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Revision 26384  View Download Blame
Modified Thu Sep 21 01:45:04 2017 UTC (4 days, 13 hours ago) by lassoan
File length: 18086 byte(s)
Diff to previous 26366
BUG: Fixed EMSegment test error due to changed selection node

Selection node has now a activePlotChartID member.

Revision 26366  View Download Blame
Modified Sat Sep 9 03:16:59 2017 UTC (2 weeks, 2 days ago) by jcfr
File length: 18086 byte(s)
Diff to previous 26360
BUG: Fix EMSegment test re-enabling BRAINSDemonWarp module

This commit re-enables the building of BRAINSDemonWarp inadvertently
disabled in r26353 (Fix macOS compilation error disabling extra BRAINSTools CLIs)
and fixes the failing test EMSegCL_Task_MRIHumanBrainExp_BRAINS_small.

Since build error originally fixed in r26353 was associated with the new
module BRAINSRefacer, it will not break the build:

```
$ make BRAINSDemonWarp
[...]
[100%] Linking CXX executable ../../../../lib/Slicer-4.7/cli-modules/BRAINSDemonWarp
Copying XML file 'BRAINSDemonWarp.xml' along side the executable
[100%] Built target BRAINSDemonWarp

```

Revision 26360  View Download Blame
Modified Fri Sep 8 17:20:26 2017 UTC (2 weeks, 2 days ago) by jcfr
File length: 18087 byte(s)
Diff to previous 26356
COMP: Update EMSegment to fix remaining CMP0020 warnings

Revision 26356  View Download Blame
Modified Thu Sep 7 22:08:16 2017 UTC (2 weeks, 3 days ago) by jcfr
File length: 18087 byte(s)
Diff to previous 26353
COMP: Update EMSegment to fix "deprecated-register" warnings

The use of the register key word is deprecated:

Slicer-bld/EMSegment/AMF/vtkMinHeap.h:235:5: warning: 'register' storage class specifier is deprecated and incompatible with C++1z
      [-Wdeprecated-register]
    register int  down;
    ^~~~~~~~~

From: Hans Johnson <hans-johnson@uiowa.edu>

Revision 26353  View Download Blame
Modified Wed Sep 6 14:31:58 2017 UTC (2 weeks, 5 days ago) by jcfr
File length: 18087 byte(s)
Diff to previous 26341
COMP: Fix macOS compilation error disabling extra BRAINSTools CLIs

Following the update of BRAINSTools in r26341, three additional modules
are available: BRAINSDemonWarp, VBRAINSDemonWarp and BRAINSRefacer

This commit disables them and avoids the follow build error on macOS:

```
Standard Error
In file included from /Users/kitware/Dashboards/Nightly/Slicer-0-build/BRAINSTools/BRAINSRefacer/BRAINSRefacer.cxx:5:
In file included from /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4/Modules/Filtering/DisplacementField/include/itkTransformToDisplacementFieldFilter.h:21:
In file included from /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4/Modules/Core/Common/include/itkDataObjectDecorator.h:31:
In file included from /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4/Modules/Core/Common/include/itkDataObject.h:31:
In file included from /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4/Modules/Core/Common/include/itkObject.h:31:
In file included from /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4/Modules/Core/Common/include/itkLightObject.h:23:
In file included from /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4/Modules/Core/Common/include/itkTimeStamp.h:33:
In file included from /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4/Modules/Core/Common/include/itkAtomicInt.h:38:
/Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4/Modules/Core/Common/include/itkAtomicIntDetail.h:42:11: fatal error: 'atomic' file not found
# include <atomic>
          ^
1 error generated.
```

Revision 26341  View Download Blame
Modified Tue Sep 5 08:34:08 2017 UTC (2 weeks, 6 days ago) by jcfr
File length: 18027 byte(s)
Diff to previous 26330
COMP: Effectively update BRAINSTools as indicated in r26331

This commit update BRAINSTools so that target "BRAINSCommonLib" is
exported.

$ git shortlog 0558e43..7994f92 --no-merges
Jean-Christophe Fillion-Robin (1):
      COMP: Export BRAINSCommonLib target for build tree

Revision 26330  View Download Blame
Modified Sun Sep 3 19:03:07 2017 UTC (3 weeks ago) by jcfr
File length: 17981 byte(s)
Diff to previous 26326
ENH: Update BRAINSTools

git shortlog 55f7e32..0558e43 --no-merges
Alexander Leinoff (36):
      ENH: Initial Commit for BRAINSDeface
      ENH: Implements most of the basic functionality of our algorithm for BRAINSDeface
      ENH: Cleanup, refactoring, for module BRAINSDeface
      ENH: Refactors The combination of BSpline and DistanceMap in module BRAINSDeface
      COMP: Code cleanup in BRAINSDeface
      ENH: Reorganize control options and input parameters for BRAINSDeface module.
      COMP: Removes unused variables in module BRAINSDeface
      ENH: Adds console output statements when writing files in module BRAINSDeface
      ENH: Creates random symmetrical B-spline control points in BRAINSDeface module.
      ENH: Some cleanup, reconfigure defaults in module BRAINSDeface
      ENH: Writes final transform to a file in module BRAINSDeface
      ENH: Adds image type information to SEM varaibles in module BRAINSDeface
      ENH: Improves implementation of B-spline creation in BRAINSDeface module.
      ENH: Adds initial Test Suite and unit tests for BRAINSDeface module!
      STYLE: Renamed BRAINSDeface to BRAINSRefacer
      ENH: Adds unit test parameters for BrainDataTest in module BRAINSRefacer
      COMP: Makes cpp11 standard by default in BRAINSRefacer
      ENH: Allows a face mask to be created from landmarks in module BRAINSRefacer
      COMP: Removes unused variables in CreateRandomBSpline in module BRAINSRefacer
      ENH: Testing the brain data is now done with a landmarks based mask in module BRAINSRefacer
      BUG: Variables should be initailized in proper scope in module BRAINSRefacer
      BUG: Removes old files in module BRAINSRefacer
      ENH: Uses Signed Maurer distance map instead of danielsson distance map in module BRAINSRefacer
      ENH: CTest - Removes labelmap as input for tests in module BRAINSRefacer
      STYLE: Refactor - rename MaskAtlasType to ImageMaskType in module BRAINSRefacer
      ENH: Clean up and add more unit tests in module BRAINSRefacer
      ENH: Creates big B-spline in module BRAINSRefacer in module BRAINSRefacer
      ENH: Adjusts range for Distance Map Scale in module BRAINSRefacer in module BRAINSRefacer
      ENH: Adds some parameters for preset "face-type" options in module BRAINSRefacer
      ENH: Moves B-spline file name SEM param to input group in module BRAINSRefacer
      ENH: Use itk Mersenne Twister instead of std::rand in module BRAINSRefacer
      ENH: Adds SEM Parameters for reusing a random seed in module BRAINSRefacer
      BUG: Fixes random number generation in module BRAINSRefacer
      ENH: Adds option to print mersenne seed to console in module BRAINSRefacer
      ENH: Puts test data onto MIDAS
      COMP: Turn on BRAINSRefacer by default

Ali Ghayoor (1):
      ENH: computing number of subsamples and stepsize in pure plugs mask

Francois Budin (2):
      ENH: Updating DCMTK and ITK (2016-10-24)
      BUG: DCMTK does not support fully C++11

Hans J. Johnson (118):
      ENH: Update to include newer ITK version.
      ENH: Revert to working version of DCMTK for C++11.
      ENH: Update ITK and ANTs.
      ENH: Add itkAverageImage filter to BRAINSTools.
      ENH: Update ITK to support sform/qfrom codes for NIFTI
      COMP: Match DCMTK build to Slicer configuration
      BUG: Testing had bad reference to atlas data
      COMP: Mac clang on 10.12 C++11 mode bugs fixed for DCMTK
      STYLE: Update version to 4.8.0 to indicate new release
      BUG: Missing loop conditions for extract meta data.
      ENH: Initial changes to provide testing suite for DCM2[NRRD|FSL].
      ENH: Reduce ambiguity for how to interpret nifti images
      BUG: Correctly compute the origin of DWI from mosaic
      ENH: Improve readability of conformance logic.
      STYLE: Organize code to simplify logic
      STYLE: Remove unnecessary multiply by identity.
      BUG: Simplify logic to avoid duplicate storage
      STYLE: Make ManualWriteNrrd a function
      ENH: Provide better defualt bvec/bval file searching.
      STYLE: Partial refactoring Cleanup and modularize.
      STYLE: Move computeScaledDiffusionVectors to converter class.
      STYLE: Moved extraction of gradientVectors to the converter class.
      STYLE: Modularize code, make logic encapsulated.
      STYLE: Move all FSL file from dicom to one function.
      STYLE: After organizing, interface can be greatly simplified.
      STYLE: Remove redundant resolution settings.
      STYLE: Remove spacing representation redundancies.
      STYLE: Removed duplicate m_LPSDirCos
      STYLE: Use const for constant value of nrrd orientation string.
      STYLE: Remove unsupported options.
      STYLE: Remove untested and probably unused features.
      STYLE: Ignore cmake build dir for intellij
      STYLE: Remove redundant m_Rows and m_Cols variables.
      STYLE: Encapsulate 3D to 4D conversion for file writing.
      STYLE: Formatting in preparation for reading/writing FSL files.
      STYLE: Reorganized code for better modularity.
      ENH: Update FSLtoNRRD to use common data structure
      ENH: Finish NRRD reader to internal data model
      ENH: Update FSL file to new bvec format.
      STYLE: Provide better typedef description for internal images.
      BUG: Remvoe debugging code.
      BUG: Need to ensure useIdentity for FSL formatted files.
      BUG: Provide consistent state for dwi gradient directions.
      ENH: Add extra testing for FSL conversions.
      ENH: Improve testing of FSL converted files.
      ENH: Add useIdentityMeasurefFrame for DWICompare
      ENH: Update command line tool for comparing BVec and BVal files.
      COMP: Remove unnecesssary variable
      STYLE: Remove execute bits from data files.
      ENH: Update test data for fixed FSL
      COMP: Separate tolerances needed
      ENH: Improve conformance with FSL based tools
      STYLE: Remove unused parameter
      STYLE: Remove redundant code for getting rows/columns of images
      STYLE: Remove TODO comments that had been sufficiently reviewed
      ENH:  Add important meta-data about the scan collection to NRRD headers
      STYLE: Organize to that data-model conversions are transactional
      BUG: Fix orientations for FSL with slice ordering.
      STYLE: Push dicom specific member functions to dicom subclass
      ENH: Improve numerical stability with conversion to/from FSL
      BUG:  Fix to/from FSL orientation settings
      COMP: Refactoring bug with respect to std::__1::endl;
      COMP: Fix backwards compatibilities to C++98
      BUG: Behavior of --allowLossyConversion was lost in refactoring
      COMP: Testing requires separate output file names
      ENH: T2 needs to be resampled to T1 data space
      COMP: GTRACT updates for DWIMetaDataValidator usage
      BUG:  Update ANTS interface now may not return a single element list.
      BUG: DTIEstim always uses the threshold
      STYLE:  Consistently use CXX_MODERN for more robust language specification.
      COMP: Remove UKF Processing for the moment.
      BUG: Converting floating point data can cause overflow problems
      BUG: FSL bvec and bval must be completely converted
      ENH: Make testing for complete template building more robust
      BUG: Incorrect file test with subject name.
      COMP: C++11 ITK_OVERRIDE in cxx files
      ENH: Update external packages for ANTs, ITK, VTK.
      ENH: Allow a file with a list of landmark files to be provided
      ENH: Update ITK to latest version with C++11 fixes.
      ENH: Make regular expression to ignore all clion build dirs.
      ENH: Improve documentation for BCD fixing.
      ENH: Minor error checking improvement
      BUG:  Failure tolerance was too narrow
      COMP: GCC 4.9 compiler errors resolved.
      ENH: SimpleITK can only read and write ASCII filenames
      COMP: Default lmk tolerance test was too small
      ENH: Provide support for the new Slicer4 fcsv file format
      ENH: ConfigParser wrapper for returning ascii strings
      ENH: Added error checking for list size.
      BUG: Need to support new Slicer landmark format
      BUG: Fix spelling error & name conversion
      BUG: Fixed errant encode to ascii on integers.
      ENH: Remove unnecessary import of csv.
      BUG: Need to have image type specified as FL for FLAIR
      COMP: Fix python 3 print statement formatting.
      STYLE: Python style conformance.
      STYLE: Format to conform to python style guides.
      ENH: Ignore *.bak files by default.
      ENH: Fixed iterator to list for length computation
      ENH: Remove encode('ascii','replace') that was unnecessary
      ENH: Read csv file as text.
      ENH: remove unncessary import commands from __init__.py
      ENH: numpy.argmax now returns 64 bit integers, that need to be converted to 32 bit.
      ENH: Fix Python3 formatting and runtime issues.
      COMP: Missing string.h for strcmp function.
      ENH: Update ITK and ANTS.
      ENH: Updaet N4 settings to increase convergence quality.
      DOC: Improve documentation for error message.
      ENH: Added feature for HessianToObjectness.
      ENH: Fix VTK download URL.
      ENH: Update ITK to latest version.
      ENH: Update RTK to the latest release
      ENH: Added new ImageFeatureExtractor tool
      ENH: Improved formatting.
      BUG: N4 BFC stability fix.
      DOC: Provide documentation for how validation was done
      DOC: Added background info about the super-resolution project.
      ENH: Update to CMake 3.5 to be inline with Slicr.

Hans Johnson (1):
      PERF: Add explicit failure for small bounding boxes.

Hui-Xie (37):
      ENH: refactor itkLoadWithMetadata method
      ENH: refactor itkSaveWithMetadata.cxx
      ENH: add new myMexprint.h file
      ENH: move content of myMexprintf.h from original load/save method to new file
      ENH: add matlabIO groundtruth file
      ENH: add matlab compare test file
      ENH: enrich compare test file of matlab
      STYLE: move function implementation into cxx file
      STYLE: move function implementation into cxx file
      ENH: add DWIConvert pulbic interface function
      ENH: add public DWI Convert lib' Ctest case
      STYLE: add DWIConvert compile switch
      ENH: modify DWI convert public lib test case
      ENH: Encapsulate Hans' DWIConvert method
      STYLE: change if statement
      STYLE: add delete converter at the method ending
      ENH: move dcmtk initialization to lib implementation
      STYLE: change cpp files' suffix name into cxx
      ENH: encapsulate DWIConvert class
      ENH: add set/get method
      ENH: change data member into private
      ENH: support 6 conversion modes [DicomToNrrd, DicomToFSL, NrrdToFSL, FSLToNrrd,NrrdToNrrd, FSLToFSL]
      Merge branch 'MatlabR_WImage' into RefactorMatlabIO
      ENH: rewrite DWIConvert infterface
      BUG: solve pullequest error in the DWIConvert Module in master
      BUG: fixes #329, use itksys::SystemTools::GetFilenameExtension instead of self defined function to avoid empty string bug
      STYLE: fix some style and Remove unnecessary commented out code.
      STYLE: replace quotation mark  with const emptyString
      BUG: fixes #331 and add corresponding test case
      BUG: disable DWIConvertMultiShellFSITest as file too big
      BUG: fix #334 without changing interface of ITK
      ENH: add a test tool program for bug #334 test case
      BUG: Fix #334. As the modification of itk::itkDCMTKFileReader::GetSpacing for getting correct zSpace using use (0020, 0032) Image Position (Patient) needs to handle the frame order of various MR vendors, e.g. Siemens Mosaic format, this work, I guess, needs a lot of time.
      BUG: fix #334 add new test cases data file
      BUG: fix #334 with passed testcase and test files
      BUG: fix #334 comment out testcase as test file can not be uploaded
      BUG: add multishell and zSpace md5 test case files

Isaiah (1):
      Update README.md

Isaiah Norton (9):
      ENH: register dcmtk codecs at startup
      BUG: check for converter factory failure
      COMP: remove unnecessary call to DCMTK loglevel
      STYLE: clean up style
      ENH: prefer inputVolume over inputDicomDirectory
      ENH: add optional "outputNiftiFile" parameter to allow Slicer GUI use
      BUG: fix path creation for bvec & bval computed path
      STYLE: more style issues for readability
      BUG: fix swapped argument order in call to constructor

Jeff Obadal (13):
      ENH: Refactors B-spline creation into a separate class in module BRAINSDeface.
      DOC: added Jeffrey Obadal to contributors and acknowledgements section in module BRAINSDeface
      BUG: Changed values used in binary threshold of label map in module BRAINSDeface
      ENH:  Changed PixelType -> ProcessPixelType, ImageType -> ProcessImageType in module BRAINSRefacer
      STYLE:  var name IOComponentType changed to OutputCompnentType_ENUM in module BRAINSRefacer
      ENH: Refactors Utility functions into a seperate file in module BRAINSRefacer
      ENH: Cleanup in module BRAINSRefacer
      ENH: Added verbose/debug functionality in module BRAINSRefacer
      ENH: Cleaned up unit tests in module BRAINSRefacer
      ENH: Added Ctest for reusing bspline in module BRAINSRefacer
      ENH: Add more labels for Slicer in module BRAINSRefacer
      ENH: Added unit test for checking pixel type in module BRAINSRefacer
      ENH: Refactored code for creating a mask from the label map into MaskFromLabelMapFilter.h in module BRAINSRefacer

Max Smolens (1):
      COMP: Fix USE_BRAINSABC default when C++11 is enabled

Tom Wright (2):
      Update git repo source
      Fix for older c++

Revision 26326  View Download Blame
Modified Thu Aug 31 22:32:18 2017 UTC (3 weeks, 3 days ago) by jcfr
File length: 17688 byte(s)
Diff to previous 26276
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 26276  View Download Blame
Modified Wed Aug 16 07:51:33 2017 UTC (5 weeks, 5 days ago) by jcfr
File length: 17688 byte(s)
Diff to previous 26250
BUG: Update EMSegment to fix libpng warning

This commit applies a fix identical to r24571 (BUG: Fix libpng warnings
in console when loading images with Qt 4.8.7) and originally authored
by Max Smolens.

It eliminates the following libpng warning seen when loading certain
PNG images using libpng 1.6.x, which is included in Qt 5:

    libpng warning: iCCP: known incorrect sRGB profile

To discover which module was introducing the warnings, a python script
(adapted from Application/SlicerApp/Testing/Python/MeasureStartupTimes.py)
was used to start Slicer excluding one module at a time.

$ cd Slicer-build
$ /path/to/Applications/SlicerApp/Testing/Python/MeasureStartupTimes.py --check-for-warnings $(pwd)/Slicer

[...]
Excluding: EMSegmentQuick
warnings: 0
****************************************
[...]



Patch applied to MeasureStartupTimes.py:

8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---
--- a/Applications/SlicerApp/Testing/Python/MeasureStartupTimes.py
+++ b/Applications/SlicerApp/Testing/Python/MeasureStartupTimes.py
@@ -173,6 +173,27 @@ def collect_startup_times_excluding_one_module(output_file, drop_cache=False, di
   with open(output_file, 'w') as file:
     file.write(json.dumps(moduleTimes, indent=4))

+def check_for_warnings_excluding_one_module(drop_cache=False, display_output=False):
+  modules = collect_modules()
+  # Collect startup times disabling each module one by one
+  moduleTimes = {}
+  for (idx, (moduleName, moduleType)) in enumerate(modules.iteritems(), start=1):
+    if moduleType == "CLI" or moduleType == "Scripted":
+      print("=> Skipping CLI or Scripted [%s]\n" % moduleName)
+      continue
+    print("[%d/%d]" % (idx, len(modules)))
+    result = runSlicerAndExit(slicer_executable, ['--testing', '--disable-scripted-loadable-modules', '--disable-cli-modules', '--modules-to-ignore', moduleName], drop_cache=drop_cache)
+    (returnCode, stdout, stderr) = result
+    if display_output:
+      if stdout: print("STDOUT [%s]\n" % stdout)
+      if stderr and returnCode == EXIT_SUCCESS: print("STDERR [%s]\n" % stderr)
+
+    print("Excluding: %s" % moduleName)
+    warnings = stderr.count("known incorrect sRGB profile")
+    print("warnings: %d" % warnings)
+    if warnings == 0:
+      print("*" * 40)
+
 def collect_startup_times_modules_to_load(output_file, modules_to_load, drop_cache=False, display_output=False):
   modules = collect_modules()
   modulesToIgnore = list(modules.keys())
@@ -201,6 +222,8 @@ if __name__ == '__main__':
   parser.add_argument("--overall", action="store_true")
   parser.add_argument("--excluding-one-module", action="store_true")
   parser.add_argument("--including-one-module", action="store_true")
+  parser.add_argument("--check-for-warnings", action="store_true")
+
   # Common options
   parser.add_argument("-n", "--repeat",  default=1, type=int)
   parser.add_argument("--drop-cache", action="store_true")
@@ -210,6 +233,11 @@ if __name__ == '__main__':
   args = parser.parse_args()

   slicer_executable = os.path.expanduser(getattr(args, "/path/to/Slicer"))
+
+  if args.check_for_warnings:
+    check_for_warnings_excluding_one_module()
+    sys.exit()
+
   all = (not args.normal
     and not args.modules_to_load
     and not args.overall
8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---

Revision 26250  View Download Blame
Modified Mon Aug 14 02:06:37 2017 UTC (6 weeks ago) by jcfr
File length: 17688 byte(s)
Diff to previous 26245
ENH: Enable C++11 for external projects and extensions

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

Revision 26245  View Download Blame
Modified Mon Aug 14 02:05:10 2017 UTC (6 weeks ago) by jcfr
File length: 17508 byte(s)
Diff to previous 26234
ENH: Update VTK project name to VTKv8

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

Revision 26234  View Download Blame
Modified Fri Aug 11 07:27:19 2017 UTC (6 weeks, 3 days ago) by jcfr
File length: 17508 byte(s)
Diff to previous 26233
ENH: Update LandmarkRegistration for Qt5 compatibility

LandmarkRegistration changes:

    $ git shortlog b2ecd4b..a8c80bc --no-merges
    Max Smolens (2):
          ENH: Make reading of DeveloperMode setting more robust
          BUG: Fix creating QMouseEvent in Qt5

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

Revision 26233  View Download Blame
Modified Fri Aug 11 07:27:17 2017 UTC (6 weeks, 3 days ago) by jcfr
File length: 17508 byte(s)
Diff to previous 26232
ENH: Update CompareVolumes for Qt5 compatibility

CompareVolumes changes:

    $ git shortlog 6d46b39..7aefebe --no-merges
    Max Smolens (1):
          ENH: Make reading of DeveloperMode setting more robust

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

Revision 26232  View Download Blame
Modified Fri Aug 11 05:32:44 2017 UTC (6 weeks, 3 days ago) by jcfr
File length: 17508 byte(s)
Diff to previous 26229
COMP: Update DataStore to add partial Qt5 support

Some more work is required to support webengine used in Qt >=5.6.0

$ git shortlog 0914dee..57c6cb7 --no-merges
Jean-Christophe Fillion-Robin (1):
      ENH: Add partial support for Qt5

Revision 26229  View Download Blame
Modified Fri Aug 11 03:00:38 2017 UTC (6 weeks, 3 days ago) by jcfr
File length: 17508 byte(s)
Diff to previous 26228
COMP: Update DataStore: Fix warnings and link error

$ git shortlog 6c3fb92..0914dee --no-merges
Hina Shah (1):
      COMP: Fix 'inconsistent-missing-override' warnings

Steve Pieper (1):
      COMP: add dependency for application singletons

Revision 26228  View Download Blame
Modified Fri Aug 11 02:50:44 2017 UTC (6 weeks, 3 days ago) by jcfr
File length: 17508 byte(s)
Diff to previous 26227
COMP: Update EMSegment: Fix 'inconsistent-missing-override' warnings

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

Revision 26227  View Download Blame
Modified Fri Aug 11 02:40:35 2017 UTC (6 weeks, 3 days ago) by jcfr
File length: 17508 byte(s)
Diff to previous 26225
COMP: Update OpenIGTLinkIF: Add Qt5 support and fix build warnings

$ git shortlog bd4d34f..06379c2 --no-merges
Hina Shah (1):
      COMP Adding VTK_OVERRIDE keyword to the overrident functions

Jean-Christophe Fillion-Robin (4):
      COMP: vtkIGTLToMRMLTrajectory: Fix deprecated declaration warning
      COMP: vtkMRMLIGTLConnectorNode: Fix sign compare warning
      STYLE: Fix unused variable warnings
      ENH: Add support for Qt5

Revision 26225  View Download Blame
Modified Fri Aug 11 00:07:23 2017 UTC (6 weeks, 3 days ago) by jcfr
File length: 17513 byte(s)
Diff to previous 26218
COMP: Update MultiVolumeExplorer: Fix 'inconsistent-missing-override' warnings

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

$ git shortlog 83866ec..b1bb131 --no-merges
Hina Shah (1):
      COMP Fix 'inconsistent-missing-override' warnings

Revision 26218  View Download Blame
Modified Tue Aug 8 06:40:27 2017 UTC (6 weeks, 6 days ago) by jcfr
File length: 17513 byte(s)
Diff to previous 26212
ENH: Update MultiVolumeExplorer adding support for Qt5

$ git shortlog c4d3b65..83866ec --no-merges
Jean-Christophe Fillion-Robin (1):
      ENH: Add support for Qt5

Revision 26212  View Download Blame
Modified Mon Aug 7 22:42:12 2017 UTC (6 weeks, 6 days ago) by jcfr
File length: 17513 byte(s)
Diff to previous 26203
STYLE: Refactor SlicerCheckCMakeHTTPS to automatically call test function

This allows to easily download the script and check that CMake
support HTTPS.

For example:

```
curl -L https://raw.githubusercontent.com/Slicer/Slicer/master/CMake/SlicerCheckCMakeHTTPS.cmake -o SlicerCheckCMakeHTTPS.cmake
./CMake-3.9.0.app/Contents/bin/cmake -P ./SlicerCheckCMakeHTTPS.cmake
```

Revision 26203  View Download Blame
Modified Fri Aug 4 19:15:50 2017 UTC (7 weeks, 2 days ago) by jcfr
File length: 17540 byte(s)
Diff to previous 26202
COMP: Update EMSegment: add VTKv8 support

Also remove CMake warnings and fix module category


More details below:

------------------------------------------------------------------------
r17134 | COMP: Fix warning removing explicit setting of CMake policy CMP0017.

Setting of CMP0017 to OLD is not needed.

This commit addresses the following warning reported when using CMake 3.9.0:

```
CMake Deprecation Warning at /home/jcfr/Projects/Slicer-2-build/EMSegment/CMakeLists.txt:12 (CMAKE_POLICY):
  The OLD behavior for policy CMP0017 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.

```

See https://github.com/Slicer/Slicer/pull/765

------------------------------------------------------------------------
r17133 | lassoan | COMP: Setting CMP0020 to NEW to remove build warnings

------------------------------------------------------------------------
r17132 | lassoan | ENH: Fixed IslandRemoval module category

It was "Filter", while the correct category name is "Filtering"

------------------------------------------------------------------------
r17131 | msmolens | ENH: Call InitializeObjectBase() in New() methods

In VTK8 it's necessary for New() methods to call InitializeObjectBase() on the
new object for proper tracking with vtkDebugLeaks. The standard macros
(vtkStandardNewMacro, vtkObjectFactoryNewMacro) handle this. For those classes
that don't use the macros, add calls to InitializeObjectBase().

Continue to support earlier versions of VTK by wrapping calls to
InitializeObjectBase() in checks for the preprocessor define
VTK_HAS_INITIALIZE_OBJECT_BASE.

It's possible that many of these implementations could be simplified by using
the standard macros.

See also:
- https://github.com/Kitware/VTK/commit/e5c793dbdf87e838bb2b60c6a5905ced0e5548f9
- http://public.kitware.com/pipermail/vtk-developers/2016-September/034332.html

Revision 26202  View Download Blame
Modified Fri Aug 4 19:15:48 2017 UTC (7 weeks, 2 days ago) by jcfr
File length: 17540 byte(s)
Diff to previous 26201
COMP: Update BRAINSTools to include support for C++11 and fix CMake warning

$ git shortlog a5cfa21..55f7e32 --no-merges
Jean-Christophe Fillion-Robin (1):
      COMP: Fix warning removing explicit setting of CMake policy CMP0017.

Max Smolens (1):
      COMP: Fix USE_BRAINSABC default when C++11 is enabled

Revision 26201  View Download Blame
Modified Fri Aug 4 19:15:46 2017 UTC (7 weeks, 2 days ago) by jcfr
File length: 17595 byte(s)
Diff to previous 26134
COMP: Update CMake minimum required version from 2.8.9 to 3.5

This commit removes few workarounds and explicit setting of CMake policies.

Note that the setting of CMP0017 to OLD (introduced in r16366 (COMP: Update
CMake policy requirements) is not needed. Slicer does not provide CMake
modules that should be included by modules distributed by CMake.

This will ensure the CMake version has:

* support for VS 2015 (introduced in CMake 3.1)

* a decent support for detecting compiler features (useful with C++11 and above)
  See https://cmake.org/cmake/help/v3.5/manual/cmake-compile-features.7.html

* as well as support for modern cmake that will be used to modernize the
  Slicer build system.
  See https://cmake.org/cmake/help/v3.5/manual/cmake-buildsystem.7.html#build-specification-and-usage-requirements

CMake 3.5 is also old enough (release in April 2016) and available (same version
or above) in distributions like these ones:

* Arch Linux
* Ubuntu LTS 14.04, 16.04
* OpenSUSE Leap 42.2, 42.3
* Debian 9, Sid
* Fedora 24/25/26
* Slackware 14.2

See https://pkgs.org/download/cmake

// ------------
Update MultiVolumeExplorer:

$ git shortlog 7e44252..c4d3b65 --no-merges
Andrey Fedorov (1):
      ENH: helper script to get stats for a mv frame

Jean-Christophe Fillion-Robin (1):
      COMP: Update CMake version to 3.5.0

// ------------
Update MultiVolumeImporter:

git shortlog 3fb2858..b2453a8 --no-merges
Jean-Christophe Fillion-Robin (1):
      COMP: Update CMake version to 3.5.0

Revision 26134  View Download Blame
Modified Sat Jun 24 19:26:54 2017 UTC (3 months ago) by fedorov
File length: 17595 byte(s)
Diff to previous 26060
ENH: update MultiVolumeImporter hash

Use scalar volume plugin to load indivudal frames of the MV node

Revision 26060  View Download Blame
Modified Tue May 30 20:19:49 2017 UTC (3 months, 3 weeks ago) by lassoan
File length: 17595 byte(s)
Diff to previous 26042
ENH: Updated EMSegment to use external iterators for shared collections

Revision 26042  View Download Blame
Modified Thu May 25 05:06:47 2017 UTC (4 months ago) by jcfr
File length: 17595 byte(s)
Diff to previous 26029
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 26029  View Download Blame
Modified Tue May 23 05:24:57 2017 UTC (4 months ago) by jcfr
File length: 17575 byte(s)
Diff to previous 26022
STYLE: BuildSystem: List one Slicer dependencies per line

Revision 26022  View Download Blame
Modified Thu May 18 15:23:11 2017 UTC (4 months, 1 week ago) by jcfr
File length: 17558 byte(s)
Diff to previous 26021
STYLE: Buildsystem: Document variable Slicer_EXTENSION_SOURCE_DIRS

Revision 26021  View Download Blame
Modified Thu May 18 15:23:09 2017 UTC (4 months, 1 week ago) by jcfr
File length: 16815 byte(s)
Diff to previous 26006
ENH: Buildsystem: Support packaging of existing extension install dirs

Configuring Slicer using

  cmake -DSlicer_EXTENSION_INSTALL_DIRS:STRING=/path/to/ext1-install-tree;/path/to/ext2-install-tree ...

will ensure the file found in each extension install directories are
packaged with Slicer.

Co-authored-by: Hina Shah <hina.shah@kitware.com>

Revision 26006  View Download Blame
Modified Sat May 6 04:52:23 2017 UTC (4 months, 2 weeks ago) by jcfr
File length: 16177 byte(s)
Diff to previous 25999
BUG: Update EMSegment: Fix "comparison of pointer with integer zero" warning

This commit is similar to r24685 but applies to vtkLevelSets
instead vtkImageLevelSets

EMSegment updates:

------------------------------------------------------------------------
r17129 | jcfr | 2017-05-06 00:48:04 -0400 (Sat, 06 May 2017) | 1 line

COMP: vtkLevelSets: Removed variable to fix unused-but-set-variable warning
------------------------------------------------------------------------
r17128 | jcfr | 2017-05-06 00:43:27 -0400 (Sat, 06 May 2017) | 21 lines

BUG: vtkLevelSets: Fix logic error in vtkLevelSets::CheckConvergence

This commit fixes logic error reported as "-Wextra" warning. It
integrates fix similar to r17108 that was specific to vtkImageLevelSets.h

8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---
/path/to/EMSegment/AMF/vtkLevelSets.cxx: In member function ‘unsigned char vtkLevelSets::CheckConvergence()’:
/path/to/EMSegment/AMF/vtkLevelSets.cxx:1279:24: warning: ordered comparison of pointer with integer zero [-Wextra]
      if (this->u[p] <= 0) total++;
                        ^
/path/to/EMSegment/AMF/vtkLevelSets.cxx:1284:65: warning: ordered comparison of pointer with integer zero [-Wextra]
      if ((this->stored_seg[p] == ON_STORED)    && (this->u[p] > 0))
                                                                 ^
/path/to/EMSegment/AMF/vtkLevelSets.cxx:1287:66: warning: ordered comparison of pointer with integer zero [-Wextra]
        if ((this->stored_seg[p] == OFF_STORED) && (this->u[p] <= 0))
                                                                  ^
/path/to/EMSegment/AMF/vtkLevelSets.cxx:1291:24: warning: ordered comparison of pointer with integer zero [-Wextra]
      if (this->u[p] <= 0)
                        ^
8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---

Revision 25999  View Download Blame
Modified Fri May 5 18:37:10 2017 UTC (4 months, 3 weeks ago) by lassoan
File length: 16177 byte(s)
Diff to previous 25960
BUG: Fixed crash when sending node via OpenIGTLink

Updated to OpenIGTLinkIF version that contains the fix (recent regression).

Revision 25960  View Download Blame
Modified Tue Apr 25 05:05:03 2017 UTC (5 months ago) by lassoan
File length: 16177 byte(s)
Diff to previous 25957
BUG: Fixed test errors

Recent changes removed extra spaces that were put in scene files when they were saved.
Baseline scene files had to be updated accordingly.

