection in itkStaticAssert.h preprocessor macro.
      BUG: Fix OpenCV version check.
      DOC: Update the SphinxExamples Remote Module.
      COMP: Wrap FlatStructuringElement before other classes.
      COMP: Workaround inconsistent OpenCV pre-processor variables.
      COMP: Update CastXML to support wrapping with GCC 6.
      ENH: Allow ITKVideoBridgeOpenCV to be built externally.

Sumedha Singla (3):
      ENH: Fixed the numeric traits for datatypes
      DOC: Added a comment to support the changes in numeric traits datatypes.
      BUG: Invalid memory access of itk::NotAlmostEquals Bug#ITK-3403



List of SimpleITK changes:

$ git shortlog 6f184b4..ee2a30c --no-merges
Bradley Lowekamp (39):
      Adding wrapping for FFT PadImageFilter
      Fix CSharp and Java boundary condition enum for test
Bradley Lowekamp (39):
      Adding wrapping for FFT PadImageFilter
      Fix CSharp and Java boundary condition enum for test
      Correcting Java and CSharp enum types
      Updating ITK Superbuild towards 4.9 along master branch
      Adding print of learning rate in OptimizerScales test
      Adding initial json file to generate filter
      Replacing json with generated source files.
      Adding manual changes to the LandmarkBasedTransformInitializer
      Expanding testing for the LandmarkBasedTransformInitializer
      Updating ITK Superbuild version
      BUG: Update ITK_DIR to match version
      Moving Python Wrapping to sub-directory
      Moving Ruby wrapping to sub-directory
      Moving Tcl and Lua wrapping for sub-directories
      Move CSharp wrapping to sub-directory
      Moving Java wrapping to separate directory
      Move R wrapping to sub-directory
      Adding SimpleITK.i to each language
      Adding script using to build anaconda distributions
      Update to new CMake policies to reduce warnings
      Add comments and working directories to Py VirtualEnv script
      Correct path for Java packaging for the dist target.
      Increase tolerance for MaskedFFTNormazliedCorrelationImageFilter
      Update ITK Superbuild version to 4.9rc3
      Updated SWIG superbuild version to 3.0.9
      Updating ImageCompare to find alternate baseline images.
      Adding alternative baseline images for ITK 4.9 changes to the algorithim
      Adding new baselines for deconvolution with FFTW
      Adding R Example for filter callbacks
      Adding documentation for R lambda callback usage
      Update tolerance for AdaptiveHistogramEqualizationImageFilter test
      Updating ITK Superbuild version along release branch
      BUG: Address HistogramMatching error with number of bins
      Updating ITK along release branch
      Disable Explicit ITK instantiation for gcc 4.1
      Adding needed quote to CMake variable to handle null strings.
      Updating to latest hash on ITK release branch for 4.9
      Revert "Disable Explicit ITK instantiation for gcc 4.1"
      BUG: Fix conversion to int in overloaded > and >= operators

David T. Chen (3):
      Added SITK_OVERRIDE macro
      Changed SITK_OVERRIDE to ITK_OVERRIDE
      Fix for CMake CMP0064 warning

Richard Beare (3):
      Use ExternalData for R data
      Use member function syntax to call member functions
      Support for using an R function as a callback.

Ziv Yaniv (3):
      BUG: Fixed bug converting between vector and set of ITK points.
      BUG: Fixed crash when reference image is not set for BSpline initialization.
      COMP: fixed failed wrapping due to method signature differences

Revision 24903  Directory Listing
Modified Thu Jan 28 05:02:16 2016 UTC (19 months, 4 weeks ago) by jcfr
ENH: Update Python to 2.7.11

Also updates 'msvc9compiler' custom version backporting change from
python/cpython@1a2c95d (Issue #4214: Remove ineffectual /pdb:none option
from msvc9compiler.py) - See https://bugs.python.org/issue4214

For the rational behind the introduction of a custom version of
msvc9compiler, see r23040 (COMP: Fix python_patched_msvc9compiler.py the
"right" way)


Reviewed-by: Max Smolens <max.smolens@kitware.com>
Suggested-by: Michael Powell <mwpowellhtx@gmail.com>

Associated python-cmake-buildsystem are listed below:

$ git shortlog ed5f9bc..b012e1e --no-merges
Chuck Atkins (3):
      Create and use append_if_absent macro for constructing compiler options
      Use the POSITION_INDEPENDENT_CODE target property instead of -fPIC
      Adjust GCC-specific compiler options to work for Clang, Intel, and PGI

Jean-Christophe Fillion-Robin (6):
      Create CONTRIBUTING.md
      Add convenience macro "check_cmake_property_exists"
      Fix distutils.sysconfig._python_build() on windows
      Fix distutils.test_get_python_inc on windows copying headers into build dir
      Fix test_get_config_h_filename in test_sysconfig.py
      Add support for python 2.7.11rc1

Matt McCormick (4):
      Add the ability to specify the Python version in the CMake configuration.
      Update remark on supported Python versions.
      Add Python 2.7.11 download support.
      Make Python 2.7.11 the default.

Simon Su (1):
      Expect BZIP2_INCLUDE_DIR when building bz2 module.

Revision 24895  Directory Listing
Modified Tue Jan 26 05:12:44 2016 UTC (20 months ago) by jcfr
ENH: ITKPython: Add support for optionally installing ITKPython Wrapping

This commit adds the option Slicer_INSTALL_ITKPython (default OFF) that
depends on Slicer_BUILD_ITKPython (also OFF by default).

When enabled, ITK Wrapping files will be installed and packaged along
side the Slicer application.

Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

From: Johan Andruejol <johan.andruejol@kitware.com>

Revision 24893  Directory Listing
Modified Tue Jan 26 05:12:40 2016 UTC (20 months ago) by jcfr
STYLE: Rename Slicer_USE_ITKPython to Slicer_BUILD_ITKPython

From: Johan Andruejol <johan.andruejol@kitware.com>

Revision 24892  Directory Listing
Modified Tue Jan 26 05:12:38 2016 UTC (20 months ago) by jcfr
BUG: ITKPython: Add PYTHONPATH support to the launcher for ITK build tree.

This commit removes pythonpath detection script that was only
working when Slicer_USE_ITKPython was enabled with an existing
build tree. Indeed, when doing a clean build, it was failing
because Slicer python interpreter was not available at configure time.

To address this, this commit configures the PYTHONPATH launcher
settings for the build tree.

Co-authored-by: Johan Andruejol <johan.andruejol@kitware.com>
Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionR@kitware.com>

From: Matt McCormick <matt.mccormick@kitware.com>

Revision 24883  Directory Listing
Modified Tue Jan 19 17:34:50 2016 UTC (20 months ago) by jcfr
BUG: Update ITKv4 to fix issue with N4ITKBiasFieldCorrection. Fixes #4130

More specifically, commit InsightSoftwareConsortium/ITK@be66cfa will fix
the following tests:
 EMSeg_SlicerCommonInterfaceTestGeneral
 EMSegCL_Task_MRIHumanBrain_2CH

It basically prevents the following error:

//---------------
itk::ExceptionObject (0x2a4c110)
Location: "void itk::MultiThreader::SingleMethodExecute()"
File: /home/jcfr/Projects/Slicer-Debug/ITKv4/Modules/Core/Common/src/itkMultiThreader.cxx
Line: 417
Description: itk::ERROR: MultiThreader(0x2a8d3b0): Exception occurred during SingleMethodExecute
/home/jcfr/Projects/Slicer-Debug/ITKv4/Modules/Filtering/ImageGrid/include/itkBSplineScatteredDataPointSetToImageFilter.hxx:621:

itk::ERROR: PointSetToImageFilter(0x2a81400): The reparameterized point component -1.97373e-16 is outside
the corresponding parametric domain of [0, 1).
//---------------


Associated ITK updates:

$ git shortlog 619f991..615607f --no-merges
Bradley Lowekamp (1):
      BUG: Fix precision with accumulation and scaling in AdaptiveHistogram

Hans Johnson (5):
      COMP: BSD command lines do not have --version
      COMP: Respect CMAKE_CXX_STANDARD during config
      COMP: Clang Override warnings removed
      BUG: Download URL was wrong for macosx
      COMP: The ComputeUpdate function is needed

Hyun Jae Kang (1):
      BUG: Exclude a test code of ITKLabelMapTestDriver on OSX 10.6

Isaiah Norton (1):
      COMP: fix build with -std=c++11 when ITK/VXL initially configured without

Jean-Christophe Fillion-Robin (1):
      COMP: Fix Slicer MacOSX extension packaging setting CMP0042 policy to OLD

Matthew McCormick (10):
      DOC: Update the location of the GNUPlot Software Guide scripts.
      DOC: Update the Software Guide repo location in Examples/README.txt.
      COMP: Add export specification for itk::ResourceProbe.
      COMP: Require NO_MODULE with DCMTK find_package.
      COMP: Update CastXML revision for C++14 VS 2015.
      BUG: Fix PythonTransformCoverage test for Python 3.4.
      BUG: Fix PythonExtras test with Python 3.
      BUG: Fix PythonTypemaps tests with Python 3.
      ENH: Do not force shared libraries when wrapping.
      ENH: Allow ITKVideoBridgeOpenCV to be built externally.

Michka Popoff (2):
      COMP: Re-enable review module for python 3 and older VTK's
      ENH: Use importlib for python 3.4 instead of imp

Nick Tustison (1):
      ENH:  Accommodate epsilon error on left side.

Sean McBride (1):
      DOC: Update some woefully out-of-date GDCM comments, and typos

Seun Odutola (1):
      BUG: Improved itkAnalyzeImageIO to handle case insensitive extensions

Revision 24867  Directory Listing
Modified Wed Jan 13 21:43:00 2016 UTC (20 months, 1 week ago) by fedorov
ENH: update DCMTK hash

The DCMTK update fixes incorrect bit packing order, which would render
invalid any segmentation object created with its API.

Revision 24864  Directory Listing
Modified Mon Jan 11 02:47:45 2016 UTC (20 months, 2 weeks ago) by jcfr
ENH: Update ITK cherry-picking "BridgeOpenCV" and "CentOS build" fixes

$ git shortlog 51760b2..619f991 --no-merges
Matthew McCormick (2):
      ENH: Allow ITKVideoBridgeOpenCV to be built externally.
      COMP: Add export specification for itk::ResourceProbe.

Sean McBride (1):
      DOC: Update some woefully out-of-date GDCM comments, and typos

Seun Odutola (1):
      BUG: Improved itkAnalyzeImageIO to handle case insensitive extensions

Revision 24839  Directory Listing
Modified Fri Jan 8 13:14:29 2016 UTC (20 months, 2 weeks ago) by jcfr
ENH: Update CTKAppLauncher to support build with older version of CentOS 5

The launcher is build with an old version of CentOS 5, which has a very
old version of glibc, to ensure better binary executable compatibility.

Co-authored-by: Matt McCormick <matt.mccormick@kitware.com>

Revision 24838  Directory Listing
Modified Fri Jan 8 04:44:03 2016 UTC (20 months, 2 weeks ago) by jcfr
BUG: Update CTKAppLauncher to avoid startup warning reported on Window >= 7

This commit updates the version of the launcher windows binaries to a new
package built against Qt4.8.6 instead of Qt 4.7.4. It will avoid to get
the startup time error message like the one report below:

  Untested Windows version 6.3 detected!

Revision 24837  Directory Listing
Modified Fri Jan 8 03:15:10 2016 UTC (20 months, 2 weeks ago) by jcfr
BUG: Update CTK to include DICOMDIR parsing fix

$ git shortlog 5f58132..caaf2c8 --no-merges

Andras Lasso (1):
      ENH: Added error logging to DICOMDIR file parsing

Andreas Fetzer (1):
      Fixed error when fetching files if resource has no name

Caspar Goch (1):
      Extend the convenience run method to accept cl args

Daniel Knorr (3):
      Added conditions for subject and experiment.     If no ID is set, then the label is used now in the resource uri.
      Creating of subjects works without ID now so setId is not neccessary anymore.     The ID of a subject should be created by XNAT itself.     This rule also is effective to the ID of an experiment.
      If the identifierPattern.exactMatch-CASE is used, the map has 2 entries (ID, content).     Now the ID is set to a lately created object.     content is unused.

Julien Finet (1):
      Support Qt 5.5 compilation

Nicole Aucoin (1):
      BUG: Add pointfile element

Revision 24836  Directory Listing
Modified Fri Jan 8 03:15:08 2016 UTC (20 months, 2 weeks ago) by jcfr
ENH: Update ITKv4 to v4.9.0 release branch

$ git shortlog 0305504..51760b2 --no-merges

Adam Snyder (1):
      PERF: Reworked MMI Threading using a per-thread buffer

Alexander Leinoff (6):
      ENH: Adds IsInteger and IsSigned to NumericTraits.
      COMP: Doxygen itkMath.h 'OneValue()' could not be resolved.
      ENH: Adds ExactlyEquals and NotExactlyEquals functions to itkMath.h
      COMP: Removes floating-point equality checks
      ENH: COMP: Adds support for complex values to Math::AlmostEquals
      ENH: Updates fftw dependency

Alexis Girault (1):
      BUG: Implement SetAutoMinimumMaximum in itkScalarImageToHistogramGenerator

Arnaud Gelas (5):
      COMP: fix warning (unused local typedef)
      COMP: simplify ITKVideoBridgeOpenCV dependency
      DOC: add doxgen documentation for BinaryImageToLevelSetImageAdaptor
      ENH: add tests to exercise itk::ThreadedIteratorRangePartitioner
      COMP: fix compilation error with OpenCV2 and OpenCV3

Betsy McPhail (1):
      BUG: Improve buffer alignment in OctreeNode .

Bill Hoffman (7):
      ENH: Use new CMake Windows export symbol dll feature.
      COMP: Put vnl_export.h in the list of sources so it gets installed.
      COMP: Put vnl_export.h in the list of sources so it gets installed.
      COMP: Put vnl_export.h in the list of sources so it gets installed.
      COMP: fix 64 bit build warnings with windows auto-export on.
      COMP: work around for VS 2015 optimizer bug causing test failures.
      COMP: work around for VS 2015 optimizer bug causing test failures.

Bill Lorensen (6):
      COMP: VTkGlue linker errors
      BUG: Inappropriate use of AlmostEquals
      ENH: Bump tag for wiki examples
      ENH: Better layout strategy
      BUG: Valgrind detected an invalid read
      BUG: nifti_read_subregion_image was leaking file pointers

Brad King (10):
      ENH: Remove use of include <itksys/ios/*> and itksys_ios::*
      ENH: Remove use of include <itksys/stl/*> and itksys_stl::*
      ENH: Update CMake Policy settings in Testing/TestExternal project
      ENH: Teach ITK module macros to support independent header-only modules
      ENH: Add script to import KWIML library source code
      ENH: Add `ITKKWIML` module to provide external KWIML library
      ENH: Port TIFF integer types from KWSys to KWIML
      ENH: Port LSM integer types from KWSys to KWIML
      ENH: Port itkIntTypes.h from KWSys to KWIML
      ENH: Drop KWSys FundamentalType component

Bradley Lowekamp (29):
      BUG: Avoid null deference in PrintSelf with default construction
      ENH: Enable base classes for templates of landmark initializer
      STYLE: Use "Swap" for ITK member name
      BUG: Demonstrate Eigen analysis failure
      BUG: Fix computation of Eigen analysis
      ENH: Update DiscreteHessianGaussian Test baseline
      ENH: Correctly demonstrate float point Eigen failure
      ENH: compile vnl_math_hypot, and use at least double
      ENH: Adding initial update script from used libpng version.
      ENH: removing non-subtree files for itkpng
      ENH: Ported ITK changes for building to subtree merged code
      ENH: Update libpng update script for v1.6.9
      BUG: Use ParameterValueType for computation of landmark affine
      ENH: Wrap LandmarkBasedTransformInitializer
      BUG: Avoid potential exception in itk::Object::UnRegister
      ENH: Update itkpng zlib, configuration, and rename
      ENH: Update itkpng name mangling
      BUG: Use const pointer in Set method for constant ReferenceImage ivar
      BUG: Increase tolerance for PhysicsBasedNonRigidRegistrationMethod
      BUG: Demonstrate side effect on registration due to BSplineScatter change
      ENH: Move MovingHistogramImageFilter base classes to ImageFilterBase
      ENH: Optimize AdaptiveHistogramEqualization with MovingHistogram base
      COMP: address sign unsigned comparison warning
      COMP: Address signed unsigned comparison warning
      COMP: Address unused member variable and methods in anonymous ns
      BUG: Fix segfault when with empty IsolatedWatershed Threshold range
      BUG: Adjust intensity tolerance for PhysicsBasedNonRigid test
      BUG: Reduce number of targets with MSVC
      ENH: Add option to choose scheme for git download

Davis Vigneault (7):
      DOC: Minor improvements to segmentation examples.
      DOC: Expanded Canny Edge Detection Example
      COMP: Warnings in FFTW Classes when compiling with c++11
      COMP: Update Git Tag for Subdivision Module
      STYLE: Address some warnings when running cppcheck
      STYLE: Use cstdlib return macros in ITK examples
      COMP: Include itkMacro.h in itkTestingMacros.h

Dženan Zukić (4):
      STYLE: better formatting of the "usage" message
      BUG: do not pass 0,0,0 to Versor.Set()
      STYLE: Removing the unused NeighborhoodRadius property
      ENH: Write out transform in DeformableRegistration15

Eugene Prilepin (1):
      BUG: Fix a template name formation in python wrappings

Floris Berendsen (1):
      STYLE: Improve naming conventions in comments.

Gert Wollny (1):
      BUG: Remove double-conversion from public interface, use system.

Hans Johnson (24):
      STYLE: Instrument for FixedParameters typedef
      BUG: Demonstrate DisplacementTransformFailure
      BUG: FixedParameters should be double precision
      STYLE: Minor code style issues for MGHIO
      COMP: Update to version for WikiExamples
      ENH: Update Sphinx for ITK 4.8.0
      ENH: Update MGHIO to be shared lib
      ENH: Provide consistent floating point comparisons
      BUG: Fix MGHIO to fix write failures
      PERF: Remove floating point as sentinal value
      COMP: Const correctness needs to be maintained
      BUG: Preserve backwards compatibility
      DOC: Provide consistent naming in comments
      ENH: Conversion between transform type tolerance
      STYLE: Prefer initialization to assignment
      ENH: Missing ITK_OVERRIDE
      COMP: Need to propagate ITKGDCM
      COMP: Need to propagate ITKGDCM
      COMP: Add missing ITK_OVERRIDE
      ENH: C++11 allows for rigorous =delete
      COMP: Remove unnecessary failing assert test
      ENH: Ignore internal files for the Clion editor
      COMP: Fix VNL compilation for wider C++11 support
      BUG: In configuration test need to mirror code

Hyun Jae Kang (49):
      BUG: Remove std::cout calls from class
      BUG: Avoid an unexpected output of static_cast
      BUG: Update python example codes for ImageRegistration
      BUG: Retrieve the missed wrap file
      BUG: itkVTKImageIO class does not handle blank lines in VTK file header.
      BUG: Fix a compilation issue on ITK4 with FFTW and shared libraries
      BUG: Fixed older XCode linking error
      ENH: Use CastXML binaries when building with x86_64 Mac OS X
      BUG: Remove std::cout calls from class
      BUG: itkVTKImageIO class does not handle blank lines in VTK file header.
      BUG: Fixed older XCode linking error
      ENH: Add automatic KWStyle build and configuration setup
      COMP: KWStyle shadow, format-nonliteral and autological-compare warning.
      COMP: Fixed the warning messages from itkGPU Module
      COMP: Fixed a warning message of unused-private-field
      COMP: Apply latest version of KWStyle
      COMP: Update KWStyle to fix its additional warning messages
      COMP: Update KWStyle to fix its additional warning messages
      COMP: Fix data-conversion warning messages on Windows
      ENH: Update itkResourceProbe to calculate statistical data
      COMP: Fix data-conversion warning messages on VS14
      COMP: Fixed 'std::sqrt' : ambiguous call to overloaded function
      ENH: Update the Report() function of itkResourceProbesCollectorBase
      COMP: Fix data-conversion warning message on itkResourceProbe
      COMP: Fix additional warning messages of KWStyle
      COMP: Fix data-conversion warning messages
      COMP: Fixed a warning message of data-conversion on VS14
      COMP: Update KWStyle to remove format-string warning message
      ENH: Use a data struct to export the system information of a probe.
      ENH: Create a test for the SpawnThread function ( ITK-3317)
      STYLE: Remove an unnecessary file (-w) from source code
      COMP: Revert itkResourceProbe to its previous version
      BUG: Fixed the failed case of itkStdStreamStateSaveTest on OS X 10.8
      BUG: Fixed the failed test case of itkThreadPoolTest on OS X 10.8
      BUG: Fixed a failed test of ITKDistanceMapTestDriver
      BUG: Fixed the failed test VideoSourceTest
      PERF: Improve the performance of a test of ITKRegistrationMethodsv4TestDriver
      COMP: Fixed the compiler error of itkDisplacementFieldToBSplineImageFilterTest
      COMP: Fixed the compiler error of ITKCommon2TestDriver on OSX 10.6
      BUG: Fixed the runtime crash of vnl_test_complex on OSX 10.6
      BUG: Fixed the runtime crash of itkTimeProbeTest2
      BUG: Fixed the runtime crash of VideoSourceTest on OSX 10.6
      BUG: Fixed the runtime crash of ITKReviewTestDriver on OSX 10.6
      BUG: Fixed the runtime crash of ITKFastMarchingTestDriver's tests on OSX 10.6
      COMP: Fixed the data conversion warning messages of itkResourceProbe
      BUG: Fixed the runtime crash of ITKStatisticsTestDriver tests on OSX 10.6
      BUG: Fixed the runtime crash of itkBinaryShapeOpeningImageFilterTest1
      BUG: Fixed the runtime crash of test_pow_log on OSX 10.6
      BUG: Fixed the runtime crash of vnl_test_numeric_traits

Jean-Christophe Fillion-Robin (26):
      BUG: Build ITKIOTransformHDF5 as shared library. See #3393
      BUG: Build ITKIOTransformMINC as shared library. See #3393
      BUG: Build ITKIOTransformMatlab as shared library. See #3393
      BUG: Build ITKIOTransformInsightLegacy as shared library. See #3393
      STYLE: TransformIOFactory: Remove obsolete declaration. See #3393
      COMP: TransformIOFactory: Add missing ctor/dtor from hxx file. See #3393
      COMP: TransformFileWriter: Remove method "OpenStream()" without definition
      COMP: TransformFileReaderTemplate: Remove undefined method "CreateTransform()"
      ENH: Update ITKIOPhilipsREC to allow static initialization. See #3393
      ENH: Update ITKIOTransformMINC to allow static initialization. See #3393
      COMP: MINC: Fix VS2008 "unknown round" build error. See #3393
      COMP: MINC: Fix VS2008 "unknown arpa/inet.h" build error. See #3393
      COMP: Configure ENABLE_SHARED into <ModuleName>.cmake file. See #3393
      COMP: Fix configuration of IOFactory header. See #3393
      STYLE: UseITK: Removed redundant code setting ImageIO factory name. See #3393
      STYLE: UseITK: Re-factor introducing _configure_IOFactoryRegisterManager
      STYLE: UseITK: Set TransformIO factory and module name using convention.
      BUG: Ensure Image IO factories are registered once. See #3393
      BUG: Ensure Transform IO factories are registered once.
      COMP: ITKIOXML: Fix VS11 "already defined std::string" link error. See #3393
      BUG: TransformIO: Implement explicit template instantiation using "extern".
      COMP: TransformIO: Fix VS build errors removing extra EXPORT
      COMP: TransformIO: Handle compiler not supporting "pragma diagnostic".
      COMP: TransformIO: TransformFile(Reader|Writer) still need to be exported.
      COMP: TransformIO: Fix explicit instantiation approach
      COMP: Fix Slicer MacOSX extension packaging setting CMP0042 policy to OLD

Johan Andruejol (1):
      ENH: Add ITK_RUNTIME_LIBRARY_DIRS for external projects

Jon Haitz Legarreta (6):
      ENH: Add test for itkStatisticsUniqueLabelMapFilter
      BUG: Fix compilation issues for StatisticsUniqueLabelMapFilterTest
      BUG: Fix comparison issues for itkStatisticsUniqueLabelMapFilter
      BUG: Test for StatisticsUniqueLabelMapFilter stability
      ENH: Add test for itkParametricStpaceToImageSpaceFilter
      ENH: Improve code coverage for itkParametricSpaceToImageSpaceMeshFilter

Julien Michel (1):
      ENH: Support of VectorImage as template parameters for WarpImageFilter

Junjie Bai (2):
      BUG: ConvertLabelMap with different LabelMapTypes
      BUG: LabelObject CopyAttribute support different LabelObject type

KWIML Upstream (1):
      KWIML 2015-12-09 (43f9f8d0)

KWSys Robot (4):
      KWSys 2015-07-10 (c9336bcf)
      KWSys 2015-07-30 (f63febb7)
      KWSys 2015-08-24 (cdaf522c)
      KWSys 2015-08-28 (dc3fdd7f)

LIBPNG Upstream (2):
      PNG 2009-04-06 (e68f5a36)
      PNG 2014-02-05 (3e753eb8)

Laurentiu Nicola (2):
      PERF: Avoid temporary smartptr in ProcessObject::GetInput
      PERF: Optimize WarpImageFilter by avoiding refcount bouncing

Luc Hermitte (8):
      PERF: itk::Image::GetPixel() performance improvment.
      PERF: Performance enhancements on VariableLengthVectors 1/...
      ENH: Dependencies on itkVariableLengthVector.h reduced
      BUG: Error in VariableLengthVector Unit Tests
      PERF: Performance enhancements on VLV 2/...
      PERF: Performances enhancements on VLV 3/...
      COMP: Fix signed/unsigned warnings
      BUG: std::copy/fill on empty VLV

Lucas Gandel (5):
      ENH: Move ImageToPathFilter from ITKReview to ITKPath module.
      BUG: Fixing ImageToPathFilter wrapping call from Review Module
      STYLE: Fix KWStyle dashboard errors
      BUG: Fix external module BUILD_SHARED_LIBS status
      BUG: PhysicsBasedNonRigidRegistrationMethod test failure on Debian 32bit

Mathieu Malaterre (1):
      BUG: Name mangle the included expat third party library.

Matthew McCormick (100):
      ENH: Change itkSystemInformationTest to itkCMakeConfigurationTest.
      ENH: Add AnisotropicDiffusionLBR Remote Module.
      ENH: Bump ITK version to 4.9.0.
      BUG: Remove std::cout calls from classes.
      COMP: Remove unused argument in ConditionVariableNoThreads.
      COMP: Add link interface specification for wrapping target_link_libraries.
      STYLE: Fix indentation in itkMINCTransformIOFactory.cxx.
      COMP: Fix MINCTransformIO factory registration.
      COMP: Add -D_LARGEFILE64_SOURCE for HDF5 with Emscripten-1.
      COMP: Remove unknown doxygen command in AnisotropicDiffusionLBR.
      ENH: Use CastXML binaries when building with x86_64 Linux.
      STYLE: Rename gccxml -> castxml in {idx,igenerator}.py.
      ENH: Use Windows binaries for CastXML.
      ENH: Add better scoping in igenerator.py.
      BUG: Fix CMAKE_BUILD_TYPE initialization with Ninja + MSVC.
      BUG: LevelSetsv4 used signed char instead of char.
      ENH: Add better scoping to idx.py.
      COMP: Define newSize and oldSize in VariableLengthVector.
      STYLE: Use prefix increment operator in ImageBase.
      DOC: Correct spelling of Continuous.
      ENH: Add more progress information to IterativeClosestPoint2.
      ENH: Add ITKModuleExternal.cmake
      COMP: Wrap Image< bool, D > for FlatStructuringElement.
      BUG: Use CastXML binary built in Release.
      BUG: ContinuousIndex should not be templated over TCoordRep.
      COMP: Set CMP0054 to new.
      COMP: Address line length too long for Software Guide.
      COMP: Fix CannyEdgeDetectionImageFilter.cxx types.
      BUG: Replace __GCCXML__ with CABLE_CONFIGURATION.
      ENH: Allow projects to build against an external module.
      ENH: Replace CABLE_CONFIGURATION with ITK_WRAPPING_PARSER.
      ENH: Rename _cable_ to _wrappers_.
      BUG: Define ITK_WRAPPING_PARSER when wrapping.
      BUG: Pass the CMAKE_CXX_FLAGS to castxml.
      ENH: Bump CastXML version to 2015-30-29.
      ENH: Bump LLVM / Clang to 3.7.0.
      COMP: Avoid itklibminc linking with ITK_USE_SYSTEM_HDF5.
      COMP: Add missing ITKIOImageBase dependency for ITKTransformMINC.
      COMP: Use itkSimpleNewMacro in ThreadedIteratorRangePartitionerTest.
      ENH: Add wrapping support for building modules externally.
      BUG: Fix KWStyle test paths when building a module externally.
      ENH: Add Cuberille Remote module.
      COMP: Remove carriage returns from Cuberille remote.
      ENH: Bump the MinimalPathExtraction Remote to 2015-10-20.
      COMP: Fix KernelTransform SetFixedParameters argument type.
      COMP: Use ITK's pygccxml by correctly setting up the sys.path
      Revert "COMP: Put vnl_export.h in the list of sources so it gets installed."
      BUG: Revert "BUG: ConvertLabelMap with different LabelMapTypes"
      ENH: Marking wrapping CMake configuration variables as advanced.
      STYLE: Rename CASTXML to CASTXML_EXECUTABLE.
      COMP: Non-virtual copy attribute members in LabelMap cannot have override.
      COMP: Add wrapping for AdaptiveHistogramEqualizationImageFilter.
      COMP: Add itkMacro.h to itkPromoteType.h for ITK_EXCEPT.
      ENH: Remove CMake version check in ITKModuleHeaderTest.cmake
      BUG: Improve KWStyle ExternalProject utilization.
      ENH: Remove old KWStyle build script.
      COMP: Address VariableLengthVector Doxygen rhs @param not found.
      ENH: Rename WRAPPING_LIBRARY_GROUPS to WRAPPING_SUBMODULE_ORDER.
      ENH: Install Python bindings into site-packages.
      ENH: Improve readability of Python site-packages path detection.
      COMP: DiscreteGaussianDerivativeImageFilter unsigned expression warning.
      BUG: ITKCommon publically depends on ITKDoubleConversion.
      COMP: Improve scoping in CovariantVectorGeometryTest.
      ENH: Improves names and export of module dependencies.
      STYLE: Improve namespace bracket style in itkIsConvertible.
      COMP: Set CMP0054 to new.
      BUG: Remove unused wrapping files.
      BUG: Do install install wrapping development files.
      ENH: Add WRAP_ITK_INSTALL_COMPONENT_IDENTIFIER.
      BUG: Remove duplicate inclusion of wrapping submodules.
      COMP: Do not use C++ style comments for Doxygen cond.
      BUG: Fix detection of the gold linker.
      BUG: Update Python package installation locations.
      ENH: Bump CMakeLists.txt version to 4.8.2.
      ENH: Change BUILD_EXAMPLES default to OFF.
      BUG: Use 'from itk import ITKCommon' in module2module test.
      COMP: Link to VTK Python when built with Kits support.
      BUG: Install itk_minc2.h header.
      COMP: ITKIOMINC has a public dependency on ITKIOImageBase.
      DOC: Remove invalid wrapping example.
      BUG: Wrap AdaptiveEqualizationHistogram.
      COMP: Ignore Doxygen endcond warning in itkIsConvertible.h.
      COMP: Fix PointDimension reference in AzimuthElevationToCartesian test.
      STYLE: Improve scoping in AzimuthElevationToCartesian test.
      STYLE: Explicitly mark the ProcessObject methods virtual in SignedMaurer.
      BUG: Do not try to install targets that do not exist when building externally.
      BUG: ITKIOMeta needs a public dependency on ITKMetaIO.
      COMP: Update LesionSizingToolkit for external build and style test failures.
      BUG: Add CMake OpenCV export code to ITKVideoBridgeOpenCV.
      COMP: Improve compatibility with OpenCV 3.
      DOC: Fix class references in StatisticsLabelMapFilter.
      STYLE: Improved readability of itkStatisticsUniqueLabelMapFilterTest1.
      DOC: Correct ReverseOrdering description in ShapeUniqueLabelMapFilter.
      STYLE: Add own copy of GenerateExportHeader
      COMP: Create _TEMPLATE_EXPORT macros.
      COMP: TransformIOBaseTemplate must be explicitly instantiated.
      BUG: Do not use dynamic_cast for DisplacementFieldType in HDF5 test.
      COMP: Do not use string(MAKE_C_IDENTIFIER with CMake < 2.8.12
      BUG: Do not perform dynamic_cast in CompositeIOTransformIOHelper.
      COMP: Do not set property on itkhdf5 with ITK_USE_SYSTEM_HDF5.

Max Smolens (1):
      BUG: VoronoiSegmentationRGBImageFilter: add pixel dimension check

Michka Popoff (10):
      ENH: Update to swig 3.0.7
      ENH: Do not link against specific Python library on OS X
      COMP: Fix wrapping warnings when building with ITK_WRAP_IMAGE_DIMS=2
      COMP: Add missing wrapping for TransformBase
      COMP: Use ITK's pygccxml by correctly setting up the sys.path
      COMP: Disable incompatible modules when using Python 3 wrapping
      COMP: Move MovingHistogramImageFilterBase wrapping to ImageFilterBase module
      COMP: Disable incompatible modules when using Python 3 wrapping
      ENH: Allow operations on Indexes and Offsets in Python
      ENH: Allow Python 3 wrapping for Glue and Review Modules with VTK 7

Mikhail Isakov (2):
      BUG: DiffusionTensor3DReconstruction segfault if no baseline image
      DOC: correction in DiffusionTensor3D Reconstruction

Nick Tustison (5):
      BUG:  Set a default b-spline epsilon.
      ENH: Adding testing for closed loop.
      BUG:  Updating B-spline classes with the same epsilon strategy.
      PERF:  Switch vnl_vectors for fixed arrays.
      ENH:  Point-set registration with time-varying B-spline.

Olivier Commowick (3):
      BUG: Correct discrepancy in tridiagonal reduction wrt VNL eigen system
      BUG: Correct under/overflows in vnl_math_hypot (taken from pythag from V3P)
      BUG: Switch eigenvalues computation to double

Pablo Hernandez-Cerdan (2):
      ENH: Help class for itkFlatStructuringElement with constructor from images.
      COMP: Fix test errors and warnings in FlatStructuringElement.

Ricardo Ortiz (1):
      BUG: Set itkBinaryImageTo*LabelMapFilter foreground/background values

Seun Odutola (3):
      COMP: Fixed name clash with Apple header (check Macro), renamed check to Check
      COMP: Corrected minc2.h path installation from libsrc2/minc2.h to minc2.h
      BUG: absolute value of tolerance taken to cater for negative spacing

Shawn Waldon (1):
      COMP: OSX set deployment target when building fftw

Simon Alexander (5):
      BUG: incorrect closest point computation
      STYLE: Change to make git bash on windows happy with the function name
      COMP: fixes for visual studio 2015update1 x86 in release mode
      COMP: fixes for visual studio 2015update1 x86 in release mode
      COMP: fixes for visual studio 2015update1 x86 in release mode

Sreekanth Arikatla (2):
      BUG: Resolved const correctness in itkMatrix.h
      ENH: Fixes the symmetry of AzimuthElevationToCartesianTransform and adds tests

Vladimir S. FONOV (8):
      BUG: Missing ITKIOMINC_EXPORT on __Private()
      COMP: Splitting up IOMINC module into two parts: MINC and Transform
      STYLE: updated comments to properly reference LIBMINC
      ENH: Add script to merge upstream MINC as a subtree
      MINC 2015-07-23 (c033d431)
      COMP: Update MINC CMake code
      MINC 2015-08-18 (6d7e3ba8)
      MINC 2015-09-13 (95cd5374)

Xiaoxiao Liu (1):
      DOC: update email address for xiaoxiao.

Zach Williamson (10):
      BUG: Use correct libraries for ImageFusion tests
      ENH: Consolidate Library Dependencies
      COMP: Add a missing link to Review module
      COMP: Use correct linking macro in DCMTK
      BUG: Use correct libraries for TestKernel tests
      COMP: Fix inconsistant naming of GPUPDEDeformableRegistration
      ENH: Use new linking system macros
      PERF: Avoid searching private dependencies for include directories
      COMP: Recover missing dependencies
      ENH: use new linking macros in Filtering module

Ziv Yaniv (2):
      BUG: Affine transformation was estimated without sufficient number of points.
      BUG: fixed BSpline initializer crash when reference image not set.

Revision 24818  Directory Listing
Modified Mon Dec 21 18:50:17 2015 UTC (21 months ago) by pieper
ENH: update DCMTK to fix segmentation object dimension error case

https://github.com/commontk/DCMTK/pull/8

From: Steve Pieper <pieper@isomics.com>

Revision 24801  Directory Listing
Modified Tue Dec 1 20:06:37 2015 UTC (21 months, 3 weeks ago) by jcfr
STYLE: Remove VTKv5 support

As discussed during the developer hangout of 2015-03-31, this commit
removes support for VTKv5.

Most of the h/cxx files have been updated automatically using the
script "slicer_remove_vtk5_support.py" [1]. See below.

The remaining of h/cxx, python and CMake files have been updated
manually.


slicer_remove_vtk5_support.py:
cd ~/Project/Slicer
~/Download/slicer_remove_vtk5_support.py $(ack -l VTK_MAJOR_VERSION)

[1] https://gist.github.com/jcfr/91d2f5d07c2a36320e48

Revision 24756  Directory Listing
Modified Fri Nov 20 02:27:20 2015 UTC (22 months ago) by msmolens
COMP: Fix configuration error with VTK OpenGL2 backend

This commit fixes a CMake error when building Slicer configured with:

    Slicer_VTK_RENDERING_BACKEND:STRING=OpenGL2

The error is:

    39>  Performing configure step for 'Slicer'
    ...
    39>  -- Found Qt4: C:/dev/Support/qt-4.8.7-64-vs2013-deb/bin/qmake.exe (found version "4.8.7")
    39>  -- Configuring Slicer with Qt 4.8.7 (using modules: QTCORE, QTGUI, QTNETWORK, QTOPENGL, QTUITOOLS, QTXML, QTXMLPATTERNS, QTWEBKIT, QTSVG, QTSQL, PHONON, QTSCRIPT, QTTEST, )
    39>  -- Configuring Slicer for [win-amd64]
    39>  CMake Error at C:/dev/SB2/VTKv6/CMake/vtkModuleAPI.cmake:120 (message):
    39>    Requested modules not available:
    39>
    39>      vtkGUISupportQtOpenGL
    39>  Call Stack (most recent call first):
    39>    C:/dev/SB2/VTKv6-build/VTKConfig.cmake:67 (vtk_module_config)
    39>    CMakeLists.txt:790 (find_package)

When using the OpenGL backend the vtkGUISupportQtOpenGL module is built because
of the CMake setting VTK_Group_Qt:BOOL=ON. When using the OpenGL2 backend it's
necessary to explicitly enable the vtkGUISupportQtOpenGL module. In this case,
the module is not part of the Qt group. See [1].

[1] https://github.com/Slicer/VTK/blob/fe92273888219edca422f3a308761ddcd2882e2b/GUISupport/QtOpenGL/module.cmake#L1-L3

Revision 24719  Directory Listing
Modified Tue Nov 10 20:04:35 2015 UTC (22 months, 2 weeks ago) by jcfr
COMP: Fix CERTIFICATE_VERIFY_FAILED build error when SimpleITK is enabled.

This commit is a follow-up of:
  * r24652 (BUG: ExtensionsWizard: Fix CERTIFICATE_VERIFY_FAILED publishing error)
  * r24662 (BUG: Fix CERTIFICATE_VERIFY_FAILED error using "urllib2.urlopen()" on MacOSX)

It updates the SlicerPython launcher settings configuration script so that
it copies the certificate file (Slicer.crt) where it is expected.

It basically fixes the error reported below:

8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---
Installed /path/to/Slicer/python-install/lib/python2.7/site-packages/SimpleITK-0.10.0.dev127-py2.7-macosx-10.11-x86_64.egg
Processing dependencies for SimpleITK==0.10.0.dev127
Searching for SimpleITK==0.10.0.dev127

Reading https://pypi.python.org/simple/SimpleITK/
Scanning index of all packages (this may take a while)

Reading https://pypi.python.org/simple/
warning: manifest_maker: standard file 'setup.py' not found

zip_safe flag not set; analyzing archive contents...
SimpleITK.SimpleITK: module references __file__

Download error on https://pypi.python.org/simple/SimpleITK/: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:590) -- Some packages may not be found!
Couldn't find index page for 'SimpleITK' (maybe misspelled?)

Download error on https://pypi.python.org/simple/: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:590) -- Some packages may not be found!
No local packages or download links found for SimpleITK==0.10.0.dev127
error: Could not find suitable distribution for Requirement.parse('SimpleITK==0.10.0.dev127')

CMake Error at /path/to/Slicer/CMake/ExternalProjectForNonCMakeProject.cmake:76 (message):
  SimpleITK: Error in install step.  See
  /path/to/Slicer/SimpleITK_install_step_output.txt and
  /path/to/Slicer/SimpleITK_install_step_error.txt
Call Stack (most recent call first):
  /path/to/Slicer/SimpleITK_install_step.cmake:3 (ExternalProject_Execute)
make[2]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-install] Error 1
[...]
8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---

Reported-by: Hans Johnson <hans-johnson@uiowa.edu>

Revision 24716  Directory Listing
Modified Tue Nov 10 03:32:03 2015 UTC (22 months, 2 weeks ago) by jcfr
STYLE: Update ITK to backport fixes for optional ITK Python wrapping support.

This update doesn't impact the regular build of Slicer
where Slicer_USE_ITKPython is disabled by default.

$ git shortlog 8989fda..0305504
Matthew McCormick (4):
      ENH: Install Python bindings into site-packages.
      ENH: Improve readability of Python site-packages path detection.
      BUG: Do install install wrapping development files.
      ENH: Add WRAP_ITK_INSTALL_COMPONENT_IDENTIFIER.

Co-authored-by: Matt McCormick <matt.mccormick@kitware.com>
Tested-by: Johan Andruejol <johan.andruejol@kitware.com>

Revision 24715  Directory Listing
Modified Tue Nov 10 01:25:00 2015 UTC (22 months, 2 weeks ago) by jcfr
BUG: Update ITK to fix segmentation fault in 2 filters. Fixes #4065

This commit integrates fixes backported from the ITK release branch:

$ git shortlog 0f346bf7..8989fda --no-merges
Bradley Lowekamp (1):
      BUG: Fix segfault when with empty IsolatedWatershed Threshold range

Mikhail Isakov (1):
      BUG: DiffusionTensor3DReconstruction segfault if no baseline image


Tested-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

Revision 24698  Directory Listing
Modified Sat Nov 7 04:36:11 2015 UTC (22 months, 2 weeks ago) by jcfr
BUG: Update VTK to include fix for vtkVariant stream operator.

$ git shortlog 8e43f69..fe92273 --no-merges
Jean-Christophe Fillion-Robin (1):
      Ensure vtkVariant stream associated with << operator is set back to "dec".

Revision 24693  Directory Listing
Modified Tue Nov 3 21:08:11 2015 UTC (22 months, 3 weeks ago) by jcfr
BUG: Update DCMTK to fix segment access via number in DcmSegmentation

Tested-by: Andriy Fedorov <fedorov@bwh.harvard.edu>

//--------------
commit commontk/DCMTK@f55f3c8
Author: Michael Onken <onken@open-connections.de>
Date:   Tue Nov 3 13:33:23 2015 -0500

    [PATCH] Fixed segment access via Segment Number.

    Fixed segment access via Segment Number which now assumes that the first
    Segment Number is not 0 as in the underlying vector, but starts with 1.

    Thanks to Andrey Fedorov <andrey.fedorov@gmail.com> for the report.
//--------------

Revision 24692  Directory Listing
Modified Tue Nov 3 20:05:09 2015 UTC (22 months, 3 weeks ago) by jcfr
BUG: Update VTK to include fix for empty corner annotation. See #4043

This commit includes the proper fix and remove the workarounds implemented
in r24649 (BUG: SliceViewAnnotations: Do not show blank when corner annotation
is off.)

$ git shortlog d620f8f..8e43f69 --no-merges
Alexis Girault (1):
      Fix bug 15787 : empty vtkCornerAnnotation text renders incorrectly

Revision 24691  Directory Listing
Modified Tue Nov 3 18:15:54 2015 UTC (22 months, 3 weeks ago) by jcfr
COMP: Update SlicerExecutionModel to include support for ITK+ExternalModule

This commit updates the SlicerExecutionModel so that it can build
against the version of ITK including ExternalModule support introduced
in the previous commit. It will fix the following error:

Linking CXX executable bin/GenerateCLP
../ModuleDescriptionParser/bin/libModuleDescriptionParser.so: undefined reference to `XML_ParserCreate'
../ModuleDescriptionParser/bin/libModuleDescriptionParser.so: undefined reference to `XML_GetErrorCode'
../ModuleDescriptionParser/bin/libModuleDescriptionParser.so: undefined reference to `XML_SetUserData'
../ModuleDescriptionParser/bin/libModuleDescriptionParser.so: undefined reference to `XML_GetSpecifiedAttributeCount'
../ModuleDescriptionParser/bin/libModuleDescriptionParser.so: undefined reference to `XML_GetCurrentLineNumber'
../ModuleDescriptionParser/bin/libModuleDescriptionParser.so: undefined reference to `XML_ErrorString'
../ModuleDescriptionParser/bin/libModuleDescriptionParser.so: undefined reference to `XML_ParserFree'
../ModuleDescriptionParser/bin/libModuleDescriptionParser.so: undefined reference to `XML_SetElementHandler'
../ModuleDescriptionParser/bin/libModuleDescriptionParser.so: undefined reference to `XML_Parse'
../ModuleDescriptionParser/bin/libModuleDescriptionParser.so: undefined reference to `XML_SetCharacterDataHandler'
collect2: error: ld returned 1 exit status


$ git shortlog 608c7b0..311eff9 --no-merges
Hans Johnson (1):
      COMP: Add missing link dependancy for ITKExpat

Lucas Gandel (5):
      ENH: Support submission of test results on CDash
      ENH: Add Docker Test file
      ENH: Reorganize docker files to support testing against multiple ITK version
      ENH: Add support for continuous integration testing using CircleCI
      ENH: Add Relevant BUILDNAME for CDash submission

Revision 24690  Directory Listing
Modified Tue Nov 3 17:47:13 2015 UTC (22 months, 3 weeks ago) by jcfr
ENH: Update ITK to include backported ExternalModule support

This will allow to build Slicer extensions based on custom ITK modules.

BRAINSTools:

$ git shortlog 26cb12b..c658c75 --no-merges
Hans J. Johnson (1):
      BUG: Incorrect library specification

ITK:

$ git shortlog 087e938..0f346bf --no-merges
Bill Lorensen (1):
      COMP: VTkGlue linker errors

Hans Johnson (2):
      COMP: Need to propagate ITKGDCM
      ENH: Missing ITK_OVERRIDE

Hyun Jae Kang (1):
      BUG: Fix a compilation issue on ITK4 with FFTW and shared libraries

Lucas Gandel (1):
      BUG: Fix external module BUILD_SHARED_LIBS status

Matthew McCormick (4):
      ENH: Add ITKModuleExternal.cmake
      ENH: Allow projects to build against an external module.
      ENH: Add wrapping support for building modules externally.
      BUG: Fix KWStyle test paths when building a module externally.

Zach Williamson (5):
      ENH: Consolidate Library Dependencies
      COMP: Add a missing link to Review module
      COMP: Use correct linking macro in DCMTK
      ENH: Use new linking system macros
      PERF: Avoid searching private dependencies for include directories

Revision 24679  Directory Listing
Modified Fri Oct 30 14:03:51 2015 UTC (22 months, 3 weeks ago) by jcfr
COMP: Fix WrapITK.pth path on windows

This error only happens with the option Slicer_USE_ITKPython enabled.

The WrapITK path isn't taking in consideration the multi-configuration
style for windows. Adding the CMAKE_CFG_INTDIR variable fixes this.

Since on other single configuration generators (like make) the variable
reduces to ".", we can simply interject it where needed.


Reviewed-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

From: Johan Andruejol <johan.andruejol@kitware.com>

Revision 24674  Directory Listing
Modified Thu Oct 29 06:53:27 2015 UTC (22 months, 4 weeks ago) by jcfr
ENH: Update SimpleITK: Use SuperBuild scripts for additional dependencies.

Configure with SimpleITK's Superbuild CMake file, to allow additional
dependencies to be build. This is done by adding a second external
project just for the download step, so that the configuration can be
done in the Superbuild sub-directory as the source directory.

$ git shortlog --no-merges 4531702..6f184

Bradley Lowekamp (72):
      Updating version for 0.10.0 development
      Update SimpleITKExamples version
      Adding SimpleITK 0.9.0 Download URLs to doxygen
      Improve exception when unable to create ImageIO
      GetGitRevisionDescription: Fix issue referencing project source
      Replace tabs with spaces.
      Adding ITK version information to the SimpleITK version info.
      Update PCRE to 9.37 in Superbuild
      WIP: Adding local transform fixes
      Using local static for itk version string
      Adding forbid download CMake option
      Forbid downloading data with option
      ADD SITK_PYTHON_USE_VIRTUAL_ENV option
      Create separate source and data tar-balls for distribution.
      Fix checking SimpleITK source directory for External data file
      Add CMake find package module for the Lua interpreter.
      Use SITK_LUA_EXECUTABLE for code generation
      Use CMake find_package for finding Lua libraries and include
      Add Lua Superbuild support
      Pass all variable beginning with SITK_ to the SimpleITK build.
      Removing integrated lua source code
      Add Superbuild of GoogleTest
      Use find_package for google test
      Remove anonymous namespace for std::vector output operator.
      Remove the GTest source code from testing
      Adding ObjectCount measurement to ConnectedComponents filter
      Use CMAKE_POSITION_INDEPENDENT_CODE property over compiler flag
      Replace superbuild fPIC with CMake property for ITK.
      Remove adding fPIC flag in language options.
      Add CMake variable to specify additional lua libraries
      Add unsigned int specifier
      Mark GTest superbuild options as advanced
      Mark additional Lua variables as advanced
      Correct variable name SimpleITK_VARS
      Adding CMake upstream FindGTest.cmake
      Fix Superbuild variable
      Install GTest with MSVC in expected directory
      Install MSVC into lib directory with out prefix
      Disable GTest using TR1::tuple with VS11
      Fix CMake syntactical errors in GTest Superbuild
      Remove quotes around ep_extra_args
      Fix CMake equals syntax.
      More CMake fixes
      Add support to join 3d image series into 4d image
      Update ITK superbuild version to 4.8 release
      COMP: Fix JoinSeries with 4DImage test
      Add support to extract 3d image from 4d.
      Require libraries when a wrapping for a language is enabled
      Update shape statistics to always use int64_t for labelmap type.
      Fix finding lua executable when not explicitly set.
      Adding wrapping for LabelIntensityStatisticsImageFilter
      Change default of SimpleITK_PYTHON_THREADS to ON
      Update SWIG to 3.0.7
      Address warnings with signed integer comparison
      Updating ITK v4.8 along release branch
      Do not pass unneeded language arguments on the command line
      add CastImageFilter to support output writing
      Do not force CMAKE_INSTALL_PREFIX if already set.
      Don't pass SITK_REQUIRED_ITK_MODULES in Superbuild
      Move CMake file to CMake directory
      WIP: Adding local transform fixes
      Adding ObjectCount measurement to ConnectedComponents filter
      Add unsigned int specifier
      Require libraries when a wrapping for a language is enabled
      Do not pass unneeded language arguments on the command line
      Updating ITK superbuild towards v4.8.1 pending release
      Add missing Java variables to the language options files
      Update ITK superbuild to 4.8.1 release
      Updating SimpleITK to 0.9.1 version for release
      Add md5 to URL for check sum
      Update Python download URLs to use https
      Adding 0.9.1 release eggs to download page

Dave Chen (2):
      Regenerated the .i files
      Regenerated the .i files

David T. Chen (7):
      Regenerate filters.csv for SimpleITK 0.9.0
      Re-regenerated filters.csv
      Fix leading space problem in doxy2swig.py
      Updated space_parse with a noLeadingSpace flag
      Rewrite Show to support Fiji
      Fix leading space problem in doxy2swig.py
      Updated space_parse with a noLeadingSpace flag

Ziv Yaniv (2):
      STYLE: change SetOptimizerAsLBFGSB parameter name to match other
      methods.
      Modified example to match parameter name change in SetOptimizerAsLBFGSB.

Reviewed-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

From: Bradley Lowekamp <blowekamp@mail.nih.gov>

Revision 24668  Directory Listing
Modified Wed Oct 28 20:53:21 2015 UTC (22 months, 4 weeks ago) by jcfr
BUG: Update VTK to fix snapshot scaling and VS2013 compilation warning

See http://www.na-mic.org/Bug/view.php?id=3885

$ git shortlog 716b0f5..d620f8f --no-merges
Max Smolens (2):
      COMP: Fix HAVE_ROUND macro redefinition build warning on Visual Studio 2013
      Fix rendering gradient background with vtkRenderLargeImage

Revision 24657  Directory Listing
Modified Fri Oct 23 19:24:42 2015 UTC (23 months ago) by jcfr
ENH: Update ITK to include latest backport to ITK release branche

It includes the following additional changes:

Bradley Lowekamp (3):
      BUG: Avoid potential exception in itk::Object::UnRegister
      BUG: Avoid null deference in PrintSelf with default construction
      BUG: Use const pointer in Set method for constant ReferenceImage ivar

Davis Vigneault (2):
      DOC: Expanded Canny Edge Detection Example
      COMP: Warnings in FFTW Classes when compiling with c++11

Eugene Prilepin (1):
      BUG: Fix a template name formation in python wrappings

Matthew McCormick (3):
      COMP: Remove unused argument in ConditionVariableNoThreads.
      DOC: Correct spelling of Continuous.
      STYLE: Use prefix increment operator in ImageBase.

Revision 24655  Directory Listing
Modified Fri Oct 23 16:46:55 2015 UTC (23 months ago) by jcfr
ENH: Update ITK to backport ITKMGHIO tweaks

A branch named "MGHIO_Remote_SlicerSync-for-release" has also been proposed
to upstream ITK
See http://review.source.kitware.com/#/q/topic:MGHIO_Remote_SlicerSync-for-release

$ git shortlog 2eb422b..0786612 --no-merges
Hans Johnson (5):
      ENH: Update Sphinx for ITK 4.8.0
      COMP: Update to version for WikiExamples
      STYLE: Minor code style issues for MGHIO
      ENH: Update MGHIO to be shared lib
      BUG: Fix MGHIO to fix write failures

Revision 24654  Directory Listing
Modified Thu Oct 22 19:51:14 2015 UTC (23 months ago) by naucoin
ENH: Update CTK to include exporting DICOM from browser

Add an option to the right click table context menus after Delete
to export patients, studies, series to disk. Also incorporates
changes from two other developers:

git shortlog 7ea654e..5f58132 --no-merges

Gert Wollny (2):
      Fix compile and link errors when using QT5 on Debian
      Remove superfluous test on fontconfig

Johan Andruejol (2):
      Add an option to the ctkConsole to add/set the completion shortcuts
      Expose option on ctkConsole to control the runFile() interface

Nicole Aucoin (2):
      ENH: add the capability to export DICOM to disk
      BUG: stop after unable to create dir.

Revision 24653  Directory Listing
Modified Thu Oct 22 02:26:55 2015 UTC (23 months ago) by jcfr
ENH: Update ITK to release branch (v4.8.1 with VS2015 and c++11 fixes)

$ git shortlog slicer-v4.8..2eb422b --no-merges
Abhishek Tiwari (1):
      BUG: "tmpImageIndex" not initialized to 0.

Davis Vigneault (2):
      DOC: Expanded TreeContainer Example
      COMP: Warnings in itkVTKImageExport when compiling with c++11

Hyun Jae Kang (1):
      BUG: Fix HDF5 CMake configuration with VS2015

Jean-Christophe Fillion-Robin (2):
      COMP: Fix Slicer MacOSX extension packaging setting CMP0042 policy to OLD
      COMP: Set policy CMP0042 only if CMake version support it.

Matthew McCormick (12):
      BUG: Implement UpdateLargestPossibleRegion for ImageToVTKImageFilter.
      BUG: Initialize mutex for 32 bit AtomicInt.
      COMP: Disable the gold linker for static builds on Ubuntu 14.04.
      BUG: Build BridgeNumPy with Visual Studio.
      BUG: Support Python 3 wrapping module initialization.
      BUG: Update itkTemplate.py for Python 3.
      BUG: Update itkExtras.py for Python 3.
      BUG: Prevent Python callback addition recursion.
      BUG: Fix test scripts for Python 3.
      BUG: Replace __GCCXML__ with CABLE_CONFIGURATION.
      COMP: Do not use C++11 alignas in itkAlignedTypedef.
      ENH: Bump CMakeLists.txt version to 4.8.1.

Michka Popoff (1):
      ENH: Do not link against specific Python library on OS X

Shawn Waldon (1):
      COMP: Set target OS X version in environment for tools using compiler

Tobias Wood (2):
      BUG: LBFGSB was printing messages even with debug switched off.
      BUG: Removed an unguarded print statement.

