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Sticky Revision:

Revision 23777 - Directory Listing
Modified Tue Nov 4 11:24:07 2014 UTC (2 years, 11 months ago) by jcfr
ENH: Branching from trunk to Slicer-4-4 at r23774

Revision 23773 - Directory Listing
Modified Sun Nov 2 15:07:38 2014 UTC (2 years, 11 months ago) by jcfr
Original Path: trunk/Modules
ENH: Update Documentation to 4.4

Revision 23771 - Directory Listing
Modified Sat Nov 1 02:53:23 2014 UTC (2 years, 11 months ago) by jcfr
Original Path: trunk/Modules
COMP: Fix VS2013 compilation issue removing unused "isnan" define.

From: Dzenan Zukic <dzenan.zukic@kitware.com>

Revision 23767 - Directory Listing
Modified Thu Oct 30 09:07:40 2014 UTC (2 years, 11 months ago) by jcfr
Original Path: trunk/Modules
COMP: Fix VS2013 compilation error including missing algorithm header

From: Dzenan Zukic <dzenan.zukic@kitware.com>

Revision 23764 - Directory Listing
Modified Wed Oct 29 21:49:14 2014 UTC (2 years, 11 months ago) by naucoin
Original Path: trunk/Modules
BUG: get the screenshot type without making a widget

From JC: avoid creation an instance of the widget to get the
value of the enum

Issue #3879

Revision 23763 - Directory Listing
Modified Wed Oct 29 21:49:07 2014 UTC (2 years, 11 months ago) by naucoin
Original Path: trunk/Modules
BUG: fix crash when editing scripted screen shots

Fixed the default screen shot type to use the defined full layout
integer.
Added checks to avoid crashes for scripts that are in extensions.

The default screen shot type was set to -1 in the python scripts
and templates, but in the Qt widget, the screen shot type was
only defined from 0-4. Trying to open the scripted screen shot
node in the Qt widget would cause a crash since the -1 type was
cast to the enumerated WidgetType in qMRMLScreenShotDialog
resulting in an invalid number and a null widget.

Issue #3879

Revision 23762 - Directory Listing
Modified Wed Oct 29 16:06:25 2014 UTC (2 years, 11 months ago) by naucoin
Original Path: trunk/Modules
ENH: link resample and check methods, add a test

Added documentation links between the method that checks
for geometry mismatch and the one that resamples to fix it.
Added basic tests for the new logic methods.

Revision 23761 - Directory Listing
Modified Wed Oct 29 16:06:21 2014 UTC (2 years, 11 months ago) by naucoin
Original Path: trunk/Modules
ENH: generalise comparing volume geometries

Added CompareVolumeGeometry and call it from CheckForLabelVolumeValidity

Revision 23758 - Directory Listing
Modified Wed Oct 29 04:15:12 2014 UTC (2 years, 11 months ago) by jcfr
Original Path: trunk/Modules
ENH: Fixed error message occurring after disabling SliceViewAnnotations

This commit fixes error message like this one:

Traceback (most recent call last):
  File "/path/to/Slicer-build/lib/Slicer-4.3/qt-scripted-modules/DataProbeLib/SliceViewAnnotations.py", line 596, in updateCornerAnnotations
    self.makeAnnotationText(caller)
  File "/path/to/Slicer-build/lib/Slicer-4.3/qt-scripted-modules/DataProbeLib/SliceViewAnnotations.py", line 838, in makeAnnotationText
    self.drawCornerAnnotations()
  File "/path/to/Slicer-build/lib/Slicer-4.3/qt-scripted-modules/DataProbeLib/SliceViewAnnotations.py", line 993, in drawCornerAnnotations
    sliceCornerAnnotation = self.sliceCornerAnnotations[self.currentSliceViewName]
KeyError: 'Red'

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

Revision 23757 - Directory Listing
Modified Wed Oct 29 04:15:09 2014 UTC (2 years, 11 months ago) by jcfr
Original Path: trunk/Modules
BUG: Fixed exception, added tooltip

Slice annotation failed with an exception when series time was empty.
Added tooltip to "Background DICOM annotations persistence" checkbox, as it was very difficult to figure out what was it for.

From: Andras Lasso <lasso@queensu.ca>

Revision 23756 - Directory Listing
Modified Wed Oct 29 04:15:06 2014 UTC (2 years, 11 months ago) by jcfr
Original Path: trunk/Modules
BUG: Fixed two minor issues of slice view annotations

* Fixed the error in the terminal No scalar values found for texture input!
* New slices that are added to the layout would have the same font
 settings as the other slices.

From: Alireza Mehrtash <mehrtash@bwh.harvard.edu>

Revision 23751 - Directory Listing
Modified Mon Oct 20 17:52:23 2014 UTC (3 years ago) by jcfr
Original Path: trunk/Modules
BUG: The items in the label statistics table should not be edit-able

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

Revision 23743 - Directory Listing
Modified Thu Oct 16 19:24:15 2014 UTC (3 years ago) by pieper
Original Path: trunk/Modules
BUG: #3873 lingering vtk5 code broke module

Need to use the newer pipeline calls for vtk 6

Revision 23742 - Directory Listing
Modified Thu Oct 16 19:14:38 2014 UTC (3 years ago) by pinter
Original Path: trunk/Modules
BUG: Prevent SliceViewAnnotations from dividing by zero

It can happen in some cases and it is important to recover gracefully, not just get a long python error.

Revision 23737 - Directory Listing
Modified Fri Oct 10 21:32:45 2014 UTC (3 years ago) by naucoin
Original Path: trunk/Modules
BUG: fix loading of derived items

A typo in a python call was masked by the catching
off an attribute error meant to catch if there
were no derived items. Fixed the call to processEvents
and now derived items will load.

Issue 3806

Revision 23735 - Directory Listing
Modified Thu Oct 2 19:07:51 2014 UTC (3 years ago) by naucoin
Original Path: trunk/Modules
COMP: fix linux compilation of Models test

Remove include of QPushButton which is causing a compilation
error on the linux factories.

File added in svn 23734.



Revision 23734 - Directory Listing
Modified Wed Oct 1 03:30:39 2014 UTC (3 years ago) by finetjul
Original Path: trunk/Modules
BUG: Do not use QItemSelectionModel::currentRowChanged()

The signal is not reliable, ot might not be triggered at the right time.
Indeed the signal is for "key" events and has not a "selection" role.
The lack of trigger can lead to a crash due to widgets still observing
nodes that are not in the scene anymore.

Revision 23726 - Directory Listing
Modified Wed Sep 24 21:55:01 2014 UTC (3 years ago) by pinter
Original Path: trunk/Modules
BUG: Fixed minor issues in subject hierarchy parse local data plugin

Show/hide icons didn't show up for non-volume displayables; If the user did a parsing, loaded further data and did a new parsing, the first batch appeared twice in the list. Both issues have been fixed.

Revision 23722 - Directory Listing
Modified Wed Sep 24 16:33:59 2014 UTC (3 years ago) by pinter
Original Path: trunk/Modules
BUG: Re-enable scrollbar for Subject hierarchy tree view

It's better to have a double scrollbar than being confused about the layout (if there are many nodes in the tree, then a scrollbar is added to both the module widget and the tree view), so I re-add the scrollbar temporarily until a better fix is made.

Revision 23721 - Directory Listing
Modified Tue Sep 23 04:43:52 2014 UTC (3 years ago) by jcfr
Original Path: trunk/Modules
ENH: Set objectName with editor PaintEffect UI element

This is particularly useful when recording macro using QtTesting or
when one need to get a reference to a widget associated with the effect
using its name.

Revision 23715 - Directory Listing
Modified Sat Sep 20 02:52:48 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
COMP: N4ITKBiasFieldCorrection - Fix compilation error with ITK_USE_64BITS_IDS

Similar to the change to vtkITK applied in previous commit (r23714), this
commit fixes the build error happening on windows when building
the CLI module N4ITKBiasFieldCorrection with the option ITK_USE_64BITS_IDS
enabled.

From: Gib Bogle <g.bogle@auckland.ac.nz>

Revision 23713 - Directory Listing
Modified Fri Sep 19 18:22:36 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
ENH: DICOM2FullBrainTractography now supports setting a new scene.

Revision 23712 - Directory Listing
Modified Fri Sep 19 18:22:33 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
BUG: Reference parent when creating DICOM2FullBrainTractography workflow

Prior to this commit, the layout was incorrectly used as a the parent
widget. This was working because the function "QLayout::layout()" return
the layout that would be otherwise returned by "parent.layout().

Revision 23711 - Directory Listing
Modified Fri Sep 19 18:22:31 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
BUG: Fix memory leak in SlicerDICOM2FullBrainTractographyModuleGenericTest

This commit sets the parent for the workflow. Doing so will ensure the
workflow and its children will be deleted.

Revision 23705 - Directory Listing
Modified Thu Sep 18 08:51:18 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
BUG: Fix crash when setting null scene on Markups widget.

This commit re-organizes the code associate with function
"onActiveMarkupMRMLNodeChanged" to prevent a crash and avoid displaying
warnings when setting a null scene.

Revision 23703 - Directory Listing
Modified Thu Sep 18 08:51:14 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
STYLE: Simplify RegisterNodes implementation in Markups and Annotation logic

This commit updates the code to use smart pointer.

Revision 23700 - Directory Listing
Modified Wed Sep 17 22:28:42 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
ENH: Simplify vtkMRMLFiberBundleNode::Add(Line/Tube/Glyph)DisplayNode methods

This commit update the functions Add(Line/Tube/Glyph)DisplayNode methods
to return null if no scene has been set. Doing so will prevent memory leak
ensuring new node are always added to the scene.