Revision 25957  View Download Blame
Modified Tue Apr 25 03:58:17 2017 UTC (5 months ago) by jcfr
File length: 16177 byte(s)
Diff to previous 25818
ENH: Install wheel and pip python packages

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

Revision 25818  View Download Blame
Modified Sun Mar 12 19:44:21 2017 UTC (6 months, 2 weeks ago) by jcfr
File length: 16145 byte(s)
Diff to previous 25815
BUG: Update EMSegment to fix -Winfinite-recursion warning

This commit fixes the following warning:

  /path/to/Slicer-build/EMSegment/MRML/vtkMRMLEMSVolumeCollectionNode.h:64:3: warning: all paths through this function will call itself [-Winfinite-recursion]
    {
    ^

Updates:

* r17126 | jcfr | 2017-03-12 14:33:29 -0400 (Sun, 12 Mar 2017) | 1 line
  COMP: vtkMRMLEMSVolumeCollectionNode: Fix -Winfinite-recursion warning

Revision 25815  View Download Blame
Modified Sun Mar 12 19:44:15 2017 UTC (6 months, 2 weeks ago) by jcfr
File length: 16145 byte(s)
Diff to previous 25801
BUG: Update OpenIGTLinkIF to include UnpackIGTLMessage fix

$ git shortlog c45030e..bfe21de --no-merges
Jean-Christophe Fillion-Robin (2):
      COMP: vtkIGTLToMRMLBase: Fix unused variable warnings
      COMP: vtkMRMLIGTLConnectorNode: Fix sign-compare warning

Longquan Chen (2):
      EHN: UnpackIGTLMessage needs to be performed if the IGTLToMRML is called from outside projects. otherwize, the InImageMessage is not initialized and causes an invalid memory access bug,
      ENN: removed unused variable, refer to ISSUE#62

Revision 25801  View Download Blame
Modified Sun Mar 12 19:43:48 2017 UTC (6 months, 2 weeks ago) by jcfr
File length: 16145 byte(s)
Diff to previous 25706
ENH: Update EMSegment to include Qt5 support and fix Clang warning

* r17125 | jcfr | 2017-03-11 18:18:35 -0500 (Sat, 11 Mar 2017) | 1 line
  STYLE: vtkEMSegmentLogic: Fix -Wabsolute-value warning using std::abs

* r17124 | jcfr | 2017-01-17 07:58:32 -0500 (Tue, 17 Jan 2017) | 1 line
  ENH: Add support for Qt5

Revision 25706  View Download Blame
Modified Mon Feb 13 21:14:55 2017 UTC (7 months, 1 week ago) by lassoan
File length: 16145 byte(s)
Diff to previous 25700
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 25700  View Download Blame
Modified Wed Feb 8 20:49:28 2017 UTC (7 months, 2 weeks ago) by lassoan
File length: 16130 byte(s)
Diff to previous 25685
ENH: OpenIGTLinkIF is capable of processing RGB image

Revision 25685  View Download Blame
Modified Wed Feb 1 20:38:35 2017 UTC (7 months, 3 weeks ago) by pieper
File length: 16130 byte(s)
Diff to previous 25652
COMP: update to latest LandmarkRegistration

Adds fixes from Adam Rankin to allow deletion of
landmarks and adds icons.  Thanks Adam!

From: Steve Pieper <pieper@isomics.com>

Revision 25652  View Download Blame
Modified Tue Jan 24 02:40:46 2017 UTC (8 months ago) by jcfr
File length: 16130 byte(s)
Diff to previous 25644
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  View Download Blame
Modified Fri Jan 20 04:18:47 2017 UTC (8 months ago) by lassoan
File length: 16130 byte(s)
Diff to previous 25547
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 25547  View Download Blame
Modified Fri Nov 18 06:34:02 2016 UTC (10 months, 1 week ago) by jcfr
File length: 16120 byte(s)
Diff to previous 25482
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 25482  View Download Blame
Modified Fri Oct 28 01:33:38 2016 UTC (10 months, 4 weeks ago) by jcfr
File length: 16052 byte(s)
Diff to previous 25422
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 25422  View Download Blame
Modified Tue Oct 11 18:26:49 2016 UTC (11 months, 2 weeks ago) by jcfr
File length: 16010 byte(s)
Diff to previous 25409
ENH: Update MultiVolumeImporter: Better support for 4D Cardiac CT

This commit updates MultiVolumeImporter plugin to include an improved
handling of certain types of 4D Cardiac CT.

Thanks to @lassoan for identifying the use case and contributing the patch.

$ git shortlog 669594f..2ebb4d2 --no-merges
Andras Lasso (1):
      ENH: Allow loading of multi-volumes when multiple series are selected in the DICOM browser

Andrey Fedorov (1):
      BUG: re-enable parsing multi-series with the IPP+AcquisitionTime strategy

From: Andrey Fedorov <andrey.fedorov@gmail.com>

Revision 25409  View Download Blame
Modified Tue Oct 4 17:45:16 2016 UTC (11 months, 3 weeks ago) by jcfr
File length: 16010 byte(s)
Diff to previous 25383
COMP: remove SlicerDMRI remote, moving -> extension

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

Revision 25383  View Download Blame
Modified Wed Sep 21 14:22:24 2016 UTC (12 months ago) by jcfr
File length: 19685 byte(s)
Diff to previous 25298
ENH: Update SlicerDMRI

$ git shortlog 248df4b..a780e4b --no-merges
Isaiah Norton (12):
      ENH: update FBStorageNode for upstream changes.
      ENH: add initial DICOM tractio features
      ENH: tractio xml updates
      COMP: tractio feature gate
      ENH: DTEstim, DTScalarMaps, Seeding GUI updates
      STYLE: fix dos line endings
      ENH: ROISeeding: move seed spacing/grid parameters to advanced
      ENH: ROISeeding: remove archaic WriteToFile option
      ENH: Intx seeding unit label consistency with ROI seeding
      COMP: remove old CLI options, ref 03d39612b
      COMP: add MRML_DATA and TEMP defs for local/extension testing
      COMP: fix and clean-up FBLabelSelect tests

zhangfanmark (2):
      EHN: FBLabelSelect: fiber resampling before selection
      ENH: Sampling faster only using points in lines

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

Revision 25298  View Download Blame
Modified Wed Aug 17 19:59:56 2016 UTC (13 months, 1 week ago) by johan.andruejol
File length: 19685 byte(s)
Diff to previous 25293
COMP: Update SlicerDMRI to include linking fix

This is to include the fix from SlicerDMRI/SlicerDMRI@f3a8545

Johan Andruejol:
   BUG: Make sure to link against CLI library in testing

Revision 25293  View Download Blame
Modified Tue Aug 16 21:53:26 2016 UTC (13 months, 1 week ago) by jcfr
File length: 19685 byte(s)
Diff to previous 25276
ENH: Update EMSegment

------------------------------------------------------------------------
r17123 | jcfr | 2016-08-16 16:43:57 -0400 (Tue, 16 Aug 2016) | 6 lines

STYLE: Improve IDE experience associating targets with folder

 Additionally, it also applies the following changes:
 * Use slicerMacroBuildLoadableModule instead of slicerMacroBuildQtModule
 * Start transitioning to lowercase CMake command names

------------------------------------------------------------------------
r17122 | johan.andruejol | 2016-08-11 13:25:49 -0400 (Thu, 11 Aug 2016) | 1 line

COMP: Include SlicerExecution_USE_FILE

Revision 25276  View Download Blame
Modified Wed Aug 10 19:39:12 2016 UTC (13 months, 2 weeks ago) by msmolens
File length: 19685 byte(s)
Diff to previous 25266
ENH: bump SlicerDMRI remote module to 2775d744ae

```
Alex Yarmarkovich (1):
      BUG: changed <geometry> tag to use  multiple="true" in order to select hierarchy nodes

Isaiah (1):
      Merge pull request #50 from ihnorton/reassign_cats

Isaiah Norton (3):
      ENH: reassign module categories to reflect workflow
      ENH: more descriptive mask-input label for DWIToDTIEstim
      ENH: CLI region-based seeding/selection categories
```

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

Revision 25266  View Download Blame
Modified Mon Aug 8 18:32:46 2016 UTC (13 months, 2 weeks ago) by fedorov
File length: 19685 byte(s)
Diff to previous 25265
BUG: fix incorrect hash and update hash

MultiVolumeExplorer hash was set for MultiVolumeImporter external module

Revision 25265  View Download Blame
Modified Fri Aug 5 18:49:09 2016 UTC (13 months, 2 weeks ago) by fedorov
File length: 19685 byte(s)
Diff to previous 25261
ENH: update MultiVolumeImporter hash

This fixes the off-by-one problem that prevented making static plots for single-
slice multivolumes

(issue reported in this thread: http://slicer-users.65878.n3.nabble.com/MultiVolume-Explorer-td4030844.html)

Revision 25261  View Download Blame
Modified Wed Aug 3 15:23:10 2016 UTC (13 months, 3 weeks ago) by msmolens
File length: 19685 byte(s)
Diff to previous 25256
ENH: bump DMRI external module to 0402024

```
git shortlog b5c262fc..b9404cdb7c
Alex Yarmarkovich (4):
      ENH: Added test datasets for DiffusionTensorScalarMeasurements module.
      ENH: Added tests for DiffusionTensorScalarMeasurements CLI
      ENH: Added tests for DWIToDTIEstimation CLI
      BUG: 4238.Right click -> Edit Properties on Fiber Bundle nodes and Fiber Bundle Display nodes in the Data module should go to the Tractography Display module.

Isaiah (2):
      Merge pull request #37 from SlicerDMRI/fbm_stats_option
      Merge pull request #43 from SlicerDMRI/fbm_clamped_msrs

Isaiah Norton (22):
      ENH: FBTractMeasurement: by default, print only specified hierarchy.
      FBTractMsr: Introduce measurement range clamping, and count excluded points
      FBTractMsr: correctly fix #36: by default print top and cluster groups, but not fiberbundles
      FBTractMsr: refactor redundant code
      FBTractMsr: update to pass tests
      FBTractMsr: fix non-C++11 compile, and more refactoring.
      FBMsr: Print NAN when no measurement value exists.
      Remove obsolute DT scalar measures, update docs.
      Update DTMsr contributor list to match wiki
      Update DTMsr contributor institutions.
      More DTScalarMsr interface updates
      Update DWIToDTIEstim module description.
      More updates to DTEstim & ScalarMeasurements desc.
      Update DWMasking module description.
      Update more module description files
      Remove newlines from FBLabelSelect xml
      FBLabelSelect description updates
      FBLabelSelect description more updates
      FBTractMeasurements description update
      TractLMSeeding module description
      COMP: fix and simplify DTScalarMeasure tests
      COMP: fix FBTractMsr tests

Lauren O'Donnell (1):
      Update README.md

zhangfanmark (1):
      EHN: Measure name consistency
```

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

Revision 25256  View Download Blame
Modified Fri Jul 29 21:23:59 2016 UTC (13 months, 3 weeks ago) by pieper
File length: 19685 byte(s)
Diff to previous 25241
ENH: update MuliVolumeImporter version

Enables cine CT viewing - see:

https://github.com/fedorov/MultiVolumeImporter/pull/19

From: Steve Pieper <pieper@isomics.com>

Revision 25241  View Download Blame
Modified Tue Jul 19 22:27:10 2016 UTC (14 months ago) by jcfr
File length: 19685 byte(s)
Diff to previous 25219
COMP: BRAINSTools: Address MacOSX packaging issue. Fix #4041

$ git shortlog 7859819..47dc8e6 --no-merges
Isaiah Norton (1):
      COMP: Address MacOSX packaging issue.

The BRAINS CMAKE_OSX_RPATH default no longer matched the Slicer default [1].

Due to this setting, the RPATH for BRAINS libraries was not being
detected and replaced correctly by the Slicer fixup_bundle procedure.

Specifically, as far as I can tell, having a pre-set `@rpath` in the
installed libraries caused the fixup_bundle procedure to copy the
(fixed) libraries into the `Slicer-4.5` base directory, rather than
fixing in-place the libraries in `Slicer-4.5/cli-modules`. This caused
two copies of the libraries to be included in the distribution bundle
[2], one of which was un-patched. This un-patched version is referred
to by all *other* libraries, causing dlopen failures. The end result
is that BRAINS could not be used in shared-library mode on Mac [3].

See:
  [1] https://github.com/Slicer/ITK/commit/8ac0d6013b76238f9d84de906c14b493addf8ac8
  [2] http://www.na-mic.org/Bug/view.php?id=4041
  [3] http://massmail.spl.harvard.edu/public-archives/slicer-users/2016/010782.html

From: Isaiah Norton <isaiah.norton@gmail.com>

Revision 25219  View Download Blame
Modified Fri Jul 8 17:53:25 2016 UTC (14 months, 2 weeks ago) by msmolens
File length: 19685 byte(s)
Diff to previous 25202
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 25202  View Download Blame
Modified Thu Jun 23 01:48:00 2016 UTC (15 months ago) by jcfr
File length: 19685 byte(s)
Diff to previous 25201
ENH: Update BRAINSTools

$ git shortlog 6763cdb..7859819 --no-merges
Jean-Christophe Fillion-Robin (2):
      COMP: CMakeLists: Consistent name between top-level and inner-project. Fixes #287
      COMP: BRAINSDemonWarpTemplates: Fix unknown SpatialObjectType error.

Revision 25201  View Download Blame
Modified Wed Jun 22 03:29:49 2016 UTC (15 months ago) by jcfr
File length: 19685 byte(s)
Diff to previous 25197
COMP: Update BRAINSTools to avoid forcing configuration types

This will avoid BRAINSTools to systematically force the configuration
types to be "Release; Debug".

Reported-by: Andras Lasso <lasso@queensu.ca>
Reported-by: Kyle Sunderland <1krs1@queensu.ca>

$ git shortlog 16526a5..eab1460 --no-merges
Alexander Leinoff (3):
      COMP: Dont build the BRAINSABC Module by default
      BUG: Fixes CMake Dependencies in DWIConvert
      ENH: Throw IO Exception when reading/writing invalid landmarks file

Ali Ghayoor (34):
      BUG: Fixed BRAINSFitTest_ROIBSpline by replacing the baseline
      ENH: Updated candidateRegionsThreshold value in BABC
      ENH: Make RC computation more stable
      BUG: Several modifications to identify bug in BCD
      BUG: Reliable computation of reflective correlation in BCD
      ENH: Add matlab companion to make a surface plot of metric
      ENH: print out CHM only in verbose mode
      ENH: Make BCD fail when we know results will be bad
      BUG: Move the physical origin to the center of the image
      BUG: Eyes ranges should be compared to aligned AC point
      BUG: Improved the input T1 test image by denoising
      BUG: Get MetaData dictionary from the reader output in BCD
      BUG: change the valid range for eye positions
      BUG: tuned valid range for eyes locations
      BUG: Generate ITK exception macro in the case of failure
      BUG: modify the threshold value for bad reflective correlation
      BUG: throw exception where needed
      BUG: Choose a reasonable search radius for mid-brain lmks
      BUG: new baselines for BCD search radius tests
      BUG: new baselines for BCD rescale intensity tests
      BUG: Fixed BCDTest_inputLandmarksEMSP
      BUG: Fixed twelve BCD test failures
      BUG: Fixed BCD forced lmks tests
      BUG: Fixed BCD lmks compare tests
      ENH: throw exception when error happens
      BUG: Fixed BRAINSTrimForeground test
      BUG: center of head mass must be passed to reflectionFunctor
      BUG: Fixed BRAINSAlignMSPTest
      ENH: RC computation is robust now, no need for repeated computation
      ENH: Consider a different threshold for RC metric
      ENH: Add correctionType to dtiestim in DWI pipeline
      ENH: Print a more informative error message in DWIConvert
      COMP: Added GTRACT as an option in cmake
      COMP: List the applications that need VTK in cmake build

Hans J. Johnson (70):
      PERF: Optimize cluster density usage
      BUG: Test for CenterOfROI had many bugs
      ENH: Make error checking robust for T1 image
      PERF: Allow running BCD with multiple cores
      ENH: Modernizing vcl_ to std::
      ENH: Update base code for fixing BAW features.
      COMP: Update for VTK 7.1 compilation
      ENH: Cleanup python code for snapshot writing.
      COMP: Remove compiler warning about unused variable.
      ENH: Update ANTs and ITK trying to resolve denoise issue
      ENH: Add ConvertBetweenFileFormats as a default build.
      ENH: RemoveVTKDependance.
      ENH: Allow building of BRAINSTools without VTK.
      COMP: Prefer _REQUIRES_VTK to BRAINSTools_REQUIRES_VTK
      COMP: Fix setting Mac OSX vars for build.
      ENH: Remove Compiler Warnings For clang c++11
      ENH: Const correctness and prefer initialization
      COMP: Compilation bug for mismatch signature.
      ENH: Update ITK to latest version.
      ENH: Hack hardcode to one file for speed.
      ENH: Added timing to computations.
      ENH: Instrument of heirarchial testing.
      ENH: Fine tune heuristic
      PERF: Use heirarcial heuristic for exhausitve search
      BUG: Replace std::__1::cout with std::cout
      ENH: Reorganize variables for readability.
      ENH: Update to new version of itkTestDriver*.inc files
      STYLE:  Put all old unused code at end of file.
      ENH: ITK, DCMTK, ANTs updated in hopes of addressing denoise empty images.
      ENH: Update version number of BRAINSTools.
      BUG: Update ANTS to fix Denoise.
      ENH: Update ITK and SlicerExecutionModel looking for linker warning resolution
      STYLE: Consolidate common typedef in one location
      COMP: Improve compilation by avoiding rebuilds of GenerateCLP
      COMP: KWSYS removed support for pre-C++98 in 2015
      COMP: Update to latest to remove compiler warnings
      COMP: CMP0063 Honor visibility properties for all target types
      ENH: Update ANTs to latest version.
      ENH: Update ITK version.
      PERF: Remove redundant assignment
      ENH: Remove shadowed typedefs
      ENH: Prefer const functions
      COMP: Address CPPCHECK warnings
      ENH: Allow specifying crash dump dir in config file.
      COMP: Incorrectly removed necessary function.
      COMP: Remove warnings about shadowed typedefs.
      ENH: Force T1 only processing for ANTS JointFusion.
      BUG: Only the first element was passing
      ENH: Update ITKv4.
      ENH: Change build for SlicerExecutionModel for visibility
      COMP: Conditionally turn off tests that require VTK
      COMP: Fix issues with SEM Hidden Symbols.
      DOC: Improve documentation for DWIConvert
      ENH: Fix regresion with respect to ITK 4.10
      ENH: Start of a test program for LinearRegression.
      BUG: Numerics for optimal averaging of images fixed
      ENH: Improve the unwrapping function
      ENH: Remove unnecessary outputs to reduce disk usage.
      ENH: Enable NIPYPE Provenance
      COMP: Remove incomplete test
      ENH: Partial additon of resampling code for all images
      ENH: Fine tune autoworkup for unwrapping and BABC candiate region thresholds.
      STYLE: Keep naming consistent with Slicer conventions.
      COMP: Silence compiler warnings
      ENH: Improve CSF and VB joint fusion results by cleanup
      BUG: Missing outputs when maxBiasOrder=0
      ENH: Improve true/false processing logic
      ENH: Use registration masks from template when available
      STYLE: Make the node name match the actual behavior
      ENH: Do not do BFC for BABC

Isaiah Norton (1):
      ENH: throw (overridable) error when attempting lossy NIFTI conversion.

Jean-Christophe Fillion-Robin (7):
      STYLE: Common.cmake: Group CMake include together and remove dead code.
      BUG: SuperBuild.cmake: Ensure calls to mark_as_superbuild are processed
      ENH: Superbuild.cmake: Simplify passing of build option to inner project.
      STYLE: CMakeLists.txt / Common.cmake: Remove commented code
      STYLE: Common.cmake: Remove unused variable ${PROJECT_NAME}_BUILD_FFTWF_SUPPORT
      BUG: Common.cmake: Do not force variable CTEST_CONFIGURATION_TYPE
      COMP: Update ExternalProjectDependency to support cache args with dbl quote

Juan Carlos Prieto (3):
      BUG: Linking error due to missing ITK libraries
      STYLE: Remove ITK version from find package
      Revert "STYLE: Remove ITK version from find package"

Regina Kim (10):
      ENH: ScreenShot script
      ENH: BCD user selected landmark option
      BUG: EMSP file error fix in BAW
      ENH: compute label volume
      ENH: Remove unused variables
      ENH: T2 is only excluded to Joint Fusion
      ENH: Stage5 Resgistration
      BUG: simpleITK BinaryThreshold
      BUG: save_state was not being used
      BUG: template and longitudinal pipeline fix

Revision 25197  View Download Blame
Modified Fri Jun 17 02:39:21 2016 UTC (15 months, 1 week ago) by jcfr
File length: 19649 byte(s)
Diff to previous 25196
BUG: Update EMSegment to fix python module import on windows

This commit updates EMSegment to fix a regression introduced in
r25128 (STYLE: Simplify import of Logic/MRML/DisplayableManager
python modules).

It ensures python modules built on system (e.g Visual Studio) using
intermediate directories (e.g Release, Debug, ...) can be imported.

All EMSegment tests are now expected to pass on Windows.

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

Revision 25196  View Download Blame
Modified Fri Jun 17 02:39:19 2016 UTC (15 months, 1 week ago) by jcfr
File length: 19649 byte(s)
Diff to previous 25193
ENH: Update EMSegment to include Python wrapping fixes for VTK 7.1

This commit updates EMSegment to include Python wrapping fixes for the current
VTK master (upcoming VTK 7.1).

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

Revision 25193  View Download Blame
Modified Tue Jun 14 12:10:29 2016 UTC (15 months, 1 week ago) by msmolens
File length: 19649 byte(s)
Diff to previous 25188
ENH: Update OpenIGTLinkIF to include compilation fixes for VTK 7.1

OpenIGTLink updates:

    $ git shortlog 9271ec5..f3ebcbd --no-merges
    Max Smolens (1):
	  Fix compilation with VTK 7.1

Revision 25188  View Download Blame
Modified Mon Jun 13 19:46:01 2016 UTC (15 months, 1 week ago) by msmolens
File length: 19649 byte(s)
Diff to previous 25184
ENH: Update EMSegment to include compilation fixes for VTK 7.1

This commit updates EMSegment to include compilation fixes for the current VTK
master (upcoming VTK 7.1).

Revision 25184  View Download Blame
Modified Mon Jun 13 04:40:57 2016 UTC (15 months, 1 week ago) by jcfr
File length: 19649 byte(s)
Diff to previous 25173
STYLE: EMSegment: Fix 'Tag already registered' warnings.

This commit updates EMSegment and vtkMRMLScene::CopyRegisteredNodesToScene
to avoid warnings like this one:

//--------
Warning: In /home/jcfr/Projects/Slicer/Libs/MRML/Core/vtkMRMLScene.cxx, line 517
vtkMRMLScene (0x2590e90): Tag LinearTransform has already been registered, unregistering previous node class vtkMRMLLinearTransformNode to register vtkMRMLLinearTransformNode
//--------

Note that calling "GetClassNameByTag" in "CopyRegisteredNodesToScene"
changes "CopyRegisteredNodesToScene" complexity from O(n) to O(n^2).

Considering that

  (1) "CopyRegisteredNodesToScene" is only called from
      "GetReferencedSubScene",  itself used only in EMSegment,

and

  (2) testing times associated with EMSegment tests does not
      increase

.. removing the warning to facilitate the understanding of the test outputs
justifies the added complexity.

Revision 25173  View Download Blame
Modified Wed Jun 8 23:10:26 2016 UTC (15 months, 2 weeks ago) by jcfr
File length: 19649 byte(s)
Diff to previous 25172
COMP: LandmarkRegistration: Update to use expected git tag

This commit update the git tag to effectively use the version of
the project mentioned in previous commit.

Revision 25172  View Download Blame
Modified Wed Jun 8 20:56:04 2016 UTC (15 months, 2 weeks ago) by pieper
File length: 19649 byte(s)
Diff to previous 25147
PERF: #4191 update landmark registration

New version avoids some duplicated work when interacting
with fiducial lists and displayable managers.

See:
https://github.com/pieper/LandmarkRegistration/commit/b6198147a57f2fe50aa9ac40194e67064a14a524

From: Steve Pieper <pieper@isomics.com>

Revision 25147  View Download Blame
Modified Thu Jun 2 03:36:07 2016 UTC (15 months, 3 weeks ago) by jcfr
File length: 19649 byte(s)
Diff to previous 25138
ENH: Add configure time check that CMake supports HTTPS

Some build targets require downloading files using the HTTPS protocol. Before
this commit, targets such as 'python-source' would fail during the build process
with errors like:

    CMake Error at python-source-prefix/src/python-source-stamp/download-python-source.cmake:27 (message):
      error: downloading
      'https://www.python.org/ftp/python/2.7.11/Python-2.7.11.tgz' failed

        status_code: 1
        status_string: "Unsupported protocol"
        log: Protocol "https" not supported or disabled in libcurl

This commit adds a configure-time check that CMake supports HTTPS. Now,
developers are made aware of the problem before building. If https is
supported it displays:

-- Checking if CMake supports https
-- Checking if CMake supports https - ok

If CMake doesn't support HTTPS, the configuration step now fails with a
descriptive error message and a suggested solution:

    CMake Error at CMake/SlicerCheckCMakeHTTPS.cmake:21 (message):
      error: This CMake does not support the HTTPS protocol.  Ensure that CMake
      is compiled with CMAKE_USE_OPENSSL enabled.

Fixes http://www.na-mic.org/Bug/view.php?id=4098

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

Revision 25138  View Download Blame
Modified Tue May 31 22:09:49 2016 UTC (15 months, 3 weeks ago) by jcfr
File length: 19410 byte(s)
Diff to previous 25135
PERF: Improve startup time by ~25% delaying import of SimpleITK

Startup time reduced from  5.1s to 3.8s (cold cache)

Stats obtained after averaging values obtained after 5 runs clearing
the file cache between runs. The following command was used:

~/Projects/Slicer/Applications/SlicerApp/Testing/Python/MeasureStartupTimes.py --drop-cache -n5 --normal ./Slicer

With a warm cache, it improve the startup time by ~32% (4s -> 2.7s)

Results have been gathered on Ubuntu 15.10 on a workstation with the
following specs: 64GB / M.2 PCIe NVMe SSD / Quad Core 3.80GHz

Revision 25135  View Download Blame
Modified Tue May 31 07:44:59 2016 UTC (15 months, 3 weeks ago) by jcfr
File length: 19410 byte(s)
Diff to previous 25119
BUG: Update EMSegment to include simpler import of python modules

This commit updates EMSegment to include updates required after
commit r25128 (STYLE: Simplify import of Logic/MRML/DisplayableManager
python modules)

Revision 25119  View Download Blame
Modified Wed May 25 19:46:00 2016 UTC (16 months ago) by jcfr
File length: 19410 byte(s)
Diff to previous 25094
BUG: Fixes widget and logic python module loading regression

This commit fixes regressions introduced in r25115 and r25116.

* Ensure vtkSlicerCLIModuleLogic (in Base/QTCLI/) python wrapping is loaded.

* Update EMSegment to a version referencing python widget and logic
from the "slicer" namespace.

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

Revision 25094  View Download Blame
Modified Fri May 20 16:44:02 2016 UTC (16 months ago) by pieper
File length: 19410 byte(s)
Diff to previous 24991
PERF: #4191 don't update widgets in batch mode

This really improves the performance of LandmarkRegistration,
particularly when there are large numbers of fiducials
being manipulated.  I haven't seen any side effects.

ENH: request future update when ignoring batch mrml event

Per suggestion from Andras, include a request for future
update to be sure that the widgets are updated
before the render happens.

BUG: #4191 update landmark registration

Addresses slowdown with large numbers of fiducials
by entering batch mode for bulk operations on the scene.

From: Steve Pieper <pieper@isomics.com>

Revision 24991  View Download Blame
Modified Tue Mar 22 23:03:16 2016 UTC (18 months ago) by jcfr
File length: 19410 byte(s)
Diff to previous 24983
ENH: Update SlicerDMRI remote module to SlicerDMRI/SlicerDMRI@b5c262fc

$ git shortlog a82fde4..b5c262f
Isaiah Norton (8):
      COMP: set  in FBMeasure test CMakeLists.txt
      STYLE: Refactor FBTractMeasurement and comments
      FBTractMeasurement: skip and record NaNs for each measure, fixes SlicerDMRI/SlicerDMRI#34
      STYLE: FBTractMeasurements clean-up
      COMP: update FBTractMeasurement tests
      COMP: update SuperBuild.cmake for external index build
      COMP: CMake updates for extension build
      ENH: add helix test data from Slicer repository, fixes SlicerDMRI/SlicerDMRI#18

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

Revision 24983  View Download Blame
Modified Mon Mar 21 22:53:52 2016 UTC (18 months ago) by jcfr
File length: 19410 byte(s)
Diff to previous 24964
ENH: Remove support for building an ExtensionsIndex directly from Slicer

This commit simplifies Slicer build system removing the (untested) support
for building extensions given a directory containing *.s4ext files.

Note that building extensions by configuring and building the project
in "Extensions/CMake" can still be done. Extensions dashboards use and
test this approach. The template extension dashboard script can be used
as a model.

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

Revision 24964  View Download Blame
Modified Thu Mar 10 18:09:30 2016 UTC (18 months, 2 weeks ago) by jcfr
File length: 19624 byte(s)
Diff to previous 24963
BUG: Update BRAINSTools to fix mask checks

This should resolve the regression introduced in r24963 that caused failing
EMSegment test. The problem was identified and solution proposed by @jcfr

$ git shortlog 29d203c...16526a5 --no-merges
Andrey Fedorov (1):
      BUG: fix mask checks for centerOfROI initializer

From: Andrey Fedorov <fedorov@bwh.harvard.edu>

Revision 24963  View Download Blame
Modified Wed Mar 9 20:42:59 2016 UTC (18 months, 2 weeks ago) by jcfr
File length: 19624 byte(s)
Diff to previous 24949
BUG: Update BRAINSTools to include BRAINSFit fix for centerOfROI initializer

Tested-by: Hans Johnson <hans-johnson@uiowa.edu>

$ git shortlog e257e62...29d203c --no-merges
Alexander Leinoff (5):
      COMP: BCD should only request VTK when building GUI
      COMP: CompareImageFilter should only use VTK when building GUI
      BUG: Replaces all baselines for BCDTests
      BUG: Fixes typo in previous commit
      BUG: Fixes version check in top level CMAKELists.txt

Ali Ghayoor (13):
      ENH: Upgrade vnl_powell to itkPowellOptimizerv4 in BCD
      ENH: Write the debug image based on requested debug level
      ENH: BCD can process input images with different dynamic range
      ENH: Change tolerance and step size for Powell optimizer
      BUG: Fixed a bug in BABC when a low debugLevel requested
      ENH: New parameters for multimodal segmentation in BABC
      ENH: Updated purePlugsThreshold value for AutoWorkup
      BUG: fixed a bug in BABC denoise filtering
      ENH: Initialize a matrix variable
      ENH: remove an intermediate variable to avoid extra memory usage
      BUG: defined an orderedmap class for BABC
      STYLE: Cleanup unnecessary if statement
      ENH: Prevent holes in created brain mask by ROIAutoFilter

Andrey Fedorov (2):
      BUG: fix centerOfROI initializer
      ENH: adjust restriction on the required registration phases

Hans J. Johnson (40):
      ENH: Update ITK, ANTS, and teem
      STYLE: Remove MinSizeRel option
      COMP: Resolve clang static analysis warnings
      BUG:  Compilation error fixed due to typo.
      ENH: Update external tools support.
      COMP: Improve coverage by using removeIntensityOutliers flag.
      COMP: Force C++11 compliance testing
      COMP: Added compatibility testing with apple and CXX11
      BUG: Nipype now reqires invert_initial_moving_transform to be set
      ENH: Selection of denoising filter improved.
      ENH: Changed options to reflect current processing
      ENH: Updated ANTs for improved DenoiseImage
      BUG: The Rician noise model fails for DenoiseImage
      ENH: Added key files for new denoised gaussian images.
      ENH: Use denoised images for atlas reference
      ENH: Add atlas images to reference atlas.
      ENH: Fine-tune denoising options in BAW.
      BUG: Need to work around nipype bug
      ENH: Use denoised t1 from atlas for registration
      ENH: Return to using Rician de-noising from ANTs
      BUG: Error in respecting the NSLOTS variable
      PERF:  Constrain memory usage for KNN phase
      PERF: Update ABC workflow to reflect memory with KNN
      BUG: Serialize printing from threaded sections
      STYLE: Print table consistently
      BUG: Need to pass all denoised images into BRAINSABC
      STYLE: Make usage of variable names consistent
      STYLE: Cleanup unsuded ComputeLabels references
      BUG: Internal ordering for dictionary missed first element
      BUG: This is an unsatisfactory solution
      BUG: Fix to allow all allocated slots to be used
      ENH: Consolidate and syncronize different ANTs run parameters
      BUG: Fix running of ANTs consistently
      ENH: Add N4 bias correction after denoising
      BUG: Missing ',' in python list.
      ENH: Improve error reporting for improper input
      STYLE: Uniformly describe registration parameters.
      PERF: New AntsJointFusion is well multithreaded
      ENH: Add automatic image unwrapping
      BUG: Fix mismatched function parameter calls.

Jean-Christophe Fillion-Robin (1):
      COMP: Force CMAKE_CONFIGURATION_TYPES only when using multi-config generator

Regina Kim (7):
      BUG: Fix Landmark Workflow
      ENH: Update antsDenoise IO specification
      ENH: Rewording to JointFusion from MALF
      ENH: Linear Regression Rescaling
      ENH: JointFusion Update for T2
      ENH: Add JointFusion masking option
      ENH: 1.5 Tesla T2-w excluded from JointFusion

From: Andrey Fedorov <fedorov@bwh.harvard.edu>

Revision 24949  View Download Blame
Modified Thu Feb 25 21:19:22 2016 UTC (18 months, 4 weeks ago) by lassoan
File length: 19622 byte(s)
Diff to previous 24943
ENH: update SlicerDMRI remote module to a82fde48

$ git shortlog --no-merges d712d9522a..a82fde4870

Isaiah Norton (3):
      DWMasking: set b-value select slider max to 20k
      DWMasking: COMP: fix test that was using old parameter
      COMP: fix windows build error due to outdated CLI entrypoint

Revision 24943  View Download Blame
Modified Tue Feb 23 20:33:55 2016 UTC (19 months ago) by fedorov
File length: 19622 byte(s)
Diff to previous 24940
ENH: update MultiVolumeImporter hash

This update fixes the issue of triggering error in MultiVolumeImporterPlugin
due to missing values of the attributes used to parse multivolumes.