Vladimir S. FONOV (2):
      BUG: Missing ITKIOMINC_EXPORT on __Private()
      COMP: Changing the order of HDF5 library components

Revision 24652  Directory Listing
Modified Wed Oct 21 02:02:28 2015 UTC (23 months ago) by jcfr
BUG: ExtensionsWizard: Fix CERTIFICATE_VERIFY_FAILED publishing error

This commit fixes SSL a regression introduced when updating the
version of python in r24526 (ENH: Upgrade to Python 2.7.10) because
of python/cpython@ae5b953 (pep 476: verify certificates by default (#22417))

The error was first reported in [1] and happened when contributing
an extension using the steps report below.

[1] http://slicer-devel.65872.n3.nabble.com/Problem-with-the-ExtensionWizard-td4035337.html

This commit fixes the issue by setting the SSL_CERT_FILE as suggested in
PEP-0476. See https://www.python.org/dev/peps/pep-0476/

Step to reproduce the problem:

// ----------------
$ bin/slicerExtensionWizard --create Slicer-MyTestExtension --addModule cli:MyTestCLI  ~
copy template
'/home/jcfr/Projects/Slicer/Utilities/Templates/Extensions/Default' to
'/home/jcfr/Slicer-MyTestExtension', replacing 'TemplateKey' -> 'Slicer-
MyTestExtension'
[...]
created module 'MyTestCLI'

$ bin/slicerExtensionWizard --publish ~/Slicer-MyTestExtension/
Creating initial commit containing the following files:
  MyTestCLI/Testing/Cxx/CMakeLists.txt
[...]
Continue y,n? y
creating github repository
Username for 'https://github.com': jcfr
Password for 'https://jcfr@github.com':
failed to publish extension: [SSL: CERTIFICATE_VERIFY_FAILED] certificate
verify failed (_ssl.c:590)
// ----------------

Reported-by: Jean-Baptiste Vimort <jvimort@umich.edu>

Revision 24603  Directory Listing
Modified Tue Oct 6 05:14:48 2015 UTC (23 months, 2 weeks ago) by jcfr
STYLE: Update CTK to fix "QSqlQuery::exec: database not open" message

This commit update CTK to fix message reported when opening
DICOM module.

$ git shortlog 6453c27..7ea654e --no-merges
Jean-Christophe Fillion-Robin (1):
      Fix runtime warning in ctkDICOMTableView

Revision 24598  Directory Listing
Modified Tue Oct 6 01:11:51 2015 UTC (23 months, 2 weeks ago) by jcfr
COMP: Fix DCMTK build error llvm-gcc-4.2 on MacOSX.

Updated version of DCMTK includes this commit:

//--------------
commit commontk/DCMTK@545de87
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Mon Oct 5 21:06:36 2015 -0400

    Fix dcmsr build error on llvm-gcc-4.2 on MacOSX.

    While maintaining the fix introduced in the previous commit, this commit
    also fixes the following error:

    Linking CXX shared library ../../lib/libdcmsr.dylib
    ld: duplicate symbol DSRTree<DSRDocumentTreeNode>::isEmpty() const  in
    CMakeFiles/dcmsr.dir/dsrdocst.cc.o and
    CMakeFiles/dcmsr.dir/dsrdoc.cc.o for architecture x86_64
    collect2: ld returned 1 exit status
    make[2]: *** [lib/libdcmsr.3.6.1.dylib] Error 1
    make[1]: *** [dcmsr/libsrc/CMakeFiles/dcmsr.dir/all] Error 2

    That was happening using the following compiler:
    i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 (Based on Apple Inc.
    build 5658) (LLVM build 2336.1.00)

    See http://slicer-devel.65872.n3.nabble.com/dcmtk-compile-regression-td4035162.html

    Reported-by: Bill Lorensen <bill.lorensen@gmail.com>
    Tested-by: Bill Lorensen <bill.lorensen@gmail.com>
//--------------

Revision 24588  Directory Listing
Modified Thu Oct 1 22:07:12 2015 UTC (23 months, 3 weeks ago) by jcfr
COMP: Update Slicer and CTK to fix DCMTK windows build error.

This commit fixes windows build error and redefined warnings introduced
by the commit r24586 (ENH: Update DMCTK to use version DCMTK-3.6.1_20150924)

Related commits:
 * r24136 (STYLE: Update CTK to fix warning related to wrapping of CTKDICOM module)
 * r23955 (COMP: Workaround to fix HAVE_STAT redefined warning in SlicerDICOMExportDialog)
 * r23952 (COMP: Workaround to fix HAVE_STAT redefined warning in qSlicerCoreApplication)

CTK updates:

$ git shortlog 7199173..6453c27 --no-merges
Jean-Christophe Fillion-Robin (2):
      Workaround refined macro warning when building CTKDICOMWidgetsPythonQt
      Fix CTKDICOMWidgetsPythonQt windows build error undefining HAVE_INT64_T

Reported-by: Andriy Fedorov <fedorov@bwh.harvard.edu>
Thanks: Andras Lasso <lasso@queensu.ca>
Thanks: Jörg Riesmeier
Thanks: Michael Onken

Revision 24587  Directory Listing
Modified Wed Sep 30 19:47:34 2015 UTC (23 months, 3 weeks ago) by jcfr
COMP: Fix DCMTK build error on Clang 3.1 on MacOSX

This commit fixes build error introduced by previous commit by updating
the version of DCMTK.

Updated version of DCMTK includes this commit:

//--------------
commit commontk/DCMTK@ade7e93
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Wed Sep 30 15:24:53 2015 -0400

    Fix dcmsr build error on clang 3.1 on MacOSX. See Slicer/Slicer#359

    This commit fixes the build error reported below by explicitly
    instantiating the DSRTree<DSRDocumentTreeNode>.

    Build error happening using Clang 3.1 downloaded from [1]
    on MacOSX SnowLeopard:

    //---------------
    $ make cmr/fast  VERBOSE=1
    make -f dcmsr/libcmr/CMakeFiles/cmr.dir/build.make dcmsr/libcmr/CMakeFiles/cmr.dir/build
    Linking CXX shared library ../../lib/libcmr.dylib
    cd /Users/kitware/Dashboards/Continuous/Slicer-0-build/DCMTK-build/dcmsr/libcmr && "/Users/kitware/Dashboards/Support/CMake 3.0.1.app/Contents/bin/cmake" -E cmake_link_script CMakeFiles/cmr.dir/link.txt --verbose=1
    "/Users/kitware/Dashboards/Support/CMake 3.0.1.app/Contents/bin/ctest" --launch --target-name cmr --build-dir /Users/kitware/Dashboards/Continuous/Slicer-0-build/DCMTK-build/dcmsr/libcmr --output ../../lib/libcmr.3.6.1.dylib --target-type SHARED_LIBRARY --language CXX -- /usr/bin/clang++    -fvisibility=hidden -D_XOPEN_SOURCE_EXTENDED -D_BSD_SOURCE -D_BSD_COMPAT -D_OSF_SOURCE -D_DARWIN_C_SOURCE -fPIC -O3 -DNDEBUG -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.6.sdk -mmacosx-version-min=10.6 -dynamiclib -Wl,-headerpad_max_install_names   -compatibility_version 7.0.0 -current_version 3.6.1 -o ../../lib/libcmr.3.6.1.dylib -install_name /Users/kitware/Dashboards/Continuous/Slicer-0-build/DCMTK-build/lib/libcmr.7.dylib CMakeFiles/cmr.dir/init.cc.o CMakeFiles/cmr.dir/logger.cc.o CMakeFiles/cmr.dir/srnumvl.cc.o CMakeFiles/cmr.dir/tid1001.cc.o CMakeFiles/cmr.dir/tid1204.cc.o CMakeFiles/cmr.dir/tid1600.cc.o CMakeFiles/cmr.dir/cid11.cc.o CMakeFiles/cmr.dir/cid29.cc.o CMakeFiles/cmr.dir/cid29e.cc.o CMakeFiles/cmr.dir/cid42.cc.o CMakeFiles/cmr.dir/cid100.cc.o CMakeFiles/cmr.dir/cid244.cc.o CMakeFiles/cmr.dir/cid244e.cc.o CMakeFiles/cmr.dir/cid4020.cc.o CMakeFiles/cmr.dir/cid4021.cc.o CMakeFiles/cmr.dir/cid4031.cc.o CMakeFiles/cmr.dir/cid4031e.cc.o CMakeFiles/cmr.dir/cid5000.cc.o CMakeFiles/cmr.dir/cid5001.cc.o CMakeFiles/cmr.dir/cid7021.cc.o CMakeFiles/cmr.dir/cid7445.cc.o CMakeFiles/cmr.dir/cid7452.cc.o CMakeFiles/cmr.dir/cid7453.cc.o CMakeFiles/cmr.dir/cid10013.cc.o CMakeFiles/cmr.dir/cid10013e.cc.o CMakeFiles/cmr.dir/cid10033.cc.o CMakeFiles/cmr.dir/cid10033e.cc.o ../../lib/libdcmsr.3.6.1.dylib ../../lib/libdcmimage.3.6.1.dylib ../../lib/libdcmimgle.3.6.1.dylib ../../lib/libdcmdata.3.6.1.dylib ../../lib/liboflog.3.6.1.dylib ../../lib/libofstd.3.6.1.dylib -lpthread
    Undefined symbols for architecture x86_64:
      "DSRTree<DSRDocumentTreeNode>::getRoot() const", referenced from:
          vtable for TID1001_ObservationContext in tid1001.cc.o
          vtable for TID1204_LanguageOfContentItemAndDescendants in tid1204.cc.o
          vtable for TID1600_ImageLibrary in tid1600.cc.o
    ld: symbol(s) not found for architecture x86_64
    clang: error: linker command failed with exit code 1 (use -v to see invocation)
    make[1]: *** [lib/libcmr.3.6.1.dylib] Error 1
    make: *** [cmr/fast] Error 2
    //---------------

    [1] http://llvm.org/releases/download.html#3.1
//--------------

Revision 24586  Directory Listing
Modified Wed Sep 30 14:21:47 2015 UTC (23 months, 3 weeks ago) by fedorov
ENH: Update DMCTK to use version DCMTK-3.6.1_20150924

The important improvements provided by the new version of DCMTK
is the support for new API that in particular greatly simplify creation of and
interaction with DICOM Segmentation image objects.

More specifically, it introduces the dcmiod, dcmfg and dcmseg classes
helpful in creating multiframe DICOM objects, such as segmentation and
parametric map objects.

Considering that standard and private dictionaries can now be  embedded
in DCMTK library, this commit partially reverts r24473 (ENH: Add support
for DCMTK private dictionary). The test DCMTKPrivateDictTest.py was updated to
not expect DCMDICTPATH environment variable that is no longer needed and is not
initialized.

List of DCMTK changes:

$ git shortlog 3366181..DCMTK-3.6.1_20150924 --no-merges

Andreas Thiel (1):
      Updated man pages for new development snapshot.

Jan Schlamelcher (86):
      Some workarounds for VC6 compiler peculiarity.
      Introduced OFunique_ptr as a fallback if std::unique_ptr is not available.
      Make use of  unique pointer (free memory if C-MOVE/C-FIND is canceled).
      Fixed dll build on windows.
      Correction of inconsistent previous commit.
      Fixed DcmSCPPool test case failing on older systems.
      Enabled shutdown functionality of DcmSCPPool.
      Fixed building with mingw-w64.
      Fixed most of the warnings in dcmjpeg.
      Fixed potential bug in dcmjpeg 12 and 16 bit variants.
      Marked SCPPool-Test (dcmnet_scp_pool) as exhaustive.
      Fixed most of the warnings in dcmdata.
      Fixed a mistake in CHANGES.361.
      Minor fixes in dcmdata.
      Added support for some C++11 types, literals and traits.
      Added documentation for the new macro "DOXYGEN".
      Fixed most of the warnings in ofstd and oflog.
      Added support for some additional C++11 traits.
      Introduced the new explicit boolean type OFExplicitBool.
      Fixed possibly wrong overload resolution in DSRCodedEntryValue.
      Minor fixes (whitespace and line ending errors).
      Modified DcmQuantColorHashTable to perform lazy initialization.
      Introduced OFoptional, implementing optional types.
      Renamed DoxygenLayout.xml to comply with filename conventions.
      Minor fixes and workarounds for Microsoft's compilers.
      Fixed ofstd_tatof error on older MSVC versions.
      Fixed DCMTK-Exports for custom module setups.
      Fixed and suppressed some warnings.
      Added 'DCMTK_USE_CXX11_STL' and 'DCMTK_CXX11_FLAGS'.
      Updated manpages.
      Updated DCMTK_ABI_VERSION for new development snapshot.
      Clarified an ambiguous configure message.
      Removed misleading comment in dcmjpeg.
      Fixed a wrong type-alias for OFintegral_constant.
      Introduced C++11-like alignment support.
      Fixed an alignment problem in OFoptional.
      Fixed building 32 bit targets with mingw-w64.
      Refined definition of numeric types and traits.
      Fixed a problem with Microsoft Safe CRT in oflog.
      Fixed a bug in dcmdata.
      Introduced DcmOutputBufferStream::filled() method.
      Fixed a problem in storescp.
      Modified some of OFoptional's comparison operators.
      Introduced OFtuple implementing generic tuples.
      Introduced move emulation for pre C++11 compilers.
      Small fixes for a previous commit about OFtuple.
      Several fixes and additions for yesterday's commits.
      Reintroduced bugfix-comment in dcmjpeg.
      Fixed autoconf install regarding ofstd variadic.
      Introduced OFnumeric_limits.
      Several fixes regarding OFnumeric_limits.
      Fixed possible arith.h generation problem on MinGW.
      Introduced basic support for assisted cross compiling.
      Fixed some problems regarding DCMTK's C++11 support.
      Added support for trusted client certificates.
      Adjusted DCMNET's default socket buffer length.
      Introduced cross compiling support for Android.
      Fixed a const correctness problem within DCMTLS.
      Introduced check-exhaustive targets to Autoconf.
      Corrections regarding recent commits.
      Modified CMake minimum version as required.
      Revised cleanup of temporary unit test files.
      Updated Autoconf dependencies.
      Updated man pages for new development snapshot.
      Updated DCMTK_ABI_VERSION for new development snapshot.
      Fixed a CMake problem with paths containing spaces.
      Moved some utility functions inside OFStandard.
      Modified fallback implementation of OFtuple.
      Added additional configuration methods for DCMTLS.
      Updated Makefile dependencies.
      Updated DCMTK_ABI_VERSION for new development snapshot.
      Moved CHANGES.361 to /docs.
      Updated Doxygen configuration files.
      Updated man pages.
      Updated default compiler flags.
      Refactored handling of some <cmath> functions.
      Fixed problems with previous commit.
      Fixed cross compiling via MinGW and Wine.
      Fixed building on FreeBSD.
      Fixed building on FreeBSD with C++11 enabled.
      Fixed inconsistent defines in CMake's osconfig.h.
      Fixed a problem in DcmAttributeFilter's unit test.
      Fixed building via GCC 4.2 on OpenBSD.
      Updated man pages for new development snapshot.
      Updated DCMTK_ABI_VERSION for new development snapshot.
      Updated CHANGES.361 for new development snapshot.

Joerg Riesmeier (511):
      Added support for CP-1236 to data dictionary.
      Added support for CP-1236 to checkAndUpdateVR() method.
      Added support for Supplement 154 to the data dictionary.
      Added support for new SOP Class UIDs from Supplement 154.
      Added support for directory record type "SURFACE SCAN".
      Added new SOP Class UID from Supplement 162.
      Added missing assignment of member variable.
      Added full support for the new Comprehensive 3D SR IOD.
      Fixed various issues in syntax usage output.
      Minor fixes in comments, e.g. typos.
      Minor fixes in comments. Also made some input parameters "const".
      Use non-throwing new and delete operator.
      Fixed two possible memory leaks.
      Added comment to variable that is currently unused.
      Fixed issue with odd-length pixel data.
      Added missing sub-directory to "make install" target.
      Added some debug output to lookForXfer() method.
      Added some debug output to read() method.
      Added new print options for SOP class output.
      Added new command line options for print output.
      Fixed bug in checkSOPClassUID() method.
      Added note on support for shared libraries.
      Added support for CP-1246 and CP-1249 to data dictionary.
      Fixed some tag key constants of recently retired attributes.
      Fixed issue with unnecessary call to clearNodeCursorStack().
      Added missing support for the new print options.
      Enhanced output to trace logger.
      Fixed inconsistencies introduced with last commit.
      Various fixes to comments. Removed trailing spaces.
      Added support for recently approved Correction Items.
      Enhanced documentation of complete flag methods.
      Added support for Supplement 157 to data dictionary.
      Added SOP Class UIDs from Supplement 157.
      Minor fixes to comments on VOI-related methods.
      Fixed bug in getTimeZoneFromString() method.
      Fixed issue with misplaced log output.
      Replaced "OFString::length() == 0" by "OFString::empty()".
      Replaced "OFString::length() != 0" by "!OFString::empty()".
      Replaced "OFString::length() > 0" by "!OFString::empty()".
      Added support for new VR "Other Double String" (OD)
      Added private tags for AGFA IMPACS 6.5.x Solution.
      Fixed wrong VR for private AGFA IMPAX tag.
      Updated version number of snapshot compilers.
      Added comment on inappropriate use of EC_IllegalCall.
      Fixed various oddities and inconsistencies:
      Replaced tabulator by space characters.
      Fixed various oddities and inconsistencies.
      Really call shouldStopAfterCurrentSOPInstance():
      Fixed further documentation issues.
      Removed trailing space characters.
      Fixed various typos.
      Added releaseAssociation() and abortAssociation()
      Fixed various typos and other Doxygen issues.
      Enable WITH_THREADS for thread-related classes.
      Added new condition constants.
      Fixed various typos.
      Use optional fields in sendSTOREResponse().
      Reimplemented sendSTOREResponse() method.
      Modified log output in loadAssociationCfgFile().
      Fixed issues with optional message fields.
      Removed unused fields from sendACTIONResponse().
      Added file missing for last commit :(
      Added progress notification to DcmSCP.
      Removed trailing spaces.
      Added global helper function createDirectory().
      Fixed some minor Doxygen issues.
      Added new class DcmStorageSCP.
      Added new command line tool "dcmrecv".
      Added comments to unused exit codes.
      Rebuilt Makefile dependencies.
      Updated man pages.
      Function createDirectory() also works on Windows:
      Updated CMake version.
      Fixed various typos.
      Deprecated closeAssociation() method.
      Added support for Supplement 163 to data dictionary.
      Added meta header to stored DICOM files.
      Fixed various typos in comments.
      Pass existing dataset to handleSTORERequest().
      Fixed various inconsistencies in comments.
      Do not copy received dataset in memory.
      Removed class name from derived method calls.
      Removed "&" from constant integer parameters.
      Fixed wrong log message in handleMOVERequest().
      Fixed various typos in comments.
      Restructured implementation of handleSTORERequest().
      Introduced dataset storage mode.
      Fixed various typos in comments.
      Receive C-STORE request dataset directly to file.
      Added new dataset storage mode.
      dded new storage mode options.
      Updated copyright dates (where appropriate).
      Added support for generating a Doxygen tag file.
      Fixed wrong Doxygen reference to a method.
      Minor fixes, e.g. added Doxygen markup.
      Fixed issue with CP-246 files and private tags.
      Slightly changed output of print() method.
      Added new print flag for showing invalid codes.
      Added new option for printing invalid codes.
      Added missing references to closed DCMTK features.
      Fixed typos.
      Added support for <InlineBinary> XML element.
      Clarified use of writeXML() flags.
      Fixed typo copied from Supplement 163.
      Output a warning message if the VR is unknown.
      Output currently processed line of input file.
      Removed superfluous footnote symbol "(*)".
      Fixed various coding style issues.
      Added trace log message on VR replacement.
      Added two new global flags for VR generation.
      Made use of new global flags for VR generation:
      Updated our email address for bug reports.
      Updated to autoconf 2.69.
      Added definition of DCMTK_PACKAGE_URL.
      Added Doxygen tag file to .gitignore.
      Added *.patch files to .gitignore.
      Also updated autoconf support files.
      Updated automake script to version 1.14.
      Fixed typos.
      Fixed various typos.
      Fixed various typos in comments.
      Added method to determine SpecificCharacterSet.
      Added 'charset' parameter to checkStringValue().
      Added new variant of checkElementValue().
      Avoid unnecessary copies of sequence elements.
      Enhanced implementation of checkCode() method.
      Report warning on unsupported character set.
      Use helper function findAndGetSequence().
      Updated comment on current character set issue.
      Fixed memory leak in log4cplus code.
      Minor fixes in comments.
      Minor changes to comments.
      Updated Doxygen configuration files.
      Removed outdated custom CSS file.
      Updated URL of DCMTK's home page.
      Fixed timeout issue in handleAssociation().
      Fixed source code formatting and various comments.
      Fixed wrong content type of XML element in DTD.
      Do not output group length in Native DICOM Model.
      Fixed outdated comment on 1st PN component group.
      Removed redundant API comment.
      Added support for CP-1268 to data dictionary.
      Added support for Supplement 168 to data dictionary.
      Added support for new UID from Supplement 168.
      Never output NULL bytes to markup string/stream.
      Adapted test cases for markup conversion.
      Iterate more efficiently over sequence items.
      Use helper method for deleting data elements.
      Added comments on missing features.
      Fixed small typos in comments.
      Added support for Real World Value Mapping objects.
      Added comment on getFrameList() method.
      Moved checkCurrentValue() to "protected" section.
      Slightly enhanced comments.
      Check return value of write() methods.
      Added support for Referenced Segment Number.
      Updated CMake version.
      Fixed small issue reported by CMake 2.8.12.
      Added Corneal Topography Map Storage SOP Class.
      Fixed bug that could cause a crash.
      Fixed doubled output of XML start tag for VR=OD.
      Added comment on wrong color model for icon images.
      Fixed issue with color icon images.
      Removed trailing white spaces from man pages files.
      Fixed build issue with shared libraries (Win32).
      Avoid CMake warning on non-installable files.
      Added missing break statements to switch cases.
      Removed redundant and outdated Word document.
      Added global flag for disabling the VR checker.
      Added new option for disabling the VR checker.
      Fixed minor Doxygen-related issue in documentation.
      Fixed name of PN component in Native DICOM Model.
      Fixed minor Doxygen-related issue in documentation.
      Fixed issue with test "ofstd_markup_6" (Win32).
      Fixed various typos in man pages.
      Fixed output of AT values in Native DICOM Model.
      Do not check valueLoaded() for Native DICOM Model.
      Completed support for <InlineBinary> XML element.
      Second try to fix the issue with "ofstd_markup_6".
      Fixed typos, comments and coding style.
      Replaced deprecated DcmSCU::closeAssociation().
      Removed check on number of command line arguments.
      Cleaned up source code in various aspects.
      Again, fixed comments to be consistent with code.
      Fixed comments and documented default values.
      Added support for recently approved CPs.
      Added support for Supplement 165 to data dictionary.
      Added support for new UIDs from Supplement 165.
      Fixed wrong/missing comment on method parameter.
      Fixed various minor documentation issues.
      Added missing module dcmrt to include directories.
      Removed comment on UID_HangingProtocolStorage.
      Added support for approved but still missing CPs.
      Added comments on some ACR/NEMA attributes.
      Fixed timeout issue in DIMSE_moveUser().
      Fixed typos in comments.
      Moved ACR/NEMA data dictionary to a separate file.
      Fixed issue with wrong check on stream compression.
      Fixed wrong VR for some retired command fields.
      Consistently use upper case letters for DICOM tags.
      Added new test cases for testing helper functions.
      Fixed typo and added comment.
      Added OFFilename versions to some helper functions.
      Added new helper function for renaming files.
      Added function for appending filename extension.
      Added wide character support to this tool.
      Added new helper function for copying files.
      Changed file mode bits back from "0755" to "0644".
      Fixed typo in comment.
      Added new command line option --create-backup.
      Avoid passing invalid values to rename().
      Avoid passing NULL to OFString, which is deprecated.
      Added support for wide chars to DICOMDIR code.
      Fixed issue when compiled with wide char support.
      Added new condition constant and fixed typo.
      Fixed issue with missing terminating NULL byte.
      Always use OFFilename() instead of "" as a default.
      Use printError() instead of OFLOG_FATAL().
      Fixed further issues with wide char support.
      Allow empty file-set ID in DICOMDIR (type 2).
      Fixed some comments.
      Fixed wrong tag in CodingSchemeIdentificationSequence.
      Made installation of tag file optional.
      Added another addContentItem() method.
      Replaced tabs by spaces and fixed indention.
      Fixed various issues in Doxygen comments.
      Fixed various minor issues in new helper class.
      Rebuilt Makefile dependencies.
      Added missing data elements to BD profiles.
      Added check for Shared Functional Groups Sequence.
      DIMSE_createFilestream() now uses an OFFilename.
      Fixed various typo.
      Pass OFString to DIMSE_createFilestream().
      Added support for CP-1090 to the data dictionary.
      Fixed issue with automatically generated classes.
      Removed superfluous quotations marks.
      Fixed small typos in comments.
      Added readPatientData() and readStudyData().
      Updated outdated comments on "log stream".
      Made sure that header file is parsed by Doxygen.
      Made sure that "Files" section is available.
      Added further header files to Doxygen documentation.
      Added support for recently approved CPs.
      Fixed some issues with wide character support.
      Added test for OFStandard::appendFilenameExtension().
      Fixed issue with untyped NULL reported by MSVC++.
      Fixed various typos in comments.
      Enhanced removeRootDirFromPathname() function.
      Enhanced createDirectory() function.
      Use non-throwing new and delete operator.
      Fixed typo in comment.
      Output to debug logger if memory allocation fails.
      Simplified creation of temporary DICOMDIR file.
      Optionally disable isFilenameValid() check.
      Added support for new UIDs from Supplement 124.
      Added support for Supplement 124 to data dictionary.
      Removed superfluous member initialization.
      Fixed typo in comments.
      Added support for determining the FrameTime.
      Access the (total) number of frames in an image.
      Fixed inconsistent parameter type.
      Added explicit type casts to avoid warnings.
      Fixed inconsistent parameter type.
      Updated data dictionary for DICOM 2013 edition.
      Fixed typos in comments.
      Added further error handling options.
      Fixed typos in comments.
      Fixed typos, added missing documentation, etc.
      Various minor fixes for development version.
      Fixed typos in comments.
      Made sure that the move originator is cleared.
      Fixed issue with text alignment in PatternLayout.
      Fixed some Doxygen related issues (and a typo).
      Consistently use "presInfo" for variables/parameters.
      Added support for Supplement 159 to data dictionary.
      Added support for new UID from Supplement 159.
      Added support for new SR IOD from Supplement 159.
      Added DcmSCP::abortAssociation() method.
      Fixed typo and updated copyright date.
      Removed meaningless layout file setting.
      Renamed Doxygen's layout file again.
      Made sure that header file is parsed by Doxygen.
      Group condition constants in Doxygen output.
      Avoid full directory path in Doxygen footer.
      Replaced CMake variable in Doxygen config file.
      Removed outdated comment on DICOM 2008 standard.
      Added missing empty line.
      Fixed typos and other minor issues.
      Updated reference to DICOM standard edition.
      Updated DCMTK's copyright date.
      Added support for CP-1125 to SR implementation.
      Fixed incomplete #include comment.
      Added support for recently approved CPs.
      Updated comment based on CP-1335.
      Added support for new Colon CAD SR constraints.
      Fixed various typos and minor Doxygen issues.
      Updated data dictionary for DICOM 2014a edition.
      Removed year component from version field.
      Minor fixes to file's comment header.
      Updated copyright date and other minor changes.
      Implemented copy constructors and added clone().
      Added explaining comment on new copy constructor.
      Removed outdated CMake exclude pattern.
      Excluded "*.md5" files from installation.
      Made sure that all top-level nodes are deleted.
      Added method counting the number of nodes.
      Added two new convenience functions.
      Fixed issue with tests run in different order.
      Fixed various Doxygen-related issues.
      Introduced new class DSRDocumentSubTree.
      Implemented copy constructors for tree classes.
      Added getPreviousNode() and getChildNode().
      Added further checking methods to cursor class.
      Added gotoFirst() and gotoLast() methods.
      Minor fixes on "const" declaration of pointers.
      Added cloneSubTree() method to tree classes.
      Changed return type of addContentItem(node*).
      Reimplemented various getXXX() methods.
      Cleaned up handling of "unknown" relationships.
      Restructured classes for nodes and trees.
      Fixed a bug in convertNewlineCharacters().
      Added insertSubTree() method to subtree class.
      Added checking of IOD-specific constraints.
      Fixed two memory leaks in recently added code.
      Clarified use of template identification.
      Removed DLL specifier from template classes.
      Slightly enhanced layout of Doxygen documentation.
      Added public method to change SR document type.
      Fixed wrong term in Doxygen documentation.
      Added removeSubTree() method to subtree class.
      Added extractSubTree() method to tree classes.
      Enhanced support for by-reference relationships.
      Further enhanced by-reference relationships.
      Insert a subtree into an empty document tree.
      Added dcmIsImageStorageSOPClassUID() function.
      Added check on valid "IMAGE" SOP Classes.
      Added support for optional JPEG fill byte.
      Removed misleading comment from checkStringValue().
      Fixed typos in comments and other minor issues.
      Added support for new value representation "UR".
      Updated data dictionary for DICOM 2014b edition.
      Added functions to enable/disable post-1993 VRs.
      Enhanced rewriting rules in DcmVR::getValidEVR().
      Use new VR "UR" for Pixel Data Provider URL.
      Fixed typo in method name.
      RLE images should not use multiple fragments.
      Added missing documentation for --propose-deflated.
      Attribute (0040,4005) has not been retired.
      Fixed wrong term "Device Driving Level".
      Updated "dcmrt" classes based on DICOM 2014b.
      Added "data correction" options to findscu.
      Fixed issue when scaling certain images.
      Removed unneeded header include.
      Fixed typo in comment.
      Fixed wrong validation of PN, LO and SH values.
      Added check for requirements clarified by CP-1401.
      Updated data dictionary for DICOM 2014c edition.
      Added support for new UIDs from DICOM 2014c.
      Fixed typo in comment.
      Added new temporarily generates files.
      Use "try and catch" block around new[].
      Fixed error handling in detachValueField().
      Fixed error handling in changeValue().
      Added new test case for VR=FD.
      Changed attribute used for the "FD" test.
      Added support for new value representation "UC".
      Added support for recently approved CPs.
      Added Mapping Resource UID from CP-1417.
      Removed outdated name suffix from EXS_xxx constant.
      Added missing standard include for assert().
      Fixed another CMake 3.1.x quotation issue.
      Updated latest tested CMake version.
      Fixed documentation of default TCP buffer length.
      Updated data dictionary for DICOM 2015a edition.
      Fixed typos in comments and other minor issues.
      Updated Makefile dependencies again.
      Updated outdated API documentation.
      Output message to logger on wrong pixel data class.
      Enhanced use of DSRCodingSchemeIdentificationList.
      Added support for recently approved CPs.
      Added support for Supplement 173 to dictionary.
      Added support for new UIDs from Supplement 173.
      Added support for recently approved CP-1425.
      Fixed test after after implementing CP-1425.
      Added further test cases for VR checker.
      Added read flag to all readXXX() methods.
      Optionally accept invalid content item values.
      Distinguish b/w invalid content items and values.
      Enhanced output to debug logger.
      Fixed wrong position counter in tree node.
      Added regression test for DSRTree::getPosition().
      Added method for counting number of child nodes.
      Fixed issue with VR checker for PN values.
      Fixed warning C4800 reported by Visual Studio.
      Updated data dictionary for DICOM 2015b edition.
      Ignore empty value for XML element 'charset'.
      Added support for optional Mapping Resource UID.
      Pass OFList parameter by-reference not by-value.
      Fixed issue with interpolation algorithm.
      Added hasTemplateIdentification() method.
      Replace the document tree of an SR document.
      Added initial support for SR templates.
      Added helpers for setting a value from dataset.
      Set observation date/time from dataset.
      Moved various methods to protected section.
      Added helpers for setting a value from element.
      Set observation date/time from element.
      Avoid using "check" parameter of SR code class.
      Introduced new error code "Unknow VR".
      Fixed source code and/or comment formatting.
      Do not check invalid UID values for IMAGE node.
      Added support for long code values (CP-1031).
      New class for "Basic Coded Entry Attributes".
      Fixed bug in time normalization code.
      Added missing empty() method to OFMap.
      Added new option for print() method.
      Added new comparison method to DSRCodedEntryValue.
      Made getAndRemoveRootNode() public.
      Fixed issue with addNode() in basic tree class.
      Added new and enhanced existing swap() function.
      Check whether a template is extensible.
      Added initial support for Supplement 186.
      Added initial support for Supplement 180.
      Made constructor and destructor "protected".
      Removed explicit name of base class from call.
      Added mechanism for remembering node positions.
      Added base class for context groups.
      Added initial version of DCM code definitions.
      Added first specific Templates and Context Groups.
      Updated "DCM" codes for DICOM 2015c edition.
      Updated data dictionary for DICOM 2015c edition.
      Fixed issue with wrong quotation marks.
      Added static initialization function (MT-safe).
      Fixed issue in OFStandard::combineDirAndFilename().
      Enhanced check on empty dataset.
      Improved documentation of disableXXXCheck().
      Consistently use "file-set" and "file format".
      Allow for disabling check on "DICOM file format".
      Renamed ANNOUNCE file (removed version suffix).
      Enhanced documentation of createNewSOPInstance().
      Added conversion operator to context group class.
      Added support for CID 42 (Numeric Value Qualifier).
      Added function that initializes all context groups.
      Updated copyright date.
      Fixed wrong documentation of return value.
      Removed superfluous OFStringStream_ends statement.
      Fixed wrong exit code on invalid input file.
      Added support for further Context Groups.
      Fixed various typos in comments.
      Enhanced handling of empty Measured Value Sequence.
      Added check for CID 42 to NUM values.
      Added support for Context Group CID 29.
      Added general information on coding scheme "DCM".
      Added easier method to set a composite reference.
      Fixed issue reported by Clang 3.5 on OpenBSD.
      Introduced condition constant EC_NotYetImplemented.
      Do not set empty concept name codes.
      Added missing DCMTK_DCMDATA_EXPORT macro.
      Added new helper method gotoEntryFromNodeList().
      Added method to look up a context group entry
      Added new mode for adding nodes to the tree.
      Fixed typos in comment.
      Added comment on reserved error codes (for "cmr").
      Fixed wrong comment.
      Introduced new flag to customize the print output.
      Added new command line options to dsrdump.
      Added specific logger for submodule "dcmsr/cmr".
      Added parameter "pos" to getStringValueFromDataset.
      Added static method setEnhancedEncodingMode().
      Clarified use of invalid coded entries.
      Added support for Context Group CID 244.
      Made sure that IOD constraint checker is used.
      Added "Extensible SR" to known document types.
      Added enhanced versions of CID 29, 244 and 4031.
      Added cleanup() function to context group classes.
      Fixed typo and other minor issues in comments.
      Added name prefix to class ContentMappingResource.
      Fixed copyright header in module "dcmsr".
      Added new optional parameter "vm" to readSequence.
      Added methods to read/write to/from sequence items.
      Fixed inconsistencies regarding the use of OFMap.
      Updated Makefile dependencies.
      Added enhanced versions of CID 10013 and 10033.
      Added initial version of SRT and UCUM codes.
      Introduced type for list of CID 7445 values.
      Updated Makefile dependencies.
      Added initial version of TID 1600 (Image Library).
      Slightly changed conversion operator.
      Extracted general information from template.
      Avoid seperator if time component is empty.
      Added support for annotating content items.
      Added support for Context Group CID 100 and 7021.
      Added support for clearing tree node annotations.
      Made sure that tree node annotations are copied.
      Made sure that "dicom.dic" is loaded for tests.
      Fixed various issues in test case.
      Fixed "cardinality" for SQ elements in comments.
      Added comment that "Big Endian" is retired.
      Removed version suffix "3" from dictionary entries.
      Check logger for debug output of template tree.
      Introduced global definitions for certain tags.
      Added CREDITS file.
      Added "YXLON" to the new CREDITS file.
      Added support for recently approved CPs.
      Added support for Supplement 156 to dictionary.
      Added support for new UIDs from Supplement 156.
      Check for recently approved multi-frame images.
      Updated currently supported compiler versions.
      Fixed various minor issues in module descriptions.
      Fixed order of modules in main HTML file.
      Added three new DCMTK modules to README.

Marco Eichelberg (5):
      Introduced OFStandard::dropPrivileges().
      Tools now use OFStandard::dropPrivileges().
      Fixed minor bug in DICOM upper layer FSM.
      Always use current dicom.dic for dcmdata unit tests.
      Removed unsupported wwwapps and perl scripts from module dcmwlm.

Michael Onken (84):
      Added (optional) originating C-MOVE AE title and message ID to C-STORE message.
      Make DcmStorageSCU make use of new MoveOriginator feature.
      Added optional status detail when sending C-MOVE response.
      Make sure memcpy does not copy to NULL destination. Thanks to Francesco Gigante     for the report.
      Added option to discard illegal characters when converting between     DICOM character sets.
      Add "Discard illegal character" support to dcmconv and classes like DcmItem.
      Make sure SCU and SCP request/response data structures are initially zeroed.
      Fixed typo (coersion -> coercion) in DIMSE status constant.
      Added missing kudos.
      Fixed too small buffer for UID in Q/R server.
      Fixed issues where JPEG marker map was not cleared if more than one JPEG     was converted using the same plugin instance.
      Fixed possible doubled destruction of association.
      Make sure oflog also compiles if threads are disabled.
      Always write meta header when receiving files. Removed Winsock comment.
      Added missing CHANGES entry.
      Warning to re-create index.dat after 20130705:
      Create DcmFileFormat from DcmDataset w/o copying.
      Do not copy DcmDataset during C-GET receive.
      Worklist SCP support for Responsible Person/Role.
      Replaced tabs with spaces.
      Support explicit item length denoting too many bytes.
      Corrected misleading transfer syntax error message.
      Fixed Comments.
      Described movescu storage SCP timeout problem.
      Make sure CMAKE_BUILD_TYPE has a default value.
      Fixed doubled tag output in XML output of VR OF.
      Avoid second OpenSSL initialization in constructor.
      Documentation for CMAKE_BUILD_TYPE default value.
      Fixed typo.
      Fixed CHANGES entries.
      Fixed some inconsistencies in documentation.
      Make sure to handle setuid() return code properly.
      Add libjpeg dependency for libtiff and minor changes.
      Fixed shared library build under Unix (configure).
      Enhanced DCMTK CMake exports for external projects.
      Capitalized all CMake key words for consistency.
      Ensure CMake v2.6 still writes DCMTKConfig.cmake.
      DCMTK.cmake and DCMTKTargets.cmake documentation.
      Added helpers to copy common modules between items.
      Fixed Makefile.dep for new files from last comit.
      Switched windows line endings to unix line endings.
      Added further module helpers and fixed small issues.
      Fixed comments and error message.
      Updated module helpers to latest DICOM 2013 draft.
      Fixed wrong ifdef syntax.
      Add connection timeout setting to SCU class.
      Fixed possible memory leak.
      Specific error if no presentation context proposed.
      Reverted false retirement status of some SOP Classes.
      Fix last commit by including implementation file.
      New compare() function for dcmdata object values.
      Make sure dcmdata tests compile with autoconf.
      Make new compare() method more reliable.
      Fixed conversion of color to palette color mode.
      Documented DCMTK's C++ cast macros.
      Fixed installation and added CHANGES file.
      Disable built-in dictionary for CMake Unix builds.
      Make sure presentation contexts do not interfer.
      Fixed iterator type.
      Introduced new modules dcmiod, dcmfg and dcmseg.
      Removed accidentially checked in test files.
      Removed more accidentially checked in test files.
      Fixed iterator dereference.
      Fixed iterator constness.
      Fixed possible DICOM VR problems.
      Removed unused method.
      Fixed mostly constness for some compilers.
      Fixed various doxygen formatting issues.
      Fixed compilers errors (mostly STL-specific).
      Removed unused link libraries.
      Made copyright header consistent in new modules.
      Build flags for internal and external dictionary.
      Updated dictionary build and code documentation.
      Added shared library export maro to IODModule.
      Added more files to be ignored by git.
      Added mising "check-exhaustive" targets.
      Replaced tab characters with spaces.
      Use static_cast instead of dynamic_cast.
      Renamed dictionary configuration build options.
      Simplified builtin dictionary infrastructure.
      Fixed typo in CMake script that can cause warnings.
      Fixed typo and made documentation more consistent.
      Fixed another typo.
      Enable private tags in builtin dictionary on CMake.

Nikolas Goldhammer (1):
      Replaced deprecated CMake expressions.

Uli Schlachter (13):
      Fixed wrong definition of Value Representation Person Name (PN)
      Removed unused local variable which shadowed a variable with the same name.
      Use ".NOTPARALLEL:" to make parallel builds (e.g. -j4) possible.
      Update rootconf for changes which were done directly to generated files.
      Fixed various issues found via cppcheck.
      Use DcmTagKey's output operator where possible.
      Don't include intrin.h on Visual Studio 2005 because of build errors.
      Fixed bug in OFString::copy() and improved unit tests.
      Fixed compiler warnings in ConvertIntegerToString with unsigned integers.
      Worked around compiler warnings on 32bit systems for too large shifts.
      Fixed crash if less than four transfer syntaxes are enabled.
      Silence some more compiler warnings about implicit casts.
      Don't set the defines for thread local storage support incorrectly.

Revision 24561  Directory Listing
Modified Thu Sep 17 19:49:35 2015 UTC (2 years ago) by msmolens
ENH: Upgrade to NumPy 1.9.2

This commit upgrades from NumPy 1.4.1 to NumPy 1.9.2.

To continue building NumPy without a Fortran compiler, a build step is
introduced that applies a patch to effectively back out the following
change:

    numpy/numpy@4a3fd1f

This new version of NumPy still compiles with Visual Studio 2008 and Visual
Studio 2010, but now also compiles with Visual Studio 2013. To make it compile
with Visual Studio 2013, this commit updates the patched version of
'msvc9compiler.py' for Python 2.7 by adding an entry in WINSDK_VERSION_MAP for
Visual Studio 2013. This fixes the following error when building NumPy with
Visual Studio 2013:

    Traceback (most recent call last):
      ...
      File "C:\dev\S4D\NUMPY\numpy\distutils\command\config.py", line 55, in _check_compiler
        self.compiler.initialize()
      File "C:\dev\S4D\python-install\Lib\distutils\msvc9compiler.py", line 500, in initialize
        vc_env = query_vcvarsall(VERSION, plat_spec)
      File "C:\dev\S4D\python-install\Lib\distutils\msvc9compiler.py", line 371, in query_vcvarsall
        for sdkver in WINSDK_VERSION_MAP[versionstr]:
    KeyError: '12.0'

NumPy test results on each platform are below:

    >>> import numpy
    >>> numpy.test(label='full')

    - Mac OS X 10.6.8 (GCC 4.2.1 Compatible Clang 3.1, Release):
        - NumPy 1.4.1, manually disabled test_multiarray.TestIO.* because many tests segfault:
            ERROR: Failure: TypeError (setting function's dictionary to a non-dict)
            FAIL: Check formatting of complex types.
            FAIL: Check formatting of complex types.
            FAIL: Check formatting of complex types.
            FAILED (KNOWNFAIL=4, SKIP=4, errors=1, failures=3)
            <nose.result.TextTestResult run=2364 errors=1 failures=3>
        - NumPy 1.9.2:
            OK (KNOWNFAIL=5, SKIP=43)
            <nose.result.TextTestResult run=5382 errors=0 failures=0>

    - Ubuntu 14.04.3 (GCC 4.8.4, Debug):
        - NumPy 1.4.1, manually disabled test_multiarray.TestIO.* because many tests segfault:
            ERROR: Failure: TypeError (setting function's dictionary to a non-dict)
            FAIL: Check formatting of complex types.
            FAIL: Check formatting of complex types.
            FAIL: Check formatting of complex types.
            FAILED (KNOWNFAIL=4, SKIP=4, errors=1, failures=3)
            <nose.result.TextTestResult run=2364 errors=1 failures=3>
        - NumPy 1.9.2:
            FAIL: test_allnans (test_nanfunctions.TestNanFunctions_Median)
            FAILED (KNOWNFAIL=5, SKIP=40, failures=1)
            <nose.result.TextTestResult run=5418 errors=0 failures=1>

    - Windows (Visual Studio 2008, Release):
        - NumPy 1.4.1, manually disabled test_multiarray.TestIO.* because many tests segfault:
            ERROR: Failure: TypeError (setting function's dictionary to a non-dict)
            FAIL: Check formatting of complex types.
            FAIL: Check formatting of complex types.
            FAIL: Check formatting of complex types.
            FAILED (KNOWNFAIL=8, SKIP=4, errors=1, failures=3)
            <nose.result.TextTestResult run=2216 errors=1 failures=3>
        - NumPy 1.9.2:
            FAIL: test_allnans (test_nanfunctions.TestNanFunctions_Median)
            FAILED (KNOWNFAIL=10, SKIP=44, failures=1)
            <nose.result.TextTestResult run=5226 errors=0 failures=1>

    - Windows (Visual Studio 2013, Debug):
        - NumPy 1.4.1:
            Unsupported compiler.
        - NumPy 1.9.2:
            FAIL: test_any_ninf (test_umath.TestArctan2SpecialValues)
            FAIL: test_any_pinf (test_umath.TestArctan2SpecialValues)
            FAIL: test_inf_ninf (test_umath.TestArctan2SpecialValues)
            FAIL: test_inf_pinf (test_umath.TestArctan2SpecialValues)
            FAIL: test_one_one (test_umath.TestArctan2SpecialValues)
            FAIL: test_zero_negative (test_umath.TestArctan2SpecialValues)
            FAIL: test_zero_nzero (test_umath.TestArctan2SpecialValues)
            FAIL: test_zero_pzero (test_umath.TestArctan2SpecialValues)
            FAIL: test_umath.TestComplexFunctions.test_branch_cuts(<ufunc 'log1p'>, -1.5, 1j, 1, -1)
            FAIL: test_umath.TestLogAddExp.test_inf
            FAIL: test_umath_complex.TestCarg.test_special_values(<ufunc '_arg'>, -inf, 1, 3.141592653589793, False)
            FAIL: test_umath_complex.TestCarg.test_special_values(<ufunc '_arg'>, inf, -1, -0.0, False)
            FAIL: test_umath_complex.TestCarg.test_special_values(<ufunc '_arg'>, -inf, inf, 2.356194490192345, False)
            FAIL: test_umath_complex.TestCarg.test_special_values(<ufunc '_arg'>, -inf, -inf, -2.356194490192345, False)
            FAIL: test_umath_complex.TestCarg.test_special_values(<ufunc '_arg'>, inf, -inf, -0.7853981633974483, False)
            FAIL: test_basic (test_function_base.TestAngle)
            FAILED (KNOWNFAIL=10, SKIP=42, failures=16)
            <nose.result.TextTestResult run=5226 errors=0 failures=16>

No new Slicer test failures are seen when running the tests manually on:
- Mac OS X 10.6.8 (Release)
- Ubuntu 14.04.3 (Debug)
- Windows (Visual Studio 2013, Debug)

Fixes #3159
Fixes #3160

From: Max Smolens <max.smolens@kitware.com>

Revision 24560  Directory Listing
Modified Thu Sep 17 19:49:27 2015 UTC (2 years ago) by msmolens
ENH: Add Python package: nose

This commit adds the Python package 'nose', a unit testing framework, to the
embedded Python installation.

The motivation for adding nose is to support testing NumPy in Slicer's Python
environment; NumPy's unit tests require nose.

For more information on nose, see https://nose.readthedocs.org.

From: Max Smolens <max.smolens@kitware.com>

Revision 24559  Directory Listing
Modified Thu Sep 17 19:49:20 2015 UTC (2 years ago) by msmolens
BUG: Fix Python test failure in Debug build on Windows

This commit fixes a Python build problem on Windows when building in Debug
configuration. Running the built-in Python test 'test_os' suggests a problem by
displaying an assertion failure in the C Runtime library (CRT):

    [...]
    File: f:\dd\vctools\crt\crtw32\Iowio\dup.c
    Line: 52

    Expression: (_osfile(fh) & FOPEN)
    [...]

This issue is that the Python library used multiple versions of the CRT. Because
Python is forced to build in Release configuration, the Python library always
uses the Multi-threaded CRT. Because the binascii and zlib Python modules
statically link to zlib, they pull in the CRT that zlib is built with, which, in
this case, is the Multi-threaded Debug CRT. When the binascii or zlib modules
are built into the Python library, the library uses both versions of the CRT,
which results in failures such as in test_os.

This commit fixes the problem by ensuring that, on Windows, the binascii and
zlib modules are not built into the Python library. Note that those two modules
might still show problems since they are built in Release configuration but pull
in the Debug CRT from zlib.

This problem was originally discovered because it prevented NumPy 1.9.2's setup
from completing in a Debug build:

    [...]
      File "C:\dev\SN\python-install\Lib\distutils\command\config.py", line 138, in _compile
	self.compiler.compile([src], include_dirs=include_dirs)
      File "C:\dev\SN\python-install\Lib\distutils\msvc9compiler.py", line 670, in compile
	extra_postargs)
      File "C:\dev\SN\NUMPY\numpy\distutils\ccompiler.py", line 59, in CCompiler_spawn
	s, o = exec_command(cmd)
      File "C:\dev\SN\NUMPY\numpy\distutils\exec_command.py", line 223, in exec_command
	use_tee=use_tee,**env)
      File "C:\dev\SN\NUMPY\numpy\distutils\exec_command.py", line 414, in _exec_command
	os.dup2(se_dup, se_fileno)
    OSError: [Errno 9] Bad file descriptor

From: Max Smolens <max.smolens@kitware.com>

Revision 24554  Directory Listing
Modified Wed Sep 16 15:47:06 2015 UTC (2 years ago) by msmolens
ENH: Update CTK (includes PythonQt crash fix, DICOM browser enhancement)

Fixes Issue #4045 (py_StandaloneEditorWidgetTest crashes on exit in PythonQt)
Fixes Issue #3792 (unable to remove one series of an exam in the dicom menu)

    // -------------------------
    commit cbf890f8eda122b8dca8e67d2bf75e85640ab297
    Author: Max Smolens <max.smolens@kitware.com>
    Date:   Tue Sep 15 15:45:30 2015 -0400

	Fix PythonQtSignalReceiver crash during cleanup

	This commit fixes a crash during PythonQt::cleanup(). While destroying the
	PythonQtPrivate instance, any remaining PythonQtSignalReceivers that are kept
	alive only by their parent object will be destroyed. The crash occurs when
	PythonQtSignalReceiver's destructor calls back into
	PythonQtPrivate::removeSignalEmitter() when the PythonQtPrivate instance is
	mostly destroyed.

	Includes test case that crashes without the fix.
    // -------------------------

    // -------------------------
    commit ea653d2cfc5be6dc846a5a54f75543af7dfd4445
    Author: Nicole Aucoin <nicole@bwh.harvard.edu>
    Date:   Mon Aug 3 18:51:07 2015 -0400

	ENH: add ability to delete individual series, studies, patients

	Add to the browser Remove button the information that it will
	delete all selected series, studies, patients.

	Add support for right click custom context menus in the
	patient, study, series tables. Translate the local points
	to global ones in terms of the table view and signal
	right clicked with the global position so that the browser
	can position the context menu appropriately.

	Add the context menu to the DICOM browser to allow
	deleting at just one level, with number of items
	selected information, and a confirmation message box with descriptive
	information that can be set to not be shown again.

	Added a test for the DICOM browser, with the ability
	to open it in interactive mode to test the right clicks.

	Add query wrappers for the DICOM database to get the patient name
	as well as descriptions for series and study. They will return empty
	strings on failure.
	Use the new queries to give more meaningful information on the right
	click pop up menu in the DICOM browser.
	Added a test for the new DICOM database accessors.

	Slicer bug:
	http://www.na-mic.org/Bug/view.php?id=3792

	When Slicer makes a custom DICOM browser, it moves the table views
	directly into the new window, extracting them from the DICOM
	table.
	With this change, the table view takes care of mapping the point to
	global, the table manager propagates the signal as a table specific
	XRightClicked signal, and the browser responds to it with a table
	specific context menu.

	Slicer Issue #3792
    // -------------------------

From: Max Smolens <max.smolens@kitware.com>

Revision 24539  Directory Listing
Modified Mon Sep 14 21:04:20 2015 UTC (2 years ago) by jcfr
ENH: Convert to using ITK version of MGHIO

The ITK supplied version of MGHIO is a derivative
work that originated in Slicer.  The ITK version
has more widespread use in non-slicer envirnments and
can be used and maintained by a larger community.

From: Hans Johnson <hans-johnson@uiowa.edu>

Revision 24538  Directory Listing
Modified Mon Sep 14 20:50:08 2015 UTC (2 years ago) by msmolens
ENH: Update CTK to include PythonQt cleanup fixes

Fixes crash on exit in py_nomainwindow_DCMTKPrivateDictTest.

// -------------------------------------------
commit commontk/CTK@ffc7f7a9
Author: Max Smolens <max.smolens@kitware.com>
Date:   Fri Sep 11 16:52:23 2015 -0400

    ctkAbstractPythonManager: revert change to clean up PythonQt before finalizing the Python interpreter

    This commit reverts commontk/CTK@77a24f2

    The original change worked in conjunction with fixes in PythonQt to avoid
    various crashes while destroying the ctkAbstractPythonManager, for example by
    calling Py_DECREF after the Python interpreter was finalized.

    Further testing shows that a better fix is indeed to finalize first to ensure
    clean destruction of PythonQt objects, and to make PythonQt's clean up step more
    robust by handling a finalized interpreter.

    An example of code which necessitates this change is creating an instance of
    class Foo:

        class Foo(object):

          def __init__(self):
        self.timer = qt.QTimer()

          def __del__(self):
        self.timer.setSingleShot(True)

    During Py_Finalize(), the Foo instance's __del__ method is called, which in turn
    calls a method on a Qt object. For this to succeed, PythonQt's data must still
    be in place.
// -------------------------------------------

From: Max Smolens <max.smolens@kitware.com>

Revision 24526  Directory Listing
Modified Wed Sep 9 14:20:24 2015 UTC (2 years ago) by msmolens
ENH: Upgrade to Python 2.7.10

This commit upgrades Slicer's Python from version 2.7.3 to version
2.7.10. The newer Python version fixes a number of build warnings seen when
building Slicer with Python 2.7.3 in Visual Studio 2013, like:

    C:\Program Files (x86)\Microsoft Visual Studio 12.0\VC\include\xtgmath.h(190): warning C4273: '_hypot' : inconsistent dll linkage [C:\dev\SN\VTKv6-build\Wrapping\PythonCore\vtkWrappingPythonCore.vcxproj]
        C:\Program Files (x86)\Microsoft Visual Studio 12.0\VC\include\math.h(538) : see previous definition of '_hypot'

and:

    C:\dev\SN\python-2.7.3\include\pymath.h(22): warning C4273: 'round' : inconsistent dll linkage [C:\dev\SN\python-build\CMakeBuild\libpython\libpython-shared.vcxproj]
        C:\Program Files (x86)\Microsoft Visual Studio 12.0\VC\include\math.h(516) : see previous definition of 'round'

In addition to specifying the Python source directory with `SRC_DIR`, this
commit makes the Python build more robust to default option changes by
explicitly specifying `-DDOWNLOAD_SOURCES:BOOL=OFF` and
`-DINSTALL_WINDOWS_TRADITIONAL:BOOL=OFF`.

Also note that 'Lib/distutils/msvc9compiler.py' did not change between Python
2.7.3 and Python 2.7.10, so the patched version remains the same.