Revision 23698 - Directory Listing
Modified Wed Sep 17 22:28:38 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
STYLE: Use vtkNew in vtkSeedTract/vtkDiffusionTensorGlyph/...

This commit simplifies code using vtkNew where it makes sense.

Revision 23697 - Directory Listing
Modified Wed Sep 17 19:59:43 2014 UTC (3 years, 1 month ago) by pieper
Original Path: trunk/Modules
ENH: improve dicom warning and tooltip for loadables

Revision 23696 - Directory Listing
Modified Wed Sep 17 19:59:41 2014 UTC (3 years, 1 month ago) by pieper
Original Path: trunk/Modules
BUG: #3847 create subseries based on image orientation in DICOM

Because the image orientation patient value can include a
comma, the logic to track the distinct values in a collection
of files failed to recognize different orientation values.
This led the only available loading option in slicer being one
with a mix of orientations, leading to incorrect geometry.
This fix allows the plugin to generate independent loadables
for each orientation, thus removing the incorrect behavior.

The issue remains that the loadable with the geometry warning
is still the highest confidence loadable which could lead
to errors.  Will address that independently.

Revision 23692 - Directory Listing
Modified Wed Sep 17 12:40:40 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
ENH: Do not set workaround to associate scalar with input tensor field.

This is not required when using VTK6.

Revision 23691 - Directory Listing
Modified Wed Sep 17 12:40:38 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
STYLE: Remove commented code from Tractography seeding modules

Revision 23690 - Directory Listing
Modified Wed Sep 17 12:40:36 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
BUG: Re-organize tractography seeding pipeline to work with VTK6. See #3845

This commit fixes pipeline incorrectly setup in r23121 by using output
port instead pipeline information (InputROIPipelineInfo)

Revision 23686 - Directory Listing
Modified Tue Sep 16 07:24:05 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
BUG: Fix qMRMLVolumePropertyNodeWidgetTest1

This commit fixes the failing test by ensuring the vtkRenderingContextOpenGL
module is initialized.

The following error was occurring on all three platforms:

// ----------
Generic Warning: In /path/to/VTKv6/Rendering/Context2D/vtkContextDevice2D.cxx, line 27
Error: no override found for 'vtkContextDevice2D'.
// ----------

For more details, see:
  http://www.vtk.org/Wiki/VTK/Build_System_Migration#How_Implementation_Modules_Are_Initialized
  http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Factories_now_require_defines


Finally, let's also note that the test executable was compiled with:

-DvtkRenderingContext2D_AUTOINIT="1(vtkRenderingContextOpenGL)"
-DvtkRenderingCore_AUTOINIT="4(vtkInteractionStyle,vtkRenderingFreeType,vtkRenderingFreeTypeOpenGL,vtkRenderingOpenGL)"
-DvtkRenderingFreeType_AUTOINIT="1(vtkRenderingFreeTypeFontConfig)"
-DvtkRenderingVolume_AUTOINIT="1(vtkRenderingVolumeOpenGL)"

and was linked against vtkRenderingContextOpenGL.

Revision 23685 - Directory Listing
Modified Tue Sep 16 03:50:18 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
COMP: Update ModelToLabelMap and remove unused dependency to ITKDeprecated

In r23660, the dependency to AnalyzeImageIO headers has been removed.
This commit also removes the now unneeded dependency to "ITKDeprecated".

Thanks to "Gib Bogle <g.bogle@auckland.ac.nz>" for reporting the problem.

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

Revision 23684 - Directory Listing
Modified Tue Sep 16 03:28:40 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
BUG: Fix OtsuThresholdImageFilterTest on Windows

This commit ensures that "SEM_LAUNCH_COMMAND" variable will be defined
for both CLIs and remote modules.

Revision 23682 - Directory Listing
Modified Tue Sep 16 02:57:09 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
COMP: Remove unused dependency to ITKDeprecated from ResampleDTIVolume

The dependency was probably added by "mistake" when the module
"Utilities/Maintenance/WhatModulesITK.py" was used to create the list of
dependent modules (r23413). Since the header "itkSemaphore.h" was
specified in the code but was commented, "WhatModulesITK" reported its
associated module ITKDeprecated as required.

This commit removes the commented code and updates the CMakeLists.txt

Thanks to "Gib Bogle <g.bogle@auckland.ac.nz>" for reporting the problem.

Revision 23681 - Directory Listing
Modified Tue Sep 16 00:51:29 2014 UTC (3 years, 1 month ago) by lassoan
Original Path: trunk/Modules
BUG: Fixed ExtensionWizard immediate scripted module loading

Problem was that settingsList returned a tuple, which is not mutable and therefore rawSearchPaths.append failed.

Revision 23676 - Directory Listing
Modified Sun Sep 14 11:28:09 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
ENH: Added icon loading for scripted module base class

Python scripted modules that use the ScriptedLoadableModule base class
now load their icon from Resources/Icons/<ModuleName>.png.
If the icon file does not exist then the default icon is kept.
Modules can override the icon setting in the module __init__ function to
use any other custom icon.

Updated extension wizard template and extension test.

Updated one more module (VectorToScalarVolume) to use
ScriptedLoadableModule base class.

From: Andras Lasso <lasso@queensu.ca>

Revision 23675 - Directory Listing
Modified Sat Sep 13 03:07:33 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
ENH: Fixed color scalar bar by using vtkPVScalarBarActor

* Color scalar bar was enhanced and the bugs were fixed by adding Paraview vtkPVScalarBarActor to module's logic
* Replaced vtkScalarBarActor with vtkPVScalarBarActor
* Made the logic sensitive to dicom volume. (for none dicom volumes the
 color scalar bar would occupy 100% of the view's width)
* Change the format of foreground volume and label opacities to percentage
(e.g. from 0.4 to 40%)

From: Alireza Mehrtash <mehrtash@bwh.harvard.edu>

Revision 23673 - Directory Listing
Modified Sat Sep 13 03:07:26 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
COMP: Slicer welcome: Fix location of qrc files in UI file.

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

Revision 23672 - Directory Listing
Modified Fri Sep 12 05:30:49 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
ENH: Update AddMarkup/Fiducial API to optionally accept the label.

When calling the AddMarkup/AddFiducial method, a default
label is associated. That said, it is not uncommon to create markup
or fiducial with a custom label.

For example, within a python script, before this commit, the following
could be done to add a fiducial and set its label:

  fiducialIndex = markups.AddFiducial(x, y, z)
  markups.SetNthMarkupLabel(fiducialIndex, "Foo")

The first issue is that the event 'MarkupAddedEvent' was triggered before the
label was set. Since when the markup is added an hypothetical callback
could retrieve other data structure based on the label, it is more
complex to do the book-keeping if the callback can't make use of the
label.

This commit ensures that callback connected to "MarkupAddedEvent" will
be able to get the custom label value.

The second issue is that the "Markup" structure is not wrapped in python.
That means it is not possible to pre-initialize a markup structure
before adding it using "AddMarkup(Markup markup)"

Note that ideally, it should be possible to pass other properties
to initialize the markup in python or c++ before the "MarkupAddedEvent"
is invoked. This commit is a trade-off between changing the Markup
structure into a more heavy weight vtkObject (so that it is wrapped) and
not being able to set the label before "MarkupAddedEvent" is invoked.

Revision 23671 - Directory Listing
Modified Fri Sep 12 05:05:44 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
ENH: Change 'AddMarkup' to also return the markupIndex on success.

This commit updates the function 'AddMarkup' to behave similarly
to 'AddMarkupWithNPoints' function.

Revision 23670 - Directory Listing
Modified Thu Sep 11 20:33:00 2014 UTC (3 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: fix crash when showing transformed markups

The module widget was getting the world coordinates by passing in a 3
element array, not a 4 element array. On some machines this was
triggering a crash. This fix avoids that by properly passing
a four element point array and then reassigning the values to
the three element array for display.

Issue #3756

Revision 23669 - Directory Listing
Modified Thu Sep 11 20:04:24 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
BUG: Consistently invoke MarkupAddedEvent specifying the markup index.

Revision 23668 - Directory Listing
Modified Thu Sep 11 19:40:59 2014 UTC (3 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: fixing fiducial projections

Turning them on for the first time was causing a null pointer crash in the
VTK 6 rendering pipeline. The glyph source hadn't been updated and the points
were undefined in the default circle glyph.

Also call the displayable manager superclass on scene close to ensure that the
fiducial projections are removed from the render window.

Issue #3821

Revision 23665 - Directory Listing
Modified Wed Sep 10 07:05:08 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
BUG: Proceed to MarkupsFiducial picking manager configuration only for VTK6.

This commit fixes regression introduced in r23648 that was preventing
Slicer from being compiled against VTK5.

Revision 23661 - Directory Listing
Modified Tue Sep 9 20:56:52 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
ENH: Change required ITK version from 4.5 to 4.6

Starting with r23373 ITK 4.6.x is used to build and test Slicer.

$ git shortlog c127db8..6b5fa1a SuperBuild/External_ITKv4.cmake
jcfr (8):
      ENH: Update (1) ITKv4 from v4.5.2 to v4.6rc01 and (2) update BRAINSTools
      BUG: Update ITKv4 project to backport fix related to GDCMIO
      BUG: Update ITKv4 - Attempt to fix ResampleDTI tests
      COMP: Update ITKv4 - Fix "unused-local-typedefs" warning
      COMP: Move most of find_package calls into each Slicer sub-project.
      ENH: Move ITKv4 towards 4.6.0rc20140719
      ENH: Update ITKv4 and BRAINSTools
      BUG: Update ITKv4 and BRAINSTools - BRAINSFit performance improvement.