Revision 24940  View Download Blame
Modified Mon Feb 22 04:52:09 2016 UTC (19 months ago) by jcfr
File length: 19622 byte(s)
Diff to previous 24939
COMP: Update SlicerDMRI to fix "CompareTxts" build errors

//---------------------------
commit SlicerDMRI/SlicerDMRI@cab6a68
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Sun Feb 21 23:15:09 2016 -0500

    COMP: CompareTxts: Fix build errors


    1) Include "cstdlib" to fix this build error:

    /home/jcfr/Projects/Slicer-Debug/DMRI/FiberTractMeasurements/Testing/CompareTxts.cxx: In function ‘int main(int, char**)’:
    /home/jcfr/Projects/Slicer-Debug/DMRI/FiberTractMeasurements/Testing/CompareTxts.cxx:20:12: error: ‘EXIT_FAILURE’ was not declared in this scope
         return EXIT_FAILURE;
                ^


    2) Construct "ifstream" using char* signature  also available with c++ older
    that c++11:

    /home/jcfr/Projects/Slicer-Debug/DMRI/FiberTractMeasurements/Testing/CompareTxts.cxx:25:40: error: no matching function for call to ‘std::basic_ifstream<char>::basic_ifstream(std::__cxx11::string&)’
       std::ifstream resultTxt(resultTxtPath);
                                            ^
//---------------------------

Revision 24939  View Download Blame
Modified Mon Feb 22 03:39:24 2016 UTC (19 months ago) by jcfr
File length: 19622 byte(s)
Diff to previous 24927
ENH: Update SlicerDMRI remote module

$ git shortlog --no-merges 86dc8ec8..17b96f4f

Alex Yarmarkovich (1):
      BUG: 3044. Disable Fiber display options when no fiber is selected

Isaiah (1):
      Update LICENSE.md formatting

Isaiah Norton (3):
      ENH: fix #26: pick baseline imgs by b-val, not |grad|
      ENH: improve DWI masking results
      DWMasking: restore input image cast for better generality

Lauren O'Donnell (2):
      Create README.md
      Create LICENSE.md

zhangfanmark (2):
      STYLE: Update module name displayed with Space
      ENH: Add testing cases for FiberTractMeasurement

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

Revision 24927  View Download Blame
Modified Wed Feb 10 21:50:45 2016 UTC (19 months, 2 weeks ago) by fedorov
File length: 19622 byte(s)
Diff to previous 24920
BUG: update MultiVolumeImporter hash

This fixes a bug where plugin would fail with certain strategy when a certain
DICOM attribute is absent or empty

Revision 24920  View Download Blame
Modified Wed Feb 10 02:57:59 2016 UTC (19 months, 2 weeks ago) by jcfr
File length: 19622 byte(s)
Diff to previous 24919
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 24919  View Download Blame
Modified Wed Feb 10 02:55:35 2016 UTC (19 months, 2 weeks ago) by fedorov
File length: 19622 byte(s)
Diff to previous 24910
ENH: update MultiVolumeImporter hash

This update adds a new strategy allowing to parse GE DSC MRI using InstanceNumber
and assigning timestamps using RepetitionTime

Revision 24910  View Download Blame
Modified Sat Jan 30 02:24:36 2016 UTC (19 months, 3 weeks ago) by jcfr
File length: 19622 byte(s)
Diff to previous 24909
COMP: SlicerDMRI: Workaround "path too long" issue for VS2013 build. Part #2

Fix error introduced in previous commit. Make sure to specify the
subdirectory to copy.

Revision 24909  View Download Blame
Modified Fri Jan 29 22:26:31 2016 UTC (19 months, 3 weeks ago) by jcfr
File length: 19607 byte(s)
Diff to previous 24889
COMP: SlicerDMRI: Workaround "path too long" issue for VS2013 build.

This commit works around the windows "path too long" issue by reorganizing
the SlicerDMRI source directory after the repository has been cloned.

For sake of consistency, and to ensure future update are tested on all
development environment, the "workaround" is applied on both Unix and
Windows.

Considering that the original source code is organized like this:

 c:\path\to\Slicer-build\SlicerDMRI\CMakeLists.txt
 c:\path\to\Slicer-build\SlicerDMRI\Modules\CLI\CLIModule1
 ...
 c:\path\to\Slicer-build\SlicerDMRI\Modules\Loadable\LoadableModule1
 ...
 c:\path\to\Slicer-build\SlicerDMRI\Modules\Scripted\ScriptedModule1

The workaround consists in creating a structure with shorter paths
similar to this one:

 c:\path\to\Slicer-build\DMRI\CMakeLists.txt
 c:\path\to\Slicer-build\DMRI\CLIModule1
 ...
 c:\path\to\Slicer-build\DMRI\LoadableModule1
 ...
 c:\path\to\Slicer-build\DMRI\ScriptedModule1

Note that the CMakeLists.txt in the new layout is generated at
configuration time.

The difference across platforms are the following:

* Unix: Symlinks are created.

* Windows: Directories are copied.


Rational for this approach:

* Updating the build system allows to keep the organization of SlicerDMRI
consistent with all other existing extension.

* Anticipating that SlicerDMRI will become a "regular" extension,
install-able through the Extension Manager", there will be no "path too long"
issue.

* Updating the CMake Visual Studio generator to have shorter "intermediate
directories" is being discussed at the time of this commit.

Revision 24889  View Download Blame
Modified Sat Jan 23 10:21:31 2016 UTC (20 months ago) by jcfr
File length: 16418 byte(s)
Diff to previous 24888
COMP: Update BRAINSTools to fix MacOSX and Linux packaging.

This commit fixes a regression originally introduced in r24881 (BUG: Update
BRAINSTools to include fixes for BRAINSFit and BRAINSResample.)

Fixes #4135

//---------------------------------------------
commit Slicer/BRAINSTools@1a8e84b
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Sat Jan 23 05:06:52 2016 -0500

    COMP: Force CMAKE_CONFIGURATION_TYPES only when using multi-config generator

    This commit fixes a regression first introduced in BRAINSia/BRAINSTools@831eab6 (ENH: Allow
    selecting C++11 from CMAKE_CXX_STANDARD) and incorrectly fixed
    in BRAINSia/BRAINSTools@8987b5d (BUG: Do not dereference a variable when checking for existance.)

    CMAKE_CONFIGURATION_TYPES variable is now forced to a value only
    if it has been defined by CMake. This ensures that project (e.g Slicer)
    directly adding BRAINSTools source tree can still rely on the
    assumption CMAKE_CONFIGURATION_TYPES is set only when multi-configuration
    generator are used.
//---------------------------------------------

Revision 24888  View Download Blame
Modified Sat Jan 23 08:44:30 2016 UTC (20 months ago) by jcfr
File length: 16418 byte(s)
Diff to previous 24881
COMP: Fix windows packaging. Fixes #4131

This commit addresses regression introduced in r24855 (ENH: Add SlicerDMRI
remote module) where the build folder became too long.

This commit introduces the concept of "REMOTE_EXTENSION" allowing to
add source directory to an extension containing multiple modules. Since
the build directory associated with remote extensions is 13 characters
shorter, it should address the windows packaging problem.

Here is an example of path before and after this change:

C:\path\to\Slicer-Release\Slicer-build\Modules\Remote\SlicerDMRI\Modules\Loadable\TractographyDisplay
C:\path\to\Slicer-Release\Slicer-build\E\SlicerDMRI\Modules\Loadable\TractographyDisplay


Notes:

To avoid doing a clean build and ensure incremental build
are successful, developers should update file:

  C:\path\to\Slicer-Release\Slicer-build\CMakeCache.txt

and remove variables of the form

  "... :INTERNAL= ... Modules\Remote\SlicerDMRI ...".

Revision 24881  View Download Blame
Modified Tue Jan 19 17:34:46 2016 UTC (20 months ago) by jcfr
File length: 16415 byte(s)
Diff to previous 24855
BUG: Update BRAINSTools to include fixes for BRAINSFit and BRAINSResample.

This commit fixes a regression introduced
by InsightSoftwareConsortium/ITK@d1e9fe2 (BUG: Ensure Transform IO
factories are  registered once.) and integrated in r24836 (ENH: Update
ITKv4 to v4.9.0 release branch).

Following this ITK commit, the ITKIO transform libraries are build as
shared and dynamic_cast can NOT be used with templated classes that are
instantiated in a translation unit different than the one where they are
defined. It will work only if the classes are explicitly instantiated
and exported.

To workaround the issue, code that was relying on dynamic_cast is updated
to (1) ensure the objects are of the right type doing string comparison
and (2) then use static_cast instead of dynamic_cast.

This patch fixes the following EMSegment test (internally using
BRAINSFit) when compiled using gcc 4.4.3 and executed on Ubuntu 10.04:

  EMSegCL_Task_BRAINS_MRIHumanBrain_scalartype_float_very_small
  EMSegCL_Task_BRAINS_MRIHumanBrain_scalartype_uint_very_small
  EMSegCL_Task_HumanEye_BRAINS_small
  EMSegCL_Task_MRIHumanBrain_BRAINS_small
  EMSegCL_Task_MRIHumanBrainExp_BRAINS_small
  EMSegCL_Task_MRIHumanBrainFullParcellation_BRAINS_small
  EMSegCL_Task_MRIHumanBrainParcellation_BRAINS_small
  EMSegCL_Task_NonHumanPrimate_BRAINS_small

It fixes runtime error like the following:

//-----------------
 Read ITK transform from file: /tmp/EMSegmentCommandLine/EMS282744605229D1c.h5
 HACK: 0  VersorRigid3DTransform
 Caught an ITK exception:

  itk::ExceptionObject (0x18ef450)
  Location: "unknown"
  File: /path/to/Slicer-0-build/BRAINSTools/BRAINSCommonLib/GenericTransformImage.cxx
  Line: 346
  Description: itk::ERROR: Error in type conversion
//-----------------

Complete list of BRAINSTools updates:

$ git shortlog c658c75..e257e62 --no-merges
Alexander Leinoff (18):
      DOC: Updates build instructions for OS X
      COMP: Updates ITK dependency and Removes Python from build system
      COMP: Allows Top-level cmake options to be passed down to BRAINSTools
      COMP: Fixes data dependency for BRAINSCommonLib test
      COMP: Fixes build errors on debain8
      COMP: Fixes some CMake dependency issues with the FindVTKUtil module
      COMP: Fixes Unused parameter warning on Linux in BRAINSCut
      COMP: Fixes sign compare warning on linux
      BUG: Fix failing BCD tests by adjusting image compare tolerences
      BUG: Fixes failing test BCDTest_rescaleIntensity
      BUG: Adds multiple baselines to BCD tests
      BUG: Adds new baseline fcsv files so BCD tests pass on ubuntu
      BUG: Fixes BCDTest_rescaleIntensity on Debian
      BUG: Adds baseline for chk_BCDTest_ForcePCPoint
      ENH: Updates compareTwoCVSFiels.py.in to work with python3
      BUG: Adds null check to string assignment in BRAINSMeasureSurface.cxx
      BUG: Fixes ctest dependencies for BRAINSTransformConvert
      BUG: TBB should only be requested when building BRAINSABC

Ali Ghayoor (18):
      ENH: Added two more tests to gtract
      ENH: Remove most calls to EncapsulateMetaData in GTRACT
      ENH: Compute seedsPerVoxel for UKF in DWI pipeline
      BUG: Fixed a bug in DWI pipeline tractography workflow
      BUG: now ANTs returns composite transform not as a list
      BUG: import necessary module from python
      BUG: Added proper python module inside the function
      BUG: Unnecessary computation of ListOfClassStatistics
      ENH: Convert a 4D image to a series of 3D images
      ENH: Change internal pixel type to float
      ENH: Increased dilate size in AtlasToSubject registration
      ENH: run multiresolution AtlasToSubject SyN registration
      ENH: NO atlasToSubject registration if transform filename exist
      ENH: Make sure there are anough samples for KNN training
      ENH: A samrter way to set the feature space values of KNN
      ENH: Generate pure plugs mask and its incorporation in BABC
      DOC: Added more detailed explanations for atlasVolume flag in BCD
      ENH: A confusing print statement was modified for BABC

Csaba Pinter (1):
      STYLE: Reconcile orphan module categories for DWICleanup and LabelStatistics

Hans J. Johnson (68):
      BUG: Update path change for neuromorphometric data.
      BUG: activate_this is not available in anaconda.
      ENH: New version of NIPYPE ants interface
      STYLE: Fixed spelling error.
      BUG: Failure multi-modal BABC is run without a T2
      BUG: Need to verify that dependant submodules are specified.
      BUG: Indexing for MALF was off
      ENH: Update ITK, ANTs
      BUG: Now that ANTs composite transform is not a list, fix code
      ENH: Improve cluster performance tuning.
      BUG: Revised MALF indexing to work both for single and multi-modal cases.
      ENH: Prepare code base for Python version 3
      ENH: Stage 2 futurize
      BUG: Remove incorrect use of relative import from non-package
      ENH: Improve fall through with sentinal values
      COMP: Fixe linkage failures with ITK changes
      COMP: Fix new linkage issues with ITK
      BUG: Force string from path
      BUG: BrainStem cleanup bug when non-identity image was used.
      BUG: MALF_SNAPSHOT_WRITER fails on non-identity images
      ENH: Zeropad output images for easier sorting.
      COMP: Remove shadow typedef warning.
      BUG: Incorrect library specification
      STYLE: Remove errant xcode build files.
      COMP: Remove compiler warnings
      ENH: Update Superbuild packages.
      ENH: Remove dependance on Boost.
      COMP: Add ITK_OVERRIDE for ICCDEF
      COMP: Improve compatibility with VTK 6.1
      COMP: Remove compiler warning.
      COMP: Fix VTK-6.3 compilation issues.
      BUG: DCMTK APPs don't build with intel compiler.
      ENH: Updated Superbuild for later C++11 support.
      ENH: Newest version of ITK.
      ENH: Updated ITKv4 for build.
      COMP: make vcl_pow command non-ambiguous
      BUG:  Updated DCMTK requires new CMAKE settings
      COMP: Remove unnecessary cmake config message.
      ENH: Merged PREDICT logic for Freesurfer script wiht main tree.
      ENH: Improve python 3 compatibility.
      ENH: Update DCMTK, ITK and ANTs
      ENH: TrackOn Freesurfer Processing.
      COMP: Remove unnecessary typedef
      COMP: Add ITK_OVERRIDE to functions
      BUG: BCD post landmark ACPC to atlas only when atlas is from same subject.
      ENH: Only allow QT 4.8 or higher.
      ENH: VTK, ITK and ANTS Updated.
      PERF: Do not use hyperthreads for ITK
      ENH: Allow selecting C++11 from CMAKE_CXX_STANDARD
      ENH: This is an initial implementation of tbb
      BUG: Fix TBB propagations to BRAINSTools
      ENH: Update BABC build only with C++11
      PERF: Replace OPEN_MP with TBB
      BUG: Need to ensure that TBB is respecting num threads specified.
      STYLE: Modernize to C++11 style conformance
      ENH:  Update version of BRAINSTools to 4.6.0
      ENH: Enable the new feature for BRAINSABC
      BUG: Do not dereference a variable when checking for existance.
      COMP: Remove unused programs unless BUILD_FOR_DASHBOARD is set
      ENH: Improve logic checking for ANTs external tool
      COMP: Make ANTs integration more robust.
      COMP: Only require VTK when requested.
      BUG: Incorrect block_range3d extents
      ENH: Add grainsize explicitly for blocked_ranges
      ENH: Parallelize preparation for KNN measurements
      PERF: Prefer pass by const reference to pass by value
      ENH: Instrument reductions with CompensatedSummationType
      ENH: Instrument std::vector reductions with CompensatedSummationType

Isaiah Norton (4):
      ENH: FSLToNrrd should default to transposed bvecs
      ENH: refactor SiemensDWIConverter::ExtractDWIData
      BUG: fix segfault when reading single-file dataset
      ENH: SiemensDWI: add support for fallback to non-CSA diffusion tags

Jean-Christophe Fillion-Robin (17):
      ENH: Allow testing to be optionally enabled in Slicer build.
      BUG: Ensure IO factory are registered.
      BUG: BRAINSResample: Fix tests removing usage of dynamic_cast with transform
      BUG: BRAINSFitHelperTemplate: Add missing static_cast
      STYLE: BRAINSResample: Remove now uneeded check.
      STYLE: VTKITKVectorReader: Remove now unneeded itkFactoryRegistration code
      BUG: BRAINSFit: Fix tests removing usage of dynamic_cast with transform
      STYLE: BRAINSFit: Remove now uneeded check.
      STYLE: Remove git merge conflict resolution artifacts
      COMP: Update ITKVtkGlue requirements to fix build with default option.
      BUG: BRAINSFitHelperTemplate: Add missing static_cast
      STYLE: BRAINSResample: Remove now uneeded check.
      STYLE: VTKITKVectorReader: Remove now unneeded itkFactoryRegistration code
      BUG: BRAINSFit: Fix tests removing usage of dynamic_cast with transform
      STYLE: BRAINSFit: Remove now uneeded check.
      STYLE: Remove git merge conflict resolution artifacts
      COMP: Update ITKVtkGlue requirements to fix build with default option.

Jessica Forbes (18):
      ENH: Splits atlas list into lists with lengths of n_modality
      ENH: Makes target_image into a list of list
      ENH: Adds atlasSmallIslandCleanup.py for pipeline
      ENH: Initial commit for WorkupAtlasDustCleanup.py
      ENH: Moves import command inside the function
      ENH: Sets inFN2/T2 input as optional/None if only T1 session
      ENH: Sets the T2 file as an optional arg for the dust cleanup script
      ENH: Removed unused BASE_DATA_GRABBER_DIR function parameter
      ENH: Adds dust cleanup workflow to baseline.py after MALF
      ENH: Specifies input params for dust cleaning workflow
      ENH: Added option to not dilate in dust cleanup script
      ENH: Includes new dilation arg for dust cleanup in pipeline
      ENH: Adds suspicious dust cleaning node before other cleaning node
      BUG: Sets includeList to str not int
      ENH: Removes unused input arg in CreateDustCleanupWorkflow
      ENH: Updates output naming schema for WorkupAtlasDustCleanup.py
      ENH: Moves dustCleanup node within Malf after injectSurfaceCSFandVBIntoLabelMap
      BUG: Fixes typo conflict left in CreateFreeSufereScripts.py

Regina Kim (20):
      COMP: Remove Unused variable
      WIP: Update interface for antsJointFusion
      BUG: ants Joint Fusion requires search_radius option
      ENH: Closes #221
      BUG: outputs should be returned with fullpath
      Update README.md
      Update README.md
      Update README.md
      ENH: BRAINSTools AutoWorkup Tutorial
      Update README.md
      Update README.md
      Update README.md
      Update README.md
      Update README.md
      Update README.md
      ENH: ITK version 4.9 Update
      ENH: ANTs Version upgrade
      ENH: ants Denoise for Auto Workup
      BUG: Denoise interface fix
      BUG: Resample T2 after BRAINSABC

Revision 24855  View Download Blame
Modified Fri Jan 8 18:53:27 2016 UTC (20 months, 2 weeks ago) by jcfr
File length: 16420 byte(s)
Diff to previous 24840
ENH: Add SlicerDMRI remote module

See http://slicerdmri.github.io/

The goal is to make Slicer core leaner and ultimately create a
SlicerDMRI extension

This remote module provides the following modules removed in previous
commits:

  FiberBundleToLabelMap (Scripted)
  DICOM2FullBrainTractography (Scripted)

  TractographyDisplay (Loadable)
  TractographyInteractiveSeeding (Loadable)

  DiffusionTensorScalarMeasurements (CLI)
  DiffusionWeightedVolumeMasking (CLI)
  DWIJointRicianLMMSEFilter (CLI)
  DWIRicianLMMSEFilter (CLI)
  DWIToDTIEstimation (CLI)
  DWIUnbiasedNonLocalMeansFilter (CLI)
  DTIImportExport (CLI)
  TractographyLabelMapSeeding (CLI)
  FiberBundleLabelSelect (CLI)
  FiberTractMeasurements (CLI)

Note that the following plugins and modules are not yet integrated
into SlicerDMRI:

  ResampleDTIVolume (CLI)
  ResampleScalarVectorDWIVolume (CLI)
  DICOMDiffusionVolumePlugin (DICOM plugin)

Additionally, the following MRML nodes are still living in Slicer core,
they will ultimately be moved out when the infrastructure will support
it:
  vtkMRMLDiffusionImageVolumeNode
  vtkMRMLDiffusionTensorDisplayPropertiesNode
  vtkMRMLDiffusionTensorVolumeDisplayNode
  vtkMRMLDiffusionTensorVolumeNode
  vtkMRMLDiffusionTensorVolumeSliceDisplayNode
  vtkMRMLDiffusionWeightedVolumeDisplayNode
  vtkMRMLDiffusionWeightedVolumeNode

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

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

Revision 24840  View Download Blame
Modified Fri Jan 8 15:36:25 2016 UTC (20 months, 2 weeks ago) by fedorov
File length: 15952 byte(s)
Diff to previous 24835
ENH: update MultiVolumeImporting

This update should resolve the regression introduced by #440 and improves
robustness by not returning multivolumes that have single frames when parsed
based on ImagePositionPatient+AcquisitionTime.

Revision 24835  View Download Blame
Modified Thu Jan 7 16:42:38 2016 UTC (20 months, 2 weeks ago) by fedorov
File length: 15952 byte(s)
Diff to previous 24817
ENH: update MultiVolumeImporter

This update adds support for parsing multivolumes from Siemens DSC MRI. The
functionality was tested on the examples provided by the QIICR MGH team.

Revision 24817  View Download Blame
Modified Mon Dec 14 21:46:47 2015 UTC (21 months, 1 week ago) by fedorov
File length: 15952 byte(s)
Diff to previous 24808
ENH: update git hash of MultiVolumeImporter

this fixes incorrect parsing of Philips trace DWI datasets that used standard
DICOM attribute for storing b-values. The issue was due to a typo in the attribute
number...

Revision 24808  View Download Blame
Modified Sat Dec 5 21:47:58 2015 UTC (21 months, 2 weeks ago) by lassoan
File length: 15952 byte(s)
Diff to previous 24802
BUG: Update Git Tag for OpenIGTLinkIF to fix issue 0004101

by Junichi Tokuda

Revision 24802  View Download Blame
Modified Wed Dec 2 00:40:35 2015 UTC (21 months, 3 weeks ago) by jcfr
File length: 15952 byte(s)
Diff to previous 24801
BUG: Update OpenIGTLinkIG to fix issues in sending PolyData.

Fixes #4095

$ git shortlog 3ad1f67..6e297b7 --no-merges
Christian Askeland (3):
      BUG: openigtlink/OpenIGTLinkIF#54 Color not supported in vtkImageData->igtl::ImageMessage.
      BUG: Fixed openigtlink/OpenIGTLinkIF#55 Segfaults in encode/decode vtkPolyData
      BUG: Fixed openigtlink/OpenIGTLinkIF#56 vtkPolyData encoding reuses data from last encoding.

Junichi Tokuda (1):
      Instead of creating a new igtl::PolyDataMessage in vtkIGTLToMRMLPolyData::MRMLToIGTL()
      to clear the content of OutPolyDataMessage, call igtl::PolyDataMessage::Clear().
      igtl::PolyDataMessage::Clear() will be reimplemented based on the discussion for
      Issue openigtlink/OpenIGTLinkIF#57.

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

Revision 24801  View Download Blame
Modified Tue Dec 1 20:06:37 2015 UTC (21 months, 3 weeks ago) by jcfr
File length: 15952 byte(s)
Diff to previous 24791
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 24791  View Download Blame
Modified Tue Dec 1 00:08:21 2015 UTC (21 months, 3 weeks ago) by jcfr
File length: 15971 byte(s)
Diff to previous 24784
STYLE: CMakeLists.txt: Set CMP0048 policy to NEW (Part2)

Similarly to what was done in r24777 (STYLE: CMakeLists.txt: Set CMP0048
policy to NEW), this commit applies same changes to DataStore and
OtsuThresholdImageFilter project.

Revision 24784  View Download Blame
Modified Mon Nov 30 19:59:20 2015 UTC (21 months, 3 weeks ago) by lassoan
File length: 15971 byte(s)
Diff to previous 24777
BUG: Updated EMSegmenter test baseline

Selection node in Slicer scene now contains an active table node ID as well.

Revision 24777  View Download Blame
Modified Thu Nov 26 22:22:31 2015 UTC (21 months, 4 weeks ago) by jcfr
File length: 15971 byte(s)
Diff to previous 24775
STYLE: CMakeLists.txt: Set CMP0048 policy to NEW

This commit also updates projects EMSegment, MultiVolumeExplorer,
OpenIGTLinkIF and SlicerSimpleFilters.

EMSegment:

r17114
STYLE: Fix CMake warning setting CMP0048 to NEW


MultiVolumeExplorer:

$ git shortlog  9cd4730..a0743dc --no-merges
Jean-Christophe Fillion-Robin (5):
      STYLE: Remove unused extension packaging code
      STYLE: Simplify CMakeLists.txt removing extra comments
      STYLE: Update CMakeLists.txt to use recommended variable names
      STYLE: Update testing/CMakeLists.txt to use slicerMacroConfigureModuleCxxTestDriver
      STYLE: Fix CMake warning setting CMP0048 to NEW


OpenIGTLinkIF:

$ git shortlog 435b1c3..3ad1f67 --no-merges
Jean-Christophe Fillion-Robin (3):
      STYLE: Simplify CMakelists directly including find_package(Slicer)
      STYLE: CMakeLists.txt: Use recommended variable names
      STYLE: Fix CMake warning setting CMP0048 to NEW


SlicerSimpleFilters:

$ git shortlog 48b7873..c58cfe5 --no-merges
Jean-Christophe Fillion-Robin (1):
      STYLE: Fix CMake warning setting CMP0048 to NEW

Revision 24775  View Download Blame
Modified Wed Nov 25 06:52:46 2015 UTC (22 months ago) by jcfr
File length: 15971 byte(s)
Diff to previous 24774
BUG: Update EMSegment to fix loading of centred atlas

This commit fixes the passing of loadAtlasNonCentered option to
LoadUserDefinedAtlas in EMSegmentCommandLine. This should allow
centred atlas to be used from the command line. (See EMSegment r17113)

Revision 24774  View Download Blame
Modified Wed Nov 25 06:52:44 2015 UTC (22 months ago) by jcfr
File length: 15971 byte(s)
Diff to previous 24707
ENH: Update EMSegment to add autoBoundaryDetection for command line module

This commit adds the option "autoBoundaryDetection" to EMSegmentCommandLine
If flag is set then the method will automatically determine the boundary
box which includes non-zero voxels in the input images. This speed things
up when working with skull stripped images. (See EMSegment r17112)

Revision 24707  View Download Blame
Modified Mon Nov 9 17:43:39 2015 UTC (22 months, 2 weeks ago) by pohl
File length: 15971 byte(s)
Diff to previous 24690
BUG: Could not load atlas in command line without it being centered

Revision 24690  View Download Blame
Modified Tue Nov 3 17:47:13 2015 UTC (22 months, 3 weeks ago) by jcfr
File length: 15971 byte(s)
Diff to previous 24685
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 24685  View Download Blame
Modified Mon Nov 2 00:51:59 2015 UTC (22 months, 3 weeks ago) by jcfr
File length: 15940 byte(s)
Diff to previous 24664
COMP: Update EMSegment: Fix "comparison of pointer with integer zero" warning

//----------
/home/jcfr/Projects/Slicer-Debug/EMSegment/AMF/vtkImageLevelSets.cxx: In member function ‘unsigned char vtkImageLevelSets::CheckConvergence()’:
/home/jcfr/Projects/Slicer-Debug/EMSegment/AMF/vtkImageLevelSets.cxx:1301:24: warning: ordered comparison of pointer with integer zero [-Wextra]
      if (this->u[p] <= 0) total++;
                        ^
/home/jcfr/Projects/Slicer-Debug/EMSegment/AMF/vtkImageLevelSets.cxx:1306:65: warning: ordered comparison of pointer with integer zero [-Wextra]
      if ((this->stored_seg[p] == ON_STORED)    && (this->u[p] > 0))
                                                                 ^
/home/jcfr/Projects/Slicer-Debug/EMSegment/AMF/vtkImageLevelSets.cxx:1309:66: warning: ordered comparison of pointer with integer zero [-Wextra]
        if ((this->stored_seg[p] == OFF_STORED) && (this->u[p] <= 0))
                                                                  ^
/home/jcfr/Projects/Slicer-Debug/EMSegment/AMF/vtkImageLevelSets.cxx:1313:24: warning: ordered comparison of pointer with integer zero [-Wextra]
      if (this->u[p] <= 0)                          ^
//----------

Co-authored-by: Kilian Pohl <pohl.kilian@gmail.com>
Reviewed-by: Steve Pieper <pieper@bwh.harvard.edu>

Revision 24664  View Download Blame
Modified Tue Oct 27 15:40:32 2015 UTC (22 months, 4 weeks ago) by fedorov
File length: 15940 byte(s)
Diff to previous 24663
ENH: Update MultiVolumeImporter hash

* use logging for debug messages
* removed 'from __main__' from the plugin

Revision 24663  View Download Blame
Modified Tue Oct 27 02:58:56 2015 UTC (22 months, 4 weeks ago) by jcfr
File length: 15940 byte(s)
Diff to previous 24607
BUG: Incorporate fix for failing MultiVolumeExplorer GUI test

Update the git tag for MultiVolumeExplorer to the version that
fixes the qSlicerMultiVolumeExplorerModuleWidgetGenericTest.

git shortlog c97e9d7b88abdd429b5410b5985d3fd03de851ec..9cd47306e7ee761072a07fef5ad1eaa7bb452816 --no-merges
Nicole Aucoin (1):
      BUG: fix failing widget generic test due to size hint

From: Nicole Aucoin <nicole@bwh.harvard.edu>

Revision 24607  View Download Blame
Modified Tue Oct 6 20:49:04 2015 UTC (23 months, 2 weeks ago) by naucoin
File length: 15940 byte(s)
Diff to previous 24581
BUG: update EMSegment to fix failing test

Updated the EMSegment testing MRML file to
include the singletonTag so that the comparison
between the baseline mrml file and the written
one will succeed. Fixes test EMSeg_MRML_DiffReadWriteNodes

Issue #4006


Revision 24581  View Download Blame
Modified Sun Sep 27 18:42:00 2015 UTC (23 months, 4 weeks ago) by fedorov
File length: 15940 byte(s)
Diff to previous 24576
BUG: update MultiVolume hash

This update fixes the crash when no labels were specified
and volume rendering was requested.

Revision 24576  View Download Blame
Modified Wed Sep 23 14:02:37 2015 UTC (2 years ago) by jcfr
File length: 15940 byte(s)
Diff to previous 24540
ENH: Update BRAINSTools to reconcile module categories. See #3844

//--------------
commit 26cb12bda02b4910fb5f80078b16bc14f46da7cf
Author: Csaba Pinter <csaba.pinter@queensu.ca>
Date:   Tue Sep 22 14:55:26 2015 -0400

    STYLE: Reconcile orphan module categories for DWICleanup and LabelStatistics

    The above two modules were in Slicer module categories that only
    contained one module, thus adding two extra categories to the already
    hard-to-navigate module list. According to a recent Slicer developer
    hangout discussion, DWICleanup was moved to Diffusion / Diffusion
    Weighted Images, and LabelStatistics to Quantification. Integrating
    it into Slicer for the release of 4.5 will make the module list a bit
    cleaner.
//--------------

Revision 24540  View Download Blame
Modified Mon Sep 14 21:58:53 2015 UTC (2 years ago) by jcfr
File length: 15930 byte(s)
Diff to previous 24517
ENH: Update BRAINSTools to version 4.5.0

Version 4.5.0 is a bug fix for DWIConvert to facilitate
generating multi-shell data from Siemens scanners where
the --useBMatrix override flag was used (i.e. VB13 data).

From: Hans Johnson <hans-johnson@uiowa.edu>

Revision 24517  View Download Blame
Modified Thu Sep 3 03:28:21 2015 UTC (2 years ago) by jcfr
File length: 15913 byte(s)
Diff to previous 24513
COMP: Allow building EMSegment with C++11

EMSegment/CommandLineApplication/EMSegmentAPIHelper.h:112:21: error: invalid suffix on literal; C++11 requires a space between literal and identifier [-Wreserved-user-defined-literal]
  cout << "Setting "Slicer_HOME_ENVVAR_NAME" ..." << endl;

From: Hans Johnson <hans-johnson@uiowa.edu>

Revision 24513  View Download Blame
Modified Fri Aug 28 18:03:59 2015 UTC (2 years ago) by fedorov
File length: 15913 byte(s)
Diff to previous 24508
ENH: update MultiVolumeExplorer

reorganization of the code

Revision 24508  View Download Blame
Modified Wed Aug 26 19:50:05 2015 UTC (2 years, 1 month ago) by fedorov
File length: 15913 byte(s)
Diff to previous 24504
ENH: update MultiVolumeExplorer

Enhancements in code organization, make the chart detachable.

Revision 24504  View Download Blame
Modified Tue Aug 25 16:56:41 2015 UTC (2 years, 1 month ago) by fedorov
File length: 15913 byte(s)
Diff to previous 24479
ENH: update MultiVolumeExplorer git hash

MultiVolumeExplorer has been refactored to facilitate reuse in other modules and
to simplify user interface. Refactoring done by Christian Herz!

Revision 24479  View Download Blame
Modified Tue Aug 4 02:41:54 2015 UTC (2 years, 1 month ago) by jcfr
File length: 15913 byte(s)
Diff to previous 24432
COMP: Add support for EMSegment when compiling with Visual Studio 2013

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

Revision 24432  View Download Blame
Modified Wed Jul 15 21:25:13 2015 UTC (2 years, 2 months ago) by jcfr
File length: 15913 byte(s)
Diff to previous 24369
BUG: Update SimpleFilters with patches for LabelMapVolume node changes.