This update has been manually tested on:
- Windows (Visual Studio 2008, Release)
- Windows (Visual Studio 2013, Debug)
- Ubuntu 14.04.3 (Debug)
- Mac OS X 10.6.8 (Release)

Release builds show the following tests as failing:
- vtkMRMLSceneImportIDModelHierarchyConflictTest
- py_StandaloneEditorWidgetTest
- py_DTINotReproducibleIssue3977
- qSlicerMultiVolumeExplorerModuleWidgetGenericTest

Debug builds show the following additional test as failing:
- vtkMRMLSceneImportTest_diffusionEditor.mrml

From: Max Smolens <max.smolens@kitware.com>

Revision 24525  Directory Listing
Modified Wed Sep 9 14:20:16 2015 UTC (2 years ago) by msmolens
ENH: Update python-cmake-buildsystem to support building Python 2.7.10

$ git shortlog 0838470ec2a0d20909571793ebb4ccc8a3292ac5..ed5f9bcee540e47f82fa17f8360b820591aa6d66 --no-merges
Chuck Atkins (9):
      Accomodate the various configurations of nbdm.h
      Use proper assembler support instead of manually assembling .S files.
      Use list(APPEND ...) to build lists avoiding excessive ";"s
      Use target_compile_definitions so defs get appended instead of replaced
      Remove dlmalloc.c from libffi's source list
      Use BUILD_EXTENSIONS_AS_BUILTIN as default but let BUILTIN_FOO override
      Mark BUILTIN_FOO and ENABLE_FOO as advanced if they use default values.
      Add additional locations to check for python source
      Fix `exec_prefix` error occurring when no extension are built shared

Gaëtan Lehmann (1):
      Automatically download the python sources

Jean-Christophe Fillion-Robin (42):
      Use official tar.gz source archive for both windows and unix
      Check MD5 of downloaded source archive
      Document DOWNLOAD_SOURCES CMake option
      Display source download messages with first letter upper-cased
      Download source archive in the parent directory
      travis: Add initial configuration
      appveyor: Add initial configuration
      pyconfig: Re-locate HAVE_UINTPTR_T macro to match position in official source
      Issue #18747: Re-seed OpenSSL's pseudo-random number generator after fork.
      Issue #20494: mmap obmalloc arenas so that they may be immediately returned to the system when unused
      pyconfig: Better comment associated with HAVE_DEV_PTMX and HAVE_DEV_PTC
      Fix for r84195: add HAVE_ALLOCA_H to configure and only include alloca.h if it's available
      Read version from python source
      Generate pybuilddir.txt and _sysconfigdata.py if python >= 2.7.5 is used
      Update default python version from 2.7.3 to 2.7.8
      Install _sysconfigdata.py
      Fix md5 used with Python-2.7.8.tgz
      Disable ctypes extension when using "Visual Studio 2008 Win64" generator.
      Disable ctypes extension when using CMake < 2.8.12 with VS2010 generators.
      Fix typo in ConfigureChecks.cmake
      Add build matrix for appveyor and travis.
      Use target_compile_definitions only if available
      Rename "append_list_in_cache" CMake macro into "_append_list_in_cache"
      Fix undeclared PyDateTimeAPI error when building _testcapi module as builtin
      Update Extensions module to support conditional requirements
      Fix link / undefined symbol error associated with "_curses_panel" extension
      Fix "pyexpat" import error when "_sqlite3" and "pyexpat" where "builtin"
      Never build '_ctypes_test' as builtin extension
      Add option BUILD_EXTENSIONS_AS_BUILTIN
      Hide BUILTIN_FOO option if FOO is disabled
      Tweak check required to conditionally exclude ctypes extensions
      Fix build of ctypes as builtin extension with Visual Studio 10
      Relocate CMake checks into its own module
      Fix error message displaying python source searched locations.
      UpdateSysconfig: Fix typo
      Fix regular dashboard removing version from project name set in CTestConfig
      Fix value of CMAKE_SYSTEM_PROCESSOR on windows when using CMake < 2.8.11
      Add support for building the windows installer
      Enable travis-ci OSX builds setting-up multi-os support
      README: Fix repository URL in clone instruction
      Speed-up travis CI build using contained-based infrastructure
      Fix openssl_md_meth_names error reported on travis

John Cary (2):
      Add option INSTALL_WINDOWS_TRADITIONAL
      Allow configuration providing the patch version. Fixes #57

John R. Cary (3):
      Fix undefined _PyTime_FloatTime symbol linker error
      Add Crypt32 library to _ssl_LIBRARIES to fix shared link.
      Exclude timemodule.c when building datemodule extension on windows.

Marcel Metz (1):
      Escape PYTHONPATH macro value separator for NMake

Matt McCormick (4):
      Expose ffi headers only for _ctypes module compiled on unix
      Add _ctypes support for x86, MSVC.
      Add support for 64-bit _ctypes with MSVC.
      Improve README overview text.

Max Smolens (4):
      Fix building on windows
      Fix failing tests on Windows by making more modules built-in
      Hide CMake policy CMP0042 warnings
      Fix Unix build when CMAKE_BUILD_WITH_INSTALL_RPATH is enabled

From: Max Smolens <max.smolens@kitware.com>

Revision 24524  Directory Listing
Modified Wed Sep 9 14:20:07 2015 UTC (2 years ago) by msmolens
ENH: Update CTK to include PythonQt cleanup fixes

$ git shortlog 35a187ff5ae15f1c590a2ac317cd102c5746a81b..3884436e0e089360c900e786513f821281a00805 --no-merges
Julien Finet (1):
      Fix compilation on Visual Studio

Max Smolens (3):
      Update PythonQt to patched-6
      ctkAbstractPythonManager: Clean up PythonQt before finalizing the Python interpreter
      Update PythonQt to patched-5, which now includes selected updates from patched-6

From: Max Smolens <max.smolens@kitware.com>

Revision 24522  Directory Listing
Modified Tue Sep 8 20:58:00 2015 UTC (2 years ago) by jcfr
COMP: Update ITKv4 to maintain support for CMake >= v2.8.9 and <= v3

// -----------------
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Tue Sep 8 16:11:02 2015 -0400

    COMP: Set policy CMP0042 only if CMake version support it.

    Thanks: Bradley Lowekamp <blowekamp@mail.nih.gov>
// -----------------

Revision 24511  Directory Listing
Modified Thu Aug 27 16:35:13 2015 UTC (2 years ago) by jcfr
COMP: Update CTK to include QtTesting fixes

$ git shortlog a1751e0..35a187f --no-merges
Jean-Christophe Fillion-Robin (4):
      ctkAbstractPythonManagerTest: Fix typo
      ctkAbstractPythonManagerTest: Improve testExecuteString to check for error
      ctkAbstractPythonManagerTest: Update testExecuteString to check function call
      QtTesting: Update Git repository URL to fix invalid cert issues.

Laurenn Lam (1):
      Fix ctkFileDialogEventTranslator bottom widget events recording

Revision 24507  Directory Listing
Modified Wed Aug 26 12:31:42 2015 UTC (2 years, 1 month ago) by fedorov
BUG: env variable was incorrectly initialized

DCMDICTPATH should be used, not DCMDICTHOME. Thanks to @jcfr for catching this.

Revision 24502  Directory Listing
Modified Wed Aug 19 03:22:15 2015 UTC (2 years, 1 month ago) by lassoan
BUG: Fixed crash caused in Model display node widget

Slicer crashed when updated a filter pipeline that generated a polydata that was used by the model node.

There was an infinite loop (and stack overflow) caused by automatically selecting the first scalar attribute when the polydata is regenerated by the pipeline.

Fixed by allowing having 'none' selected as displayed scalar in the model widget and therefore avoiding automatic scalar selection when scalars are added to the data set and so avoiding infinite loop.

Revision 24494  Directory Listing
Modified Wed Aug 12 03:13:48 2015 UTC (2 years, 1 month ago) by jcfr
COMP: Update ITK to fix Slicer MacOSX extension packaging. Fixes #4029

// ------------------
commit 0905a43149320d8c2993e83ecf6c8a9d6b2b4232
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Tue Aug 11 22:53:36 2015 -0400

    COMP: Fix Slicer MacOSX extension packaging setting CMP0042 policy to OLD

    Most likely because the version of CMake used on the factory has been
    updated from CMake 2.8.12 to CMake 3.0.2, Slicer extension packaging was
    failing.

    Waiting the packaging of extension on MacOSX is improved to directly
    leverage CMake 3.x to set @rpath appropriately for both build and install
    tree, this commit reverts the policy to OLD.
// ------------------

Revision 24491  Directory Listing
Modified Tue Aug 11 22:44:45 2015 UTC (2 years, 1 month ago) by naucoin
BUG: Update CTK (update message box don't show again)

Among other changes it updates ctkMessageBox to include the
text on the button that will be the default if the don't
show again option is checked.

> git shortlog 7081550..e0c8fd5 --no-merges
Andreas Fetzer (1):
      Fixed another qt 5.5 build error

Nicole Aucoin (1):
      ENH: Give more information for not showing the message box again

Issue #3965

Revision 24490  Directory Listing
Modified Mon Aug 10 23:21:09 2015 UTC (2 years, 1 month ago) by jcfr
COMP: Fix build error in External_DCMTK.cmake

Reported-by: Erich Bremer <erich.bremer@stonybrook.edu>
Thanks: Steve Pieper <pieper@bwh.harvard.edu>

This commit fixes a regression introduced in r24483 (BUG: fix support
for DCMTK DICOM dictionaries) where a line continuation character
is used. It turns out that this character caused parsing issue with older
version of CMake (< v3.0.0)

//-------------------------------
CMake Error at SuperBuild/External_DCMTK.cmake:99 (set):
   Syntax error in cmake code at

     /home/erich/MyProjects/trunk/SuperBuild/External_DCMTK.cmake:100

   when parsing string

     DCMDICTHOME=<APPLAUNCHER_DIR>/${Slicer_SHARE_DIR}/dicom.dic<PATHSEP>\

   <APPLAUNCHER_DIR>/${Slicer_SHARE_DIR}/private.dic

   syntax error, unexpected cal_SYMBOL, expecting $end (89)
 Call Stack (most recent call first):
   CMake/ExternalProjectDependency.cmake:593 (include)
   SuperBuild/External_ITKv4.cmake:14 (ExternalProject_Include_Dependencies)
   CMake/ExternalProjectDependency.cmake:593 (include)
   CMake/ExternalProjectDependency.cmake:639 (ExternalProject_Include_Dependencies)
   SuperBuild.cmake:323 (ExternalProject_Include_Dependencies)
   CMakeLists.txt:670 (include)
//-------------------------------

Revision 24484  Directory Listing
Modified Tue Aug 4 22:18:42 2015 UTC (2 years, 1 month ago) by jcfr
BUG: Update VTK - Re-enable GPU VR on Mac fixing a Slicer/VTK rebase mistake

This commit

   (1) reverts Slicer specific commit disabling the failing color transfer
       function improvements and include the fix done by Cory.

   (2) re-enable GPU volume rendering on MacOSX fixing a rebase mistake
       introduced in r24461 (ENH: Update VTK to master (soon to be v6.3.0) and also update CTK)


// --------------
$ git log --no-merges d645b35..716b0f5
commit 716b0f56fc4bd4b9fcca05f386ec375bcd674122
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Tue Aug 4 17:49:39 2015 -0400

    Fix error preventing GPU volume rendering from working on MacOSX

    This commit fixes error introduced when rebasing commit Slicer/VTK@add058e
    (Enable GPU Raycast volume mapper for recent NVIDIA drivers on Mac OS X)

commit 74733a0e7d5dd55f5eb52ca411c06ecbb3431ed2
Author: Cory Quammen <cory.quammen@kitware.com>
Date:   Thu Jul 23 22:45:26 2015 -0400

    Fix crash where vtkColorTransferFunction has 0 nodes

    Thanks to Jean-Christophe Fillion-Robin for pointing this out.

    See

    https://github.com/Slicer/Slicer/commit/f59a689a0f6d2912538ed72dad16efc70601f0ed#commitcomment-9407867

    for reference.

    A basic test for vtkColorTransferFunction is added that crashes
    prior to this patch and succeeds with this patch.

    Tested-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

commit 7b51a097aead0c872f199a2039d010f28c96e2f5
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Tue Aug 4 15:08:41 2015 -0400

    Re-enable "6657: Add out-of-range colors to color maps"

    This reverts commit Slicer/VTK@d645b35.

    Thanks: Cory Quammen <cory.quammen@kitware.com>
// --------------

Revision 24483  Directory Listing
Modified Tue Aug 4 03:52:36 2015 UTC (2 years, 1 month ago) by fedorov
BUG: fix support for DCMTK DICOM dictionaries

See issue 4013, followup on commit 24473. Dictionaries passed to DCMTK in
DCMDICPATH override embedded dictionaries, and standard dictionary needs to be
specified together with the private one, as shown in example here:

http://support.dcmtk.org/redmine/projects/dcmtk/wiki/Howto_Dictionaries

This commit installs dicom.dic and initializes the environment variable.

Revision 24478  Directory Listing
Modified Tue Aug 4 02:41:52 2015 UTC (2 years, 1 month ago) by jcfr
COMP: Add support for OpenSSL when compiling with Visual Studio 2013

The OpenSSL packages available on packages.kitware.com are
compiled using the following script:

  https://gist.github.com/jcfr/6030240

From: Max Smolens <max.smolens@kitware.com>

Revision 24473  Directory Listing
Modified Wed Jul 29 23:44:26 2015 UTC (2 years, 1 month ago) by jcfr
ENH: Add support for DCMTK private dictionary

See issue 4013 and related discussion here:

  http://slicer-devel.65872.n3.nabble.com/Enabling-support-for-DCMTK-private-dictionary-td4034305.html

This change implements the following changes:

 (1) install private.dic of DCMTK in a runtime location

 (2) update launcher setting to set DCMDICTPATH environment
     variable

 (3) on MacOSX, update application to ensure DCMDICTPATH is set when
     Slicer is started using Slicer.app bundle (in that case no launcher
     is used)

This will allow for more robust interpretation of DICOM private tags
based on the information contained in the DCMTK private dictionary.

Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

Revision 24472  Directory Listing
Modified Wed Jul 29 01:44:21 2015 UTC (2 years, 1 month ago) by jcfr
BUG: Fix VTK library path configured into build tree launcher setting on unix

Thanks: Francois Budin <fbudin@email.unc.edu>

Revision 24468  Directory Listing
Modified Fri Jul 24 23:25:16 2015 UTC (2 years, 2 months ago) by jcfr
BUG: Ensure only one version of itcl library is built and packaged

Following the update of the tcl version in r23613 (COMP: Update version
of tcl/tk/incrTcl used on Linux/MacOSX. Issue #3809), it turns out that
the associated source package contains the source of itcl 4.0.0.

Since the external project External_incrTcl also install the version 4.0.1,
duplicate version are built.

This commit explicitly disables all packages available in the source
archive of tcl by deleting the "pkgs" directory. (see below of a complete
list).

The list of disabled packages:
  sqlite3.8.0
  tdbcmysql1.0.0
  tdbcpostgres1.0.0
  thread2.7.0
  itcl4.0.0
  tdbc1.0.0
  tdbcodbc1.0.0
  tdbcsqlite3-1.0.0

Revision 24461  Directory Listing
Modified Fri Jul 24 23:25:05 2015 UTC (2 years, 2 months ago) by jcfr
ENH: Update VTK to master (soon to be v6.3.0) and also update CTK

CTK updates:

$ git shortlog 7bb708c..7081550 --no-merges
Jean-Christophe Fillion-Robin (2):
      Fix link error when linking against VTK build with KITS enabled.
      Tweak logic specifying libraries to link against VisualizationVTKCore

Rostislav Khlebnikov (1):
      DEBUG variable renamed to DEBUG_FLAG

VTK Updates:

$git shortlog 4b46455..d645b35 --no-merges
Aashish Chaudhary (41):
      Maximize or minimize each component for independent components
      Fixed additive blending for independent components
      Added initial support for 2 and 3 components
      Fixed style
      Fixed bad switch case
      Compute the range correctly when dealing with 2-3 components
      Keep the comments in the final shader string
      Added support for dependent components
      Match tokens with method names
      Fixing shader for 2 & 3 component
      Fixed dependent component test failing
      Fix GL extensions not reported on Mac OpenGL2 context
      Reset active texture to texture 0
      Saving and restoring GL state
      Fixed comment
      Clamp texture unit to 0 and GL_MAX_TEXTURE_IMAGE_UNITS
      Fixed accessing invalid texture unit manager
      Using a consistent style within a method
      Compute light position only once
      Optimize lighting code some more
      Reset number of lights
      Some more optimizations for better performance
      Respect interpolation type set on volume property
      Fixed invalid variable names used for gradient computation
      Fixed check on interpolation type
      Updated default interpolation type for test
      Fixed style
      Added check on when to update volume parameters
      Do not update light parameters if shading is OFF
      Fixed compiler warning
      Some more optimizations
      Do not compute color if opacity is zero
      Updated code to new computeColor signature
      Avoid computation of fragment world position repeatedly
      Fixed failing VTK tests
      Removed debug message
      Fixed issues with interactive volume rendering
      Fixed styles and added notes
      Fixed ReductionFactor not initialized that was causing tests to hangup
      Added alternate baseline with jitter for GL2
      Updated test to new ivar to turn off auto adjust sample distance

Andras Lasso (1):
      BUG: Fixed vtkImageReslice HitInputExtent update

Andrew Bauer (6):
      Fix for bad cached cell id for flow path filters.
      Particle path fixes.
      Getting rid of unused variable warning in release builds.
      Fixed memory issue and reinject frequency counter.
      Adding in piece information for XMLPMultiBlockDataWriter.
      Fix issue if there aren't any blocks.

Andrew Maclean (20):
      Remove the unnecessary find_package command.
      Visual Studio 2013 requires the <algorithm> header.
      Visual Studio 2013 requires the <algorithm> header.
      A minor fix eliminating a CMP0043 warning.
      Added TestEmptyInput.py
      Refactoring TestEmptyInput.py
      Convert TestSetGet from TCL to Python.
      Added a new class to exclude.
      Missing comma.
      Adding another class to exclude in an attempt to fix release mode on OSX.
      Removing two classes in LinuxExceptions.
      Adding back some classes to the exception list.
      Test - see if vtkView as a friend is causing failures.
      Reverting
      Reverting
      A patch from Utkarsh
      These scripts only run using Python 2.6 or greater.
      Display information about the VTK test folders.
      Converted more Tcl scripts to Python.
      BUG: This import is unnecessary.

Arnaud Gelas (1):
      Fix typo in FindTBB.cmake which makes it impossible to use TBB on MacOSX

Ben Boeckel (38):
      windows: compile the vtkpython.rc file separately
      vtkpython: avoid vtkpythonrc hack in Visual Studio
      docs: add buildbot information
      docs: buildbot label is no more
      python: silence warnings about round redefinition
      vtkMPICommunicator: check for 2.0
      java: remove screamake and quote paths
      java: refactor out writing paths to the file
      java: quote arguments
      java: add missing java files
      python: add the generated files to the list as well
      freetype: update baselines to support freetype 2.5.3
      testing: set PROCESSORS property for MPI tests
      FindJsonCpp: add version detection
      ThirdParty: add minimum version support
      jsoncpp: mark that 0.7.0 is the minimum version
      vtkFFMPEGWriter: conditionalize a GCC pragma
      FindJsonCpp: fix typo in regex
      JsonCpp: the VERSION_VAR is a separate signature
      QVTKWidget2: call the direct parent class
      QVTKWidget2: use Superclass typedef internally
      doxygen: generate SVG images
      vtkRAdapter: move R_NO_REMAP to the header
      mpi4py: strip trailing whitespace from the include dir
      typos: fix 'writting' -> 'writing'
      vtkWin32ProcessOutputWindow: fix string literal
      vtkXMLUnstructuredDataWriter: also check for string output
      qtgraphicsview: remove unused vtkgl.h includes
      vtkGenericOpenGLRenderWindow: add PushState/PopState methods
      QVTKGraphicsItem: support the OpenGL2 backend
      vtkOpenGLRenderUtilities: move Render{Quad,Triangle}
      IOXML: add test for outputting to a string
      modules: use the export name for the file
      Testing: fix unused variable warnings
      FiltersStatisticsGnuR: fix R_NO_REMAP juggling
      FiltersStatisticsGnuR: fix warnings in tests
      semanticDiffVersion: use the returncode
      python: split wrapping functions

Berk Geveci (14):
      Fixed issue with vtkPointSet::FindCell().
      Impoved check for ascii file in PLOT3D reader.
      Fixed compiler warning
      Initial point data support in AMR base reader
      Added point array support to vtkAMRBaseReader
      Moved Plot3D reader to IO/Parallel.
      Making the Plot3D reader parallel.
      Improved ghost array generation.
      Do not rexecute based on ghosts for serial execution
      Do not override DATA_NUMBER_OF_GHOST_LEVELS() unnecesarily.
      Cleaned up error handling in plot3d reader.
      Fixed warnings.
      BUG: Was using the wrong extent in computation.
      Fixed bug with loading 2D or ASCII datasets in parallel.

Bill Hoffman (1):
      Use Qt5 COMPNENTS in find_package instead of finding each package directly.

Bill Lorensen (18):
      COMP: Member template function use on Mac
      COMP: Member template function use on Mac
      ENH: Modernize RIBExporter and RIBProperty
      COMP: Memory leak in new test
      ENH: define VTK_MAXPATH
      COMP: Typo causes compile error
      COMP: Memory leak in vtkOBJImporter
      STYLE: OBJImporter style
      COMP: Adjust fuzzy compare tolerance
      COMP: Adjust fuzzy compare tolerance for scalar divide
      BUG: PentagonalPrism bug
      COMP: TestPentagonalPrism mempry leak
      ENH: Unit Test for Linear, Quadratic and BiQuadratic Cells
      ENH: Remove unused tcl tests
      ENH: Restore Common/DataModel Cxx tests
      BUG: Missing data file
      ENH: Removed unused vtkExplicitCell
      ENH: Remote module capability

Brad King (45):
      setup-stage: Optionally reconfigure topic stage
      setup-gerrit: Allow ssh-only repo URLs
      setup-stage: Allow 'url' without 'pushurl'
      Tell Git how to check GitSetup config files
      Add 'git-gerrit-push' script
      setup-hooks: Create .git hooks directory if necessary
      Avoid bash history expansion in developer setup scripts
      ExternalData: Allow local stores without any URL templates
      ExternalData: Add support for custom download scripts
      ExternalData: Add support for custom algorithm-to-URL mapping
      ExternalData: Update documentation to match CMake copy
      git-gerrit-push: Refine topic name validation
      git-gerrit-push: Append topic to refspecs instead of overwriting
      git-gerrit-push: Avoid bash history expansion
      git-gerrit-push: Fetch 'master' before checking refspecs
      Add 'setup-upstream' script to help users configure preferred upstream
      Add 'setup-gitlab' script to configure GitLab access
      Add 'git-gitlab-push' script to help users push to their GitLab fork
      git-gitlab-push: Print follow-up instructions and links for user
      git-gitlab-push: Keep user fork 'master' up to date if possible
      git-gitlab-push: Document options on multiple lines in usage
      git-gitlab-push: Require a '--force' option to force-push the topic
      Teach our 'git-gitlab-push' script to push ExternalData content
      Drop mention of Gerrit from instructions in third-party README files
      Disable gerrit-push and stage aliases
      Switch developer setup to use the GitLab workflow
      Tell Git how to check Markdown (.md) source files
      Documentation: Add VTK Git instructions
      CONTRIBUTING: Update for GitLab workflow
      README.md: Add document introducing VTK and linking to resources
      README.html: Remove out-dated document
      Documentation: Revise Merge Request creation instructions
      Documentation: Add links to GitLab markdown documentation
      Documentation: Revise Git development docs to mention fork step
      setup-upstream: Tolerate lack of existing upstream pushurl
      Report developer setup-upstream failure explicitly
      CONTRIBUTING: Restore link to dev/git/README.md document
      Documentation: Explain how to keep a GitLab fork `master` in sync
      Documentation: Explain to reviewers how to fetch Merge Request changes
      Fix 'git-gitlab-push' ExternalData push for duplicate objects
      Documentation: Update required Git version to 1.7.2
      Documentation: Define reviewer vote shortcuts and meanings
      KWSys: Tell Git not to export .gitattributes
      Add vtkPeriodicDataArray to list of sources in its module
      vtkhdf5: Suppress VS 2015 assertion failure popup during try_run

Burlen Loring (1):
      buffering issue in vtkweb

Chris Harris (3):
      Wait for resize notification in SetSize(...)
      Revert "Wait for resize notification in SetSize(...)"
      vtkWeb: Ensure that we get the image size requested

Chuck Atkins (1):
      ADIOS: Remove block-index calculations to use new APIs

Cory Quammen (14):
      Added vtkPolyLineSource
      Added vtkPolyLineRepresentation and vtkPolyLineWidget
      Added base class for representations of curves
      Tests for vtkPolyLine{Widget,Source,Representation}
      Added checking for NULL pointer in a few locations
      BUG 15365: Fixed crash in function called from multiple threads
      BUG: Fixed error in area-weighted normal
      Initialized all member variables in vtkCurveRepresentation
      Various fixes for vtkPolyLine{Source,Representation}
      Initialized test values
      BUG: added output points precision for structured grids
      Added test for vtkDataSetSurfaceFilter
      BUG: Direct scalar coloring with string arrays caused crash
      Move table resizing out of core mapping routine

Dan Lipsa (42):
      Solve warnings on the ICC compiler.
      Redesign "vtkGhostLevels" arrays and related ghost functionalties.
      Fix warnings.
      Solve windows warnings.
      Remove warning when a array name for labeling is not found.
      Use previous version for XML files if there is no vtkGhostType array.
      BUG #15199: EnSightReader does not crash if you change CaseFileName
      VTK XML files are saved using previous version if possible.
      Update documentation for save VTK XML using previous version.
      BUG: Fix valgrind complaint about uninitialised values.
      BUG: Blanked cell is marked as a blanked point.
      ENH: Remove legacy code from before vtk-6.1 (2014-01-21)
      ENH: Add GatherV for vtkDataObjects
      BUG: Mismatch between # of points and # of tcoords results in segfault
      BUG: XMLMultiBlockDataWriter always pointed to vtp files.
      BUG: Add additional baselines to deal # of digits in exponent.
      BUG: Fix uninitialized values that caused segfault.
      BUG: Skiped a number when adding a baseline.
      BUG: Skipped a number when adding a baseline.
      BUG: Test passed because two wrongs made it right.
      ENH: Ghost changes documentation update.
      BUG: Fix initialization and typo problems.
      BUG: Enable vtkFiltersSourcesPython-squadViewer only if Module_vtkRenderingTk
      BUG: vtkTestingInteractor cannot create timers which results in errors.
      BUG: Fix link warnings for static build on windows.
      BUG: Teach ImageSlice and ImageSliceMapper to deal with empty slices
      BUG: InteractorEventRecorder bug results warning about passive observer.
      BUG: Fix test volume of interest to match data extents
      ENH: TestChangeInformation does not print error message.
      BUG: Fix warning 'Resetting view-up since view plane normal is parallel'
      BUG: Fix warning 'Resetting view-up since view plane normal is parallel'
      BUG: This fixes a valgrind complaint.
      BUG: We need a Renderer for HasTranslucentPolygonalGeometry
      BUG: Fix version for ghost documentation.
      BUG: Get rid of error printouts from TestRIBExporter
      BUG: Replace deprecated functions.
      BUG: vtkProbeFilter stored state which did not work for multi-block data.
      BUG: Initialize grids before adding them to the AMR dataset.
      BUG: Test basic representation after you setup the object
      ENH: CanReadFile does not fail for newer file version.
      ENH: Move test that discovers inconsistent structured grids in an AMR grid.
      BUG: Fix uninitialized value.

Dave DeMarle (3):
      Increment version to VTK 6.3.0
      fix no newline comp warning
      expose texture so manta can intercept

David C. Lonie (59):
      Enable freetype tests when matplotlib is not found.
      Use a default text property in the labeled contour mapper.
      Don't use offscreen FBOs when multisampling is requested.
      Disable multisampling in the OSCone test.
      Enable MPL tests only if the vtk module is enabled.
      Allow vtkTextActor* to handle empty inputs.
      Account for actor matrix in vtkLabeledContourMapper.
      Add a debug-only yellow dot at the text alignment point.
      Ensure that the background is rendered behind the text.
      Improve appearance of small-sized mathtext.
      Add missing ReleaseGraphicsResources implementation.
      Move test file (s/cpp/cxx)
      Remove unimplemented private method.
      Fix transformed contour label placement on OpenGL backend.
      Fix kerning on rotated fonts.
      Update sources in chart symbol glyphs.
      Add missing ReleaseGraphicsResources implementation.
      Release actor resources in vtkLegendScaleActor.
      Use vtkTextRenderer in the default label render strategy.
      Do not set vtkProperties on vtkTextMappers.
      Fix vtkBiDimensionalRepresentation2D to work with new text mapper.
      Use string width, not length, to determine longest labels.
      Remove tcl [info command "rtExMath"] check from test.
      Print image name on test failure.
      Update vtkTextMapper's alignment to match current conventions.
      Align to a fixed-height font bbox, rather than a "tight" one.
      Remove the RenderingFreeTypeOpenGL module.
      Exercise the new default vtkTextMapper implementation.
      Update baselines.
      Add new baselines for dash3's continuous build.
      Number baselines consecutively.
      Baselines from nightlies.
      Fix typo/platform issues in GLUT test.
      Call glewInit() from test to setup GL function pointers.
      Move PreserveColorBuffer to vtkRenderer.
      Fix glut header in test.
      Fix variable type.
      Allow an explicit mapping between tprops and scalars for contour labels.
      Update make_pair call to work with newer MSVC.
      Clean up Rendering/OpenGL2/vtkGenericOpenGLRenWin.
      Remind MSVC that NULL is a pointer. Fix tclPrintOtherTest.
      Change comment text to use a gentler tone.
      Release shaders after rendering is complete.
      Define missing typedefs.
      Fix typo.
      Add vtkWindow::DetectDPI.
      Add DPI awareness to text rendering.
      Apply kerning to bounding box calculations.
      Don't glyph hidden points in vtkGlyph2D.
      Mark ticks as dirty when enabling/disabling log scale.
      Performance cleanup.
      Account for TileScale in RenderWindowToImage filter.
      Fix vtkAxis scaling when TileScale is set on the renwin.
      Defer matplotlib initialization for text rendering.
      Update Get macro for paraview parsers.
      Use max(tdx, tdy) to determine string bound scaling...
      Add a warning if there is not a scene set on the vtkAxis instance.
      Ensure that input data is synced.
      Make ScalarBarRepresentation orientation set-able.

David E DeMarle (1):
      Fix depth peeling with antialiasing

David Gobbi (22):
      BUG 15358: Remove inappropriate cast from pointer to long.
      Add the vtkBoundingBox type to the Python wrappers.
      Fix Java build, different extensions for file properties.
      Allow wrappers to properly support "using" methods.
      Apply using declarations that hadn't been "used".
      Add missing hints for color conversion methods.
      Add virtual data method CopyInformationToPipeline.
      Fix vtkParseMerge uninitialized variable warnings.
      Allow TestEmptyInput to work with python 2.5.
      Fix a null deref when wrapping "using" declarations.
      Enable the "using" declaration in vtkTypedArray.h.
      Fix nifti sform, qform when qfac=-1.
      Fix uninitiazed array warning in vtkBSPlineInterpolator.
      Put back some Visual Studio 2003 compatibility code.
      Temporary wrapper fix, pointers to vtkSmartPointer.
      Code style fixes.
      Allow NIFTI reader and writer to handle planar RGB files.
      Close the DICOM file immediately after reading it.
      Fix blank slices that appear in some TIFF volumes.
      Replace the O(n^2) median algorithm with an O(n) one.
      Fix the median computation in vtkImageMedian3D.
      Fix normal computation in vtkContourTriangulator.

Ethan Brodsky (4):
      ENH: Added edge annotations to vtkCornerAnnotation
      CMP: Eliminated warnings relating to for loop iterator scoping
      BUG: Updated test baseline output for edge annotation
      ENH: Modified vtkCornerAnnotation testing to improve code coverage

Isaiah Norton (1):
      Visual Studio 2013 requires the <algorithm> header.

Jean-Christophe Fillion-Robin (15):
      Maintenance: 'main' function in WhatModulesVTK can now be re-used
      Maintenance: Update WhatModulesVTK to support rendering backend
      Do not force manifest selection for vtkhdf5 libraries
      modules: Re-order RenderingOpenGL libraries to fix VTK_ENABLE_KIT link error
      python: Add wrapping of kits if VTK_ENABLE_KITS is ON
      python: Update python module dependency to account for VTK_ENABLE_KITS
      python: Configure PythonInit file for kit when VTK_ENABLE_KITS is ON
      python: Update wrapping function to support kit
      python: Add VTK_ENABLE_KITS to VTKConfig
      python: Update wrapping tool to support multiple hierarchy files
      python: Do not create a new hints file if a kit bundles only one module
      python: Update vtkWrapPython to add mutable object when building kit
      Disable Chemistry module to workaround issue #15255
      KWSys-SystemTools: Fix memory leak in DetectFileType
      Revert "6657: Add out-of-range colors to color maps"

Joachim Pouderoux (9):
      Bug #0015217: Fix tet aspect ratio computation.
      Fix filter crash when input data is not temporal
      Add more support of Quadratic Polygon cells.
      Fix TessellatorFilter so it does not crash with quadratic polygon cells.
      Enhance and optimize Xdmf2 reader and writer to support static meshes.
      code cleaning
      Fix error with java wrapping
      fix header test
      Add test and fix reader

John Tourtellott (6):
      Apply WRAP_EXCLUDE to the vtkGDAL not vtkGDAL.h
      Add return value to vtkPythonInterpreter::RunSimpleString()
      Add field data to vtkUniformGrid to save GDALDataset NoDataValue
      Fix indentation and restore empty line
      Move variable declaration inside loop to limit its scope
      Change iterator from postincrement to preincrement

Julien Finet (13):
      Kill TDX timer when using no WindowHandle
      Add TDX_INCLUDE_DIR CMake variable
      Add multitouch support to QVTKWidget and QVTKWidget2
      Add support for drawing multiple line segments
      Add vtkPlot::Selectable
      Add vtkPlotBag::BagVisible
      Fix crash in vtkPlotHistogram2D
      Exposes vtkHighestDensityRegionStatistics::ComputeHDR() to the public API
      Fix unsorted range error in vtkChartSelectionHelper::BuildSelection
      Fix compilation by adding DrawLines() to OpenGL context devices
      Fix unsafe mix of bool and int types
      Enable GPU Raycast volume mapper for recent NVIDIA drivers on Mac OS X
      GPU raycast volume rendering now supports textures larger than 1024

Julien Jomier (1):
      BUG: Internal title box should be initialized

KWSys Robot (3):
      KWSys 2015-04-16 (1ea01a46)
      KWSys 2015-04-19 (4f39791b)
      KWSys 2015-05-12 (b1d560a0)

Karsten Tausche (3):
      fix copied noise extent in vtkImageDataLIC2D
      fix memory leak in vtkImageDataLIC2D
      Remove vtkFreeTypeUtilities.h from vtkScalarBarActorInternal.h

Ken Martin (135):
      Fix a couple issues
      Fix a regression and new failing test
      Fix interactions of depth peeling with the point gaussian mapper.
      Fix a case where glyphic was failing on unlit primitives
      A couple depth peeling fixes
      A number of transparency related issues fixed
      Forgot to comment out debug statement
      Fix for the case when there is nothing to draw
      Rename class back to the old name for better compatability
      Add in support for below and above range LUTs
      Remove power of two requirement from image slice mapper
      Remove window size change
      Add back in LIC for OpenGL2
      Rebased and merged due to conflicts
      Fix a compiler warning
      Some lic cleanup for ES 2 and ES 3
      A few dashboard fixes as described below
      Fix a few issues with ImageDataLIC2D
      A few more VR fixes I missed the first time
      Fix PV text composite with cell data issues
      Fix issues with composite dataset luts issues
      Fixes for composite id when selecting on OpenGL2
      Fix failing test and add new convenience func
      Add a valid image and a slight change to generated normals
      Convert Context2D to use more modern OpenGL
      I should learn to test on intel too before committing
      Some fixes for bigmac
      Fix for draw pixels shows up in PV rubberband selection
      Add some debugging code
      Minor compile fix for GL ES 20
      Fix bad destructor
      redo how cell data is handled and picking
      Add support for picking indirection arrays
      Managed to get scale and bias for voluem rendering working
      Make VTK work with OpenGL 3.2 Core
      Make X windows default to a 3.2 context
      Convert Cocoa to default to OpenGL 3.2
      Some more fixes for apple to make VTK more 3.2 core compliant
      Even more OSX 3.2 changes
      More 3.2 OpenGL fixes
      Minor compiler warning fix
      Minor change to pass line width calls through
      Added valid images for cases where line width is over 1.0
      Add missing ReleasGraphicsResources call
      Some exit cleanup fixes for debug mesa
      redo how cell data is handled and picking
      Add support for picking indirection arrays
      Convert Cocoa to default to OpenGL 3.2
      Even more OSX 3.2 changes
      Minor compiler warning fix
      Add missing releasegraphicsresources
      Rebasing from master
      Fix compile error
      Make sure GL_R32F is available on old 2.1 context
      Fix for apple
      Some fixes for mesa master runs
      Fix some compiler warnings
      Some compile fixes for OpenGLES
      Fix a few issues exposed by PV testing
      Fix two compiler warnings.
      A couple more picking fixes these related to processor id
      Better Tk support for OpenGL2
      Instanced arrays require OpenGL 3.3 not 3.2
      Remove old style rendering check
      Fix for cell normals to use RGBA32F textures
      Renamed XOpenGLRenderWindowInteractor back to original name
      Added valid image for Sphere widget
      Fix for independent components on mesa
      Pare down the test to be about 40% faster
      Some X window fixes and make two slow tests faster
      Update the alternate image as well
      Fix apple ifdef
      Fix for some systems
      Type fix
      Some fixes for checking framebuffer depths
      New valid image due to line widths
      Tiny fix for OpenGL ES 3
      And whoa I committed a png undo that
      Add method for external codes
      Support use of FieldDataTupleId in scalar coloring opengl2
      Add a geometry shader and some cleanup and fixes
      Do not use GeometryShaders on ES
      Test out ogl2 as the default for buildbot systems
      More fixes based on test dashboard
      Fix a couple more issues
      Duh fix bas cmake code
      Always use our glew
      Update to backend logic
      Fix check for multisample support
      Newer logic so apps can set a default rendering backend
      Set default back to OpenGL1 for commit
      Clenup some OpenGL2 code
      More cleanups
      Rebased to master
      Maybe fix memory leak
      Fix a compiler issue with PV
      Fix for compile issue on OpenGLES
      Test fix for applie AMD primitiveID bug
      Better warning message
      Add support for 2D
      Another apple fix
      Fix memory leak
      Another compiler fix
      Another fix due to multiple VBOs
      Make the VAO code bind the bufferobject
      Remove reference to old header file
      Trying something
      Sticking with basic approach
      Fix an atom rendering performance regression
      Remove a leftover test setting
      Some more code cleanups, this time shader related
      Remove some unused ivars
      Add ability for PointGaussianMapper to also just draw points
      Fix test that was creating an ill defined camera
      Update test to have more debugging
      Support wide lines in the polydata mappers on 3.2
      Fix prim id issue on mac
      More cleanup and fixes for 2D this time
      Fixes for failing tests
      Fix issue on Apple
      A couple minor fixes that PV exposed
      More minor fixes
      Some fixes for PV ColorOpacityTableEditing
      Make sure PV texture fix hits the other use cases
      Fix for clear depth call on es
      Thick lines only use a GS when the hardware lacks support
      Fix compiler issue on gcc
      Update to fix failing tests
      Better handling of thick lines in a couple places
      Fix some recent compile issues
      Some compiler fixes for Android
      Fix missing header
      Fix issue with compositepolydatamapper2 with scalar colors
      Add valid image for non AA systems
      Apply fix to the generic version as well.

Lin Ma (6):
      Tested merge
      Added vector for memoizing
      Modified vtkMath::Factorial
      Recursive stored intermediate results
      Fixed bugs
      Changed map to vector

Marcus D. Hanwell (4):
      Added support for writing TIFF volume stacks
      Fix compiler warning - unsigned int -> int
      Removed unused sstream include, add Windows logic
      Fix bug with bad TIFF tag on char/short format

Mathieu Westphal (20):
      Reimplementing AppendData using vtkDataArrayIteratorMacro and std::copy
      Adding surface streamlines
      VTK Style
      Adding Angular Periodic Filter and Angular Periodic Array to VTK.
      Correcting multiple bugs with periodic data array
      AngularPeriodicDataArray : Use of sin instead of sinf
      Correcting bugs in vtkCell implementation
      Correcting pcoords in vtkTriangle
      Add a degenerate Triangle test in IntersectWithLine
      Correcting degenerate triangle
      Missing initialization of a member
      Fixing coincident point in stream tracer output
      Correcting a warning in vtkLargeInteger
      Adding another image for test
      Checking for Null vtkPoints in Angular Periodic Filter
      Fixing 14897 mantis bug, adding VTKTargets.cmake in install
      fixup python testing
      Deprecating FrontBuffer member and double passing tests if necesssary
      First bug fix fro periodic filter
      Fixing parallel periodic filter

MetaIO developers (1):
      MetaIO 2015-03-18 (ebdd30dd)

Nathan Fabian (6):
      Fixed possible nulls when FieldData are string arrays.
      Detect when we're writing sets and don't write them as blocks.
      NodeSets finally write out.
      Side sets now write out correctly.
      Replaced the missing const
      Replaces iterator pointers with SmartPointers to avoid possible leaks.

Robert Maynard (7):
      FindTBB: Updated implementation to version proposed for CMake.
      Get SynchronizedTemplates3D to work with more than 4GB.
      Get ThreadedSynchronizedTemplates3D to work with more than 4GB.
      CONTRIBUTING: Add an overview of the development process
      You can't close a null tiff pointer.
      Mark the entire Accelerators Piston module as legacy as of 6.3
      Mark the entire Accelerators Dax module as legacy as of 6.3

Rolf Eike Beer (2):
      ExternalData: Replace MATCHES with STREQUAL where possible
      ExternalData: Clean up duplicate regex matches with CMAKE_MATCH_<n>

Sankhesh Jhaveri (69):
      Clipping test with oblique clipping planes
      Explicitly set sample distance for timing test
      Make sure most voxels are rendered for timing test
      Make the AMR Volume mapper available for GL2 backend
      Added test with shading
      Fix volume cropping issue
      Circumvent crash in volume mapper when context changes
      Added test for change related to releasing resources
      Added ivar for ContextChanged
      Laxed restrictions on input data required by OpenGL2 volume mapper
      GPU volume mapper test for two independent components
      Added interaction and baseline to the two independent components test
      Fix error in OpenGL2 volume mapper for multiple components
      Test for GPU volume mapper with three independent component scalar data
      Test for two dependent component scalar data
      Modify test for three components
      Fix two dependent components case for volume mapper
      Reset scale and bias after loading volume
      Take per component range for setting default transfer functions
      Use the appropriate components for transfer functions
      Fix crash due to wrong index fetching of tables
      Use the right component for opacity functions
      Added baselines for new tests
      New baseline for the independent components MinIP test
      Fix lights issue in external render environments
      Set spot parameters on the newly created lights
      Changed GLUT test to remove VTK lights
      Added ability to automatically resize external window
      Account for window position when drawing in external context
      Fix lighting for external rendering environments
      Update the GLUT test baseline
      Added Generic OpenGL RenderWindow to OpenGL2 pipeline
      Enable OpenGL2 support for vtkRenderingExternal module
      Provide extension manager support to external rendering module
      Removed redundant tests and fixed crop test
      Streamlined testing without VolumeOpenGLNew tests
      Remove trailing references to VolumeOpenGLNew
      Remove module VolumeOpenGLNew
      Remove context caching from the volume mapper
      Remove unused variable warning
      Add API for auto-adjust sample distances to smart volume mapper
      Add convenience API to smart volume mapper
      Fix data trunctation issues with 32 bit int types
      Enforcing GPU breaks old mapper compatibility for test
      Fix AMR volume mapper for recent smartvolume mapper changes
      Remove debug print messages
      PrintSelf newly added variable
      Add new external light object
      Ability to modify externally created lights in the external renderer
      Modify existing lights each render call
      Documentation changes
      Change default for vtkExternalLight
      Performance optimization in external renderer
      Fix external window stereo mode position for OpenGL2 backend
      Fix near plane offset clipping when camera inside
      New test for camera inside volume calculations
      Added camera inside test for small spacing
      Update comment to reflect documentation
      Add resolution specification capability to circle glyphs
      Add test for glyph 2D circle resolution
      Fix test failure due to vtkMath::Random
      Fix constant array size issue
      Fix crash due to un-set point ID
      Fix compile error when compiling vtkRenderingExternal
      Added test for GPU volume mapper jagged edges issue
      Restore concept of InteractiveUpdateRate for vtkSmartVolumeMapper
      Compute initial sample distance based on dataset spacing
      Interactively adjust sample distance for vtkSmartVolumeMapper
      Improve documentation of new variable in vtkSmartVolumeMapper

Scott Wittenburg (8):
      Support pvweb color editor widget and use of local storage by apps.
      Add a completely standalone tool for generating color swatch images.
      Support retrieving geometry for all timesteps in paraviewweb.
      Change framerate stats to show two decimals places.  Fix stat table.
      Update autobahn client/server as well as vtkweb connect for longpoll.
      Allow clients to know when a render occurred that was not stale.
      Fix how we import our argparse fallback implementation.
      Add synchronous methods to Base64-encode image data as png or jpg.

Sean McBride (88):
      Unified mixed unsigned char/int usage to bool
      Unconfused cppcheck by removing unneeded null check
      Moved dereference to after null check
      Fixed typo: - should be ->
      Fixed || that should be &&
      Fixed contradictory ‘if’ statements
      Fix division by zero cppcheck warnings
      Fix clang warnings about implicit float->bool
      Add asserts to silence clang analyzer warning
      Return upon error, otherwise invalid file reference is used
      Fixed memory leaks found by cppcheck
      Fix incorrectStringCompare cppcheck warning
      Fixed cppcheck signConversion warning
      Made various float to bool conversions explicit
      Removed unneeded casting
      Fixed stack allocation to be properly aligned
      Replace size() with empty()
      Copy-paste error, duplicate ORing
      Add parens for less ambiguity, fix cppcheck warning
      Refactor & simplify to avoid cppcheck false positive
      Reverse order of AND statements
      Removed simple dead stores/statements found by cppcheck
      Refactor old school alignment test to use offsetof()
      Remove the addition of a few inappropriate vtkErrorMacro
      Fix more include guards to not start with __vtk
      Removed dead code found by cppcheck
      Removed unneeded c_str() usage
      Silence clang analyzer warning
      Fixed minor format string mismatch
      Fixed possible array overrun found by cppcheck
      Move index ‘i’ check after usage
      Removed _probably_ dead code
      Reformulate assert to pacify cppcheck
      Fix null deref, likely due to && vs || typo
      Fixed cppcheck warning about all-const params to strncmp
      Check ResizeAndExtend error result and bail
      Fixed division by zero found by cppcheck
      Merged private function into destructor
      Removed code dead since 2001.
      Removed code dead since 2003.
      Removed code dead since 2001.
      Removed code dead since 2010.
      Removed code dead since 2006.
      Added static to many private globals
      Fixed -Wformat-pedantic warnings
      Removed dead code
      Fixed all -Wswitch-enum warnings
      Revert warning fix that caused another warning
      Fixed mismatch between ivars and get/set macros
      Changed many int to vtkIdType
      Fixed implicit float/double to bool conversion
      Added explicit casts to fix Wconversion warnings
      Fixed memory leak in Cocoa code (regression)
      Fixed dead code warning on OS X
      Fixed unused parameter warning
      Fixed warning caused by warning fixes from other branch
      Fixed compiler error with div() introduced with Wconversion fixes
      Changed vtkWriter::Write()'s return value
      Fixed illegal left shift of negative number
      Fixed some warnings from PGI compiler dashboard
      Fixed blunder in merge request #51
      Added missing #include, causing some bots to not build
      Fixed -Wextra-semi warnings within VTK macros
      Fixed -Wextra-semi warnings in ThirdParty/alglib
      Fixed -Wextra-semi warnings in ThirdParty/ftgl
      Fixed -Wextra-semi warnings in ThirdParty/utf8
      Fix -Wimplicit-fallthrough warnings; introduce VTK_FALLTHROUGH
      Modernized Cocoa code to use NSTrackingArea
      Removed many unneeded null checks before delete
      Changed placeholder value from 0.0 to 1.0, fixing undefined behaviour
      Disambiguated use of term “kilobyte”
      Fix possible null deref by bailing early
      Workaround cppcheck warning by refactoring loop
      Removed dead store found by cppcheck
      Fix warning about identical comparisons
      Avoid cppcheck division by 0 warning
      Fixed null deref found by cppcheck
      Fixed division by zero
      Fixed STLReader regression vs VTK 5.10.1
      Fixed mismatch array new/delete found by clang -Wmismatched-new-delete
      Removed branches for _MSC_VER <= 1400.
      Removed branches for gcc 4.0 and lower.
      Added #error for known old unsupported compilers
      Restored support for Apple gcc 4.2
      Hopefully suppress ‘used uninitialized’ warnings
      Replace VTKGL2 define with VTK_OPENGL2
      Fixed ‘no newline at end of file’ warnings
      Added VTK_FALLTHROUGH in case without break

Sebastien Jourdain (1):
      Allow GetTuple6 to be preperly Wrapped

Shawn Waldon (10):
      Handle datatypes other than single precision float
      Add overloads to parallel communication methods
      Update the documentation on data array subclasses
      Make java wrapping give files to javac via a response file
      Add higher timeouts for some long running tests
      Force tests to run in serial
      Remove "have tcoords" print statement
      Add a reader for the MRC image file format
      Add test for MRC reader
      Add test data

Steve Pieper (1):
      BUG: WIP: fix vtkPickingManager interaction with widgets

Steven Hahn (1):
      Change while loop condition for osx.

Sujin Philip (19):
      Fix for windows warning suppressions not working
      Fix SMP compile warning in VC++
      vtkThreadedSynchronizedTemplatesCutter3D
      Remove double underscores from header guard.
      Add support tbb in local build dirs, and from composer installs.
      Improvements to vtkAtomicInt
      Fixes for vtkAtomicInt issues from dashboard tests
      Improve OS X support in FindTBB
      Fix errors detected on Windows dashboards
      Fix usage of CriticalSectionGuard
      Change vtkAtomicInt to vtkAtomic
      Re-enable use of long for 64-bit vtkIdType
      Added Improved FindOpenMP module
      OpenMP backend for SMP
      Add vtkAtomic support headers to list of sources
      Fix testing of MTime in TestAtomic
      Fix cmake error when ${POLICY_VAR} is empty
      Fix "#pragma warning" warning in gcc
      Intel compiler 11.1 template typedef issue

Utkarsh Ayachit (36):
      Added fake-stereo mode.
      Modified Matrix when it changes.
      Make PushImageToScreen() virtual.
      Add test to demonstrate TIFF reader issue.
      Support random access in compressed tiff files.
      Remove invalid error message.
      Avoid modifying vtkAxis unless things changed.
      Adding area plot (vtkPlotArea).
      Fix leaks in vtkExtractArraysOverTime.
      Add alternative baseline for dashlin1.
      Add missing 'close' to vtkPythonStdStreamCaptureHelper.
      BUG #14721: Add support for quadratic pyramid for Exodus reader.
      Revert "FIX: We don't select 2D annotations."
      Overcome wrapping issue with client-server wrappings in ParaView.
      Fixed warnings.
      Extending API to get information about picked location.
      BUG #15438: Handle NaN when computing array range.
      BUG #0015512: Added ability to hide plots from the legend.
      BUG #15321: Fix mode_shape array.
      Remove vtkExodusIIReader::UpdateTimeInformation().
      Cleanup initialization of TimeStepRange/ModeShapeRange.
      Expose mode-shape-range meta-data to downstream filters.
      BUG #15155: Fix issues with temporal interpolator.
      Use AllGather instead of custom implementation of the same.
      BUG #15445: Handle empty input datasets in vtkDistributedDataFilter.
      BUG #14897: Fix periodic boundary issues with vtkNetCDFCAMReader.
      Avoid segfaults for multiblocks of vtkTable.
      Fixed invalid #ifs in vtkByteSwap.
      Make vtkMultiBlockPLOT3DReader factory overridable.
      Add vtkMPIMultiBlockPLOT3DReader -- MPI-IO enabled reader for Plot3D.
      Adding a basic test to test vtkMPIMultiBlockPLOT3DReader.
      Cleaning python testing macros.
      Win64 fixes for vtkMultiBlockPLOT3DReader.
      Fix typo in call to superclass method.
      Error checking: check status of collective call.
      Fix uninitialized memory reported by valgrind.

Vincent Chen (4):
      Fixing outptr traversal bug in vtkImageResize
      Modify Stencil Iterator to work under block mode.
      vtkVolumeRayCastSpaceLeapingImageFilter,
      vtkImageBlend row traversal bug

Vittorio Parrella (2):
      Fixed crash in PokeMatrix(NULL) if not called before with valid data.
      Refactoring of Set/Get filename to model reader classes.

Will Schroeder (8):
      Fixed HandleDirection issues.
      Performance improvements via templating and SMP
      Cleaned up dashboard warnings
      New Guassian splatter class, added multithreading
      Using typename instead of class for templates
      Work around brain dead compiler
      Another method made public to work around compiler
      Another method made public to work around compiler(2)

peter karasev (19):
      add obj importer with test. fetches textured mtl files for test.
      re-add test file that was quashed unintentionally
      cleanup style issues per comments in gitlab
      update cmake for external data usage
      update style and remove console output
      more robust handling of path to texture files
      update test robustness, use freely distributable model files
      exclude header so that vtkSmartPointer can be used ...
      update md5 files in repo
      remove previous md5 refs
      touch data files to get dashboard greener
      remove previous files
      dont show warning about comments in MTL file unless debug mode on
      add support for mixing usemtl and vertex definitions, add test for this.
      touch files; previous commit encountered gitlab error
      make a pass at cleaning up warnings on cdash
      disable warning in impl file.
      add test files
      fix importing to work for no mtl file + no warnings for empty texture image

Revision 24459  Directory Listing
Modified Tue Jul 21 21:13:45 2015 UTC (2 years, 2 months ago) by naucoin
ENH: support fiducial file transfer between Slicer and CLIs

Requires the updates to the SlicerExecutionModel to define the new XML
tag --pointfile, the pull request was merged, so the external project
file is updated.
Expands the application logic to support reading and writing fiducial files.
Expands the CLI module UI helper to create a fiducial node selection combo
box when a point file type is detected.
Expands the CLI module logic to manage fiducial files. Need to link to the
Markups storage node to set the coordinate system flag, and to remove a circular
dependency between the Markups Module and QTCLI, moved that class into Libs MRML Core.
Currently setting an attribute on the fiducial node to pass the coordinate
system flag along to ApplyTask where the files get written to disk.
Added CreateDefaultDisplayNodes for the fiducial node so it can be called for
output node setup.
Add input and output fiducial file examples with coordinate
systems set to LPS to the execution model tour.

Revision 24439  Directory Listing
Modified Fri Jul 17 05:00:47 2015 UTC (2 years, 2 months ago) by jcfr
BUG: Update VTK to include fix for memory leak in vtkSys SystemTools.

See Slicer/VTK@4b46455

Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Thu Jul 16 14:54:10 2015 -0400

    KWSys-SystemTools: Fix memory leak in DetectFileType

    A more elaborated patch including update of the test case has been
    pushed upstream: http://review.source.kitware.com/#/c/20003

    This commit fixes the leak found using valgrind memcheck tool:

    ==29339== 512 bytes in 2 blocks are definitely lost in loss record 2,179 of 2,448
    ==29339==    at 0x4C2B800: operator new[](unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
    ==29339==    by 0x28396AB8: vtksys::SystemTools::DetectFileType(char const*, unsigned long, double) (SystemTools.cxx:4142)
    ==29339==    by 0x1018F9229: vtkSlicerColorLogic::FindColorFiles(std::vector<std::string, std::allocator<std::string> > const&) (vtkSlicerColorLogic.cxx:177)
    ==29339==    by 0x1018F86EA: vtkSlicerColorLogic::FindDefaultColorFiles() (vtkSlicerColorLogic.cxx:100)
    ==29339==    by 0x9844613: vtkMRMLColorLogic::AddDefaultFileNodes() (vtkMRMLColorLogic.cxx:1016)
    ==29339==    by 0x983DAF6: vtkMRMLColorLogic::AddDefaultColorNodes() (vtkMRMLColorLogic.cxx:144)
    ==29339==    by 0x983D673: vtkMRMLColorLogic::OnMRMLSceneNewEvent() (vtkMRMLColorLogic.cxx:85)
    ==29339==    by 0x983D629: vtkMRMLColorLogic::SetMRMLSceneInternal(vtkMRMLScene*) (vtkMRMLColorLogic.cxx:78)
    ==29339==    by 0x982B4F9: vtkMRMLAbstractLogic::SetMRMLScene(vtkMRMLScene*) (vtkMRMLAbstractLogic.cxx:281)
    ==29339==    by 0x8E70F0A: qSlicerAbstractCoreModule::setMRMLScene(vtkMRMLScene*) (qSlicerAbstractCoreModule.cxx:168)
    ==29339==    by 0x101492780: qSlicerColorsModule::setMRMLScene(vtkMRMLScene*) (qSlicerColorsModule.cxx:132)
    ==29339==    by 0x8EA2B1A: qSlicerModuleFactoryManager::loadModule(QString const&, QString const&) (qSlicerModuleFactoryManager.cxx:181)

Revision 24438  Directory Listing
Modified Fri Jul 17 05:00:45 2015 UTC (2 years, 2 months ago) by jcfr
BUG: Update CTK (include fix for memory leak in ctkDoubleSpinBox)

Among other changes, it include fixes and improvement for:
  ctkColorPickerButton
  ctkDoubleSpinBox
  ctkVTKTextPropertyWidget
  ctkXNAT

$ git shortlog 9e5af26..7bb708c --no-merges
Andreas Fetzer (45):
      Initial commit
      Removed unused function declaration
      Added new class ctkXnatResourceFolder.
      Adapted documentation. Currently the remove() function does not modify the object on the server
      Added possibility to set a default file download path to ctkXnatSession.     If the specified location does not exist its value will be set to the current     working directory
      Since some of the ctkXnatObject support retrieving a last modification time (e.g. project)     this function should be virtual so that is can be overwritten by the according subclasses
      Also check if path is empty
      Continued refactoring of the upload functions:
      Added convenience method for adding a resource to a xnatObject
      Enhanced xnatTreeBrowser so that resource creation and file upload can be tested
      Fixed build error and removed useless upload function from xnatTreeModel
      Some minor fixes.
      Added dirty flag to indicate whether a xnat object was modified
      Don't update the modified flag after an object was saved on the server and the ID was set afterwards
      cosmetic changes
      If a file with the given name already exits on the server set the overwrite flag to true
      Added rudimentary check whether the file upload was successful.     Right now just the filesize is compared. Checksum would be better.
      Setting correct filename for upload
      Added file upload validation to saveImpl of ctkXnatFile
      Fixed iteration over md5 results
      Adapted add(child) function of ctkXnatObject
      Added function for adding a new child node to ctkXnatTreeModel
      Return resource folder after creation
      Added overwrite flag for file upload
      Use QXmlStreamReader instead of deprecated QXml module classes
      Some Qt5 adaptions
      Added tests for:
      Cleaned up code
      Fixed build error on Mac
      Removed unused modified flag again
      Further cleanup
      Fixed possible invalid directory path
      Improved check for valid directory path
      Removed function calls that were made for testing reasons
      Replaced for loop with iterators.
      Only add folder if it not exists
      Added refesh function to ctkXnatTreeModel
      Fixed crash which might happen if the xnatObject is null
      Added name and label getters to all XNAT folder objects
      Synchronize deleted objects as well
      Use iterator instead of foreach
      Fixed query parameters for httpPut
      Fixed build error on Mac OS X
      Added include for QScopedPointer and QObject
      Added include for QSharedPointer

Benjamin BENEY (3):
      Add text size in ctkVTKTextPropertyWidget
      Change icon for invalid color in ctkColorPickerButton
      Fix ctkColorPickerButton build error

Jean-Christophe Fillion-Robin (1):
      Fix memory leak associated with ctkDoubleSpinBox ensuring pimpl is deleted

Revision 24406  Directory Listing
Modified Fri Jul 10 16:00:26 2015 UTC (2 years, 2 months ago) by jcfr
COMP: Fix regression in ITKv4 external project properly setting INSTALL step

This commit fixes the following error:

CMake Error at cmake_install.cmake:36 (file):
  file cannot create directory: /usr/local/lib/cmake/ITK-4.8.  Maybe need
  administrative privileges.