Revision 23660 - Directory Listing
Modified Tue Sep 9 19:54:01 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
ENH: Remove ITK AnalyzeImageIO registration

Originally introduced in r824, the ITK AnalyzeImageIO have been
deprecated. The NIFTI ImageIO implementation is now able to read
analyze .img or .hdr files as well as the original Analyze ImageIO.

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

Revision 23659 - Directory Listing
Modified Mon Sep 8 07:08:36 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
BUG: Fix crash in AddArchetypeScalarVolume checking MRMLScene validity

Revision 23657 - Directory Listing
Modified Sat Sep 6 20:28:02 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
ENH: Added a test for the ExtractSkeleton CLI. Fixes #3333

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

From: Dirk Padfield <padfield@ge.com>

Revision 23656 - Directory Listing
Modified Sat Sep 6 19:29:46 2014 UTC (3 years, 1 month ago) by pieper
Original Path: trunk/Modules
BUG: 3808: fix failing test - add some pointer checks

Fixes regression detected here:

http://slicer.cdash.org/testDetails.php?test=5704490&build=266935

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

Revision 23652 - Directory Listing
Modified Fri Sep 5 22:00:17 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
ENH: Update GetCoefficientImage to GetCoeffiecientImages

Function renamed, and only available with ITKv3 compatibility.

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

Revision 23651 - Directory Listing
Modified Fri Sep 5 22:00:15 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
ENH: Update to Testing::ComparisionImageFilter

Update deprecated usage of ComparisonImageFilter to
TestingComparisonImageFilter.

Migration:
http://itk.org/migrationv4/index.php?action=artikel&cat=3&id=113&artlang=en&highlight=ComparisonImageFilter

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

Revision 23649 - Directory Listing
Modified Fri Sep 5 20:58:45 2014 UTC (3 years, 1 month ago) by pieper
Original Path: trunk/Modules
ENH: fixed issue #2771 kill preivious storescp executables

The new logic will get the os process list and if (other) storescps are on
the list, it would warn the user and through a dialog asks for killing
these executables. The start listener button is checkable now and it is only
checked when the listner is running.

From: Alireza Mehrtash <mehrtash@bwh.harvard.edu>

Revision 23648 - Directory Listing
Modified Fri Sep 5 20:16:45 2014 UTC (3 years, 1 month ago) by pieper
Original Path: trunk/Modules
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 23646 - Directory Listing
Modified Fri Sep 5 16:00:20 2014 UTC (3 years, 1 month ago) by pieper
Original Path: trunk/Modules
STYLE: add comments to SampleData class

Revision 23645 - Directory Listing
Modified Wed Sep 3 21:17:51 2014 UTC (3 years, 1 month ago) by lassoan
Original Path: trunk/Modules
BUG: Fixed slice annotation not displayed for patient names containing international characters

Error log before the fix:

[INFO][Stream] 03.09.2014 17:00:41 [] (unknown:0) - Traceback (most recent call last):
[INFO][Stream] 03.09.2014 17:00:41 [] (unknown:0) -   File "C:/S4D/Slicer-build/lib/Slicer-4.3/qt-scripted-modules\DataProbeLib\SliceViewAnnotations.py", line 594, in updateCornerAnnotations
[INFO][Stream] 03.09.2014 17:00:41 [] (unknown:0) -     self.makeAnnotationText(caller)
[INFO][Stream] 03.09.2014 17:00:41 [] (unknown:0) -   File "C:/S4D/Slicer-build/lib/Slicer-4.3/qt-scripted-modules\DataProbeLib\SliceViewAnnotations.py", line 825, in makeAnnotationText
[INFO][Stream] 03.09.2014 17:00:41 [] (unknown:0) -     self.drawCornerAnnotations()
[INFO][Stream] 03.09.2014 17:00:41 [] (unknown:0) -   File "C:/S4D/Slicer-build/lib/Slicer-4.3/qt-scripted-modules\DataProbeLib\SliceViewAnnotations.py", line 976, in drawCornerAnnotations
[INFO][Stream] 03.09.2014 17:00:41 [] (unknown:0) -     sliceCornerAnnotation.SetText(i, cornerAnnotation)
[INFO][Stream] 03.09.2014 17:00:41 [] (unknown:0) - TypeError: SetText argument 2: (unicode conversion error)


Revision 23639 - Directory Listing
Modified Sun Aug 31 02:45:34 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
BUG: EditBox: Ensure state variable are initialized before calling "create()"

This commit fixes regression introduced by r23636.

The following tests are now passing:
 * py_StandaloneEditorWidgetTest
 * py_ThresholdThreadingTest
 * py_NeurosurgicalPlanningTutorialMarkupsSelfTest

The associated error was:

Traceback (most recent call last):
  File "/path/to/Slicer-build/lib/Slicer-4.3/qt-scripted-modules/Editor.py", line 244, in setup
    self.createEditBox()
  File "/path/to/Slicer-build/lib/Slicer-4.3/qt-scripted-modules/Editor.py", line 280, in createEditBox
    self.toolsBox = EditorLib.EditBox(self.editBoxFrame, optionsFrame=self.effectOptionsFrame)
  File "/path/to/Slicer-build/lib/Slicer-4.3/qt-scripted-modules/EditorLib/EditBox.py", line 74, in __init__
    self.create()
  File "/path/to/Slicer-build/lib/Slicer-4.3/qt-scripted-modules/EditorLib/EditBox.py", line 289, in create
    self._onParameterNodeModified(self.editUtil.getParameterNode())
  File "/path/to/Slicer-build/lib/Slicer-4.3/qt-scripted-modules/EditorLib/EditBox.py", line 105, in _onParameterNodeModified
    self._onEffectChanged(caller.GetParameter("effect"))
  File "/path/to/Slicer-build/lib/Slicer-4.3/qt-scripted-modules/EditorLib/EditBox.py", line 336, in _onEffectChanged
    if self.currentOption:
AttributeError: 'EditBox' object has no attribute 'currentOption'

Revision 23636 - Directory Listing
Modified Fri Aug 29 19:01:53 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
ENH: Editor: Effects are checkable and updated based on the parameter node

This commit ensures the button effect are checked or unchecked based
on the 'effect' property stored in the parameter node.

It also extends the EditUtil API adding function allowing to more easily
set and get the 'EraseLabel' state.

Revision 23635 - Directory Listing
Modified Fri Aug 29 19:01:50 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
ENH: EditBox: Simplify observation introducing the use of VTKObservationMixin

Revision 23632 - Directory Listing
Modified Fri Aug 29 18:23:48 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
COMP: Always set SOURCE_DIR variable for CLI modules

This commit will allow ResampleScalarVectorDWIVolume to be built
even if ResampleDTI is disabled.

This is needed because ResampleScalarVectorDWIVolume references
the source of ResampleDTI using the variable ResampleDTI_SOURCE_DIR

Revision 23628 - Directory Listing
Modified Wed Aug 27 22:39:24 2014 UTC (3 years, 1 month ago) by pieper
Original Path: trunk/Modules
ENH: Fixed issues 3579, 3798 and other dicom browser improvements

Improvements:
* Added the table density control to the slicer dicom browser for
 controlling table densities in three levels: comact, cozy and
 comfortable. The default value would be compact. Changing the settings
 would be saved in slicer user settings.
* Re-arranged the patient, study and series search boxex so that the
 search box will be on the top of tables for both horizontal and vertical
 cases (This will add more space to dicom tables)
tables)
* The bug with browser size change on advanced view is fixed (issue #3798)
* The feature to resize tables based on contents was added to the tables.

From: Alireza Mehrtash <mehrtash@bwh.harvard.edu>

Revision 23618 - Directory Listing
Modified Mon Aug 25 00:40:14 2014 UTC (3 years, 1 month ago) by jcfr
Original Path: trunk/Modules
BUG: Made color scalar bar RepositionableOff

This is a quick temporary fix for color scalar bar re-positioning
behavior which not works in horizontal mode.

For more details, see http://slicer-devel.65872.n3.nabble.com/Slice-annotations-comments-tp4032290p4032305.html

From: Alireza Mehrtash <mehrtash@bwh.harvard.edu>

Revision 23612 - Directory Listing
Modified Fri Aug 22 20:26:28 2014 UTC (3 years, 1 month ago) by pieper
Original Path: trunk/Modules
ENH: Add Slice Annotations to DataProbe module

This commit enhance the DataProbe module providing an
easy way to show/hide/customize corner annotations, ruler and color bar in the
Slice viewers.

Associated setting are saved in the general settings common to
all version of Slicer installed on the workstation.

The implementation of slice view annotations in DataProbe is a part of QIICR Project [1] includes the following features:

* Corner text annotations including basic DICOM annotations.
* Interactive Color scalar bar widget for background and foreground volumes.
* Scaling ruler

[1] QIICR Slicer infrastructure projects

ENH: Add method vtkMRMLSliceLogic::GetForegroundWindowLevelAndRange

STYLE: Remove dead code

ENH: Added the following enhancements and fixes

* Added color scalar bar actors to color bar widget instead of adding it
directly to renderer. The user can move the color bar now.
* The height of color bar is now sensitive to the top right annotations.
When top right is deactive the height would be almost 100%
* Replaced the hard-coded UI with Qt Designer UI file.
* Fixed the vtk warning:
                   vtkTextActor::SetInput was passed an uninitialized
		   string
* Fixed issues with user settings
* An option added to have persistent background layer dicom annotation.
* Restore default values for all of the default settings was added.