48b7873 Remove input based automatic LabelMap output restriction.
c90a778 Replace LabelMap checkbox with option in output combo box
d3f3bf1 Restore support for label map volumes as input
a560064 Correct nodeType to be a list of one element.
2f392a5 Update to use new MRMLLabelmapNode

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

Revision 24369  View Download Blame
Modified Thu Jul 2 17:09:00 2015 UTC (2 years, 2 months ago) by fedorov
File length: 15913 byte(s)
Diff to previous 24366
BUG: Fix bug in vtkMRMLIGTLTrackingDataBundleNode::GetTransformNode() (See issue 4011)

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

Revision 24366  View Download Blame
Modified Tue Jun 30 17:52:52 2015 UTC (2 years, 2 months ago) by fedorov
File length: 15913 byte(s)
Diff to previous 24348
BUG: update MultiVolumeExplorer SHA

This fixes missing 'import math'

Revision 24348  View Download Blame
Modified Fri Jun 19 20:35:53 2015 UTC (2 years, 3 months ago) by jcfr
File length: 15913 byte(s)
Diff to previous 24309
BUG: Update BRAINSTools to fix loading of bspline transform

Note that the corresponding change has also been submitted as
a pull request in the official BRAINSTools repo.
See https://github.com/BRAINSia/BRAINSTools/pull/194

// -------------
Author: Andras Lasso <lasso@queensu.ca>
Date:   Fri Jun 19 15:33:03 2015 -0400

    BUG: Fixed loading of bspline transform

    The transformFileType and typename were inconsistent.
// -------------

Revision 24309  View Download Blame
Modified Tue Jun 16 19:45:01 2015 UTC (2 years, 3 months ago) by jcfr
File length: 15913 byte(s)
Diff to previous 24301
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 24301  View Download Blame
Modified Fri Jun 5 13:40:49 2015 UTC (2 years, 3 months ago) by pieper
File length: 15454 byte(s)
Diff to previous 24300
ENH: update CompareVolumes to support label map nodes

https://github.com/pieper/CompareVolumes/pull/5

Revision 24300  View Download Blame
Modified Fri Jun 5 13:23:00 2015 UTC (2 years, 3 months ago) by lassoan
File length: 15454 byte(s)
Diff to previous 24299
BUG: Fixed  EMSegCL_Task_MRIHumanBrainFullParcellation_BRAINS_small test

Revision 24299  View Download Blame
Modified Fri Jun 5 00:56:44 2015 UTC (2 years, 3 months ago) by jcfr
File length: 15454 byte(s)
Diff to previous 24295
BUG: Update EMSegment to fix regression introduced in labelmap node support

This commit fixes a regression introduced in r24291 (ENH: Use vtkMRMLLabelMapVolumeNode
class for labelmap volumes).

The issue has been found thanks to the following unused variable warning:

/home/jcfr/Projects/Slicer-Debug/EMSegment/CommandLineApplication/EMSegmentCommandLineFct.cxx:44:1: warning: unused parameter ‘labelMap’ [-Wunused-parameter]
 AddNewScalarArchetypeVolume(vtkMRMLScene* mrmlScene,

EMSegment commit:
------------------------------------------------------------------------
r17103 | jcfr | 2015-06-04 20:51:49 -0400 (Thu, 04 Jun 2015) | 4 lines

BUG: Fix unused variable warning fix regression introduced in previous commit.

Update AddNewScalarArchetypeVolume function to create either a scalar volume node
or a labelmap volume node.
------------------------------------------------------------------------

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

Revision 24295  View Download Blame
Modified Thu Jun 4 22:22:36 2015 UTC (2 years, 3 months ago) by fedorov
File length: 15454 byte(s)
Diff to previous 24291
ENH: update MultiVolumeExplorer hash

This fixes the issues related to the new label node, contributed by Andras Lasso

Revision 24291  View Download Blame
Modified Thu Jun 4 20:12:02 2015 UTC (2 years, 3 months ago) by lassoan
File length: 15454 byte(s)
Diff to previous 24287
ENH: Use vtkMRMLLabelMapVolumeNode class for labelmap volumes

Before vtkMRMLScalarVolumeNode was used for both scalar and label map
volumes and the LabelMap custom MRML node attribute was used for
distinguishing between them (0=scalar; 1=label map volume).
This made conversion between labelmap/scalar volumes very easy but made
it difficult to customize behavior, display, processing of segmentation
information.

Now a new vtkMRMLLabelMapVolumeNode class is used for storing segmentation
information (still using vtkMRMLScalarVolume used as base class for backward
compatibility; but in the future the base class may be changed to reflect
that segmentation can be represented in various ways, not just as volumes).

Notes:

A new "segmentation" node has been developed that is based on vtkMRMLLabelMapVolumeNode,
which can store segmentation information in various ways (not just labelmaps but planar
contours, closed surfaces, etc). To allow using of this new segmentation node,
first the vtkMRMLLabelMapVolumeNode has to be integrated into the Slicer core.

When reading a scene that was saved with an old version of Slicer, label maps are stored
in vtkMRMLScalarVolumeNode with label map attribute set to 1. Added a check for this case
and handle it by converting the vtkMRMLScalarVolumeNode to a vtkMRMLLabelMapVolumeNode during import.

Revision 24287  View Download Blame
Modified Wed Jun 3 21:35:23 2015 UTC (2 years, 3 months ago) by fedorov
File length: 15454 byte(s)
Diff to previous 24283
ENH: update MultiVolumeImporter tag

* added parsing of DWI by (0018,9087) DiffusionBValue
* corrected b-value units

Revision 24283  View Download Blame
Modified Mon Jun 1 21:15:08 2015 UTC (2 years, 3 months ago) by jcfr
File length: 15454 byte(s)
Diff to previous 24261
BUG: Address SimpleFilters FlipImageFilter

$ git shortlog  73add6..ceb133
Bradley Lowekamp (1):
      BUG: Add method for vector of bool changed

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

Revision 24261  View Download Blame
Modified Fri May 15 23:12:19 2015 UTC (2 years, 4 months ago) by jcfr
File length: 15454 byte(s)
Diff to previous 24252
COMP: Update BRAINSTools to fix windows build error

// ----------------------------------------------------------------
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Fri May 15 19:09:32 2015 -0400

    COMP: Fix windows build error related to non existing std::isnan function

    std::isnan has been introduced in C++11 and Visual Studio 2008 doesn't
    support it.

// ----------------------------------------------------------------
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Fri May 15 18:56:16 2015 -0400

    COMP: Fix windows build error due to already defined GetBValue macro

    This commit applies as fix similar to InsightSoftwareConsortium/ITK@8ec410c0

    It avoids the windows macro "GetBValue" to conflict with the
    declaration of DWIMetaDataDictionaryValidator::GetBValue()

    On windows, the macro is usually defined in "WinGDI.h" itself included by
    "Windows.h".

Revision 24252  View Download Blame
Modified Wed May 13 18:41:46 2015 UTC (2 years, 4 months ago) by jcfr
File length: 15454 byte(s)
Diff to previous 24249
COMP: Update BRAINSTools - fix configure warning with Slicer SVN source tree

On the factory, Slicer is checked out using SVN. Since in that case there
are no ".git" directory in the source tree, the configuration was failing
with the following warning:

// --------------------------
CMake Warning at /Users/kitware/Dashboards/Continuous/Slicer-0-build/BRAINSTools/CMake/ProjectSourceVersion.cmake:56 (message):
  git tag: "HEAD-HASH-NOTFOUND" does not match expected version format!
Call Stack (most recent call first):
  /Users/kitware/Dashboards/Continuous/Slicer-0-build/BRAINSTools/Version.cmake:10 (include)
  /Users/kitware/Dashboards/Continuous/Slicer-0-build/BRAINSTools/BRAINSTools.cmake:14 (include)
  /Users/kitware/Dashboards/Continuous/Slicer-0-build/BRAINSTools/CMakeLists.txt:68 (include)
// --------------------------

This commit fixes the described above. Finally, to fix a following error
related to extraction of tag information. The tag v4.3.0 has also been
pushed on the Slicer/BRAINSTools fork.

// --------------------------
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Wed May 13 14:28:25 2015 -0400

    COMP: GetGitRevisionDescription: Fix issue referencing project source

    In the case BRAINSTools is integrated using "add_subdirectory(source_dir
    [binary_dir])" [1] (this is the case in Slicer), the variable
    CMAKE_SOURCE_DIR [2] where  resolving to Slice source tree instead of
    BRAINSTools one.

    This commit fixes the module by consistently using PROJECT_SOURCE_DIR [3]
    and PROJECT_BINARY_DIR [4] variable.

    [1] http://www.cmake.org/cmake/help/v3.2/command/add_subdirectory.html
    [2] http://www.cmake.org/cmake/help/v3.2/variable/CMAKE_SOURCE_DIR.html
    [3] http://www.cmake.org/cmake/help/v3.2/variable/PROJECT_SOURCE_DIR.html
    [4] http://www.cmake.org/cmake/help/v3.2/variable/PROJECT_BINARY_DIR.html
// --------------------------

Revision 24249  View Download Blame
Modified Wed May 13 08:20:45 2015 UTC (2 years, 4 months ago) by jcfr
File length: 15454 byte(s)
Diff to previous 24242
ENH: Update BRAINSTools to include DWIConvert bug fixes

BRAINSTools DWIConvert module has been updated
to address a problem identified the BWH team regarding
images being loaded up-side-down.

In addition, some types of nifti/nrrd conversions could result
in improper orientation of the images.  A comprehensive bug fix
was implemented to refactor the fragile old code into a consistent
paradigm for managing image directions.

$ git shortlog 73a6e2d..980803c --no-merges
Alexander Leinoff (2):
      DOC: Changes README file extension to .md
      DOC: Adds intructions for OS X users to install xcode command line tools.

Ali Ghayoor (40):
      ENH: Add new gtractResampleDWIInPlace tests for image meta data
      ENH: Fix a bug in nrrd file header changes by gtractResampleDWIInPlace
      BUG: BRAINSResample should have a default value for warpTransform
      ENH: Add new gtractResampleDWIInPlace tests for image meta data
      ENH: Fix a bug in nrrd file header changes by gtractResampleDWIInPlace
      ENH: Add DWIWorkflow python file to AutoWorkup directory
      ENH: Separate Cache dir from result dir in DWI pipline
      ENH: add CorrectedDWI to dataSink of DWI pipeline
      ENH: Add a python script to compute IPD
      ENH: Improve DWIWorkflow with better registrtion
      ENH: Write output transforms of BFit and BABCD in float
      ENH: AutoWorkup runs antsRegistration and BRINSFit in float mode
      ENH: Add a set of workflows for DWI data processing
      ENH: Add recordLength to UKF traits
      BUG: Fixed a bug in DWI measurement workflow
      BUG: Avoid dtiprocess to stop nipype processing
      BUG: Fix dtiestim cmdline parameters
      ENH: freeSurfer extended labels config file is update with new label
      ENH: Add MultiProc plugin to DWI pipeline
      ENH: Add overwrite to DataSink of DWI pipeline
      ENH: Run UKFTractography in a separate workflow
      ENH: Use cubic BSpline interpolation for RIS
      ENH: Add RIS computations from non compressed sensing DWI image
      ENH: giving proper names to the dataSink outputs
      ENH: Used FloatAlmostEqual for image info comaprison
      ENH: Use vnl_vector/matrix.isequal to compare images information
      ENH: Add comparison of the voxel values to DWICompare
      Revert "BUG: Refactoring introduced direction swap error."
      BUG: Fixed DWIConverter based on last changes to itkDCMTKFileReader
      BUG: A hack solution for FslToNrrd test failure
      ENH: Use vtp extension for output of UKFTractograhy
      ENH: Add correction option to dtiprocess in estimationWF
      ENH: Add correction option to SEMTools for dtiprocess and dtiestim
      BUG: Enhance the non-negative preserving resampling
      ENH: Fixed, enhanced and tested DWIMetaDataDictionaryValidator
      BUG: Fixed FSLToNrrd converter
      BUG: Fixed DeleteGradientTable bug in DWIMetaDataValidator
      ENH: Update gtractResampleDWIInPlace using MetaDataDictionaryValidator
      ENH: Provided build consistency with c++03
      BUG: changing codes that were only compatible with c++11

Dave Welch (6):
      WIP: adding a cross validation workflow for ANTs JointFusion()     TODO: Test workflow (how?)           Run and validate workflow outputs
      STYLE: Added Ubuntu build directions for 14.04
      STYLE: Fixed README.md formatting
      STYLE: Added missing 3rd step to Ubuntu build
      ENH: Python variables pass correctly to external projects
      ENH: Python variables pass correctly to external projects

David Ellis (7):
      COMP: Fixes compilation warning
      BUG: Updates vtkImageGenus0MarchingCubes to the new vtk pipeline format.
      BUG: Fixes bug causing the filter to abort.
      BUG: Fixes GenusZeroImageFilter failure to output vtk file.
      BUG: Fixes issues with the GenusZeroImageFilter tests
      BUG: Fixes the failing tests for BRAINSAssignSurfaceFeatures
      BUG: Fixes the COMPARE_SurfaceLabelCleanup test

Hans J. Johnson (30):
      BUG: The program and python paths should be part of input args
      BUG: add T2 and labelMap paths to input args of DWI pipeline
      ENH: Added UKF Tractography to end of pipeline.
      ENH: First pass at adding version control
      ENH: Update many packages to be in sync with NEP
      ENH: Improve mask processing for PREDICT-HD to include better FSWM defintions.
      ENH: Syncronized Artichoke with Slicer updates (name change).
      BUG: Fixed bugs in the BRAINSABC test suite
      DOC: Improve documentation for error condidtions.
      ENH: Update to syncronize with recent Artichoke commit fixes.
      ENH: Updated to latest SVN version of teem.
      COMP: Match cmake policy options of slicer.
      ENH: Update support packages in preparation for UKF updates
      BUG: Fixed tag for ANTS
      BUG: Testing of images needs to verify all data
      BUG: Refactoring introduced direction swap error.
      ENH: Fixed automatic versioning
      ENH: Added consistent tagging for xml's
      BUG: Consistently use git tag for version
      BUG: Automatic versioning based on git
      BUG: Update itkDCMTKFileReader code
      BUG: Backwards compatible with older ITK versions
      COMP: Temporarily remove BRAINSCut, Need OpenCV 3.0
      ENH: Syncronize with Slicer and NAMICExternalProjects.
      ENH: Add utility class for managing DWI MetaData
      ENH: Added mailmap
      ENH: Second mailmap improvement.
      ENH: Syncronized with NEP.
      BUG: Incorrect initialiation
      COMP: Syncronize with NEP configurations.

Jon Pipitone (1):
      Updated README with some markdown formatting fixes

Regina Kim (11):
      ENH: Add FreeSurfer Lobar Pacellation Mapping
      ENH: Lobar Label fix
      ENH: Add BRAINSCut README file to support usage
      Update README.md
      Update README.md
      Update README.md
      Update README.md
      Update README.md
      Update README.md
      Update README.md
      ENH: name change from sample to training set

From: Hans Johnson <hans-johnson@uiowa.edu>

Revision 24242  View Download Blame
Modified Tue May 12 14:44:12 2015 UTC (2 years, 4 months ago) by jcfr
File length: 15454 byte(s)
Diff to previous 24191
BUG: Update SimpleFilters to fix failing py_SimpleFiltersModuleTest

$ git shortlog 625d941..73add6b --no-merges
Jean-Christophe Fillion-Robin (2):
      Prevent already destroyed widget exception occurring on Slicer exit
      Remove broken 'STAPLEImageFilter'

Revision 24191  View Download Blame
Modified Sat Apr 25 21:43:47 2015 UTC (2 years, 5 months ago) by pohl
File length: 15454 byte(s)
Diff to previous 24190
BUG: took out class 10 as the structure shown inside the probability atlas was very thin and so caused issue for whene executing tests involved _Human-Eye.mrml - all EMSegment  tests pass now on ubuntu 

Revision 24190  View Download Blame
Modified Sat Apr 25 02:40:37 2015 UTC (2 years, 5 months ago) by fedorov
File length: 15454 byte(s)
Diff to previous 24189
ENH: update MultiVolumeImporter

added explicit import of DICOMLib

Revision 24189  View Download Blame
Modified Fri Apr 24 21:54:55 2015 UTC (2 years, 5 months ago) by fedorov
File length: 15454 byte(s)
Diff to previous 24164
BUG: fix unresolved os module

No explicit import of os module was needed in the past, but is causing problems now.

Revision 24164  View Download Blame
Modified Thu Apr 9 07:14:24 2015 UTC (2 years, 5 months ago) by jcfr
File length: 15454 byte(s)
Diff to previous 24145
ENH: Update LandmarkRegistration to show warning if plugin failed to be loaded

See pieper/LandmarkRegistration@13d7b32

Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Wed Apr 8 00:20:27 2015 -0400

    Display a warning when a built-in registration plugin failed to be loaded.

    For example, if Slicer is build without SimpleITK support, the following
    is displayed:

    8<----8<----8<----8<----8<----8<----8<----8<----
    [...]
    Number of registered modules: 139
    Registration: Failed to import 'LocalSimpleITK' plugin: No module named SimpleITK
    Number of instantiated modules: 139
    [...]
    8<----8<----8<----8<----8<----8<----8<----8<----

Revision 24145  View Download Blame
Modified Thu Apr 2 18:05:13 2015 UTC (2 years, 5 months ago) by fedorov
File length: 15454 byte(s)
Diff to previous 24144
ENH: update MultiVolumeImporter

Fix from jcfr@github: Rename lib module to 'MultiVolumeImporterLib'. This will avoid conflict when Slicer issue #3549 (Import scripted module as python module) will be addressed.

Revision 24144  View Download Blame
Modified Wed Apr 1 21:51:48 2015 UTC (2 years, 5 months ago) by jcfr
File length: 15454 byte(s)
Diff to previous 24130
BUG: Update LandmarkRegistration to fix failing generic test

This commit will fix "py_nomainwindow_qSlicerLandmarkRegistrationModuleGenericTest"

$ git shortlog c1c65ce..0bcbcce --no-merges
Jean-Christophe Fillion-Robin (1):
      Fix generic test checking for cropVolume availability

Revision 24130  View Download Blame
Modified Mon Mar 30 20:02:22 2015 UTC (2 years, 5 months ago) by pieper
File length: 15454 byte(s)
Diff to previous 24129
ENH: include updated LandmarkRegistration

Fixes startup issue due to local refinement plugins
not being included in the package.  (Fixes from Jim
Miller and Andras Lasso)

Revision 24129  View Download Blame
Modified Mon Mar 30 14:46:17 2015 UTC (2 years, 5 months ago) by lassoan
File length: 15454 byte(s)
Diff to previous 24087
BUG: Updated OpenIGTLinkIF

Contains fixes for bugs in outgoing node sending.

Revision 24087  View Download Blame
Modified Fri Mar 20 18:53:56 2015 UTC (2 years, 6 months ago) by pieper
File length: 15454 byte(s)
Diff to previous 24063
COMP: update LandmarkRegistration to include landmark refinement

206db9e Merge remote-tracking branch 'millerjv/6-add-landmark-refinement'
63763b2 Add gui to control verbosity. Connected ROI sizes to gui.
655d28b Added Brad's SimpleITK implementation to its own plugin
fa140f5 Moved timing instrumentation
bf85e25 Plugin support for local refinement algorithms
9ab24fc Hide the display nodes during cropping

Revision 24063  View Download Blame
Modified Fri Mar 13 15:05:14 2015 UTC (2 years, 6 months ago) by fedorov
File length: 15454 byte(s)
Diff to previous 24044
ENH: Updated revision number for MultiVolumeImporter

Explicit import of re is apparently needed on some systems. See
https://github.com/fedorov/MultiVolumeImporter/issues/10.

Revision 24044  View Download Blame
Modified Tue Mar 10 05:20:47 2015 UTC (2 years, 6 months ago) by jcfr
File length: 15454 byte(s)
Diff to previous 24027
BUG: Update EMSegment to fix "EMSeg_MRML_DiffReadWriteNodes" test

// -----------------
r17095 | jcfr | 2015-03-10 00:46:54 -0400 (Tue, 10 Mar 2015) | 3 lines

BUG: Fix EMSeg_MRML_DiffReadWriteNodes test

Add missing attribute 'placeModePersistence' into mrml scene used for the Tutorial tests
// -----------------

Revision 24027  View Download Blame
Modified Thu Mar 5 23:40:30 2015 UTC (2 years, 6 months ago) by jcfr
File length: 15454 byte(s)
Diff to previous 24026
ENH: Enable SSL support by default.

OpenSSL is needed:
 * for python to provide the integration with github
 when using the extension wizard
 * by the extension manager to display images hosted using https
 * for python to install packages downloaded from https server

Note that Qt is required to be built with openssl support. The default
version of OpenSSL used on windows is "1.0.1h" and it matches the version
used by the packages available on sourceforge.net/projects/qtx64/files/qt-x64/4.8.6/msvc2008/

To build Qt from source, instruction are provided on the Slicer wiki.
See http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Build_Instructions

Co-authored-by: Hans Johnson <hans-johnson@uiowa.edu>

Revision 24026  View Download Blame
Modified Thu Mar 5 23:20:04 2015 UTC (2 years, 6 months ago) by jcfr
File length: 15223 byte(s)
Diff to previous 24024
ENH: Update SimpleFilter with latest SimpleITK json support

This SimpleFilter adds some new filters include noise filters, more
fast marching, and registration image filters ( although they have not
been testing in the SimpleFilters framework )

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

Revision 24024  View Download Blame
Modified Thu Mar 5 22:41:18 2015 UTC (2 years, 6 months ago) by jcfr
File length: 15223 byte(s)
Diff to previous 23992
ENH: Add slicerMacroBuildAppLibrary and slicerMacroBuildApplication

Facilitate maintenance introducing two new marcos allowing to more easily
create application executable and library.

Revision 23992  View Download Blame
Modified Thu Feb 26 22:42:12 2015 UTC (2 years, 6 months ago) by lassoan
File length: 15291 byte(s)
Diff to previous 23961
ENH: Updated OpenIGTLinkIF

Enhancements for better OpenIGTLink string command support
https://github.com/openigtlink/OpenIGTLinkIF/pull/48

Revision 23961  View Download Blame
Modified Thu Feb 5 00:11:16 2015 UTC (2 years, 7 months ago) by jcfr
File length: 15291 byte(s)
Diff to previous 23954
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 23954  View Download Blame
Modified Tue Feb 3 14:54:25 2015 UTC (2 years, 7 months ago) by jcfr
File length: 15291 byte(s)
Diff to previous 23874
COMP: Update OpenIGTLinkIF to fix sign-compare warnings

//-----------
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Tue Feb 3 00:27:38 2015 -0500

    COMP: Fix sign-compare warnings in vtkIGTLToMRMLPolyData::IGTLToMRML

    This commit fixes the following warnings:

    //------------
    /path/to/OpenIGTLinkIF/MRML/vtkIGTLToMRMLPolyData.cxx: In member function ‘virtual int vtkIGTLToMRMLPolyData::IGTLToMRML(igtl::MessageBase::Pointer, vtkMRMLNode*)’:
    /path/to/OpenIGTLinkIF/MRML/vtkIGTLToMRMLPolyData.cxx:171:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (unsigned int i = 0; i < npoints; i ++)
                                      ^
    /path/to/OpenIGTLinkIF/MRML/vtkIGTLToMRMLPolyData.cxx:190:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (unsigned int i = 0; i < nvertices; i ++)
                                      ^
    /path/to/OpenIGTLinkIF/MRML/vtkIGTLToMRMLPolyData.cxx:213:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(unsigned int i = 0; i < nlines; i++)
                                     ^
    /path/to/OpenIGTLinkIF/MRML/vtkIGTLToMRMLPolyData.cxx:238:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(unsigned int i = 0; i < npolygons; i++)
                                     ^
    /path/to/OpenIGTLinkIF/MRML/vtkIGTLToMRMLPolyData.cxx:263:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(unsigned int i = 0; i < ntstrips; i++)
                                     ^
    /path/to/OpenIGTLinkIF/MRML/vtkIGTLToMRMLPolyData.cxx: In member function ‘virtual int vtkIGTLToMRMLPolyData::MRMLToIGTL(long unsigned int, vtkMRMLNode*, int*, void**)’:
    /path/to/OpenIGTLinkIF/MRML/vtkIGTLToMRMLPolyData.cxx:399:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (unsigned int i = 0; i < npoints; i ++)
    //------------
//-----------

Revision 23874  View Download Blame
Modified Fri Jan 9 17:23:53 2015 UTC (2 years, 8 months ago) by jcfr
File length: 15291 byte(s)
Diff to previous 23872
BUG: Update EMSegment to avoid using invalid BRAINSFit argument. Fixes #3939

// ---------------------
BUG: Remove invalid BRAINSFit argument

This commit removes deprecated (and unused for a long time) command line options
from the most recent version of BRAINSTools. These command line options have
been NO-OP operations for a long time. They have been removed in the version
of BRAINSTools now used in Slicer r23872.

Thanks to "Hans Johnson <hans-johnson@uiowa.edu>" for providing the patch.
// ---------------------

Revision 23872  View Download Blame
Modified Fri Jan 9 14:15:36 2015 UTC (2 years, 8 months ago) by jcfr
File length: 15291 byte(s)
Diff to previous 23866
ENH: Update BRAINTools

Ali Ghayoor (50):
      BUG: fix BRAINSFitTest_ROIBSpline test failure
      BUG: increase the tolerance for BRAINSFitTest_ROIBSpline
      BUG: Symmetric bounding box in training and detection phases of BCD
      ENH: perform the local search of BCD in Freq domain
      ENH: Add version number to input template and LLS model files
      ENH: add the new template files to ReferenceAtlas/20140916_BCD directory
      ENH: Update the current address of BCD model files to the new one
      ENH: Remove irrelevent parameters from BRAINSFit
      ENH: add the new template files to ReferenceAtlas/20141004_BCD directory
      ENH: Remove wrong model files and update AutoWorkup scripts
      ENH: Update the BCD model files for internal TestSuite
      ENH: Integration of ANTs Multimodal Registration into BRAINSFitHelper
      ENH: Add multi-modal capsbilities to BRAINSFit
      ENH: Change the classifier in BRAINSABC
      ENH: Update the ITK tag
      ENH: Write different posteriors for EM and KNN
      BUG: Fix BCD test failures
      BUG: Initialized m_UseKNN member variable on constructor
      ENH: Add itkCompensatedSummation for MSP estimation
      BUG: Fix 23 BCD test failures on medusa
      ENH: Avereged warped intra subjects
      ENH: Write debug warped intra subject images to the disk
      ENH: InitializeTransformsPerStage is set on BFit
      BUG: save-state transform should be cloned from the result transform in BFit
      BUG: Update ITK tag and a temporary tag for ANTs so BTools can be compiled
      BUG: Update save-state in BFit based on the last changes to ANTs
      BUG: Update temporary tags for ITK and ANTs based on bia versions
      BUG: Fix a bug in BABC when intial atlasToSubjectTx is missing
      BUG: Avoid writing the inverse of the state file
      ENH: Convert savedState file to the restored forward and inverse composites
      BUG: Fix BRAINSABC Failure for single modal images
      BUG: Fixed some bugs in BRAINSTransformConvert and verified its outputs
      ENH: BRAINSLandmarkInitializer works with multiple transformTypes
      BUG: No limit on usage of CompositeTransform for intialization in BABC
      BUG: MultiModal registration bug in BRAINSABC and BRAINSFit
      ENH: Add a GenerateCLP command line for GenerateAverageLmkFile
      BUG: Fixed BCD Test failures on Dashboard
      BUG: Fix BRAINSFitTest_ROIBSpline test failure
      BUG: Replace the baselines of BCD tests based on CDash build
      BUG: Fix a bug in BRAINSFit SyN registration
      BUG: Fixed a bug in GenericTransformImage
      BUG: Fixed output origin in ResampleInPlaceImageFilter
      ENH: Add a regression test to BRAINSResample for ResampleInPlace
      BUG: ReadTransformFromDisk can process a list of transforms now
      BUG: Fixed a bug in gtractResampleDWIInPlace
      ENH: Add a test for gtractResampleDWIInPlace
      BUG: Fixed a bug BRAINSHoughEyeDetector
      ENH: add reading from landmark file to BRAINSTalairach
      ENH: Add a python script to create inputLmkFile for BTalairach
      BUG: Fix BFit crash when only one value is set for splineGridSize

Hans Johnson (86):
      ENH: Update to include ITKv4 Mattes Performance fixes.
      ENH: Per requests of the slicer community, defaults changed.
      ENH: Added --dry-run feature
      WIP: Needs more work on SEM tools. DO NOT SUBMIT THIS.
      COMP: ITK Components needed for build.
      WIP: Removed BRAINSSurface building.
      ENH: Updated SEMTools to new command line usage.
      BUG: Filenames needed to change from hdf5 to h5 extension in autoworkup.
      BUG: Eliminate unnecessary handling of version
      COMP: Remove compiler warning
      ENH: Added UseKNN on the command line.
      STYLE: Remove unnecessary CLUSTER tag from config file
      ENH: Improve SyN registration in BABC
      ENH: Trying to add sqrt of multiplied posteriors
      ENH: Automatically calculate the number of sampels to use
      ENH: Add initial masking to Averaged images
      ENH: Update to include SEM generated interfaces.
      ENH: Fix BRAINSABC for AutoWorkup.
      ENH: Improved fine grained control of processing
      ENH: Added fixes for ITK FixedParameters.
      ENH: Cleaned up logic for isolating separate processing steps
      ENH: Added new command line for ANTS
      BUG: Fixed order of imports
      ENH: Updated Workflow for ANTs state saving.
      ENH: Add saveState and storeState to BFit and BABC
      ENH: Added stub restoring ANTs registration
      ENH: Improved linkage of SyN to BRAINSABC.
      ENH: Testing new ANTs registration values.
      ENH: Provide consistent registration for ANTs.
      ENH: ANTs testing with separate stages.
      ENH: Remove requirement for atlasToSubjectIntialTransform flag.
      ENH: Added cluster flags and remove debugging.
      ENH: Fixed segmentation phase of processing
      BUG: Need to ensure range of threads are integer values.
      ENH: Improved registration parameters for optimization.
      STYLE: Remove aliasing that was confusing
      ENH: Added debugging info.
      BUG: Missing update on averaging filter
      STYLE:  ::Zero and ::One have been deprecated since 2012
      ENH: Syncronize with NAMICExternalProjects.
      ENH: Improve logic for choosing registration mode.
      ENH: Improve T1 only segmentations
      ENH: Optimize registration parameters for ANTs template building.
      BUG: Command line to limit subjects to process was incorrect.
      STYLE: Hide debugging information.
      ENH: Fine tuning ANTs registration to take less time
      ENH: Limit the number of iterations for full size SyN
      BUG: matplotlib is not a requirement.
      ENH: Conversion to composite files continued
      ENH: Provide skipping logic for template building phase.
      ENH: FIXING BUGS IN template use for phase 3.
      ENH: Added GenerateAverageLmkFile interface.
      ENH: Split required and optional items from datagrabber.
      BUG: Incorrect syntax for custom pipeline arguments
      ENH: Try to fix Brainstem segmentations.
      BUG:  Connections to Segmentation were incorrect
      ENH: Make segmentation connection.
      ENH: Add feature for using ROIAuto for registration masking
      ENH: Add r/l hemisphere separation.
      COMP: Improve Compilation for ITK modules
      ENH: Adding MALF label fusion to autoworkup
      COMP: Fix compilation linkage errors.
      ENH: Initial code copied directly from BRAINS3/src/iplProg/GenusZero
      STYLE: Clean code for easier maintenance.
      ENH: Copy vtkITK from Slicer
      ENH: Migrate to Slicer version of vtkITK, and update to VTK version 6
      COMP: Remove compilation warning of returning without value.
      COMP: Fixed compilation problems
      ENH: Improve quality of MALF outputs
      ENH: Update ITKv4 to include performance fixes.
      COMP: Incorrect function signature.
      ENH: Lastest alpha ITK 4.7 release.
      COMP: Consolidated duplicate code, fix include directory
      ENH: Merged fusion and other knowlege
      ENH: Update external packages.
      COMP: C++11 style nullptr usage
      COMP: Use C++11 keyword override for code maintenance
      COMP: Remove unused typedefs
      ENH: Updated VTK.
      COMP: Improve VTK compilation options.
      BUG: Changes to Fix 'space directions' field in the NRRD Header
      BUG: Prevent infiinte loop for bad cases in BABC
      COMP: Missing ITK_OVERRIDE substitution.
      COMP: Fix VTK QT relationship builds.
      ENH: Syncronized with NAMICExternalProjects.
      ENH: Deprecate ::Zero and ::One

Kent Williams (14):
      COMP: remove ITKV3_COMPATIBILITY entireley
      COMP: Removed deprecated V3 filters
      COMP: Remove shadow declaration warnings
      COMP: fix core dump due to premature object destruction
      COMP: Replace Rigod{2,3}Transform with derived classes
      COMP: Initialize m_AtlasToSubjectInitialTransform
      COMP: Turn off ITKV3Compatibility and ITKDeprecated
      BUG: Fix scaling of vectors by b-values
      COMP: fix some gcc 4.9.2 warnings
      COMP: gcc4.9.1 warnings for ANTs
      COMP: Enable BRAINSSurfaceTools by default
      COMP: Fix warningsCOMP: get BRAINSSurfaceTools to build.
      COMP: Remove gcc 4.9 warnings
      COMP: Remove more gcc 4.9 warnings

Regina Kim (9):
      ENH: BRAINSABC multimodal functionality
      WIP: BRAINSABC multimodal functionality
      WIP: working version with the local option
      WIP: SyN Registration parameter tunning
      BUG: Fix the bug introduced by merging
      BUG: Multimodal registration into BABC
      BUG: kNN output were improperly propagated. Fixed
      ENH: By pass denoising for BCD failures
      BUG: BRAINSCut DG move and template building fix     BRAINSCut probablity DataGrabber were placed into segmentation     section instead of default section.

eunyoung regina kim (2):
      Update README
      Create MALFLabel_neuromorphometrics_colortable.txt

fbudin69500 (1):
      ENH: Addition of an option in DWIConvert to read input BVector files that are transposed when converting FSL images to     NRRD images.

Revision 23866  View Download Blame
Modified Fri Jan 9 06:45:26 2015 UTC (2 years, 8 months ago) by jcfr
File length: 15649 byte(s)
Diff to previous 23856
COMP: Remove ITKv3Compatibility dependency from EMSegment

// ---------------
ENH: Remove dependency on ITKv3Compatibility module.

Thanks to "Bradley Lowekamp <blowekamp@mail.nih.gov>" for providing the patch.

See http://itk.org/migrationv4/index.php?action=artikel&cat=3&id=143&artlang=en for
more details
// ---------------

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

Revision 23856  View Download Blame
Modified Thu Jan 8 05:20:22 2015 UTC (2 years, 8 months ago) by fedorov
File length: 15649 byte(s)
Diff to previous 23853
ENH: update DICOMMultiVolumePlugin 

Include TR and TE attributes for FA-separated multivolume nodes, as these are necessare for T1 calculation

Revision 23853  View Download Blame
Modified Wed Jan 7 05:24:59 2015 UTC (2 years, 8 months ago) by fedorov
File length: 15649 byte(s)
Diff to previous 23827
ENH: Update SHA tag for MultiVolumeImporter. This updates MultiVolume DICOM plugin to include FlipAngle in the list of tags to consider while parsing multi-series multi-volume. This issue prevented loading of the MGH variable FA multivolume.