Revision 24405  Directory Listing
Modified Fri Jul 10 15:26:20 2015 UTC (2 years, 2 months ago) by jcfr
ENH: Add option "Slicer_USE_ITKPython" to turn on ITK Python wrapping.

The option is disabled by default.

Note: This is currently only tested on the build tree with Linux.

This change depends on InsightSoftwareConsortium/ITK@13b368b fixing for
the WrapITK.pth

Reviewed-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

From: Matt McCormick <matt.mccormick@kitware.com>

Revision 24404  Directory Listing
Modified Fri Jul 10 15:26:18 2015 UTC (2 years, 2 months ago) by jcfr
ENH: Update ITK to v4.8

$ git shortlog 5f95aa6..3388d7b --no-merges
Bradley Lowekamp (4):
      BUG: Remove reliance on exceptions in StringTools::ToData methods
      BUG: Remove reliance on exceptions in StringTools::ToData methods
      BUG: Fix WriteCellsAsBinary and valgrind defects
      COMP: Explicitly export SingleValuedNonLinearVnlOptimizerv4

Davis Vigneault (1):
      COMP: C++11 Warnings in thirdparty PNG module.

Matthew McCormick (13):
      COMP: Address may bu used uninitialized in IdentityTransformTest.
      COMP: Address array subscript above bounds in VTKPolyDataReader.
      COMP: Work around GDCM test segfault with Clang 3.5+.
      BUG: Do not use pthreads with Emscripten.
      COMP: Fix unused parameter warnings in itkMultiThreaderNoThreads.
      BUG: Do not output CMake log files in itkSystemInformationTest.
      COMP: Work around segfaults with VS12 in RegionOfInterestImageFilter.
      DOC: Update Wiki Examples Remote to June 26, 2015.
      COMP: Update ParabolicMorphology to address doxygen warning.
      COMP: Add missing exports in the ITKFEM module.
      BUG: Use CMAKE_LIBRARY_OUTPUT_DIRECTORY for build tree WrapITK.pth.
      DOC: Document grafting the input image in composite filters.
      DOC: Bump SphinxExample remote module version to 2015-07-02.

Michka Popoff (1):
      ENH: Update PyInit for Python 3

From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

Revision 24368  Directory Listing
Modified Thu Jul 2 14:15:25 2015 UTC (2 years, 2 months ago) by fedorov
BUG: Revert "ENH: add support of DCMTK private dictionary"

This reverts commit 1c20e6fc3adad65c72bc3bc3091e636b5e7080c0.

For unknown reason, this commit appears to break the dashboard.
The messages reported on dashboard are contradicting, since config
and build errors are reported on the front page, but not for the Slicer4
project, see

http://slicer.cdash.org/index.php?project=Slicer4&date=2015-07-01

Experiments trying to package Slicer on mac failed, with or without this
commit, as documented in

https://github.com/Slicer/Slicer/pull/299

Revision 24367  Directory Listing
Modified Tue Jun 30 21:21:28 2015 UTC (2 years, 2 months ago) by fedorov
ENH: add support of DCMTK private dictionary

See issue 4013 and related discussion here:

http://slicer-devel.65872.n3.nabble.com/Enabling-support-for-DCMTK-private-dictionary-td4034305.html

This change installs private.dic of DCMTK in a runtime location,
and sets DCMDICTPATH launcher variable. This will allow for more robust
interpretation of DICOM private tags based on the information
contained in the DCMTK private dictionary.

Revision 24365  Directory Listing
Modified Sun Jun 28 02:45:49 2015 UTC (2 years, 2 months ago) by jcfr
COMP: Fix pcre package Linux download error relocating file on midas.

This commit is an attempt to fix the following download error
happening on linux:

// -----------------
CMake Error at PCRE-stamp/download-PCRE.cmake:27 (message):
  error: downloading
  'http://downloads.sourceforge.net/project/pcre/pcre/8.12/pcre-8.12.tar.gz'
  failed

    status_code: 7
    status_string: "couldn't connect to server"
    log: About to connect() to downloads.sourceforge.net port 80 (#0)
    Trying 216.34.181.59... connected

  Connected to downloads.sourceforge.net (216.34.181.59) port 80 (#0)

  GET /project/pcre/pcre/8.12/pcre-8.12.tar.gz HTTP/1.1

  User-Agent: curl/7.16.1

  Host: downloads.sourceforge.net

  Accept: */*



  HTTP/1.1 302 Found

  Server: nginx

  Date: Sat, 27 Jun 2015 03:14:40 GMT

  Content-Type: text/html; charset=UTF-8

  Connection: close

  content-disposition: attachment; filename="pcre-8.12.tar.gz"

  Set-Cookie:
  sf_mirror_attempt="pcre:superb-dca2:pcre/8.12/pcre-8.12.tar.gz";
  expires=120; Path=/

  Location:
  http://superb-dca2.dl.sourceforge.net/project/pcre/pcre/8.12/pcre-8.12.tar.gz


  Content-Length: 337

  Closing connection #0

  Issue another request to this URL:
  'http://superb-dca2.dl.sourceforge.net/project/pcre/pcre/8.12/pcre-8.12.tar.gz'


  About to connect() to superb-dca2.dl.sourceforge.net port 80 (#0)

    Trying 209.61.193.20... Connection timed out

  couldn't connect to host

  Closing connection #0

  couldn't connect to server
// -----------------

Revision 24363  Directory Listing
Modified Fri Jun 26 18:47:09 2015 UTC (2 years, 3 months ago) by jcfr
BUG: Update VTKv6 to include fix for vtkhdf5 libraries DLL manifest

At the time of this commit the associated change hadn't been integrated
in VTK master and were under review here:

   https://gitlab.kitware.com/jcfr/vtk/tree/fix-hdf5-manifest

Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Fri Jun 26 14:15:47 2015 -0400

    Do not force manifest selection for vtkhdf5 libraries

    Following e16fac1, hdf5 libraries are build with -D_BIND_TO_CURRENT_VCLIBS_VERSION=1.

    When building VTK using VS2008, the result of this is that
    (1) VTK libraries all reference "9.0.21022.8" manifest expect the hdf5
    ones that reference "9.0.30729.1" and (2) in some case prevent application
    built against VTK from starting.

    The problem can also be detected when running CMakeVerifyManifest.cmake
    against the application install tree. It basically returns a message
    similar to the following one:

    8<----8<----8<----8<----8<----8<----8<----
    ERROR: C:/Program Files/AwesomeApp 1.0.0/bin/vtkhdf5_hl-6.2.dll uses 9.0.30729.6161 not found in shipped manifests:[9.0.21022.8].
    CMake Error at C:/D/Support/cmake-3.2.2-win32-x86/share/cmake-3.2/Modules/CMakeVerifyManifest.cmake:118 (message):
      This distribution embeds dll versions that it does not ship, and may not
      work on other machines.
    8<----8<----8<----8<----8<----8<----8<----

    Here are some more information copied from the convenience script allowing
    to patch the manifest from VS2008.

    Source:  https://gist.github.com/jcfr/3c7bef3f8b32f9f6ad4b

    8<----8<----8<----8<----8<----8<----8<----8<----

    .SYNOPSIS
        Patch manifests in the redist folder of Visual Studio 9 (2008)
    .DESCRIPTION
        To avoid the dll hell associated with runtime libraries distribution. There are
        two approaches:
         (1) edit the manifest file to have "9.0.21022.8" from the "9.0.30729.XXX" that is there, you "trick"
             your executable into using the newer dlls.  There appears to be no ill effects from this.
             The executables work, and you are using a newer version of the run time library.
         (2) add -D_BIND_TO_CURRENT_VCLIBS=1 to ALL files being compiled, then all of your executable files
             and dll files will refer to "9.0.30729.XXX" and you can use the redist files without any edits.
             However, you have to be careful here to recompile everything with this.  By default the compiler
             will build for "9.0.21022.8".

        This script will consider approach (1). If not already done, this script will first backup the
        manifest files and then patch them.

        See:
          * http://www.kitware.com/blog/home/post/4
          * http://stackoverflow.com/questions/8097733/how-to-distribute-c-run-time-crt-libraries

    8<----8<----8<----8<----8<----8<----8<----8<----

Revision 24361  Directory Listing
Modified Thu Jun 25 23:32:58 2015 UTC (2 years, 3 months ago) by jcfr
COMP: Update ITKv4 to fix MacOSX compilation issue.

//------------------
commit 5f95aa6712c508a637a12faaea119d35e574208c
Author: Bradley Lowekamp <blowekamp@mail.nih.gov>
Date:   Thu Jun 25 10:25:11 2015 -0400

    COMP: Explicitly export SingleValuedNonLinearVnlOptimizerv4

    Address the following linking issue:

    Undefined symbols for architecture x86_64:
      "typeinfo for itk::SingleValuedNonLinearVnlOptimizerv4", referenced
      from:
          typeinfo for itk::LBFGSOptimizerBasev4<vnl_lbfgsb> in
          libSimpleITKRegistration-0.9.a(sitkImageRegistrationMethod_CreateOptimizer.cxx.o)
    ld: symbol(s) not found for architecture x86_64
    clang: error: linker command failed with exit code 1 (use -v to see
    invocation)
//------------------

Revision 24360  Directory Listing
Modified Thu Jun 25 02:47:09 2015 UTC (2 years, 3 months ago) by jcfr
ENH: Update to ITKv4.8rc2

$ git shortlog 38398fb..650d169 --no-merges

Alexander Hewer (1):
      COMP: fixed error "Dunno about this gcc" for gcc 5.1

Arnaud Gelas (13):
      ENH: add MinimalPathExtraction as a remote module
      ENH: fix KWStyle errors for SubdivisionQuadEdgeMesh
      COMP: fix warning with non default template parameter for OutputImage
      COMP: missing ';' in itkSetClampMacro
      STYLE: no need to expose internal type
      DOC: add explanations about input and out filters
      COMP: missing include in IterativeTriangleCellSubdivision
      BUG: memory leaks when calling itk::Mesh::Graft
      DOC: Improve documentation for ParameterizationQuadEdgeMeshFilter
      BUG: not all combinations were actually test
      ENH: add an exception in BorderQuadEdgeMeshFilter if no boundaries
      COMP: fix CMake warning in ITKModuleHeaderTest
      BUG: fix memory leaks in BorderQuadEdgeMeshFilter using itk::AutoPointer

Bill Lorensen (6):
      ENH: Update to KWStyle conformant version
      ENH: Add interpolate capability
      ENH: WikiExamples QuickView Update
      COMP: VTK AUTOINIT redefinition warnings
      COMP: Compiler hidden visibility on Mac compiler
      COMP: EventMacro backward compatibility

Brad King (24):
      ENH: ExternalData: Allow local stores without any URL templates
      ENH: ExternalData: Warn on missing file instead of failing
      ENH: ExternalData: Add support for custom download scripts
      ENH: ExternalData: Add support for custom algorithm-to-URL mapping
      DOC: ExternalData: Update documentation to match CMake copy
      ENH: Teach UpdateThirdPartyFromUpstream to support spaces in path
      ENH: Improve UpdateThirdPartyFromUpstream for initial imports
      ENH: Require CMake 2.8.9 or greater
      ENH: Do not produce ITKGDCM library when using system GDCM
      ENH: Drop gdcm source subtree to prepare for fresh import
      ENH: Add script to update GDCM from upstream
      STYLE: Tell Git not to check whitespace in GDCM
      STYLE: Tell Git about larger files in GDCM
      COMP: Configure GDCM to build inside ITK
      COMP: Fix GDCM to handle older expat library
      COMP: Cleanup CMP0022 warnings in GDCM module
      COMP: Add missing include in GDCM source
      COMP: Teach GDCM to honor ITK_DYNAMIC_LOADING option
      ENH: KWSys: Tell Git not to export .gitattributes
      COMP: Remove cmake_minimum_required calls from GDCM
      COMP: Remove extra CMake policy settings in GDCM
      COMP: Use more standard SSE intrinsics in GDCM copy of OpenJPEG
      COMP: Fix GDCM std::accumulate initial value type
      ENH: Update version of CastXML built for wrapper generation

Bradley Lowekamp (38):
      PERF: Use ImageAlgorithm::Copy in ImageSeriesWriter
      ENH: Refactor versor to matrix transform code
      DOC: Clarify that Scale Skew Versor does addition
      BUG: Correct Simularity3D Jacobian
      BUG: Ensure OptimizerParameters doesn't leak its helper
      PERF: Remove frequent dynamic allocations used with std::vector
      BUG: Restore IO support for BSplineDeformableTransform
      BUG: Replace std::cout message Warning marco
      BUG: Correct ExtractImageFilters Type macro
      DOC: Separately document IsNull and IsNotNull
      ENH: Modularize KWStyleTests
      BUG: Remove ExhaustiveOptimizer ivar which was unused
      STYLE: Update IOFDF to address KWStyle issues
      BUG: Fix undefined signed integer shift
      BUG: Fix IOFDFInDoxygenGroup test
      BUG: Update MGHImageIO for header guarder style
      BUG: Fix itkFDFImageIOTest link error on windows
      STYLE: Update SCIFIO for KWStyke failures
      BUG: Use base's NumberOfIterations for stopping condition
      PERF: Report progress for linear transform only at scanline completion
      BUG: Avoid underflow in gradient range calculation
      ENH: Use return by value for ImageAlgorithm::EnlargeRegionOverBox
      BUG: No exception for 0 parameter transforms
      COMP: Address conversion compilation warning
      ENH: Use PrinSelfObjectMacro
      BUG: Use module's libraries for linking header test.
      ENH: Add export specifications to FFT library
      COMP: Address conversion compilation warning
      COMP: This patch address linking errors with WrapITK
      DOC: Improving documentation for the names inputs of the ProcessObject
      BUG: Isolate CannyEdgeDetection's internal filter from external
      PERF: Refactor ExpandImageFilter loop
      ENH: Add AtmoicInt class, use TimeStamp & LightObject
      COMP: Address signed to unsigned comparison warning in AtomicInt Test
      ENH: Move IsPrime and GreatestPrimeFactor to compiled cxx file
      COMP: Add export missing export specifications
      BUG: Fix reading HDF5 images into different dimension.
      Revert selection "ENH: Add shared libraries for ITK libraries"

Brian Helba (2):
      ENH: Add scripts for automated updating of ThirdParty libraries
      ENH: Make Vector construction from scalar value explicit

Christopher Mullins (10):
      STYLE: Keep codesnippet lines under 80 characters.
      STYLE: Fix Latex blocks in documentation to include newlines.
      COMP: Fix clang warnings
      DOC: Fix Latex underscore for SoftwareGuide
      DOC: Use the dilated version of the FivePoints image
      COMP: Use c++11 noexcept declarator.
      COMP: Fix override warnings on clang with GPU module and MINC
      COMP: Fix clang override warnings for Review module.
      COMP: Fix more clang warnings in review module
      COMP: Fix more clang override warnings in Review module.

Cyril Mory (3):
      BUG: Fixed itkWarpImageFilter wrong result in some cases
      ENH: Method to compute InputRequestedRegion in itkWarpImageFilter
      ENH: Moved some of itkWarpFilter from private to protected

David Froger (2):
      ENH: Check regions in HDF5 streaming test
      BUG: Fix HDF5 write streaming test.

Davis Vigneault (5):
      STYLE: Minor style and documentation changes to ITK examples.
      DOC: Minor changes and clarifications to the registration chapter of Book 2.
      STYLE: Minor wording and formatting changes to Software Guide Mesh examples.
      COMP: Build failure using EuclideanDistancePointMetric with mismatched meshes.
      STYLE: Minor typographical changes in ParameterizationQuadEdgeMeshFilter

Dženan Zukić (3):
      ENH: adding reverse iteration test
      ENH: using scanline iterator instead of linear iterator
      DOC: Improve docs for ConnectedComponentImageFilter

GDCM Upstream (1):
      GDCM 2015-04-29 (81e551fc)

Gary JIA (1):
      BUG: Fix memory leak at GPUCommon

Gaëtan Lehmann (21):
      BUG: fix extra carriage return in python callbacks
      ENH: use castxml in wrapping
      COMP: almost fix java build
      ENH: use modern cmake list operations in wrapping
      COMP: hide compiler warnings when building pcre and swig
      COMP: fix the IOFDF module name used in wrapping
      COMP: fix last python runtime warnings about unknown types
      COMP: fix undefined __float128 type with gcc
      BUG: reactivate PythonGetNameOfClass and fix the FDFImageIOFactory name
      COMP: fix warnings due to double MultipleValuedCostFunction wrapper
      BUG: fix ipython custom completion
      BUG: fix runtime information for cross correlation filters
      ENH: let the user choose the tradeoff between size and speed in fft operations
      ENH: update progress in ImageFileReader
      ENH: initialize the progress in ImageFileWriter
      BUG: fix extra line return in terminal progress display
      BUG: fix missing space before "done" in progress display
      ENH: pass ActualXDimensionIsOdd through the pipeline
      COMP: fixes for SizeGreatestPrimeFactor
      ENH: Add itkFFTPadImageFilter
      ENH: factorize shared code in itk::PadImageFilterBase

Gert Wollny (1):
      COMP: defining ITK_USE_FLOAT_SPACE_PRECISION

Hans Johnson (40):
      COMP: Add c++11 override designation
      COMP: Identify null pointer assignments
      STYLE: rm explicit void for parameterless function
      STYLE: Use ITK_NULLPTR to utilize c++11 features
      BUG: Incorrect addition of ITK_OVERRIDE
      COMP: Use STREQUAL instead of MATCH
      BUG: return type defaults to zero.
      BUG: ImageType, CofficientImageArray types missing
      DOC: Invalid doxygen return for void function.
      COMP: _Pragma suppress fltpnt equality warnings
      COMP: Allow exact floatpnt equality checks.
      COMP: Avoid floatpnt equality check
      COMP: Floatpnt equality for divisor
      COMP: Avoid unnecessary float pnt equality checks.
      PERF: Improve perf of ANTSNeighborhoodCorrelation
      BUG: Test depending on itkMesh.h in Common
      COMP: Make DCMTK header functions const
      Revert "COMP: VTK AUTOINIT redefinition warnings"
      COMP: VTK and ITK H5 build program collision
      COMP: Create out-of-line virtual method defintions
      COMP: Create out-of-line virtual method macros
      DOC: Clarify strange syntax for itk::MetaEvent
      COMP: Fix ENABLE_SHARED variable name
      STYLE: Remove outdated cmake version support
      STYLE: Move SymmetricEigenAnalysis to Deprecated
      COMP: Prefer modern CMake visibility settings
      STYLE: Use ITK_NOEXCEPTION macro
      ENH: Continue to deprecate ::Zero and ::One
      ENH: Avoid need for const_cast, ensure consistency
      BUG: Incorrect function signature
      COMP: Intel compiler warning suppression
      ENH: Add shared libraries for ITK libraries
      ENH: Remove unnecessary const_cast
      STYLE: Move utility TransformIOHelper to cxx file
      BUG: Missing ITKIOMINC_EXPORT on __Private()
      STYLE: Fixed AnalyzeObjectMap header guard style.
      COMP: Missing exports for templates
      ENH: Update MGHIO for consistency with ITK.
      BUG: Remove shared specifications from TransformIO
      STYLE: Use consistent names in template parameters

Ivan Setiawan (2):
      BUG: Fix initial ImageTrueMax to the most negative value.
      BUG: Test case to verify fix of ImageTrueMax in MattesMI.

Jan Bergmeier (1):
      DOC: Changed indices for steps in ExhaustiveOptimizer.

Jon Haitz Legarreta (9):
      ENH: New test for the BinaryStatisticsKeepNObjectsImageFilter
      ENH: New test for the itkLabelShapeKeepNObjectsImageFilter
      ENH: Add test for itkShapeRelabelImageFilter
      ENH: Add test for the itkLabelStatisticsKeepNObjectsImageFilter
      ENH: Add test for itkBinaryShapeKeepNObjectsImageFilter
      ENH: Add test for itkLabelStatisticsOpeningImageFilter
      DOC: Correct documentation typo.
      ENH: Increase code coverage for itkCustomColormapFunction
      ENH: New test for the itkMetaGaussianConverter

Julien Jomier (1):
      BUG: Output pointer origin is not set causing a memory access error.

KWSys Robot (3):
      KWSys 2015-04-19 (4f39791b)
      KWSys 2015-05-12 (b1d560a0)
      KWSys 2015-05-18 (9a6b7c3f)

Kevin H. Hobbs (1):
      COMP: new baseline for building against VTK master

Marius Staring (2):
      BUG: workaround for 64bit VS2013 Release segfaults
      COMP: workaround for 64bit VS2013 Release ICE

Matthew McCormick (142):
      ENH: Add BridgeNumPy Remote Module.
      COMP: Bump AnalyzeObjectMapIO to fix doxygen warning.
      STYLE: Style changes for itkGaussianDerivativeImageFunctionTest.
      ENH: Test GaussianDerivativeImageFunction with unsigned short.
      DOC: Add C++11 macros to doxygen configuration.
      ENH: Remove FindNUMARRAY.cmake.
      STYLE: Too many spaces before semi-colon in PCAShapeSignedDistanceFunction.
      COMP: Bump Wiki Examples revision to fix Doxygen warnings.
      COMP: Fix ITK_OVERRIDE update DebugMacro build errors.
      DOC: Updates to GettingStarted.txt.
      BUG: Remove Testing/Temporary/CTestCostData.txt.
      ENH: Update doxygen.config for Doxygen 1.8.9.1.
      ENH: Bump CMakeLists.txt version to 4.8.0.
      DOC: Rename duplicate doxygen section.
      Revert Doxygen version 1.8.9.1 to 1.8.5 config to clean up dashboard
      DOC: Fix Doxygen override, nullptr, noexcept definitions.
      DOC: Note that push access is not required to get patches merged.
      DOC: Clean up some wrapping comments.
      STYLE: Clean up inter-definition space for Image,ImageBase,ProcessObject.
      ENH: Fetch source tarball external data from midas3.kitware.com.
      BUG: Fix BridgeNumPy signed / unsigned short correspondance.
      DOC: Improve ImageScanlineIterator documentation.
      ENH: Add missing {Set,Get}Element methods to Array2D.
      BUG: Fix linking SmoothingRecursiveYvvGaussianFilter with install tree.
      BUG: Add CMake export code for ITK_USE_SYSTEM_GDCM.
      ENH: Pass CMAKE_GENERATOR to ExternalProject's.
      ENH: Update LLVM/Clang ExternalProject to 3.6.0.
      ENH: Update MetaIO License from Upstream.
      ENH: Bump MetaIO to latest upstream.
      COMP: Do not include tests/ directory in clang tarball.
      ENH: Add Azure Storage as ExternalData source.
      STYLE: Update SplitComponents module for KWStyle fixes.
      STYLE: Style fixes for LevelSetsv4 and related classes.
      BUG: Move MagnitudeAndPhaseToComplex filter wrapping to ITKImageIntensity.
      ENH: Document testModules.sh and move to Utilities/Maintenance
      BUG: Fix Python tests on Windows with Ninja generator.
      STYLE: Update IOSTL module for KWStyle test.
      BUG: Suppress wrapping type conversions warnings with MSVC.
      COMP: Address quoted MSVC variable in GDCM.
      BUG: WrapITK.pth should contain the lib/ directory with VS.
      COMP: Suppress swig build configure warning.
      ENH: Use CMAKE_CROSSCOMPILING_EMULATOR to run HDF5 detection.
      BUG: Do not use EXECUTABLE_OUTPUT_PATH for vcl tests.
      BUG: Do not enable floating point exceptions in tests with MinGW.
      DOC: Update KWStyle location.
      BUG: Add QuickViewTest baseline for Mac.
      ENH: MetaIO use UpdateThirdPartyFromUpstream.sh
      ENH: Arrange MetaIO sources for UpdateThirdPartyFromUpstream.sh.
      ENH: Add root snapshot commit support to UpdateThirdPartyFromUpstream.sh
      COMP: Do not try to generate tiff_fax3sm.c when cross compiling.
      COMP: Android does not currently have posix_memalign.
      COMP: The Android pwd.h passwd struct does not have a pw_gecos entry.
      COMP: Android does not have pthread_setcancelstate.
      COMP: Do not do __errno_location workaround on Android.
      COMP: Removed unused parameters in itkThreadPoolTest.
      BUG: Address detection of TransformReadWriteTest as executable.
      ENH: Set CMP0056 to NEW.
      COMP: Work around test file too big with x64_64-w64-mingw32.
      COMP: Increase itkMattesMutualInformationImageToIMageMetricv4Test tolerance.
      COMP: Address NumericTraits warning related to POWER8 char.
      BUG: Add new ResampleImageFilter9Test baseline for MinGW.
      BUG: Add MinGW baseline for VoronoiPartitioningImageFilterTest1.
      COMP: Fix vnl_sample.cxx for srand48 but no drand48.
      ENH: Add ITK_DYNAMIC_LOADING CMake option.
      COMP: Support S_IRUSR and S_IWUSR.
      COMP: Do not log swig configure output.
      BUG: NumericTraits< char > does not have Self typedef.
      ENH: Do not use TestBigEndian from CMAKE_ROOT.
      COMP: Use sizeof(void *) instead of sizeof(size_t) for address model.
      COMP: Do not use GCC demangling with emscripten.
      ENH: Use try_run to determine if double correction required.
      COMP: Suppress Swig configure output.
      COMP: Set CMP0058 to NEW.
      COMP: Add missing InternalLabelType.
      BUG: Specify absolute path to double-conversion-configure.h for install.
      DOC: Clarify the UpdateThirdPartyFromUpstream.sh commit message.
      COMP: Pass --quiet to swig's configure script.
      STYLE: Update HigherOrderAccurateGradient module for style fixes.
      ENH: Mark ITK_DYNAMIC_LOADING as an advanced CMake variable.
      COMP: Ignore swig-prefix warnings.
      BUG: GDCM set default ultrasound spacing when not found.
      COMP: Initialize arrays in itkCurvatureFlowFunction.
      COMP: Add itkIntTypes.h header for SizeValueType in itkVnlFFTCommon.h
      STYLE: Style fixes for RayCastHelper::CalcRayIntercepts
      COMP: Run the SWIG configure step in a CMake script.
      STYLE: Bump IOFDF module for style and cleanup.
      BUG: Fix DoxygenInGroup test from .zip release files.
      COMP: Do not wrap exotic QuadEdgeMesh CellInterface types.
      COMP: Remove FFTWGlobalConfiguration param doxygen keyword.
      COMP: Do not reference ::MetaEvent in itkMetaEvent.h docs.
      DOC: itkSymmetricEigenSystem is now in the ITKDeprecated module.
      BUG: Fix TestDriver executable for itkSymmetricEigenSystemTest.
      BUG: Use consistent SizeGreatestPrimeFactor in deconvolution tests.
      COMP: Use signed char in ImageToImageMetricv4 test.
      COMP: Do not include itkDynamicLoader in header tests.
      COMP: Include byteswap.h for Android in GDCM.
      COMP: Use signal.h instead of sys/signal.h in GDCM.
      COMP: Not all versions of Android have posix_memalign.
      COMP: Initialize variable in PointSetToListSampleAdaptorTest.
      COMP: Suppress getpwnam warning with static executables.
      COMP: Tighten LandmarkWarping2 lines for Software Guide.
      ENH: Allow skip of FloatPointExceptions implementation for absent fenv.h.
      COMP: Define feenableexcept for Emscripten.
      BUG: HDF5 do not force CMake CheckTypeSize on include.
      STYLE: Style fixes to itkVideoStream.e
      COMP: Ignore build warnings for libs unfound by emscripten.
      BUG: Run HDF5 H5detect in working directory with the executable.
      BUG: HDF5 use CMAKE_EXECUTABLE_SUFFIX.
      COMP: Work around Emscripten internal compiler crash in VideoStream.
      COMP: Use byteswap.h with GDCM with Emscripten.
      COMP: Recognize Emscripten in socket++.
      BUG: Remove HDF5's own internal CheckTypeSize.cmake.
      ENH: Enable cross-compiling of the wrapping.
      COMP: Missing semi-colon in FFT Hermitian filters.
      ENH: Add ExternalData_NO_SYMLINKS option.
      ENH: Mount local filesystem in the test driver for Emscripten.
      BUG: Do not install wrapping with CMAKE_PREFIX_PATH.
      ENH: Define CPACK_PACKAGE_CONTACT.
      ENH: Add post-commit hook for third party library patches.
      ENH: Pass the CastXML flags directly.
      STYLE: Rename GCC-XML references to CastXML.
      ENH: Send an error when CMAKE_CXX_COMPILER_TARGET is not set.
      ENH: Bump CastXML version for cross-compiling target fix.
      BUG: Use STRING type for PY_SITE_PACKAGES_PATH.
      BUG: Continue when IPython.get_ipython throws an AttributeError.
      ENH: Add ITK_USE_SYSTEM_LIBRARIES
      STYLE: Fix indentation in ITKSetStandardCompilerFlags.cmake.
      COMP: Do not enable ITK_HAVE_SYNC_BUILTINS with Emscripten.
      COMP: Fix MinGW ITK_HAVE_SYNC_BUILTINS detection.
      ENH: Split testing data tarball form source tarball.
      COMP: Do not use ITK_NULLPTR as sentinel.
      ENH: Use gold linker on Linux with GCC.
      COMP: Add try_compile check for gold linker.
      COMP: Do not build dsrc2c.c with -fvisibility-inlines-hidden.
      BUG: Remove shared specifications from IOTransformBase.
      BUG: Required GCC version for gold linker is 4.8.3.
      BUG: Fix ITKIOMINCExport.h capitalization.
      BUG: Add missing include directory required after MINC update.
      BUG: Bring in IOFDF license updates.
      COMP: Add missing HDF5 include for MINC.
      COMP: Add missing HDF5 include directory for ITKIOMINC.
      COMP: Fix itkVTKImageExport.h header name in VtkGlue.i.

MetaIO Maintainers (2):
      MetaIO 2015-04-12 (b7969294)
      MetaIO 2015-04-21 (dc4f7d16)

Michka Popoff (20):
      COMP: Use c++ style comments in pyBase.i
      ENH: Update to swig 3.0.3
      STYLE: Cleanup up cmake files (if, endif, foreach, endforeach).
      ENH: Update to SWIG 3.0.5
      COMP: Fix PythonReadDicomTagTest on OS X
      ENH: Improve wrapping for Vector image types
      ENH: Cleanup itkComposeImageFilter wrapping
      ENH: Setup correct wrapping of GradientRecursiveGaussianImageFilter
      ENH: Add Get/SetSigmaArray to GradientRecursiveGaussianImageFilter
      ENH: Add checks for base types when wrapping more complex types
      COMP: Fix DiffeomorphicDemonsRegistration Wrapping
      STYLE: Rename ITK_WRAP_DIMS to ITK_WRAP_IMAGE_DIMS
      ENH: Add ITK_WRAP_VECTOR_COMPONENTS option
      STYLE: Replace GCCXML by CASTXML
      BUG: Wrap FixedArray sizes also for vector components
      ENH: Wrap MersenneTwisterRandomVariateGenerator
      ENH: Wrap CustomColormapFunction
      ENH: Update to PCRE 8.37
      ENH: Enable wrapping of 4 dimensional vectors
      ENH: Remove inline namespace fix for Wrapping

Nick Tustison (11):
      ENH:  Adding point set reg. capabilities for SyN.
      PERF:  Tolerance for testing needs to be increased.
      BUG:  Coverity divide by zero complaint.
      BUG:  Metric evaluation had an incorrect sign.
      ENH:  Making the point set type visible.
      BUG:  Need to check if maxNorm == 0.
      BUG:  Pixel type shouldn't be initialized with scalar.
      ENH:  Cleaning up point set reg. in BSplineSyN
      ENH:  Adding tangent space calculation for SyN methods.
      BUG:  Added sampling only within the specified mask.
      BUG:  Added sampling only within the specified mask.

Niels Dekker (2):
      BUG: workaround for 64bit VS2013 Release segfault
      COMP: Fixed MSVC warnings, "warning D9025: overriding '/W1' with '/w'"

Richard Beare (3):
      ENH: LabelErodeDilate as a remote module
      ENH: remote.cmake for parabolic morphology
      ENH: Use SHA for LabelErodeDilate module.

Rolf Eike Beer (2):
      STYLE: ExternalData: Replace MATCHES with STREQUAL where possible
      STYLE: ExternalData: Clean up duplicate regex matches with CMAKE_MATCH_<n>

Sean McBride (14):
      COMP: Changed KWStyle check for header include guard names
      COMP: Remove double underscore in header guards (.h & __itk*_h form)
      COMP: Remove double underscore in header guards (.hxx & __itk*_h form)
      COMP: Remove double underscore in header guards (.in & __itk*_h form)
      COMP: Remove remaining double underscore in header guards (__itk form)
      COMP: Remove unnecessary header guards in .cxx files
      COMP: Manually search for "__itk" and clean up double underscore usage
      COMP: fixed clang -Wkeyword-macro warning by removing invalid #undef
      COMP: Suppress clang -Wdocumentation-unknown-command false positive
      COMP: properly escape @ char in doxygen comments
      COMP: Escaped @ character in doxygen comments
      BUG: updated libminc SHA to newest
      COMP: Update MINC to upstream 85145dca36
      BUG: updated MINC to a77da29

Ziv Yaniv (1):
      BUG: Versor initialized with null axis (0,0,0) did not throw exception.

Revision 24359  Directory Listing
Modified Thu Jun 25 02:47:07 2015 UTC (2 years, 3 months ago) by jcfr
STYLE: Remove of Slicer_ITKV3_COMPATIBILITY build option

Since r23960 (ENH: Disable ITKv3 compatibility to enable 64-bit ids on
windows), this option has been disabled by default. This commit simplifies
the maintenance of the build system by removing the option.

Revision 24309  Directory Listing
Modified Tue Jun 16 19:45:01 2015 UTC (2 years, 3 months ago) by jcfr
COMP: Update Slicer, CTK and BRAINSTools to fix outdated builds on VS2012

High-level build did not build external projects in VS2012. The BUILD_ALWAYS flag is a relatively new CMake feature (added in 3.1), therefore the following workaround was added into SuperBuild.cmake:

# This custom external project step forces the build and later
# steps to run whenever a top level build is done...
ExternalProject_Add_Step(${proj} forcebuild
  COMMAND ${CMAKE_COMMAND} -E remove
    ${CMAKE_CURRENT_BINARY_DIR}/Slicer-prefix/src/Slicer-stamp/Slicer-build
  COMMENT "Forcing build step for '${proj}'"
  DEPENDEES build
  ALWAYS 1
  )

This does not work with Visual Studio, where the stamp file is in Debug/Release/etc. subdirectory:
${CMAKE_CURRENT_BINARY_DIR}/Slicer-prefix/src/Slicer-stamp/${CMAKE_CFG_INTDIR}/Slicer-build

Co-authored-by:

// ----------------
Update CTK to integrate similar fix:

git shortlog fd3a2b1..9e5af26 --no-merges
Andras Lasso (1):
      Fixed outdated builds on VS2012

Andreas Fetzer (1):
      Update ctk user password for central.xnat.org, which was expired

Sascha Zelzer (1):
      Provide an explicit resolve operation for plug-ins.


// ----------------
Update BRAINSTools to integrate similar fix:

$ git shortlog 0dd3268..30f43a7 --no-merges
Andras Lasso (1):
      COMP: Fixed outdated builds on VS2012

Revision 24272  Directory Listing
Modified Thu May 21 16:30:05 2015 UTC (2 years, 4 months ago) by pieper
BUG: #3993 fix update of render window when transform changes

Full credit to Andras Lasso for debugging this at the VTK level!

Issue is described on the bug report:

http://na-mic.org/Mantis/view.php?id=3993

Revision 24247  Directory Listing
Modified Wed May 13 02:56:49 2015 UTC (2 years, 4 months ago) by jcfr
ENH: Update SimpleITK to v0.9.0

$ git shortlog  0bbbd33..4531702 --no-merges
Bradley Lowekamp (22):
      Keep updating on the ITK release tail
      Propagate CMAKE_MAKE_PROGRAM to superbuild probjects
      Add https as back up URL for midas test data downloads
      Update examples to use new transform specific interface
      Update ITK along release branch
      Updating json Doxygen fields from ITK XML doxygen
      Updating json with the python beautify script.
      BUG: Fix MaskImageFilters's output value for vector images
      Add Mask test with RGB images
      Include gz extension in ITK Tag file URL
      Add ToPixelType utility methods
      Updating along ITK release branch
      Improve SetInitialMovingTransform documentation.
      Add explicit keyword to single argument transform constructors.
      Add brief comment and ITK doxygen link to transform classes.
      BUG: Uses template parameter for input scalar in ToPixelType
      Minor tweaks and corrections to transform documentation.
      Address uninitialized anonymous variable warning.
      DOC: Adding brief and ITK links to ImageRegistrationMethod
      run doxyall.py to generate SWIG .i docstring file.
      Fix brief Doxygen command typeo
      Updating R version

Ziv Yaniv (2):
      Updating transform usage to new (transform specific) style.
      Updating conventions.

Revision 24246  Directory Listing
Modified Wed May 13 02:56:47 2015 UTC (2 years, 4 months ago) by jcfr
ENH: Update ITK to v4.7.2

$ git shortlog 9c9b310..38398fb --no-merges
Arnaud Gelas (3):
      COMP: fix warning with non default template parameter for OutputImage
      COMP: fix warning with non default template parameter for OutputImage
      BUG: fix BinaryImageToLabelMapFilter with negative OutputBackgroundValue

Bill Lorensen (1):
      COMP: Only require the minimal VTK modules

Bradley Lowekamp (5):
      BUG: Enable VectorImage to work with the ImageSeriesWriter
      BUG: Move LBFGSB callback helper to parent
      BUG: Update AmoebaOptimizer NumberOfIterations
      BUG: Use base's NumberOfIterations for stopping condition
      BUG: Correct convergence string check

Gaëtan Lehmann (1):
      BUG: fix runtime information for cross correlation filters

Hans Johnson (1):
      COMP: VTK and ITK H5 build program collision

Jean-Christophe Fillion-Robin (1):
      Ensure ITKDeprecated is always excluded from the default module list.

Jon Haitz Legarreta (1):
      ENH: Increase code coverage for itkCustomColormapFunction

Marius Staring (2):
      BUG: workaround for 64bit VS2013 Release segfaults
      COMP: workaround for 64bit VS2013 Release ICE

Matthew McCormick (15):
      COMP: Fix wrapping runtime warning on unknown itk::Matrix.
      COMP: Add missing types for MeshTraits wrapping.
      COMP: Do not wrap the Container types for CellInterface * types.
      COMP: Add wrapping for CellTraitsInfo.
      COMP: Wrap missing Mesh templates.
      ENH: Add wrapping for ITKImageNoise module.
      BUG: Export ITK_FFTW_INCLUDE_PATH as CMake path.
      COMP: Fix LevelSetsv4 tests with libc++.
      BUG: Set ITK_BUILD_SHARED in ITKConfig.cmake on Windows.
      COMP: Address quoted MSVC variable in GDCM.
      COMP: Remove duplicate InternalLabelType typedef.
      BUG: Link to VTK 6 rendering backend modules.
      BUG: Add VTK modules for annotation rendering.
      BUG: Link vtkRenderingFreeType in the VTK modules.
      ENH: Bump release branch version to 4.7.2.

Revision 24228  Directory Listing
Modified Mon May 11 02:51:34 2015 UTC (2 years, 4 months ago) by jcfr
ENH: Update CTK to include new PythonQt C++/Python ownership tracking feature

This will allow to greatly simplify python code by avoiding the need to
explicitly keep reference to object that are expected to be own by cpp.

From updated Python Qt documentation:

8<----8<----8<----8<----8<----8<----8<----8<----8<----8<----8<----
 Source: PythonQtDoc.h

 Ownership Ownership management

 In PythonQt, each wrapped C++ object is either owned by Python or C++.
 When an object is created via a Python constructor,
 it is owned by Python by default. When an object is returned from a
 C++ API (e.g. a slot), it is owned by C++ by default.
 Since the Qt API contains various APIs that pass the ownership from/to
 other C++ objects, PythonQt needs to keep track of
 such API calls. This is achieved by annotating arguments and return
 values in wrapper slots with magic templates:

 - PythonQtPassOwnershipToCPP
 - PythonQtPassOwnershipToPython
 - PythonQtNewOwnerOfThis

 These annotation templates work for since C++ pointer types. In addition
 to that, they work for QList<AnyObject*>, to pass the ownership for each
 object in the list.
8<----8<----8<----8<----8<----8<----8<----8<----8<----8<----8<----

$ git shortlog e771b4a..fd3a2b1 --no-merges
Jean-Christophe Fillion-Robin (1):
      Update to PythonQt 3.0

Marco Nolden (1):
      Make BuildUrl more robust for file urls

Sascha Zelzer (3):
      Correctly rethrow exceptions and improve error messages.
      Fix regression making sure the Qt4 moc considers target include paths.
      Introduced another framework option for controlling the plugin start options.

Revision 24205  Directory Listing
Modified Fri May 1 02:31:56 2015 UTC (2 years, 4 months ago) by jcfr
ENH: Update CTK

$ git shortlog b643fd8..e771b4a --no-merges
Jean-Christophe Fillion-Robin (2):
      Do not override widget visibility if already set in a layout view factory
      Do not require QWidget in decorator generated by ctkWrapPythonQt

Julien Finet (4):
      Fix compilation error with Qt < 5.2.1
      Add Qt5 support for VTK.
      Add Qt5 support to QtTesting module
      Fix ctkFileDialogEventTranslatorPlayerTests

Sascha Zelzer (6):
      Added application support and improved debugging mechanism.
      Fixed installing plug-ins via symbolic names.
      Fixed class / struct forward decls and incomplete type.
      Improved test output.
      Visual Studio seems to need the full class definition.
      During shutdown of the plugin framework, also stop all plug-ins.

Revision 24193  Directory Listing
Modified Mon Apr 27 04:47:54 2015 UTC (2 years, 5 months ago) by jcfr
ENH: Update CTK

$ git shortlog  d6171b8..b643fd8 --no-merges
Andras Lasso (1):
      BUG: Enable Ctrl-C shortcut in Python console in the history area

Andreas Fetzer (2):
      Fixed again duplicate signal connection
      Removed redundant call of hideUIDColumns

Csaba Pitner (1):
      BUG: Clear box icon renamed to be considered

Julien Finet (1):
      Add white border to clear icon

Laurenn Lam (1):
      Add setChecked method to ctkButtonGroup

Sascha Zelzer (2):
      QAtomicInt does not have a int conversion operator any more.
      Fixed deprecated warning with Qt5.

Revision 24192  Directory Listing
Modified Sun Apr 26 18:31:09 2015 UTC (2 years, 5 months ago) by jcfr
ENH: Update SimpleITK

This will also fix intermittent build failure happening when doing
parallel build. See 6fda1a4 (Adding dependency of SimpleITKBasicFilters1
on GeneratedCode target)

$ git shortlog d5b32be..0bbbd33 --no-merges
Ali Ghayoor (1):
      Adding AmoebaOptimizer to registration method

Bradley Lowekamp (45):
      ENH: Add explicit instantiation of common ITK classes
      Adding missing itk::ImageSource long long explicit instantiation
      Disable Explicit when shared libraries are enabled.
      Add missing Export specification for explicitly instantiated class.
      Made explicit instantiation code generator work for SimpleITK
      Manually adding long long type to explicitly instantiated classes
      Reordering explicit headers to reduce gcc attribute warnings
      Fix incorrect preprocessor define for exporting
      Use Explicit library by default, always static on windows
      Address CMP0054 warning for CMP0054
      Adding check of dimension and size to named inputs
      Compare Size instead of individual elements.
      Fix error message to specify what doesn't match
      Adding test for checking of name parameters match size
      Fixing size check with optional
      Add generated code for validate testing size of named inputs
      Extend Typelist to 30 elements at max.
      Adding Transform constructor which does try casts to determine type
      Refactor ReadTransform method to utilize casting Transform constructor
      Removing typename usage in not template function
      Relax transform type check to support base classes
      Convert transform to Composite transform if required in InternalInitialize
      Add BSpline and Displacement support for casting constructors
      Adding testing to check conversion after reading a transform
      Adding testing for setting scales estimators for registration
      Use raw pointer to get ITK transform base
      Adding checking of hashed for 4d Image tests
      Moving 4D ImageIO test to exclusive 4D tests
      Increase support variadic template support for vs11
      Increasing variadic templates for vs11 for the Image class
      Add CDash suppression for SWIG python keyword warning
      Suppress shift conversion warning on Visual Studio
      Move CRT warning suppression before first include
      Adding newline at end of file
      Adding CDash suppressing for unused parameter in tr1
      Adding initial test for the amoeba optimizer
      Adding dependency of SimpleITKBasicFilters1 on GeneratedCode target
      Adding Amoeba options withRestarts
      Update ITK superbuild with optimizer patches
      Updating towards v4.7.2
      Adding trace option to LBFGSB optimizer
      Add LBFGSB test with iteration check
      Update examples with corrected LBFGSB iteration limits
      Updating ITK Superbuild to 4.7.2
      Fix gtest unsigned warning

Hans Johnson (1):
      Adding initial script used for generate explicit instantiated ITK

Kasper Marstal (6):
      Added 4D image support via CMake option
      Added 4D support to HashImageFilter
      Added 4D support to HashImageFilterTest
      Added tests for 4D image support
      Added 4D I/O support
      Added tests for 4D image I/O

Ziv Yaniv (3):
      BUG: ImageSeriesReader did not check if file names were set.
      BUG: ImageSeriesReader did not check if file names were set.
      Adding tests to series file writer, dealing with empty file list.

Revision 24187  Directory Listing
Modified Wed Apr 22 15:31:47 2015 UTC (2 years, 5 months ago) by jcfr
COMP: Update teem to fix windows build error

$ git shortlog b83e546..e474608
Jean-Christophe Fillion-Robin (1):
      COMP: Fix MSVC build error in encodingZRL.c

Revision 24185  Directory Listing
Modified Tue Apr 21 17:06:27 2015 UTC (2 years, 5 months ago) by jcfr
ENH: Update teem

$ git shortlog a0ae38a..b83e546 --no-merges
kindlmann (14):
      initial (broken) implementation of nrrdEncodingZRL, and adding nrrdSpaceRightUp and nrrdSpaceRightDown; both of which are reasons for using nrrd magic 6
      forgot to add this
      adding mysteriously missing dyeSpace airEnum, and a utility for command-line image space conversion
      added dieSpace
      whoa! key/value pairs were never saved correctly in plain text files!
      the road ahead
      long-overdue update to logic test after signed->unsigned change
      added airBitsSet
      comment about importance of large values for seekContext->pldArrIncr
      removing copy/paste code from gzip
      first pass at ZRL decompression
      fix from Adam J Shaw
      no need
      fixed bug caused by saving a 3D 1-by-X-by-Y array to an image format like PNG, with fields like space directions that can be usefully preserved in the image meta data: 3 space directions were saved in the image, not two.  This fix is a pretty simplistic one, but it is used in a very targeted way, so it seems safe

rjosest (23):
      fixing double/float precision warnings
      fixing double/float precision warnings
      COMP: Add try_compile to test AIR_EXISTS MACRO
      COMP: adapt to older version of libpng that's part of VTK 5.1
      COMP: Get rid of warnings.
      COMP: fix warning
      COMP: remove debug print from CMakeLists.txt
      COMP: Build/Install modernization
      STYLE: Convert CMake-language commands to lower case
      STYLE: Remove CMake-language block-end command arguments
      COMP: Fix cmake warnings
      STYLE: Remove end-of-line spaces to improve maintenance
      COMP: Update to cmake 2.8 compatibility.
      ENH: Prefer to use $<TARGET_FILE:tgt> for testing
      STYLE: Remove outdated cmake variable
      STYLE: Remove unnecessary conditionals for cmake 2.6
      COMP: Associate component with teem install rules
      COMP: Restore library output path to "lib" folder
      COMP: Prevent target double inclusion with older version of CMake
      COMP: Remove discardd qualifiers warning
      COMP: Remove compiler warnings
      COMP: Fixes a set-but-not-used warning
      COMP: Fixes array-bounds warnings that occur when using O2 optimization on GNUC compilers

Revision 24168  Directory Listing
Modified Fri Apr 10 03:14:46 2015 UTC (2 years, 5 months ago) by jcfr
COMP: Fix build of tcl on Windows 32-bit (See #3984)

This commit fixes regression introduced by r23702 (BUG: Create zip
archive and move tcl binaries onto slicer.kitware.com)

Suggested-by: Christopher Mullins <christopherrmullins@gmail.com>
Tested-by: Sharp, Gregory C. <GCSHARP@mgh.harvard.edu>

Revision 24160  Directory Listing
Modified Tue Apr 7 15:09:03 2015 UTC (2 years, 5 months ago) by jcfr
BUG: Update CTK to fix python interactor regression

$ git shortlog 16aa095..d6171b8 --no-merges
Andras Lasso (2):
      ctkConsole: Do not allow moving before the interactive position
      ctkConsole: Added direct backspace key handling

Revision 24157  Directory Listing
Modified Sun Apr 5 01:20:00 2015 UTC (2 years, 5 months ago) by jcfr
BUG: Update CTK to fix qMRMLSliceControllerWidgetEventTranslatorPlayerTest1

$ git shortlog 2ecb028..16aa095 --no-merges
Eric Heim (1):
      Add support for python wrapping when building against Qt5

Jean-Christophe Fillion-Robin (1):
      Fix qMRMLSliceControllerWidgetEventTranslatorPlayerTest1 on MacOSX

Revision 24156  Directory Listing
Modified Sun Apr 5 01:00:08 2015 UTC (2 years, 5 months ago) by jcfr
BUG: Update CTK to fix python interactor keyboard shortcuts

$ git shortlog d72ab0c..2ecb028 --no-merges
Andras Lasso (3):
      BUG: Fixed Console Shift+Home behavior
      BUG: Fixed more keyboard shortcuts in console
      ENH: Removed low-level key processing from ctkConsolePrivate::keyPressEvent

Revision 24136  Directory Listing
Modified Wed Apr 1 07:01:43 2015 UTC (2 years, 5 months ago) by jcfr
STYLE: Update CTK to fix warning related to wrapping of CTKDICOM module

$ git shortlog 8011739..d72ab0c --no-merges
Jean-Christophe Fillion-Robin (1):
      Workaround to fix HAVE_STAT redefined warning related to DICOM module wrapping

Revision 24135  Directory Listing
Modified Wed Apr 1 06:00:15 2015 UTC (2 years, 5 months ago) by jcfr
ENH: Update CTK to fix warning and include ctkButtonGroup tweaks

$ git shortlog 657853b..8011739 --no-merges
Jean-Christophe Fillion-Robin (1):
      Fix -Wuninitialized in ctkDICOMTableManager

Julien Finet (2):
      Preserve button ids in ctkButtonGroup
      Add QButtonGroup::buttonToggled support

Revision 24120  Directory Listing
Modified Fri Mar 27 07:22:07 2015 UTC (2 years, 6 months ago) by jcfr
BUG: Update CTK to include logger fixes

$ git shortlog 3d972114..657853b --no-merges
Andras Lasso (2):
      BUG: Prevent infinite recursion in Qt log handler
      BUG: Fixed heap corruption error by log handlers

Jean-Christophe Fillion-Robin (3):
      Fix UseCTK.cmake to work for very simple project
      Simplify ctkDICOMTableView constructor removing redundant call
      Fix unused parameter warning in ctkLayoutViewFactory

Revision 24110  Directory Listing
Modified Thu Mar 26 03:30:40 2015 UTC (2 years, 6 months ago) by jcfr
COMP: Update VTKv6 to include fix for vs2013 compilation

//--------------
commit c501ccc5df46d33fa15ae1e5df94459f3b98c52b
Author: Isaiah Norton <isaiah.norton@gmail.com>
Date:   Wed Mar 25 22:51:37 2015 -0400

    Visual Studio 2013 requires the <algorithm> header.
//--------------

Revision 24109  Directory Listing
Modified Wed Mar 25 22:17:51 2015 UTC (2 years, 6 months ago) by jcfr
BUG: Update CTK to include DICOMTableView fixes

$ git shortlog a358caf..3d97211 --no-merges
Andreas Fetzer (2):
      Fixed duplicate connection to Qt signal/slots in ctkDICOMTableView
      init now calls setDicomDatabase, which then calls setUpTableView

Jan Zieher (1):
      getter for XNAT sessionId

Jean-Christophe Fillion-Robin (1):
      DICOMTableView: Do not clear selection if user click outside of existing rows

Sascha Zelzer (2):
      Fixed missing include dirs for plug-in test drivers.
      Don't treat CTKData as a CMake package. Fixes a small issue in #532.

Revision 24107  Directory Listing
Modified Wed Mar 25 07:59:09 2015 UTC (2 years, 6 months ago) by jcfr
ENH: Update SimpleITK to v0.9b01 with few patches

This update includes:

d5b32be Merge topic 'SIMPLEITK-457_AddExhaustiveOptimizer'
2e4af8c Merge topic 'SIMPLEITK-622_LevelSetMotionFixImageNames'
a15c3f2 Merge topic 'SIMPLEITK-623_AddOptmizerWeights'

From: Bradley Lowekamp <blowekamp@mail.nih.gov>

Revision 24048  Directory Listing
Modified Tue Mar 10 17:10:49 2015 UTC (2 years, 6 months ago) by jcfr
ENH: Update VTK to v6.2.0

$ git shortlog d733280..v6.2.0 --no-merges
Aashish Chaudhary (6):
      Do not assume initial min and max values
      Attempt to fix failing independent component tests
      GLSL 120 does not support sampler arrays
      Added missing header
      Fixed errors found using valgrind leak check
      Silenced compiler warnings

Andrew Bauer (1):
      Getting rid of compiler warnings.

Andrew Maclean (2):
      Visual Studio 2013 requires the <algorithm> header.
      Remove the unnecessary find_package command.

Arnaud Gelas (1):
      Limiting number of ModifiedEvent when calling vtkTransform::SetMatrix

Ben Boeckel (19):
      IOXdmf3: remove excess MPI stuff
      install: install missing module-related files
      netcdf: support a system netcdf
      cmake: reformat java compilation commands
      java: add an option to set the target for java compiles
      wxVTKRenderWindow: support wxPython 3.0
      wrapping: find superclasses that are templates
      examples: add shebang lines
      doxygen: remove obsolete options
      doxygen: add an option to disable CHM files
      release: add scripts for release maintenance
      python: don't export Python modules as targets
      maint: use "git checkout" rather than reset
      maint: ignore css files for ctags as well
      metaio: remove stray reject file
      vtkModuleTop: handle UsrMove-like setups
      vtkWrap: use size_t for sizes
      vtkPistonMapper: fix a overload-virtual warning
      vtkWrapTcl: hide dString when there are no methods

Dan Lipsa (1):
      BUG: Fix mispelled excluded class and print out all exclusions.

Dave DeMarle (2):
      per bug 14586 fix external vtkLocal
      allow examples to be built without tests

David C. Lonie (4):
      Fix an error in setting an array length.
      Fix conic point identification in the path renderer.
      Fix warning in vtkLabeledContourMapper.cxx
      Allow the initial GL2PS buffer size to be set.

David Gobbi (1):
      Fix arg conversion of const ref arg via constructor.

Jean-Christophe Fillion-Robin (4):
      vtkRenderer: Fix null pointer crash in ViewToWorld() with no active camera
      vtkhdf5: Fix build error when building on system with glic >= 2.19
      per bug 14826 make find_package vtk more lenient
      vtkCornerAnnotation: Add convenience TextPosition enum

John Tourtellott (6):
      Set geo-origin and -spacing in RequestInformation() call
      Add vtkGDAL class & MAP_PROJECTION key for pipeline data and field data
      Change missing geotransform from error to warning.
      Fix ctest errors
      Turn off wrapping for vtkGDAL.h
      Declare vtkGDAL constructor & destructor private, since class is static

Ken Martin (6):
      Some updates to the timing test
      Fix molecular rendering in parallel projection
      Fix an issue with mapper requiring a polydata input
      Update to a cleaner way of solving the issue
      Fix a couple issues
      A fix for shader link error reporting an molecules with lightkit

Sean McBride (1):
      Remove the addition of a few inappropriate vtkErrorMacro

Shawn Waldon (3):
      Add an option to set default radius of point gaussian
      Fix triangle size for sprites with radius > 1
      Made Point Gaussian mapper handle scale arrays not in dataset

Sujin Philip (4):
      VTK SMP implementation of SynchronizedTemplates3D
      Fix SMP compile warning in VC++
      Use the correct TBB lib based on the build config
      Fix for SMP examples compile issues

Tim Thirion (2):
      Update Android toolchain file (now support NDKs r5 through r10d)
      Add one-pass Android build

acbauer (1):
      Fixing issue of wrong celldata output order from vtkGeometryFilter.