ENH: Modified the logic to use dicom tag cache and the following fixes:

* Added dialog box for notifying slicer users about the new slice
 annotation feature
* Made Color Scalar bar off in default mode
* Code refactored in creating lines for ruler and other minor bugs fixed

From: Alireza Mehrtash <mehrtash@bwh.harvard.edu>

Revision 23603 - Directory Listing
Modified Wed Aug 20 21:26:54 2014 UTC (3 years, 2 months ago) by jcfr
Original Path: trunk/Modules
COMP: Fix unused-but-set-variable warning in vtkImageErode

This commit fixes the following warning happening when building Slicer
in Release:

/path/to/Slicer/Modules/Scripted/EditorLib/Logic/vtkImageErode.cxx: In instantiation of ‘void vtkImageErodeExecute(vtkImageErode*, vtkImageData*, T*, vtkImageData*, int*, int) [with T = double]’:
/path/to/Slicer/Modules/Scripted/EditorLib/Logic/vtkImageErode.cxx:217:26:   required from here
/path/to/Slicer/Modules/Scripted/EditorLib/Logic/vtkImageErode.cxx:76:25: warning: variable ‘tDiff’ set but not used [-Wunused-but-set-variable]
   clock_t tStart, tEnd, tDiff;

Revision 23599 - Directory Listing
Modified Wed Aug 20 21:26:47 2014 UTC (3 years, 2 months ago) by jcfr
Original Path: trunk/Modules
COMP: Removed legacy module OtsuThresholdSegmentation. See #3401

For future reference, code has been moved into a dedicated repository.
See https://github.com/Slicer/Slicer-OtsuThresholdSegmentation

Revision 23598 - Directory Listing
Modified Wed Aug 20 21:26:43 2014 UTC (3 years, 2 months ago) by jcfr
Original Path: trunk/Modules
COMP: Removed legacy module OtsuThresholdImageFilter. See #3401

For future reference, code has been moved into a dedicated repository.
See https://github.com/Slicer/Slicer-OtsuThresholdImageFilter

Revision 23597 - Directory Listing
Modified Wed Aug 20 21:26:40 2014 UTC (3 years, 2 months ago) by jcfr
Original Path: trunk/Modules
COMP: Removed legacy module MultiResolutionAffineRegistration. See #3401

For future reference, code has been moved into a dedicated repository.
See https://github.com/Slicer/Slicer-MultiResolutionAffineRegistration

Revision 23596 - Directory Listing
Modified Wed Aug 20 21:26:36 2014 UTC (3 years, 2 months ago) by jcfr
Original Path: trunk/Modules
COMP: Removed legacy module BSplineDeformableRegistration. See #3401

For future reference, code has been moved into a dedicated repository.
See https://github.com/Slicer/Slicer-BSplineDeformableRegistration

Revision 23595 - Directory Listing
Modified Wed Aug 20 21:26:34 2014 UTC (3 years, 2 months ago) by jcfr
Original Path: trunk/Modules
COMP: Removed legacy module RigidRegistration. See #3401

For future reference, code has been moved into a dedicated repository.
See https://github.com/Slicer/Slicer-RigidRegistration

Revision 23594 - Directory Listing
Modified Wed Aug 20 21:26:32 2014 UTC (3 years, 2 months ago) by jcfr
Original Path: trunk/Modules
COMP: Removed legacy module LinearRegistration. See #3401

For future reference, code has been moved into a dedicated repository.
See https://github.com/Slicer/Slicer-LinearRegistration

Revision 23593 - Directory Listing
Modified Wed Aug 20 21:26:30 2014 UTC (3 years, 2 months ago) by jcfr
Original Path: trunk/Modules
COMP: Removed legacy module AffineRegistration. See #3401

For future reference, code has been moved into a dedicated repository.
See https://github.com/Slicer/Slicer-AffineRegistration

Revision 23592 - Directory Listing
Modified Wed Aug 20 21:26:27 2014 UTC (3 years, 2 months ago) by jcfr
Original Path: trunk/Modules
COMP: Removed unused module MRIBiasFieldCorrection. See #3401

For future reference, code has been moved into a dedicated repository.
See https://github.com/Slicer/Slicer-MRIBiasFieldCorrection

Revision 23590 - Directory Listing
Modified Tue Aug 19 15:39:30 2014 UTC (3 years, 2 months ago) by pieper
Original Path: trunk/Modules
BUG: #3807 fix crashes when cloning non-scalar volumes

Since nodes are strongly typed, it's important to get the right
subclass when making the copy.  Unfortunately New is not virtual
and there's currently not a good way to make this code polymorphic.
We should investigate doing a sweeping change to MRML so that
the vtkStandardNewMacro is used appropriately but that is a bigger
change than is needed to fix this particular bug.

Revision 23588 - Directory Listing
Modified Tue Aug 19 14:34:09 2014 UTC (3 years, 2 months ago) by jcfr
Original Path: trunk/Modules
COMP: Do not install CLIROITest

Revision 23579 - Directory Listing
Modified Sun Aug 17 23:30:28 2014 UTC (3 years, 2 months ago) by jcfr
Original Path: trunk/Modules
ENH: Simplified transform storage node. See #3788

From: Andras Lasso <lasso@queensu.ca>

Revision 23574 - Directory Listing
Modified Sun Aug 17 23:30:12 2014 UTC (3 years, 2 months ago) by jcfr
Original Path: trunk/Modules
ENH: WIP - Add .h5 formated transform storage of BSplines. See #3788

Partial implementation for reading itkBSplineTransform (for ITKv4)

Mostly implemented but the transform that gets read in is identity
and not the one in the file. Probably something wrong with
this cast:

+  typedef itk::BSplineTransform< T,VTKDimension,BSPLINE_TRANSFORM_ORDER > BSplineTransformType;
+  typename BSplineTransformType::Pointer bsplineItk =
+    dynamic_cast< BSplineTransformType* >( warpTransformItk.GetPointer() );

The transformation itself is not populated with correct data,
so need to reach inside to get spacing, origin, etc.

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

Revision 23569 - Directory Listing
Modified Fri Aug 15 20:49:16 2014 UTC (3 years, 2 months ago) by pieper
Original Path: trunk/Modules
COMP: fix case of Qt method in VTK branch

Qt methods start with lower case and probably this
branch never got tested on VTK5.

Revision 23566 - Directory Listing
Modified Thu Aug 14 18:10:10 2014 UTC (3 years, 2 months ago) by jcfr
Original Path: trunk/Modules
ENH: Add enhanced scalarbar actor class based on VTK6. Fixes #2919

The VTK6 vtkScalarBarActor class allows displaying annotations in
conjunction with labels. However, in Slicer we want to sample the
annotations for display just like color values since some color
tables have more than 10000 values and annotations.

The vtkSlicerScalarBarActor is based on vtkScalarBarActor class and
only overrides its LayoutTicks method to slightly modify the method
to enable sampling the annotations and display it as labels.

Additional remarks:

* Change colors module logic using the new class.

* Keep backward compatibility to VTK5.

* Added a python selftest based on scripted module superclass.

* Added a check box to toggle using the color names as labels, and set
default label formats when it's toggled to support strings or numbers.

* Added simple label format testing to avoid crashes that were seen when
using a string format with a number value.

* Regular expression associated with LabelFormat could be improved. This
is tracked by issue 3802

Co-authored-by: Nicole Aucoin <nicole@bwh.harvard.edu>

From: Kevin Wang <kevin.wang@rmp.uhn.ca>

Revision 23563 - Directory Listing
Modified Tue Aug 12 18:31:31 2014 UTC (3 years, 2 months ago) by pinter
Original Path: trunk/Modules
BUG: Fixed clone when cloned volume does not have display node. Fixes #3795

Fixing second function doing that (rev23561 fixed only vtkSlicerVolumesLogic::CloneVolume, this commit fixes vtkSlicerVolumesLogic::CloneVolumeWithoutImageData)

Revision 23562 - Directory Listing
Modified Fri Aug 8 16:18:21 2014 UTC (3 years, 2 months ago) by pinter
Original Path: trunk/Modules
BUG: Handled scene context request in SceneViews subject hierarchy plugin

Revision 23561 - Directory Listing
Modified Thu Aug 7 18:45:02 2014 UTC (3 years, 2 months ago) by jcfr
Original Path: trunk/Modules
BUG: Fixed crash when cloned volume does not have display node. Fixes #3795

From: Csaba Pinter <csaba.pinter@queensu.ca>

Revision 23551 - Directory Listing
Modified Wed Aug 6 02:21:59 2014 UTC (3 years, 2 months ago) by pinter
Original Path: trunk/Modules
ENH: Added SceneViews and Segment plugins to subject hierarchy

SceneViews is a role plugin for scene view nodes. Provides an icon and allows restoring scene views (request of Sonia)
Segment is a function plugin that adds a context sub-menu ("Segment this using...") to volumes. There is only one action under the sub-menu so far that takes the user to the Editor module, sets the volume as master and creates a labelmap as merge volume.

Revision 23550 - Directory Listing
Modified Tue Aug 5 17:58:19 2014 UTC (3 years, 2 months ago) by jcfr
Original Path: trunk/Modules
BUG: Fixed issue of DICOM browser not closed after loading a volume

Browser was not closed after loading a volume even if "Persistent" checkbox was unchecked.

Also added a settings (DICOM/BrowserPersistent) to remember the checkbox setting.