Revision 23827  View Download Blame
Modified Wed Dec 10 21:29:20 2014 UTC (2 years, 9 months ago) by jcfr
File length: 15649 byte(s)
Diff to previous 23814
ENH: Update OpenIGTLinkIF: Improve support for POINT and POLYDATA message

Fixes #3875 and #3907

$ git shortlog 2ffd26b..d56c985 --no-merges
Junichi Tokuda (10):
      ENH: Use MarkupsFiducial node for POINT messages
      STYLE: Rename vtkIGTLToMRMLPointMetaList to vtkIGTLToMRMLPoint
      STYLE: Rename vtkIGTLToMRMLPoint to vtkIGTLToMRMLPoints.
      ENH: Initial implementation of the PolyData converter.
      ENH: Export PolyData through OpenIGTLink. Attributes are not exported.
      ENH: Export attributes. All features for the POLYDATA converter are implemented.
      ENH: Simplify vtkIGTLToMRMLPolyData::MRMLToIGTL() using vtkIGTLToMRMLPolyData::VTKToIGTLCellArray() function.
      ENH: Simplify vtkIGTLToMRMLPolyData::MRMLToIGTL() using vtkIGTLToMRMLPolyData::VTKToIGTLAttribute() function.
      ENH: Clean up the code.
      STYLE: Remove debug code.

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

Revision 23814  View Download Blame
Modified Wed Dec 3 05:21:05 2014 UTC (2 years, 9 months ago) by fedorov
File length: 15649 byte(s)
Diff to previous 23765
ENH: enable parsing of Philips DWI datasets

Philips private tag added to allow parsing multi-b acquisitions as multivolumes by the plugin.

Revision 23765  View Download Blame
Modified Wed Oct 29 23:34:58 2014 UTC (2 years, 10 months ago) by pieper
File length: 15649 byte(s)
Diff to previous 23752
ENH: update landmark registration

commit fbf515ecd91b26177bad25e0336c24deec8bf69b
Author: Steve Pieper <pieper@bwh.harvard.edu>
Date:   Wed Oct 29 19:32:50 2014 -0400

    ENH: improve the support for imported fiducial lists for LandmarkRegistration

    - detect and set display style
    - add associated node linkage
    - avoid detecting storage nodes
    - trigger registration when switching registration plugins

Revision 23752  View Download Blame
Modified Mon Oct 20 23:22:47 2014 UTC (2 years, 11 months ago) by pohl
File length: 15649 byte(s)
Diff to previous 23748
STYLE: change BRAINSFIT setting to accomodate new version

Revision 23748  View Download Blame
Modified Fri Oct 17 20:08:35 2014 UTC (2 years, 11 months ago) by pohl
File length: 15649 byte(s)
Diff to previous 23738
BUG: #3561 did not check if index < 0, which causes crashes

Revision 23738  View Download Blame
Modified Mon Oct 13 22:53:42 2014 UTC (2 years, 11 months ago) by pohl
File length: 15649 byte(s)
Diff to previous 23736
BUG: #3561 tcl file was not updated to VTK6

Revision 23736  View Download Blame
Modified Fri Oct 10 03:01:32 2014 UTC (2 years, 11 months ago) by fedorov
File length: 15649 byte(s)
Diff to previous 23733
BUG: fix static charting

Revision 23733  View Download Blame
Modified Sat Sep 27 02:09:31 2014 UTC (2 years, 11 months ago) by jcfr
File length: 15649 byte(s)
Diff to previous 23729
COMP: Update BRAINSTools to fix build issue related to ITKDeprecated.

This commit is a follow-up of r23729 where BRAINSTools hasn't been updated
by mistake.

The update of BRAINSTools now includes the following commit:

// ----------------
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Thu Sep 25 10:52:17 2014 -0400

    COMP: Remove ITKDeprecated from the list of ITK components.

    This commit is a follow-up of BRAINSia/BRAINSTools@13969f3

    An issue has been reported upstream, see BRAINSia/BRAINSTools#154
// ----------------

Revision 23729  View Download Blame
Modified Thu Sep 25 19:49:02 2014 UTC (3 years ago) by jcfr
File length: 15554 byte(s)
Diff to previous 23707
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 23707  View Download Blame
Modified Thu Sep 18 22:15:03 2014 UTC (3 years ago) by jcfr
File length: 15554 byte(s)
Diff to previous 23704
STYLE: Fix typo "protocol" instead of "protocole"

Revision 23704  View Download Blame
Modified Thu Sep 18 08:51:16 2014 UTC (3 years ago) by jcfr
File length: 15555 byte(s)
Diff to previous 23683
BUG: Update EMSegment - Do not display warning when setting a null scene.

Before this commit, setting an null scene on the EMSegent widgets was
outputting the following:

335: Warning: In /path/to/EMSegment/vtkEMSegmentLogic.cxx, line 400
335: vtkEMSegmentLogic (0x4d35da0): InitializeEventListeners: no scene to listen to!
335:
335: Warning: In /path/to/EMSegment/vtkEMSegmentLogic.cxx, line 400
335: vtkEMSegmentLogic (0x4d264c0): InitializeEventListeners: no scene to listen to!

Revision 23683  View Download Blame
Modified Tue Sep 16 03:18:00 2014 UTC (3 years ago) by jcfr
File length: 15555 byte(s)
Diff to previous 23679
BUG: Update EMSegment to fix EMSeg_SlicerCommonInterfaceTestGeneral test

This commit ensures the ITK IO factory associated with
executable vtkSlicerCommonInterfaceTest are registered.

Revision 23679  View Download Blame
Modified Mon Sep 15 19:34:18 2014 UTC (3 years ago) by jcfr
File length: 15555 byte(s)
Diff to previous 23678
COMP: Update BRAINStools to include fixes for shadowed declarations.

$ git shortlog 868c290d..6f9986
Jean-Christophe Fillion-Robin (2):
      Revert "COMP: Fix unused variable warning in BRAINSFitHelperTemplate"
      Revert "COMP: Fix shadowed declaration warning"

Kent Williams (2):
      COMP: Removed deprecated V3 filters
      COMP: Remove shadow declaration warnings

Revision 23678  View Download Blame
Modified Mon Sep 15 15:49:04 2014 UTC (3 years ago) by jcfr
File length: 15516 byte(s)
Diff to previous 23655
COMP: Update BRAINSTools - Remove ITKv3 compatibility / Tweak BRAINSFit.xml

See #3829

$ git shortlog slicer-2014-08-27-6b15c2b..slicer-2014-09-15-411dee9
David Welch (2):
      ENH: Modified atlas xml name
      ENH: Added print statement to diagnose missing sentinal file

Hans Johnson (6):
      BUG: Uniformly apply modify_qsub_args for configuring qsub_args.
      BUG: Fixed logic for set notation.
      PERF: Fixed job submission logic to speed job start.
      BUG: Add consistent use-sentinal file.
      ENH: Added missing __init__.py file for SEMTools module.
      ENH: Per requests of the slicer community, defaults changed.

Jean-Christophe Fillion-Robin (2):
      Revert "COMP: fine-tune VTK dependencies"
      Revert "COMP: move find_package(VTK) down to individual project directories"

Kent Williams (3):
      COMP: Allow BRAINSTransformConvert without output transform file
      COMP: Remove global declarations from GenericTransformImage.h
      COMP: remove ITKV3_COMPATIBILITY entireley

Regina Kim (3):
      ENH: Allow template building to only do new files
      ENH: Add code for identifying the brain stem
      BUG: ATLAS_DIRECTORY to ATLAS_INSTALLING_DIRECTORY

Revision 23655  View Download Blame
Modified Sat Sep 6 17:08:11 2014 UTC (3 years ago) by pieper
File length: 15351 byte(s)
Diff to previous 23653
ENH: Update LandmarkRegistration and CompareVolumes

Several improvements to the documentation and features.

From: Steve Pieper <pieper@bwh.harvard.edu>

Revision 23653  View Download Blame
Modified Sat Sep 6 17:07:21 2014 UTC (3 years ago) by pieper
File length: 15351 byte(s)
Diff to previous 23648
ENH: upgrade CompareVolumes

commit 583d4a78b0b2b9609e023b5a37f64ed154e0d180
Author: Steve Pieper <pieper@bwh.harvard.edu>
Date:   Thu Aug 28 19:03:29 2014 -0400

    Add lightbox render mode and extra controls

commit 1370b2bf6990db182cb12bc23bfaa414af3f1278
Author: Steve Pieper <pieper@bwh.harvard.edu>
Date:   Thu Aug 28 14:41:01 2014 -0400

    Fix issue with cursor not being turned back on after reveal

From: Steve Pieper <pieper@bwh.harvard.edu>

Revision 23648  View Download Blame
Modified Fri Sep 5 20:16:45 2014 UTC (3 years ago) by pieper
File length: 15351 byte(s)
Diff to previous 23644
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 23644  View Download Blame
Modified Wed Sep 3 17:41:56 2014 UTC (3 years ago) by pohl
File length: 15351 byte(s)
Diff to previous 23642
BUG: disabled calcDFVolumeNode as it calls a BRAINS function that does not work

Revision 23642  View Download Blame
Modified Tue Sep 2 03:09:44 2014 UTC (3 years ago) by fedorov
File length: 15351 byte(s)
Diff to previous 23640
BUG: seriesNumber tag was not initialized, leading to series parsing failure

Revision 23640  View Download Blame
Modified Mon Sep 1 21:52:34 2014 UTC (3 years ago) by pohl
File length: 15351 byte(s)
Diff to previous 23638
BUG: Tests failed bc BRAINS non-rigid registration took too long; EMSegmenter failed if the auto sampling of covariance matrix resulted in 0 entries in the diagonal; Add info to error message to simplify tracing down the issue; Changed one of the Tests so that they only perform affine registration; Fixed naming convention for atlases that are loaded in through api instead of mrml

Revision 23638  View Download Blame
Modified Sat Aug 30 00:51:01 2014 UTC (3 years ago) by pohl
File length: 15351 byte(s)
Diff to previous 23637
BUG: Integrated BRAINSTransformConvert as original cmd did not work with BRAINS anymore

Revision 23637  View Download Blame
Modified Fri Aug 29 21:36:48 2014 UTC (3 years ago) by jcfr
File length: 15351 byte(s)
Diff to previous 23627
ENH: Allow BRAINSTransformConvert without output transform file

$ git shortlog 68303b3..4fb59c3
Kent Williams (1):
      COMP: Allow BRAINSTransformConvert without output transform file

Revision 23627  View Download Blame
Modified Wed Aug 27 19:51:35 2014 UTC (3 years ago) by jcfr
File length: 15351 byte(s)
Diff to previous 23611
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 23611  View Download Blame
Modified Fri Aug 22 03:35:22 2014 UTC (3 years, 1 month ago) by jcfr
File length: 15362 byte(s)
Diff to previous 23609
BUG: Legacy module OtsuThresholdImageFilter needed by EMSegment. Issue #3815

This commit fixes a regression introduced by r23598 which removed
the source of OtsuThresholdImageFilter. This ensures EMSegment will
work as expected by integrating the source of the CLI as a
remote module [1].

[1] http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Build_system/Remote_Module

For future reference, the EMSegment test
"EMSeg_SlicerCommonInterfaceTestGeneral" was failing with:

// ---------------
[...]
Test 7 : PreprocessingBiasFieldCorrection
ERROR: In /home/kitware/Dashboards/Nightly/Slicer-0-build/EMSegment/vtkSlicerCommonInterface.cxx, line 609
vtkSlicerCommonInterface (0x226d940): Could not find path to OtsuThresholdImageFilter

ERROR: In /home/kitware/Dashboards/Nightly/Slicer-0/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx, line 367
vtkMRMLVolumeArchetypeStorageNode (0x235fd00): ReadData: Cannot read file as a volume of type Volume[fullName = /tmp/EMSD1388245976wJ71mE/mask.nrrd]
    Number of files listed in the node = 0.
    File reader says it was able to read 0 files.
    File reader used the archetype file name of /tmp/EMSD1388245976wJ71mE/mask.nrrd []
[...]
// ---------------

Revision 23609  View Download Blame
Modified Thu Aug 21 22:56:51 2014 UTC (3 years, 1 month ago) by jcfr
File length: 14942 byte(s)
Diff to previous 23571
BUG: Fix OpenIGTLinkIF performance issue with PlusRemote. Issue #3813

$ git shortlog fb1a29..2ffd26 --no-merges
Andras Lasso (1):
      ENH: Prevent continuous changing of connector node state while waiting for connection

Jean-Christophe Fillion-Robin (2):
      STYLE: Remove end-of-line spaces
      COMP: Fix uninitialized variable warning in vtkIGTLToMRMLTrajectory.

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

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

Revision 23571  View Download Blame
Modified Sat Aug 16 21:45:18 2014 UTC (3 years, 1 month ago) by jcfr
File length: 14942 byte(s)
Diff to previous 23570
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 23570  View Download Blame
Modified Sat Aug 16 02:54:06 2014 UTC (3 years, 1 month ago) by pohl
File length: 14950 byte(s)
Diff to previous 23560
BUG: Script exited with error when writting out intermediate results with tasks that included subparcellation

Revision 23560  View Download Blame
Modified Wed Aug 6 22:03:51 2014 UTC (3 years, 1 month ago) by pieper
File length: 14950 byte(s)
Diff to previous 23544
ENH: new LandmarkRegistration feature

Helps when registering two non-overlapping volumes.

Revision 23544  View Download Blame
Modified Sun Aug 3 05:14:38 2014 UTC (3 years, 1 month ago) by jcfr
File length: 14950 byte(s)
Diff to previous 23543
BUG: Update MultiVolumeExplorer to fix issue due to missing cast to int

See fedorov/MultiVolumeExplorer@f9222a25a
and fedorov/MultiVolumeExplorer@9135996ae

From: Andrey Fedorov <fedorov@bwh.harvard.edu>

Revision 23543  View Download Blame
Modified Sun Aug 3 05:14:36 2014 UTC (3 years, 1 month ago) by jcfr
File length: 14950 byte(s)
Diff to previous 23542
BUG: Update MultiVolumeImporter to fix DICOM.instanceUIDs initialization

See fedorov/MultiVolumeImporter@fb38cbbd00

From: Andrey Fedorov <fedorov@bwh.harvard.edu>

Revision 23542  View Download Blame
Modified Sat Aug 2 05:43:13 2014 UTC (3 years, 1 month ago) by jcfr
File length: 14950 byte(s)
Diff to previous 23532
COMP: Update Datastore to fix build introduced when trying to fix warning

See Slicer/Slicer-DataStore@713f1f8

Revision 23532  View Download Blame
Modified Fri Aug 1 07:31:10 2014 UTC (3 years, 1 month ago) by jcfr
File length: 14950 byte(s)
Diff to previous 23526
COMP: Update DataStore to fix "No resources" warning

$ git shortlog 4ac766c..6081f84
Jean-Christophe Fillion-Robin (1):
      Fix "No Resources" warning in Widgets library

Revision 23526  View Download Blame
Modified Thu Jul 31 16:27:20 2014 UTC (3 years, 1 month ago) by pieper
File length: 14950 byte(s)
Diff to previous 23521
ENH: Update to latest landmark registration

Improved point placement through transforms

Revision 23521  View Download Blame
Modified Wed Jul 30 21:03:39 2014 UTC (3 years, 1 month ago) by jcfr
File length: 14950 byte(s)
Diff to previous 23507
BUG: Update MultiVolumeExplorer - Fix frame scrolling

This fixes an issue due to missing cast from float to int that disabled
frame scrolling. See fedorov/MultiVolumeExplorer@f9222a25a

From: Andrey Fedorov <fedorov@bwh.harvard.edu>

Revision 23507  View Download Blame
Modified Wed Jul 30 00:36:31 2014 UTC (3 years, 1 month ago) by jcfr
File length: 14950 byte(s)
Diff to previous 23496
BUG: Partial fix for EMSegment/BRAINSFit integration. See #3561, #2741, #3779

This commit is a follow up of EMSegment commit r23496. It updates BRAINSFit
to integrate the fix done by Kent to specifically address the naming
of .h5 transform files written by BRAINSFit.

// ---------------------
commit e46c99795cedd4c6aeec98e881af9c2b28dc5cf5
Author: Kent Williams <norman-k-williams@uiowa.edu>
Date:   Tue Jul 29 15:24:11 2014 -0500

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
given was already for an HDF5 file.
// ---------------------

Revision 23496  View Download Blame
Modified Tue Jul 29 23:07:53 2014 UTC (3 years, 1 month ago) by pohl
File length: 14934 byte(s)
Diff to previous 23486
BUG: BRAINS can only now read in h5 files

Revision 23486  View Download Blame
Modified Sat Jul 26 04:10:03 2014 UTC (3 years, 2 months ago) by pohl
File length: 14934 byte(s)
Diff to previous 23485
BUG: cli-modules were not included in PATH of installed version of MAC so added it to search path

Revision 23485  View Download Blame
Modified Fri Jul 25 21:28:37 2014 UTC (3 years, 2 months ago) by pohl
File length: 14934 byte(s)
Diff to previous 23480
BUG: Fixed error with intensity sampling; removed code not used under Slicer4

Revision 23480  View Download Blame
Modified Wed Jul 23 16:59:10 2014 UTC (3 years, 2 months ago) by jcfr
File length: 14934 byte(s)
Diff to previous 23477
BUG: Ensure MultiVolume modules work with VTK 5 and 6

This commit updates the modules to check for the version
of VTK (using `vtk.VTK_MAJOR_VERSION`). This is required
because the MacOSX factory is still building against VTK5.

For more details see:

  fedorov/MultiVolumeExplorer@1053c40
  fedorov/MultiVolumeImporter@351226a

From: Andrey Fedorov <fedorov@bwh.harvard.edu>

Revision 23477  View Download Blame
Modified Wed Jul 23 03:01:25 2014 UTC (3 years, 2 months ago) by jcfr
File length: 14934 byte(s)
Diff to previous 23474
STYLE: Add "python-" prefix to GitPython, Github and pydicom module

Consistently name python package.

Revision 23474  View Download Blame
Modified Tue Jul 22 09:54:34 2014 UTC (3 years, 2 months ago) by jcfr
File length: 14906 byte(s)
Diff to previous 23468
COMP: Update setuptools to support parallel install. See #3757

This commit removes the complex and un-maintainable "lock" mechanism
first introduced in r23465. Instead it updates the version of setuptools
to use a patched version able to support parallel build.

Revision 23468  View Download Blame
Modified Sun Jul 20 20:07:26 2014 UTC (3 years, 2 months ago) by jcfr
File length: 16768 byte(s)
Diff to previous 23465
COMP: Provide Updates to BRAINSFit and DWIConvert

After the NAMIC meeting, several changes were made to address issues
with BRIANSFit and DWIConvert (Fixes #3736).

Reference atlas is a new module and is not needed by Slicer.

From: Hans Johnson <hans-johnson@uiowa.edu>

Revision 23465  View Download Blame
Modified Fri Jul 18 23:20:33 2014 UTC (3 years, 2 months ago) by jcfr
File length: 16714 byte(s)
Diff to previous 23442
COMP: Do not package GitPython and PyGithub test directories. Fixes #3749

This commit reverts r23088 and now ensures that the test directories from
the GitPython and PyGithub python module install tree are removed. This
should fix the packaging issue caused by two long paths reported in
issue #3749 when install rules in "SlicerBlockInstallPython.cmake" where
executed.

To conveniently delete folders from the install tree, the CMake function
"ExternalProject_PythonModule_InstallTreeCleanup" has been introduced. Note
that it doesn't yet belong to the Slicer API and exists purely as an
implementation detail.

Revision 23442  View Download Blame
Modified Wed Jul 16 21:39:41 2014 UTC (3 years, 2 months ago) by pieper
File length: 16728 byte(s)
Diff to previous 23441
BUG: fix method name difference between vtk 5 and 6

Fixes failing test on vtk 6.

Revision 23441  View Download Blame
Modified Wed Jul 16 18:46:49 2014 UTC (3 years, 2 months ago) by pieper
File length: 16728 byte(s)
Diff to previous 23434
ENH: LandmarkRegistration improvements (and fixed test on vtk5 and vtk6)

Revision 23434  View Download Blame
Modified Tue Jul 15 15:21:33 2014 UTC (3 years, 2 months ago) by pieper
File length: 16728 byte(s)
Diff to previous 23433
BUG: fix type of argument to SetGridExtent for LandmarkRegistration

Exposed by vtk v5 vs v6 testing.

Revision 23433  View Download Blame
Modified Tue Jul 15 00:01:37 2014 UTC (3 years, 2 months ago) by pieper
File length: 16728 byte(s)
Diff to previous 23429
ENH: update to new LandmarkRegistration

Now with interactive ThinPlate registration!
- uses real-time nonlinear transform updates
- compatible with transform visualization

Other improvments and upgrades, like VTKv6 support and
generalization of the plugin architecture.

Revision 23429  View Download Blame
Modified Mon Jul 14 17:21:06 2014 UTC (3 years, 2 months ago) by jcfr
File length: 16728 byte(s)
Diff to previous 23426
ENH: Update OpenIGTLinkIF - Add new message converters. Fixes #3548 & #3738

Also update GUI to allow users to push MRML nodes (#3738)

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

Revision 23426  View Download Blame
Modified Thu Jul 10 03:48:59 2014 UTC (3 years, 2 months ago) by pohl
File length: 16728 byte(s)
Diff to previous 23423
BUG: Extesions did not look in right directory - in addition CMTK could pass even if CMTK was not installed as EMSegmenter automatically switches to Brains

Revision 23423  View Download Blame
Modified Tue Jul 8 16:37:40 2014 UTC (3 years, 2 months ago) by pohl
File length: 16728 byte(s)
Diff to previous 23422
BUG: depreciated flag of BRAINS was changed

Revision 23422  View Download Blame
Modified Fri Jul 4 22:02:11 2014 UTC (3 years, 2 months ago) by jcfr
File length: 16728 byte(s)
Diff to previous 23416
STYLE: Improve comment associated with lock variable.

This commit updates the text illustrating why a lock variable should
be used. For reference, the lock variable has been introduced in r23409.

Revision 23416  View Download Blame
Modified Fri Jul 4 06:36:09 2014 UTC (3 years, 2 months ago) by jcfr
File length: 16691 byte(s)
Diff to previous 23409
COMP: Fix BRAINSTools configure error related to missing ITKVtkGlue

Commit Slicer/BRAINSTools@94d53a64:

//---------------
COMP: Conditionally specify ITK component "ITKVtkGlue" to fix Slicer build.

This commit conditionally append "ITKVtkGlue" to the list of components
introduced in commit 2c751a5. Considering that (1) Slicer does NOT build
the module BRAINSConstellationDetector and ConvertBetweenFileFormats
depending on "ITKVtkGlue" and (2) Slicer does NOT build ITK with
module ITKVtkGlue enabled, this commit will ensure BRAINSTools can
be built within Slicer.

Ideally, every module should specify the list of ITK components it expects.

To find out which module depended on "ITKVtkGlue", assuming the source of
ITKv4 are in /path/to/src/ITKv5, the following one-liner has been used:

cd /path/to/src/BRAINSTools

for i in `ls -d */`; do \
  echo Directory [$i]; \
  ../ITKv4/Utilities/Maintenance/WhatModulesITK.py \
    ../ITKv4 $(find $i -type f) | ack -i ITKVtkGlue; \
done
//---------------

Revision 23409  View Download Blame
Modified Thu Jul 3 02:59:40 2014 UTC (3 years, 2 months ago) by jcfr
File length: 16691 byte(s)
Diff to previous 23396
COMP: Ensure that easy-install.pth is not concurrently updated. Fixes #3757

Project that can NOT be built in parallel should set the
variable _EP_<projectName>_<lockname>_LOCK to 1.

For example, to address issue #3757 and ensure that project
building and python module are not updating the file 'easy-install.pth'
concurrently, these project are setting the variable:

    set(_EP_${proj}_SETUPTOOLS_LOCK 1)

Then, by calling the function "_ep_setup_lock", we are
sure that they won't be run in parallel.

Since "gitdb", "async" and "NUMPY" project are not updating easy-install.pth,
there is no need to "lock" them.

Revision 23396  View Download Blame
Modified Mon Jun 30 13:18:21 2014 UTC (3 years, 2 months ago) by jcfr
File length: 14866 byte(s)
Diff to previous 23388
COMP: Remove unused CLIs MIDASApplications and BatchMakeApplications

See #3401

Revision 23388  View Download Blame
Modified Fri Jun 27 14:03:29 2014 UTC (3 years, 2 months ago) by jcfr
File length: 14945 byte(s)
Diff to previous 23379
ENH: Update SimpleFilters

This commit updates both SimpleFilters documentation strings
presented in the help section, and json description used to described the
filters.

b27cdf6 Remove statistics only filters
148d863 Update help and acknowledgment text
bcdabde Fix json syntax issue StatisticsImageFilter
c62f9a8 Removing Filters which produce labelmaps as outputs
77fb3ac SimpleITK cd897256 Filter descriptions (reduced)
85d1ab2 Add utility script to generate Wiki table of filter

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

Revision 23379  View Download Blame
Modified Thu Jun 26 13:33:48 2014 UTC (3 years, 3 months ago) by pieper
File length: 14945 byte(s)
Diff to previous 23377
ENH: update to latest LandmarkRegistration code

Revision 23377  View Download Blame
Modified Thu Jun 26 06:24:31 2014 UTC (3 years, 3 months ago) by jcfr
File length: 14945 byte(s)
Diff to previous 23374
COMP: Update MultiVolumeExplorer project to fix unused-local-typedefs warnings

$ git shortlog 17a9095..d68663f --no-merges
Jean-Christophe Fillion-Robin (1):
      COMP: Fix unused-local-typedefs warnings

Revision 23374  View Download Blame
Modified Thu Jun 26 06:24:27 2014 UTC (3 years, 3 months ago) by jcfr
File length: 14945 byte(s)
Diff to previous 23373
BUG: Update BRAINSTools to include DWIConvert interface tweaks.

See #3693

$ git shortlog 8d870f0..ce609cb
Hans Johnson (2):
      ENH: Improve Slicer interface to DWIConvert
      ENH: Fine tuning the GUI for ease of use.

Revision 23373  View Download Blame
Modified Thu Jun 26 06:24:25 2014 UTC (3 years, 3 months ago) by jcfr
File length: 14945 byte(s)
Diff to previous 23369
ENH: Update (1) ITKv4 from v4.5.2 to v4.6rc01 and (2) update BRAINSTools

// ------------------------
BRAINSTools

 * Compliant with ITKv4 registration framework. This changes
the fundamental methods for registration to use the ITKv4 framework,
while maintaining both the API and the same results for all regression tests.

 * DWIConvert tool also add features for reading additional scanner types.
// ------------------------


// ------------------------
ITKv4 - New Features

* CMake improvements
 - Improved Remote Module support
 - Add ITK_FORBID_DOWNLOADS for package maintainers
 - ITK_USE_SYSTEM_EXPAT available

* Filtering Improvements
 - Moved TransformToDisplacementField out of Review
 - An entire noise image generation module
   - http://hdl.handle.net/10380/3158
 - Better pipeline support for ResampleImageFilter
 - Move MagnitudeAndPhaseToComplexImageFilter out of Review
 - Setters for LabelMap overlay filters
 - More consistent filter progress reporting

* ImageO improvements
 - Register the GE image formats by default
 - More IO modules are built as shared libraries
 - OpenFileForReading/Writing methods in ImageIO
 - Support for system tiff 4.0.0-4.0.2 (e.g. some Ubuntu versions)
 - Mangling to internal OpenJPEG
 - SCIFIO improvements

* Infrastructure improvements
 - MetaDataObject print specialization for common types
 - Improvements to ResourceProbe and RealTimeClock
 - More Solve methods for VNLSparseLUSolverTraits
 - Output stream operator for LightObject exposed
 - FFTW bump to 3.3.3

* New Remote Modules
 - Skull stripper
   - http://hdl.handle.net/10380/3353
 - Wiki examples
 - Sphinx examples
 - Variational registration
   - http://hdl.handle.net/10380/3460
 - AnalyzeObjectMapIO
   - http://hdl.handle.net/1926/593
 - FDFImageIO
 - SplitComponents
   - http://hdl.handle.net/10380/320

* Registrationv4 improvements
 - v4 regular step gradient descent optimizer
 - v4 amoeba optimizer
 - v4 exhaustive optimizer
 - v4 Powell optimizer
 - v4 one-plus-one-evolutionary optimizer
 - v4 LBFGS optimizer improvements
 - Use registration method classes as pipeline filters

* Performance improvements
 - Registrationv4
 - Histogram computation
 - Improved SmartPointer copy
 - CompositeTransform
 - Registration Jacobian re-use

* Wrapping improvements
 - pygccxml 1.0.0
 - .pth symlink usable in a virtualenv
 - Cleaner CMake configuration
 - SWIG and PCRE updated to 3.0.2, 8.34
 - Latest GCCXML, which works with GCC 4.9
 - Sweeping wrapping generation cleanup


* Many style improvements -- ITK gets more stylish with every release!

* Improved code coverage -- some measures put us over 85%!
// ------------------------

Co-authored-by: Hans Johnson <hans-johnson@uiowa.edu>

Revision 23369  View Download Blame
Modified Wed Jun 25 22:50:42 2014 UTC (3 years, 3 months ago) by pieper
File length: 14909 byte(s)
Diff to previous 23367
ENH: update to new LandmarkRegistration

Makes use of the new fiducial end moving event

Revision 23367  View Download Blame
Modified Tue Jun 24 15:30:06 2014 UTC (3 years, 3 months ago) by finetjul
File length: 14909 byte(s)
Diff to previous 23366
BUG: Fix VTK6 support for vtkImageIslandFilter

Closes #3746

Revision 23366  View Download Blame
Modified Mon Jun 23 17:57:45 2014 UTC (3 years, 3 months ago) by pohl
File length: 14909 byte(s)
Diff to previous 23365
BUG: Added Test 6 to expose crash of vtkImageIslandFilter due to VTK6 transition

Revision 23365  View Download Blame
Modified Mon Jun 23 16:36:03 2014 UTC (3 years, 3 months ago) by finetjul
File length: 14909 byte(s)
Diff to previous 23364
COMP: Remove vtkImageLabelPropagation::AllocateScalarsOutput

declaration in VTKv6.

Revision 23364  View Download Blame
Modified Mon Jun 23 15:35:19 2014 UTC (3 years, 3 months ago) by finetjul
File length: 14909 byte(s)
Diff to previous 23356
BUG: Fix vtkImageLabelPropagation VTK 6 support

Fixes vtkSlicerCommonInterfaceTest1

Revision 23356  View Download Blame
Modified Sat Jun 21 16:20:05 2014 UTC (3 years, 3 months ago) by jcfr
File length: 14909 byte(s)
Diff to previous 23345
COMP: Find qRestAPI package only where required.

This commits moved the discovery of the qRestAPI module in both QTCore
library and DataStore remote module.

Revision 23345  View Download Blame
Modified Thu Jun 19 20:11:58 2014 UTC (3 years, 3 months ago) by pohl
File length: 14909 byte(s)
Diff to previous 23341
BUG: Fixed bug with respect to Image inhomogeneity; included vtkImageLabelPropagation in SlicerCommonInterFaceTest1 so it would fail as this is also the reason for EMSegCL_Task_MRIHumanBrainFullParcellation_BRAINS_small failing

Revision 23341  View Download Blame
Modified Wed Jun 18 13:53:25 2014 UTC (3 years, 3 months ago) by jcfr
File length: 14909 byte(s)
Diff to previous 23335
COMP: Update EMSegment project to fix VTKv6 build error.

//------------------
r17058 | jcfr | 2014-06-18 09:47:30 -0400 (Wed, 18 Jun 2014) | 9 lines

COMP: Fix compilation against VTKv6.

This commits fixes build error introduced by r17053.

Few tests are still failing due to memory leaks and will
be fixed at a later time:
* EMSegCL_Task_MRIHumanBrain_BRAINS_small
* EMSegCL_Task_MRIHumanBrainFullParcellation_BRAINS_small
//------------------

Revision 23335  View Download Blame
Modified Tue Jun 17 17:59:25 2014 UTC (3 years, 3 months ago) by pohl
File length: 14909 byte(s)
Diff to previous 23334
BUG: Replaced outdated sliceWidgetRed_interactorStyle slicer.sliceWidgetRed_sliceLogic

Revision 23334  View Download Blame
Modified Tue Jun 17 16:21:11 2014 UTC (3 years, 3 months ago) by pohl
File length: 14909 byte(s)
Diff to previous 23332
BUG: Test failed as MRML node now also include version number in mrml file 

Revision 23332  View Download Blame
Modified Mon Jun 16 23:04:12 2014 UTC (3 years, 3 months ago) by pohl
File length: 14909 byte(s)
Diff to previous 23329
BUG: data() is not part of std::vector on windows compilers

Revision 23329  View Download Blame
Modified Fri Jun 13 02:17:26 2014 UTC (3 years, 3 months ago) by pohl
File length: 14909 byte(s)
Diff to previous 23328
BUG: vtkSlicerCommonInterface did not define the right plugin path to plugins when EMSEgmenter was run by installed package

Revision 23328  View Download Blame
Modified Wed Jun 11 21:42:39 2014 UTC (3 years, 3 months ago) by pohl
File length: 14909 byte(s)
Diff to previous 23327
BUG: N4ITK changes the image range which can cause problems for images of scalar type short if they fall outside the range

Revision 23327  View Download Blame
Modified Wed Jun 11 19:23:11 2014 UTC (3 years, 3 months ago) by pieper
File length: 14909 byte(s)
Diff to previous 23314
STYLE: update to latest CompareVolumes code

Changes style of slice view name.

Revision 23314  View Download Blame
Modified Sat Jun 7 16:04:44 2014 UTC (3 years, 3 months ago) by jcfr
File length: 14909 byte(s)
Diff to previous 23304
COMP: Update EMSegment to fix narrowing and non virtual dtor warnings.

Issue #3419

------------------------------------------------------------------------
r17052 | jcfr | 2014-06-06 21:29:01 -0400 (Fri, 06 Jun 2014) | 3 lines

COMP: Avoid implicit narrowing casts

Explicitly cast initializers in {} array initializer where the assigned
type is smaller than the value type. This avoids implicit narrowing in a
{} initializer, which is ill-formed in C++11.

------------------------------------------------------------------------
r17051 | jcfr | 2014-06-06 21:21:39 -0400 (Fri, 06 Jun 2014) | 3 lines

COMP: Remove gratuitous virtual

Remove 'virtual' specifier of private class in source file, where said
class is not and (due to being in a source file) never will be derived.
This avoids needing an explicit (virtual) dtor in order to avo
id a -Wnon-virtual-dtor warning.

From: Matthew Woehlke <matthew.woehlke@kitware.com>

Revision 23304  View Download Blame
Modified Wed Jun 4 14:51:03 2014 UTC (3 years, 3 months ago) by jcfr
File length: 14909 byte(s)
Diff to previous 23267
BUG: Update OpenIGTLinkIF Git Tag. Fixes #3724

Transforms don't update after loading from saved scene.

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

Revision 23267  View Download Blame
Modified Fri May 30 22:43:00 2014 UTC (3 years, 3 months ago) by mwoehlke
File length: 14909 byte(s)
Diff to previous 23226
ENH: Add python-chardet external project

Add external project for chardet Python module used in the previous
commit, so that we have actual detection available and not just ASCII
vs. "don't know". Like GitPython and friends, this is only enabled if
Python and extension manager support are enabled, and system Python is
not used.