Revision 24043  Directory Listing
Modified Tue Mar 10 03:52:04 2015 UTC (2 years, 6 months ago) by jcfr
BUG: Update CTK to include fix for VTK log message parsing regexp

$ git shortlog 6983ecc..a358caf --no-merges
Andras Lasso (1):
      Fixed VTK log message parsing regexp

Revision 24025  Directory Listing
Modified Thu Mar 5 23:20:03 2015 UTC (2 years, 6 months ago) by jcfr
ENH: Update SimpleITK to v0.9b01 with Registration beta

$ git shortlog 1fe2f56..v0.9b01 --no-merges
Bradley Lowekamp (58):
      Update CastITKToImage to take CovarientVector Images
      Adding initial implementation of FastMarchingUpwindGradientImageFilter
      Add template support for a "point_vec" class of members
      Fixup functions name for adding a seed point
      Block SWIG from processing private method
      Add initial wrapping interface for the CollidingFronts filter.
      Adding CollidingFronts test and updating test generation
      Fixing CollidingFronts tests for wrapped lanuages
      Improved UpwindGradient to include TargetPoints
      Fix initial unsigned integer type warning in test
      Adding baseline images for fast marching colliding fronts and upwind
      Update PCRE superbuild to 8.36
      Update superbuild SWIG to 3.0.5 release
      Add typeid check for transform interfaces
      Fix typeo in name of transform initialize test
      Adding test to prevent polymorphic conversion
      Adding method to set using image gradient filter
      Updating ITK Superbuild version along 4.7 release branch
      Add missing headers to source files
      Moved CreateMetric method to separate file with explicit instantiation
      Adding automatic displacement parameter adapter across scales
      Updating displacement test to follow ITK's SimpleRegistrationTest1
      Adding baseline images to displacement registration tests
      Make displacement example baselines CMake external data with DATA{}
      Adding C++ DisplacementField image registration example
      Fix warning unused parameter warning
      Fix SWIG warning in python about hidden self variable
      Add GetOptimizerLearningRate active measurement for registration
      Adding GetCurrentLevel method to registration method
      Updating StopCondition to be active measurement
      Adding GetOptimizerConvergenceValue active metric
      Improve callback in Displacement registration examples
      Factored out common metric setup code
      Adding Evaluate method to the registration method
      Must initialize metric before it is evaluated
      Correct construction of the composite initial transform.
      Rename Evaluate to MetricEvaluate to be more inline with conventions
      Adding testing for the MetricEvaluate method
      Adding documentation for the MetricEvaluate method
      Fix RegionGrowning template to pass point list by reference
      Update Colliding Fronts testing for Tcl and Lua
      Renaming FastMarchingImageFilter to FastMarchingBaseImageFilter
      Fixing the FastMarchingBase StoppingValue to match ITK
      Adding original FastMarchingImageFilter
      Add support for fast marching seed values
      Adding test for writing VectorImages with the series writer
      Adding baseline image for FastMarchingImageFilter test
      Updating along ITK 4.7 release
      Adding C++ Example for BSpline registration with LBFGSB optimizer
      Remove todo comments in Python example
      Fix erroneous extra character
      Adjusting tolerance for results on the dashboard
      Adding CTest warning suppression for internal header for gcc 4.1.2
      rename typedef to avoid shadowing typename
      Adding a utility script to convert the HTML release notes to Wiki
      Add missing space in wiki link output
      Updating the SWIG doc strings from SimpleITK doxygen
      Update ITK Superbuild version tag v4.7.1

Ziv Yaniv (2):
      ENH: Added non default constructors to all global transformations.
      STYLE: Changed variable names to be consistent with usage in other methods.

From: Bradley Lowekamp <blowekamp@mail.nih.gov>

Revision 24007  Directory Listing
Modified Mon Mar 2 19:29:43 2015 UTC (2 years, 6 months ago) by jcfr
COMP: Simplify logic selecting if OpenSSL project should be built or not

OpenSSL will *NOT* be built if one of these condition is true:

  - OPENSSL_LIBRARIES is defined
  - LIB_EAY_DEBUG and SSL_EAY_DEBUG are defined
  - LIB_EAY_RELEASE and SSL_EAY_RELEASE are defined
  - Slicer_USE_SYSTEM_OpenSSL is True

Revision 24006  Directory Listing
Modified Mon Mar 2 19:29:41 2015 UTC (2 years, 6 months ago) by jcfr
ENH: Improve OpenSSL external project automatically setting OPENSSL_LIBRARIES

Revision 24005  Directory Listing
Modified Mon Mar 2 19:29:40 2015 UTC (2 years, 6 months ago) by jcfr
COMP: Fix download url associated with OpenSSL 1.0.1l

The previous url were using "bitstream id" instead of "item id"

Revision 24003  Directory Listing
Modified Mon Mar 2 13:58:01 2015 UTC (2 years, 6 months ago) by jcfr
COMP: Properly pass url and url_md5 to OpenSSL external project

Revision 24002  Directory Listing
Modified Mon Mar 2 13:33:59 2015 UTC (2 years, 6 months ago) by jcfr
COMP: Fix typo in OpenSSL external project introduced by r23999

Revision 24000  Directory Listing
Modified Mon Mar 2 01:54:34 2015 UTC (2 years, 6 months ago) by jcfr
ENH: Add OpenSSL 1.0.1l as a valid version for both unix and windows

This version will be expected if Slicer is configured with
-DOPENSSL_DOWNLOAD_VERSION:STRING=1.0.1l

Revision 23999  Directory Listing
Modified Mon Mar 2 01:54:32 2015 UTC (2 years, 6 months ago) by jcfr
ENH: Add OPENSSL_DOWNLOAD_VERSION option allow to select OpenSSL version

This commit introduces a new option allowing to
 (a) select the OpenSSL source archive to download on unix system
 (b) select the OpenSSL pre-compiled package to download on winows system

Currently there is only one version supported for either linux or windows.

Revision 23998  Directory Listing
Modified Mon Mar 2 01:54:30 2015 UTC (2 years, 6 months ago) by jcfr
COMP: Fix OpenSSL configure step to use expected zlib include and lib dir

On system without zlib header and library installed, openssl project
couldn't be built. This commit adds a custom step copying the zlib library
to the name expected by openssl build system and uses --with-zlib-{lib|include}
option as required bu Configure script.

While the "threads" option was the default, it is now explicitly specified.

Revision 23997  Directory Listing
Modified Mon Mar 2 01:54:28 2015 UTC (2 years, 6 months ago) by jcfr
COMP: Ensure default env option are considered when building OpenSSL

Revision 23995  Directory Listing
Modified Sun Mar 1 17:49:12 2015 UTC (2 years, 6 months ago) by jcfr
ENH: Simplify windows download for OpenSSL external project

Since version "e" and "h" are expected to be 100% backward compatible [1],
this commit removes the special OpenSSL download for Qt 4.8.5.

[1] http://upstream.rosalinux.ru/versions/openssl.html

Revision 23983  Directory Listing
Modified Wed Feb 25 18:53:07 2015 UTC (2 years, 6 months ago) by jcfr
BUG: Update VTK to revert changes associated with vtkColorTransferFunction

It turns out the proposed fix (http://review.source.kitware.com/#/c/19012/)
does not completely address the problem. This commit revert it and also
revert the VTK commit kitware/VTK@238163f (6657: Add out-of-range colors
to color maps) as it was done in r23910.

The following tests are now passing (tested on Ubuntu 14.04):

     py_sceneImport2428
     py_ThresholdThreadingTest
     py_StandaloneEditorWidgetTest
     py_RSNAVisTutorial
     py_RSNAQuantTutorial
     py_RSNA2012ProstateDemo
     py_JRC2013Vis
     py_NeurosurgicalPlanningTutorialMarkupsSelfTest
     py_NeurosurgicalPlanningTutorial

$ git shortlog e0dda5f..c9fd5fb
Jean-Christophe Fillion-Robin (2):
      Revert "Fix crash where vtkColorTransferFunction has 0 nodes"
      Revert "6657: Add out-of-range colors to color maps"

Revision 23982  Directory Listing
Modified Tue Feb 24 22:46:41 2015 UTC (2 years, 7 months ago) by jcfr
ENH: Update VTK version to release branch of 2015-02-24

This is the list of changes specific to the
Slicer VTK fork (cherry-picked from the previous Slicer/VTK branch):

$ git shortlog 70bad0e..e0dda5f --no-merges
Ben Boeckel (1):
      python: split wrapping functions

Cory Quammen (1):
      Fix crash where vtkColorTransferFunction has 0 nodes

Jean-Christophe Fillion-Robin (12):
      modules: Re-order RenderingOpenGL libraries to fix VTK_ENABLE_KIT link error
      python: Add wrapping of kits if VTK_ENABLE_KITS is ON
      python: Update python module dependency to account for VTK_ENABLE_KITS
      python: Configure PythonInit file for kit when VTK_ENABLE_KITS is ON
      python: Update wrapping function to support kit
      python: Add VTK_ENABLE_KITS to VTKConfig
      python: Update wrapping tool to support multiple hierarchy files
      python: Do not create a new hints file if a kit bundles only one module
      python: Update vtkWrapPython to add mutable object when building kit
      python: Fix vtkWrapPython compiler error ensuring type declaration are first.
      vtkCornerAnnotation: Add convenience TextPosition enum
      Disable Chemistry module to workaround issue #15255

Julien Finet (2):
      Enable GPU Raycast volume mapper for recent NVIDIA drivers on Mac OS X
      GPU raycast volume rendering now supports textures larger than 1024

Steve Pieper (1):
      BUG: WIP: fix vtkPickingManager interaction with widgets

This is the list of new changes specific to VTK:

$ git shortlog d733280..70bad0e --no-merges
Aashish Chaudhary (6):
      Do not assume initial min and max values
      Attempt to fix failing independent component tests
      GLSL 120 does not support sampler arrays
      Added missing header
      Fixed errors found using valgrind leak check
      Silenced compiler warnings

Andrew Bauer (1):
      Getting rid of compiler warnings.

Arnaud Gelas (1):
      Limiting number of ModifiedEvent when calling vtkTransform::SetMatrix

Ben Boeckel (19):
      IOXdmf3: remove excess MPI stuff
      install: install missing module-related files
      netcdf: support a system netcdf
      cmake: reformat java compilation commands
      java: add an option to set the target for java compiles
      wxVTKRenderWindow: support wxPython 3.0
      wrapping: find superclasses that are templates
      examples: add shebang lines
      doxygen: remove obsolete options
      doxygen: add an option to disable CHM files
      release: add scripts for release maintenance
      python: don't export Python modules as targets
      maint: use "git checkout" rather than reset
      maint: ignore css files for ctags as well
      metaio: remove stray reject file
      vtkModuleTop: handle UsrMove-like setups
      vtkWrap: use size_t for sizes
      vtkPistonMapper: fix a overload-virtual warning
      vtkWrapTcl: hide dString when there are no methods

Dan Lipsa (1):
      BUG: Fix mispelled excluded class and print out all exclusions.

Dave DeMarle (1):
      per bug 14586 fix external vtkLocal

David C. Lonie (4):
      Fix an error in setting an array length.
      Fix conic point identification in the path renderer.
      Fix warning in vtkLabeledContourMapper.cxx
      Allow the initial GL2PS buffer size to be set.

David Gobbi (1):
      Fix arg conversion of const ref arg via constructor.

Jean-Christophe Fillion-Robin (3):
      vtkRenderer: Fix null pointer crash in ViewToWorld() with no active camera
      vtkhdf5: Fix build error when building on system with glic >= 2.19
      per bug 14826 make find_package vtk more lenient

John Tourtellott (6):
      Set geo-origin and -spacing in RequestInformation() call
      Add vtkGDAL class & MAP_PROJECTION key for pipeline data and field data
      Change missing geotransform from error to warning.
      Fix ctest errors
      Turn off wrapping for vtkGDAL.h
      Declare vtkGDAL constructor & destructor private, since class is static

Ken Martin (5):
      Some updates to the timing test
      Fix molecular rendering in parallel projection
      Fix an issue with mapper requiring a polydata input
      Update to a cleaner way of solving the issue
      Fix a couple issues

Shawn Waldon (3):
      Add an option to set default radius of point gaussian
      Fix triangle size for sprites with radius > 1
      Made Point Gaussian mapper handle scale arrays not in dataset

Sujin Philip (2):
      VTK SMP implementation of SynchronizedTemplates3D
      Fix SMP compile warning in VC++

Tim Thirion (2):
      Update Android toolchain file (now support NDKs r5 through r10d)
      Add one-pass Android build

acbauer (1):
      Fixing issue of wrong celldata output order from vtkGeometryFilter.

Revision 23971  Directory Listing
Modified Fri Feb 13 22:34:44 2015 UTC (2 years, 7 months ago) by jcfr
ENH: Update CTK to include pythonqt wrapping improvements

$ git shortlog 59dfc7f..6983ecc --no-merges
Alex Yarmarkovich (1):
      ENH: Improve ctkVTKHistogram/ctkTransferFunctionItem pythonqt wrapping

Revision 23970  Directory Listing
Modified Thu Feb 12 07:27:24 2015 UTC (2 years, 7 months ago) by jcfr
ENH: Update VTKv5/VTKv6 to include vtkCornerAnnotation API improvement

//-----------
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Tue Feb 10 19:43:30 2015 -0500

    vtkCornerAnnotation: Add convenience TextPosition enum

    Note: This changed has been submitted on gerrit for its integration
    into VTK  master. See http://review.source.kitware.com/#/c/19191/

    This commit extends the API of the corner annotation by introducing
    an enum named "TextPosition".

    Considering that enums are also wrapped in Python, this will improve
    the readability of both python and c++ code.

    The words Lower{Left|Right} and Upper{Left|Right} have been selected
    to be consistent with vtkLabelPlacer API
//-----------

Revision 23968  Directory Listing
Modified Mon Feb 9 22:19:11 2015 UTC (2 years, 7 months ago) by jcfr
COMP: Update CTK to fix Slicer packaging issue on windows and linux

This commit fixes a regression introduced in r23958 and discussed in [1]

[1] http://slicer-devel.65872.n3.nabble.com/Windows-and-Linux-nightly-packages-tp4033451p4033452.html

// -------------
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Mon Feb 9 17:02:42 2015 -0500

    Ensure PYTHONQT_INSTALL_DIR is not reset in project including CTK

    This commit is an attempt to fix a regression introduced by commontk/CTK@fc92239
    that was causing the Slicer packaging to fail (mainly because the
    variable PYTHONQT_INSTALL_DIR was reset to an empty value after
    "find_path" was called in FindPythonQt.cmake)

    Note that this a workaround, the issue is being discussed with CMake
    developer.
// -------------

Revision 23967  Directory Listing
Modified Sun Feb 8 02:06:16 2015 UTC (2 years, 7 months ago) by jcfr
COMP: Update VTK to fix hdf5 build error on system with glibc >= 2.19

//--------------
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Sat Feb 7 20:59:51 2015 -0500

    vtkhdf5: Fix build error when building on system with glic >= 2.19

    A topic has been pushed on VTK gerrit: http://review.source.kitware.com/#/c/

    As described in [1], since _BSD_SOURCE has been deprecated,
    _DEFAULT_SOURCE should now be used.

    This commit fixes the following build error happening when buiding
    on Ubuntu 14.04 LTS (with gcc (Ubuntu 4.8.2-19ubuntu1) 4.8.2,
    GNU C Library (Ubuntu EGLIBC 2.19-0ubuntu6.5)):

    $ make H5detect
    [...]
    /home/jcfr/Projects/Slicer-Release/VTKv6/ThirdParty/hdf5/vtkhdf5/src/H5detec
     static H5JMP_BUF jbuf_g;

    [1] http://www.sourceware.org/ml/glibc-cvs/2014-q1/msg00252.html
//--------------

Revision 23963  Directory Listing
Modified Thu Feb 5 18:57:31 2015 UTC (2 years, 7 months ago) by jcfr
BUG: Update VTKv6 - Potential fixes for #3949 and #3950 related to OpenGL2

Aashish Chaudhary (27):
      Re-added volume benchmark test
      Typedef the volume test
      Updated volume test
      Tweaked opacity function to force more computation
      Clean up cmake a bit
      Adding GPU independent component feature
      Updated test to highlight mappings
      Adding support for multiple components in GPU RayCast
      Remove limiting check for independent components
      Adding support for multi RGB tables
      Fixed erroneous logic
      Updating shader code to support independent components
      Adding support for independent components for opacity and color function
      Some more updates to support independent components
      Fixed composite blend mode
      Added independent support for min and max projections
      Pass component weights to the shader
      Fixed testing
      Renaming classes for consistency
      Added support for independent components for gradient opacity
      Improved the test a bit
      Reinitialize transfer functions if the property changes
      Independent component is not supported in OpenGL GPU mapper
      Fixed MIP independent shader
      Fixed independent component computing for min intensity projection
      Fixing volume tests not passing on intel machine
      Removed unused code and check

Andrew Bauer (1):
      Improving testing of deleting cells from a polydata.

Ben Boeckel (1):
      vtkRenderingVolumeOpenGL2: remove copy_shaders target

Berk Geveci (1):
      Improved unstructured grid support in dataset_adapter.

Burlen Loring (2):
      vtkweb: buffering issue
      vtkweb: connect to existing session issue

Chris Harris (2):
      vtkWeb: Use unbuffered file read/write for stdout
      vtkWeb: Cleanup python processes that timeout on startup

Christoph Kolb (1):
      Add a method to enable multisampling in the QVTKWidget2

Cory Quammen (1):
      Fixed memory leak when RGBPoints are read

Dan Lipsa (3):
      Accumulate strings printed to console by Python and send them in one piece.
      Fix style problems.
      BUG: Buffer output only for RunSimpleString.

Dave DeMarle (1):
      COMP: fix macro redefinition comp warning

David C. Lonie (3):
      Reenable GL2PS MathText tests.
      Add background color/opacity settings to vtkTextProperty.
      Use the new background color rendering for the labeled contour test.

Jean-Christophe Fillion-Robin (3):
      Fix regression ensuring macro VTK_MAKE_INSTANTIATOR3 configure files
      Fix component names in "vtkhdf5-hl" install rules. Fixes #15282
      Fix MacOSX build error related to OpenGL2/vtkOpenGL.h. See #15285

Joachim Pouderoux (2):
      Small fixes to allow empty cells.
      Fix EnSight Reader BUG 0015268

Julien Jomier (1):
      BUG: RenderedAreaPicker was not using the PickFromList

Ken Martin (14):
      Add valid image for OpenGL2
      Use MCDCMatrix in shaders
      Use MCDCMatrix in shaders
      Fix a compiler warning
      Add two valid images
      Add a subclass for faster composite dataset mapping
      Fix compile issues for es2
      Expose more methods in opengles3
      Fix GLES3
      Add support for vtkTextures Transform ivar
      Fix some dashboard warnings
      Fix for systems with spaces in the path
      Fix memory leak in helper class holding input data
      Fix two compiler warnings

Marcus D. Hanwell (6):
      Benchmarking triangles, chart that updates
      Made a benchmark module, moved the benchmark tools
      Added a --timeout option, default to 1 second
      Call Write on the delimited text writer
      Just make the benchmark module depend on volume rendering
      Use the resolution variable to set the cube size

Matt McCormick (1):
      Reset VTK_MODULES_REQUESTED to all modules with multiple calls.

Paul Edwards (1):
      Fixing how polydata cells are deleted.

Roger Bramon (1):
      Fix QVTKWidget problem on Windows with Aero off and Qt5

Scott Wittenburg (5):
      In the vtkweb loader, add css specific to the proxy editor widget.
      Changes to viewports supporting capturing screenshots for pvweb.
      Support vtkweb and pvweb servers using http only (no websockets).
      Added missing import which broke http-only servers not serving content.
      Updating launcher to include a complete set of example profiles.

Shawn Waldon (2):
      Made sure composite data iterators were deleted properly
      Made vtkPointGaussianMapper handle NULL arrays

Sujin Philip (4):
      Toolchain files for MICs on stampede
      Fix compile warnings in SMP under Windows
      Additions to SMP API
      Fix SMP examples warnings

Tim Thirion (5):
      Create iOS framework in one pass through CMake config
      Clean up iOS build script
      Make vtkVersion available sooner in CMakeLists.txt
      iOS build: check install directories before any compilation
      iOS build: pass OpenGL ES version string to child builds

Utkarsh Ayachit (4):
      Fix inverted ifdef NDEBUG in commit f1a90fd2.
      Forward InteractionEvent to Interactor.
      Miscellaneous vtkContextInteractorStyle fixes.
      Fix missing headers.

Will Schroeder (1):
      Progress reporting was broken

Revision 23961  Directory Listing
Modified Thu Feb 5 00:11:16 2015 UTC (2 years, 7 months ago) by jcfr
ENH: Improve build targets organization in IDE that support folders

This commit set the FOLDER property on all targets to group them
into meaningful "units". This will make development easier ensuring
it is possible to quickly re-build and open the source files associated
with the targets of either a given module, the core libraries or even
the Slicer application.

Currently the grouping is:
* App-SlicerApp
* CMakePredefinedTargets
* Core-Base
* Core-Libs
 * FreeSurfer
 * ITKFactoryRegistration
 * [...]
* Module-<NameOfModule>
* [...]

If for some reason, the folder organization needs to be disabled. Slicer
could be configured with Slicer_USE_FOLDERS set to OFF.

Projects updated in this commit:
* CTK
* SlicerExecutionModel
* OtsuThresholdImageFilter

Notes:

 (1) some of the targets (EMSegment, BRAINSTools, MultiVolume, ...)
are still associated to the root and not yet categorized.

 (2) ideally few more  macros/functions should be introduced: one to
easily configure subject hierarchy plugin, and one to easily configure
tests associated with a CLI.


CTK changes:

// -------------
commit commontk/CTK@ac1370e
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Wed Feb 4 14:47:09 2015 -0500

    Add FOLDER parameter to ctkMacroBuildQtPlugin

    If specified, the target(s) associated with designer, icon engine and
    style plugins will be added into the specified folder when the project is
    configured for an IDE supporting it.

    For more details, see http://www.cmake.org/cmake/help/v2.8.9/cmake.html#prop_tgt:FOLDER
// -------------


SlicerExecutionModel changes:

// -------------
commit Slicer/SlicerExecutionModel@0b780eb
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Wed Feb 4 18:06:25 2015 -0500

    ENH: SEMMacroBuildCLI - Add possibility to associate FOLDER with CLI targets

    In project building a lot of modules (i.e Slicer), whenever possible, it
    is better to keep the huge list of targets organized. To help with this,
    CMake allows to set a FOLDER target property.

    See http://www.cmake.org/cmake/help/v2.8.3/cmake.html#prop_tgt:FOLDER

    This commit extends the SEMMacroBuildCLI API to accept an optional FOLDER
    parameter. If not set, the folder name will default to:

      <SlicerExecutionModel_DEFAULT_CLI_TARGETS_FOLDER_PREFIX><MODULE_NAME>

    By default the prefix is set to an empty string and the folder will be
    named after the module name.

    There are two ways to specify a default prefix value:

     (1) Set the variable SlicerExecutionModel_DEFAULT_CLI_TARGETS_FOLDER_PREFIX
    in the current scope before calling 'SEMMacroBuildCLI'

     (2) Configure the SlicerExecutionModel project with the option
    SlicerExecutionModel_DEFAULT_CLI_TARGETS_FOLDER_PREFIX

    Note that:
     - FOLDER support has been introduced in CMake >= 2.8.3
    and
     - it can optionally be enabled in a project by setting the global
    property named USE_FOLDERS.

    See http://www.cmake.org/cmake/help/v2.8.3/cmake.html#prop_global:USE_FOLDERS

    Finally, to associate CLI test expected to be in the same "FOLDER",
    a variable named <MODULE_NAME>_TARGETS_FOLDER is conveniently set in the
    current scope each time the macro SEMMacroBuildCLI is called.

commit Slicer/SlicerExecutionModel@e84d231
Author: Matt McCormick <matt.mccormick@kitware.com>
Date:   Thu Aug 7 11:09:39 2014 -0400

    BUG: Fix ModuleDescriptionParser test data dir.

    Fixes Parser1Test{1,2}.

    Simplify by consolidation of variables.
// -------------


OtsuThresholdImageFilter changes:

// -------------
commit :Slicer/Slicer-OtsuThresholdImageFilter@5efe412
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Wed Feb 4 18:08:28 2015 -0500

    Associate folder with test targets.
    [...]
// -------------

Revision 23959  Directory Listing
Modified Wed Feb 4 05:37:05 2015 UTC (2 years, 7 months ago) by jcfr
ENH: Update SimpleITK

$ git shortlog 57e6a52..1fe2f56 --no-merges
Bradley Lowekamp (47):
      Adding preliminary displacement transform interface
      Adding additional PimpleTransform method for SetIdentity
      Adding MakeUnique before set methods are called
      Implementing Setting of smoothing parameters and interpolators
      COMP: Default template arguments cannot be used with function
      Fix incorrect argument place holder for DisplacementTrasform functor
      Fix typeo in name of internal function
      WIP: hacking at displacement example
      Add documentation note for the GetDisplacementField methods
      Adding comprehensive testing for displacement field transform
      adding testing for setting interpolator for displacement field
      Adding testing for transformation of point by displacement field
      Adding initial implementation of ImageSeriesWriter
      Adding testing for ImageSeriesWriter class
      Fix up documentation for image series writer.
      BUG: Move show in example to conditional block
      DOC: Improving docs in internal transform class
      Suppress warning about sprintf warning in image series writer.
      Update ITK superbuild version to 4.7.0+
      Don't always display with Displacement examples
      Reduce tolerance for RMS
      Fix leaking of DisplacementField Pimples
      Adding accessors for global physical tolerance of images
      Update ITK Superbuild version along ITK 4.7 release branch
      Fix Doxygen warnings in Command page
      Fix clang warning in lua
      BUG: Disable SimpleITKExamples Superbuild project with flag
      Rename MakeUniqueForWrite to MakeUnique
      Change MakeUnique's access-specifier to public
      Improve ImageRegistrationMethod::SetInitialRegistration copy handling
      Adding testing for new const argument SetInitialTransform method
      Adding implementation of the ScaleTransform
      Adding comprehensive testing for the ScaleTransform class
      improve style in translation transform
      Fixing indenting
      Moving implementation from header file
      Remove unneeded conditional
      Rename r variable to avoid CMP0054 warning
      Updating Java an Python DocStrings
      Updating superbuild along ITK v4.7.0 release branch
      Updating Scalar transforms to expect fixed parameters
      Adding SetMatrix method to Transform classes
      Adding testing for the SetMatrix methods
      Change matrix to pi/2 rotation
      Adding GetName for SimpleITK class
      Include SimpleITK class type in transform ToString
      Adding testing for GetName via ToString methods

Jean-Christophe Fillion-Robin (1):
      Simplify if() conditions on check result variables

Matt McCormick (1):
      ENH: Update doxygen.config for Doxygen version 1.8.9.1.

Ziv Yaniv (1):
      BUG: default translation vector corrected from 3D to 2D

Revision 23958  Directory Listing
Modified Wed Feb 4 05:29:16 2015 UTC (2 years, 7 months ago) by jcfr
ENH: Update CTK to include python decorator update and external project fix

$ git shortlog e23537d..d8cd14e --no-merges
Jean-Christophe Fillion-Robin (2):
      Improve ctkVTKHistogram metaobject for better pythonqt wrapping
      Extend ctkTransferFunction*Item for better pythonqt wrapping

Sascha Zelzer (5):
      Removed left-over method from git merge without implementation.
      Support CMAKE_DEBUG_POSTFIX for CTK superbuild and external DCMTK.
      Ensure find_package() is called in CTKConfig.cmake for external projects.
      Some systems need PYTHON_INCLUDE_DIR2 for FindPythonLibs.cmake.
      Added custom moc options again when moc'ing plug-in headers.

Revision 23956  Directory Listing
Modified Tue Feb 3 18:18:38 2015 UTC (2 years, 7 months ago) by jcfr
COMP: Configure ITKv4 with python executable

If on the build machine there is a python installed on the system, this one
will be found by the ITKModuleHeaderTest.cmake module. To keep the
SlicerConfig.cmake sanity checks quiet, this commit ensure ITKv4 will be
configured with the same python executable accross the entire Slicer build
tree.

Revision 23946  Directory Listing
Modified Tue Feb 3 05:34:59 2015 UTC (2 years, 7 months ago) by jcfr
ENH: Update version of ITK to 4.7.1

$ git shortlog 0f6c2b3..9c9b310 --no-merges
Brad King (1):
      COMP: Fix variable reference in ITKVtkGlue module files

Bradley Lowekamp (7):
      BUG: Enable setting all zeroes for fixed parameters for displacement
      COMP: Fix unsafe usage of sprintf
      BUG: Fix incorrectly ordering of template parameters
      COMP: check for search.h in libtiff
      BUG: restore the center point fixed parameters for scale transforms
      COMP: Use _timezone for Visual Studio
      BUG: Restore IO support for BSplineDeformableTransform

Christopher Mullins (2):
      BUG: Return a correct voronoi partition in Danielsson filter example.
      STYLE: Fix Latex blocks in documentation to include newlines.

Dženan Zukić (2):
      COMP: VS 2012+ compile fixes and CMake warnings
      COMP: fixing quote matching in vtkGlue-related .cmake file

Jean-Christophe Fillion-Robin (1):
      Ensure ITKDeprecated is always excluded from the default module list.

Julien Jomier (1):
      BUG: Output pointer origin is not set causing a memory access error.

Matthew McCormick (3):
      ENH: Bump CMakeLists.txt version to 4.8.0.
      ENH: Bump release branch version to 4.7.1.
      BUG: Clear TransformIO's list of transforms in TransformFileReader.

Niels Dekker (1):
      BUG: workaround for 64bit VS2013 Release segfault

Revision 23936  Directory Listing
Modified Sat Jan 31 03:14:08 2015 UTC (2 years, 7 months ago) by jcfr
COMP: Update teem to allow configuration with CMake < 2.8.12.1

Thanks to the following community members for their investigation and
issue reports:
  Anderle, Kristjan <K.Anderle@gsi.de>
  Andras Lasso <lasso@queensu.ca>
  Sharp, Gregory C. <GCSHARP@mgh.harvard.edu>
  Steve Pieper <pieper@isomics.com>
  Csaba Pinter <csaba.pinter@queensu.ca>
  Matthew Woehlke <matthew.woehlke@kitware.com>
  Christopher Mullins <christopher.mullins@kitware.com>

// ------------------
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Fri Jan 30 22:00:50 2015 -0500

    COMP: Prevent target double inclusion with older version of CMake

    This commit fixes a regression introduced by Slicer/teem@e590e60c
    (COMP: Build/Install modernization) where "export(TARGETS tee, ...)"
    call has been introduced.

    With older version of CMake, the generated target file didn't have the
    multiple inclusion safe guard. Since this feature has been introduced
    in CMake < 2.8.12.1 [1], this commit removes the existing
    test and add a valid multiple inclusion guard.

    [1] http://slicer-devel.65872.n3.nabble.com/Problems-with-building-Slicer-tp4033327p4033330.html
// ------------------

Revision 23921  Directory Listing
Modified Mon Jan 26 22:48:05 2015 UTC (2 years, 7 months ago) by jcfr
COMP: Update VTKv6/OpenGL2 to fix MacOSX build error

// ----------------
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Mon Jan 26 17:10:01 2015 -0500

    Fix MacOSX build error related to OpenGL2/vtkOpenGL.h. See #15285

    This commit ensures the file defining VTK_USE_{CARBON|COCOA} is included
    and fixes the following build error caught by Slicer dashboard:

    // ---------
    In file included from /Users/kitware/Dashboards/Experimental/Slicer-0/Modules/Loadable/VolumeRendering/VolumeRenderingReplacements/vtkSlicerOpenGLRayCastImageDisplayHelper.cxx:25:
    /Users/kitware/Dashboards/Experimental/Slicer-0-build/VTKv6/Rendering/OpenGL2/vtkOpenGL.h:26:11: fatal error: 'GL/gl.h' file not found
    # include  // Include OpenGL API.
              ^
    1 error generated.
    // ---------

// ----------------

Revision 23916  Directory Listing
Modified Fri Jan 23 19:14:09 2015 UTC (2 years, 8 months ago) by jcfr
COMP: Update VTKv6 to include fix for hdf5-hl library install rule

This commit will ensure vtk module can be imported from an installed tree.

//--------------
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Fri Jan 23 13:53:13 2015 -0500

    Fix component names in "vtkhdf5-hl" install rules
//--------------

Revision 23915  Directory Listing
Modified Fri Jan 23 17:55:28 2015 UTC (2 years, 8 months ago) by jcfr
ENH: Allow vtk module to be imported from Slicer python

This commit update launcher settings associated with VTKv6 project so that
"import vtk" can be successfully executed from the python interpreter
executed in the Slicer environment.

./Slicer --launch python -c 'import vtk'

Revision 23914  Directory Listing
Modified Fri Jan 23 17:55:26 2015 UTC (2 years, 8 months ago) by jcfr
BUG: Fix qSlicerLoadableModuleWithPythonTest

To fix the failing test due to a regression introduced by r23828,
this commit
  (1) updates CTK to include update to ctk/__init__.py
  (2) update slicer/__init__.py
to ensure "slicer" module can be imported without an instantiated
  (3) update launcher settings associated with CTK external project to
allow ctk module to be imported without having a qSlicerCoreApplication
instantiated. (See function "pythonPaths" at line 65 of
qSlicerCorePythonManager.cpp)
QApplication.

CTK changes:

$ git shortlog a3d8aa9..e23537d --no-merges
Andreas Fetzer (32):
      Use same way to display data like in the ctkXnatTreeModel
      Make root object protected to allow access to the root object from     within subclasses.
      Use lower case property keys consistently.
      Use label instead of abstractresourceid since a newly generated resource may not have an id yet
      Fixed resource uri for ctkXnatFile
      Added new file which contains all the xnat object fields that are accessible via the xnat rest api
      Use properties for fields that are accessible via the rest api instead of members     of the private implementation.     Use the object field constants for accessing the properties.
      Use constants for accessing the properties of an object
      Use constants for accessing the properties of an subject
      Use constants for accessing the properties of an xnat object
      Added convenience methods for setting file properties
      Added missing includes
      Use constant for accessing properties
      Added functions for getting/setting the description of a project
      The description which is displayed as a tooltip by the Tree- and TableModel     must not be synchronized with the XNAT server.     Hence it should be a member of the private implementation
      Don't store the ID within a property. Since the ID is created automatically     and cannot be changed afterwards it should be stored as a field of the private     implementation.
      Added convenience methods for setting xnatScan properties
      Overwrote the ID and name accessors for xnatResource
      Fixed return type
      Fixed fetching xnatObjects by using the correct properties/fields
      Reverted changes regarding ID handling. ID is no longer stored within the private     implementation but as property again.     Overwrote ID getters and setter where this was necessary.
      Added get/set label methods to xnatResource, since the xnatResource object has no     field name.
      Fixed access to reconstruction file names
      Removed debug messages
      Fixed property access
      Stylistic improvements
      Made id getter and setter virtual
      Added more missing virtual declarations
      Fixed compiler warning. No longer returning reference to local temporary object.
      Removed file with xnat constants. The respective constants are now located in     the according xnat object implementation
      Removed unused includes
      Removed commented-out legacy code

Ivo Wolf (1):
      Refactored and extended download

Jean-Christophe Fillion-Robin (1):
      BUG: Allow ctk to be imported if neither Core or Widget kit are loaded

Revision 23913  Directory Listing
Modified Fri Jan 23 10:39:09 2015 UTC (2 years, 8 months ago) by jcfr
COMP: Update curl project to fix more CMP0054 warnings

This commit fixes warnings occurring when using CMake >= 3.1.0

// ---------------
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Fri Jan 23 05:33:51 2015 -0500

    Simplify an other if() conditions on check result variables

    Remove use of an old hack that takes advantage of the auto-dereference
    behavior of the if() command to detect if a variable is defined.  The
    hack has the form:

     if("${VAR} MATCHES "^${VAR}$")

    where "${VAR}" is a macro argument reference.  Use if(NOT DEFINED) instead.
    This also avoids warnings for CMake Policy CMP0054.
// ---------------

Revision 23912  Directory Listing
Modified Fri Jan 23 10:39:07 2015 UTC (2 years, 8 months ago) by jcfr
COMP: Update DCMTK to fix additional CMP0054 warnings

This commit fixes warnings occurring when using CMake >= 3.1.0

//------------
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Fri Jan 23 05:17:58 2015 -0500

    Simplify if() conditions on check result variables

    Remove use of an old hack that takes advantage of the auto-dereference
    behavior of the if() command to detect if a variable is defined.  The
    hack has the form:

     if("${VAR} MATCHES "^${VAR}$")

    where "${VAR}" is a macro argument reference.  Use if(NOT DEFINED) instead.
    This also avoids warnings for CMake Policy CMP0054.
//------------

Revision 23911  Directory Listing
Modified Fri Jan 23 10:39:05 2015 UTC (2 years, 8 months ago) by jcfr
COMP: Update python to fix CMP0054 warnings

This commit fixes warnings occurring when using CMake >= 3.1.0

$ git shortlog ee53f7..0838470 --no-merges
Chuck Atkins (1):
      Allow system BZip2

Jean-Christophe Fillion-Robin (1):
      Simplify if() conditions on check result variables to fix CMP0054 warnings

Revision 23910  Directory Listing
Modified Fri Jan 23 09:15:44 2015 UTC (2 years, 8 months ago) by jcfr
BUG: Update VTK - Fix tests reverting commit updating

After reverting kitware/VTK@238163f (6657: Add out-of-range colors
to color maps) , the following tests are now passing (tested on MacOSX
10.6.8):

 py_sceneImport2428
 py_ThresholdThreadingTest
 py_StandaloneEditorWidgetTest
 py_labelToggleBug2049
 py_RSNAVisTutorial
 py_RSNAQuantTutorial
 py_JRC2013Vis
 py_NeurosurgicalPlanningTutorialMarkupsSelfTest
 py_NeurosurgicalPlanningTutorial

Revision 23906  Directory Listing
Modified Fri Jan 23 00:05:01 2015 UTC (2 years, 8 months ago) by jcfr
BUG: Update VTK to fix crash when opening Volumes module after loading MRHead

//--------------
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Thu Jan 22 19:02:46 2015 -0500

    Fix vtkColorTransferFunction crash most likely introduced by kitware/VTK@238163f

    Crash happen when calling AdjustRange() with [0, 279]
//--------------

Revision 23899  Directory Listing
Modified Wed Jan 21 08:17:53 2015 UTC (2 years, 8 months ago) by jcfr
COMP: Update CTK to fix unused variable warnings

//----------
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Wed Jan 21 03:15:35 2015 -0500

    Fix unused variable warnings in ctkLayoutViewFactory
//----------

Revision 23898  Directory Listing
Modified Wed Jan 21 08:12:35 2015 UTC (2 years, 8 months ago) by jcfr
COMP: Update CTK to fix CMP0054 warning

This commit fixes warnings occurring when using CMake >= 3.1.0

//------------
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Wed Jan 21 03:09:53 2015 -0500

    Set CMake policy CMP0054 to shut-up associated warning

    This commit will avoid the following warning:

    CMake Warning (dev) at /path/to/cmake-3.1/Modules/ExternalProject.cmake:919 (if):
      Policy CMP0054 is not set: Only interpret if() arguments as variables or
      keywords when unquoted.  Run "cmake --help-policy CMP0054" for policy
      details.  Use the cmake_policy command to set the policy and suppress this
      warning.

      Quoted variables like "PYTHONQT_INSTALL_DIR" will no longer be dereferenced
      when the policy is set to NEW.  Since the policy is not set the OLD
      behavior will be used.
    Call Stack (most recent call first):
      /path/to/cmake-3.1/Modules/ExternalProject.cmake:1764 (_ep_write_initial_cache)
      /path/to/cmake-3.1/Modules/ExternalProject.cmake:1997 (_ep_add_configure_command)
      SuperBuild.cmake:37 (ExternalProject_Add)
      CMakeLists.txt:977 (include)
    This warning is for project developers.  Use -Wno-dev to suppress it.
//------------

Revision 23897  Directory Listing
Modified Wed Jan 21 07:56:30 2015 UTC (2 years, 8 months ago) by jcfr
COMP: Update DCMTK to fix Syntax warning

This commit fixes a warning occurring when using CMake >= 2.8.12

//--------------
Author: Joerg Riesmeier <dicom@jriesmeier.com>
Date:   Wed Jan 21 02:49:54 2015 -0500

    Fixed small issue reported by CMake 2.8.12.

    A trailing "/" had to be removed in order to keep CMake 2.8.12 quiet.
//--------------


This commit fixes the following warning:

CMake Warning (dev) at CMake/dcmtkPrepare.cmake:317 (INCLUDE):
  Syntax Warning in cmake code at

    /path/to/Slicer-0-build/DCMTK/CMake/3rdparty.cmake:9:70

  Argument not separated from preceding token by whitespace.
Call Stack (most recent call first):
  CMakeLists.txt:8 (INCLUDE)
This warning is for project developers.  Use -Wno-dev to suppress it.

Revision 23896  Directory Listing
Modified Wed Jan 21 07:56:28 2015 UTC (2 years, 8 months ago) by jcfr
COMP: Update DCMTK to fix CMP0054 warning

This commit fixes warnings occurring when using CMake >= 3.1.0

//------------
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Wed Jan 21 02:39:50 2015 -0500

    Simplify if() conditions on check result variables

    Remove use of an old hack that takes advantage of the auto-dereference
    behavior of the if() command to detect if a variable is defined.  The
    hack has the form:

     if("${VAR} MATCHES "^${VAR}$")

    where "${VAR}" is a macro argument reference.  Use if(DEFINED) instead.
    This also avoids warnings for CMake Policy CMP0054.

//------------

Revision 23895  Directory Listing
Modified Wed Jan 21 07:56:26 2015 UTC (2 years, 8 months ago) by jcfr
COMP: Update libarchive to fix CMP0054 and CMP0026 warnings

This commit fixes warnings occurring when using CMake >= 3.1.0

//----------------
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Wed Jan 21 02:23:46 2015 -0500

    Fix CMP0026 warning related to usage of GET_TARGET_PROPERTY with LOCATION property

    Backported from libarchive/libarchive@c62d30e

    This commit fixes warning like this one:

    CMake Warning (dev) at tar/CMakeLists.txt:41 (GET_TARGET_PROPERTY):
      Policy CMP0026 is not set: Disallow use of the LOCATION target property.
      Run "cmake --help-policy CMP0026" for policy details.  Use the cmake_policy
      command to set the policy and suppress this warning.

      The LOCATION property should not be read from target "bsdtar".  Use the
      target name directly with add_custom_command, or use the generator
      expression $<TARGET_FILE>, as appropriate.

Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Wed Jan 21 02:14:37 2015 -0500

    Fix warnings for CMake Policy CMP0054

    This commit ensures the variables CMAKE_C_COMPILER_ID and
    CMAKE_C_COMPILER_ID will always be interpreted by removing
    the double quotes.

    It fixes warnings like this one:

    CMake Warning (dev) at CMakeLists.txt:91 (IF):
      Policy CMP0054 is not set: Only interpret if() arguments as variables or
      keywords when unquoted.  Run "cmake --help-policy CMP0054" for policy
      details.  Use the cmake_policy command to set the policy and suppress this
      warning.

      Quoted variables like "CMAKE_C_COMPILER_ID" will no longer be dereferenced
      when the policy is set to NEW.  Since the policy is not set the OLD
      behavior will be used.
    This warning is for project developers.  Use -Wno-dev to suppress it.
//----------------

Revision 23894  Directory Listing
Modified Wed Jan 21 07:56:23 2015 UTC (2 years, 8 months ago) by jcfr
COMP: Update curl project to fix CMP0054 warning

This commit fixes warnings occurring when using CMake >= 3.1.0

// ---------------
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Wed Jan 21 01:47:56 2015 -0500

    Simplify if() conditions on check result variables

    Backported from bagder/curl@fba9f41

    Remove use of an old hack that takes advantage of the auto-dereference
    behavior of the if() command to detect if a variable is defined.  The
    hack has the form:

     if("${VAR} MATCHES "^${VAR}$")

    where "${VAR}" is a macro argument reference.  Use if(DEFINED) instead.
    This also avoids warnings for CMake Policy CMP0054.
// ---------------

Revision 23891  Directory Listing
Modified Tue Jan 20 02:13:55 2015 UTC (2 years, 8 months ago) by jcfr
ENH: Add Slicer_VTK_RENDERING_BACKEND configure option

By default set to "OpenGL", this commit introduces an option allowing
to build VTK using the new "OpenGL2" backend.

Note that the VTK build directory have to be completely removed when
switching between "OpenGL" and "OpenGL2" backend.

See http://www.kitware.com/source/home/post/144

Revision 23890  Directory Listing
Modified Tue Jan 20 02:13:50 2015 UTC (2 years, 8 months ago) by jcfr
ENH: Update VTK to version of 2015-01-19

$ git shortlog 563cc62..751982c --no-merges

Aashish Chaudhary (228):
      Fixed headlight not working right when using the ext renderer
      Fixed missing display, window, and context id not being set
      Fixed splitviewport stereo rendering
      Added new volume rendering code
      Fixed texture state being dirty
      Use correct local bounds
      Fixed rotation bug
      Fixed style
      Fixed geometry beign missing after volume render
      Fixed indent
      Silenced cast warnings
      Fixed style and naming conventions
      Added copyright
      Embedded volume shaders into C++ units
      Fixed broken volume rendering because of uninitialized variable
      Fixed code document style a bit
      Added method to validate volume rendering
      Enable sample distance control
      Enabled additive and composite blend mode
      Use depth buffer to terminate ray
      Fixed incorrect mix geometry and volume rendering
      Added string replacement code
      First pass on compositing shader for the rendering
      Formalizing the grammar for the shader replacement
      Updated volume code to use new compositing mode
      Updating shader to be fully programmable
      Fixed loose ends
      Using appropriate variable names
      Rebuild shader if necessary
      Rename Helper to ShaderComposer as thats best suited
      Added tests for the new volume mapper
      Consolidating shading and color accumulation
      Got maximum intensity working
      Pass mapper to composer calls as its needed to query volume params
      Simplified the code a bit
      Fixed minor calculation bug
      Got rid of hard-coded maximum number of samples
      Removed references to vtkgl
      Separated lookup for clarity
      Compute and store actual max value
      Fixed bad gl state at the start of volume rendering
      Implemented cropping feature
      Using a better amplitude for the noise texture
      Use boolean to skip or consider a pixel for rendering
      Build cropping shader dynamically
      Condensed preprocessor tags
      Perform close bounds check
      Updated tests
      Got clipping working
      Passing size and data for clip planes in a single uniform array
      Implemented clipping via substitution
      Fixed clipping for multiple clip planes
      Fixed normals not getting passed correctly
      Fixed crash on resizing
      Updated clip test planes to reasonable values
      Following consistent way of checking for uninitiliazed values
      Removed hard-coded sample distance
      Adding minimum intensity blend capability
      Fixed wrong initial value of the min value
      Fixed biased not being passed to the shader
      Some more minor fixes
      Fixed rendering of short and some other types
      Added support for double (and other 8 bytes) datatypes
      Adding alpha blending
      Fixed issues with additive blending
      Renaming so that we can replace the old one with the new one
      Porting new volume mapper to proper vtk
      Got new mapper working
      Renamed the new volume module
      Fixed cropping
      Some more fixes
      Removed experimental code on cropping flags
      Updated lighting parameters
      Adding gradient opacity
      Implementing gradient opacity
      Added gradient opacity table to the mapper
      Added some more pieces for the gradient opacity
      Enabled auto-adjust sample distance
      Fixed style
      Added new gradient opacity test
      Added debug code
      Adding gradient opacity calculation
      Fixing / cleaing variables that are not required
      Fixed access from the texture
      Fixing the scaling of the gradients
      Fixing long data types volumes
      Using GLSL version 120
      Making gradient opacity optional
      Removed check for gl error for now
      Fixed shader issues on MAC
      Fix white edge showing up
      Fixed wrong invert matrix being passed
      Revert "Removed experimental code on cropping flags"
      Fixed cropping test
      Fixing gradient vector computation
      Added support for 4 components
      Adding support for mask type
      Fixing shading
      Adding support for label mask type
      Fixing issues
      Restructured the code a bit more to make it flexible
      Fixed some more issues
      Fixed lighting issues
      Clean up some code
      Improvig code readability
      VTK style fixes
      Adding support for parallel projection
      Got parallel projection working
      Disabled the gradient opacity test for now
      Fixed cpp issues
      Silenced compiler warnings
      Implemented release graphics method
      For now set reduction ratio to 1.0
      Fixed texture units
      Fixed wrong bounds used to pass bound values to shader
      Few style fixes
      Updated vtk point picker
      Added support for rendering when clipping by near plane
      Fixed volume geomety not updated
      Using smallest possible delta to offset precision issues
      Fixed release graphics resources
      Re-added gradient opacity
      Wrapped long lines
      Organzied the code bit better
      Disabled the gradient opacity test for now
      Fixed failing tests
      Added missing API to set uniform
      Updating to use vtk shader API
      Removed calls to old API
      Fixed volume not showing up
      Removed unused files
      Fixed licensing
      Removed unused file from cmake
      Updated to use vtkTextureObject
      Use vtkTextureObject if set
      Updated ray cast image display helper to use GL2
      Removed unused code
      Fixed casting to wrong type; copy-paste error
      Updated headers
      Fixed test failing by restoring defaults
      Updated logic for testing for translucency
      Updated logic to check for external texture object
      Updated display helper
      Improved code by removing redundant code
      Fixed style issues
      Added more volume tests that are passing now
      Removed unused header files
      Set referencee to render window for external texture object
      Fixed typo
      Mark as translucent if 1,2 or 4 components
      With Ken, fixed resources not release issue
      Added notes, comments
      Updated volume rendering to use shader cache
      Added error checks for volume render calls
      Using render window shader cache
      Fixed volume tests failing because of shader cache
      ShaderCache should release its graphics resources
      Removed unnecessary call and added notes
      Let shader cache invoke release graphics resources on shader
      Attempt to fix failing test by removing calls to interactor
      Added second baseline to fix failing test on some systems
      Adding support for light kit
      Passing required parameters to the shaders
      Handling more lighting cases
      Fixing headlight
      Fixed gradient opacity computation
      Implementing positional light
      Adding test for testing light kit and fixed shader issues
      Enabling reduction factor for large volumes
      Updated so that we can compute the time to draw correctly
      Updating tests for consistent dashboard results
      Silenced compiler warnings
      Updated baseline and test for light kit
      Removed dead code
      Fixing lighting computation for lightkit
      Added convenient method to check for gradient opacity
      Updated code to use check on availability of gradient opacity
      Removed dead code
      Check for two sided lighting
      Attempt to fix failing tests
      Added a note on the workaround as well
      Commented out debug code
      Renamed for consistency
      Fixed positional light calculation
      Fixing positional light bugs
      Clean up code
      Compute appropriate matrix for normal transformation
      Fixed variable not found
      Fixing variable names
      Fixed style issues
      Fixed various lighting and formatting issues
      Silenced compiler warnings
      Fixed smart volume mapper crashes because of gradient opacity
      Fixed smart volume mapper level test
      Added GDAL based raster reader
      Fixed various minor issues
      Added baseline and data for the testing
      Addressed minor code clean up issues
      Fixed various cleanup issues
      Fixed bad sampling issues when dealing with large sample distances
      Fixed incorrect name used for the test file
      Update texture with the data
      Fixed data not showing up
      Use last texture units for 3D textures
      Added ability to set depth mode formats
      Added ability to use texture modes
      Set texture parameters before creating the texture
      Adding support for 3D textures
      Fixed check for depth texture mode
      Apply scale and bias in the shader
      Added ability to set texture attributes directly
      Make sure to release graphics resources
      Updating volume masks
      Handle large data type textures
      Fixing various issues
      Updated and improved texture object implementation
      Allow reuse of texture units
      Removed debug messages
      Fixing MIP issues
      Fixing some more issues
      Fixed memory leaks and release of textures
      Removed dead code
      Removed code for depth texture mode as they are deprecated
      Style fixes
      Fixed loose ends
      Removed extra flag to force re-computation of texture format
      Updated code so that applications will still work in OpenGL2
      Fixed when mappers try to reuse the same texture

Andrew Bauer (18):
      Adding in a filter to append structured grids together.
      Adding the ability to merge structured grids for composite data sets.
      Fixed issue with ghost cells not being deleted properly.
      Removing temporary file that accidentally got added.
      Fixed issue of possibly modifying other polydatas.
      Removing Tcl tests the duplicate existing Python testing.
      Fixed incorrect cell data output.
      Making some cell locators more efficient.
      Giving a warning if trying to create a subcontroller with 0 procs.
      Temporary fixes for finding ADIOS.
      Fixing flow paths correct injection time and ability to add extra arrays.
      Renaming CurrentTime to CurrentTimeValue due to windows mangling issues.
      Fixing particle paths to have proper SimulationTime output.
      Adding in SimulationTimeStep output for particle paths.
      Getting rid of clang analyzer warnings.
      Skipping the wasteful and unnecessary inverse sin computation.
      Cosmetic change to be consistent with file codeing convention.
      Fix parallel flow paths filters.

Andrew Maclean (5):
      Make the generation of random hills consistent across all platforms.
      Add a missing header in vtkCompositePolyDataMapper2
      ENH: Restore / convert Infovis examples
      Lots of minor changes for Examples to build with OpenGL2
      This fixes the c2039 error in VS2013.

Arnaud Gelas (1):
      Handle properties are not properly set up when starting vtkBoxwidget2

Ben Boeckel (117):
      python: use typedef names
      python: add reference counting to the object map
      FindPythonModules: use a function
      FindPythonModules: search if not found
      vtkmpi4py: empty out Py_{UN,}BLOCK_THREADS
      web: support Image from PIL in testing
      web: print the traceback from errors as well
      vtkPStreamTracer: remove unused function
      vtkModuleMacros: use STREQUAL rather than MATCHES
      cmake: use functions instead of macros
      cmake: minor style nits
      vtkPythonAlgorithm: print out all the error information
      tk: update to support 8.6
      vtkEnSightReader: use memmove for overlapping regions
      vtkFFMPEGWriter: use av_malloc to match the av_free
      vtkChartXY: check the scene before use
      otherByteSwap: fix calls for byteswapping
      netcdf: don't use the cache to set variables in the parent scope
      HeaderTesting: skip non-vtk* files
      HeaderTests: only run if VTK_SOURCE_DIR is set
      vtkChartXYZ: use dummy bounds rather for bounds calculation
      vtkChartXYZ: don't copy the points out
      RenderingOpenGL: remove unused file
      cmake: fix CMP0054 warnings
      cmake: remove variable dereferences in if statements
      windows: use the proper format specifier for DWORD
      windows: put parentheses around mixed && and || operators
      vtkWin32OpenGLRenderWindow: avoid narrowing warnings
      vtkWin32Header: support 64-bit properly on non-MSVC
      vtkWin32Header: always use {Get,Set}WindowLongPtr
      hdf5: avoid CMP0054 warning
      vtkPythonPackages: use IN LISTS syntax in foreach
      vtkPythonPackages: avoid CMP0054 warnings
      vtkOpenGLTexture: don't check for a mapped window
      cmake: remove arguments to else and endfoo commands
      cmake: remove arguments from else and endfoo in alglib
      cmake: remove arguments from else and endfoo in exodusII
      cmake: remove arguments from else and endfoo in expat
      cmake: remove arguments from else and endfoo in freerange
      cmake: remove arguments from else and endfoo in freetype
      cmake: remove arguments from else and endfoo in ftgl
      cmake: remove arguments from else and endfoo in gl2ps
      cmake: remove arguments from else and endfoo in hdf5
      cmake: remove arguments from else and endfoo in jpeg
      cmake: remove arguments from else and endfoo in libproj4
      cmake: remove arguments from else and endfoo in libxml2
      cmake: remove arguments from else and endfoo in mpi4py
      cmake: remove arguments from else and endfoo in netcdf
      cmake: remove arguments from else and endfoo in oggtheora
      cmake: remove arguments from else and endfoo in png
      cmake: remove arguments from else and endfoo in sqlite
      cmake: remove arguments from else and endfoo in TclTk
      cmake: remove arguments from else and endfoo in tiff
      cmake: remove arguments from else and endfoo in verdict
      cmake: remove arguments from else and endfoo in VPIC
      cmake: remove arguments from else and endfoo in xdmf2
      cmake: remove arguments from else and endfoo in xdmf3
      cmake: remove arguments from else and endfoo in zlib
      cmake: remove arguments to else and endfoo commands
      cmake: remove @var@ expansions
      FindTBB: fix up typo'd logic
      cmake: fix up some version checks
      zlib: remove empty if statements
      vtkInformationDataObjectKey: move to CommonDataModel
      numpy_support: always support [u]int64
      numpy_support: raise an error if a type cannot be found
      Revert "vtkInformationDataObjectKey: move to CommonDataModel"
      numpy_support: support using dtype array types
      cmake: use COPYONLY rather than COPY_ONLY
      vtkWrap: some uses of COPY_ONLY weren't even wrong
      numpy_support: don't convert array types if possible
      numpy_support: deep copy for type mismatched array data
      numpy: test numpy_to_vtk when requesting specific types
      vtkParticleTracerBase: remove unused function
      vtkImageCanvasSource2D: add missing newline at eof
      vtkKdNode, vtkOctreePointLocatorNode: don't assign after a short-circuit
      vtkPolyhedron: initialize the iterator
      HyperTree example: use the iterator before invalidating it
      Widgets example: fix up logic around planeSource
      vtkYoungsMaterialInterface: plug memory leaks
      vtkUnstructuredGridGeometryFilter: plug memory leak
      vtkPKdTree: plug memory leak
      vtkDistributedDataFilter: plug memory leaks
      vtkKMeansStatistics: plug memory leak
      vtkAMRFlashReaderInternal: don't return a pointer to temporary memory
      vtkExodusIIWriter: use a larger buffer
      TestIncrementalOctreePointLocator: close file handles
      vtkCGMWriter: fix typo
      vtkNIFTIImageReader: plug memory leaks
      vtkSLCReader: plug memory leak
      vtkPLY: handle realloc errors properly
      vtkEnSightWriter: terminate buffers properly
      vtkImagePlaneWidget: avoid divide-by-zero
      vtkResliceCursorRepresentation: avoid divide-by-zero
      vtkParseMain: handle realloc errors properly
      vtkParseMain: close the input file
      vtkParsePreprocess: handle realloc errors properly
      vtkParsePreprocess: fix up some free() logic for params
      vtkWrapHierarchy: handle realloc errors properly
      TestIncrementalOctreePointLocator: use malloc
      vtkParse: regenerate lex.yy.c
      vtkParse: address cppcheck messages
      vtkReebGraph: add a comment about realloc usage
      vtkOpenGLPolyDataMapper2D: comment possible divide-by-zero
      TestIncrementalOctreePointLocator: remove dead code
      vtkWin32OpenGLRenderWindow: use size_t for integer storage of pointers
      vtkWin32OpenGLRenderWindow: wrap assignments in while() in parens
      hdf5: check for the right policy
      python: remove echo from custom target
      FindMPI: search for msmpi as well
      FindMPI: fix a CMP0054 warning for CMake
      FindMPI: add in the SDK path
      FindMPI: support newer MSMPI
      hdf5: remove conflict markers
      FindMPI: convert to a safer path representation.
      vtkDataArrayTemplate: fix support for compilers without explicit instantiation
      Copyright: bump the year

Berk Geveci (11):
      Added a SeedIds array to the output of stream tracer.
      Added support for specifying split mode.
      Added VTKPythonAlgorithmBase - base class for Python algorithms.
      Fixed vtkImageGradient in parallel.
      Added Python support for making new information keys.
      Removed mrmpi ThirdParty, which was not used.
      Fixed quadratic quad and biquadratic quad derivatives.
      Added a new example demonstrating developing SMP algorithms.
      Added another SMP example.
      Fixed bug in vtkExecutive::CopyDefaultInformation.
      Fixed bug in vtkMaskPoints that caused corrupt output.