From: Andras Lasso <lasso@queensu.ca>

Revision 23547 - Directory Listing
Modified Mon Aug 4 01:48:15 2014 UTC (3 years, 2 months ago) by jcfr
Original Path: trunk/Modules
BUG: Create new indexer for each file

Suggested by Steve Pieper as a way to work around potential issues in CTK

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

Revision 23546 - Directory Listing
Modified Mon Aug 4 01:48:12 2014 UTC (3 years, 2 months ago) by jcfr
Original Path: trunk/Modules
ENH: Adding the capability to process derived items

DerivedItems is a list of file names attributes on the
loadable with the DICOM instances produced by the plugin,
which will be added to the database after loading
the loadable.

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

Revision 23545 - Directory Listing
Modified Sun Aug 3 20:08:26 2014 UTC (3 years, 2 months ago) by pinter
Original Path: trunk/Modules
ENH: Minor subject hierarchy enhancements

If a subject hierarchy node is deleted that has children, the user is given the option to delete branch.
Subject hierarchy added to favorite module list (still not appearing, because QSettings is pre-loaded from somewhere)

Revision 23541 - Directory Listing
Modified Sat Aug 2 05:43:11 2014 UTC (3 years, 2 months ago) by jcfr
Original Path: trunk/Modules
STYLE: Simplify qSlicerModelsModuleWidget introducing vtkNew smartpointer

Using vtkNew avoid to manually manage reference and simplify the
code.

Revision 23540 - Directory Listing
Modified Fri Aug 1 23:09:51 2014 UTC (3 years, 2 months ago) by pinter
Original Path: trunk/Modules
ENH: Show volume and model information in subject hierarchy

Show extended information for volumes and models in their tooltips in subject hierarchy

Fixes #1424

Revision 23538 - Directory Listing
Modified Fri Aug 1 21:23:13 2014 UTC (3 years, 2 months ago) by pinter
Original Path: trunk/Modules
BUG: Minor fixes in subject hierarchy

There was a double scrollbar in case of many nodes (one for the module panel, one for the tree view), which was not convenient or nice. The tree view scrollbar has been disabled, so now the same behavior can be seen as in the Data module.
Parse local data plugin fixed so that data nodes do not stay around after creating subject hierarchy from them.

Revision 23536 - Directory Listing
Modified Fri Aug 1 19:46:04 2014 UTC (3 years, 2 months ago) by pinter
Original Path: trunk/Modules
BUG: Fixed extra spaces in names of DICOM volumes

Spaces were added after each character of the name of a volume that was loaded from DICOM. This has now been fixed by encoding to Latin-1 (which conversion is used throughout the code).

Fixes #3688

Revision 23535 - Directory Listing
Modified Fri Aug 1 19:17:40 2014 UTC (3 years, 2 months ago) by pinter
Original Path: trunk/Modules
BUG: Fixed issues caused by LazyUpdate in subject hierarchy model

Complete scene update triggered by LazyUpdate in subject hierarchy after batch processing caused a crash in certain conditions. This has been fixed by only triggering it at scene import, which is necessary.
invalidateModels replaced with invalidateFilter, which his called when filtering needs to be refreshed, e.g. when removing nodes by plugins

Revision 23534 - Directory Listing
Modified Fri Aug 1 15:08:03 2014 UTC (3 years, 2 months ago) by pieper
Original Path: trunk/Modules
ENH: #3753 make ResampleVolumeToReferenceVolume static

Per request from Kevin who reports this was overlooked
in the first version.

Revision 23533 - Directory Listing
Modified Fri Aug 1 07:31:12 2014 UTC (3 years, 2 months ago) by jcfr
Original Path: trunk/Modules
COMP: Fix unused variable warning in qSlicerSubjectHierarchyAbstractPlugin

This commit fixes regression introduced in r23489

Revision 23527 - Directory Listing
Modified Thu Jul 31 20:53:12 2014 UTC (3 years, 2 months ago) by pinter
Original Path: trunk/Modules
BUG: Fix update issues in subject hierarchy when module active

Subject hierarchy tree was not properly updated when reparenting programatically or importing/restoring scene when module was active. This has been fixed and some unnecessary code removed.
More testing added to SubjectHierarchyGenericSelfTest.

Revision 23525 - Directory Listing
Modified Wed Jul 30 22:49:51 2014 UTC (3 years, 2 months ago) by naucoin
Original Path: trunk/Modules
BUG: respect don't show again on fiducials conversion

Define a new button with an AcceptRole to have it saved
in the config file, following the pattern of the Delete
pop up boxes.

Issue #3663



Revision 23508 - Directory Listing
Modified Wed Jul 30 02:32:01 2014 UTC (3 years, 2 months ago) by jcfr
Original Path: trunk/Modules
COMP: Specify list VTK_MAKE_INSTANTIATOR3 input as list of cxx files only.

This commit fixes a build error introduced by kitware/VTK@5c3241b9d8
It ensures there are no duplicated entries in the instantiator files.

The error (reported below) was first discovered when building Slicer
on MacOSX 10.6 with the option VTK_ENABLE_KITS while working on issue
#3741.

// ------------------------
$ make vtkSlicerTransformsModuleMRMLDisplayableManager/fast
[ 59%] Building CXX object Modules/Loadable/Transforms/MRMLDM/CMakeFiles/vtkSlicerTransformsModuleMRMLDisplayableManager.dir/TransformsInstantiator.cxx.o
/path/to/Slicer-build/Modules/Loadable/Transforms/MRMLDM/TransformsInstantiator.cxx: In function 'vtkObject* vtkInstantiatorvtkMRMLTransformsDisplayableManager2DNew()':
/path/to/Slicer-build/Modules/Loadable/Transforms/MRMLDM/TransformsInstantiator.cxx:10: error: redefinition of 'vtkObject* vtkInstantiatorvtkMRMLTransformsDisplayableManager2DNew()'
/path/to/Slicer-build/Modules/Loadable/Transforms/MRMLDM/TransformsInstantiator.cxx:9: error: 'vtkObject* vtkInstantiatorvtkMRMLTransformsDisplayableManager2DNew()' previously defined here
/path/to/Slicer-build/Modules/Loadable/Transforms/MRMLDM/TransformsInstantiator.cxx: In function 'vtkObject* vtkInstantiatorvtkMRMLTransformsDisplayableManager3DNew()':
/path/to/Slicer-build/Modules/Loadable/Transforms/MRMLDM/TransformsInstantiator.cxx:12: error: redefinition of 'vtkObject* vtkInstantiatorvtkMRMLTransformsDisplayableManager3DNew()'
/path/to/Slicer-build/Modules/Loadable/Transforms/MRMLDM/TransformsInstantiator.cxx:11: error: 'vtkObject* vtkInstantiatorvtkMRMLTransformsDisplayableManager3DNew()' previously defined here
make[1]: *** [Modules/Loadable/Transforms/MRMLDM/CMakeFiles/vtkSlicerTransformsModuleMRMLDisplayableManager.dir/TransformsInstantiator.cxx.o] Error 1
make: *** [vtkSlicerTransformsModuleMRMLDisplayableManager/fast] Error 2
// ------------------------

The content of the associated instantiator file was:

// ---------------
$ cat Modules/Loadable/Transforms/MRMLDM/TransformsInstantiator.cxx

[...]

vtkInstantiatorNewMacro(vtkMRMLTransformsDisplayableManager2D)
vtkInstantiatorNewMacro(vtkMRMLTransformsDisplayableManager2D)
vtkInstantiatorNewMacro(vtkMRMLTransformsDisplayableManager3D)
vtkInstantiatorNewMacro(vtkMRMLTransformsDisplayableManager3D)

[...]
// ---------------

This commit avoid the duplicated entries in the instantiator file.

Revision 23506 - Directory Listing
Modified Tue Jul 29 23:59:34 2014 UTC (3 years, 2 months ago) by jcfr
Original Path: trunk/Modules
ENH: Added developer mode and base classes for scripted modules

* Added "Enable developer mode" option in the application settings
(Developer section, next to Enable QtTesting)

* Added base classes for scripted module, widget, logic, and test: they
make scripted modules simpler and shorter and also more functions and
helper methods can be added in the future without changing each scripted
module
** Module handles selftest registration
** Widget handles reload&test (shown on GUI only in developer mode)
** Logic and Test contains delayDisplay utility function

* As an example, updated ScriptedLoadableModuleTemplate and SurfaceToolbox to use the new base classes

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

Revision 23505 - Directory Listing
Modified Tue Jul 29 23:43:49 2014 UTC (3 years, 2 months ago) by pinter
Original Path: trunk/Modules
BUG: Fixed SubjectHierarchyGenericSelfTest
Fixes #3754

Additional minor fixes in handling potential nodes in the subject hierarchy tree (removed unavailable context menu items)
Removed potential subject hierarchy node list and related classes (model, proxy model, designer plugin)

Revision 23494 - Directory Listing
Modified Tue Jul 29 22:35:30 2014 UTC (3 years, 2 months ago) by pieper
Original Path: trunk/Modules
BUG: check for valid transform pointers to avoid crash

On scene close and possibly other circumstances there can be transform
nodes that don't have valid transforms, so check the pointers.

Revision 23493 - Directory Listing
Modified Tue Jul 29 22:27:54 2014 UTC (3 years, 2 months ago) by naucoin
Original Path: trunk/Modules
BUG: test for active camera before enabling fiducials

Removes the error message that world to view and view to world
can't compute result due to a missing active camera. Delaying
setting the handles and widgets to be enabled if there's
no active camera defined on their renderers seems to work well
since the next time through the update code once the layout
has stabilised and the renderers are updated, the seeds 
will get positioned and enabled.