Revision 23226  View Download Blame
Modified Thu May 22 15:11:21 2014 UTC (3 years, 4 months ago) by pieper
File length: 14894 byte(s)
Diff to previous 23214
BUG: fix failing landmark registration test

Update the remote module to better handle scene events.

Revision 23214  View Download Blame
Modified Tue May 20 15:04:54 2014 UTC (3 years, 4 months ago) by pohl
File length: 14894 byte(s)
Diff to previous 23159
BUG: Expanded vtkSlicerCommonInterfaceTest1.cxx to expose bug that makes multiple tests fail of EMSegmenter

Revision 23159  View Download Blame
Modified Tue May 13 08:52:13 2014 UTC (3 years, 4 months ago) by jcfr
File length: 14894 byte(s)
Diff to previous 23152
BUG: Restore color image support in OpenIGTLinkIF. Fixes #3685

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

Revision 23152  View Download Blame
Modified Tue May 13 03:52:15 2014 UTC (3 years, 4 months ago) by jcfr
File length: 14894 byte(s)
Diff to previous 23144
COMP: Simplify MRML Scene API removing "Edited()" method. Fixes #3472

For sake of consistency, remove Edited method. Indeed, this was the only
event triggered using this approach and it was not observed. For reference,
this method was first introduced by commit r7727.

Revision 23144  View Download Blame
Modified Thu May 8 19:57:12 2014 UTC (3 years, 4 months ago) by finetjul
File length: 14894 byte(s)
Diff to previous 23141
STYLE: Remove error message when loading volume with VTK6

Revision 23141  View Download Blame
Modified Thu May 8 15:16:28 2014 UTC (3 years, 4 months ago) by mwoehlke
File length: 14894 byte(s)
Diff to previous 23138
BUG: Fix force build for Slicer

Replace the 'build depends on always run step' rule for Slicer (which
does not work with at least Ninja) with a rule to remove the stamp for
the build step. This more reliably ensures that the build step for
Slicer is always executed.

Revision 23138  View Download Blame
Modified Thu May 8 04:34:09 2014 UTC (3 years, 4 months ago) by jcfr
File length: 14848 byte(s)
Diff to previous 23136
COMP: Fix unused-local-typedefs warnings

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

Revision 23136  View Download Blame
Modified Wed May 7 17:45:27 2014 UTC (3 years, 4 months ago) by finetjul
File length: 14848 byte(s)
Diff to previous 23122
COMP: Fix EMSegment python wrapping for VTK6

Issue #3514

Revision 23122  View Download Blame
Modified Fri May 2 21:55:04 2014 UTC (3 years, 4 months ago) by finetjul
File length: 14848 byte(s)
Diff to previous 23121
ENH: Add VTK 6 support 2/2

Issue #3514

Revision 23121  View Download Blame
Modified Fri May 2 21:49:48 2014 UTC (3 years, 4 months ago) by finetjul
File length: 14780 byte(s)
Diff to previous 23107
ENH: Add VTK 6 support 1/2

1) Support vtk6 to build system.
http://www.vtk.org/Wiki/VTK/Build_System_Migration
Give users a build option between vtk5 and vtk6.
Solve vtk library python wrapping for VTK 6
Use system zlib (this is a hack)
Use system png (this is a hack)

2) Update dependency projects in superbuild including VTK, CTK, OpenIGTLinkIF, MultiVolumeExplorer.

3) Remove deprecated Macro.
The following two macros were deprecated in VTK 5.0 that were still supported, but have now been eliminated:
vtkTypeRevisionMacro has been replaced with vtkTypeMacro; vtkCxxRevisionMacro has been removed.
http://www.visitusers.org/index.php?title=VTK_6.0_Upgrade

The following two macros were deprecated in VTK 6.0 if VTK_LEGACY_REMOVE is on:
VTK_LARGE_INTEGER and VTK_LARGE_FLOAT
https://github.com/Kitware/VTK/blob/9a0fbb8da1a1701dc1b44c71467b969b3302efad/Common/Core/vtkType.h#L158-159

vtkFloatingPointType is replaced with double.
http://review.source.kitware.com/#/t/1667/

vtkType deprecations
http://www.vtk.org/Wiki/VTK/VTK_6_Migration/vtkType_deprecations

4) Replace SetInput() with SetInputData() and SetInputConnection(), the same kind of functions include SetInput1(), SetInput2(), AddInput() and SetSource().
http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Replacement_of_SetInput

5) Remove GetProducerPort() from vtkDataObject.
http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Removal_of_GetProducerPort

6) Remove Execute
http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Removal_of_Execute

7) Remove SetWholeExtent() from vtkDataObject
http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Removal_of_SetWholeExtent

8) Remove Methods for Manipulating Update Extent
http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Removal_of_Methods_for_Manipulating_Update_Extent

9) Change AllocateOutputData() in vtkImageAlgorithm.
http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Change_to_AllocateOutputData

10) Remove CopyInformation and CopyTypeSpecificInformation from vtkDataObject and vtkImageData.
http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Removal_of_CopyInformation

11) Remove GetPipelineInformation and GetExecutive from vtkDataObject.
http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Removal_of_GetPipelineInformation

12) VTK6 requires #include <vtkVersion.h> to use the VTK_xxx_VERSION preprocessor directives.
http://vtk.org/Wiki/VTK/VTK6/Migration/WikiExamples#Improve

13) Remove Methods for Manipulating Update Extent.
http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Removal_of_Methods_for_Manipulating_Update_Extent.
http://vtk.org/Wiki/VTK/VTK6/Migration/WikiExamples#Improve.

14) Change scalars manipulation functions
http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Changes_to_Scalars_Manipulation_Functions.
http://vtk.org/Wiki/VTK/VTK6/Migration/WikiExamples#Improve.

15) Remove Pipeline Update Methods from vtkDataObject.
http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Removal_of_Update

16) Remove Pipeline Update Methods from vtkDataObject.
http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Removal_of_Update.

17) Refactor functions in vtkMRMLModelNode and sublcasses.

18) Refactor functions in vtkMRMLVolumeNode and its subclasses.
Use ImageDataPort instead of ImageData

Issue #3514

From Yuzheng Zhou <yuzheng.zhou@kitware.com>

Revision 23107  View Download Blame
Modified Thu Apr 17 20:35:11 2014 UTC (3 years, 5 months ago) by jcfr
File length: 13635 byte(s)
Diff to previous 23088
ENH: Update OpenIGTLinkIF SHA1 to add color image support. See #3649

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

Revision 23088  View Download Blame
Modified Fri Apr 11 23:57:15 2014 UTC (3 years, 5 months ago) by jcfr
File length: 13635 byte(s)
Diff to previous 23077
COMP: Fix windows packaging error disabling GitPython and PyGithub

The problem is that the directory structure is too deep. Some path
have a length greater than 260 characters and seems to be an issue
for the CMake install command due to the windows maximum path
length limitation [1]

Waiting this issue is addressed, this commit disables the package on
Windows to ensure packages will be uploaded.

[1] http://msdn.microsoft.com/en-us/library/windows/desktop/aa365247%28v=vs.85%29.aspx#maxpath

Revision 23077  View Download Blame
Modified Fri Apr 11 04:10:41 2014 UTC (3 years, 5 months ago) by jcfr
File length: 13621 byte(s)
Diff to previous 23076
ENH: Remove ITKv3 support

As discussed on the mailing list [1] and reported on the Roadmap [2],
this commit removes all conditional code that was allowing Slicer4 to be
compiled against ITKv3.

Code that was building only against ITKv3 has also been removed. This
includes DicomToNrrdConverter CLI module
and SlicerITKv3N4MRIBiasFieldCorrectionImageFilter class.

[1] http://slicer-devel.65872.n3.nabble.com/Removal-of-ITKv3-support-tt4031364.html

[2] http://wiki.slicer.org/slicerWiki/index.php/Roadmap#Deprecation_.2F_API_Changes

Revision 23076  View Download Blame
Modified Thu Apr 10 18:33:30 2014 UTC (3 years, 5 months ago) by jcfr
File length: 14991 byte(s)
Diff to previous 23067
BUG: Fix gitdb and async build error explicitly setting build environment

In addition to update the install step of these two projects, this commit
also revert commit r23065 that was disabling the build of PyGithub
and GitPython projects.

Revision 23067  View Download Blame
Modified Thu Apr 10 00:58:35 2014 UTC (3 years, 5 months ago) by pieper
File length: 14993 byte(s)
Diff to previous 23065
BUG: fix error condition in LandmarkRegistration

See commit log for info.

Revision 23065  View Download Blame
Modified Wed Apr 9 21:13:48 2014 UTC (3 years, 5 months ago) by jcfr
File length: 14993 byte(s)
Diff to previous 23060
COMP: Disable 'GitPython' and 'PyGithub' waiting build error are fixed.

This is a temporary solution waiting I finish to generalize the system
used to configure/make/install NUMPY. When done, a similar mechanism
will be used to build python modules requiring a build environment / compiler.

Revision 23060  View Download Blame
Modified Tue Apr 8 21:56:17 2014 UTC (3 years, 5 months ago) by jcfr
File length: 14991 byte(s)
Diff to previous 23059
ENH: Do not install EMSegment testing data. See #2397

Revision 23059  View Download Blame
Modified Tue Apr 8 21:15:52 2014 UTC (3 years, 5 months ago) by mwoehlke
File length: 14991 byte(s)
Diff to previous 23058
ENH: Add GitPython and PyGithub external projects

Add external projects for GitPython, PyGithub, and their dependencies
(python-setuptools, python-gitdb, python-async, python-smmap). These are
required for full functionality of the SlicerWizard package.

These are only built if Python and extension manager support are both
enabled, and system Python is not used. Additionally, PyGithub is only
requested if Python SSL support is enabled.

Note that Python must be built with SSL support for PyGithub to be
usable.

Issue #3269

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

Revision 23058  View Download Blame
Modified Tue Apr 8 17:41:15 2014 UTC (3 years, 5 months ago) by jcfr
File length: 14568 byte(s)
Diff to previous 23008
ENH: Associate a component with install rules

Revision 23008  View Download Blame
Modified Wed Mar 19 17:41:09 2014 UTC (3 years, 6 months ago) by lassoan
File length: 14565 byte(s)
Diff to previous 22920
ENH: Several fixes and improvements in transform handling

Major fixes:
* Added mechanism to prevent immediate invocation of TransformModified events (similarly to Modified events) to allow atomic changes of transforms and prevent multiple event invocations (fixes #3610, #3611).
* Fixed vtkITKBSplineTransform inverse computation (the bulk component was ignored in the inverse computation due to a shadow variable)
* Fixed DeepCopy of vtkITKBSplineTransform.cxx (InternalDeepCopy method had to be implemented)
* Use vtkTransform's ability to compute inverse transforms instead of keeping separate transforms for forward and inverse transforms (still kept the two member variables in the transform node base class to allow storing of forward and inverse transform if they are both computed, e.g., some Demons registration provides both the forward and inverse transforms as outputs).
* Fixed ReadWriteAsTransformToParent logic in the storage node class (as inverse warp transforms usually cannot be written, the flag should point to the forward transform class). For convenience, the flag is updated automatically when a To/FromParentTransform is set in the transform node.
* Fixed transform node copy: now a true deep copy is performed (earlier only the pointer of the transforms were copied, therefore changing a transform in a node changed the copied node, too)
* Removed vtkMRMLNonlinearTransformNode, as non-linear transforms are not special cases anymore: the base transform class can manage them the same way as linear transforms.
* Changed Get/SetMatrixTransformToParent and Get/SetMatrixTransformFromParent method to make it clear that it makes a copy of the input and output, so changing a matrix is only possible by using the Set... method (and not Get...()->DeepCopy(...)). Kept the old functions to prevent build errors, but they are deprecated and a warning is logged if they are used (as the behavior of the Get... function is changed from a shallow copy to a deep copy). This API change required changing of a lot of file in the Slicer core and extensions.

Minor fixes:
* Made vtkMRMLTransformNode non-abstract: this is the class that can handle arbitrarily complex composite transforms (e.g., grid transform hardened on a bspline transform).
* Fixed invalid NonLinearTransformScene.mrml scene: wrong storage node ref ID caused warnings in the tests
* Changed the Bspline-f-m.tfm test data to include larger bulk component to make errors more detectable
* Added tests for composite transforms (e.g., hardened combination of grid and bspline transform)
* Split the transform node's huge read/write methods to separate smaller methods (one for each transform type)
* Added the option of loading a .mha file as a grid transform

Extensions updated according to the API change: OpenIGTLinkIF, SlicerIGT, SlicerRT, and TransformVisualizer. See details at:
https://github.com/openigtlink/OpenIGTLinkIF/pull/25
https://github.com/SlicerIGT/FiducialRegistrationWizard/pull/14
https://github.com/SlicerIGT/BreachWarning/pull/1
https://github.com/SlicerIGT/PivotCalibration/pull/13
https://github.com/SlicerIGT/TransformFusion/pull/2
https://www.assembla.com/spaces/slicerrt/tickets/563

Tests performed:

* All automatic tests passed (except those that are known to fail in the nightly builds)

* Load MRBrainTumor1 & MRBrainTumor2 sample
* Create model of MRBrainTumor2, threshold=50
* Linear registration with BRAINS (fixed: MRBrainTumor1 & moving: MRBrainTumor2)
* VERIFY: the resampled output image should look the same as the dynamically transformed moving volume, checked on several slices
* Save the transform as tfm from file, load the transform from file, apply the transform to the moving image
* VERIFY: the resampled output image should look the same as the dynamically transformed moving volume
* Apply transform to the model
* VERIFY: model is deformed in the 3D view, aligned with the volume slices
* Harden transform to the model
* VERIFY: model in the 3D view doesn’t change, model slice intersections are aligned with the volume
* Harden the transform on the volume
* VERIFY: the image doesn’t change too much

* BSpline registration with BRAINS (fixed: MRBrainTumor1 & moving: MRBrainTumor2)
* VERIFY: the resampled output image should look the same as the dynamically transformed moving volume
* Save the transform as tfm from file, load the transform from file, apply the transform to the moving image
* VERIFY: the resampled output image should look the same as the dynamically transformed moving volume
* Apply transform to the model
* VERIFY: model is deformed in the 3D view, aligned with the volume slices
* Harden transform to the model
* VERIFY: model in the 3D view doesn’t change, model slice intersections are aligned with the volume
* Insert linear transform between bspline and volume, move sliders
* VERIFY: volume deforms as it travels through the BSpline region
* Harden the transform on the volume
* VERIFY: the image doesn’t change too much

* Create a two markup list (each having 15 points), all but 3 in the same position
* Landwarp registration with Plastimatch with the markup lists, save the displacement field to file
* Load the displacement field
* VERIFY: the resampled output image should look the same as the dynamically transformed moving volume
* Apply the displacement field to the moving fiducials
* VERIFY: all the fiducials are now in the same position
* Harden the transform on the fiducials
* VERIFY: the fiducials don’t move
* Apply transform to the model
* VERIFY: model is deformed in the 3D view, aligned with the volume slices
* Harden transform to the model
* VERIFY: model in the 3D view doesn’t change, model slice intersections are aligned with the volume
* Harden the transform on the volume
* VERIFY: the image doesn’t change too much

* Load MRI head, create new linear transform, apply to the volume, move the sliders
* VERIFY: the volume moves in the slice viewer, the numbers change in the matrix
* Click Invert, Identity
* VERIFY: volume jumps to other side, to the center
* Connect to an OpenIGTLink server, apply a transform to a volume
* VERIFY: transform matrix values updated in transforms module, volume moves

Revision 22920  View Download Blame
Modified Tue Mar 4 04:40:37 2014 UTC (3 years, 6 months ago) by fedorov
File length: 14565 byte(s)
Diff to previous 22917
BUG: fix interactive plotting feature

The feature was broken by the changes in SliceLayerLogic API:

https://github.com/Slicer/Slicer/commit/40f74cdf870f213847f77b86351032c7869762d3#diff-228dc8288779dec5ad07baedef604899

Revision 22917  View Download Blame
Modified Mon Mar 3 14:38:14 2014 UTC (3 years, 6 months ago) by jcfr
File length: 14565 byte(s)
Diff to previous 22908
ENH: Adding SimpleITK Python threading, and progress/abort to SimpleFilters

Enabling SimpleITK Python threading. This unlock the Python GIL while
inside C++ code in ITK, while still having safe commands on events.

Updated SimpleFilters with support for SimpleITK 0.8rc1, and adding a
progress bar and abort button.

$ git log --oneline 3bc2fdc5ca5c72b3fbfc596213eecf89cec31b32..
c939ce0 Update to use namespace KernelEnum types for morphology
34e55c9 Verify the update-sitk update branch does not exist before json update
5cb03ef Merge branch 'sitk-upstream'
f46c414 SimpleITK 9f758175 Filter descriptions (reduced)
18db32e Adding Cancel button to abort filter processing.
757d0fe Adding ProgressBar and SimpleITK events

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

Revision 22908  View Download Blame
Modified Wed Feb 26 21:37:40 2014 UTC (3 years, 6 months ago) by pieper
File length: 14565 byte(s)
Diff to previous 22907
ENH: update the versions of CompareVolumes and LandmarkRegistration

Improved plugin support for plastimatch (SlicerRT) and also improved
visualization via the RevealCursor and Rock modes.

Also fix the tests by selecting the module at the start of the
test (when running as a self test slicer starts with the default
module).

Revision 22907  View Download Blame
Modified Wed Feb 26 19:25:38 2014 UTC (3 years, 6 months ago) by jcfr
File length: 14565 byte(s)
Diff to previous 22902
COMP: Simplify how BRAINSTools project options are specified

Source repository, revision and associated CMake options are not
all set in a single location.

Revision 22902  View Download Blame
Modified Tue Feb 25 22:53:02 2014 UTC (3 years, 6 months ago) by jcfr
File length: 12623 byte(s)
Diff to previous 22892
ENH: Update tag for OpenIGTLinkIF in response to issue #3596.

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

Revision 22892  View Download Blame
Modified Fri Feb 21 01:11:21 2014 UTC (3 years, 7 months ago) by jcfr
File length: 12623 byte(s)
Diff to previous 22857
COMP: Update OpenIGTLinkIF to fix TDATA segfault

For reference, see:

  https://github.com/openigtlink/OpenIGTLinkIF/pull/23

and

  https://github.com/SlicerIGT/OpenIGTLinkRemote/issues/18

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

Revision 22857  View Download Blame
Modified Tue Feb 4 15:17:14 2014 UTC (3 years, 7 months ago) by pieper
File length: 12623 byte(s)
Diff to previous 22844
ENH: Updating SimpleFilter remote module

This updates adds a check box to set output as LabelMap, A Restore
defaults button, and print of filter to be run in python code to set
filter.

$ git log --oneline fc1f06..3bc2f
3bc2fdc Adding button "Restore" defaults
0d27412 ENH: improving responsiveness of main_queue_process
51d14b7 STYLE: move apply bottom to match CLI interface
49ec882 ENH: print object oriented python code to create filter before running
5d0a528 ENH: When a labelmap input is selected the output changes to labelmap
aa7ddc5 Update node selector and checkbox with LabelMap state
d4a5116 move output box and labelmap checkbox to self variables
648f736 Adding CheckBox to set output volume as label map

Revision 22844  View Download Blame
Modified Thu Jan 23 18:58:54 2014 UTC (3 years, 8 months ago) by fedorov
File length: 12623 byte(s)
Diff to previous 22843
ENH: set the multivolume loadable name as requested by the caller

Revision 22843  View Download Blame
Modified Thu Jan 23 17:14:31 2014 UTC (3 years, 8 months ago) by fedorov
File length: 12623 byte(s)
Diff to previous 22835
BUG: fix incorrect function name in MultiVolumeImporter

Revision 22835  View Download Blame
Modified Sat Jan 18 18:24:45 2014 UTC (3 years, 8 months ago) by fedorov
File length: 12623 byte(s)
Diff to previous 22815
ENH: use a sort procedure based on numbers instead of alphanumeric. Fixes issue
3487. Fix contributed by Yanlling Liu.

Revision 22815  View Download Blame
Modified Sun Jan 12 20:24:38 2014 UTC (3 years, 8 months ago) by pieper
File length: 12623 byte(s)
Diff to previous 22792
ENH: Add 'pydicom' python module as external project.

"pydicom is a pure python package for working with DICOM files. It
was made for inspecting and modifying DICOM data in an easy "pythonic"
way. The modifications can be written again to a new file. As a pure
python package, it should run anywhere python runs without any other
requirements.

pydicom is not a DICOM server, and is not primarily about viewing
images. It is designed to let you manipulate data elements in DICOM
files with python code.

Limitations -- the main limitation of the current version is that
compressed pixel data (e.g. JPEG) cannot be altered in an intelligent
way as it can for uncompressed pixels. Files can always be read and
saved, but compressed pixel data cannot easily be modified."
See http://code.google.com/p/pydicom/

The module being licensed under MIT license, it is compatible with
the Slicer BSD like license.

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

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

Revision 22792  View Download Blame
Modified Tue Dec 31 22:21:06 2013 UTC (3 years, 8 months ago) by pieper
File length: 12503 byte(s)
Diff to previous 22787
ENH: update LandmarkRegistration to support RegistrationPlugins

Still some work to do on the built-in plugins, but the framework
is now in place for extensions (like SlicerRT/Plastimatch) to provide
registration plugins.

Affine registration is now a plugin and it works like the previous
version of LandmarkRegistration which supported only Affine.

Revision 22787  View Download Blame
Modified Wed Dec 18 21:40:09 2013 UTC (3 years, 9 months ago) by jcfr
File length: 12503 byte(s)
Diff to previous 22786
ENH: Add 'DataStore' to top-level module category.

Revision 22786  View Download Blame
Modified Wed Dec 18 15:30:42 2013 UTC (3 years, 9 months ago) by fedorov
File length: 12503 byte(s)
Diff to previous 22785
BUG: check that the frame image has been initialized

Fixes #3535

Revision 22785  View Download Blame
Modified Tue Dec 17 23:42:15 2013 UTC (3 years, 9 months ago) by pieper
File length: 12503 byte(s)
Diff to previous 22780
ENH: Add prototype LandmarkRegistration and CompareVolumes modules

These are still work-in-progress modules, but should be usable to
support interatcive registration.

See https://github.com/pieper/LandmarkRegistration

Revision 22780  View Download Blame
Modified Tue Dec 17 10:36:40 2013 UTC (3 years, 9 months ago) by jcfr
File length: 11725 byte(s)
Diff to previous 22776
COMP: Add DataStore module as remote module.

See [1] for details about remote module.

Fixes #3400

[1] http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Build_system/Remote_Module

Revision 22776  View Download Blame
Modified Tue Dec 17 06:07:46 2013 UTC (3 years, 9 months ago) by jcfr
File length: 11422 byte(s)
Diff to previous 22773
COMP: Easier maintenance simplifying process to add remote module source

Following this commit, adding a remote module source to Slicer can
simply be done calling:

 Slicer_Remote_Add(Foo
   GIT_REPOSITORY git://github.com/john/foo
   GIT_TAG abcdef
   OPTION_NAME Slicer_BUILD_Foo
   LABELS REMOTE_MODULE
   )

As a side effect, (1) the option "Slicer_BUILD_Foo" will automatically be
added as an advanced option and (2) the CMake variables "Slicer_BUILD_Foo"
and "Foo_SOURCE_DIR" will be passed to Slicer inner build.

Additionally, by associating the "REMOTE_MODULE" label, the corresponding
source directory will be added automatically using a call 'add_directory'
similar to this one:

 add_directory(
   /path/to/Slicer-build/Foo
   /path/to/Slicer-build/Slicer-build/Module/Remote/Foo)

This happen in the Slicer/Modules/Remote/CMakeLists.txt file.

Finally, note that a new module named "ExternalProjectAddSource" has been
added, it is still experimental and should be considered as
internal to Slicer without any promise to keep backward compatibility.

Revision 22773  View Download Blame
Modified Sun Dec 15 08:02:44 2013 UTC (3 years, 9 months ago) by jcfr
File length: 8712 byte(s)
Diff to previous 22756
COMP: Simplify external project includes & passing of CMake vars to project

A new module named "ExternalProjectDependency" has been introduced, it is
equivalent to the Artichoke module at revision commontk/Artichoke@70ed903.

This new module is now used within Slicer to support its build system. To
maintain backward compatibility with existing extensions, the modules
"SlicerMacroEmptyExternalProject" and "SlicerMacroCheckExternalProjectDependency"
are kept around.

Revision 22756  View Download Blame
Modified Tue Dec 3 22:09:36 2013 UTC (3 years, 9 months ago) by jcfr
File length: 18094 byte(s)
Diff to previous 22747
COMP: Add Slicer_ADDITIONAL_REQUIRED_QT_MODULES to add QT modules

 * Manually prefix the modules because some modules (e.g. PHONON) may not
have the "QT" prefix.
 * Synchronize the required modules with the packaged modules

From: Julien Finet <julien.finet@kitware.com>

Revision 22747  View Download Blame
Modified Fri Nov 29 06:10:29 2013 UTC (3 years, 9 months ago) by jcfr
File length: 17775 byte(s)
Diff to previous 22746
COMP: For consistency rename OpenSSL_* variables into OPENSSL_*

Revision 22746  View Download Blame
Modified Fri Nov 29 06:10:26 2013 UTC (3 years, 9 months ago) by jcfr
File length: 17778 byte(s)
Diff to previous 22740
COMP: Fix OpenSSL install rules

Commit r22724 updated the External_* project files to support
Slicer_USE_SYSTEM_* variables. For sake of consistency, it also
changed variable "EP_OpenSSL_LIBRARIES" into "OPENSSL_LIBRARIES".
Since not all variables have been updated, this commit updates
the remaining variables to fix the OpenSSL install rules.

Revision 22740  View Download Blame
Modified Tue Nov 26 05:37:17 2013 UTC (3 years, 10 months ago) by jcfr
File length: 17781 byte(s)
Diff to previous 22739
COMP: Optionally configure Slicer inner project with OpenSSL options.

This is needed because following commit r22734 RemoteIO library is
linked against OpenSSL.

Revision 22739  View Download Blame
Modified Tue Nov 26 01:05:59 2013 UTC (3 years, 10 months ago) by jcfr
File length: 17258 byte(s)
Diff to previous 22728
COMP: External_curl: Fix build issue + Build against patched 7.34.0 release

This commit install the project so that all needed headers are all
in the same folder.

It also change the version of curl to 7.34.0 with an additional patch
adding CURL_STATICLIB to curlbuild.h to fix build issue on windows
and unix system.

Finally, it reverts r22728 which was incorrectly addressing the build
error described in the corresponding commit message.

Revision 22728  View Download Blame
Modified Mon Nov 25 03:48:44 2013 UTC (3 years, 10 months ago) by jcfr
File length: 17514 byte(s)
Diff to previous 22726
COMP: Fix MacOSX RemoteIO build error by building against system CURL

Trying to build against our own version of curl end up in a mixing
of headers causing a build error:

// ---------------
In file included from /Developer/SDKs/MacOSX10.6.sdk/usr/include/curl/curl.h:43,
                 from /Users/kitware/Dashboards/Continuous/Slicer4/Libs/RemoteIO/vtkHTTPHandler.h:8,
                 from /Users/kitware/Dashboards/Continuous/Slicer4/Libs/RemoteIO/vtkHTTPHandler.cxx:1:
/Users/kitware/Dashboards/Continuous/Slicer4-build-64bits-QT4.8.5-PythonQt-With-Tcl-CLI-Release-continuous/curl-build/include/curl/curlbuild.h:151: error: 'socklen_t' does not name a type
In file included from /Developer/SDKs/MacOSX10.6.sdk/usr/include/curl/curl.h:44,
                 from /Users/kitware/Dashboards/Continuous/Slicer4/Libs/RemoteIO/vtkHTTPHandler.h:8,
                 from /Users/kitware/Dashboards/Continuous/Slicer4/Libs/RemoteIO/vtkHTTPHandler.cxx:1:
/Developer/SDKs/MacOSX10.6.sdk/usr/include/curl/curlrules.h:174: error: 'curl_socklen_t' was not declared in this scope
/Developer/SDKs/MacOSX10.6.sdk/usr/include/curl/curlrules.h:184: error: 'curl_socklen_t' was not declared in this scope
// ---------------

While not providing a definite explanation regarding the root cause of
the problem, we circumvent it by building against the system version
of the library.

See #1739

Revision 22726  View Download Blame
Modified Sun Nov 24 20:40:51 2013 UTC (3 years, 10 months ago) by jcfr
File length: 17258 byte(s)
Diff to previous 22724
COMP: Consistently pass LibArchive parameters when configuring Slicer

This will ensure LibArchive is properly found.

See #1739

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

Revision 22724  View Download Blame
Modified Sun Nov 24 08:09:34 2013 UTC (3 years, 10 months ago) by jcfr
File length: 17264 byte(s)
Diff to previous 22721
COMP: Support Slicer_USE_SYSTEM_* option. Fixes #1739

This commit implements four main changes:

  (1) it updates Slicer build system to support configuring Slicer passing
      Slicer_USE_SYSTEM_* CMake variables

  (2) it updates to a newer version of CTK able to understand CTK_USE_SYSTEM_*
      options. List of CTK contribution associated with this update are
      reported below.

  (3) it changes curl library from "slicerlibcurl/cmcurl/curl" v7.12.1
      to the more recent official CMake'ified curl v7.33.0. This has the
      benefit of making it easier to build against the corresponding
      system library.

  (4) It implements workaround allowing some CLIs to built on Debian-like
      distribution that is providing DCMTK 3.6.0.
      See http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=637687
      EMSegment project has also been updated to implement a similar
      workaround.

The macro "SlicerMacroCheckExternalProjectDependency" allowing to
recursively traverse the external project dependency tree has been
updated.

The traversal is now done in two passes. The first pass traverses the
complete tree to set the value of Slicer_USE_SYSTEM_*.

The second pass invokes the "ExternalProject_Add" function and displays
informative messages. In addition to the usual "[OK]" and "[INCLUDED]"
suffixes, an additional text "(SYSTEM)" is displayed. It means the
corresponding libraries (and headers) installed on the system will be
used.

On Ubuntu 13.10, support for the following options have been
tested simultaneously:
  -DSlicer_USE_PYTHONQT_WITH_OPENSSL:BOOL=ON
  -DSlicer_USE_SYSTEM_python:BOOL=ON
  -DSlicer_USE_SYSTEM_DCMTK:BOOL=ON
  -DSlicer_USE_SYSTEM_LibArchive:BOOL=ON
  -DSlicer_USE_SYSTEM_curl:BOOL=ON
  -DSlicer_USE_SYSTEM_teem:BOOL=ON
  -DSlicer_USE_SYSTEM_OpenIGTLink:BOOL=ON
  -DSlicer_USE_SYSTEM_OpenSSL:BOOL=ON # Implicitly set because python depends
                                      # on OpenSSL.
  -DSlicer_BUILD_OpenIGTLinkIF:BOOL=OFF # Only openigtlink version1 are available
                                        # and code does NOT supports only v2.

To successfully build Slicer against system libraries, the corresponding
packages have been installed:
  sudo apt-get install libssl-dev \
    libdcmtk-dev \
    libarchive-dev \
    libpython2.7-dev \
    python-numpy \
    libcurl4-openssl-dev \
    libteem-dev \
    tk-dev \
    tcl-dev \
    itcl3-dev \
    libopenigtlink1-dev

While not tested, support for the following option has also been
implemented:
  -DSlicer_USE_SYSTEM_ITKv4:BOOL=ON
  -DSlicer_USE_SYSTEM_VTK:BOOL=ON

CTK updates:

$ git shortlog  91cdf9e0f...02ecc27d0

Jean-Christophe Fillion-Robin (39):
      Ensure CTK_INSTALL_QTPLUGIN_DIR is properly set
      Ensure "CMAKE_INSTALL_PREFIX" is properly passed to inner project.
      By default, do not install application headers
      Install CTK's *.cmake files
      Merge branch '65-packaging-support' into 403-relocatable-ctkconfig-usectk
      Set plugin install rules for target and include files
      Remove commented code and unused vars from CTKConfig / CTKGenerateCTKConfig
      Explicitly set default value for CTK_INSTALL_QTPLUGIN_DIR
      Remove explicit setting of CMake policies.
      Improve FindDCMTK.cmake documentation
      Add DCMTK 3.6.0 support to ctkDICOMUtil.cpp
      Ensure DCMTK libraries can be found on system without setting DCMTK_DIR
      FindDCMTK - Workaround bug in packaging of DCMTK 3.6.0 on Debian.
      Add support for install-able and relocatable package.
      Merge branch '382-fix-find-dcmtk-issue'
      Merge branch '403-relocatable-ctkconfig-usectk'
      Merge branch '405-support-dcmtk-360'
      Fix -Wunused-but-set-variable in transfer function tests
      Merge branch '209-fix-vtk-transfer-function-test-warnings'
      Fix linking of VTKCoreCppTest by adding a check for linker capabilities
      Merge branch 'fix-vtk-core-test-link-error'
      COMP: FindDCMTK - Exclude -D from DCMTK_DEFINITIONS for easier re-use
      Merge branch '382-fix-find-dcmtk-issue'
      Associate DCMTK_DEFINITIONS to CTKDICOMCore
      Merge branch '413-associated-dcmtk-definitions-to-ctkdicomcore'
      Merge pull request #410 from NifTK/409-widgets-on-ctkPopupWidget-do-not-get-keyboard-focus
      Add DCMTK 3.6.0 support to CTK application.
      Merge branch '405-support-dcmtk-360'
      Fix configuration of CTKConfig based on DCMTK_HAVE_CONFIG_H_OPTIONAL value
      Merge branch '413-associated-dcmtk-definitions-to-ctkdicomcore'
      Add convenience function "ctk_list_to_string"
      Automatically reformat list passed to "CTK" inner build.
      COMP: Add support for CTK_USE_SYSTEM_* options
      Merge branch '418-support-use-system-option'
      FindDCMTK - Do not explicitly set DCMTK_DEFINITIONS
      FindDCMTK - Clean white spaces
      Merge branch '382-fix-find-dcmtk-issue' into 413-associated-dcmtk-definitions-to-ctkdicomcore
      Associate CTKDICOMCore with DCMTK_DEFINITIONS in build and install tree
      Merge branch '413-associated-dcmtk-definitions-to-ctkdicomcore'

Miklos Espak (1):
      Active window flag transferred on RequestSoftwareInputPanel event

Steve Pieper (2):
      Put all tags for a given instance into a list for a single batch insert
      Merge pull request #415 from pieper/414-batch-insert-tags

See #1739

Revision 22721  View Download Blame
Modified Sun Nov 24 08:09:12 2013 UTC (3 years, 10 months ago) by jcfr
File length: 16354 byte(s)
Diff to previous 22718
COMP: ExternalProject - Rename zlib variables with slicer independent name

Revision 22718  View Download Blame
Modified Sun Nov 24 08:09:03 2013 UTC (3 years, 10 months ago) by jcfr
File length: 16375 byte(s)
Diff to previous 22706
COMP: ExternalProject - Rename python variables with a slicer independent name

Revision 22706  View Download Blame
Modified Fri Nov 15 02:56:47 2013 UTC (3 years, 10 months ago) by finetjul
File length: 16392 byte(s)
Diff to previous 22375
COMP: Propagate cmake variable Slicer_QTSCRIPTEDMODULES_DISABLED

to the Slicer inner build configuration.