Bill Hoffman (2):
      Fix build with mingw 4.8.2 and qt 5.3.2, bug #14735
      Detect win32 or pthread model in a mingw gcc build.

Bill Lorensen (13):
      BUG14463 vtkMy does not work for vtk6
      BUG: 0013057: bad xml input to XML Reader's causes exception
      BUG14527: Subdivision fails for non-manifold data
      BUG: ImageAccumulate overflows for large images
      BUG: Some types of files are not closed after processing
      COMP: A more robust way to check file descriptor leaks
      ENH: Add support to read tiled tiff images
      COMP: Add execption for vtkJSONWriter
      ENH: Restore missing Infovis classes
      ENH: Unit Test FunctionParser
      COJMP: More robust fuzzy results checking
      BUG: Memory leaks detectd by valgrind
      COMP: Prefix HDF5 cmake messages with HDF5:.

Brad King (2):
      ENH: Use if(DEFINED) to simplify conditions
      COMP: Include "vtk_glew.h" instead of "GL/glew.h"

Casey Goodlett (4):
      Ignore files in project.xcworkspace
      Fix names of texture and normal arrays in the OBJ reader
      Fix libpng "Not recognizing known sRGB profile that has been edited"
      Skip install of .pdb files for hdf5 on windows

Chris Harris (3):
      vtkWeb: parseObject now returns an array of actors
      Export same scalar bar title as is displayed by actor
      Update VGL version

Chuck Atkins (21):
      Remove leftover debug messages
      Expose WriteAllTimeSteps as a setable parameter for ADIOS
      Properly handle WriteAllTimeSteps = false for vtkADIOSWriter
      vtkIOADIOS: Fix incorrect multi-block multi-step scalar values.
      vtkIOADIOS: Ensure time values always get written, even if just the step.
      vtkIOADIOS: Collection of small fixes
      jsoncpp: Update to use the seperate-file version
      vtkIOGeometry: Correct typos in older jsoncpp API calls
      jsoncpp: Fix vs7 build error from missing C99 functions
      COMP: Suppress warnings on PGI with commonly used patterns
      COMP: Remove unreachable break; statements following returns
      BUG: Replace a few previously removed exit conditions
      BUG 14681: Allow for early exit when no data can be decoded.
      BUG 14681: Close leftover file handles on exit
      XMLReader: Prevent streams from being closed when they don't exist.
      ADIOS: Resize the write buffer to the known required size.
      ADIOS: Update FindADIOS to match upstream
      ADIOS: Add an initial polydata write-readback test
      HDF5: Fix build errors for PGI on Linux
      ADIOS: Properly handle variable sized data.
      ADIOS: Fix memory leaks by adding deletes

Cory Quammen (26):
      Removed unused types and member variables, fixed formatting
      Rename local functions and embed in anonymous namespace
      Change clamping range for texture coordinates
      Turn on edge clamping
      Fixed errors exposed by changes to clamping of texture coordinates
      Replaced buggy and redundant implementation of GetRGBPoints()
      Updated baseline for when test uses alpha blending
      Improved comments and made some formatting improvements
      Removed code mistakenly introduced during a merge
      Updated test baseline
      Removed unneeded function argument
      Enabled easier specification of custom test name
      Re-enabled some tests overlooked by vtk_add_test_*
      Fixed some file extensions in documentation
      6657: Add out-of-range colors to color maps
      CMake was complained about unknown arguments to find_package
      BUG: Fixed how the header size is computed
      BUG 10708: Fix vtkPolyDataMapper2D color mapping
      Avoid insertion of extra newlines when adding comments
      BUG: Added missing build of lookup table
      Handle coloring by field data
      Enable coloring by indexed lookup for vtkStringArrays
      Added previous signature back for MapScalars() method
      Fixed memory errors in newly added tests
      Fixed test to work on older graphics hardware
      Added alternative baseline image for TestActor2D

Dan Lipsa (25):
      FIX: Get rid of dependent properties.
      FIX: Set the hue range for the default lookup table.
      FIX: NULL data in RequestInformation causes a segfault.
      Fix compilation after upgrade to hdf5-1.8.13
      Build static hdf5 and build on VS 2003 7.1
      Fix mingw release build.
      snprintf from HDF5 conflicts with the one from GMVReader
      Make hdf5 properties advanced.
      Add VTK_COLOR_MODE_DIRECT_SCALARS. See vtkScalarsToColors::MapScalars.
      Fix KdTree::GenerateRepresentation and add test.
      Add a test for VTK_COLOR_MODE_DIRECT_SCALARS
      Fix hdf5 library names.
      Remove lib prefix from windows libraries and mangle additional symbols.
      Fix hdf5 library names for VTK (and ParaView).
      FIX: We don't select 2D annotations.
      Add data_index to Exodus driver
      FIX: remove warning declaration of ‘’ shadows a previous local
      Prefix BUILD_STATIC_EXECS with HDF5 and make it advanced.
      Add missing numpy functions previously available in ParaView 4.1.
      Rename data_index to mode_shape in Exodus reader.
      BUG: Writing an Exodus file in parallel segfaults.
      Stop all processes if one process stops.
      Reshape VTKArrays so that they can be combined through operators.
      BUG: Account for gradient G + mean(G,0)
      Fix conflicts in cmake files from hd5 upgrade.

Dave DeMarle (18):
      Add render mode in which values are drawn as recoverable 24bit colors.
      fix a compilation warning
      Fix test failure
      Fix test failure
      Revert "Fix test failure"
      Revert "Fix test failure"
      now 000 is reserved as the no value (background) color
      fix dashboards that lack multisampling
      make area picker respect prop transformations
      prevent possibly uninitialized ivar use
      java install shouldn't delete /usr/bin !
      shrink size of xdmf3 written files
      fix a bug in value painting for cell arrays
      fix a bug in triangle frustum intersection
      COMP: fix a valgrind leak in new test
      update cdash scrapers to use https
      COMP: fix unused warning
      edge clipping fallback path needs correct edges

David C. Lonie (46):
      Check if the selection array exists before dereferencing it.
      Ignore blanked cells in vtkCellDataToPointData.
      Error if attribute arrays are incorrectly sized in vtkGlyph2D.
      Remove unused variable.
      Don't attempt to render NULL strings.
      Add DebugTextures to FreeTypeTools to show texture background.
      Use unrotated faces to determine text height metrics.
      Move templated methods to private visiblity.
      Style cleanup in vtkTextActor3D.
      Remove pointer tests for ImageActor in vtkTextActor3D.
      Strip newlines from GL2PS comments.
      Always upload test image if a regression test fails.
      Improve aligned and rotated text.
      Update tests and baselines.
      Account for frame width in ScalarBarActor title position.
      Use Round vs Floor(+.5).
      Update baselines due to text rendering changes.
      Fix shadowed variable warning.
      Cache number of points used in asserts.
      Simplify and inline much of the logic in vtkStructuredData.
      Update vtkExtractStructuredGridHelper to remove data descriptions args.
      Batch copy point data.
      Add API to copy ranges of tuples efficiently.
      Copy ranges of points during VOI extraction, if possible.
      Move InsertTuples implementation to helper class.
      Fix "uninitialized usage" warnings.
      Make a clear distinction between extent indices and values.
      Add helper functions for computing partitioned structured data.
      Fix bugs in vtkStructuredImplicitConnectivity.
      Fix vtkPExtractRectilinearGrid extent issues.
      Fix vtkPExtractVOI extent issues.
      Fix vtkPExtractStructuredGrid extent issues.
      Fix a buffer overrun in vtkExtractStructuredGridHelper.
      Remove redeclared variable.
      Fix bool -> int conversion.
      Clamp global VOI to the output whole extent in subset filters.
      More warning cleanup from nightly dashboards.
      Rearrange inline methods in vtkStructuredData.h.
      Move vtkTextActor and vtkTextActor3D into Rendering/Core.
      Add unary minus (negation) to vtkVectorOperators.h.
      Fix c/v qualifier on vtkVector::Normalized and Cross methods.
      Manually mark text buffer images as modified.
      Add a vtkLabeledContourMapper for producing inline labels on isolines.
      Added ability to turn label visibility ON/OFF
      Add vtkTextPropertyCollection.
      Allow multiple text properties to be used in vtkLabeledContourMapper.

David Cole (8):
      Rendering: Use AdjustWindowRect to ensure pixel perfect client size
      Rendering: Retrieve the full screen size in GetScreenSize
      Rendering: Use AdjustWindowRect to ensure pixel perfect client size
      vtkTesting: Refactor RegressionTest, eliminating hard-coded cout
      vtkTesting: If test fails with back buffer, try front buffer too
      VRMLImporter: Fix memory leaks and crashes
      VRMLImporter: Fix crash. Avoid dereferencing NULL pointer (#1624)
      vtkVRMLImporter: if non-NULL, delete CurrentTransform in destructor

David Gobbi (73):
      Add wrap hints for vtkPoints2D and vtkRenderWindow.
      Reactivate the RenderingImage tests.
      Replace python mutable with its value in GetValue().
      Clean up cocoa input event handling.
      Interpret OS X Command key as Ctrl instead of Alt.
      Initialize interactor in Start() if not done yet.
      Fix illegal extent request in ImageThresholdConnectivity.
      14445: Fix vtkImageStencilData IsInside upper bound.
      14552: Check python interp and lib versions.
      12098: Mangle void_p like other swig pointers.
      Exit the Cocoa event loop when the window closes.
      Readability improvements to vtkCocoaGLView event code.
      14999: Python Tk widgets fail to load on Tcl 8.6.
      Remove InstallMessageProc flag from OS X interactors.
      Reduce code duplication for Start() method.
      Ensure python header version matches lib version.
      Remove the deprecated PYTHON_INCLUDE_PATH variable.
      Fix Initialize() and Start() interactor documentation.
      Revert "Remove the deprecated PYTHON_INCLUDE_PATH variable."
      Remove obsolete PYTHON_INCLUDE_PATH from CMakeLists.
      Do not cache deprecated PYTHON_INCLUDE_PATH.
      Make streaming optional for the 3D image mappers.
      14042: Numerical stability of vtkPolyDataToImageStencil.
      BlackmanHarris4 fourth coefficient was ignored.
      Default parameter for Kaiser window is wrong.
      Fix copy-paste parameter name.
      Add missing newline to end of file.
      Fix handling of tolerance in vertical direction.
      Deprecate the obsolete InsertLine method signature.
      Add test for LassoStencilSource orientations.
      Re-enable vtkPolyDataToImageStencil tolerance.
      Python init config used COPYONLY instead of ONLY.
      Fix unreachable-code-break warnings.
      Check whether volume property is null.
      Before c99, variable decls go before other statements.
      Before c99, variable decls go before other statements.
      Before c99, variable decls go before other statements.
      Before c99, variable decls go before other statements.
      Refactor vtkWrapPython into smaller source files.
      Wrap enum constant members for non-vtkObject types.
      Add an enum type to the python wrappers.
      Fix two previously undetected wrapper bugs.
      Wrap namespaces in python.
      Allow use of all enum types as method parameters.
      Move VTK_BUILD_SHARED_LIBS check to generated code.
      Wrap constants more efficiently.
      Avoid creating duplicate wrapped namespaces.
      Only wrap namespaces that have useful contents.
      Update the readme file for new wrapping capabilities.
      Fix compile warnings for vtkParse.tab.c.
      Use a wider integer for the parser stack.
      Fix warnings due to anonymous namespace.
      Revert "Use a wider integer for the parser stack."
      Allow enum types to be used as method parameters.
      Fix "conversion from size_t to int" warning.
      Remove NULL check on reference.
      Fix potential vtkUnicodeStringArray instability.
      Fix warnings due to anonymous namespace.
      Fix type-punned pointer dereference warning.
      Fix warning about comma at end of enum list.
      Fix incorrect index types for loops.
      NumberOfArrays is int, so use int as counter type.
      Fix warning for possible uninitialized array access.
      Fix a bug caused by recent tolerance fixes.
      Fix error when kernel size is greater than slab thickness.
      Remove some unecessary casts.
      Revert "Remove some unecessary casts."
      Allow absence of i64 suffix when __int64 exists.
      Increase tolerance for UnitTestParametricSpline.
      Increase numerical tolerance in UnitTestFunctionParser.
      A "Set" method in the constructor caused a UMC.
      Revert last commit to UnitTestFunctionParser.cxx.
      Make wrappers ignore scoped class definitions.

David Thompson (2):
      Remove MD5 test-data MD5 file.
      Fix SetAllArrayStatus on the ExodusII reader.

Dženan Zukić (1):
      VS2013 compile fix

HDF Group (1):
      hdf5-1.8.13-r25462-reduced

Hans Johnson (1):
      DOC:  Remove documentation that is not relevant to VTK6

Joachim Pouderoux (19):
      Fix code formating & style to VTK coding-style rules.
      Add algorithm header for std::lower_bound function call.
      Fix non Delaunay internal edges added by RecoverEdge().
      Add missing NoBlockSend(vtkIdType) method.
      Remove compilation warnings on some platforms.
      Add support for EDGEFLAG attributes in legacy reader & writer.
      Add a new test for EDGEFLAGS point attributes.
      Fix vtkHyperOctree copy functions.
      Disable edgeflag test if Mesa driver is detected.
      Fix and clean VRML importer code.
      Make vtkContextScene ButtonPress/ReleaseEvent invoke a button event.
      Fix a memory leak that occures when Uniform Variables are updated
      Fix Xdmf3 CMake file to export symbols in DLL.
      Add functions to get data bounds and number of plotted bars.
      Fix Xdmf2 writer: array type was not respected. Also save block name.
      Enhance Xdmf3 writer to save block names.
      Fix a warning (variable shadows a parameter)
      Optimize data array range computation functions.
      Clean and fix STL reader.

Johan Andruejol (1):
      Refactor parts of vtkLookupTable

John Tourtellott (1):
      Fix memory leak in vtkGDALRasterReader::RequestData()

Julien Finet (9):
      Fix vtkAbstractPolygonalHandleRepresentation3D visibility
      Fix crash in vtkFixedSliceHandleRepresentation3D
      Add vtkPlot::SelectionPen and vtkPlot::SelectionBrush
      vtkPlotPoints selections must be sorted
      Add vtkChart::SELECTION_COLUMNS
      Add vtkAbstractContextItem::StackAbove and StackUnder
      Reorder the columns of vtkExtractFunctionBagPlot
      Apply selection pen opacity when drawing selected points
      Fix crash when vtkPlotPoints has no Axis

Julien Jomier (7):
      ENH: Added back support for TDx
      COMP: GLEW_STATIC should be defined with MSVC2010 when building static
      COMP: Missing type for vtkWindow GetScreenSize()
      COMP: Q_OS_X11 doesn't exist with Qt4 replacing it back to Q_WS_X11
      ENH: Added support for ClampToBorder (as it was in OpenGL)
      ENH: Added function to initialize volume
      BUG: AreaPicker doesn't consider position/orientation of assembly

KWSys Robot (6):
      KWSys 2014-08-11 (32023afd)
      KWSys 2014-09-08 (80e852f6)
      KWSys 2014-09-19 (6aa1f800)
      KWSys 2014-09-25 (29ffaf43)
      KWSys 2014-10-31 (88c8cc7f)
      KWSys 2014-11-12 (5843f590)

Ken Martin (175):
      dashboard fixes and debug leak
      some fixes for macs
      fix glyph memory leak and issue on intel
      cleanup reorg and fix some memory leaks
      minor doc fix
      fix unit memory issue
      in progress ios
      more iOS changes and depth peeling fix
      some minor cleanups to wrapped classes
      lighting fix for generated normals
      remove unimplemented methods
      fix a number of dashbaord issues
      fix for lines that are exactly horizontal or vert plus cleanup
      fix for lines that are exactly horizontal or vert plus cleanup
      add support for cell normals
      add support for cell normals
      fix a bad test
      minor cleanup to a test
      forgot to update the python version
      yank test for a feature we do not plan to support
      fix an initialization issue with image reslice
      fix incorrect filename
      added valid image for line lighting in opengl2
      removed broken test form opengl corrected for opengl2
      more ios changes
      some good cleanup
      ** working **  app and some cleanup
      fix for iphone test
      minor fix to cover vtkcompiletools
      remove some extra files that we do not need
      make sure modules are really turned off
      in progress need rebase
      turn off more modules by default
      in progress
      working clean prepping for opengl instancing
      some minor cleanups
      really turn shared libs off
      Fix compile warning in TextureObject
      update toolchains to ios8
      Fix scalar colors using textures
      Fix image mapper positions
      Fix the tcl and python cells test
      Fix otherPrint and TestEmptyInput tests
      fix for failing mac dashbaords
      Remove setting of ambient to 1.0
      Add support for backface properties
      use GL_EXT_gpu_shader4 when picking
      Rename TextureUnitManager to not have the OpenGL
      Rename texture unit manager to not have OpenGL in it
      Forgot to uncomment line on prior commit
      Add support for OpenGL32 instancing in GlyphMapper
      Had to rebase as master had comflicts
      fix opengl es issues with glyphing code
      Try adding support for ARB_instanced_arrays
      Handle case with no lights on
      Remove extra call to set the divisor
      Forgot to add the image hash
      Replace some valid images lost with the big merge and a pick bug
      Fix error in glyphing and extend to mac
      Fix fast path on apple
      Fix cleanup issue
      Fix two glyph issues
      trivial compiler warning fix
      Forgot a file dangit
      Exclude freetype form iOS and andriod
      Remove EdgeFlags test from OpenGL2
      Support edge flags.
      Fix for the 1 0 1 edge flag case.
      Minor cleanup
      Another attempt.  I think this one should work.
      Update the ios example to use GLKit View and put most logic in controller
      temporarily turn of mesa test until Joachim ets a chance to look at it
      Add in support for clipping planes
      Add back in the edge test
      Some suggested changes form Casey and remove user files
      A first cut at a CompositePolyDataMapper2
      Fix compiler warning and increase test threshold
      Cache camera and actor matrices for performance
      Remove the unused old code
      Fix compiler error
      Fix issue with mesa and gl_FrontFacing
      make it so that this test works on the old OpenGL backend
      Fix a MTime check in the matrix cache
      Fix header test warning
      Minor fix for glyphing using CurrentInput
      Fix float to integer comparison in shader code
      Cleanup some indentation
      Convert Projected Tetrahedra class to OpenGL2 backend
      Fix up compiler warning of shadowed variables
      Fixing ray cast image display helper
      Fix a few compiler warnings
      Cleanup a C style cast to keep it real plus a bug fix
      Fix a compile warning
      Remove bad transpose of normal matrix
      Remove some unused headers and code
      Updated API to force use of vtkShaderCache
      Remove some extra code that isnt required
      Get render passes working in OpenGL2
      Restore file that was accidentally changed
      Fix some compiler errors that show up on other compilers
      Add in depth peeling pass and a couple other passes
      A number of Parallel and MPI fixes for OpenGL2
      Fix use of undefined vector behavior.
      Fix for out of range memcpy
      Fix three dashbaord issues
      Fix clearzpass on opengl ES 2
      Fix edge color with composite polydata mapper 2
      Added some ifdef needed for OpenGL ES 20
      Fix a bad merge
      Fix RenderingParallel when wrapped and fix a compiler warning
      Make the old freetype code work with OpenGL2
      Minor fix for clearing the zbuffer
      Add support for imposters for molecular rendering
      Make it so that fragment shaders can modify vertexVC
      Fix some OpenGLES compile issues
      Significantly better performance with EdgeVisibilityOn
      Add two more valid images
      Fix failing cursor2D test and some minor cleanup
      Fix bas valid image size and a couple NULL copies in SLACReader
      Fix Context2D to clear the current shader before drawing.
      Fix lighting overdrive on ImagePlaneWidget
      Camera was caching when shared between multiple renderers
      Fix unnormalized interpolated normals
      Update the Composite Mapper to reflect changing in Edge Rendering
      Fix for shadowed variable warning
      Fail gracefully if depth peeling is not supported
      Fix 2d transparent annotation after depth peeling
      Fix an coordinate issue with CopyToFrameBuffer
      Minor compiler cleanup
      make sure glsl extensions are requested at the start of a shader
      Fixes for wrong case in include file name
      Fixes for composite poly data mapper2
      Make sure scale is included in the normal matrix
      Make sure molecule mapper works with depth peeling
      Fix lighting to use Blinn-Phong specular model
      Reduce the size of the test it was too big for my macbook
      Add valid image for other systems (not AA etc)
      Add in support for OpenGL ES 3.0
      trivial fix for es 2.0
      Fixes so the recent scalar changes compile on OpenGL2
      Improve picking support in OpenGL2
      Minor compile fix for ES
      Fix a few issues with parallel passes in VTK
      remove some leftover debugging code
      A fix for rendering coincident polygons or lines.
      Remove old references to vtkOpenGL.h and fix comment
      Enable IO/Export (minus gl2ps) for OPenGL2
      Fix SynchronizedRenderers to work with use OpenGL2
      Fix gcc warnings and build error with gl2ps
      Fix a bad array reference
      More changes needed to get iceT working and cleanup
      Fix compiler warning
      Add valid image due to different z buffer
      Fix some release graphics resource issues
      Ifdef out some code for OpenGLES systems
      Add a point gaussian mapper for cosmology and cleanup
      Remove test I added from old OpenGL backend
      Fix up some dashboard issues
      Minor fix to the picking code
      Fix floating point issue with chart test
      Add a timing framework in for testing rendering performance
      Filename case issue
      Add another valid image as this test is sensitive to zbuffer
      Fix a simple compiler warning.
      Break the UpdateVBO method into smaller pieces.
      Fix missing virtual destructors
      Improve the performance of the parametric function source
      Add a molecule test
      Uh maybe fixing a cmake issue
      Cleanup the CMake build a bit
      Add aother valid image
      Added another valid image
      Fix a couple long lines
      Add virtual destructors again
      Fix dashbaord compile error and some long lines

Kenneth Moreland (4):
      Change vtkDaxMarchingCubes to vtkDaxContour
      Add compute scalars to Dax contour filter.
      Support Dax marching tetrahedra
      Support passing point field data in Dax threshold filter.

Marcus D. Hanwell (19):
      Added some code to fix Tcl and its use of OpenGL backends
      Added excludes for OpenGL2 headers
      Enable the Java rendering test for OpenGL2 too
      Actually define GLX_GLXEXT_LEGACY to prevent the include
      Update to the upstream GLEW 1.11.0 release
      Added logic for OSMesa contexts
      Add support for OSMesa builds of OpenGL2
      Added colored bar charts, along with a test
      Expand support for the OpenGL2 backend
      Restore test deps for matplotlib tests
      Disable some widget tests building for OpenGL2
      BUG: Fix bug #14378, ensure observer is removed in dtor
      Added a non-const form of vtkTesting::AddArguments
      Trivial fixes for API change in OpenGL2 shaders
      BUG: Fixed error in passing position of key press
      Fix compile failures seen with latest FreeType
      Make the VBO update more selective for picking
      Convert the file name to a const char*
      Minor fixes for code style, indentation, use vtkNew

Matthew Woehlke (2):
      Fix rotation handling in vtkTransformInterpolator.
      Fix operation order in vtkTransformInterpolator.

Nicolas Gallego (1):
      IntersectWithLine method documentation update

Orion Poplawski (1):
      thirdparty: support defaulting all third party library sources

Patric Schmitz (1):
      Include vtkPythonPackages in Web/JavaScript/CMakeLists.txt

Robert Maynard (2):
      Correctly detect that we are compiling with MSVC.
      Enable the output of the number of triangles in the benchmark.

Ronald Römer (1):
      bugfix 14459: Iterating through polydata cells incorrectly.

Sankhesh Jhaveri (107):
      ENH: New RenderingExternal module
      ENH: Added custom renderer and camera classes for external support
      Variable renamed to maintain consistent syntax
      ENH: Cleaned up the ExternalRenderWindow
      Set light transform matrix irrespective of light type
      ENH: Added test for vtkRenderingExternal
      Replace baseline with MD5 sum
      Fix lighting for the external rendering module
      ENH: Fetch viewport size for the existing OpenGL context
      Cleaned debugging code
      Updated baseline for TestGLUTRenderWindow
      FIX: vtkRenderingExternal module is OFF by default
      ENH: Synchronize camera focalpoint
      ENH: External renderer preserves buffers by default
      Using the external renderwindow always uses current context
      ENH: Add ExternalVTKWidget
      STYLE: Fixed indentation as per VTK style guidelines
      ENH: Added interactor to ExternalVTKWidget
      ENH: Compute the window size when initializing from context
      Moved the eye determination code to Start
      ENH: Make sure VTK does stereo rendering
      Use vtkGenericOpenGLRenderWindow
      Attempt at fixing light issues across multiple screens
      Renamed module to vtkRenderingVolumeOpenGLNew
      ENH: Changed dependency from glew to vtkglew
      FIX: Build error due to misplaced colon and style fixes
      ENH: Implement PrintSelf
      STYLE: Fix lines larger than 80 chars
      FIX: Failing HeaderTest and rename vtkGLSLShader
      Bring back deleted files
      FIX: VertexArray issue on APPLE machines
      ENH: Additional tests for new volume mapper
      ENH: Added baselines based generated using old volume mapper
      FIX: Exclude the vtkRenderingOpenGLNew module from BUILD_ALL_MODULES
      FIX: Use RegressionTestImage instead of InteractorEventLoop
      FIX: Disable new volume rendering tests for old mapper
      FIX: Exclude vtkRenderingVolumeOpenGLNew from vtkOpenGL kit
      FIX: Reset clipping planes
      FIX: Remove all vtkgl dependencies for vtkRenderingVolumeOpenGLNew
      Fix unused variable warning
      ENH: Added new vtkOpenGLGPUVolumeRayCastMapper to VolumeOpenGL2
      ENH: Add all GPURayCast tests for OpenGL2 backend
      Remove unused shader files
      Fix cmake string issue
      STYLE: Rename shader variables to maintain consistency
      ENH: Initial take at SmartVolumeMapper support
      ENH: Removed all vtkVolumeTextureMapper3D refs from OpenGL2 module
      Port warning and style fixes from VolumeOpenGL2
      ENH: Sorted out python and tcl tests for new volume rendering
      Make SmartVolumeMapper available for VolumeAMR
      ENH: Volume Mapper benchmark test
      FIX: Make sure context is present
      FIX: Bypass testing if OpenGL extensions not supported
      STYLE: Ensure change follows VTK style
      FIX: Python testing was saving foo_1.valid.png style files
      Removed use of unrequired variable
      FIX: Disable antialiasing in new gpu volume tests
      FIX: Nice axis bounds calculation when flipped
      FIX: Tooltips not showing up when axis inverted.
      ENH: Tests for inverted axis functionality
      Test new volume mapper against positional lights
      BUG: Representation not updating when volume input changed
      Fix crash when running VolumeUpdate test
      Test for large sample distance in volume mapper
      Test against geometry rendering
      Changed the noise generator amplitude to 0.1
      Add baseline for new sample distance test
      Convert RGB Table to use vtkTextureObject
      ENH: Ability to load create alpha textures from raw data
      Minor semantic changes
      ENH: Use texture object for opacity tables
      ENH: Use vtkTextureObject for gradient opacity table
      ENH: Make sure the new API for opacity tables is supported by mapper
      Initial null value for pointer
      ENH: Convert noise and depth textures to use texture object
      Initial work to reformat the window level test
      Started working on gradient opacity test for new mapper
      Added new gradient opacity test
      Test the new mapper for gradient opacity support
      BUG: Fix an issue in the shader code that supports gradient opacity
      Pre-compute gradient function to reduce computation overhead
      Replaced old window level test for a better one
      Check if extensions are supported for the new window level test
      Turn off auto adjust sample distances
      Set parameters before activating texture
      Free the texture object memory at destruction time
      Safety checks before deleting objects
      Safeguard against bad memory access
      Bring back the smart volume mapper window level test
      ENH: Use generic render window to support multiple platforms
      Fix GLUT API include header for Mac OSX and Windows
      Maintain consistent style across classes
      Baseline for SmartVolumeMapper window level test
      Additional baseline for failing test
      Prevent releasing graphics resources on the same memory twice
      Removed unwanted commented out code
      If check against bad memory access
      Support multiple renderers in the ExternalVTKWidget
      Fix segfault due to invalid pointer address
      Fix viewport size change when renderwindow resizes
      Removed redundant commented out code
      Exclude vtkRenderingExternal from BUILD_ALL_MODULES
      Improved style and documentation
      Deleted unrequired commented debug code
      GLUT test as an example for ExternalVTKWidget use
      Disable vtkRenderingExternal module for OpenGL2 backend
      Remove debugging code

Scott Wittenburg (6):
      Properly override ApplicationSession c-tor, supports Crossbar.io.
      This should fix problems with paraviewweb and python 2.6.
      Added alternate jQuery catalyst view constructor.
      Added an rpc method to exit after a delay instead of immediately.
      Update vtkweb loader to support addition of scalar opacity widget.
      Use "-dr" in lauch examples to encourage disabling registry for pvweb.

Sean McBride (94):
      Added comments about the danger of not clamping.
      Fix clang warning about comparision that's always true.
      Added TODOs to indicate source of TestQuadricLODActor failure
      Change #include style from <> to "" for some vtk files
      Changed #include <limits.h> to <climits>
      replaced #include <stdlib.h> with <cstdlib>
      replaced most <time.h> with <ctime> includes
      changed some <assert.h> to <cassert>
      changed some <stddef.h> to <cstddef>
      Fix gcc warning about possible use of uninitialized variable
      Added check for null before dereference, for bug #14671
      cleanup all uses of fclose() in vtkSTLReader, for bug #14515
      Removed dead code in test by using #if 0
      Moved unused var suppression to suppressed dead code warning
      Removed unneeded break statements in switches
      Fixed inconsistent #include style, from <> to ""
      Fixed inconsistent #include style, changed <> to ""
      Fixed SimpleCocoaVTK Xcode project to build properly.
      Fixed bug #14266: fix observation of NSView size change
      Fixed unused const var warning
      Fixed a backwards ‘if’ test, and memory leak
      Eliminated unneeded null checks before using delete/free
      Fixed indentation level
      Fixed ‘null deref’ warning
      Simplified memory deallocation
      Removed useless assignment
      Fixed warning about using null with memcpy
      Removed useless assignments
      Misc cleanup and refactoring
      Bail early on null parameter
      Sync up Cocoa code between OpenGL and OpenGL2
      Added partial/initial support for Cocoa ARC memory management
      Remove dead store to fix warning.
      Added some consts in a few places
      Put initial assignment at declaration
      Fixed analyzer warning by removing null check
      Fixed analyzer warning about possible null deref
      Fixed a few dead store warnings
      Fixed dead store warning by removing redundant 'break'
      Fixed dead store warning by reformulating loop
      Fixed null dereference
      Fixed false positive warning about null deref
      Fixed null dereference
      Fixed obvious null dereferences
      Hopefully supress dashboard compiler warning in QT header
      Fixed use of memory after its deallocation
      Fixed incorrect indentation
      Prevent null deref of ‘null’
      Prevent null deref of ‘composite’ fn pointer
      Init memory to prevent it being used uninitialized
      Removed dead store to ‘j’
      Removed dead stores
      Suppress numerous warnings about using uninitialized memory
      Remove a likely dead store
      Prevent null dereferences
      Fixed null deref and whitespace/indentation
      Fixed obvious dead stores
      Fixed null deref by returning upon error
      Fixed memory leaks and malloc(0)
      Removed minor dead stores, to fix warnings
      Refactor to make intent clear to clang analyzer
      Fixed warning about possible null deref
      Fix clang analyzer warning by adding temp variable
      Fixed warning about using ‘volBounds’ uninitialized
      Only react to NSView frame changes if VTK itself created the NSView
      Suppress clang analyzer warning
      Suppress warning about dead store
      Suppress warning about ‘x’ used uninitialized
      Move warning check to prevent ‘fd’ null deref
      Return after warning to prevent ‘dsa’ null deref
      Simplify and exit quickly if input point ids empty
      Another try to suppress warnings from Qt headers
      Advance null check to before cast
      Fix possible null deref of ‘dsa’
      Added vtkErrorMacro to code paths that give null ptrs
      Removed harmless-looking dead code
      Another attempt to silence warning from Qt header
      Fixed -Wstring-conversion warnings
      Whitespace/spelling
      Fix warning about use-after-free
      Fix possible null deref warnings
      Made some copy-pasted code more self-similar
      Fixed types of some copy-pasted code
      Move some declarations closer to use.
      Removed useless null check
      Return early to avoid null to strcmp()
      Removed dubious #undef of keywords
      Refactoring and cleanup of Cocoa NSWindow and NSView observations
      Remove double underscore in header guards (.txx & __vtk*_txx form)
      Remove double underscore in header guards (.in & __vtk*_h form)
      Remove double underscore in header guards (__vtk*_cxx form)
      Manual tweak of .hxx include guard naming
      Remove double underscore in header guards (.h & __vtk*_h form)
      Manual search and cleanup of "__vtk"

Sebastien Jourdain (5):
      Fix import with latest Autobahn update
      Add missing call to properly handle webgl rendering
      Remove loading of native lib from vtk classes
      Add Get/SetTuple6 methods
      Add additional information for Java package build

Shawn Waldon (13):
      Fix the vtkPolyPlane implicit function
      Change vtkProbeFilter to expose the 'in' threshold
      Move static data in vtkVRMLImporter to local struct
      Assume block request produced what was requested
      Add a documentation module that contains information keys
      Add block amount of detail information key
      Block opacity and color are now more independent
      Add a baseline for block opacity with no depth peeling
      Adding a key to indicate the current process has the block
      Legacy reader/writers for composite data now save field data
      Added comment on required invocation order
      Prefer vtkDoubleArray::GetValue to GetTuple for single component arrays
      Made vtkGaussianSplatter handle composite data input

Sujin Philip (1):
      Fix for buffer overflow in vtkCubeAxesActor class

Tim Thirion (7):
      Prefer xcrun when querying for iOS-related SDK elements
      Add CMake option to select OpenGL ES 2.0 or 3.0
      Add x86_64 to list of archs for iOS simulator
      Surfaces example ported to iOS
      Add CMake script to allow user to `make framework` for iOS
      Remove shell script for creating VTK framework; update iOS readme
      Update CMakeLists for iOS examples

Utkarsh Ayachit (21):
      Refactoring CMake code for Python modules.
      BUG #14971. Fix invalid sprintf() in vtkPNGWriter.
      Add missing <algorithm> include. Needed for std::max/min.
      Handle case when make_vector is called with NumPy arrays.
      Make vtkScalarsToColorsPainter respect ScalarMaterialMode.
      Update TestScalarMaterialMode test image size.
      BUG #14779. Fixes for vtkDistancePolyDataFilter.
      BUG 14693: Fixed vtkAssignAttribute for unnamed arrays.
      BUG #12753: Fixed support for large images.
      BUG #11607: Fixed support for large images.
      Add support for vtkTable to vtkExtractSelectedThresholds.
      Fixed warnings with shadowed variables.
      BUG #15046, BUG #15020: Fix issues with OpenGL 1.2.
      BUG #15058: Fixes unclipped grid.
      BUG #14809: Use title size when placing title in vtkChartXY.
      vtkPlotGrid draws grid even when axis is invisible.
      BUG #15132: Fix incorrect flag check.
      Disable OpenGL error checks in release builds.
      Adding alternate baseline for TestLinePlotAxisFonts.
      Change invalid extent error to a debug message.
      Fixed typo in commit 031f7f6371.

Will Schroeder (5):
      Added hints for vtkBox.GetBounds()
      Updated documentation
      Select internal tetra tessellation based on scalar change
      New data file for QuadraticTetra
      Alternative test image

Revision 23875  Directory Listing
Modified Sat Jan 10 01:05:54 2015 UTC (2 years, 8 months ago) by jcfr
BUG: Update ITKv4 to fix Resample DTIVolume/ScalarVectorDWIVolume tests

This commit fixes a regression introduced by the update of ITK in r23858

// ----------------
BUG: Clear TransformIO's list of transforms in TransformFileReader.

Since TransformFileReaderTemplate and TransformIO do not have very good const
correctness and encapsulation, it is possible to manipulate their members and
change their state in a way they might not expect.

In InsightSoftwareConsortium/ITK@81faafe29, a m_TransformIO member
was added. This is used in
TransformFileReaderTemplate's Update() step instead of creating a new
TransformIOBase instance on every Update.  To keep completely consistent
with the previous behavior, we must clear the TransformIOBase's
internal transform list at the time the class was previously instantiated.

Thanks to Jean-Christophe Fillion-Robin and the Slicer community for
identifying this regression.

Change-Id: If5dfd03b32b31ba765c6781d689e91edb944be3f
// ----------------

Revision 23873  Directory Listing
Modified Fri Jan 9 16:41:54 2015 UTC (2 years, 8 months ago) by jcfr
COMP: Fix linux package using correct teem library folder in launcher settings

Thanks to "Francois Budin <fbudin@unc.edu>" for reporting the problem.

Revision 23871  Directory Listing
Modified Fri Jan 9 07:29:43 2015 UTC (2 years, 8 months ago) by jcfr
BUG: Update CTK so that platform specific end-of-line is used in ctkFileLogger

$ git shortlog 07222d0..e47ac49 --no-merges
Andras Lasso (1):
      ENH: Use platform-specific EOL character in log file

Sascha Zelzer (2):
      Use modern CMake features in plugin build macro.
      Bumped the number of max degrees.

Revision 23865  Directory Listing
Modified Fri Jan 9 00:58:22 2015 UTC (2 years, 8 months ago) by jcfr
COMP: Update teem to fix MacOSX packaging issue

$ git shortlog 93ba14a..71e15b1 --no-merges
Jean-Christophe Fillion-Robin (1):
      COMP: Restore library output path to "lib" folder

From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

Revision 23864  Directory Listing
Modified Fri Jan 9 00:58:20 2015 UTC (2 years, 8 months ago) by jcfr
BUG: Update teem to fix issue #3455

$ git shortlog 9142f9a..93ba14a
Jean-Christophe Fillion-Robin (1):
      COMP: Associate component with teem install rules

From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

Revision 23863  Directory Listing
Modified Fri Jan 9 00:58:17 2015 UTC (2 years, 8 months ago) by jcfr
ENH: Update teem version from 1.10.0 to 1.12.0 with Slicer specific changes

The list of contributors for this update:

$ git shortlog -s 1.10.0..9142f9a
     8  Hans Johnson
     3  Kent Williams
     3  MichelKitware
     1  bigler
     9  blezek
     3  chaircrusher
     5  dlrdave
     2  dmwsci
     5  jbm139
     1  jefferis
     2  jorikb
  1847  kindlmann
     2  matthewbrett
    20  michaelcallahan
    28  michelkitware
     1  olduvaihand
     1  rchoudhury
    15  rjosest
    14  samquinan
    60  tststs

The list of all changes can be visualized here:

   https://github.com/Slicer/teem/compare/1.10.0...9142f9a

Co-authored-by: Hans Johnson <hans-johnson@uiowa.edu>
Co-authored-by: Alex Yarmarkovich <alexy@bwh.harvard.edu>

From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

Revision 23861  Directory Listing
Modified Thu Jan 8 22:23:50 2015 UTC (2 years, 8 months ago) by jcfr
COMP: Update VTK to fix build error on Debian "Jessie". Fixes #3906

Co-authored-by: "Sharp, Gregory C." <GCSHARP@mgh.harvard.edu>

This commit fixes the following build error:

// ----------------
[ 35%] Building CXX object Rendering/OpenGL/CMakeFiles/vtkRenderingOpenGLObjects.dir/vtkXOpenGLRenderWindow.cxx.o
In file included from /usr/include/GL/glx.h:333:0,
                 from /home/gsharp/build/slicer-4/Slicer-build/VTKv6/Rendering/OpenGL/vtkXOpenGLRenderWindow.cxx:30:
/usr/include/GL/glxext.h:480:143: error: ‘GLintptr’ has not been declared
 typedef void ( *PFNGLXCOPYBUFFERSUBDATANVPROC) (Display *dpy, GLXContext readCtx, GLXContext writeCtx, GLenum readTarget, GLenum writeTarget, GLintptr readOffset, GLintptr writeOffset, GLsizeiptr size);
// ----------------

$ git shortlog ea7cdc4..563cc62 --no-merges
Marcus D. Hanwell (1):
      Actually define GLX_GLXEXT_LEGACY to prevent the include

Revision 23858  Directory Listing
Modified Thu Jan 8 19:52:08 2015 UTC (2 years, 8 months ago) by jcfr
ENH: Update ITKv4, SimpleITK and Swig

Co-authored-by: Hans Johnson <hans-johnson@uiowa.edu>

// ------------------------------
ITKv4 changes:

Alexander Schmidt-Richberg (1):
      ENH: Updated Remote Module VariationalRegistration to new git tag

Ali Ghayoor (11):
      ENH: Make ITKv4 compatible with ITKSoftwareGuide
      ENH: Add GetCurrentStepLength to RegularStepGradDescentOptv4
      ENH: Convert three ImageRegistration Examples to ITKv4
      ENH: Add multi-Res and multistage registration Examples to ITKv4
      ENH: Convert DeformableReg examples to ITKv4 reg framework
      BUG: Expand a test to reflect multi-metric registration bug
      BUG: Fix multi metric point sampling bug in ImageRegistrationMethodv4
      ENH: Add direct initialization to SyN registration
      ENH: Direct initialization of SyN by restoring the state
      ENH: LandmarkBasedTransformInitializer supports BSplineTransformType
      DOC: Revise the registration examples of ITKSoftwareGuide

Arnaud Gelas (15):
      COMP: use find_package(VTK COMPONENTS) for LevelSetsv4Visualization
      ENH: Importing Laplacian Deformation for QuadEdgeMesh
      DOC: Add more explanation about SmoothingQuadEdgeMeshFilter's usage
      ENH: SmoothingQuadEdgeMeshFilter::SetCoefficientMethod calls Modified()
      ENH: Add progress report in itk::SmoothingQuadEdgeMeshFilter
      COMP: missing cast when calling gdcm::DataElement::SetByteValue
      ENH: increase LaplacianDeformation code coverage
      STYLE: use typedef rather than inheritance
      BUG: split include directories into appropriate cmake variables HDF5
      BUG: missing gdcm libraries when using system GDCM
      DOC: fix doxygen documentaiton for itk::LaplacianDeformationQuadEdgeMeshFilter
      ENH: Add one method to erase a tag into MetaDataDictionary
      ENH: Adding SubdivisionQuadEdgeMeshFilters to ITK as remote module
      COMP: address clang -Winconsistent-missing-override in ITKQuadEdgeMesh
      COMP: fix warnings on dashboard for Subdivision remote module

Bill Lorensen (5):
      ENH: Specify required VTK modules
      COMP: Wiki examples require additional vtk modules
      ENH: Modify WikiExamples remote config
      COMP: Bad test signature
      COMP: Update tag for wiki examples

Brad King (5):
      ENH: Use if(DEFINED) to simplify conditions
      COMP: Fix vxl_config_macros checks broken by refactoring
      COMP: Fix one more vxl_config_macros check broken by refactoring
      BUG: Fix itk_module_config for repeated calls
      BUG: Fix itk_module_config for repeated calls

Bradley Lowekamp (51):
      PERF: Remove dynamically allocated temporary in evaluate method
      BUG: Implement ITK Style Singleton design pattern
      ENH: Add no throw exception specification for UnRegister methods
      COMP: Must specify order as "noexcept override"
      BUG: Add GetInverse for IdentityTransform
      ENH: Adding SetIdentity method to base DisplacementField class
      BUG: Remove unused redefinition of NULL
      BUG: Don't print to std::cout in PrintSelf
      ENH: Prefer the PrintSelfObjectMacro for printing nested objects
      BUG: Use METER of sCAL scale unit
      BUG: Use PNG_SCALE_METER for PNG sCAL unit
      COMP: Fix signed to unsigned int comparison
      ENH: Extract TiffReaderInternal to separate file
      ENH: Refactor ReadTwoSamplePerPixelImage into template function
      ENH: Refactor GenericReadImage into template function
      BUG: Remove Zeiss 2-channel support code in TIFFImageIO ( and LSMImageIO )
      ENH: Refactor method to convert RGBA image to output buffer
      ENH: Refactor duplicated code to read a page
      BUG: Fix right oriented tiff images
      BUG: Remove dead separated plannar code, add test
      STYLE: Fix minor kwstyle defects in test and test results
      BUG: Use array delete operator for array new allocations
      ENH: add arbitrary TIFF TAGs to meta-data dictionary
      ENH: Reduce code duplicate in TIFFImageIO::ReadCurrentPage
      BUG: Address Coverity warning about null pointer dereferences
      ENH: Remove support for TIFF tile as 3D and dead code
      ENH: RGBA read images should stay unchanged.
      BUG: Override method to MakeOutput by name
      ENH: Refactor per pixel conversion function to per scan-line method
      PERF: Refactor color table lookup
      BUG: Adding missing parentheses around boolean expression
      ENH: adding TIFFImageIO test for RGB palette images
      PERF: Improve recursive Gaussian perfromance with VectorImages
      ENH: Query libtiff to determine compression support
      BUG: Support TIFF tiled image with TIFFReadRGBAImage
      BUG: Use SizeValueType for length of scanline
      PERF: Store causal results directly in output buffers
      COMP: Add explicit conversion to const char
      COMP: Explicitly add override to GetNameOfClass method
      COMP: Address internal segmentation fault with Intel compiler
      ENH: Adding method to set global physical space tolerance
      COMP: Explicitly add override to GetNameOfClass method
      BUG: Add new TypeMacro for non-overloaded classes
      BUG: Fix obscure race condition on access thread pool initialization
      BUG: Updating FDFImageIO remote module
      BUG: Fix segfault when setting displacement field as null
      BUG: Don't enable SSE rounding with OSX and gccxml
      BUG: Add portable access to Tiff field name
      BUG: Fix conversion compilation error
      BUG: Rename remote module FDFImageIO -> IOFDF
      BUG: IOFDF remote module should stay with InsightConsortium repo

Christopher Mullins (22):
      COMP: Allows latex to compile for ITKSoftwareGuide
      COMP: Wrap MeshBase templates
      COMP: Fix warning in BlockMatchingImageFilter
      STYLE: Line lengths in examples should be no longer than 80 chars.
      COMP: Wrap the remaining MeshBase and MeshToMeshFilter types.
      COMP: Fix LaTeX warnings.
      STYLE: Fix formatting/punctuation errors.
      STYLE: Formatting and punctuation fixes.
      DOC: Edits for Book 2 Chapter 1 documentation in the Examples.
      DOC: Edits for book 2 chapter 2.
      DOC: More chapter 2 edits
      DOC: Book 2 Chapter 3 edits (part 1)
      DOC: book 2 chapter 4 Segmentation edits
      STYLE: Fix line length in OpenJPEG license for 80 character.
      DOC: Finish the ImageLinearIteratorWithIndex example.
      DOC: Text and picture problems, book2
      BUG: Fix text in margin issues
      DOC: Edits for the beginning of chapter 5, Statistics
      DOC: Fix empty code block.
      DOC: Fix code overlapping figure
      STYLE: Keep the text in the margins
      STYLE: Put newline before long doxygen reference

Cory Quammen (2):
      COMP: Avoid including VTK_USE_FILE within ITK
      BUG: Fix segfaults in ITKExamples

Danny Perry (2):
      BUG: adding test for vnl_sparse_matrix::mult()
      BUG: size of q buffer should actually be (this->rows())*pcols.

Dirk Padfield (1):
      BUG: Corrected processing of last sigma

GCC-XML Upstream (1):
      ENH: pygccxml v1.6.2 (reduced)

Hans Johnson (12):
      COMP: Add tolerance for comparing floating point
      PERF: Remove non-threadable algorithm components
      BUG: Syntax error in comment
      PERF: Add non-blocking mutex locking.
      ENH: Use TryLock minimize thread stalls
      BUG: ThreadedIndexedContainerPartitioner is inclusive
      STYLE: Remove include_regular_expression from Examples
      BUG: Demonstrate Inv(Inv(T)) != T
      BUG: Ensure Inv(Inv(T)) == T for transforms
      COMP: Valgrind detects uninitialized memory read
      COMP: Missing required base class API component
      ENH: Expand interface for selecting threadpool

Ismael Belghiti (1):
      DOC: Spelling Error in PatchBasedDenoisingBaseImageFilter

Jean-Christophe Fillion-Robin (1):
      Ensure ITKDeprecated is always excluded from the default module list.

Jim Miller (1):
      STYLE: Removing what appears to be a temporary file

Johan Andruejol (1):
      ENH: Fix normalization for null vectors and return the norm

Jon Haitz Legarreta (1):
      ENH: New test for itkLabelShapeOpeningImageFilter

KWSys Robot (3):
      KWSys 2014-09-08 (80e852f6)
      KWSys 2014-10-31 (88c8cc7f)
      KWSys 2014-11-12 (5843f590)

Kent Williams (10):
      COMP: use find_package(VTK COMPONENTS) to specify just needed VTK Components
      BUG: ImageSources/test/CMakeLists.txt incorrect library var reference
      COMP: Fix coverity defects related to RegistrationV4 examples
      COMP: silence warning of vnl_vector_fixed_ref::assert_size
      COMP: Fix various Coverity warnings
      COMP: Fix a typo in an error message print statement.
      COMP: itk::Command-derived class used pointless dynamic_cast.
      PERF: Don't recompute InternalInverse repeatedly
      COMP: Correct orientation/spacing for Philips MultiFrame
      ENH: Add test to exercise issue with Transform::GetInverse

Mark Hiner (2):
      ENH: Update SCIFIO remote module hash
      BUG: Fix duplicate variables in Windows

Matthew McCormick (90):
      DOC: Fix itkSetGetDecoratedInputMacro Doxygen macro.
      ENH: Move FFTComplexToComplexImageFilter out of Review.
      ENH: Add VnlComplexToComplexFFTImageFilter.
      BUG: Use fixed seed for Vnl FFT tests for repeatibility.
      ENH: Bump CMakeLists.txt version to 4.7.0.
      BUG: Do not run vnl_test_na with broken libc++.
      DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx.
      DOC: Remove duplicate text in LaplacianRecursiveGaussian example.
      BUG: Uninitialized m_TransformDirection in ComplexToComplexFFTImageFilter.
      BUG: Fix offset[2] in PointSetToSpatialObjectDemonsRegistrationTest.
      STYLE: Fix style in VoronoiDiagram2D.
      BUG: Fix invalid assignment of second VoronoiBoundaryOrigin.
      BUG: Remove unused m_{SplitEpsilon,SigmoidPrimeOffset}.
      BUG: Fix Win MultiThreader check for successful process creation.
      BUG: Fix VTKPolyDataMeshIO writing for 2D second rank tensor.
      COMP: Fix ImageRegistration8RegisteredSlice.png baseline name.
      DOC: itk::statistics -> itk::Statistics.
      COMP: Fix transform type for ITKv3/IterativeClosestPoint2.
      COMP: Improve const correctness of GradientRecursiveGaussianImageFilter.
      COMP: ThreadJob NULL not defined.
      COMP: Remove unused typedefs in LevelSetsv4Visualization.
      COMP: Remove unused typedef's in VtkGlue.
      ENH: Mark BSplineWarping2Test as RUNS_LONG.
      COMP: Remove call for non-existent variable in Nifti debugging.
      BUG: Close the file on Read and Write in HDF5TransformIO.
      BUG: Remove InsightLegacy test code from TransformHDF5Test.
      ENH: Add {Set,Get}TransformIO for TransformFile{Reader,Writer}.
      STYLE: Use SeriesUIDContainerType and FileNamesContainerType
      ENH: Allow specification of orthogonality tolerance in rigid transforms.
      BUG: TransformFileReader does not clear its TransformList.
      BUG: Prevent dangling pointer in HDF5TransformIO.
      COMP: Do not use _stat64 with MinGW-32.
      COMP: Address LaplacianDeformation Doxygen warnings.
      COMP: Do not wrap the FixedArray of Image SmartPointer's.
      COMP: Add missing wrapping for TransformIOBaseTemplate.
      COMP: Mark DeformableRegistration6Test as RUNS_LONG.
      BUG: Use -py3 when building wrapping for Python 3.
      DOC: Improve ImageRegistration4 grammar.
      ENH: Add IOTransformDCMTK Remote module.
      DOC: Add migration guide for GDCM Rescale slope intercept apply on write.
      COMP: Remove unused typedef's in GPU code.
      STYLE: Improve style of HoughTransform2DLinesImageFilter example.
      COMP: Use ConceptChecking for IterativeInverse dimension check.
      COMP: Wrap TransformIOBaseTemplate for const SmartPointer.
      COMP: Add warning exceptions for third party pcre, swig, gccxml.
      ENH: Bump ITK version to 4.6.1.
      BUG: Add missing ITK_OVERRIDE to ITKImageeSources module.
      BUG: Remove GaussianImageSource members shadowing GenerateImageSource.
      STYLE: Style fixes to ITKImageSources module.
      BUG: GaussianSpatialFunction and GaborImageSource use SpacePrecisionType.
      BUG: Do not perform itk_download_attempt_check when not building ITK.
      DOC: Update GDCMImageIO rescale slope intercept doc.
      BUG: Only register requestion IO COMPONENT modules.
      BUG: Fix wrapping .i, .idx CMake dependencies.
      COMP: Add VTK Python module when wrapping ITKVtkGlue.
      STYLE: Remove NULL definition in itkVoronoiDiagram2DGenerator.
      STYLE: VoronoiDiagram2DGenerator defines a VoronoiDiagramType typedef.
      COMP: Add missing VTK module dependency for LevelSetsv4Visualization.
      BUG: By default, do not create any fixed parameters.
      STYLE: Remove trivial method comments in itkTransform.hxx.
      BUG: PolylineMask Filter's GenerateData is protected / virtual.
      ENH: Add HigherOrderAccurateGradient Module.
      BUG: Use input RequestedRegion Index in SliceBySliceImageFilter internal.
      COMP: Remove extra semi-colon, variable scope in DCMTKFileReader.
      STYLE: Style fixes for Transform classes.
      DOC: Increase Doxygen LOOKUP_CACHE_SIZE.
      BUG: MatrixOffsetTransformBase::GetFixedParameters not thread safe.
      DOC: Index Wiki examples with Doxygen.
      COMP: Bump SphinxExamples remote module.
      DOC: Index Sphinx examples in Doxygen.
      COMP: Remove old java examples.
      COMP: Remove duplicate DiffusionTensor3DReconstruction example reference.
      COMP: Address GradientAnisotropicDiffusionImageFilter example settings.
      COMP: Bump Sphinx Examples remote.
      COMP: Bump WikiExamples remote.
      BUG: Register AzimuthElevationToCartesianTransform to factories.
      DOC: Update texture feature class references.
      BUG: Fix texture feature correlation computation for constant image.
      STYLE: Put ImageToImageFilterCommon in its own file.
      BUG: Wrap ImageToImageFilterCommon.
      STYLE: Put ImageSourceCommon in its own file.
      COMP: Add missing itkImageRegionSplitterBase to ImageSourceCommon.
      BUG: Reset ITK_MODULES_REQUESTED to all modules with multiple calls.
      BUG: Configure against VTK 5.
      COMP: Add ITK_SOURCE_DIR to doxygen EXAMPLE_PATH.
      COMP: Increase DOT_GRAPH_MAX_NODES.
      DOC: Add Doxygen macros for itkSetGetDecoratedObjectMacro.
      ENH: Warning when reading a PNG with UNKNOWN unit and non-unit spacing.
      BUG: Fix VTK5 module export code.
      BUG: Fix LevelSetsv4Visualization VTK variable names.