Issue #3761


Revision 23492 - Directory Listing
Modified Tue Jul 29 22:11:12 2014 UTC (3 years, 2 months ago) by pieper
Original Path: trunk/Modules
ENH: Added a method in VolumesLogic class to resample volume node.

Also added a new CloneVolume method which does not clone the imageData. Changed the LabelStatistics.py to use the new resample logic to make labelmap same as input volume.

From: Kevin Wang <kevin.wang@rmp.uhn.ca>

Revision 23491 - Directory Listing
Modified Tue Jul 29 22:11:10 2014 UTC (3 years, 2 months ago) by pieper
Original Path: trunk/Modules
ENH: Added a method in VolumesLogic class to resample volume node.

Also changed the LabelStatistics.py to use the new resample logic to make labelmap same as input volume.

From: Kevin Wang <kevin.wang@rmp.uhn.ca>

Revision 23489 - Directory Listing
Modified Mon Jul 28 22:06:04 2014 UTC (3 years, 2 months ago) by pinter
Original Path: trunk/Modules
BUG: Subject hierarchy UI update issues fixed
Fixes #3714

- qMRMLSceneSubjectHierarchyModel::nodeIndex rewritten to generate correct indices, parentNode also fixed. Workarounds removed
- New subject hierarchy nodes get simpler names
- Setting icons is not so simple as it should be due to a bug in Qt (https://bugreports.qt-project.org/browse/QTBUG-20248), which raises the need to check if the icon to be set is the same as the current icon of an item. This introduces one more thing to remember to the developer. Thus, instead of having the plugins set icons on items, they just return it (or an empty one), and the model does the check. This way developing plugins is not harder than before.
- Changed copyright information in all subject hierarchy files
- Instead of having the potential nodes list on the bottom of the module, those nodes are shown in the subject hierarchy tree on the top-level without icons. They can be shown/hidden with a checkbox under the tree, and can be handled the same way as in the potential list before.


Revision 23488 - Directory Listing
Modified Mon Jul 28 13:56:08 2014 UTC (3 years, 2 months ago) by jcfr
Original Path: trunk/Modules
BUG: Fix CheckForLabelVolumeValidity warning. Fixes #3776

This commit fixes a regression introduced in r23406 [1]
where calling CheckForLabelVolumeValidity with two volumes that have
the same dimension was returning a wrong warning, e.g. "IJKToRAS mismatch
at [0, 3] (-89.6207 != -89.6207)", "IJKToRAS mismatch
at [1, 1] (0.000542851 != 0.000542851)", and "IJKToRAS mismatch
at [2, 0] (4.32616e-09 != 4.32616e-09) IJKToRAS mismatch
at [2, 2] (0.0752821 != 0.0752821)", and "IJKToRAS mismatch
at [2, 3] (176.197 != 176.197)".

Thanks to "safir" for reporting the problem and suggesting a solution.

[1] http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=23406

Revision 23484 - Directory Listing
Modified Thu Jul 24 14:20:37 2014 UTC (3 years, 2 months ago) by pinter
Original Path: trunk/Modules
STYLE: Removed testing code from previous commit

Revision 23483 - Directory Listing
Modified Thu Jul 24 14:18:44 2014 UTC (3 years, 2 months ago) by pinter
Original Path: trunk/Modules
BUG: Fixed accented character display of series and studies in subject hierarchy

Fixes #3688

Revision 23473 - Directory Listing
Modified Mon Jul 21 20:51:00 2014 UTC (3 years, 3 months ago) by pieper
Original Path: trunk/Modules
BUG: unicodeify date to fix subject hierarchy

Revision 23472 - Directory Listing
Modified Mon Jul 21 20:50:56 2014 UTC (3 years, 3 months ago) by pieper
Original Path: trunk/Modules
BUG: 3688 unicode characters from dicom

Add a utility to handle unicode conversion.  It works in the
ScalarVolume plugin but not in the Subject Hiearchy
code.  I want to run this by @pinter for help.

Revision 23464 - Directory Listing
Modified Fri Jul 18 18:43:28 2014 UTC (3 years, 3 months ago) by lassoan
Original Path: trunk/Modules
BUG: Fixed distorted sphere brush in editor paint tool

Out-of-plane dimension of the sphere brush was computed incorrectly. When a volume with anisotropic spacing was loaded then the bursh shape became ellipsoid.
(e.g., load the MRHead volume, set Z spacing to 10mm, draw in the sagittal view => enormous blobs appear on the axial and coronal slices).

The problem was that out-of-plane voxel size was computed incorrectly.

Revision 23453 - Directory Listing
Modified Fri Jul 18 04:45:59 2014 UTC (3 years, 3 months ago) by jcfr
Original Path: trunk/Modules
COMP: Fix doxygen warnings and tweak doxygen layout

This commit also updated the main page to include an "important link"
section. It has been inspired by the Blender main page.

Revision 23450 - Directory Listing
Modified Fri Jul 18 00:04:38 2014 UTC (3 years, 3 months ago) by jcfr
Original Path: trunk/Modules
COMP: Silence unused variable warning in qMRMLTransformInfoWidget

Revision 23425 - Directory Listing
Modified Wed Jul 9 08:17:39 2014 UTC (3 years, 3 months ago) by jcfr
Original Path: trunk/Modules
BUG: vtkNRRDReader filename ambiguity. Fixes #3766

Slicer has a class vtkNRRDReader in Libs/vtkTeem. VTKv4 has a class
vtkNrrdreader in VTK/IO/Image. On case insensitive file systems
(e.g. Windows and some Macs), the statement #include "vtkNRRDReader.h"
will actually include the file vtkNrrdReader (from VTKv6). The
compiler will report the error: error: ‘vtkNRRDReader’ was not
declared in this scope.

CLI's that explicitly include vtkNRRDReader will have these
errors.
Prior to check-in:
https://github.com/Slicer/Slicer/commit/f0f0df61038b9591e895ccb4a40256167e5366d3
a cmake statement:
include_directories(BEFORE ${vtkTeem_INCLUDE_DIRS})
insured that the Slicer vtkNRRDReader would be found.

This patch restores the
include_directories(BEFORE ${vtkTeem_INCLUDE_DIRS})
with a more descriptive comment to prevent its removal in the future.

From: Bill Lorensen <bill.lorensen@gmail.com>

Revision 23424 - Directory Listing
Modified Wed Jul 9 03:34:30 2014 UTC (3 years, 3 months ago) by lassoan
Original Path: trunk/Modules
BUG: Fixed VTK 6 incompatibility in LabelStatistics

Revision 23413 - Directory Listing
Modified Fri Jul 4 01:34:23 2014 UTC (3 years, 3 months ago) by jcfr
Original Path: trunk/Modules
COMP: Move most of find_package calls into each Slicer sub-project.

To help address issue #3741 [1], call to find_package associated to CTK,
DCMTK, ITK and SlicerExecutionModel have been moved in every Slicer
sub project, library or module expecting it.

This allows to reduce both the number of include directories and
the number of libraries passed to the compiler.

Moving forward, every Slicer sub project, library or module will be
responsible to call find_package (optionally specifying a list of
components) and (if it applies) include the associated "use file".

Note that call to find_package(VTK) is still done at the top-level, before
moving the call to the expected sub-directories, the CTKConfig.cmake
will have to be updated to call find_package(VTK) specifying the required
components where it is needed.

[1] http://na-mic.org/Mantis/view.php?id=3741

Revision 23412 - Directory Listing
Modified Fri Jul 4 01:33:36 2014 UTC (3 years, 3 months ago) by jcfr
Original Path: trunk/Modules
COMP: Disable VTK find_package/use_file_include in sub directory.

Calling "find_package(VTK)/include(${VTK_USE_FILE})" in both the top-level
directory and sub-directories is undefined. Indeed, If we include
VTK_USE_FILE (UseVTK.cmake) in the top level then it is probably adding
the autoinit definitions to the COMPILE_DEFINITIONS directory property.
Then that inherits to the sub-directory and could conflict with any such
property defined there. Thanks to Brad King for his insight.

Revision 23410 - Directory Listing
Modified Thu Jul 3 18:18:27 2014 UTC (3 years, 3 months ago) by naucoin
Original Path: trunk/Modules
BUG: fix the path to the ruler scene file for test

Pass the Input data directory via the CMakeLists file on the command line.
Avoids the hard coded path that assumes a specific directory name for
the Slicer source code check out.

Issue #3758


Revision 23406 - Directory Listing
Modified Wed Jul 2 20:44:13 2014 UTC (3 years, 3 months ago) by pieper
Original Path: trunk/Modules
ENH: move duplicated code into volumes logic

Both the Editor and LabelStatistics modules had code to check
that volume geometry matched for a label map.  The duplicated
code is removed and there is a test in LabelStatistics.

Revision 23405 - Directory Listing
Modified Wed Jul 2 13:56:15 2014 UTC (3 years, 3 months ago) by pinter
Original Path: trunk/Modules
STYLE: Reduced debug messages related to subject hierarchy

Didn't delete them, just commented out, so that they can be restored when debugging plugin ownership changes and other issues.

Revision 23396 - Directory Listing
Modified Mon Jun 30 13:18:21 2014 UTC (3 years, 3 months ago) by jcfr
Original Path: trunk/Modules
COMP: Remove unused CLIs MIDASApplications and BatchMakeApplications

See #3401

Revision 23387 - Directory Listing
Modified Fri Jun 27 02:51:54 2014 UTC (3 years, 3 months ago) by jcfr
Original Path: trunk/Modules
ENH: Added mouse cursor position to vtkMRMLCrosshairNode.