It originally was a typo: eq_superbuild_extra_args instead of
ep_superbuild_extra_args which was latter replaced into
EXTERNAL_PROJECT_OPTIONAL_ARGS

Revision 22375  View Download Blame
Modified Sat Aug 31 02:32:38 2013 UTC (4 years ago) by jcfr
File length: 16386 byte(s)
Diff to previous 22220
COMP: Suggest "insteadof" git config only for ITKv3.

Since ITKv4 doesn't use submodule (see fab42d0ef) it only applies to ITKv3.

Fixes #2751

Revision 22220  View Download Blame
Modified Sat Jul 20 02:16:35 2013 UTC (4 years, 2 months ago) by jcfr
File length: 16337 byte(s)
Diff to previous 22201
ENH: Add SSL support

Having the application interacting with services or downloading resources
served over https protocol is now required. More particularly,
it became necessary to access resources stored on Github (extension
manager - issue #2354) or to download python packages from pip server
at run time.

The CMake option "Slicer_USE_PYTHONQT_WITH_OPENSSL" allowing to enable or
disable OpenSSL support has been introduced is set to OFF by default.

Building OpenSSL
================

On Windows, since Perl is required, OpenSSL binaries have been
generated and uploaded on kitware packages server. See [1]

The project allowing to re-generate the Windows OpenSSL archive is currently
hosted here [2].

On unix-like system, OpenSSL is built has part of the Superbuild. To ensure
is can be built in parallel, a patch is also applied [3].

Finally, since python is built with OpenSSL support, the python launcher
is now configured on all platform so that python can properly load the built
OpenSSL shared library when it is used to build project like numpy.

[1] http://packages.kitware.com/packages/application/view?applicationId=20
[2] https://gist.github.com/jcfr/6030240
[3] https://raw.github.com/Alexpux/Qt-builds/master/patches/openssl/openssl-1.0.1-parallel-build.patch

OpenSSL support in Qt, python, curl
===================================

Practically, it means that library like Qt, python, curl need to be
built with OpenSSL support.

This commit only address OpenSSL support for Python and Qt.

Curl support is not yet enabled.

For Qt OpenSSL support, Qt has to be built with the flags:
  -openssl
  -I /path/to/OpenSSL/include
  -L /path/to/OpenSSL/lib

On unix-like system, available binaries are already OpenSSL ready, Qt
has to be explicitly built only on windows. On windows, Qt will have to
be built.

Certificates
============

In case X.509v3 certificates are available on the system where Slicer is
executed, a certificate bundle "Slicer.crt" is also provided. The set of
scripts allowing to generate the bundle are provided by BLFS
(Beyond Linux From Scratch).
More details in Base/QTCore/Resources/Certs/README

Application integration
=======================

The Slicer core application will load the Slicer.crt bundle if needed.

qSlicerExtensionsInstallWidget now derives from a re-usable widget
named qSlicerWebWidget.

qSlicerSslTest has been added to check that "https" connection can
be established using Qt library.

Fixes #2998
Fixes #2355
Fixes #2354

Revision 22201  View Download Blame
Modified Tue Jul 16 19:52:28 2013 UTC (4 years, 2 months ago) by jcfr
File length: 16018 byte(s)
Diff to previous 22133
ENH: adding SimpleFilters as internal modules via externalproject

Following the example of MultiVolumeImporter, a new external project
was added to download the SimpleFilters repository, the source
directory is propagated into the Slicer project and it is added as a
sub-directory to the build in scripted modules.

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

Revision 22133  View Download Blame
Modified Wed Jul 3 22:12:40 2013 UTC (4 years, 2 months ago) by jcfr
File length: 15783 byte(s)
Diff to previous 22118
COMP: Adding option for SimpleITK as a shared library

SimpleITK has large internal libraries, which take an extremely long
time to link on windows when they are static. Creating shared
SimpleITK internal libraries can reduce linking time. Also the size
of the debug libraries are monstrous. Using shared libraries for
debug, reduce disc requirements, and can improve linking
times. However, these shared libraries take longer to load than the
monolithic target from static libraries.

This commits updates the build system:
1) Propagate SimpleITK_DIR into Slicer config.
2) Add SimpleITK lib path to runtime library path for build.
3) Add SimpleITK to be installed as a cmake project.
4) Add CMake variable Slicer_USE_SimpleITK_SHARED to turn on SimpleITK
as a shared library.

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

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

Revision 22118  View Download Blame
Modified Fri Jun 21 14:29:17 2013 UTC (4 years, 3 months ago) by finetjul
File length: 15623 byte(s)
Diff to previous 22029
COMP: Pass Slicer_PLATFORM_CHECK to inner build

Otherwise, if Slicer_PLATFORM_CHECK is OFF at the superbuild level,
the variable is not defined in the inner build, and automatically set to
ON by SlicerBlockPlatformCheck.cmake

Revision 22029  View Download Blame
Modified Wed May 22 22:02:30 2013 UTC (4 years, 4 months ago) by jcfr
File length: 15599 byte(s)
Diff to previous 22026
COMP: Use qRestAPI instead of deprecated qMidasAPI project

In addition to provide Midas support, qRestAPI also provides
support for XNat (qXnatAPI.h)

See https://github.com/commontk/qRestAPI

Revision 22026  View Download Blame
Modified Mon May 20 02:16:03 2013 UTC (4 years, 4 months ago) by jcfr
File length: 15602 byte(s)
Diff to previous 21997
COMP: Simplify external project removing CMake 2.8.8 compatibility

Revision 21997  View Download Blame
Modified Tue May 14 22:29:23 2013 UTC (4 years, 4 months ago) by jcfr
File length: 16040 byte(s)
Diff to previous 21996
COMP: Fix unused CMake variable warning related to DOCUMENTATION_* variable

Revision 21996  View Download Blame
Modified Tue May 14 22:29:21 2013 UTC (4 years, 4 months ago) by jcfr
File length: 15918 byte(s)
Diff to previous 21995
COMP: Fix CMake warning related to WITH_MEMCHECK CMake variable

Commented the variable waiting the build system is updated to support
running of the test using valgrind.

Revision 21995  View Download Blame
Modified Tue May 14 22:29:20 2013 UTC (4 years, 4 months ago) by jcfr
File length: 15917 byte(s)
Diff to previous 21989
COMP: Remove unused Slicer superbuild boolean variable

The variable "Slicer_BUILD_Extensions" originally introduced
by commit r21550 is not used.

Revision 21989  View Download Blame
Modified Tue May 14 18:50:19 2013 UTC (4 years, 4 months ago) by jcfr
File length: 15943 byte(s)
Diff to previous 21963
COMP: Consistently specify optional external project CMake arguments

Easier maintenance of the build system by using the variable
"EXTERNAL_PROJECT_OPTIONAL_ARGS" to accumulate optional CMake arguments.

Revision 21963  View Download Blame
Modified Wed May 1 04:45:20 2013 UTC (4 years, 4 months ago) by jcfr
File length: 16186 byte(s)
Diff to previous 21960
COMP: Use internally consistent zlib

The zlib libraries are used by many differnt packages
includeing ITKv4, LibArchive, VTK, python, and teem.

This patchset builds a single version of zlib
that is mangled with a slicer namespace, and uses
that one library for all zlib operation through the
"USE_SYSTEM_ZLIB" options.

The mangling for vtk_zlib is disabled for teem because
it is not needed when using the External_zlib build.

From: Hans Johnson <hans-johnson@uiowa.edu>

Revision 21960  View Download Blame
Modified Wed May 1 03:34:50 2013 UTC (4 years, 4 months ago) by jcfr
File length: 16028 byte(s)
Diff to previous 21849
COMP: Remove python patch step related to "dll boundaries" hack

As explained in r21863, patching pythonrun.h and pythonrun.c was
required to prevent crash (related to dll boundaries [1][2]) when
building Slicer debug against a released python.

[1] http://stackoverflow.com/questions/2322095/why-does-this-program-crash-passing-of-stdstring-between-dlls
[2] http://social.msdn.microsoft.com/Forums/en-US/vcgeneral/thread/57e0d522-a42c-4add-963d-c87c6e76f161

Applying the approach discussed on the Blender mailing list[3], the
hack is not required anymore. This is made possible by using
"PyRun_String" function combined with the "execfile" statement.

[3] http://lists.blender.org/pipermail/bf-python/2008-May/005253.html

When transitioning to Python3 [4], use of "exec" and "compile" could be
considered:

  with open('foo.py', 'r') as fh:
    code = compile(fh.read(), 'foo.py', 'exec'); exec(code);

[4] http://stackoverflow.com/questions/436198/what-is-an-alternative-to-execfile-in-python-3-0

Approach making use of the "imp"  module could also be investigated [5][6]

[5] http://www.ragestorm.net/blogs/?tag=execfile
[6] http://docs.python.org/2/library/imp.html

Finally, let's note that overall approach to load module could be
revised to prevent side effect as the one described in
"qSlicerScriptedFileDialog::setPythonSource"

Revision 21849  View Download Blame
Modified Fri Mar 29 02:18:07 2013 UTC (4 years, 5 months ago) by jcfr
File length: 16073 byte(s)
Diff to previous 21848
COMP: Fix DCMTK build error using a working implementation of DCMTKConfig.cmake

For details: See https://github.com/commontk/DCMTK/commit/f461865d1759854db56e4c840991c81c77e45bb9

Revert commits r21842, r21841

Revision 21848  View Download Blame
Modified Fri Mar 29 02:15:04 2013 UTC (4 years, 5 months ago) by jcfr
File length: 16221 byte(s)
Diff to previous 21842
COMP: Add HAVE_PYRUN_{CLOSE, OPEN}FILE anticipating build against system python

Anticipating the possibility to build Slicer against a system python,
introduced variable HAVE_PYRUN_CLOSEFILE and HAVE_PYRUN_OPENFILE variable
to be able to conditionally build Slicer library with fopen/fclose
built-in the python library.

Revision 21842  View Download Blame
Modified Tue Mar 26 21:30:48 2013 UTC (4 years, 6 months ago) by hjohnson
File length: 16176 byte(s)
Diff to previous 21839
COMP: Fix pathing bug in packaging

For the preferred directory for DCMTK install packages and
DCMT_DIR are not consistent.  THis patch passes the correct pathing
to the bin directory needed for packaging.

Revision 21839  View Download Blame
Modified Sun Mar 24 21:05:57 2013 UTC (4 years, 6 months ago) by hjohnson
File length: 16028 byte(s)
Diff to previous 21791
ENH: Updates for BRAINSTools and ITKv4

This is a set of updates to try to address reported
issues with 32bit windows builds related to the new
double-convert to ASCII functionality.

Worked with ITKv4 team (Bill Lorensen and Kent Williams mostly) to
add the DoubleConversion featues directly to ITKv4.  This simplyfies
adding this functionality to other tools (like BRAINSTools, Slicer,
ANTs, etc..), and also provides more extensive testing of ITKv4.

Revision 21791  View Download Blame
Modified Tue Mar 12 11:20:05 2013 UTC (4 years, 6 months ago) by jcfr
File length: 16114 byte(s)
Diff to previous 21790
COMP: Fix double-convert external project so that it works as intended

1) The previous version was working because the double-conversion project
was exporting its build tree in the cmake package registry.

See http://www.cmake.org/cmake/help/v2.8.10/cmake.html#command:export

Since the package was exported, the find_package(double-conversion ..) within
BRAINSTools was working. Line like the following weren't not used at all:

  list(APPEND ${CMAKE_PROJECT_NAME}_SUPERBUILD_EP_VARS ${extProjName}_DIR:PATH)

2) Remove dependency to DCMTK. See https://github.com/BRAINSia/BRAINSTools/issues/5

Revision 21790  View Download Blame
Modified Tue Mar 12 03:00:06 2013 UTC (4 years, 6 months ago) by hjohnson
File length: 16042 byte(s)
Diff to previous 21775
COMP:  DoubleConvert needs to be included

In order to build BRAINSTools, the External_DoubleConvert.cmake needs
to be built prior to building the BRAINSTools.

Revision 21775  View Download Blame
Modified Sun Feb 24 20:38:50 2013 UTC (4 years, 7 months ago) by jcfr
File length: 16028 byte(s)
Diff to previous 21722
COMP: Fix warning "Slicer_BUILD_SkullStripper" is unused.

The option has been added by r18797, then when SkullStripper
has been converted to be a regular extension (r20088) the variable
"Slicer_BUILD_SkullStripper" should have been removed from SuperBuild.cmake.

Revision 21722  View Download Blame
Modified Sat Feb 16 02:38:39 2013 UTC (4 years, 7 months ago) by jcfr
File length: 16057 byte(s)
Diff to previous 21667
COMP: Remove build system option related to ChangeTracker

Follow up of commit r21716

Revision 21667  View Download Blame
Modified Thu Feb 7 15:24:55 2013 UTC (4 years, 7 months ago) by jcfr
File length: 16327 byte(s)
Diff to previous 21638
COMP: Change slicer_external_update to ${PROJECT_NAME}_EP_UPDATE_IF_GREATER_288

The new variable name better represents the intent of this variable
and it is more appropriate for the many other non-slicer
projects that use derivatives of these External_*.cmake
files.

Contributed by Hans Johnson

Revision 21638  View Download Blame
Modified Fri Jan 25 09:06:34 2013 UTC (4 years, 8 months ago) by jcfr
File length: 16283 byte(s)
Diff to previous 21551
COMP: Remove WebGLExport module from Slicer core - Will be distributed as extension.

See https://github.com/xtk/SlicerWebGLExport/pull/2

Revision 21551  View Download Blame
Modified Mon Dec 31 12:48:54 2012 UTC (4 years, 8 months ago) by finetjul
File length: 16565 byte(s)
Diff to previous 21550
COMP: Propagate Slicer_ADDITIONAL_DEPENDENCIEs for packaging

Pass Slicer_ADDITIONAL_DEPENDENCIES to SlicerCPack.cmake for installing
the project targets.

Revision 21550  View Download Blame
Modified Mon Dec 31 12:48:48 2012 UTC (4 years, 8 months ago) by finetjul
File length: 16421 byte(s)
Diff to previous 21549
ENH: Add support for external projects passed as configuration parameter

Revision 21549  View Download Blame
Modified Mon Dec 31 12:48:38 2012 UTC (4 years, 8 months ago) by finetjul
File length: 15500 byte(s)
Diff to previous 21548
ENH: Add Slicer_BUILD_DIFFUSION_SUPPORT

Controls whether Diffusion related modules are built or not.
It concernes all the DWI, DTI and Tractography modules.

Revision 21548  View Download Blame
Modified Mon Dec 31 12:48:26 2012 UTC (4 years, 8 months ago) by finetjul
File length: 15467 byte(s)
Diff to previous 21510
ENH: Make the applications to build customizable

By passing Slicer_APPLICATIONS_DIR, the applications to build can be
changed.

Revision 21510  View Download Blame
Modified Sat Dec 8 18:20:36 2012 UTC (4 years, 9 months ago) by jcfr
File length: 14639 byte(s)
Diff to previous 21506
COMP: Fix Windows build ensuring CMAKE_CONFIGURATION_TYPES is properly passed

This is a follow up of commit r21499

List can't be passed directly to ExternalProject, they have to be converted
to string with a separator different from ";".

The function "list_to_string" allows to easily convert list to string
using a given separator.

Revision 21506  View Download Blame
Modified Sat Dec 8 02:46:40 2012 UTC (4 years, 9 months ago) by jcfr
File length: 14348 byte(s)
Diff to previous 21499
COMP: Pass CMAKE_CONFIGURATION_TYPES only if it applies

This will avoid CMake "unused variable" warning when using generator that
don't support multiple config. (i.e Makefile)

Revision 21499  View Download Blame
Modified Fri Dec 7 22:58:37 2012 UTC (4 years, 9 months ago) by pieper
File length: 14265 byte(s)
Diff to previous 21482
COMP: allow restriction only one build type at cmake time

By including only a single configuration type, visual studio
will bring that up by default.  This helps when building
release on windows, since you can restrict the projects to
only support release and avoid getting builds with both
libraries by mistake.  By passing this to the slicer project
you can open that and build without needing to remember to
change the build type.

Revision 21482  View Download Blame
Modified Fri Dec 7 00:23:59 2012 UTC (4 years, 9 months ago) by jcfr
File length: 14197 byte(s)
Diff to previous 21457
ENH: Support per user per revision extensions settings

There is now a clear distinction between:
 - userSettings -> i.e. ~/.config/NA-MIC/Slicer.ini
 - revisionUserSettings -> i.e. ~/.config/NA-MIC/Slicer-<revision>.ini

The following slicer settings are now revision specific:
 - Extensions/ManagerEnabled
 - Extensions/ServerUrl
 - Extensions/InstallPath
 - Modules/AdditonalPath
 - Modules/IgnoreModules

Additionally, the launcher version has also been updated to be able to
consider settings associated with a user, application and revision. This is
captured by the new parameter APPLICATION_REVISION, ORGANIZATION_DOMAIN,
ORGANIZATION_NAME and USER_ADDITIONAL_SETTINGS_FILEBASENAME passed to the CMake
function "ctkAppLauncherConfigure".

qSlicerCoreApplication API has also been extended and now includes methods
like:
  - QSettings* userSettings()  [settings() method is deprecated and kept for backward compatibility]
  - QSettings* revisionUserSettings()
  - QString launcherRevisionUserSettingsFilePath()
  - QString slicerUserSettingsFilePath()
  - QString slicerRevisionUserSettingsFilePath()

In addition to the settings, the extensions install path is also revision
specific, it means that it's now possible to have multiple version of slicer
running with different set of extensions.

Fixes #2791, #2143, #2720, #2533


Since the version of the launcher is updated, launcher will return EXIT_FAILURE
also when no application is been set in the launcher settings.

Fixes #2767

Revision 21457  View Download Blame
Modified Wed Nov 21 15:26:52 2012 UTC (4 years, 10 months ago) by jcfr
File length: 14265 byte(s)
Diff to previous 21443
COMP: Systematically disable update for non CMake-ified projects

Re-configuring of non cmake-ified project was causing the rebuild of
VTK, CTK and Slicer. For example, in case of python, the headers were
re-installed, the associated timestamp updated ... hence the recompilation
of VTK.

Revision 21443  View Download Blame
Modified Mon Nov 19 00:00:53 2012 UTC (4 years, 10 months ago) by hjohnson
File length: 14195 byte(s)
Diff to previous 21319
ENH: Added DWIConvert

Revision 21319  View Download Blame
Modified Tue Nov 6 14:53:59 2012 UTC (4 years, 10 months ago) by jcfr
File length: 13926 byte(s)
Diff to previous 21206
COMP: Complain if git config "insteadof" are not as expected

See http://na-mic.org/Mantis/view.php?id=2731

Fixes #2731

Revision 21206  View Download Blame
Modified Wed Oct 17 18:38:58 2012 UTC (4 years, 11 months ago) by jcfr
File length: 12828 byte(s)
Diff to previous 21112
COMP: Remove unused CLI/Java directory

The associated code has been moved into the Slicer "Attic".
See https://github.com/Slicer/Attic/commit/1889649f20bf3ec2b9adc9f26c973954ce821e38

See http://www.na-mic.org/Bug/view.php?id=2651

Fixes #2651

Revision 21112  View Download Blame
Modified Fri Oct 5 14:39:27 2012 UTC (4 years, 11 months ago) by jcfr
File length: 12961 byte(s)
Diff to previous 20881
COMP: Fix CDash errors/warnings reporting for unix parallel build

Setting the variable CTEST_USE_LAUNCHERS_DEFAULT in the environment
to enable CTest launcher reliably will be supported by default in either
CMake 2.8.10 or 2.8.11.

In the mean time, your local installation of CMake can be modified based on
the following topic: https://github.com/jcfr/CMake/tree/fix-ctest-use-launchers-for-superbuild

See http://na-mic.org/Mantis/view.php?id=2468

Fixes #2468

Revision 20881  View Download Blame
Modified Mon Aug 27 22:06:48 2012 UTC (5 years ago) by jcfr
File length: 13310 byte(s)
Diff to previous 20849
COMP: Make sure Slicer_BUILD_DICOM_SUPPORT is passed to the inner build

Thanks to Steve Pieper for suggesting that change

Revision 20849  View Download Blame
Modified Thu Aug 23 22:47:22 2012 UTC (5 years, 1 month ago) by jcfr
File length: 13281 byte(s)
Diff to previous 20836
COMP: Use variable Slicer_BINARY_INNER_SUBDIR instead of hard-coding "Slicer-build"

See http://www.na-mic.org/Bug/view.php?id=2390

Fixes #2390

Revision 20836  View Download Blame
Modified Thu Aug 23 14:40:40 2012 UTC (5 years, 1 month ago) by jcfr
File length: 13264 byte(s)
Diff to previous 20664
COMP: Make sure Update command is disabled using CMake < 2.8.9

While commit r20834 allowed Slicer to be configured using CMake 2.8.9, it
also prevented the UPDATE_COMMAND from being disabled using version < 2.8.9.

This commit revert it and fix the issue by re setting LOG_UPDATE 1

Revision 20664  View Download Blame
Modified Tue Jul 24 06:45:33 2012 UTC (5 years, 2 months ago) by jcfr
File length: 13251 byte(s)
Diff to previous 20650
COMP: Honor option Slicer_BUILD_DICOM_SUPPORT by conditionally building DCMTK

Revision 20650  View Download Blame
Modified Fri Jul 20 19:37:46 2012 UTC (5 years, 2 months ago) by jcfr
File length: 13176 byte(s)
Diff to previous 20633
COMP: Reinstate UPDATE_COMMAND only for CMake >= 2.8.9

It's only in CMake 2.8.9 that the update of SHA1 won't trigger a
configure and build. See http://cmake.org/Bug/view.php?id=12564

Revision 20633  View Download Blame
Modified Thu Jul 19 16:15:41 2012 UTC (5 years, 2 months ago) by pieper
File length: 13163 byte(s)
Diff to previous 20619
COMP: build DCMTK as external project and use it to build CTK

This will allow us to use the same DCMTK for both CTK and ITKv4.

This move is also motivated by the need to use a version of DCTMK that
includes dcmrt, as needed for the SlicerRT effort.

Currently this build points to the master branch of the dcmkt.git.rt
repository, but should be migrated to a release branch as soon
as one is available.

Revision 20619  View Download Blame
Modified Fri Jul 13 13:44:20 2012 UTC (5 years, 2 months ago) by jcfr
File length: 13157 byte(s)
Diff to previous 20615
COMP: External project command should be passed as list of parameters

Revision 20615  View Download Blame
Modified Fri Jul 13 11:54:29 2012 UTC (5 years, 2 months ago) by mccormic
File length: 13161 byte(s)
Diff to previous 20576
BUG: Reinstate ExternalProject UPDATE_COMMAND.

The UPDATE_COMMAND stage of CMake ExternalProject_Add calls had been removed by
setting it to "".  This was likely to prevent unneccessary clones.  However, the
buggy behavior was fixed in CMake >=2.8.8.

  http://cmake.org/gitweb?p=cmake.git;a=commit;h=987c017f6b1b49ab832c244166e30e07260432da

And the UPDATE_COMMAND step is required to keep the ExternalProject in sync if
the desired Git tag changes.

In this commit, the UPDATE_COMMAND ExternalProject step is restored for CMake >=
2.8.8.

Revision 20576  View Download Blame
Modified Thu Jul 5 22:45:53 2012 UTC (5 years, 2 months ago) by jcfr
File length: 12859 byte(s)
Diff to previous 20550
ENH: Extensions can now be built with Slicer proper

Assuming the top-level folder name matches the extension name, it is now
possible to configure Slicer so that it also builds a chosen set of
extension source directories. If a package is generated,
these extensions will also be packaged.

Configuring Slicer passing the option "Slicer_EXTENSION_SOURCE_DIRS" will
achieve the desired goal.

For example, if we want to bundle within Slicer extensions "MinimalistiCli" and "SkullStripper",
the following could be done:

 cmake -DSlicer_EXTENSION_SOURCE_DIRS:STRING=/home/jchris/Projects/MinimalistiCli\;/home/jchris/Projects/SkullStripper .

The associated build tree will then be located in:
  /path/to/Slicer-Superbuild-Release/Slicer-build/Extensions/MinimalistiCli and
/path/to/Slicer-Superbuild-Release/Slicer-build/Extensions/SkullStripper

See http://na-mic.org/Mantis/view.php?id=2293

Fixes #2293

Revision 20550  View Download Blame
Modified Tue Jul 3 17:07:23 2012 UTC (5 years, 2 months ago) by christopher.mullins
File length: 12785 byte(s)
Diff to previous 20546
COMP: Provide a mechanism to disable one or more scripted modules at configure time.

Modules appended to Slicer_QTSCRIPTEDMODULES_DISABLED list won't be built.

See http://na-mic.org/Mantis/view.php?id=2283

Fixes #2283

Revision 20546  View Download Blame
Modified Mon Jul 2 21:28:10 2012 UTC (5 years, 2 months ago) by christopher.mullins
File length: 12556 byte(s)
Diff to previous 20514
COMP: Provide mechanism to disable one or more CLI modules at configure time.

Module appended to Slicer_CLIMODULES_DISABLED list won't be built.

See http://na-mic.org/Mantis/view.php?id=2284

Fixes #2284

Revision 20514  View Download Blame
Modified Thu Jun 28 20:40:21 2012 UTC (5 years, 2 months ago) by benjamin.long
File length: 12388 byte(s)
Diff to previous 20464
ENH: Internationalized Slicer

Added Internationalization setting panel to enable/disable this behavior.
Added language combo box into general setting panel if enabled.
Added function to load language when we start the application.

Revision 20464  View Download Blame
Modified Fri Jun 22 15:32:10 2012 UTC (5 years, 3 months ago) by hjohnson
File length: 12360 byte(s)
Diff to previous 20088
COMP: The compiler options must be propogated

Compiler options selected in the main Slicer4
Superbuild harness needs to be propogated to
each of the subsequent External_project builds.

This was tested by setting
export CC=/dev/null
export CXX=/dev/null
cmake -DCMAKE_C_COMPILER:PATH=/usr/bin/gcc -DCMAKE_CXX_COMPILER:PATH=/usr/bin/g++
and then compiling all of Slicer.

Propogate the necessary compiler flags to each
external package consistently.  Additionally,
only propogate the flags that are explicitly needed
for that external project.  In many cases, only the
C compiler options need to be propogated.

Slicer compiler options needed by Extensions as well.
The extension need to have the same compiler used
as the primary Slicer build.

Revision 20088  View Download Blame
Modified Wed May 16 17:13:17 2012 UTC (5 years, 4 months ago) by jcfr
File length: 12365 byte(s)
Diff to previous 20087
COMP: SkullStripper being an extension, remove code to build it as built-in module.

Revision 20087  View Download Blame
Modified Wed May 16 15:47:06 2012 UTC (5 years, 4 months ago) by jcfr
File length: 12623 byte(s)
Diff to previous 20062
COMP: Ensure Slicer can be build when Extension manager support is OFF. Fixes #2012

See http://www.na-mic.org/Bug/view.php?id=2012

This commit is a follow up of r20063

Revision 20062  View Download Blame
Modified Thu May 10 20:44:17 2012 UTC (5 years, 4 months ago) by pieper
File length: 12606 byte(s)
Diff to previous 19971
COMP: enable LibArchive independent of extensions

Revision 19971  View Download Blame
Modified Tue May 1 00:11:14 2012 UTC (5 years, 4 months ago) by jcfr
File length: 12606 byte(s)
Diff to previous 19959
COMP: Provide a mechanism to overwrite the auto-discovered Slicer_WC_REVISION

Such mechanism allows to overwrite the discovered Slicer_WC_REVISION
and build extensions against an expected revision associated with
a Slicer release.

While the core functionality (API/ABI) of slicer wouldn't be modified by a
newer Slicer revision, the extension build system could be improved or
fixed by a more recent set of patches. In that specific case, the option
Slicer_FORCED_WC_REVISION could be used.

Revision 19959  View Download Blame
Modified Mon Apr 30 23:11:21 2012 UTC (5 years, 4 months ago) by benjamin.long
File length: 12538 byte(s)
Diff to previous 19821
ENH: Add Qt Testing support

Expose signals/slots on some widget APIs for qttesting recording/replay

Revision 19821  View Download Blame
Modified Sun Apr 8 05:25:54 2012 UTC (5 years, 5 months ago) by jcfr
File length: 12515 byte(s)
Diff to previous 19819
COMP: Facilitate maintenance by keeping overwrite of warning level in one location.

Revision 19819  View Download Blame
Modified Sun Apr 8 03:06:50 2012 UTC (5 years, 5 months ago) by jcfr
File length: 12683 byte(s)
Diff to previous 19756
COMP: Ensure external projects are compiled with a warning level 2.

* Considering Slicer itself is now compiled with a warning level of 2,
it make sens to compiled all external project with a warning level
lower or equal.

See also r19791, r19805 and r19817

Revision 19756  View Download Blame
Modified Fri Mar 30 18:41:17 2012 UTC (5 years, 5 months ago) by jcfr
File length: 12515 byte(s)
Diff to previous 19689
COMP: Specifying a custom value for Slicer_REQUIRED_QT_VERSION should work

* The value wasn't propagated when configuring Slicer inner project

Revision 19689  View Download Blame
Modified Fri Mar 23 02:45:04 2012 UTC (5 years, 6 months ago) by hjohnson
File length: 12445 byte(s)
Diff to previous 19640
ENH:  Cleaned up the installation of SimpleITK

This patch removes the agressive compilation with fPIC.  A
patch to SimpleITK was created that removes some of the complexity
in selecting the fPIC compilation option.

Revision 19640  View Download Blame
Modified Sun Mar 18 13:20:32 2012 UTC (5 years, 6 months ago) by hjohnson
File length: 12969 byte(s)
Diff to previous 19570
COMP: Fortify SimpleITK building on Linux.

Revision 19570  View Download Blame
Modified Mon Mar 12 17:40:44 2012 UTC (5 years, 6 months ago) by finetjul
File length: 12445 byte(s)
Diff to previous 19402
COMP: On Windows 64b, pass INCR_TCL_VERSION_DOT to inner build

On Windows, tcl is not built but pre-built. Itcl is packaged with tcl and doesn't require the external project itcl. Make sure
INCR_TCL_VERSION_DOT and INCR_TCL_VERSION are passed to the inner build so that their path are added into the launcher configuration file.
Failing test: qSlicerApplicationTpyclTest1
Note that the fix is not enough, and itcl34.dll is still failing to load. It seems to use a bad version of msvcr90.dll

Revision 19402  View Download Blame
Modified Sun Feb 26 20:35:15 2012 UTC (5 years, 6 months ago) by jcfr
File length: 12443 byte(s)
Diff to previous 19401
COMP: Simplify how external project options and list of dependencies are specified

* Since the cmake macro CMAKE_DEPENDENT_OPTION is used to "link" build option
together, the logic allowing to determine if any CMake code that
should be executed according to these option can be simplified.

Before:

if(Slicer_Build_Foo)
  message("Oohoh")
  if(Slicer_Build_Bar)
    message("yeahh")
  endif()
endif()


After:

if(Slicer_Build_Foo)
  message("Oohoh")
endif()

if(Slicer_Build_Bar)
  message("yeahh")
endif()


This is possible because option B is specified using the following:

CMAKE_DEPENDENT_OPTION(
  Slicer_Build_Bar "Build Bar." OFF
  "Slicer_Build_Foo" OFF)

See http://www.cmake.org/cmake/help/cmake-2-8-docs.html#module:CMakeDependentOption

Revision 19401  View Download Blame
Modified Sun Feb 26 20:35:13 2012 UTC (5 years, 6 months ago) by jcfr
File length: 12935 byte(s)
Diff to previous 19340
COMP: Integrate SlicerWebGLEXport as an external project

* By keeping the source code of this project in its own github repository,
it makes review of the code, contribution, integration and
development of the code an easier process.

Revision 19340  View Download Blame
Modified Wed Feb 22 20:22:56 2012 UTC (5 years, 7 months ago) by jcfr
File length: 12575 byte(s)
Diff to previous 19330
BUG: Fix integration of MultiVolumeExplorer and MultiVolumeImporter

* Option Slicer_MULTIVOLUME_SUPPORT renamed into Slicer_BUILD_MULTIVOLUME_SUPPORT
and set as advanced

* Introduced option Slicer_BUILD_MultiVolumeImporter and Slicer_BUILD_MultiVolumeExplorer
depending on Slicer_BUILD_MULTIVOLUME_SUPPORT. These options are also advanced.

* Updated the CMakeLists.txt in both Scripted and Loadable folder so
that the source corresponding to these two modules is considered.

Revision 19330  View Download Blame
Modified Wed Feb 22 16:18:39 2012 UTC (5 years, 7 months ago) by fedorov
File length: 12563 byte(s)
Diff to previous 19329
BUG: fixed typo

Revision 19329  View Download Blame
Modified Wed Feb 22 16:16:50 2012 UTC (5 years, 7 months ago) by fedorov
File length: 12561 byte(s)
Diff to previous 19254
ENH: adding external projects for multivolume support

Revision 19254  View Download Blame
Modified Tue Feb 7 22:44:28 2012 UTC (5 years, 7 months ago) by hjohnson
File length: 11930 byte(s)
Diff to previous 19225
ENH: Compiler from SuperBuild.master needs to be propogated to sub-projects.

Revision 19225  View Download Blame
Modified Mon Feb 6 21:04:28 2012 UTC (5 years, 7 months ago) by jcfr
File length: 11922 byte(s)
Diff to previous 19222
ENH: Extensions are now downloaded from Midas instead of CDash

* Use qMidasAPI library instead of qCDashAPI

* Configuring an extension description file using package name is not required
anymore. Metadata associated with a package will be directly sent to MIDAS
using the web API.

Revision 19222  View Download Blame
Modified Mon Feb 6 21:04:22 2012 UTC (5 years, 7 months ago) by jcfr
File length: 11922 byte(s)
Diff to previous 19087
ENH: Update and improve extension build system

* Use recently added function SlicerFunctionMIDASUploadExtension

* Add a CMakeLists to Slicer/Extensions/CMake allowing to build the extensions
as a standalone project independently of Slicer.