Michka Popoff (38):
      ENH: Fixes for python 3 support
      BUG: Add VTK_VERSION for older VTK versions
      BUG: Improve SWIG version check
      COMP: Add wrapping for ThreadPool and ThreadJob
      COMP: Remove unimplemented DestroyPool method
      COMP: Fix itkVnlComplexToComplexFFTImageFilter wrapping
      COMP: Do not hide pygccxml warnings
      ENH: Update links in readme file
      STYLE: Remove trailing whitespaces
      STYLE: Set ITK_USE_SYTEM_ZLIB and ITK_USE_SYTEM_SZIP
      BUG: Fix memory leak in MetaImageIO after exception
      ENH: Add script to update pygccxml from upstream
      ENH: Remove Sun OS compatibility for the wrappings
      COMP: Fix for conversion to non-pointer like type warning
      STYLE: LabelObject style
      DOC: Remove broken link from LabelObject class description
      ENH: Do not setup the python tests if not asked
      ENH: Add new GetTypes() and GetTypesAsList() methods to the template class
      COMP: Fix CMP0054 warnings in wrappings
      STYLE: Remove old cmake < 2.8.4 specific code
      STYLE: Remove old cmake < 2.8.5 specific code
      ENH: Update to PCRE 8.36
      COMP: Refactor Wrapping setup and fix legacy warnings
      ENH: Add wrapping configuration to ITKConfig.cmake
      STYLE: Some minor code cleanup in the wrapping setup
      DOC: Fix typo in RelabelComponentImageFilter
      ENH: Deprecate VectorResampleImageFilter
      DOC: Add migration guide for ::Zero and ::One
      ENH: Deprecate ::Zero and ::One
      ENH: Add option to disable sorting by size in itkRelabelComponentImageFilter
      ENH: Add Vector and RGB wrapping to linear interpolator
      STYLE: Remove SORT macro in wrappings
      COMP: Fix warning for InterpolateImageFunction wrapping
      COMP: Add a check for Blocks in GPU module
      COMP: Bump SCIFIO to fix test build warnings
      COMP: Fix wrapping of itkImageFunctionBase
      ENH: Add CVD and CVF types to VectorIndexSelectionCastImageFilter wrappings
      DOC: Improvements for Book1, Chap4

Nick Tustison (7):
      BUG:  Need to explicitly specify spline order.
      ENH:  Initializing the transform center.
      BUG:  Need to check the dynamic cast before any calls.
      ENH:  Adding modifications for point set metrics.
      BUG:  Need to specify TInternalComputationValueType for default metric.
      ENH:  Adding sparse points to B-spline field estimate.
      BUG:  Uninitialized variables.

Richard Beare (1):
      ENH: Include TIFF tags in the MetaDataDictionary

Taylor Braun-Jones (1):
      BUG: Fix SliceBySliceImageFilter doesn't propagate information internally

Umang B (1):
      ENH: Use thread pool to dispatch multithreading tasks

Vivien Delmon (2):
      BUG: ExtractImageFilter::CollapseToSubMatrix fix
      ENH: Add a test on extracted directions in CollapseToSubMatrix mode

Vladimir S. FONOV (1):
      BUG: Fixing incorrect MINC style inverse transform

Ziv Yaniv (1):
      COMP: fixed warnings from gcc4.1.2, made implicit casts explicit


// ------------------------------
SimpleITK changes:

$ git shortlog f2241a13..57e6a526 --no-merges
Bradley Lowekamp (199):
      Adding ANTS neighborhood correlation to registration method
      BUG: UseHistograms was not getting set on ITK filter
      Updating ITK tag along 4.6.0 release
      Hide visibility warnings
      Adding Compare class for transform classes.
      Adding basic comparison driver to compare a transformation
      Adding basic test of the transform compare driver
      Don't automatically convert to md5 hashes for files.
      Moving Python tests to the AdditionalTests file
      Update Python Examples and manual unit tests with standard DATA{}
      Remove the fixed image used for reference
      Adding TRANSFORM_COMPARE option to sitk_add_test
      rename cmake support file with sitk prefix
      Moving sitk custom add test function to separate cmake file
      rename variable SITK_DATA_ROOT to SimpleITK_DATA_ROOT
      Move python add_test wrapper to separate cmake file
      Moving CXX Example testing to examples directory
      Moving python example tests to example directory
      Moving Ruby Lua and TCL example tests to example directory
      remove check for build examples from add tests
      Use if COMMAND to detect if a function is defined
      Move Java test examples to example directory
      Moving R add test wrapper to common cmake file
      Adding missing R SimpleGaussian example
      Moving CSharp examples test to example directory
      Always allow sitk_add_?_test
      In test assert array is not empty
      Adding comparison for ImageRegistrationMethod1 example
      Improve CXX ImageRegistration2
      Switching to JointHistogram MI metric
      Adding verification of for python ImageRegistrationMethod2
      Adding baseline image for demons registration examples
      Always print dart measurement for RMSDifference
      Use "true" for bool values to avoid int to bool comparison warnings
      Adding initial Euler3DTransform class
      Adding Euler3DTransform to header and wrapping
      BUG: Add check for correct size of parameters to transforms
      Add virtual method to set pimple transform
      Core improvements to Euler3DTransform
      Adding comprehensive test of the Euler3DTransform.
      Fix some style issues with EulerTransform interface
      Adding specific translation transform interface
      Adding specific interface for the affine transform
      Adding specific interface for Euler2D transform
      Adding specific versor transform interface
      Adding transform interfaces for 2d and 3d similarity transforms
      Fix PatchBasedDenoising warning for double to in conversion
      Fix unused variable warning
      Set Scale function pointer to null
      Use setter methods for Euler3D constructor with values
      Adding skeleton test place holders for transforms
      Using const vector & for function object parameters
      Fix wrong function called for GetCenter
      COMP: VS11+ requires C++11 nullptr for assignment to std::function
      Detect C++11 nullptr keyword define SITK_NULLPTR as it or NULL
      Adding testing for affine transformation
      Adding gtest predicate and macro for tolerant vector compares
      completed testing for affine transformation
      Adding comprehensive testing for euler2d transform
      Fix default argument to euler2d constructor
      Set old function pointers to null before initializing
      Adding Set/GetTranslation method to Similarity3D
      Adding comprehensive test for Similarity3D Transform
      Remove reference to double for Scale variable
      Adding comprehensive test for similarity 2d transform
      Remove extra Translate method from Versor transform
      Adding specific interface for VersorRigid3D transform
      Adding tests for the versor rigid3d transform
      Remove pre argument for Translate methods
      Adding more testing for transforming points
      COMP: Fix operator<< for std:vector in custom gtest predicate
      Adding missing header files for testing
      Refine logic of using c++11 nullptr
      Adding testing for Similarity2D constructor
      Adding rough json file to generate initial code
      Adding initial generated code from json
      Rename CenterVersorTransformInitializer to add Filter Suffix
      Correct the Versor Initialization wrapping code
      Print parent process object and minor documentation tweaks
      Adding initial testing for Versor transform initializer
      Fixing conversion double to uint8_t conversion warning in test
      Improve error message for transform initializers
      Adding explicit constructor from base transform to vesor
      Moving vector testing facilities to SimpleITKTestHarness
      Must include test harness before gtest
      Moving VectorDoubleRMS Predicate to cxx file
      Adding inline keyword to functions in anonymous namespace
      Adding explicit conversion constructor to transform from base class
      Adding comprehensive testing for the versor initializer
      Explicitly use Self qualifier for virtual method in constructor
      Adding wrapping for ScaleSkewVersorTransform
      Adding comprehensive testing for ScaleSkewVersorTransform
      Don't take address of zero sized std::vector
      Move Matrix/Direction conversion function to TemplateFunctions header
      Adding protected constructor for derived classes to construct pimple
      Adding transform specific interface for bspline transforms
      Adding basic testing for BSplineTransform
      Adding testing of point transform and skew setter
      Adding rough json file to generate initial code
      Adding initial generate code from json
      Rename initial generated files
      Modify generate code for BSplineTransformInitializerFilter
      Adding testing for the BSplineTransfromInitalizerFilter
      Correct skewed point expected value
      Updated ITK super build to tag v4.6.0
      Updating to the official ITK v4.6.0 tag
      Adding GetCoefficientImages method
      Convert <sp\> tag to a space
      Updating JSON doc string from ITK 4.6 with spacing corrections.
      Fix errors in the BSpline test
      Setting BSpline functions pointers to null before initialization
      ENH: Adding masking of fixed and moving image for registration
      BUG: exit with failure code when not enough arguments are specified.
      Adding BSpline registration examples based on ITK DeformableRegistration4
      ITKv4.6 changes the results, renaming old baseline
      Update FFTConvolution baseline for change in origin
      Rename the registration tests file to sitkMethodRegistrationTests
      Create itk SpatialObject from image with conversion
      Move the logic for checking the dimensions of mask match
      Adding testing of mask with registration
      Fix miss matched parenthesizes.
      Fix logic in assert statement.
      Add basic filters library to registration
      ENH: Adding MultiResolutionIterationEvent
      Adding a Python example for multi-resolution BSpline registration
      Adding baseline for new bspline example
      Add SetIdentity method to transform interface
      Adding comprehensive testing for SetIdentity.
      Fix test not clearing string
      Add Transform IO support for BSpline of order 1,2,4
      Addd BSpline::GetOrder method
      Support creation of bspline of order 1,2,3,4
      Adding testing for bspline order
      BSplines of order 0,1,2,3 are support, not 4
      Use unsigned int for bspline order type
      Add support for different bspline order in the initializer.
      Adding GetInverse method to transforms
      Adding doxygen comment for SetInverse
      Adding comprehensive testing for GetInverse method
      Adding missing declaration of GetInverse in PimpleTransform base
      Adding Transform::IsLinear method
      BUG: Use fix image as reference image for bspline transform
      Rename registration SetTransform to SetInitialTransform
      Adding testing for registration transform inplace option
      Adding documentation for SetInitialTransform method
      Adding new registration methods to set moving and fixed transforms
      Adding testing for the initial transforms
      Adding doxygen documentation for initialize transform methods.
      Fix header guarder name to match file
      Use helper macro to set member function pointers
      BUG: Delete pimple before setting
      Remove extra std::auto_ptr in transform pimple
      Adding ScaleVersorTransform interface.
      Adding Get/Set Matrix method to affine transform
      Use the transform helper set macro in versor transforms too
      Add GetMatrix method to matrix offset based transforms
      Adding implementation of GetInverse method for transform class.
      Adding doxygen documentation to the GetInverse method.
      Adding testing for transform's GetInverse method
      Adding testing for GetMatrix method
      Adding testing for transform SetMatrix method
      Add accessor method to get the optimizer scales.
      Adding doxygen documentation for the GetOptimizerScales method
      Adding example which utilizes center estimator and scales estimator
      Adding baseline images and testing for the registration3 example
      Adjust RMS error for displacement field for IRM3 test
      Updating generated documentation strings for SWIG.
      Manually updating R package version.
      Update BugReports URL for R wrapping
      Updating ITK Superbuild version to 4.6.1
      BUG: Pass system search paths from system build to external builds
      Do a try import on setuptools then fall back to distutils
      Add setupegg.py which uses ez_setup to get setuptools
      When installing the wheel package use ez_setup
      Fix Python Download URL
      BUG: Adding missing cmake error variable for wheel process
      Replaced python execfile with python 3 compatible code
      Update ITK External superbuild to ITK 4.7rc01
      Add export specification for instantiated Transform::InternalInitialization
      Fix Registration library's dependency on library with Cast filter
      Make BasicFilters1 library manually specified.
      Correctly do explicit instantiation of member function with specified linkage.
      Updating ITK superbuild towards 4.7rc2
      Fixing conversion double to uint8_t conversion warning in test
      ENH: Updating JSON from ITK doxygen
      Revert "Updating generated documentation strings for SWIG."
      Add Doygen grouping to overloaded procedural methods
      Adds space before for ulink doxygen nodes to SWIG
      Updating SWIG doc strings from latest updated json files.
      Updating Lua Example to latest registration
      Update to v4.7rc01 tag for ITK superbuild
      Fix png inputs sCal flag
      Fixing png sCal field to METER
      Update ITK superbuild to the official 4.7.0 release
      Updating SimpleITK version to v0.8.1
      Updating PythonDownloadPage with 0.8.1 eggs
      BUG: Correct check for empty string for CMake variable type
      Explicitly use DEFINED to check if variable is set
      BUG: Apply escape sequence to problematic characters.

Dave Chen (3):
      Patch to remote -k flag for gzip
      Added missing commas in new JSON files
      DOC: Fixed spacing in the XML to JSON script

David T. Chen (4):
      ENH: Perform download of ITK tag file during build time
      Changed useSeriesDetails default to false
      Fixed for Python 3
      Added ImageRegistrationMethod1 example

Ziv Yaniv (1):
      COMP: CMake change that ensures ITK required modules are on.

Revision 23844  Directory Listing
Modified Wed Dec 24 18:23:19 2014 UTC (2 years, 9 months ago) by jcfr
BUG: Fix python path associated with build tree launcher settings.

Since python_DIR resolved to /path/to/python-install directory, the
intermediate directory is not needed.

Revision 23841  Directory Listing
Modified Sun Dec 21 03:15:09 2014 UTC (2 years, 9 months ago) by jcfr
BUG: Update CTK to fix Fix warning related to missing active camera

// ----------
vtkLightBoxRendererManager - Fix warning related to missing active camera

This issue was occurring after (1) adding a markup and (2) registering
a custom Slicer layout having at least on Slice view.

It addresses the following warning:

  WorldToView: no active camera, cannot compute world to view, returning 0,0,0

The "no active camera" warning/issue is also discussed in Slicer issue
#1690 but note that this commit does NOT address that problem.
// ----------

$ git shortlog cb53ac3..07222d0 --no-merges
Jean-Christophe Fillion-Robin (1):
      vtkLightBoxRendererManager - Fix warning related to missing active camera

Revision 23830  Directory Listing
Modified Tue Dec 16 00:22:43 2014 UTC (2 years, 9 months ago) by jcfr
COMP: Update ITKv4 and VTKv6 to include fix for multiple call to find_package

// --------------
VTKv6 changes:

$ git shortlog b55dad7..ea7cdc4 --no-merges
Matt McCormick (1):
      Reset VTK_MODULES_REQUESTED to all modules with multiple calls.

// --------------
ITKv4 changes:

$ git shortlog 8012adeb..f5e429a --no-merges
Arnaud Gelas (1):
      COMP: use find_package(VTK COMPONENTS) for LevelSetsv4Visualization

Bill Lorensen (2):
      ENH: Specify required VTK modules
      ENH: Modify WikiExamples remote config

Cory Quammen (1):
      COMP: Avoid including VTK_USE_FILE within ITK

Jean-Christophe Fillion-Robin (1):
      COMP: Wiki examples require additional vtk modules

Kent Williams (1):
      COMP: use find_package(VTK COMPONENTS) to specify just needed VTK Components

Matthew McCormick (6):
      COMP: Remove unused typedef's in VtkGlue.
      COMP: Add VTK Python module when wrapping ITKVtkGlue.
      COMP: Remove unused typedefs in LevelSetsv4Visualization.
      COMP: Add missing VTK module dependency for LevelSetsv4Visualization.
      BUG: Configure against VTK 5.
      BUG: Reset ITK_MODULES_REQUESTED to all modules with multiple calls.

Michka Popoff (1):
      STYLE: Remove old cmake < 2.8.4 specific code

Revision 23823  Directory Listing
Modified Wed Dec 10 18:27:19 2014 UTC (2 years, 9 months ago) by jcfr
ENH: Update CTK to also wrap set/get for ctkErrorLogContext File attribute

$ git shortlog 0d2a634..cb53ac3a --no-merges
Jean-Christophe Fillion-Robin (1):
      Update PythonQt decorator of ctkErrorLogContext to include set/get for file

Revision 23822  Directory Listing
Modified Tue Dec 9 22:52:07 2014 UTC (2 years, 9 months ago) by jcfr
ENH: Update CTK to ensure ctkErrorLogContext is available from python

From python, it is now possible to execute the following:

errorLogModel = slicer.app.errorLogModel()
errorLogModel.addEntry(qt.QDateTime.currentDateTime(), \
  slicer.app.applicationPid(), \
  ctk.ctkErrorLogLevel.Debug, \
  "Python", \
  ctk.ctkErrorLogContext("This is a message"), \
  "This is a message")


$ git shortlog 42700cf..0d2a634 --no-merges
Jean-Christophe Fillion-Robin (1):
      Add PythonQt decorator for ctkErrorLogContext

Revision 23815  Directory Listing
Modified Wed Dec 3 19:06:21 2014 UTC (2 years, 9 months ago) by jcfr
BUG: Update CTK to ensure python error a written to stderr

$ git shortlog f341589..42700cf --no-merges
Andras Lasso (1):
      BUG: Fixed issue of writing Python errors to stdout instead of stderr

Revision 23806  Directory Listing
Modified Wed Nov 26 22:02:25 2014 UTC (2 years, 9 months ago) by jcfr
COMP: Update python - Fix configuration error on 32-bit system of type i686

The commit fixes the following error:

// ---------------
CMAKE_SYSTEM_PROCESSOR:i686

/home/thiele/Slicer-SuperBuild-Debug/python-build/../Python-2.7.3/Modules/_ctypes/libffi/src/i686/ffi.c

  Tried extensions .c .C .c++ .cc .cpp .cxx .m .M .mm .h .hh .h++ .hm .hpp
  .hxx .in .txx
Call Stack (most recent call first):
  cmake/extensions/CMakeLists.txt:183 (add_python_extension)

// ---------------

[python]

$ git shortlog 47845c5..ee53f79 --no-merges
Jean-Christophe Fillion-Robin (1):
      Fix configuration of ctypes extension in case system processor is i686



Thanks to  "Thiele Kobus <TKOBUS@partners.org>" for his help identifying
the issue.

Revision 23805  Directory Listing
Modified Wed Nov 26 22:02:23 2014 UTC (2 years, 9 months ago) by jcfr
ENH: Update build system to more robustly check bitness using void ptr size

This commit update the build system so that void pointer size is used
instead of system process name.

[CTK]

$ git shortlog 9e8f66f..f34158 --no-merges
Jean-Christophe Fillion-Robin (1):
      Check bitness using void ptr size instead of system processor name

[DMCTK]

$ git shortlog f461865..042de27 --no-merges
Jean-Christophe Fillion-Robin (1):
      Update CMake build system to more robustly check bitness using void pointer size

Revision 23801  Directory Listing
Modified Wed Nov 26 05:44:15 2014 UTC (2 years, 10 months ago) by jcfr
COMP: Update CTK to fix generator expression introduced in previous commit

$ git shortlog 6dfdb85..9e8f66fd --no-merges
Jean-Christophe Fillion-Robin (1):
      Fix generator expression introduced in previous commit d779b43

Revision 23800  Directory Listing
Modified Wed Nov 26 05:21:15 2014 UTC (2 years, 10 months ago) by jcfr
COMP: Fix CMake 3.x warnings related to CMP0054 and CMP0026

* Update ExternalProjectDependency based on commontk/Artichoke@6725b6a

* This commit fixes warning like these ones:

// ----------------------
CMake Warning (dev) at CMake/ctkMacroCheckExternalProjectDependency.cmake:345 (if):
  Policy CMP0054 is not set: Only interpret if() arguments as variables or
  keywords when unquoted.  Run "cmake --help-policy CMP0054" for policy
  details.  Use the cmake_policy command to set the policy and suppress this
  warning.

  Quoted variables like "SB_SECOND_PASS" will no longer be dereferenced when
  the policy is set to NEW.  Since the policy is not set the OLD behavior
  will be used.
Call Stack (most recent call first):
  CMake/ctkMacroCheckExternalProjectDependency.cmake:596 (ExternalProject_Message)
  CMakeExternals/Log4Qt.cmake:9 (ExternalProject_Include_Dependencies)
  CMake/ctkMacroCheckExternalProjectDependency.cmake:568 (include)
  CMake/ctkMacroCheckExternalProjectDependency.cmake:614 (ExternalProject_Include_Dependencies)
  CMake/ctkBlockCheckDependencies.cmake:132 (ExternalProject_Include_Dependencies)
  CMakeLists.txt:970 (include)
// ----------------------

// ----------------------
1>-- Configuring Loadable module: Transforms [qSlicerTransformsModuleExport.h]
1>CMake Warning (dev) at C:/D/P/SonoEQ-0-build/Slicer-build/CTK/CMake/ctkMacroBuildQtPlugin.cmake:168 (get_target_property):
1>  Policy CMP0026 is not set: Disallow use of the LOCATION target property.
1>  Run "cmake --help-policy CMP0026" for policy details.  Use the cmake_policy
1>  command to set the policy and suppress this warning.
1>  The LOCATION property should not be read from target
1>  "qSlicerAnnotationsModuleWidgetsPlugins".  Use the target name directly
1>  with add_custom_command, or use the generator expression $<TARGET_FILE>, as
1>  appropriate.
1>Call Stack (most recent call first):
1>  C:/D/P/SonoEQ-0-build/Slicer-build/CTK/CMake/ctkMacroBuildQtPlugin.cmake:181 (ctkMacroBuildQtPlugin)
1>  Modules/Loadable/Annotations/Widgets/DesignerPlugins/CMakeLists.txt:36 (ctkMacroBuildQtDesignerPlugin)
// ----------------------


* Updates of the associated projects are reported below:

[Artichoke]
$ git shortlog c3eb170..6725b6a
Jean-Christophe Fillion-Robin (12):
      Rename Artichoke into ExternalProjectDependency
      Add cmake sphinx extension based on Kitware/CMake@3c8226e59
      Add explicit support for function and macro directive
      Add sphinx gitignore
      Add sphinx documentation
      Convert README into rst and reference it from index.rst
      Include "indices and tables" only if generating html
      Add docs badge
      Merge pull request #8 from mwoehlke-kitware/installable-external-projects
      Fix tests including the correct module (broken after commit 9106d3d)
      Tweak test in ExternalProject_Message to avoid warning related to CMP0054
      Update tests setting policy CMP0054 to OLD.

Matthew Woehlke (1):
      Add function to install external CMake projects

[CTK]
$ git shortlog 1c97e54..6dfdb85 --no-merges
Andreas Fetzer (1):
      Remove empty build command and set install command empty. Thus is cannot happen     that the dcmtk libraries are installed to some unintended location.     Setting dcmtk_dir to dcmtk-build directory

Christian Askeland (4):
      fixed crashing line in ctkFileDialog for Qt5.
      improved in-code description of previous ctkFileDialog crash fix
      Fixed broken doxygen generation for Plugin Framework
      set doxygen variable ensuring macro definitions of type MY_FOO(arg) dont mess up doc generation

Jean-Christophe Fillion-Robin (2):
      Update ExternalProjectDependency based on commontk/Artichoke@388fc33
      Update ctkMacroBuildQtPlugin to fix CMake warning related to CMP0026

Sascha Zelzer (1):
      Removed custom QT5_INSTALL_PREFIX variable.

Revision 23797  Directory Listing
Modified Mon Nov 24 18:37:46 2014 UTC (2 years, 10 months ago) by jcfr
BUG: Update ITKv4 to include fixes for TIFF Reader/Writer

$ git shortlog 56fae27..8012ade --no-merges
Bradley Lowekamp (22):
      ENH: Extract TiffReaderInternal to separate file
      ENH: Refactor ReadTwoSamplePerPixelImage into template function
      ENH: Refactor GenericReadImage into template function
      BUG: Remove Zeiss 2-channel support code in TIFFImageIO ( and LSMImageIO )
      ENH: Refactor method to convert RGBA image to output buffer
      ENH: Refactor duplicated code to read a page
      BUG: Fix right oriented tiff images
      BUG: Remove dead separated plannar code, add test
      STYLE: Fix minor kwstyle defects in test and test results
      BUG: Use array delete operator for array new allocations
      ENH: add arbitrary TIFF TAGs to meta-data dictionary
      ENH: Reduce code duplicate in TIFFImageIO::ReadCurrentPage
      BUG: Address Coverity warning about null pointer dereferences
      ENH: Remove support for TIFF tile as 3D and dead code
      ENH: RGBA read images should stay unchanged.
      ENH: Refactor per pixel conversion function to per scan-line method
      PERF: Refactor color table lookup
      BUG: Adding missing parentheses around boolean expression
      ENH: adding TIFFImageIO test for RGB palette images
      ENH: Query libtiff to determine compression support
      BUG: Support TIFF tiled image with TIFFReadRGBAImage
      COMP: Add explicit conversion to const char

Matthew McCormick (1):
      COMP: Do not use _stat64 with MinGW-32.

Richard Beare (1):
      ENH: Include TIFF tags in the MetaDataDictionary

From: Bradley Lowekamp <blowekamp@mail.nih.gov>

Revision 23792  Directory Listing
Modified Wed Nov 19 13:52:57 2014 UTC (2 years, 10 months ago) by jcfr
BUG: Update VTKv5 to include fix for vtkRenderer and  HandleRepresentation3D

$ git shortlog d8540e7e..dbbeaad --no-merges
Julien Finet (1):
      Fix vtkAbstractPolygonalHandleRepresentation3D visibility

Nicole Aucoin (1):
      BUG: fix null pointer crash in view to world with no active camera

Revision 23770  Directory Listing
Modified Sat Nov 1 02:53:20 2014 UTC (2 years, 10 months ago) by jcfr
COMP: Update CTK project - Fix compilation error when python is disabled

$ git shortlog 68a1ce2..1c97e54 --no-merges
Dzenan Zukic (1):
      Ensure CTKVisualizationVTKWidget build with VTK6 and python disabled.

Sascha Zelzer (2):
      Added an option to skip install commands for plugins.
      Using : as separator might conflict with absolute paths on Windows.

From: Dzenan Zukic <dzenan.zukic@kitware.com>

Revision 23760  Directory Listing
Modified Wed Oct 29 15:42:12 2014 UTC (2 years, 10 months ago) by jcfr
COMP: Update VTK to fix VS2013 compilation errors.

Co-authored-by: Dzenan Zukic <dzenan.zukic@kitware.com>

// -------------
$ git shortlog c9862c5..b55dad7 --no-merges
Jean-Christophe Fillion-Robin (1):
      Fix VS2013 compilation. Add missing <algorithm> include. Needed for std::max

Utkarsh Ayachit (1):
      Add missing <algorithm> include. Needed for std::max/min.

Revision 23750  Directory Listing
Modified Mon Oct 20 17:49:56 2014 UTC (2 years, 11 months ago) by jcfr
BUG: Update CTK to fix issue with ctkMenuComboBox

$ git lg 19c9668..68a1ce2 --no-merges
* a2cce54 - ctkXnatResource download function implemented (11 days ago) <Tom Doel>
* 6ab9b11 - BUG: Fixed missing list elements problem (25 hours ago) <Andras Lasso>
* d3af228 - Replaced Qt5::Gui dependency with Qt5::Widgets. (4 days ago) <Stefan Kislinskiy>
* b9393da - Set QT_INSTALLED_LIBRARY_DIR in case of Qt5. (7 days ago) <Stefan Kislinskiy>
* 055c319 - Change sleep duration from 200ms to 250ms. (11 days ago) <Stefan Kislinskiy>
* 30d745a - Add NOMINMAX definition to global compile flags. (11 days ago) <Stefan Kislinskiy>
* 5002282 - Fixed incompatibilities between Windows.h and Qt 5 (NOMINMAX). (12 days ago) <Stefan Kislinskiy>
* a1f5a9e - Fixed Qt4/5 MOC issues regarding QIconEngineV2. (13 days ago) <Stefan Kislinskiy>
* 8f8208d - Add missing error log context parameter. (13 days ago) <Stefan Kislinskiy>
* 4f9073e - ENH: Clear box icon replaced with a less harsh one, a simple 'x' that does not indicate error (3 weeks ago) <Csaba Pitner>
* c2b9c56 - Add ctkCollapsibleButton::flat property (3 weeks ago) <Julien Finet>
* 553ecd7 - Add documentation for ctk*PopupWidget (8 weeks ago) <Julien Finet>
* 8e9b0a0 - Added a Signal which is used to do something before the session is closed. (8 weeks ago) <Daniel Knorr>

Revision 23730  Directory Listing
Modified Thu Sep 25 19:56:17 2014 UTC (3 years ago) by jcfr
ENH: Add option Slicer_ITKV3_COMPATIBILITY. See #3825

This option enabled by default will allow (if disabled) to build Slicer
with ITKv3 compatibility later disabled and ITK_USE_64BITS_IDS enabled.

Co-authored-by: Bradley Lowekamp <blowekamp@mail.nih.gov>

Revision 23729  Directory Listing
Modified Thu Sep 25 19:49:02 2014 UTC (3 years ago) by jcfr
COMP: Remove dependency on ITKDeprecated. See #3830

This commit updates ITK to include custom Slicer patch ensuring that
independently of the value of the ITKV3_COMPATIBILITY option,
ITKDeprecated is not include in the list of default modules.

It updates

  (1) BRAINSTools to remove ITKDeprecated from the list
      of required ITK components.

  (2) EMSegment to explicitly call find_package(ITK..) and use
      ITK_LIBRARIES variable when executable and library are added.

Note that at the time of this commit the pull request updating the
LASegmenter extension  to remove ITKDeprecated dependency is pending.
See https://github.com/ljzhu/LASegmenter/pull/2

// -------------
BRAINSTools updates:

$ git shortlog 6f99866..b82c7c8
Jean-Christophe Fillion-Robin (1):
      COMP: Remove ITKDeprecated from the list of ITK components.

// -------------
ITKv4 updates:

$ git shortlog baf8174bb..56fae278
Jean-Christophe Fillion-Robin (1):
      Ensure ITKDeprecated is always excluded from the default module list.

Revision 23728  Directory Listing
Modified Thu Sep 25 19:49:00 2014 UTC (3 years ago) by jcfr
ENH: Update ITKv4 to include fix for repeated call to "find_package(ITK ..)"

Associated gerrit topic is:

  http://review.source.kitware.com/#/c/16963/

// ----------
Author: Brad King <brad.king@kitware.com>
Date:   Wed Sep 10 09:22:34 2014 -0400

    BUG: Fix itk_module_config for repeated calls

    Fix use of _${ns}_${mod}_USED settings to block reporting a module more
    than once in a single itk_module_config call.  Do not leak the
    _${ns}_${mod}_USED settings outside a single call to itk_module_config
    so that a future call to the macro with the same ${ns} will use a fresh
    set of modules.

Revision 23727  Directory Listing
Modified Thu Sep 25 19:48:58 2014 UTC (3 years ago) by jcfr
ENH: Update ITKv4 project to include latest release branch changes

This commit updates the version of ITK to what will be the 4.6.1 patch
release.
$ git shortlog 056d97b66..554e46a1
Christopher Mullins (1):
      COMP: Wrap MeshBase templates

Revision 23724  Directory Listing
Modified Wed Sep 24 19:36:11 2014 UTC (3 years ago) by jcfr
ENH: Refactor management of external project launcher settings.

This commit moves the definition of launcher setting into each external
projects.

The different type of setting (listed below) are passed to the the main
project (Slicer) using labels set using "mark_as_superbuild" function.

Type of settings and associated labels:

  Build tree:

    * LIBRARY_PATHS_LAUNCHER_BUILD
    * PATHS_LAUNCHER_BUILD
    * PYTHONPATH_LAUNCHER_BUILD
    * ENVVARS_LAUNCHER_BUILD

  Install tree:

    * LIBRARY_PATHS_LAUNCHER_INSTALLED
    * PYTHONPATH_LAUNCHER_INSTALLED
    * PATHS_LAUNCHER_INSTALLED
    * ENVVARS_LAUNCHER_INSTALLED

This patch has been tested on factory-win7, factory-south-ubuntu and
factory. The SlicerLauncherSetting.ini and SlicerLauncherSettingToInstall.ini
file have been compared with / without this patch and the file are
similar. The few differences are explained below:
* nonexistent path are not configured anymore
* on unix, following r23613, a new version of incrTcl is used and path
have been updated to reflect this. Since there are to version of incrTcl
(4.0.0 and 4.0.1), the path to "4.0.1" are considered.

Revision 23723  Directory Listing
Modified Wed Sep 24 19:36:08 2014 UTC (3 years ago) by jcfr
STYLE: Rename variable used to configure python launcher

This change is done anticipating a simplification of how additional
library path and python path are associated with either the different
launchers.

Revision 23716  Directory Listing
Modified Sat Sep 20 05:17:14 2014 UTC (3 years ago) by jcfr
BUG: Update ITKv4 - Fix GDCMImageIO and TIFFImageIO

The fix related to TIFFImageIO (InsightSoftwareConsortium/ITK@6791b4a3)
should help when building Slicer with option ITK_USE_64BITS_IDS enabled.

// -----------
$ git shortlog c768e9b..056d97b --no-merges
Arnaud Gelas (1):
      BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is false

Bradley Lowekamp (1):
      BUG: Fix overflows computing size of read tiff image

Matthew McCormick (1):
      BUG: gdcm::StringFilter recognizes backslash delimiter.

Revision 23710  Directory Listing
Modified Fri Sep 19 02:25:53 2014 UTC (3 years ago) by jcfr
COMP: Fix windows numpy build error.

This commit is an attempt to fix the following error:

      File "numpy\core\setup_common.py", line 247, in long_double_representation
      24>    raise ValueError("Could not lock sequences (%s)" % saw)
      24>ValueError: Could not lock sequences (None)

To explain the changes, the content of the file "SLICER_README.txt"
now bundled in the archive is reported below:

// ------------
This archive has originally been downloaded from sourceforge.

  URL http://sourceforge.net/projects/numpy/files/NumPy/1.4.1/
  MD5: 5c7b5349dc3161763f7f366ceb96516b


The patches located in the "patches" subdirectory have all been
applied and are descibed below:

  0001-BLD-fix-build-error-on-Windows-with-MSVC9.-Thanks-to.patch

     Generated using: git format-patch c17738a..4872cac

     Applied using: Did NOT apply cleanly. File numpy/core/setup_common.py
                    manually updated.

     The issue addressed by this patch has been reported on
     the Slicer list [1] on Sept 18th 2014 and has also been
     discussed on the numpy list [2] on July 10th 2011.

     The error message was:

      File "numpy\core\setup_common.py", line 247, in long_double_representation
      24>    raise ValueError("Could not lock sequences (%s)" % saw)
      24>ValueError: Could not lock sequences (None)

     [1] http://slicer-devel.65872.n3.nabble.com/Numpy-build-error-on-trunk-tt4032488.html
     [2] http://mail.scipy.org/pipermail/numpy-discussion/2011-July/057614.html
// ------------

Revision 23709  Directory Listing
Modified Thu Sep 18 22:15:06 2014 UTC (3 years ago) by jcfr
ENH: Update ITKv4 project to integrate BSpline registration improvements.

Thanks to "Andras Lasso <lasso@queensu.ca>" for testing.

From Andras:

"I’ve done some tests and it seems that with the new ITK version
computation time of BSpline registration is significantly decreased
(by a factor of about 1.5-2x), while the computed transforms look
the same.

[...]

MR brain tumor, rigid, 0.01
Nightly: 9 sec
ITK-c768e9b: 8 sec

MR brain tumor, rigid+bspline, 0.01
Nightly: 106 sec
ITK-c768e9b: 49 sec

Dental surgery CBCT, rigid, 0.002
Nightly: 14 sec
ITK-c768e9b: 15 sec

Dental surgery CBCT, rigid, 0.01
Nightly: 66 sec
ITK-c768e9b: 57 sec

Dental surgery CBCT, rigid+bspline, 0.002
Nightly: 76 sec
ITK-c768e9b: 55 sec

Dental surgery CBCT, rigid+bspline, 0.01
Nightly: 1200+ sec (could not wait for it to finish)
ITK-c768e9b: 623 sec
"

// ----------
$ git shortlog 7c3a15eb..c768e9b87c --no-merges
Arnaud Gelas (2):
      BUG: fix gdcm version in GDCMImageIO.
      COMP: missing cast when calling gdcm::DataElement::SetByteValue

Girish Mallya (1):
      BUG: Tests added for BinaryImageToLabelMapFilter for single-row images.

Hans Johnson (9):
      PERF: Revert Remove large foot print of PDF derivatives.
      STYLE: Test against almost equal for floating point values
      STYLE: Non-exact floating point testing
      PERF: Distribute initialization per thread buffers
      ENH: Remove unnecessary mutable qualifier.
      STYLE: Remove comment with no meaning.
      ENH: Moved accumlator logic to main MI class
      ENH: Allow staggering of accumulations per thread.
      PERF: Zero reset thread buffers during finalize

Matthew McCormick (6):
      STYLE: Improve style in BinaryImageToLabelMapFilter.
      BUG: Fix BinaryImageToLabelMapFilter on 1D image.
      ENH: Improve precision of the joint PDF sum
      BUG: Fix BinShrinkImageFilter for different input/output image types.
      COMP: Fix transform type for ITKv3/IterativeClosestPoint2.
      COMP: Add missing wrapping for TransformIOBaseTemplate.

Revision 23706  Directory Listing
Modified Thu Sep 18 22:15:01 2014 UTC (3 years ago) by jcfr
STYLE: Fix typo "nonexistent" instead of "non-existing "

Revision 23702  Directory Listing
Modified Wed Sep 17 23:14:12 2014 UTC (3 years ago) by jcfr
BUG: Create zip archive and move tcl binaries onto slicer.kitware.com

This should help address issue preventing binaries from being downloaded
on some version of Windows. The error reported was:

// -----------
1>------ Build started: Project: tcl, Configuration: Release x64 ------

1>Performing download step (SVN checkout) for 'tcl'

1>svn: E175002: Unable to connect to a repository at URL 'http://svn.slicer.org/Slicer3-lib-mirrors/trunk/Binaries/Windows/tcl85-x64-build'

1>svn: E175002: Unexpected HTTP status 413 'Request Entity Too Large' on '/Slicer3-lib-mirrors/trunk/Binaries/Windows/tcl85-x64-build'

1>Project : error PRJ0019: A tool returned an error code from "Performing download step (SVN checkout) for 'tcl'"

1>Build log was saved at "file://c:\build\s3d\tcl.dir\Release\BuildLog.htm"
// --------------

For more details, see http://slicer-devel.65872.n3.nabble.com/SVN-TCL-donwload-issue-tt4032460.html

Thanks to "Bradley Lowekamp <blowekamp@mail.nih.gov>" for reporting the problem.

Solution suggested by "Steve Pieper <pieper@bwh.harvard.edu>"

Revision 23701  Directory Listing
Modified Wed Sep 17 23:14:10 2014 UTC (3 years ago) by jcfr
ENH: Relocate numpy and teem source archives onto slicer.kitware.com

Revision 23667  Directory Listing
Modified Wed Sep 10 18:23:15 2014 UTC (3 years ago) by jcfr
BUG: Fix packaging of libtk8.6.dylib on MacOSX. Fixes #3822

This commit fixes a regression introduced by r23613 (attempts to
address #3809 by updating tcl version)

Tk 8.6 build system has a known problem building the tk shared library.
To ensure fixup_bundle properly process the _tkinter.so python module,
we implemented the following workaround to fix the library id.
For more details
  http://sourceforge.net/p/tcl/mailman/message/30354096/
  http://na-mic.org/Mantis/view.php?id=3822

Revision 23664  Directory Listing
Modified Wed Sep 10 06:13:08 2014 UTC (3 years ago) by jcfr
ENH: Update ITKv4 version to current release branch (7c3a15e-2014-09-03)

$ git shortlog 372991d..7c3a15ebc --no-merges
Bradley Lowekamp (2):
      BUG: Use METER of sCAL scale unit
      BUG: Use PNG_SCALE_METER for PNG sCAL unit

Christopher Mullins (1):
      COMP: Allows latex to compile for ITKSoftwareGuide

KWSys Robot (2):
      KWSys 2014-07-18 (65b36ede)
      KWSys 2014-08-04 (e787837a)

Matthew McCormick (9):
      BUG: Fix alpha assignment for RGBA TIFF.
      BUG: Improve thread-safety and performance of PCAShapeSignedDistanceFunction.
      DOC: itk::statistics -> itk::Statistics.
      DOC: Remove duplicate text in LaplacianRecursiveGaussian example.
      DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx.
      BUG: TransformFileReader does not clear its TransformList.
      BUG: Prevent dangling pointer in HDF5TransformIO.
      COMP: Fix missing prefix in ITKv3ImageRegistration20Test.
      BUG: Do not return SmartPointers in TimeVaryingVelocityFieldTransform

Revision 23661  Directory Listing
Modified Tue Sep 9 20:56:52 2014 UTC (3 years ago) by jcfr
ENH: Change required ITK version from 4.5 to 4.6

Starting with r23373 ITK 4.6.x is used to build and test Slicer.

$ git shortlog c127db8..6b5fa1a SuperBuild/External_ITKv4.cmake
jcfr (8):
      ENH: Update (1) ITKv4 from v4.5.2 to v4.6rc01 and (2) update BRAINSTools
      BUG: Update ITKv4 project to backport fix related to GDCMIO
      BUG: Update ITKv4 - Attempt to fix ResampleDTI tests
      COMP: Update ITKv4 - Fix "unused-local-typedefs" warning
      COMP: Move most of find_package calls into each Slicer sub-project.
      ENH: Move ITKv4 towards 4.6.0rc20140719
      ENH: Update ITKv4 and BRAINSTools
      BUG: Update ITKv4 and BRAINSTools - BRAINSFit performance improvement.

Revision 23650  Directory Listing
Modified Fri Sep 5 21:30:31 2014 UTC (3 years ago) by jcfr
COMP: Update VTK to reference updated Slicer/VTK fork. Issue #3808

Steve changes related to issue #3808 have been integrated into the
Slicer/VTK fork and this commit updates the external project accordingly.

Revision 23648  Directory Listing
Modified Fri Sep 5 20:16:45 2014 UTC (3 years ago) by pieper
BUG: fixes for 3808 fiducial picking issue

See http://na-mic.org/Bug/view.php?id=3808

Note that fixing this requires the corresponding fixes
to VTKv6 and LandmarkRegistration

https://github.com/pieper/LandmarkRegistration/commit/d9393f515b4798d9904fdd0383d959b91fc1edfb

https://github.com/pieper/VTK/commit/f3d6cc2503375724e60dd73d9a93ba9c764be26e

COMP: fix repository url and error macro usage

From: Steve Pieper <pieper@bwh.harvard.edu>

Revision 23630  Directory Listing
Modified Thu Aug 28 10:46:35 2014 UTC (3 years ago) by jcfr
COMP: Update VTK to fix windows compiler error

$ git shortlog 0a186e2..003cbd4 --no-merges
Jean-Christophe Fillion-Robin (1):
      python: Fix vtkWrapPython compiler error ensuring type declaration are first.

Revision 23629  Directory Listing
Modified Thu Aug 28 06:22:30 2014 UTC (3 years ago) by jcfr
BUG: Update VTK to include fixes for VTK kits wrapping. Issue #3809

$ git shortlog 898e51a..0a186e2 --no-merges
Jean-Christophe Fillion-Robin (3):
      python: Update wrapping tool to support multiple hierarchy files
      python: Do not create a new hints file if a kit bundles only one module
      python: Update vtkWrapPython to add mutable object when building kit

Revision 23627  Directory Listing
Modified Wed Aug 27 19:51:35 2014 UTC (3 years ago) by jcfr
BUG: Update ITKv4 and BRAINSTools - BRAINSFit performance improvement.

(1) This commit updates the tag to use ITK release branch as of
2014-08-16 and integrate the two patches improving MattesMutualInformation
metric provided by Hans and Ali.

(2) It also update the version of BRAINS to use the master branch as of
2014-08-27. More specifically, it updates the BRAINSFit xml code to
have a new set of default parameters for the LBFGSB optimizerv4.

Let's note that it excludes the commit re-organizing find_package(VTK)
calls. These changes would have to be integrated when Slicer itself will
be re-organizing its call to find_package(VTK...)

For sake of completeness, here are the comments reported by Ali:

[BEGIN-ALI-COMMENT]
Although an enormous speed improvement to the previous versions of
Mattes metric and BRAINSFitv4, the current version of BRAINSFit is
still slower than the old BRAINSFitv3 by a factor of 1.7  if both are
run by their default parameters. The factor 1.7 is computed by averaging
over running times of several experiments that are different in the
number of used samples.

In the case of the experiments reported in this google doc (choosing
100,000 for the number of samples):

    Registration process is converged in 1 min 35 sec in BRAINSFitv3 using default parameters for BSpline registration.
    Registration process is converged in 2 min 46 sec in BRAINSFitv4 using default parameters for BSpline registration.

Also, an independent Mattes metric was used after the registration
process to compare the outputs of ITKv3 and ITKv4 registrations with
the input  fixed atlas image. It generated -0.773 and -0.757 for the
outputs of BFitv3 and BFitv4 respectively that are different by %2.1.

[1] https://docs.google.com/document/d/1j8Hy3di54YG42Nr7MGPDWn2XJIAF1oFzC17iV-LJGWI/edit
[END-ALI-COMMENT]


This work has been possible by having the following people
working together (in alphabetical order):

  Ali Ghayoor <ali-ghayoor@uiowa.edu>
  Andras Lasso <lasso@queensu.ca>
  Bradley Lowekamp <blowekamp@mail.nih.gov>
  Csaba Pinter <csaba.pinter@queensu.ca>
  Hans Johnson <hans-johnson@uiowa.edu>
  Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
  Kent Williams <norman-k-williams@uiowa.edu>
  Kevin Wang <kevin.wang@rmp.uhn.on.ca>
  Kilian Pohl <pohl.kilian@gmail.com>
  Matt McCormick <matt.mccormick@kitware.com>
  Steve Pieper <pieper@bwh.harvard.edu>

//-----------
ITKv4 changes
//-----------
$ git shortlog 3147239..372991d --no-merges
Brad King (1):
      COMP: Fix vxl_config_macros usage of CMake check macros

Hans Johnson (2):
      PERF: Revert Remove large foot print of PDF derivatives.
      PERF: Distribute initialization per thread buffers

Matthew McCormick (1):
      BUG: Fix Nifti IO read with large images.

//-----------------
BRAINSTools changes
//-----------------
$ git shortlog dd996be..68303b3 --no-merges
Ali Ghayoor (10):
      ENH: Use BSplineTransformInitializer for BSpline Registration
      BUG: fix BRAINSFitTest_ROIBSpline test failure
      BUG: fix BRAINSFitTest_ROIBSpline test failure
      ENH: Add observer for BSpline regsitration in BRAINSFitv4
      ENH: Print selective parameters in BSpline observer
      ENH: Generalize the legacy PerformTestMMI
      ENH: Add lbfgsb optimizer parameters to commandline
      BUG: fix ROIBSpline test failure in linux system
      ENH: Use a new default parameters set for LBFGSBoptv4
      COMP: Updated ITK tag to BRAINSiaITK

David Welch (6):
      BUG: Fixed typo in singleSession for T2 passing to inputSpec of segmentation workflow
      ENH: Added commandline option to use T1 as sentinal file (off by default)
      BUG: VIRTUALENV option is optional
      BUG: Fixed typo in configFileParser.py     STYLE: Ran autopep8 on AutoWorkup.py     ENH: Added commandline testing for configFileParser.py
      ENH: CLUSTER config section included in ENV section
      BUG: Deprecated local processing until code can be updated

Hans Johnson (5):
      ENH: Remove outdated and non-functioning md5 files.
      ENH: Added Sentinal output file checking for Workflows
      STYLE: Only give debugging information when requested
      ENH: Add logic for better skipping
      ENH: Add new Mattes Mutual Information implementation.

Jean-Christophe Fillion-Robin (2):
      Revert "COMP: fine-tune VTK dependencies"
      Revert "COMP: move find_package(VTK) down to individual project directories"

Kent Williams (4):
      COMP: move find_package(VTK) down to individual project directories
      COMP: Switch back to official ITK repo
      COMP: Silence warnings
      COMP: fine-tune VTK dependencies

Revision 23626  Directory Listing
Modified Wed Aug 27 18:34:10 2014 UTC (3 years ago) by jcfr
BUG: Update VTK and re-enable KITS on Windows/Linux. Issue #3809

This commit updates VTK to basically include commit Slicer/VTK@fbcabbf
VTK kit module are now wrapped similarly to module and this fixes
the issue preventing some VTK object from being available.

Before this change, if a KIT was bundling module A, B, C. Only the object
associated with object A where available from an install tree. After this
commit all objects will be available.

Revision 23625  Directory Listing
Modified Wed Aug 27 02:54:28 2014 UTC (3 years, 1 month ago) by jcfr
BUG: Enable VTK_ENABLE_KITS only on MacOSX. Issue #3809

On Linux, enabling VTK_ENABLE_KITS prevent the vtk package from
being properly imported from an install tree.

For example, the "vtk.vtkTextActor" is not available after starting
Slicer from an install tree. On the other hand, after Slicer is started,
doing the following allow to access the 'vtkTextActor':

import vtk.vtkRenderingKit
vtk.vtkRenderingKit.vtkTextActor

Revision 23622  Directory Listing
Modified Tue Aug 26 23:41:20 2014 UTC (3 years, 1 month ago) by jcfr
BUG: Update version of VTK to use VTK_ENABLE_KITS.  Issue #3809

This commit updates to the latest version of VTK including Slicer
specific patches (branch: slicer-v6.2.0-7167ad1_2014-08-21)

Additionally:
* Update VTK to include kit support for VTK python modules.
* Tweak vtkMacroKitPythonWrap to consider VTK kits.
* Enable VTK_ENABLE_KITS only if CMake >= 3
* Explicitly specify vtkRenderingContextOpenGL. Basically following
kitware/VTK@c5121871,  the OpenGL override for vtkContextDevice2D has been
moved int Rendering/ContextOpenGL, we have to make sure that we link
to vtkRenderingContextOpenGL.  See [1] for more info.

[1] http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Factories_now_require_defines

// --------------------------------
$ git shortlog df24b795..e59c76c --no-merges
Ben Boeckel (1):
      python: split wrapping functions

Jean-Christophe Fillion-Robin (5):
      python: Add wrapping of kits if VTK_ENABLE_KITS is ON
      modules: Re-order RenderingOpenGL libraries to fix VTK_ENABLE_KIT link error
      python: Update python module dependency to account for VTK_ENABLE_KITS
      python: Configure PythonInit file for kit when VTK_ENABLE_KITS is ON
      python: Add VTK_ENABLE_KITS to VTKConfig

// ---------------------------------
$ git shortlog slicer/slicer-v6.1.0..df24b795 --no-merges

Andrew Bauer (8):
      Need to check for static targets before adding abi visibility flags.
      Composite data writers weren't passing down the HeaderType info.
      Passing missing parallel writer options to piece writers.
      Fixing overflow issue that appeared with GCC compilers.
      Fix the way point and cell data arrays are marked for reading.
      Adding in arctan2 through numpy.
      Adding the ability to not delete the passed in arrays.
      Fixed memory leak in test and added in comments for clarification.

Andrew Maclean (8):
      Remove WindowLevelInterface.tcl and WindowLevelInterface.py
      Revert Remove WindowLevelInterface.tcl and WindowLevelInterface.py
      Sphere widget behaves better when scaled down to zero
      ENH: VTK Parametric surfaces - modernised the code.
      ENH: Remove the need to manually regenerate the hill data.
      DOC: Update vtkRandomHills documentation.
      BUG: Fix by adding a new keyword.
      ENH: Add option to return an ordinal lookup table.

Antonio Cervone (1):
      Fixed the BiQuadraticQuad interpolator

Ben Boeckel (117):
      STLWriter: Raise an error for non-triangles
      STLReader: Close the file when an error occurs
      ExodusIIReader: Add the title to the field data
      STLReader: Fix error signaling when reading files
      AVIWriter: Don't overflow the fourcc storage
      AVIWriter: Fix a comment typo
      Exodus: Always attach the title to the output fields
      Rewrite the testing macros
      Update the Cxx test call sites
      Update the MPI test call sites
      Update the Python test call sites
      Update Tcl test call sites
      Minor CMake logic simplification
      Copy Statistics tests to StatisticsGnuR
      Infovis: Add an include for newer Boost versions
      ParallelMPI: Add missing return statement
      Allow arguments to be passed directly to Python
      Skip adding the executable if no tests are created
      Allow for overriding the data directory in tests
      Allow overriding the baseline directory in tests
      Build the VTK test data directory properly
      Support custom baselines in tests
      Store VTK's ExternalData in its source directory
      Support VTKExternalData_OBJECT_STORES as well
      Support custom ExternalData targets for tests
      Support flags to tests common at the module level
      Support JUST_VALID for Python tests
      Support Python+MPI testing
      Use VTK_TEST_OUTPUT_DIR rather than rebuilding the path
      examples: Fix typo in testing calls
      ParallelGeometry: Fix Grid symbol scoping
      testing: Use vtk-example as a fallback for prefix
      Fix test function signatures
      testing: Don't look for tests when making an executable
      FiltersGeometry: Remove unnecessary links
      Filters/Geometry: Remove some unused functions from tests
      Filters/Geometry: Hide WriteGrid if ENABLE_IO isn't on
      testing: add some missing TEST_DEPENDS
      pythoncore: extract python objects from arguments
      wrapping: add function to check for Python objects
      wrapping: wrap PyObject* in python code
      python: accept any argument for PyObject* arguments
      vtkAlgorithm: fix a typo
      FiltersPython: create a vtkPythonAlgorithm class
      python: fix leaks when setting constants in wrappers
      vtkPythonAlgorithm: support older pythons
      vtkpython: add site-packages to the path
      vtkFiltersPython: Disable without Python wrapping
      wrapping: add variables to exclude from language-specific wrapping
      vtkFiltersPython: exclude from Java and Tcl wrapping
      java: get the list of java modules properly
      testing: append the tests to the given variable
      pythonalg: use keyword arguments rather than members
      pythonalg: raise an error in RequestData by default
      wrapping: remove the ${module}_WRAP_PYTHON variable
      vtkStructuredImplicitConnectivity: fix msvc warnings
      typo: fix some typos
      unused: remove unused functions
      mpi4py: add module information
      mpi4py: link to CMAKE_DL_LIBS
      testing: skip test executables with no tests
      IOVPIC: include MPI headers as SYSTEM headers
      cmake: set policy 0053 if available
      cmake: set policy 0053 in thirdparty cmake
      mpi4py: add a class to convert communicators
      wrapping: check for Tcl wrapping exclusion for warnings
      vtkAMRUtilities: split out vtkParallelAMRUtilities
      hierarchy: use a .txt extension
      GenerateExportHeader: support object libraries as well
      vtk_module: support a KIT argument
      modules: add modules to "kits"
      linking: wrap tll() with a module-aware function
      export: OBJECT libraries may not be exported
      modules: output kit information in the module tree
      modules: topo-sort modules with kits as well
      modules: build kits from the member modules
      module: depend on the dependent module object library
      python: add an option to disable vtkpython
      testing: check for pvtkpython before using it
      vtkpython: don't install if not enabled
      vtkAVIWriter: make a more informative error message
      IO/Geometry: add obj index tests
      FiltersParallelGeometry: move functions to the sources
      vtkMPICommunicator: avoid deprecated MPI functions
      vtkInstantiator: remove instantiator macro from main sources
      typo: remove duplicate source listing
      vtkCompositePolyDataMapper2: cache opacity check
      vtkCompositePolyDataMapper2: include <algorithm> for std::max
      vtkCompositePolyDataMapper2: avoid a NULL dereference
      OpenGL: use STATUS for the OSMesa message
      vtkPStreamTracer: conditionalize functions
      vtkPTemporalStreamTracer: remove useless code
      unused: add a macro to mark functions as "unused"
      vtkChartBox: initialize segmentIndex
      nit: remove extra semicolon
      vtkMPI: install so that vtk_mpi_link is available
      python: install packages properly
      opengl2: use STATUS for the OSMesa message
      Maintenance: recognize the KIT keyword in scripts
      module: add comment to update maintenance scripts too
      Maintenance: recognize language exclusion keywords
      warnings: fix narrowing warnings
      TestSurfacePlot: loop using vtkIdType
      vtkQuaternionInterpolator: call the constructor properly
      warnings: remember values with the proper type
      warnings: use static casts to point out precision loss
      warnings: use floating point intermediate values
      warnings: resolve unused variables
      vtkOpenGLImageMapper: fix unintentional shadowing
      warnings: fix signed/unsigned comparison warnings
      vtkOpenGLProperty: remove unused function
      unused: use the vtkNotUsed macro
      Q4VTKWidgetPlugin: only define qDebug if not already defined
      mpi4py: use the output, not the result
      cmake: remove unnecessary condition copies
      vtkSmartPyObject: ignore warning C4127 on MSVC
      mpi4py: use old code with Python 2.6 as well

Berk Geveci (52):
      Removed priority based streaming and fast path.
      Removed unused code from vtkModelMetaData and vtkExodusModel
      COMP: Fixed compiler error - needed to remove functions from .h.
      Improved test to increase vtkDistributedDataFilter's coverage.
      Cleaned up the Exodus metadata.
      Fixed minor typo - case sensitivity issue.
      Removed verts from streaklines - lines are enough.
      Removed unnecessary recursion in pipeline streaming.
      Filter was modifying self in request. Fixed.
      Fixed minor typo in documentation.
      Added test for vtkTableBasedClipDataSet.
      Added caching to temporal interpolator.
      Fixed minor bug in the ensight gold reader.
      Added EnSight tests to increase coverage.
      Added initial ghost points support to vtkDataSetSurfaceFilter.
      PERF: Parallel streamline was slow. Fixed.
      Refactored how pieces and extents are handled.
      Update the XML readers and writers to work with pipeline changes.
      Cleaned up and fixed transmit filters for structured data.
      Fixed bug in send structured data.
      Fixed legacy parallel reader and writer.
      BUG: Was using array of wrong size.
      Fixed compiler warnings.
      Changed synchronized templates class for new pipeline behavior.
      Removed unused keys.
      Updated filters and sources to work with new pipeline logic.
      Moved key.
      Cleaned up extent translators.
      Removed unnecessary reference to extent translator
      ExtractSelection was not managing pieces corretly. Fixed.
      Filters should silently handle empty input
      Fixed multiple issues with resample/probe filters.
      Fixed contour filters
      Fixed issues in the group filter.
      Fixed crash in the empty input test.
      Fixed vtkXdmfReader for parallel structured data.
      Parallel Exodus writer was not asking for pieces. Fixed.
      Added new meta-data and request capability to the pipeline.
      PERF: Removed unnecessary function call.
      Added an ensemble source.
      Added documentation and testing to vtkPythonAlgorithm.
      Fixed no newline at end of file warnings.
      Executive was setting update extent initialized falsely.
      PERF: Removed unnecessary garbage collection.
      Fixed indentation and style to match VTK's.
      BUG: Filter was overwriting input scalars. Fixed.
      Added modules that create a numpy type interface.
      Certain MPI types were not being recognized by mpi4py.
      Improved TestNumpyInterface to cover various append implementations.
      Added sum and mean per block to Python algorithms.
      Added support for CompositeDataSet.Points.
      Fixed innaccurate comments.