Now cursor (now only mouse position in 2D Slice view, but later also
other pointing devices can be supported) position can be obtained by
observing the vtkMRMLCrosshairNode singleton node.

The feature is used in:
* DataProbe window
* Transform info window (showing the transform displacement vector value
  at the current mouse position in real-time)

After the integration into the Slicer core is done, it will be also used
in MultiVolume, Multidimensional data for live 3D graphing.

Also separated SetCursorPositionRAS and SetCursorPositionXYZ methods to
allow 3D-only positioning devices to specify the cursor position
(when no 2D slice position is available)

From: Andras Lasso <lasso@queensu.ca>

Revision 23384 - Directory Listing
Modified Thu Jun 26 20:57:14 2014 UTC (3 years, 3 months ago) by pieper
Original Path: trunk/Modules
ENH: Add prostate MR-Ultrasound to sample data

Revision 23380 - Directory Listing
Modified Thu Jun 26 16:02:06 2014 UTC (3 years, 3 months ago) by jcfr
Original Path: trunk/Modules
STYLE: Simplify qMRMLScene canBeAChild/canBeAParent implementation

Revision 23378 - Directory Listing
Modified Thu Jun 26 12:52:07 2014 UTC (3 years, 3 months ago) by pieper
Original Path: trunk/Modules
ENH: document string for markups event enum

Revision 23371 - Directory Listing
Modified Wed Jun 25 23:59:02 2014 UTC (3 years, 3 months ago) by pinter
Original Path: trunk/Modules
ENH: Subject hierarchy study name now contains date

To facilitate easy differentiation between studies with same name

Revision 23370 - Directory Listing
Modified Wed Jun 25 23:58:06 2014 UTC (3 years, 3 months ago) by pinter
Original Path: trunk/Modules
BUG: Two fixes in vtkSlicerSubjectHierarchyModuleLogicTest

Still fails due to transform hardening issue (investigating)

Revision 23368 - Directory Listing
Modified Wed Jun 25 22:50:40 2014 UTC (3 years, 3 months ago) by pieper
Original Path: trunk/Modules
ENH: add an event type for the end of a fiducial interaction

This can be used to trigger execution at the end of the interaction
instead of doing it on every mouse move.

Revision 23358 - Directory Listing
Modified Sun Jun 22 15:44:02 2014 UTC (3 years, 3 months ago) by jcfr
Original Path: trunk/Modules
COMP: Fix "RCC No resources warning" by removing empty resource files.

Revision 23355 - Directory Listing
Modified Sat Jun 21 16:20:03 2014 UTC (3 years, 4 months ago) by jcfr
Original Path: trunk/Modules
COMP: Find LibArchive/CURL/OpenIGTLink/ZLIB package where required.

This commit complements commit r23350 and will help reducing the number
of parameters passed to the compiler/linker. See #3741

Revision 23354 - Directory Listing
Modified Sat Jun 21 16:19:59 2014 UTC (3 years, 4 months ago) by jcfr
Original Path: trunk/Modules
STYLE: FiberBundleLabelSelect - Clean up CMakeLists.txt

This commit removes reference to empty variable vtkTeem_LIB_DIR, additionally
vtkTeem being a target this is not needed.

Change *_(BINARY|SOURCE)_DIR with their *_INCLUDE_DIRS equivalent

Revision 23349 - Directory Listing
Modified Fri Jun 20 13:37:28 2014 UTC (3 years, 4 months ago) by finetjul
Original Path: trunk/Modules
BUG: Fixes auto level for DTI images

* CalculateAutoLevel was not called in VTK 6 when the image was modified
* CalculateAutoLevel was aborting with Diffusion tensor display node
because the scalar image data did not have a Scalars array
* Also use GetDisplayScalarRange() in qSlicerScalarVolumeDisplayWidget

Revision 23347 - Directory Listing
Modified Fri Jun 20 13:37:23 2014 UTC (3 years, 4 months ago) by finetjul
Original Path: trunk/Modules
BUG: Fix vtkTeemEstimateDiffusionTensor

* The nrrd reader did not properly propagate the scalar type to the
pipeline on time.
* vtkTeemEstimateDiffusionTensor did not use a proper pipeline of filters
for the baseline and averagedwi outputs.

Fixes DWIToDTIEstimationTest and DiffusionTensorScalarMeasurementsTest

Revision 23343 - Directory Listing
Modified Wed Jun 18 15:02:14 2014 UTC (3 years, 4 months ago) by jcfr
Original Path: trunk/Modules
COMP: Fix Slicer build warnings

This commit addresses two types of warnings:
 - unused variable warnings
 - RCC: Warning: No resources in '/path/to/foo.qrc

Revision 23331 - Directory Listing
Modified Fri Jun 13 18:17:44 2014 UTC (3 years, 4 months ago) by alexy
Original Path: trunk/Modules
BUG: 3231. Added MRML scene version check and warning on scene load.

Revision 23330 - Directory Listing
Modified Fri Jun 13 02:37:02 2014 UTC (3 years, 4 months ago) by jcfr
Original Path: trunk/Modules
BUG: N4ITKBiasFieldCorrection - Change output type to float

Cast of the output to the input type led to occasional overflows. Output of this
module is inherently floating point, as it is a multuplication of the recovered
bias field by the input image.

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

Revision 23325 - Directory Listing
Modified Wed Jun 11 19:12:09 2014 UTC (3 years, 4 months ago) by pieper
Original Path: trunk/Modules
BUG: don't try updating a 2D displayable manager if there is no slice node

This is an invalid condition that can lead to errors being generated
by the rest of the displayable manager code.  The condition that this
checks for happens when a slice view is being created but has not
yet been fully configured (that is, this can be triggered when the
scene is assigned to the slice view, but the slice node has not
yet been assigned; in this case the slice node being assigned will
trigger the needed update).

Revision 23324 - Directory Listing
Modified Tue Jun 10 19:31:35 2014 UTC (3 years, 4 months ago) by naucoin
Original Path: trunk/Modules
BUG: calculate range of active scalar

Getting the scalar range on the poly data was returning an
incorrect tuple. Get the range of the active scalar array instead.

Issue #3672

Revision 23317 - Directory Listing
Modified Mon Jun 9 17:02:01 2014 UTC (3 years, 4 months ago) by mwoehlke
Original Path: trunk/Modules
COMP: Remove gratuitous virtual

Remove 'virtual' specifier of private classes in source files where said
classes are not and (due to being in a source file) never will be
derived. This avoids needing an explicit (virtual) dtor in order to
avoid a -Wnon-virtual-dtor warning.

Revision 23315 - Directory Listing
Modified Mon Jun 9 16:43:06 2014 UTC (3 years, 4 months ago) by naucoin
Original Path: trunk/Modules
BUG: Persist 'dont show message' selection when deleting markups

This fix addresses Mantis item #3663. The ctkMessageBox expects a
ButtonRole of AcceptRole. Created a custom button for 2 reasons.
First, it allows us to set the correct role and secondly a "Delete"
and "Delete All" button more clearly aligns with the action being
performed.

From: David Stoup <david.stoup@kitware.com>

Revision 23310 - Directory Listing
Modified Thu Jun 5 21:59:23 2014 UTC (3 years, 4 months ago) by jcfr
Original Path: trunk/Modules
BUG: N4ITKBiasFieldCorrection: Fix test updating the baseline

This commit updates the baseline to match the default parameter value
updated in r23306.

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

Revision 23307 - Directory Listing
Modified Wed Jun 4 21:04:30 2014 UTC (3 years, 4 months ago) by jcfr
Original Path: trunk/Modules
ENH: Editor: paint using pixel mode if brush size is too small

For volumes with anisotropic spacing the minimum brush size in the paint
tool may be smaller than the pixel size. When a the brush size is smaller
than the pixel size then no pixels are filled when the user clicks on the
image, which is very confusing for the user.

Implemented solution: added a check in the PaintEffect tool so that if
the brush size is too small then pixels are painted using paintPixel mode.

From: Andras Lasso <lasso@queensu.ca>

Revision 23306 - Directory Listing
Modified Wed Jun 4 18:42:44 2014 UTC (3 years, 4 months ago) by jcfr
Original Path: trunk/Modules
ENH: N4ITKBiasFieldCorrection: Restore original default for iteration number.

This commit reverts the change added as part r21845 to resolve issue #3034

To be compatible with code expecting the original default value, the value
is changed back to to "50,40,30".

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

Revision 23302 - Directory Listing
Modified Tue Jun 3 21:20:12 2014 UTC (3 years, 4 months ago) by mwoehlke
Original Path: trunk/Modules
BUG: Fix (another) bug reading settings list

Write a helper function to read a QSettings value explicitly as a list
in Python, in order to work around PythonQt's implicit conversion of
QVariant. Use this everywhere it is applicable in the Extension Wizard
module. This allows us to simplify some places where we iterate over
settings lists, and (more importantly) fixes (another) bug where we try
to iterate over a list that might be empty.

See also r23285.

Revision 23301 - Directory Listing
Modified Tue Jun 3 19:07:41 2014 UTC (3 years, 4 months ago) by mwoehlke
Original Path: trunk/Modules
BUG: Reenable Extension Wizard module

The previous commit should resolve the issue that was causing the
Extension Wizard module to crash Slicer; therefore, revert r23297,
making it enabled again.

Revision 23297 - Directory Listing
Modified Sun Jun 1 18:42:10 2014 UTC (3 years, 4 months ago) by jcfr
Original Path: trunk/Modules
BUG: Disable ExtensionWizard to avoid crash on Windows

Time the runtime crash happening on Windows is resolved. The module
is disabled.