For example:
 mkdir SlicerExtentions-build
 cd SlicerExtentions-build
 cmake -DSlicer_UPLOAD_EXTENSIONS:BOOL=ON -DSlicer_DIR:PATH=/home/jchris/Projects/Slicer4-Superbuild-Debug/Slicer-build/ ../Slicer4/Extensions/CMake/
 make

* Mote that it's still possible to build Slicer with the options Slicer_BUILD_EXTENSIONS
and Slicer_UPLOAD_EXTENSIONS

What's next?
 * Integrate qMidasAPI library instead of qCDashAPI and update extension manager
 * On macosx, update extension packaging (or installation) to properly
fix up extension libraries.

Revision 19087  View Download Blame
Modified Sun Jan 15 19:05:29 2012 UTC (5 years, 8 months ago) by millerjv
File length: 12284 byte(s)
Diff to previous 18988
ENH: Initial ChartView checkin for charts that can be packed in layouts

Contains ChartView, ChartWidget, ChartControllerWidget, ChartViewNode, ChartNode.

Two temporary layouts defined to hold charts, name "*Quantitative"

Data to plot is held in DoubleArrayNodes and added to ChartNodes

Uses jqPlot to plot within a QWebView.

ChartControllerWidget is a place-holder.

Plots can only be generated programmatically. See Libs/MRML/Widgets/Testing/qMRMLChartViewTest.py for an example.

Todo: property specifications
Todo: rework javascript code to be more modular.
Todo: fix packing issues with QWebView in a larger layout.
Todo: remove or implement proper ChartViewDisplayableManager and ChartViewInteractorStyle.

Revision 18988  View Download Blame
Modified Mon Dec 26 21:12:05 2011 UTC (5 years, 9 months ago) by finetjul
File length: 12228 byte(s)
Diff to previous 18931
ENH: Pass CMAKE_DISABLE_FIND_PACKAGE_Java to inner build

On Mac OS X, java is not installed by default.
However, there is a java binary in /usr/bin, when run, the user is asked if he/she wants to install Java.
So for CMake, Java is found (which is true). There need a way for the user to prevent Java to be found.
Solution works only on CMake > 2.8.6

Revision 18931  View Download Blame
Modified Thu Dec 15 07:45:25 2011 UTC (5 years, 9 months ago) by jcfr
File length: 12095 byte(s)
Diff to previous 18929
ENH: Add Slicer_BUILD_EXTENSIONMANAGER_SUPPORT option

* If disabled:
 - extension manager won't be integrated
 - external project qCDashAPI and LibArchive won't be checkedout

Revision 18929  View Download Blame
Modified Thu Dec 15 07:45:18 2011 UTC (5 years, 9 months ago) by jcfr
File length: 11907 byte(s)
Diff to previous 18893
COMP: Add Slicer_BUILD_CLI_SUPPORT

* When disabled, neither the CLI factories or the CLI modules will be built.

Revision 18893  View Download Blame
Modified Fri Dec 9 14:23:42 2011 UTC (5 years, 9 months ago) by finetjul
File length: 11684 byte(s)
Diff to previous 18881
COMP: Propagate SkullStripper build flag from Superbuild to Slicer internal build

Revision 18881  View Download Blame
Modified Thu Dec 8 09:34:04 2011 UTC (5 years, 9 months ago) by jcfr
File length: 11599 byte(s)
Diff to previous 18880
COMP: Add Slicer_BUILD_OpenIGTLinkIF option allowing to build the corresponding module

* The source of the module are checked out using an external project

* The source are then added conditionally similarly to a regular source directory

Revision 18880  View Download Blame
Modified Thu Dec 8 09:34:01 2011 UTC (5 years, 9 months ago) by jcfr
File length: 11331 byte(s)
Diff to previous 18799
COMP: OpenIGTLink external project is disabled by default

Revision 18799  View Download Blame
Modified Fri Dec 2 14:19:28 2011 UTC (5 years, 9 months ago) by jcfr
File length: 11261 byte(s)
Diff to previous 18797
COMP: Provide mechanism to disable one or more loadable modules at configure time.

Module appended to Slicer_QTLOADABLEMODULES_DISABLED list won't be built.

Revision 18797  View Download Blame
Modified Fri Dec 2 13:30:44 2011 UTC (5 years, 9 months ago) by jcfr
File length: 11032 byte(s)
Diff to previous 18786
COMP: Add advanced option to disable/enable the building of ChangeTrackerPy, EMSegment and SkullStripper

Revision 18786  View Download Blame
Modified Thu Dec 1 02:14:19 2011 UTC (5 years, 9 months ago) by jcfr
File length: 10644 byte(s)
Diff to previous 18691
COMP: Integrate SkullStripper extension as an external project

Revision 18691  View Download Blame
Modified Tue Nov 15 22:30:28 2011 UTC (5 years, 10 months ago) by hjohnson
File length: 10546 byte(s)
Diff to previous 18677
ENH: Add slicer/sitk python interface.

Revision 18677  View Download Blame
Modified Fri Nov 11 23:27:29 2011 UTC (5 years, 10 months ago) by finetjul
File length: 10464 byte(s)
Diff to previous 18520
ENH: Add option to build Slicer with no console on Windows

Add Slicer_BUILD_WIN32_CONSOLE at superbuild and build level

Revision 18520  View Download Blame
Modified Fri Oct 28 02:27:53 2011 UTC (5 years, 10 months ago) by jcfr
File length: 10396 byte(s)
Diff to previous 18515
COMP: Superbuild.cmake - Fix typo

Revision 18515  View Download Blame
Modified Fri Oct 28 01:29:10 2011 UTC (5 years, 10 months ago) by jcfr
File length: 10385 byte(s)
Diff to previous 18514
COMP: Remove option Slicer_BUILD_WITH_ITKv4 and add ITK_VERSION_MAJOR

Revision 18514  View Download Blame
Modified Fri Oct 28 00:56:12 2011 UTC (5 years, 11 months ago) by jcfr
File length: 10627 byte(s)
Diff to previous 18512
COMP: Cleaner integration of SimpleITK

* Slicer_USE_SimpleITK option depends on Slicer_BUILD_WITH_ITKv4
* Expect Swig_DIR to be defined on windows platform
* Fix indent

Revision 18512  View Download Blame
Modified Thu Oct 27 23:28:06 2011 UTC (5 years, 11 months ago) by jcfr
File length: 10670 byte(s)
Diff to previous 18494
COMP: Superbuild - Pass CTEST_USE_LAUNCHER to Slicer inner project if it applies

* Doing so seems to help in having error properly reported on CDash

Revision 18494  View Download Blame
Modified Thu Oct 27 16:51:01 2011 UTC (5 years, 11 months ago) by jcfr
File length: 10321 byte(s)
Diff to previous 18473
ENH: Adding SimpleITK for Linux/Mac

This is a first pass at incorporating
SimpleITK in to Slicer4 with ITK.  It works
on Linux/Mac, but not windows yet.  There is
a known way to make windows work, but that
is going to take some time.

This set of patches will allow for
a parallel set of development improvements
to the Slicer/SimpleITK integration while
the windows swig integration is worked out by
more fully qualifed windows experts.

Revision 18473  View Download Blame
Modified Wed Oct 26 02:21:12 2011 UTC (5 years, 11 months ago) by jcfr
File length: 10039 byte(s)
Diff to previous 18466
STYLE: Rename SlicerBRAINSTools into BRAINSTools

* The project is named "BRAINSTools"

Revision 18466  View Download Blame
Modified Tue Oct 25 21:17:02 2011 UTC (5 years, 11 months ago) by jcfr
File length: 10057 byte(s)
Diff to previous 18461
COMP: Set Slicer_SKIP_ROOT_DIR_MAX_LENGTH_CHECK to ON when configuring inner project

Revision 18461  View Download Blame
Modified Tue Oct 25 19:50:44 2011 UTC (5 years, 11 months ago) by jcfr
File length: 10058 byte(s)
Diff to previous 18430
COMP: Pass Slicer_SKIP_ROOT_DIR_MAX_LENGTH_CHECK:OFF to slicer inner project. Fixes #1480

* The first test already account for the length of the inner directory.

Revision 18430  View Download Blame
Modified Mon Oct 24 07:23:52 2011 UTC (5 years, 11 months ago) by jcfr
File length: 9950 byte(s)
Diff to previous 18426
COMP: Include BRAINSTools dependency

* Similarly to what's done with EMSegment and ChangeTrackerPy, the source
code is checked out using an External project. Then, the corresponding
source directory is added as a "regular" Slicer directory.

Revision 18426  View Download Blame
Modified Mon Oct 24 07:23:38 2011 UTC (5 years, 11 months ago) by jcfr
File length: 9777 byte(s)
Diff to previous 18425
COMP: Superbuild.cmake - Rename "slicer_superbuild_*_args" into "ep_superbuild_*_args"

* Use "ep" prefix to make ease the re-use of Slicer superbuild in other project

Revision 18425  View Download Blame
Modified Mon Oct 24 07:23:33 2011 UTC (5 years, 11 months ago) by jcfr
File length: 9849 byte(s)
Diff to previous 18423
COMP: Superbuild.cmake - Use ${CMAKE_PROJECT_NAME} to declare USE_GIT_PROTOCOL variable

* Doing so make it easier to re-use the Slicer superbuild structure
in other projects.

Revision 18423  View Download Blame
Modified Mon Oct 24 07:23:28 2011 UTC (5 years, 11 months ago) by jcfr
File length: 9827 byte(s)
Diff to previous 18282
COMP: External projects - Rename "ep_common_flags" into "ep_common_compiler_args"

Revision 18282  View Download Blame
Modified Thu Oct 6 01:06:03 2011 UTC (5 years, 11 months ago) by jcfr
File length: 9819 byte(s)
Diff to previous 18253
COMP: Fix "CMake unused variable" warning

* Slicer_USE_SYSTEM_PYTHON is not used

Revision 18253  View Download Blame
Modified Sat Oct 1 03:17:08 2011 UTC (5 years, 11 months ago) by jcfr
File length: 9859 byte(s)
Diff to previous 18249
ENH: ChangeTrackerPy source code is now checked out from github.com/fedorov

* Note that the module is currently disable since the MRML sub-directory
seems to be missing.

Revision 18249  View Download Blame
Modified Sat Oct 1 02:23:14 2011 UTC (5 years, 11 months ago) by jcfr
File length: 9753 byte(s)
Diff to previous 18157
COMP: Remove EMSegment source code

Revision 18157  View Download Blame
Modified Wed Sep 21 19:50:42 2011 UTC (6 years ago) by jcfr
File length: 9671 byte(s)
Diff to previous 17885
STYLE: Remove year from Kitware copyright

Revision 17885  View Download Blame
Modified Tue Aug 30 06:25:50 2011 UTC (6 years ago) by jcfr
File length: 9676 byte(s)
Diff to previous 17849
COMP: Unconditionally rebuild "Slicer" inner project.

* Since the superbuild project doesn't have any dependency on Slicer source
files, adding the "forcerebuild" step will ensure Slicer build tree
is always up-to-date.

* ExternalProject_Add_Step requires COMMAND parameter with VisualStudioi. See #32
 A bug has been reported on CMake bug tracker
 See http://public.kitware.com/Bug/view.php?id=12430

* Update CTK tag so that the similar problem happening in CTK is fixed.

* See http://massmail.spl.harvard.edu/public-archives/slicer-devel/2011/007079.html

Revision 17849  View Download Blame
Modified Fri Aug 26 21:26:19 2011 UTC (6 years, 1 month ago) by jcfr
File length: 9370 byte(s)
Diff to previous 17797
STYLE: SuperBuild.cmake - Remove extra empty lines

Revision 17797  View Download Blame
Modified Tue Aug 23 01:38:39 2011 UTC (6 years, 1 month ago) by hjohnson
File length: 9297 byte(s)
Diff to previous 17786
ENH: Turn on building BRAINSTools by default.

Revision 17786  View Download Blame
Modified Mon Aug 22 01:26:00 2011 UTC (6 years, 1 month ago) by hjohnson
File length: 9420 byte(s)
Diff to previous 17632
COMP: Set BRAINSTools building for ITKv3 and ITKv4

BRAINSTools is built quite differently for ITKv3 and
ITKv4.  This separates they way they are configured.

Added BRAINSTools as an External_Project for ITKv4,
and left it as an internal build for ITKv3.

Revision 17632  View Download Blame
Modified Fri Jul 29 16:15:56 2011 UTC (6 years, 1 month ago) by jcfr
File length: 9322 byte(s)
Diff to previous 17630
STYLE: To be consistent, rename External_Insight into External_ITKv3

Revision 17630  View Download Blame
Modified Fri Jul 29 16:15:52 2011 UTC (6 years, 1 month ago) by jcfr
File length: 9333 byte(s)
Diff to previous 17597
COMP: SuperBuild.cmake - Remove unused variable ITK_LIBRARY_DIR_NAME

Revision 17597  View Download Blame
Modified Fri Jul 29 01:06:32 2011 UTC (6 years, 1 month ago) by hjohnson
File length: 9414 byte(s)
Diff to previous 17596
ENH:  Updated ITKv4 build parameters.

Revision 17596  View Download Blame
Modified Fri Jul 29 01:06:30 2011 UTC (6 years, 1 month ago) by hjohnson
File length: 9310 byte(s)
Diff to previous 17486
ENH: Add option to build slicer with ITKv4.

A new external package was created for building
with ITKv4.  A few code modificaitons were
required to get this to build with
the 4.0.alpha07 release of ITKv4.

The default is to use ITKv3.20.

Revision 17486  View Download Blame
Modified Wed Jul 13 23:53:01 2011 UTC (6 years, 2 months ago) by jcfr
File length: 8996 byte(s)
Diff to previous 17405
ENH: Superbuild - Pass variable Slicer_SUPERBUILD_DIR to Slicer inner project

Revision 17405  View Download Blame
Modified Sat Jul 9 04:31:43 2011 UTC (6 years, 2 months ago) by jcfr
File length: 8942 byte(s)
Diff to previous 17340
ENH: INCR_TCL_VERSION and TCL_TK_VERSION are passed to Slicer through superbuild

Revision 17340  View Download Blame
Modified Tue Jul 5 22:54:22 2011 UTC (6 years, 2 months ago) by jcfr
File length: 8637 byte(s)
Diff to previous 17287
STYLE: Rename "libarchive" external project into "LibArchive"

Revision 17287  View Download Blame
Modified Fri Jul 1 04:15:51 2011 UTC (6 years, 2 months ago) by jcfr
File length: 8749 byte(s)
Diff to previous 17217
ENH: SlicerExecutionModel is now an external project

* A single find_package(SlicerExecutionModule) can be used.

* Calling find_package(SlicerExecutionModule ...) will systematically define the
ModuleDescriptionParser_DIR, GenerateCLP_DIR and TCLAP_DIR

* Assuming ModuleDescriptionParser_DIR, GenerateCLP_DIR or TCLAP_DIR are defined,
the corresponding find_package() call are still valid.

* Call of the form find_package(SlicerExecutionModule REQUIRED GenerateCLP) or
find_package(SlicerExecutionModule REQUIRED ModuleDescriptionParser) are valid and
will:
  - include the target of the specified components
  - set SlicerExecutionModel_INCLUDE_DIRS, SlicerExecutionModel_LIBRARIES appropriately.

* Known issue: SlicerExecutionModel_LIBRARY_DIRS is not defined. Since the
list of library SlicerExecutionModel_LIBRARIES is defined and the associated
CMake target imported. If CMake 2.6 or above is used, this shouldn't be a problem.

Revision 17217  View Download Blame
Modified Thu Jun 23 21:13:12 2011 UTC (6 years, 3 months ago) by jcfr
File length: 8637 byte(s)
Diff to previous 17208
COMP: Pass CMAKE_OSX_* variable to Slicer inner project

Revision 17208  View Download Blame
Modified Thu Jun 23 19:18:09 2011 UTC (6 years, 3 months ago) by jcfr
File length: 8269 byte(s)
Diff to previous 17193
STYLE: Rename Doc/copyright/copyright.txt into COPYRIGHT.txt

Revision 17193  View Download Blame
Modified Thu Jun 23 03:28:28 2011 UTC (6 years, 3 months ago) by jcfr
File length: 8283 byte(s)
Diff to previous 17191
COMP: OpenIGTLink can now be properly referenced within Extension

* Note also that Slicer_USE_OPENIGTLINK has been changed into Slicer_USE_OpenIGTLink

Revision 17191  View Download Blame
Modified Thu Jun 23 01:39:37 2011 UTC (6 years, 3 months ago) by jcfr
File length: 8283 byte(s)
Diff to previous 17096
STYLE: Move CMake commands to match new conventions

The next step in removing end-of-lines is to run through all the
CMakeLists.txt files and clean them up.

This also changes all the key words to lower
case. The primary reason for changing key words is that all documentation for
CMakeLists.txt now shows the key words as lower case. Even the printed
“Mastering CMake v5” uses lower case. I’ve come across this several
times in my class where students stumble over the fact that the
documentation about Cmake does not match the implementation in ITK.

I have a script (a wrapper around a vim macro) written that can make
these substituions reliably (Tested on the BRAINS tree, the Slicer3
tree, and the ITK tree without causing any errors).  More complete
documentation can be found in
ITK/Utilities/Maintenance/HowToCreateTheCMakeCaseConversion.txt

Revision 17096  View Download Blame
Modified Sat Jun 18 00:05:55 2011 UTC (6 years, 3 months ago) by jcfr
File length: 8291 byte(s)
Diff to previous 17078
BUG: Superbuild - Remove hardcoded value associated with CMAKE_CTEST_COMMAND

Revision 17078  View Download Blame
Modified Fri Jun 17 07:26:23 2011 UTC (6 years, 3 months ago) by jcfr
File length: 8376 byte(s)
Diff to previous 17028
ENH: Add option Slicer_UPLOAD_EXTENSIONS AND Update extension build system

If WITH_EXTENSION is OFF, slicer superbuild behaves as usual
otherwise, option Slicer_UPLOAD_EXTENSIONS is added:

* Slicer_UPLOAD_EXTENSIONS is OFF

  It means the extensions are added to superbuild as regular "external"  project
  depending on Slicer. The different "external" project are  named after
  the <extension_name>.

  For convenience, an "external project" named <extension_name>-rebuild is added.
  This project doesn't depend on Slicer and can be used to rebuild only
  the extension without waiting for Slicer and its dependencies(VTK, CTK, ...)
  to be configured, built ..


* Slicer_UPLOAD_EXTENSIONS is ON

  It means the extensions are added to superbuild as "ctest-fied" project.
  In other word, the BUILD_COMMAND of the external project is set to
  execute a ctest script that will configure, build, test, package and upload
  the packages to CDash.

  The configure/build/test results and also the packages are submitted to either
  Extensions-Nightly, Extensions-Continuous or Extensions-Experimental track.

  Similarly to the previous case, external project named <extension_name>-rebuild
  are also added.

When setting up dashboard, Slicer_UPLOAD_EXTENSIONS should be set to TRUE.
Within the Slicer dashboard driver script, both Slicer_BUILD_EXTENSIONS
and Slicer_UPLOAD_EXTENSIONS are set if WITH_EXTENSIONS is TRUE.

Revision 17028  View Download Blame
Modified Thu Jun 16 06:27:06 2011 UTC (6 years, 3 months ago) by jcfr
File length: 7961 byte(s)
Diff to previous 17000
ENH: Superbuild - Additional option related to optional external project are now conditionally added.

This will have the advantage of shuting down CMake warning related
to unused variable.

Revision 17000  View Download Blame
Modified Mon Jun 13 07:33:26 2011 UTC (6 years, 3 months ago) by jcfr
File length: 7452 byte(s)
Diff to previous 16978
ENH: Add external project qCDashAPI

This external project hosted on github.com/jcfr/qCDashAPI is
a small Qt based library allowing to easily query a CDash server.

Revision 16978  View Download Blame
Modified Sun Jun 12 17:53:23 2011 UTC (6 years, 3 months ago) by jcfr
File length: 7384 byte(s)
Diff to previous 16976
COMP: SuperBuild / SlicerConfig - Remove obsolete reference to OPENCV

Revision 16976  View Download Blame
Modified Sun Jun 12 07:14:14 2011 UTC (6 years, 3 months ago) by jcfr
File length: 7404 byte(s)
Diff to previous 16973
COMP: incrTcl external project is a dependency of Slicer only

Revision 16973  View Download Blame
Modified Sun Jun 12 07:14:09 2011 UTC (6 years, 3 months ago) by jcfr
File length: 7305 byte(s)
Diff to previous 16967
COMP: Superbuild.cmake -  Update comment and definition of Slicer_DEPENDENCIES

Slicer dependencies are not required to be topologically ordered since
each external project specifies its dependencies.

Revision 16967  View Download Blame
Modified Sun Jun 12 07:13:59 2011 UTC (6 years, 3 months ago) by jcfr
File length: 7388 byte(s)
Diff to previous 16966
COMP: Rename "scipy" project into "SciPy" so that the External project file and the project name are the same

Revision 16966  View Download Blame
Modified Sun Jun 12 03:21:16 2011 UTC (6 years, 3 months ago) by jcfr
File length: 7388 byte(s)
Diff to previous 16964
COMP: ExternalProject definition are now automatically included given their respective dependencies.

At configuration time, an output of the following form is also printed:

-- SuperBuild - Slicer => Requires libarchive, cmcurl, OpenIGTLink, teem, CTKAPPLAUNCHER, python, NUMPY, VTK, Insight, CTK,
-- SuperBuild -   libarchive[OK]
-- SuperBuild -   cmcurl[OK]
-- SuperBuild -   OpenIGTLink[OK]
-- SuperBuild -   teem => Requires VTK,
-- SuperBuild -     VTK => Requires python,
-- SuperBuild -       python => Requires incrTcl, tcl, tk,
-- SuperBuild -         incrTcl => Requires tcl, tk,
-- SuperBuild -           tcl[OK]
-- SuperBuild -           tk => Requires tcl[INCLUDED],
-- SuperBuild -           tk[OK]
-- SuperBuild -         incrTcl[OK]
-- SuperBuild -       python[OK]
-- SuperBuild -     VTK[OK]
-- SuperBuild -   teem[OK]
-- SuperBuild -   CTKAPPLAUNCHER[OK]
-- SuperBuild -   NUMPY => Requires CLAPACK, python[INCLUDED],
-- SuperBuild -     CLAPACK[OK]
-- SuperBuild -   NUMPY[OK]
-- SuperBuild -   Insight[OK]
-- SuperBuild -   CTK => Requires VTK[INCLUDED], Insight[INCLUDED], python[INCLUDED],
-- SuperBuild -   CTK[OK]
-- SuperBuild - Slicer[OK]

Revision 16964  View Download Blame
Modified Sun Jun 12 03:21:09 2011 UTC (6 years, 3 months ago) by jcfr
File length: 8784 byte(s)
Diff to previous 16963
COMP: Dependencies of each external project are now specified in their respective definition file.

Revision 16963  View Download Blame
Modified Sun Jun 12 03:21:04 2011 UTC (6 years, 3 months ago) by jcfr
File length: 9665 byte(s)
Diff to previous 16962
COMP: Rename External_Tcl,Tk}.cmake into External_{tcl,tk}.cnake

* Name of external project definition file and project name now match

Revision 16962  View Download Blame
Modified Sun Jun 12 03:21:01 2011 UTC (6 years, 3 months ago) by jcfr
File length: 9665 byte(s)
Diff to previous 16961
COMP: Add SlicerBlockCheckExternalProjectDependencyList

By adding that CMake block in each external project definition, we ensure
that all dependent external project definition have been included beforehand.

Revision 16961  View Download Blame
Modified Sun Jun 12 03:20:58 2011 UTC (6 years, 3 months ago) by jcfr
File length: 9641 byte(s)
Diff to previous 16960
COMP: Rename "itcl" into "incrTcl" so that the project is uniquely identified.

* Also removed unused itcl_configure_step.cmake.in

Revision 16960  View Download Blame
Modified Sun Jun 12 03:20:56 2011 UTC (6 years, 3 months ago) by jcfr
File length: 9638 byte(s)
Diff to previous 16957
COMP: To be consistent with the project name, rename External_Python26 into External_python

Revision 16957  View Download Blame
Modified Sun Jun 12 03:20:48 2011 UTC (6 years, 3 months ago) by jcfr
File length: 9640 byte(s)
Diff to previous 16955
COMP: Remove obsolete external "iwidgets" project definition

File External_iwidgets has been move to the Slicer/Attic repository
See https://github.com/Slicer/Attic/commit/949d9488a3d946c3cb59e1979ddf0269676a1220

Revision 16955  View Download Blame
Modified Sun Jun 12 03:20:43 2011 UTC (6 years, 3 months ago) by jcfr
File length: 9685 byte(s)
Diff to previous 16865
COMP: Superbuild - CTK is directly added slicer_DEPENDENCIES

Revision 16865  View Download Blame
Modified Wed Jun 8 09:27:41 2011 UTC (6 years, 3 months ago) by jcfr
File length: 9718 byte(s)
Diff to previous 16864
COMP: Conditionally configure Slicer inner project with BUILD_BRAINSTOOLS

If Slicer_BUILD_CLI is OFF, this option shouldn't be set or used..

This should shut down the following warning:

CMake Warning: The variable, 'BUILD_BRAINSTOOLS', specified manually, was not used during the generation.

Revision 16864  View Download Blame
Modified Wed Jun 8 09:27:39 2011 UTC (6 years, 3 months ago) by jcfr
File length: 9649 byte(s)
Diff to previous 16845
COMP: Configured Slicer with CTEST_CONFIGURATION_TYPE only if the variable is defined

This should shut down the following warning reported on Linux dashboard:

CMake Warning: The variable, 'CTEST_CONFIGURATION_TYPE', specified manually, was not used during the generation.

Revision 16845  View Download Blame
Modified Tue Jun 7 22:47:07 2011 UTC (6 years, 3 months ago) by jcfr
File length: 9493 byte(s)
Diff to previous 16816
COMP: Do not INCR_{TCL,TK}_LIBRARY from superbuild - These Variables are not used anymore

Revision 16816  View Download Blame
Modified Mon Jun 6 16:06:17 2011 UTC (6 years, 3 months ago) by jcfr
File length: 9591 byte(s)
Diff to previous 16815
COMP: Explicitly set CMAKE_BUILD_TYPE on external project

By explicitly setting the build type, CMake warnings related to unused
CMAKE_BUILD_TYPE variable in project which doesn't rely on CMake
will be avoided.

Revision 16815  View Download Blame
Modified Mon Jun 6 16:06:14 2011 UTC (6 years, 3 months ago) by jcfr
File length: 9712 byte(s)
Diff to previous 16804
COMP: Explicitly disable TESTING on external project

By explicitly disabling testing, CMake warnings related to unused
BUILD_TESTING variable in project without testing capabilities will be
avoided.

Revision 16804  View Download Blame
Modified Sat Jun 4 06:56:07 2011 UTC (6 years, 3 months ago) by jcfr
File length: 9739 byte(s)
Diff to previous 16649
COMP: Add Slicer_BUILD_BRAINSTOOLS option at superbuild level.

Doing so will allow to dashboard to either enable or disable the built
of that module.

Note that the module is currently disable since the associated CLI
libraries can't be properly loaded in Slicer and also because the mac bundle
failed to be generated if it is enabled.

Revision 16649  View Download Blame
Modified Mon May 23 19:33:22 2011 UTC (6 years, 4 months ago) by partyd
File length: 9657 byte(s)
Diff to previous 16617
COMP: When building 64-bit on Windows we need to compile with /bigobj as building ITK will exceed the number of entries allowed in an .obj file built 64-bit.

Revision 16617  View Download Blame
Modified Wed May 18 17:28:13 2011 UTC (6 years, 4 months ago) by jcfr
File length: 9536 byte(s)
Diff to previous 16396
COMP: Remove obsolete external "blt" project definition

Since r15923, KWWidgets related code has been removed and
blt isn't required anymore.

Revision 16396  View Download Blame
Modified Tue Apr 26 08:30:22 2011 UTC (6 years, 5 months ago) by jcfr
File length: 9569 byte(s)
Diff to previous 16373
ENH: Add option Slicer_BUILD_EXTENSIONS

By default disabled.

If enabled, the *.s4ext file within the Extensions directory will be
parsed and an ExternalProject target specific to each one of them and
depending on Slicer will be added.

Revision 16373  View Download Blame
Modified Tue Apr 26 08:29:42 2011 UTC (6 years, 5 months ago) by jcfr
File length: 9288 byte(s)
Diff to previous 16371
COMP: Factor out code related to C/CXX flags to that it could be re-used within extension

Revision 16371  View Download Blame
Modified Tue Apr 26 08:29:39 2011 UTC (6 years, 5 months ago) by jcfr
File length: 9190 byte(s)
Diff to previous 16353
COMP: Update SlicerBlockFindQtAndCheckVersion, and also reorganize VTK, CTK and Qt discovery

VTK and CTK should be found first, then using the block SlicerBlockFindQtAndCheckVersion
it's easy to make sure the Qt version used to build both CTK and VTK are equal
and satisfy Slicer_REQUIRED_QT_VERSION condition.

Revision 16353  View Download Blame
Modified Tue Apr 26 08:28:44 2011 UTC (6 years, 5 months ago) by jcfr
File length: 9612 byte(s)
Diff to previous 16173
COMP: Remove occurences of Slicer_USE_QT variable

Revision 16173  View Download Blame
Modified Sat Apr 2 05:53:55 2011 UTC (6 years, 5 months ago) by jcfr
File length: 9700 byte(s)
Diff to previous 16115
ENH: Modernize doxygen Documentation generation mechanism

Revision 16115  View Download Blame
Modified Sat Mar 26 14:57:00 2011 UTC (6 years, 6 months ago) by jcfr
File length: 9542 byte(s)
Diff to previous 15923
ENH: Pass ITK_DIR to CTK external project and enable "CTK_LIB_ImageProcessing/ITK/Core" option

Revision 15923  View Download Blame
Modified Sun Jan 30 01:47:13 2011 UTC (6 years, 7 months ago) by jcfr
File length: 9534 byte(s)
Diff to previous 15905
COMP: Remove ref to KWWidgets, Slicer_USE_PYTHON, Slicer_BUILD_MODULES, ...

KWWidgets external project has been removed

Reference to Slicer_USE_PYTHON have been removed

Reference to Slicer_BUILD_MODULES has been removed

Launcher.tcl also has been cleaned

Deprecated function from qSlicerCoreApplication have been removed

Reference to Tcl wrapping within the core component of Slicer have been
removed. note that Slicer/Libs haven't been updated. Indeed, in case other
project want to benefit from Tcl wrapping ...

Revision 15905  View Download Blame
Modified Thu Jan 27 05:36:46 2011 UTC (6 years, 8 months ago) by finetjul
File length: 10275 byte(s)
Diff to previous 15830
COMP: Propagate CTEST_CONFIGURATION_TYPE to Slicer project

The superbuild may get CTEST_CONFIGURATION_TYPE from the dashboard driver script, in that case, it should propagate the option to the Slicer project

Revision 15830  View Download Blame
Modified Thu Jan 13 15:10:51 2011 UTC (6 years, 8 months ago) by partyd
File length: 10209 byte(s)
Diff to previous 15556
BUG: properly adjust Slicer dependencies so Batchmake and be disabled.

Revision 15556  View Download Blame
Modified Tue Dec 14 06:45:12 2010 UTC (6 years, 9 months ago) by finetjul
File length: 10100 byte(s)
Diff to previous 15525
ENH: Add LibArchive into Slicer launcher

Revision 15525  View Download Blame
Modified Fri Dec 10 23:17:57 2010 UTC (6 years, 9 months ago) by partyd
File length: 10056 byte(s)
Diff to previous 15410
ENH: Build libarchive as an external project.

Revision 15410  View Download Blame
Modified Mon Dec 6 02:34:05 2010 UTC (6 years, 9 months ago) by jcfr
File length: 9841 byte(s)
Diff to previous 15195
COMP: Re-add option Slicer_USE_NUMPY - enabled by default

Revision 15195  View Download Blame
Modified Fri Oct 29 15:54:29 2010 UTC (6 years, 10 months ago) by jcfr
File length: 9793 byte(s)
Diff to previous 15192
COMP: Use CMAKE_{C/CXX}_FLAGS_INIT to initialize ep_common_{c/cxx}_flags

Doing so will ensure that all compiler specific flags are specified

Revision 15192  View Download Blame
Modified Fri Oct 29 03:27:01 2010 UTC (6 years, 10 months ago) by jcfr
File length: 9886 byte(s)
Diff to previous 15190
COMP: ADDITIONAL_{C/CXX}_FLAGS are added to ep_common_{c/cxx}_flags

Doing so allow to pass flags like /MP to all external projects

Revision 15190  View Download Blame
Modified Fri Oct 29 03:26:57 2010 UTC (6 years, 10 months ago) by jcfr
File length: 9840 byte(s)
Diff to previous 15175
COMP: C/CXX flags common to external project are grouped into ep_common_{c,cxx}_flags variable

Revision 15175  View Download Blame
Modified Thu Oct 28 00:00:19 2010 UTC (6 years, 11 months ago) by jcfr
File length: 9648 byte(s)
Diff to previous 15174
ENH: Add ADDITIONAL_{C,CXX}_FLAGS options

These options allow to pass flags that will be appended to the ones
internally determined.

The variable CMAKE_{C,CXX}_FLAGS will then be set using:
 - the list of internal flags: Slicer_{C,CXX}_FLAGS
 - the additional flags passed at configuration time: ADDITIONAL_{C,CXX}_FLAGS

Revision 15174  View Download Blame
Added Thu Oct 28 00:00:17 2010 UTC (6 years, 11 months ago) by jcfr
File length: 9552 byte(s)
ENH: Simplify and optimize superbuild

External project specification have been added to SuperBuild.cmake

Running:
  1) "cmake ../Slicer4" => Build using SuperBuild
  2) "cmake -DSlicer_SUPERBUILD:BOOL=OFF ../Slicer4" => Build without Superbuild

In case (2), all external dependencies (VTK, ITK, ...) will have
to be specified manually.

Layout of the CMakeLists.txt has been reviewed to improve readability

Factored out cmake code and use macro SlicerMacroEmptyExternalProject
in VTK, ITK and CTK external project description.

${ep_common_args} has been introduced to contain option common
to all external project.

launcher.tcl.in has been updated to properly behave when KWWidgets_*_DIR
are not specified.

CTestCustom files has been merged into one file now located
in CMake subdirectory

SlicerFindQt.cmake has been removed, Qt discovery is now handled
directly in both CMakeLists.txt and SuperBuild.cmake

{Subversion_SVN, GIT}_EXECUTABLE are now discovered at superbuild
configure time. In case of error a message will be immediately thrown
in case of problem.

Dashboard template and driver script have been updated to reflect new
directory layout.

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