Bill Lorensen (26):
      COMP: Test driver array bounds error
      BUG0013829: vtkAssembly::GetBounds adds bounds which are uninitialized
      BUG0014331: Filter skips VTK_CUBIC_LINE
      COMP: Restore TestTessellator test
      ENH: Added tests that were removed during modularization
      COMP: Refactored TestDataObjectIO
      COMP: test require NO_VALID modifier
      ENH: Add removed tests
      COMP: Improve coverage of vtkMeshQuality
      COMP: Missing NO_VALID
      ENH: Improve code coverage script
      BUG: Flawed logic for NO_OUTPUT
      COMP: Python unittest requies NO_OUTPUT
      COMP: Performance warning: int to bool
      COMP: Remove QtInitialization from otherPrint test
      ENH: Remove ThirdParty code from coverage results
      COMP: Remove bogus line info from generated files
      ENH: Unit test for ParametricSpline
      ENH: Coverage for MultiThreshold.
      BUG: CreateDefaultLookupTable crashes if Input is NULL.
      ENH: Add some more coverage for MultiThreshold
      ENH: Improve code coverage for UnicodeStringArray
      ENH: Unit test for vtkMath
      COMP: Adjust tolerances
      COMP: Guard against infinite loop in vtkClearOpenGLErrors
      ENH: Provide PlaybackFile for recorded interaction events

Brad King (35):
      COMP: Drop invalid custom commands from HDF5
      COMP: Drop missing dependencies of target 'vtkpython_pyc'
      vtkhdf5: Remove extra calls to cmake_minimum_required
      Accelerators/Dax: Remove extra call to cmake_minimum_required
      Refactor top-level CMake Policy settings as loop
      Examples: Set required CMake version and policies before project()
      Set CMake Policies CMP0025 and CMP0042 as necessary
      Rendering/Volume: Convert new baseline to ExternalData content link
      Wrapping/Tcl: Fix CMake Policy CMP0050 warnings
      IO/XML: Remove unnecessary <sstream> include
      IO/XML: Add missing <string> include
      IO/XML: Fix HeaderTest for this module
      vtkOStreamWrapper: Support std::string
      Revert "vtkOStreamWrapper: Support std::string"
      vtkOStreamWrapper: Support std::string
      Revert "vtkOStreamWrapper: Support std::string"
      vtkOStreamWrapper: Support std::string
      Allow custom TestTM3DLightComponents timeout
      Allow custom TestProp3DFollower timeout
      Honor VTK_INSTALL_NO_DEVELOPMENT for archive libraries
      Use vtkMPI.cmake helper for all module MPI tests
      Set MACOSX_RPATH property default consistently across CMake versions
      ExternalData: Add backtrace to missing file warning
      Export the locations of Qt5 packages on which modules depend
      Allow configuration of external module dependency locations
      Views/Infovis: Add another baseline for TestConeLayoutStrategy
      Allow custom Interaction/Widgets test timeouts
      Fix ExternalData pre-commit hook on msysGit
      Add option to exclude VTKData target from default build
      mpi4py: Suppress warnings in third-party code
      vtkFFMPEGWriter: Fix build with libavcodec55
      Exclude classes requiring a QApplication from VTK smoke tests
      module: fix export macros with kits
      vtkglew: Install glew header files
      IO/ADIOS: Exclude module from VTK_BUILD_ALL_MODULES

Burlen Loring (1):
      surface LIC - stl and NULL

Chris Harris (22):
      Add failure filter to session.auth(...) deferred
      Add error function to vtk:mouseInteraction RPC
      vtkWeb: Add newline to end of each proxy map entry
      vtkWeb: Teach launcher.py to wait for ready_line
      vtkWeb: Add appropriate error codes for launch requests
      vtkWeb: Don't reset viewer to null on updateViewer(...)
      vtkWeb: Propagate mouse events to VGL
      vtkWeb: Fix calls to old VGL API
      vtkWeb: Rename ogs.vgl => vgl
      Rename md5 => sceneMD5 to avoid confusion
      Update canvas size before creating viewer
      Prevent mouse event handlers be bound multiple times
      Update VGL to master
      Update version of VGL
      Prevent scene and clipping range from being reset
      Update VGL to lastest version
      vtkWeb: Refactor fetchObject(..) to use cached objects
      Add code to clean of VGL actor cache
      Add missing initialization of member
      Fix typo introduce by 06aaa805 session => m_session
      Update to modern CMake style
      Allow location of OSMesa install to be specified

Chuck Atkins (1):
      Initial ADIOS readers and writers

Cory Quammen (7):
      BUG: Fix build failure in RenderingParallelLIC on Intel compiler
      Added "sticky" axes mode to vtkCubeAxesActor
      Fixed linkage problem in Windows
      Improved comment handling
      KW00001404: Major overhaul of vtkAppendFilter
      Fixed memory leak and improper erasing of std::set elements
      Fixed error in appending cell data

Dan Lipsa (9):
      Report an error when writing a file with changing topology.
      Update documentation.
      Remove debugging printouts.
      Name enum LEFT, BOTTOM, ... Location.
      Add component-wise set functions for Border and Gutter (vtkChartMatrix)
      Set Bold and Italic axis label properties for ScatterPlotMatrix.
      vtkMultiProcessStream: Add insert and extract operators for bool
      Fix Windows compilation warning.
      Forces the compiler to convert a char* to a string rather than a bool.

Dave DeMarle (35):
      Increment version to VTK 6.2.0
      Add a test for the VPIC reader
      document arguments to test macros
      move dashboard management scripts into better place
      fix link errors that happened when I turned on InfovisParallel
      deprecate this module
      fix a compilation warning
      make rubber band look correct on scenes with textures
      optimize geojson writer
      more optimization of geojson writer
      fix variety of dashboard problems
      Put libxdmf into a namespace so that libxdmf3 can coincide with it.
      Adapt libxdmf to build within VTK.
      add cmakescript infrastructure to make libxdmf a VTK module
      Add a reader and writer for the new xdmf library.
      Fixes for xdmf3 regression test data.
      Fix issues the dashboards turned up.
      Fix more issues the dashboards turned up.
      Really fix on of the issues the dashboards turned up
      Fix a regression in the xdmf bump
      STYLE: improve comments and organize internal classes
      fix a case of discarded arrays
      Remove stray debugf.
      bring back subsets
      put array reuse in
      Fix dashboard warnings and test failure.
      disable a balky test until we can fix it
      Add file series reading and top level spatial partitioning
      fill in time varying graphs
      STYLE: pull helpers out and format all for vtkstyle
      move strict partition multipiece constuction out to reader level
      disable oggtheora on cray too
      Fix problems that the dashboards turned up.
      remove MetaIO to replace with updated content
      exclude matlab from the "all" modules set

David C. Lonie (14):
      Tie vtkUnstructuredGridBase into the dataset type system.
      Update baseline
      Handle empty array initialization in numpy_support.
      Don't reset traversal location in each iteration of box clip filter.
      Process facestream in vtkExtractUnstructuredGridPiece::RequestData.
      Handle polyhedra in vtkUnstructuredGridWriter.
      Disable FP frame buffer when GL_ARG_texture_float is not present.
      Return early if ProjectedTetrahedra volume rendering is unsupported.
      Add new baseline for rendering without floating point buffers.
      Add new baseline for dashlin1.
      Pass std::strings through the OStreamWrapper.
      Revert "Pass std::strings through the OStreamWrapper."
      Return early in TransformPoints if input is NULL.
      Update system font test baseline.

David Cole (6):
      Add a vtkMath method to compute the angle between two vectors
      Tests: Re-activate the old TestResliceCursorWidget tests
      Tests: Add test for the vtkCornerAnnotation class
      - Follow on commit to use the right style #include ("", not <>)
      BUG: Add missing header files to enable try_run tests to run without crashing
      Testing: Call SetMultiSamples(0) from tests

David Gobbi (19):
      14196: Allow unicode path in vtkLoadPythonTkWidgets.py.
      In wrappers, guard against #including dirs.
      Fix cell picker for images with negative spacing.
      Fix uninitialized array warnings.
      Fix unreachable code warning in otherCellTypes.cxx.
      Fix a crash when deleting vtk-python objects.
      Fix bad SetColor/GetColor interaction in vtkProperty.
      Fix the extent for tiled tiff files.
      Two fixes for certain lsm (zeiss) tiff images.
      Add reader/writer for NIFTIv1 and NIFTIv2 files.
      Add SetSlabModeToSum() to vtkImageResliceMapper.
      Clean up vtkMedicalImageProperties PrintSelf.
      NIFTI makes IOImage module depend on vtkzlib.
      Fix warning about trailing comma in enum list.
      Bad null pointer check in vtkBSplineTransform.
      Fix segfault if vtkImageWeightedSum's inputs don't match.
      Rewrite the comments for vtkDataArray::GetRange.
      Add generic PyObject support to vtkPythonOverload.
      Provide a method to set the sample spacing for slab modes.

David Stoup (1):
      Add multi-layer support to the vgl interface.

David Thompson (6):
      Bug 14713: Read LS-Dyna point coordinates properly.
      Add a regression test for bug 14713.
      Small fixes to docs, comments, and formatting.
      Add support for reading polyhedra.
      Test reading a polyhedral Exodus dataset.
      Add test data with multiple polyhedra.

Eli Kahn (4):
      Adding mousewheel support to Java GUI components.
      Fix java code formatting.
      Add java file to generated jar file.
      In java code, handle situation when wheel rotation value is zero.

Georg Hammerl (1):
      Add caching for time steps in EnSightGoldReader binary reader.

George Zagaris (18):
      Disable I/O in TestStructuredAMRGridConnectivity
      ENH: DuplicateNodes property to RCB partitioners
      BUGFIX: Fix integer overflow in vtkStructuredData
      ENH: FieldData deserialization to a subextent
      ENH: Add blanking to vtkXMLUniformGridAMRReader
      ENH: Implicit structured data connectivity
      COMP: Update vtkFiltersParallelMPI tests
      ENH: Rename nodes to points in vtkStructuredData
      BUGFIX: Add guards for NULL ivars in PrintSelf
      BUGFIX: Fix issue with unigrid enzo datasets
      COMP: Correct ParallelMPI module test dependencies
      COMP: Remove HyperTreeGridGeometry::UpdateExtent()
      ENH: Update extract structured data filters
      ENH: Use vtkImageData in implicit connectivity
      ENH: RectilinearGrid implicit connectivity support
      ENH: MPI structured data extraction filters
      COMP: Fix a few compiler warnings
      ENH: Added broadcast implementation for RMI triggers

Jacob Becker (1):
      Fix bad check for incomplete polygons, fix div-by-zero.

Jameson Merkow (1):
      Add files, and made modifications for MatlabMex to wotk in vtk 6

Jean-Christophe Fillion-Robin (3):
      vtkPythonCommand - Add support for additional call data types
      vtkPythonCommand - Fix indent and variable names
      Configure VTKConfigVersion consistent with VTK's compatibility guarantees

Jeffrey Baumes (1):
      Fixing array bounds issue

Joachim Pouderoux (19):
      Introduce Robust PCA.
      Introduce box plot and the corresponding chart.
      Introduce Compute Quartiles filter to generate box plots tables.
      Enhance bag plot API to allow specify line and points properties.
      Fix bag plot legends.
      Fix black box plots issue.
      Fix double to unsigned char cast error on clang compiler.
      Fix bag plot and functional bag plots tests.
      Fix and enhance the box plot and chart
      Fix and enhance bag plots.
      Fix bug in picking of invisible props in an assembly.
      Clean an enhance hypertree grids.
      Fix potential compiler error with ternary operator.
      Replace a verbose cout by a vtkDebugMacro()
      Fix clang errors on array initialization
      Fix and clean vtkWin32OpenGLRenderWindow class.
      Fix functional bag plot.
      Clean and uniformize vtkPoints & vtkPoints2D.
      Fix crash on normal computation when polygon is empty.

John Stark (2):
      Add a test for vtkImageImport / vtkImageExport
      Fix pipeline update issues in vtkImageExport

Jorge Perez (1):
      Upgrading the Tcl examples wrt. VTK 6.x

Julien Finet (4):
      Prevent error message when deep copying vtkGridTransform
      Change GetInputConnection error message into a debug warning message
      Enable GPU Raycast volume mapper for recent NVIDIA drivers on Mac OS X
      GPU raycast volume rendering now supports textures larger than 1024

Julien Jomier (2):
      ENH: Fixes for ActiViz.Net
      BUG: Wrong transformation used to restore original parameters

KWSys Robot (1):
      KWSys 2014-03-12 (dd873734)

Ken Martin (115):
      some rough changes to the VBO polydata mapper
      some more cleanup
      added light override
      compute cam matrix, add posiitonal light in progress
      updates to support positional lights
      change how object factory is done
      some fixes to normals etc
      added ambient color in
      some module changes override actor change bunny color
      changes in normal calcs
      moved property over and started gutting it
      fix normals on test
      minor changes
      some bug fixes and start on mapper2D
      allow testing using old mapper
      bug fix
      added cxx for Helper
      duh
      many updates to 2d mapper
      bug fix
      lots of rough changes
      moved renderer over, moved init code
      in progress
      in progress cell scalars
      some cleanup and fixes
      lots of changes in progress
      more fixes
      fix array bounds issue and memory leak
      fix performance issue
      add fast path for float points no col no norm and fix bug
      started on texture mapping
      first cut a tmap support
      add textured backgrounds and fix issue with gradients
      bug fixes
      clean up a bit
      change opacity clean some texture stuff
      minor fixes
      fix crash on test
      fix crash on test
      add fragment shader lighting of lines
      support textured luts some cleanup
      some support for resolving coincident polys
      ambient color fix
      some minor fixes
      start working on image slice mapper
      add baseine images
      updated baseline images
      updated baseline image
      minor backwards compatability change
      basic ImageSliceMapper conversion
      some more fixes
      moved render window over
      bug fix in old VTK
      bunch of optimization more to come
      bad optimizations and missing classes'
      doh forgot really key line
      bug fix and minor cleanup
      fix a glyph bug and minor cleanup
      another bug fix
      better picking support some cleanup
      move interface closer to old Rendering API
      convert ImageMapper
      some bug fixes
      another valid image, remove unused test
      fix SetPixelData and fix picking issue
      add depth peeling
      make wider so we can see errors
      some win32 fixes
      rename VBO mapper
      cleaned up the mapper a bit
      minor cleanup
      minor lighting fix for intel
      handle wireframe tstrips
      some bug fixes etc
      more fixes
      more fixes
      add support for edge visibility
      modify API to be a bit more future proof
      fix some picking issues
      some fixes for andriod
      some fixes for andriod
      remove some old code
      some fixes for andriod
      more andriod glew changes
      more andriod glew changes
      many changes to support glew and android
      many changes to support glew and android
      many changes to support glew and android
      first working in quotes android app
      first working in quotes android app
      comment out more modukles by default
      some warning fixes and minor cleanups
      fix some more warnings
      fix some more warnings
      make vtkOpenGLTexture use vtkTextureObject
      convert depth peeling to use more texture objects
      a tad more depth peeling cleanup
      add android output window
      better debugging out for shader programs
      clean up some shader code
      new android interactor and cleanup
      some shader cleanup
      some android fixes in progress
      improved release graphics resources
      improved release graphics resources
      minor change to be more compatible with some opengl hardware
      fix android resize and lingering glew issue
      added multitouch framework and support on windows and android
      fix java issue
      in progress
      in progress
      more reasonable first cut at java android
      clean up some shader code and classes
      removed unused includes
      fix some warnings

Kenneth Moreland (2):
      Dax marching cubes now uses input array not active scalars.
      Allow Dax marching cubes and threshold to work with doubles.

Lisandro Dalcin (1):
      import mpi4py 1.3

Marco Cecchetti (5):
      vtkColorString - Helper class for defining a color through a string.
      Merged vtkColorString into vtkNamedColors.
      I added a RGBAToHTMLColor and made some minor changes.
      Tentative fix for Windows build issue.
      Tentative fix for big-endian machine issue.

Marcus D. Hanwell (98):
      Added a test for biquadratic quad interpolation
      Exclude the vtkgl.* files (generated code) from coverage
      Make consistent with vtkBiQuadraticQuad
      Added back the QtSQL test for the database class
      Removed misleading comment - test is built
      Added back various rendering tests
      Added back the named components test in FiltersCore
      Removed a few remaining Cg related files
      Refactored the TIFF reader, add support for floats
      Added progress updates when reading a volume
      Remove redundant checks for old JPEG compression
      Copy simple TIFF images into buffers more directly
      First pass at a new render widget
      Implement a basic VBO based poly data mapper
      Basic support for color from property
      Add the find module for Eigen 3
      Added a hack to override OpenGL overrides with GL2
      Roughly mapping the colors/scalars, updates to shaders
      Normalize the colors, and put the light the other side...
      Added the dragon model (already in external data store)
      Moved the VBO and IBO creation to helper functions
      Use the vtkPolyDataNormals filter to calculate normals
      Added a points/lines test, added point/line rendering
      Added in a program for lines, change
      Moved the replace function into the helper header
      Refactoring a little, movig IBO stuff into structs
      Added a polyline, and basic support for rendering it
      Refactor uniforms a little, enable point rendering again
      Small changes for point size and line width
      Minor clean up for includes in the mappers
      Ensure we set the active shaders
      Removed commented code/classes from the test
      Added in the case for multiple renders/VBO updates
      Refactor the shader API to comply with VTK style
      Refactor API, comply with VTK style
      Refactor the shader program API to comply with VTK style
      Added a Vertex Attribute Object (VAO) class
      Enable textures now that the vtkTexture class doesn't do it
      Set the z-spacing in a TIFF to match x-spacing
      Early attempt at getting the 3D glyph mapper working
      Hackish, map the colors for the glyphs
      Keep the color mapper around, shallow copy for settings
      Fixed the normal matrix, now molecules look much better
      Make it compile on Linux/X again
      Bring over the Cocoa classes for Mac
      Intel GLSL compiler is much fussier about type...
      Removed the vtkFiltersCore dep
      Removed vtkRenderingOpenGL as a dep now too!
      Made vtkRenderingOpenGL2 independent of vtkRenderingOpenGL
      The PainterDeviceAdaptor is abstract, can be NULL
      Rename vtkOpenGL2* -> vtkOpenGL*
      Very judicious use of sed, vtkOpenGL2* -> vtkOpenGL*
      Added a concept of backends, added OpenGL and OpenGL2
      File moves necessary to create a context backend
      Context OpenGL and OpenGL2 backends
      Some minor tweaks to get the tests passing again
      Some modules only in groups if correct backend selected
      Missed these OpenGL2 variants with the mass rename
      Brought more of the OpenGL module logic over
      OpenGL and OpenGL2 are mutually exclusive
      If enabled, always override in OpenGL 2
      Unused include for a file that was deleted
      Disable multitexturing in Geovis class
      Moving rendering tests to more appropriate places
      More test moves into more appropriate locations
      Removed the TDx classes from OpenGL 2
      Only enable backends for interface modules being built
      Disable test for render widget
      Changed the default CDash URL for VTK
      Move several TEST_DEPENDS to switch on backend
      Create object factory CMake file, move vtk_add_override
      Now generate the object factory files in a function
      Revert "updated baseline images"
      Revert "updated baseline image"
      Some dependency updates now vtkRenderingContext2D is abstract
      Don't exclude the module from wrapping - initialization
      Made the label tests pass again!
      Make TCL wrapping happy - no numbers in module names
      Added include for std::string
      Save the rendering backend used to the config file
      Avoid early termination when collecting actors
      vtkOpenGLContextActor should subclass vtkContextActor
      One of the tests needs a context device to render
      Removed unused variable - used in subclasses
      These classes are abstract, fix smoke tests
      Fix for Windows mangling issue
      Must be marked WRAP_EXCLUDE too for Tcl smoke tests
      Reduce the number of renders (avoid time outs)
      Move device adapter initialization to the OpenGL module
      BUG: Make selections more permanent, linked to object
      STYLE: Some basic style fixes
      Removed sorts as the inputs were already sorted
      Added a test to exercise bar graph selection
      Remove the wrap exclusion at the module level
      More exclusions, avoid setting ABSTRACT twice
      TCL doesn't like numbers in module names
      Comment out the animated PDB renders
      CMake's exec_program is deprecated, revert back

MetaIO developers (1):
      MetaIO 2014-07-09 (53aa417f)

Nicole Aucoin (1):
      BUG: fix null pointer crash in view to world with no active camera

Patrick O'Leary (1):
      added paraviewweb widget for catalyst workbench

Paul Edwards (2):
      Fix for polyhedron cells.
      Bug fix for dataset surface filter.

Robert Maynard (15):
      Update Dax Accelerator to use the new tll signature.
      Update the Dax Accelerator to use the new dispatcher classes.
      Correct warnings about negative unsigned constant values.
      Properly implement the factory for the dax filters.
      EnSight Binary uses 64bit longs so explicitly use those instead of long.
      Netcdf now handles different directories for c and cxx bindings.
      Improve the performance of vtkDataArray::ComputeScalarRange.
      Improve the performance of vtkDataArray::ComputeVectorRange.
      Move all free functions in vtkDataArray into an anonymous namespace.
      Update ComputeVectorRange based on gerrit feedback.
      Update DataArray and DataArrayTemplate to use vtkTypeTraits.
      Correct ComputeScalarRange when dealing with multiple components.
      Improve ComputeScalarRange when we have a single component.
      Correct an issue with converting dax data to vtk polydata.
      Refactor GetRange to compute all ranges at the same time.

Sandeep Menon (1):
      vtkOBJReader: accept relative indices in OBJ files

Sankhesh Jhaveri (12):
      BUG: Fix failing EnSightBlow5ASCII tests
      BUG: Turned multisampling OFF for certain tests failing on linux with ATI
      Fixed multisampling issues for some tests on ATI
      ENH: Script to generate API differences between two git revisions
      ENH: Added test for vtkImageCroppingRegionsWidget to improve coverage
      ENH: Enable selection of translucent geometry
      BUG: VTK_JAVA_SOURCE_VERSION to accomodate different java versions
      Re-enabling tests disabled during modularization for Interaction/Widgets
      BUG: Duplicate class definition in TestSeedWidget2
      BUG: Duplicate class definition of vtkSeedCallback2
      Additional baseline for TestAreaSelections
      BUG: Border visibility from underlying vtkScalarBar actor

Scott Wittenburg (9):
      Added code to draw current selection rectangle in viewport.
      Added code to support a cache option for filebrowser widget.
      Added canvas based image zooming and panning capabilities.
      Fixed a null reference by surrounding the call with a check.
      Support faster configuration times by checking dependencies at runtime.
      Changed to make tests run serially, async nature was causing collisions.
      Replace an import which disappeared and broke all dashboard web tests.
      Updating to Autobahn python version 0.8.13 to get http long poll endpoints.
      Added latest Autobahn JS (0.9.4) to support pvweb authentication.

Sean McBride (47):
      bug #14418: Remove addition of "-Wno-deprecated" compiler flag
      Fix clang analyzer warning about passing null to strcmp
      Fixed clang analyzer warning about passing null to memcpy
      Fixed clang analyzer warning about reading uninitialized memory
      Fixed clang analyzer waring about a dead store.
      Fixed clang analyzer warning about dead store
      Fixed clang analyzer warning about dead store.
      Fixed clang analyzer warning about dead store.
      Fixed clang analyzer warning about dead store.
      Fixed clang analyzer warning about dead store.
      Fixed clang analyzer warning about 2 dead stores.
      Fixed clang analyzer warning about dead store.
      Fixed clang analyzer warning about reading past an array.
      Fixed several clang analyzer warnings.
      Fixed clang analyzer warning about reading uninitialized memory.
      Fixed clang analyzer warning about dead store to 'pd'.
      Fixed clang analyzer warning about passing null to memcpy.
      Fixed clang analyzer warning about dead store to 'index'.
      Fixed clang analyzer warning about dead store to 'bestTime'.
      Workaround clang analyzer warning by creating temp variable.
      Fixed clang analyzer warnings about dead stores.
      Misc cleanup of code nearby clang analyzer warnings.
      Fixed clang analyzer warnings about dead stores.
      Fixed clang analyzer warning about dead store at very end of method.
      Fixed clang analyzer warning about dead store to 'itr'.
      Fixed clang analyzer warning about dead store to 'cptr'.
      Fixed null deref found by clang analyzer
      Fixed clang analyzer warnings about dereferences
      Suppress clang analyzer warning
      Fixed clang analyzer warning about null deref
      Fixed clang analyzer warning about reading uninitialized data.
      Fixed infinite recursion in vtkBitArray::RemoveFirstTuple()
      Improved code coverage of vtkScalarsToColors by adding more tests
      Added tests for a few uncovered vtkMatrix3x3 methods
      Fixed error in vtkFiltersCoreCxx-TestClipPolyData test
      Removed -fobjc-gc from VTK_REQUIRED_OBJCXX_FLAGS
      Various Cocoa improvements and fixes
      Fixed a bunch of clang -Wabsolute-value warnings
      Removed all uses of deprecated NSOpenGLPFACompliant
      Assume UTF8 for vtkCarbonRenderWindow::SetWindowName
      Remove unnessary 'if' before 'delete[]'
      Add #error when trying to build as Cocoa ARC
      Fixed confusing indentation, no behaviour change
      Fixed unused variable warning in release
      Rewrote vtkCoreGraphicsGPUInfoList to not use deprecated API
      Removed checks for antique Borland versions
      Changed public API of vtkGPUInfo to return vtkTypeUInt64 for memory sizes.

Sebastien Jourdain (55):
      Add catalyst web widget into VTK
      Add NaN support in web chart rendering
      Add a resampling filter
      Add JSON writer for ImageData
      Extend vtkImageMapToColors to support Mask color and Non Active Scalar input
      Use / for path separator to prevent Windows related issue with escape char
      Improve implementation of Catalyst viewer
      Add image resampler catalyst web widget
      Remove test dependency to data when not needed
      Remove usage of the keyword with to allow old python
      Add new set of catalyst web widgets
      Attempt to handle some system raise condition
      Add catalyst web composite widget
      Better composite catalyst web widget
      better UI for catalyst re-sampler web widget
      Various VTK-web improvement
      Fix vtkweb catalyst css
      Add cost information in workbench analysis
      Improve web compositing for dynamic interaction
      Properly handle background selector visibility
      Fix composite rendering widget for search
      Add sorting capabilities
      Refresh workbench UI and workflow
      Fix Composite Javascript for WebKit
      Improve ParaView cinema UI
      Improve basic search in web-catalyst
      Fix catalyst web - cost time computation
      Improve catalyst web UI
      Catalyst web: Minor Web UI change
      Catalyst-web: Improve composite search experience
      Add image width column
      Add cost estimate for Catalyst Web
      Catalyst-Web estimate UI fix
      Change catalyst-web analysis API to expect full URL
      Fix center of rotation for WebGL renderer
      Fix WebGL background orientation
      Fix basic catalyst viewer with theta
      Add runtime libraries on Windows for Java binary package
      Fix several catalyst web UI issue
      Add configuration pass to Catalyst PVW workflow
      Add support for mobile device interaction
      Catalyst Web - Composite improvement
      Catalyst web
      Add new rendering class API based on vtkPanel class
      Remove @Override annotation to prevent compilation issue on old Java compiler
      Upgrade autobahn version to 0.8.9
      Upgrade Twisted version to 14.0.0
      Upgrade ZopeInterface version to 4.1.1
      Add SixPython module for Autobahn dependency
      Update Autobahn/JS library version
      Update VTK Web Python code to handle WAMP v2
      Update Web applications to support new protocol API
      Fix python for vtkweb
      Allow arbitrary WebSocket endpoint
      Add bottstrap3 + pv lib in loader

Shawn Waldon (2):
      Add a smartpointer for PyObjects
      Format comments according to VTK stlye guide

Shinya Onogi (1):
      fix_GPU_resource_handling

Thomas Vaughan (1):
      Set origin and spacing in vtkSurfaceReconstructionFilter. Ref: Mantis 0002826.

Tristan Coulange (5):
      BUG: fix some xdmf writer crashes
      BUG: Add a missing include for VS 2013
      Add support for original ids for generic dataset
      BUG: fix xdmf test failure
      BUG: Fix the quads evaluate location

Utkarsh Ayachit (31):
      Adding a new test for TestSocketCommunicator.
      Added test to test vtkSynchronizedRenderers.
      Deprecate vtkOpenGLPolyDataMapper.
      Fix segfault with TestSetGet.
      Fix build issues with deprecated vtkOpenGLPolyDataMapper.
      Add a delay between process launches.
      Fixed mismatches cell arrays in vtkPStreamTracer.
      Added ability to probe filter to allow disabling of passing field data.
      Add support for empty strinngs in SetInputArrayToProcess.
      Make it possible to override ClampPos.
      Remove OpenGL error checks that were causing errors.
      BUG #14244: Fix stereo image captures.
      Add helper method to convert from SelectionField to AttributeType.
      Fix appending of scalar arrays.
      Fix DataSet reference in when input array is passed to output.
      Avoid exceptions on StringArrays.
      Fixed exceptions with older numpy version.
      Cleanup MPI controller properly.
      vtkExtractSelectedRows only works with IdTypeArray.
      BUG #14828: Keep surface color from interacting with scalar color.
      Handle append scalar in CompositeDataSetAttributes.
      BUG: Fixed opacity mapping when scalar array is vtkUnsignedChar.
      BUG #14813: Fix range reported for mode shapes.
      BUG #14599: Handle double values properly.
      Fix issue with empty arrays with numpy 1.2.1.
      Don't glyph masked points in vtkUniformGrid.
      BUG: Fix invalid return value check in vtkClientSocket.
      vtkScalarBarRepresentation doesn't call Superclass.
      Fixed logic to work when an empty vtkSelection is passed.
      Fix handling of empty selection on ParallelCoordinates.
      Fixed issue with selection frame line style.

Will Schroeder (7):
      Disabling translation and scaling now works.
      Added the ability to specify a clip tolerance.
      Fixed bug causing plane to disappear on boundary.
      InsertNextCell and related method now return the proper vtkIdType.
      Create vtkPolyData instead of vtkUnstructuredGrid when passing points.
      Extended filter to support culling unused points.
      Added ability to control alpha shape output

XDMF Developers (3):
      export xdmf for import into vtk
      export xdmf for import into vtk
      export xdmf for import into vtk

Xabi Riobe (1):
      BUG: The method vtkClipPlanesPainter::UpdateBounds must not be implemented.

Zack Galbreath (25):
      fix lingering off-by-one error
      new writer: vtkPhyloXMLTreeWriter
      attempt to silence "possible loss of data" warning
      improve the thoroughness of TestPhyloXMLTreeWriter
      add baseline directory
      get the baseline file's path from the command line
      add option to write XML to string instead of file
      fix failing tests revealed by gerrit
      fix the format of PhyloXML references
      fix blank newline in XML output
      vtkXMLReader can now read from an input string
      new class: vtkPhyloXMLTreeReader
      consolidate tests for PhyloXML
      silence unused parameter warning
      change signatures for wrapping
      copy row names from R to vtkTable
      do not assume 1st column holds row names
      fix failing SetGet test forvtkHeatmapItem
      preserve R data.frame row names
      break vtkRCalculatorFilter's input/output symmetry
      style cleanup
      add SSL support to VTKWeb server
      fix potential segmentation fault
      change the way we shut down the R interface
      fix failing R tests reported by CDash

xabi riobe (4):
      Fix memory leak in vtkPNGWriter when OutOfDiskSpaceError
      Initialize row_pointers
      Fix numerical precision problem in vtkCellLocator::IntersectWithLine
      Add default value for argument

Revision 23615  Directory Listing
Modified Fri Aug 22 20:55:55 2014 UTC (3 years, 1 month ago) by jcfr
BUG: Update CTK to fix "invalid drawable" error on MacOSX >= 10.8. Issue #3809

$ git shortlog 790155..19c966 --no-merges
Jean-Christophe Fillion-Robin (2):
      BUG: Prevent VTK render call in ctkVTKRenderView::setupRendering
      Fix unused-variable warning in ctkLayoutViewFactory::createViewFromXML

Julien Finet (1):
      Separate viewFromXML to createViewFromXML

Revision 23614  Directory Listing
Modified Fri Aug 22 20:55:54 2014 UTC (3 years, 1 month ago) by jcfr
COMP: Remove un-needed external project step 'CHMOD_incrTcl_configure'

Following previous commit updating the version of incrTcl, this
custom step is now unnecessary.

Revision 23613  Directory Listing
Modified Fri Aug 22 20:55:52 2014 UTC (3 years, 1 month ago) by jcfr
COMP: Update version of tcl/tk/incrTcl used on Linux/MacOSX. Issue #3809

In an attempt to help addressing #3809, this commit updates the ancient
version of Tcl from 8.4 to 8.6 and also update incrTcl from 3.2 to 4.0.

This should fix potential issues specific to MacOSX 10.9 and above.

Also remove unused CMake script 'SlicerBlockStringFindReplace.cmake'

Revision 23608  Directory Listing
Modified Thu Aug 21 21:32:17 2014 UTC (3 years, 1 month ago) by jcfr
COMP: Fix build error when building on MacOSX 10.8/10.9. Issue #3405

This commit updates the python build system and ensure tk can be configured
when X11 header and libraries are in non-system location.

Python build system changes:

$ git shortlog 3c5864f2..47845 --no-merges
Jean-Christophe Fillion-Robin (12):
      Update .gitignore
      README: Re-organize README using markdown
      README: Associate Apache 2.0 License
      README: Update curl command to follow redirect
      README: Add instruction to check MD5 sum of the downloaded source package
      README: Add instruction to extract Python source archive
      README: Reference license file using relative link
      README: Format list of CMake options
      Display system processor
      Fix get_target_property warning related to non existent target
      Fix readline build error occurring when targeting MacOSX SDK 10.4
      Find X11 library and header to fix tkinter compile error. Fixes #33

Matt McCormick (3):
      Update Python version in README 2.7.1 -> 2.7.3.
      Support build for Linux/ARM.
      Reformat README from Markdown to reStructuredText.

Yann Collette (2):
      Simplify handling of python version introducing PY_VERSION CMake variable
      Fix failed uint{32,64}_t / int{32,64}_t detection on some platforms.

Revision 23571  Directory Listing
Modified Sat Aug 16 21:45:18 2014 UTC (3 years, 1 month ago) by jcfr
ENH: Update ITKv4 and BRAINSTools

The commit BRAINSia/BRAINSTools@7311363 related to the re-organization of
the "find_package(VTK)" call has not been included, this will be done
when Slicer itself will be re-organized.

// -----------------
ITK changes:

$ git shortlog v4.6.0...3147239 --no-merges
Bradley Lowekamp (4):
      ENH: Adding License file from upstream MetaIO
      ENH: Adding script to update MetaIO from upstream
      ENH: Remove ITK MetaIO to prepare for upstream import
      COMP: Fix variable type for Set/Get macros

David T. Chen (1):
      DOC: Fixed HistogramThresholdImageFitler

Gert Wollny (1):
      COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease)

Hans Johnson (3):
      COMP: Add tolerance for comparing floating point
      PERF: Remove non-threadable algorithm components
      PERF: Remove large foot print of PDF derivatives.

Matthew McCormick (13):
      BUG: ArchiveTestingData.py future imports must occur at the beginning.
      DOC: Remove Image2.cxx reference from Book 2.
      DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx.
      DOC: Remove references to Book 1 sections from Book 2.
      DOC: Make BinaryThresholdImageFilter not floating.
      DOC: Fix Software Guide figure caption for FlipImageFilter.
      DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx.
      DOC: Remove duplicate figure in LaplacianRecursiveGaussianImageFilter2.cxx.
      DOC: ImageRandomConstIteratorWithIndex table reference.
      BUG: Bump GCCXML to 2014-08-06.
      BUG: Fix invalid assignment of second VoronoiBoundaryOrigin.
      BUG: Call clear instead of empty on PatchBasedDenoising EmptyCaches().
      BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's.

MetaIO Maintainers (1):
      MetaIO (reduced)

Michka Popoff (4):
      BUG: Improve SWIG version check
      BUG: Add VTK_VERSION for older VTK versions
      BUG: Update VTK minimum version (for release)
      BUG: Fix memory leak in MetaImageIO after exception


// -----------------
BRAINSTools changes:

$ git shortlog slicer-e5c9c8c_2014-07-29...slicer-57c31ab_2014-08-08 --no-merges
Ali Ghayoor (2):
      BUG: Fix cmake bug and replace a test baseline
      BUG: Fix ValidateBRAINSResampleTest4 by increasing tolearance

David Welch (9):
      WIP: Initial testing with one session/subject
      WIP: Run one session/subject successfully
      ENH: Refactored workflow with new config variable and singleSession.py executable
      STYLE: Updated configuration template file
      BUG: singleSession.py can now be called as an executable w/o modifying PYTHONPATH     BUG: Fixed --session flag to take in one or more session IDs
      BUG: Fixing the template running stage.
      STYLE: Remove python warning and reorganize imports
      STYLE: Removed master_config dictionary in favor of descriptive dictionary names
      ENH: Fixed command line for singleSession and template     STYLE: Moved imports in template to top of file     BUG: Fixed DataGrabber for template workflow     BUG: Fixed session checking in singleSe

Hans Johnson (27):
      ENH: Utilize new mattes with improved threading
      BUG: Fixed bugs in singleSession
      COMP: Address dependencies on tests.
      BUG: Incomplete refactorings done for Autoworkup
      ENH: Add convience alias for pushing changes.
      ENH: Allow XML files to have relative paths to images
      COMP: Add warning suppressions for OpenCV.
      COMP: Add second suppression for OpenCV.
      BUG: Missed brainmask read read wrapping
      ENH: Refactoring template.py for consistent data sinks.
      ENH: More changes to get atlas generation cleaned up.
      BUG: Incorrect file was used for selecting the brain mask.
      STYLE: Remove unnecessary code.
      BUG: Data grabber changes required dictionary changes
      BUG: The master atlas should be specified from config file
      STYLE: Remove global code from __init__.py
      BUG: Command line wfrun argument was not being respected
      STYLE: Remove unnecessary checking
      BUG: The logitudinal processing could not occur previously
      ENH: Add separate config variables specific to each workphase
      BUG: Premature return from loop
      ENH: Updated to latest ITK+Gerrit Mattes patch
      ENH: Update to latest version of ANTS.
      COMP: Erroneous closing ')'
      ENH: Remove outdated and non-functioning md5 files.
      ENH: Added Sentinal output file checking for Workflows
      STYLE: Only give debugging information when requested

Jean-Christophe Fillion-Robin (2):
      COMP: Move ITK find_package calls into each sub-project.
      COMP: Fixes tests by explicitly specifying list of ITK IO components

Kent Williams (15):
      COMP: get rid of ITKv3 Compatibility ifdefs
      COMP: Sync with NAMICExternalProjects
      COMP: fix teem build and ITK->VTK dependency
      BUG: don't extend composite transform filenames needlessly.there was some deficient logic that was changing the filename of composit transforms to force them to hdf5 format, even if the filename give
      BUG: don't extend composite transform filenames needlessly.there was some deficient logic that was changing the filename of composit transforms to force them to hdf5 format, even if the filename give
      COMP: update teem tag
      COMP: Make FSLToNrrd synthesize bval/bvec filenames if none are given.
      COMP: Move find_package(ITK) into a macro
      COMP: tune module list
      COMP: streamlined FindITKUtil commands
      COMP: cleaned up CMakeLists.txt with respect to FindITKUtil
      COMP: slight changes to address compiler errors in BRAINSSurfaceTools
      COMP: iccdef changes to work with ITKv4
      COMP: add new parameter for FSLToNrrd conversion
      COMP: reorganize path processing

Revision 23565  Directory Listing
Modified Wed Aug 13 02:32:22 2014 UTC (3 years, 1 month ago) by jcfr
ENH: Update OpenIGTLink from 1.10.4 to 1.10.10 to include bug fixes.

$ git shortlog 3ac5311..849b434 --no-merges
Andras Lasso (1):
      Add the MSG_NOSIGNAL flag to socket send calls to prevent application crash on disconnect on linux systems

Gergely Zombori (1):
      Bug #1912 - Merged the changes and enhancements from upstream into 'master'

Isaiah Norton (1):
      BUG: use shutdown() instead of close() for sockets

Junichi Tokuda (7):
      BUG: Address issue #29: copy igtl_win32hearder.h to the install directory.
      ENH: Update patch number.
      STYLE: Update patch number.
      COMP: Fix compilation error due to lack of MSG_NOSIGNAL option in send() in Mac OS X. For Mac OS X, call setsockopt() with SO_NOSIGPIPE instead.
      STYLE: Update revision number.
      BUG: Set timestamp zero, when no timestamp object is registered to image meta message.
      STYLE: Update patch number

Laurent Chauvin (1):
      BUG: Initialize ImageMessage matrix to identity (issue #39)

Matt Clarkson (3):
      #44: Put nanosleep in loop to ensure sleep is for the correct time.
      #49: Avoid crash on division by zero, which should never happen
      #50: Convenience methods to set/get igtl_image matrix from 4x4 array of floats

z0022myy (1):
      BUG: Intializing pointer should not be in a loop

Revision 23564  Directory Listing
Modified Tue Aug 12 20:53:10 2014 UTC (3 years, 1 month ago) by pinter
ENH: Log to file

Enabled file logging in CTK error log model, bumping up hash. The number of files to keep and the log file paths are stored in the revision settings. The log files are saved in the temp folder with file name Slicer_[revision]_[date]_[time].log. If number of log files is larger than number of files to keep, then the old log file is deleted.

Revision 23558  Directory Listing
Modified Wed Aug 6 07:11:38 2014 UTC (3 years, 1 month ago) by jcfr
ENH: Update CTK to remove extra debug statements related to ctkDICOMDatabase

Before this commit:

// -------
$ ./Slicer
Number of registered modules: 142
Register compression libraries
TagCacheDatabase not open

TagCacheDatabase verified!

Number of instantiated modules: 142
Number of loaded modules: 142
// -------

After:

// -------
$ ./Slicer
Number of registered modules: 142
Number of instantiated modules: 142
Number of loaded modules: 142
// -------


Summary of changes:

$ git shortlog 9e1c0258..62675d0 --no-merges
Jean-Christophe Fillion-Robin (2):
      Remove qDebug statement from registerCompressionLibraries()
      Do not display debug info when tagCacheExists method works as expected.

Revision 23553  Directory Listing
Modified Wed Aug 6 04:33:12 2014 UTC (3 years, 1 month ago) by jcfr
COMP: External_OpenSSL - Fix typo introduced in previous commit r23552

Use "OpenSSL_(URL|MD5)" instead of "OPENSSL_(URL|MD5)" variables.

Revision 23552  Directory Listing
Modified Wed Aug 6 02:43:36 2014 UTC (3 years, 1 month ago) by jcfr
COMP: Add support for building on windows using Qt 4.8.6 and OpenSSL 1.0.1h

For more details see inlined comment. Also copied below for convenience:

8<----8<----8<----8<----8<----8<----8<----8<----8<----
# Starting with Qt 4.8.6, we compiled [1] OpenSSL binaries specifically for each
# version of Microsoft Visual Studio. To understand the motivation, read below.
#
# As explained in [2][3], if a library meets these two conditions:
#   (a) exposes a pure C interface
#   (b) is linked against static version of the CRT
# the version of the compiler and runtime used to build the library
# shouldn't matter.
#
# That said, since OpenSSL is built as a shared library using the '/MD' [4]
# flag, it is not possible to use the same library with different runtime
# libraries.
#
# We found out that '/MD' was used by inspecting the the file 'ms/ntdll.mak'
# generated atfer configuring OpenSSL.
#
# If you find mistake in this explanation, do not hesitate to submit a patch
# to fix this text. Thanks.
#
# [1] Script used to compile OpenSSL: https://gist.github.com/jcfr/6030240
# [2] http://siomsystems.com/mixing-visual-studio-versions/
# [3] http://bytes.com/topic/net/answers/505515-compile-different-versions-visual-studio
# [4] http://msdn.microsoft.com/en-us/library/2kzt1wy3.aspx
8<----8<----8<----8<----8<----8<----8<----8<----8<----

Revision 23548  Directory Listing
Modified Mon Aug 4 17:01:13 2014 UTC (3 years, 1 month ago) by jcfr
ENH: Update VTK6 to include backported bug fixes and tweaks

$ git shortlog 169b37b..6c6e5d3
Andrew Bauer (1):
      Fixing overflow issue that appeared with GCC compilers.

Ben Boeckel (4):
      python: fix leaks when setting constants in wrappers
      STLWriter: Raise an error for non-triangles
      STLReader: Close the file when an error occurs
      STLReader: Fix error signaling when reading files

Bill Lorensen (1):
      BUG0013829: vtkAssembly::GetBounds adds bounds which are uninitialized

Brad King (1):
      Examples: Set required CMake version and policies before project()

Cory Quammen (1):
      Added "sticky" axes mode to vtkCubeAxesActor

David C. Lonie (1):
      Handle empty array initialization in numpy_support.

David Gobbi (7):
      Fix a crash when deleting vtk-python objects.
      Fix warning about trailing comma in enum list.
      In wrappers, guard against #including dirs.
      Fix cell picker for images with negative spacing.
      Fix uninitialized array warnings.
      Bad null pointer check in vtkBSplineTransform.
      Fix bad SetColor/GetColor interaction in vtkProperty.

Jean-Christophe Fillion-Robin (2):
      vtkPythonCommand - Add support for additional call data types
      vtkPythonCommand - Fix indent and variable names

John Stark (1):
      Fix pipeline update issues in vtkImageExport

Julien Finet (2):
      Prevent error message when deep copying vtkGridTransform
      Change GetInputConnection error message into a debug warning message

Sankhesh Jhaveri (1):
      BUG: Border visibility from underlying vtkScalarBar actor

Sean McBride (30):
      Fix clang analyzer warning about passing null to strcmp
      Fixed clang analyzer warning about passing null to memcpy
      Fixed clang analyzer warning about reading uninitialized memory
      Fixed clang analyzer waring about a dead store.
      Fixed clang analyzer warning about dead store
      Fixed clang analyzer warning about dead store.
      Fixed clang analyzer warning about dead store.
      Fixed clang analyzer warning about dead store.
      Fixed clang analyzer warning about dead store.
      Fixed clang analyzer warning about 2 dead stores.
      Fixed clang analyzer warning about dead store.
      Fixed clang analyzer warning about reading past an array.
      Fixed several clang analyzer warnings.
      Fixed clang analyzer warning about reading uninitialized memory.
      Fixed clang analyzer warning about dead store to 'pd'.
      Fixed clang analyzer warning about passing null to memcpy.
      Fixed clang analyzer warning about dead store to 'index'.
      Fixed clang analyzer warning about dead store to 'bestTime'.
      Workaround clang analyzer warning by creating temp variable.
      Fixed clang analyzer warnings about dead stores.
      Misc cleanup of code nearby clang analyzer warnings.
      Fixed clang analyzer warnings about dead stores.
      Fixed clang analyzer warning about dead store at very end of method.
      Fixed clang analyzer warning about dead store to 'itr'.
      Fixed clang analyzer warning about dead store to 'cptr'.
      Fixed null deref found by clang analyzer
      Fixed clang analyzer warnings about dereferences
      Suppress clang analyzer warning
      Fixed clang analyzer warning about null deref
      Fixed clang analyzer warning about reading uninitialized data.

Thomas Vaughan (1):
      Set origin and spacing in vtkSurfaceReconstructionFilter. Ref: Mantis 0002826.

Tristan Coulange (1):
      BUG: Add a missing include for VS 2013

Utkarsh Ayachit (3):
      BUG #14599: Handle double values properly.
      Add support for empty strinngs in SetInputArrayToProcess.
      BUG #14244: Fix stereo image captures.

Will Schroeder (1):
      Fixed bug causing plane to disappear on boundary.

Xabi Riobe (1):
      BUG: The method vtkClipPlanesPainter::UpdateBounds must not be implemented.

xabi riobe (2):
      Fix numerical precision problem in vtkCellLocator::IntersectWithLine
      Add default value for argument

Revision 23528  Directory Listing
Modified Fri Aug 1 02:12:59 2014 UTC (3 years, 1 month ago) by jcfr
COMP: Revert back to VTK 6.1. See #3741

It turns out that updating the version of XCode  used on the factory
(running Snow Leopard) from 3.2.6 to 4.2 avoids to get the rather
obnoxious errors of the form:

// ---------------------
[ 53%] Built target vtkSlicerAtlasCreatorModuleLogic
Linking CXX shared library ../../../../lib/Slicer-4.3/qt-loadable-modules/libvtkSlicerAtlasCreatorModuleLogicPythonD.dylib
ld: warning: duplicate dylib /Users/kitware/Dashboards/Experimental/Slicer4-SB/python-install/lib/libpython2.7.dylib
ld: two level namespace mach-o files can link with at most 253 dylibs, this link would use 257 dylibs
collect2: ld returned 1 exit status
// ---------------------

This has been confirmed doing

(1) a clean build of Slicer r23525 using:
 Slicer/VTK@169b37b
 CMake 2.8.12

(2) a clean build of CarreraSlice against the Slicer build tree
obtain in (1) also using CMake 2.8.12

More particularly, this commit reverts r23512, r23513, r23514 and r23515
The code checking for the version of CMake and enabling the option
VTK_ENABLE_KITS only available with kitware/VTK@a609ca has been removed.

XCode before:

 * Xcode: 3.2.6 - uildVersion: 10M2518
 * gcc-4.0: i686-apple-darwin10-gcc-4.0.1 (GCC) 4.0.1 (Apple Inc. build 5494)
 * gcc-4.2: i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3)
 * llvm-gcc: i686-apple-darwin10-llvm-gcc-4.2 (GCC) 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.6)
 * clang: Apple clang version 1.7 (tags/Apple/clang-77) (based on LLVM 2.9svn

XCode after:

 * Xcode: 4.2 - Build version 4C199
 * gcc-4.0: i686-apple-darwin10-gcc-4.0.1 (GCC) 4.0.1 (Apple Inc. build 5494)
 * gcc-4.2: i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3)
 * llvm-gcc: i686-apple-darwin10-llvm-gcc-4.2 (GCC) 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.1.00)
 * clang: Apple clang version 3.0 (tags/Apple/clang-211.10.1) (based on LLVM 3.0svn)

The XCode configuration details has been obtained using the following
one-liner adapted from the one available on XcodeVersionInfo macports
page [1]:

// --------------------
echo -en " * Xcode: $(/usr/bin/xcodebuild -version |head -n1) - $(/usr/bin/xcodebuild -version |tail -1)\n\
$(test -x /usr/bin/gcc-3.3\
&& echo " * gcc-3.3: $(/usr/bin/gcc-3.3 --version 2>/dev/null |head -1)\n")\
$(test -x /usr/bin/gcc-4.0\
&& echo " * gcc-4.0: $(/usr/bin/gcc-4.0 --version 2>/dev/null |head -1)\n")\
$(test -x /usr/bin/gcc-4.2\
&& echo " * gcc-4.2: $(/usr/bin/gcc-4.2 --version 2>/dev/null |head -1)\n")\
$((test -x /usr/bin/llvm-gcc-4.2 || test -x /Developer/usr/bin/llvm-gcc-4.2)\
&& echo " * llvm-gcc: $((/usr/bin/llvm-gcc --version 2>/dev/null || /Developer/usr/bin/llvm-gcc --version 2>/dev/null) |head -1)\n")\
$((test -x /usr/bin/clang || test -x /Developer/usr/bin/clang)\
&& echo " * clang: $((test -x /usr/bin/clang\
&& /usr/bin/clang --version 2>&1 || /Developer/usr/bin/clang --version 2>&1) |head -1)\n")"
// --------------------

Note also that running this on-liner using the freshly installed version
of XCode return the following message:

** INTERNAL ERROR: Uncaught exception **
Exception: *** -[NSConcreteFileHandle writeData:]: Broken pipe


Finally, for future reference, the package allowing to install xcode is
named "xcode_4.2_for_snow_leopard.dmg" and the associated
MD5 is "428b006e1c12eaa644a442a598c6f13f". It has been installed using
the default option in the "/Developer" folder.

[1] https://trac.macports.org/wiki/XcodeVersionInfo

Revision 23515  Directory Listing
Modified Wed Jul 30 11:03:47 2014 UTC (3 years, 1 month ago) by jcfr
COMP: Update VTK to configure a more friendly VTKConfigVersion file

// -------------------
commit 15fac7625d2b817aee4326376871f2cc2bbf53cd
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Wed Jul 30 06:51:28 2014 -0400

    Configure VTKConfigVersion consistent with VTK's compatibility guarantees

    Since the minimum CMake version required by VTK is 2.8.8, this commit
    uses the module CMakePackageConfigHelpers available in that version of
    CMake.
// -------------------

Revision 23512  Directory Listing
Modified Wed Jul 30 09:41:26 2014 UTC (3 years, 1 month ago) by jcfr
COMP: Update VTK6 to include support for VTK_ENABLE_KITS. See #3741

This commit updates the version of VTK so that the changes introduced
in commit r23509 can have an effect.

An attempt to cherry-pick only the commits introducing the VTK_ENABLE_KITS
feature has been done. It turned out that the kits feature and the
introduction of the support for different backend were too much tangled.

After reviewing the list of changes, most them includes bug fixes, addition
of VTK tests, fixes for memory initialization, optimization.
More specifically, here is a list of the one that are of interest
for Slicer are:

  kitware/VTK@504036 : Added "sticky" axes mode to vtkCubeAxesActor
  kitware/VTK@196bbe : Refactor GetRange to compute all ranges at the same time.
                       [...] improves the total runtime by 1.5x to 3x.
  kitware/VTK@87291c : Improve ComputeScalarRange when we have a single component.
                       In testing this takes the ComputeScalarRange on 600^3 from ~430 ms to ~20ms.
  kitware/VTK@cbd488 : Fix a crash when deleting vtk-python objects.
  kitware/VTK@e76153 : BUG: vtkProp3D - Wrong transformation used to restore original parameters

Following discussion with Berk [1], the OpenGL backend remains the
same and the corresponding changes are backward compatible. (There are
some exceptions but Slicer code base is not impacted)

[1] http://www.kitware.com/blog/home/post/703

For a complete list of changes:

  git shortlog 169b37..0d4202 --no-merges

Revision 23511  Directory Listing
Modified Wed Jul 30 06:03:55 2014 UTC (3 years, 1 month ago) by jcfr
COMP: Download openssl-1.0.1e source packages from packages.kitware.com

Since openssl.org is not always up, the source archive has been
mirrored on midas.

Revision 23509  Directory Listing
Modified Wed Jul 30 03:00:19 2014 UTC (3 years, 1 month ago) by jcfr
COMP: Fix VTK6 link error on MacOSX 10.6. Fixes #3741

To reduce the number of libraries passed to the linker, this commit build
VTK6 with the VTK_ENABLE_KITS option enabled.

If building on MacOSX 10.6 without CMake 3.0, it also updated the build
system to output a fatal error message explaining that a more recent
version of CMake is required.

Revision 23487  Directory Listing
Modified Sun Jul 27 21:57:16 2014 UTC (3 years, 1 month ago) by finetjul
BUG: Fix IconEngine and d&d of QStandardItems with icons

When doing drag&drop, the mime data failed to stream the QIcon because
qSlicerIconEnginePlugin was not a subclass of QIconEngineV2.
Regression when adding Qt5 support in CTK.
Closes #3778

Revision 23478  Directory Listing
Modified Wed Jul 23 06:51:17 2014 UTC (3 years, 2 months ago) by jcfr
BUG: Update SlicerExecutionModel - Fixes #2712

This commit updates SlicerExecutionModel to include an updated version
of ModuleDescription::ReadParameterFile function that support string
parameter without value. The Slicer/SlicerExecutionModel@05af78d also
adds corresponding test checking that parameter file with and without
value can still be read.

$ git shortlog feef59e..a6616b52 --no-merges
Jean-Christophe Fillion-Robin (1):
      BUG: Support parameter file with empty value

Revision 23477