Details about the crash are reported here:

 http://slicer-devel.65872.n3.nabble.com/Fwd-ctk-build-error-in-slicer-tt4031747.html

To avoid the crash in existing build tree, the following two files
will have to be removed from the build tree:

 lib/Slicer-4.3/qt-scripted-modules/ExtensionWizard.py
 lib/Slicer-4.3/qt-scripted-modules/ExtensionWizard.pyc

Revision 23293 - Directory Listing
Modified Fri May 30 22:43:30 2014 UTC (3 years, 4 months ago) by mwoehlke
Original Path: trunk/Modules
ENH: Also find templates in build (source) tree

Add slicer.util.sourceDir() convenience method to retrieve the Slicer
source directory, when running from a local build tree. Change Extension
Wizard module to prefer to use templates from the same, if available.

Revision 23291 - Directory Listing
Modified Fri May 30 22:43:27 2014 UTC (3 years, 4 months ago) by mwoehlke
Original Path: trunk/Modules
STYLE: Add icon for Extension Wizard module

Reorganize Extension Wizard module resources to account for the
directory structure being conducive to generating a compiled resource
script in a reasonable location. Add rules to generate and import the
same. Add code to set the module icon resource.

Revision 23288 - Directory Listing
Modified Fri May 30 22:43:23 2014 UTC (3 years, 4 months ago) by mwoehlke
Original Path: trunk/Modules
STYLE: Create icon for Extension Wizard module

Add icon images ("same" icon, multiple resolutions) and source SVG's for
the same for the Extension Wizard module. (The XSmall resolution is just
the Medium SVG rendered at 16x16, hence no source SVG.)

These aren't being used yet.

Revision 23287 - Directory Listing
Modified Fri May 30 22:43:22 2014 UTC (3 years, 4 months ago) by mwoehlke
Original Path: trunk/Modules
ENH: Use installed templates, if available

Refactor template path handling in the Extension Wizard module to reduce
duplication of key literals. Add a helper function to try to get the
location of the "standard" templates (e.g. from an install), and use
these if available. Also, display this path (non-editable) in the
settings panel.

Revision 23285 - Directory Listing
Modified Fri May 30 22:43:19 2014 UTC (3 years, 4 months ago) by mwoehlke
Original Path: trunk/Modules
BUG: Don't choke on empty path value

Fix logic that loads list of template paths from settings to not choke
(i.e. throw an unexpected exception) in case the key value is None.
Also, remove some stray debugging statements that were accidentally
committed.

Revision 23284 - Directory Listing
Modified Fri May 30 22:43:18 2014 UTC (3 years, 4 months ago) by mwoehlke
Original Path: trunk/Modules
ENH: Add UI for modifying template paths

Create a settings panel for the Extension Wizard module that allows
editing the list of paths used to find templates. Change how we read
settings to work with the way ctkSettingsPanel stores lists.

Issue #3603

Revision 23282 - Directory Listing
Modified Fri May 30 22:43:16 2014 UTC (3 years, 4 months ago) by mwoehlke
Original Path: trunk/Modules
ENH: Create editable directory list

Create utility widget class DirectoryListWidget, which provides a
standard interface of supplemental buttons to support a user editable
qSlicerDirectoryListView. (Surprisingly, no such class previously
exists; existing occurrences of this pattern reimplement the
supplemental UI in the parent, for each occurrence!)

This will allow us to trivially create multiple instances of editable
lists.

Revision 23281 - Directory Listing
Modified Fri May 30 22:43:15 2014 UTC (3 years, 4 months ago) by mwoehlke
Original Path: trunk/Modules
ENH: Implement loading of extension modules

Hook up the loading of modules in the Extension Wizard when requesting
to do so. (See previous two commits.)

Issue #3603

Revision 23279 - Directory Listing
Modified Fri May 30 22:43:12 2014 UTC (3 years, 4 months ago) by mwoehlke
Original Path: trunk/Modules
ENH: Prompt to load extension modules (WIP)

Create a dialog to prompt the user if they want to load modules
available from a selected extension. (Also used to ask the user if they
want to load a newly-created module immediately.) The UI is implemented,
but the actual loading requires changes to the C++ interfaces, and so is
not hooked up yet.

Issue #3603

Revision 23278 - Directory Listing
Modified Fri May 30 22:43:11 2014 UTC (3 years, 4 months ago) by mwoehlke
Original Path: trunk/Modules
ENH: Implement creation of extension modules

Add ability to create modules for extensions to extension wizard module.
Refactor CreateExtensionDialog into more generic CreateComponentDialog
so that it can be shared for this purpose.

Issue #3603

Revision 23277 - Directory Listing
Modified Fri May 30 22:43:10 2014 UTC (3 years, 4 months ago) by mwoehlke
Original Path: trunk/Modules
ENH: Select from location of selected extension

Change extension selection in the extension wizard module to use the
location of the currently selected extension (when applicable) as the
initial directory for choosing another extension.

Issue #3603

Revision 23276 - Directory Listing
Modified Fri May 30 22:43:09 2014 UTC (3 years, 4 months ago) by mwoehlke
Original Path: trunk/Modules
ENH: Use I-beam cursor for information fields

Tweak the read only line edits used to show information about the
currently selected extension in the Extension Wizard module to use the
I-beam cursor, to make it more obvious that the text can be selected.

Revision 23275 - Directory Listing
Modified Fri May 30 22:43:08 2014 UTC (3 years, 4 months ago) by mwoehlke
Original Path: trunk/Modules
ENH: Implement editing of extension metadata

Create dialog for editing extension metadata and hook up to necessary
bi-directional manipulation of the same in the extension project and
description classes.

Issue #3603

Revision 23272 - Directory Listing
Modified Fri May 30 22:43:05 2014 UTC (3 years, 4 months ago) by mwoehlke
Original Path: trunk/Modules
ENH: Create editable tree widget

Create utility widget class EditableTreeWidget, for extension wizard
module. This will be useful for editing extension metadata that takes
the form of lists, e.g. contributors.

Revision 23271 - Directory Listing
Modified Fri May 30 22:43:04 2014 UTC (3 years, 4 months ago) by mwoehlke
Original Path: trunk/Modules
STYLE: Use properties in CreateExtensionDialog

Change CreateExtensionDialog classes to subclass object, which is needed
to give them properties (they weren't originally as there seems to be
some problem if a module's primary classes derive from object). Change
accessor methods of the same to Python properties, which are slightly
more convenient and "more Pythonic".

Revision 23269 - Directory Listing
Modified Fri May 30 22:43:02 2014 UTC (3 years, 4 months ago) by mwoehlke
Original Path: trunk/Modules
ENH: More work on in-Slicer Extension Wizard

Add some widgets to the 'edit extension' section to show basic
information about the selected extension, and hook up the ability to
select an extension. There is a not-yet-implemented 'edit metadata'
action that will likely be joined eventually by other actions.

Issue #3603

Revision 23268 - Directory Listing
Modified Fri May 30 22:43:01 2014 UTC (3 years, 4 months ago) by mwoehlke
Original Path: trunk/Modules
ENH: Improve styling of wizard actions

Replace the QPushButton extension wizard actions with "flat"
QToolButton's, using (for now) a forward-arrow icon. This gives a
cleaner look than the odd stack of unusually wide buttons, that is
loosely based on Windows wizards (which were the only example of a
list-of-possible-actions - as opposed to list-of-steps - type wizard I
could find).

Revision 23265 - Directory Listing
Modified Fri May 30 22:42:57 2014 UTC (3 years, 4 months ago) by mwoehlke
Original Path: trunk/Modules
ENH: Create in-Slicer Extension Wizard (skeleton)

Create the initial skeleton of the in-Slicer Extension Wizard. This will
provide a graphical front-end to (some of) the Extension Wizard
functions. Right now, only creation is implemented.

Issue #3603

Revision 23257 - Directory Listing
Modified Wed May 28 22:04:21 2014 UTC (3 years, 4 months ago) by jcfr
Original Path: trunk/Modules
COMP: Fix unused variable warnings in qSlicerSubjectHierarchyDefaultPlugin

Revision 23252 - Directory Listing
Modified Wed May 28 07:42:51 2014 UTC (3 years, 4 months ago) by jcfr
Original Path: trunk/Modules
STYLE: Improve error output of subject hierarchy TestTransformBranch

Revision 23251 - Directory Listing
Modified Wed May 28 07:42:48 2014 UTC (3 years, 4 months ago) by jcfr
Original Path: trunk/Modules
STYLE: Update vtkMRMLSubjectHierarchyNode to use vtkNew

Also fixes indent

Revision 23250 - Directory Listing
Modified Wed May 28 07:42:46 2014 UTC (3 years, 4 months ago) by jcfr
Original Path: trunk/Modules
ENH: Update subject hierarchy PopulateScene to check nodes are added.

This commit basically removed the assert and add corresponding
test.

Revision 23248 - Directory Listing
Modified Wed May 28 07:42:40 2014 UTC (3 years, 4 months ago) by jcfr
Original Path: trunk/Modules
STYLE: Improve error output of TestTreeOperations in subject hierarchy test

Revision 23247 - Directory Listing
Modified Wed May 28 07:42:38 2014 UTC (3 years, 4 months ago) by jcfr
Original Path: trunk/Modules
STYLE: Improve readability of subject hierarchy logic test using vtkNew

Revision 23245 - Directory Listing
Modified Tue May 27 21:45:09 2014 UTC (3 years, 4 months ago) by jcfr
Original Path: trunk/Modules
STYLE: SubjectHierarchy - Fix build warnings and indentation

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

Revision 23243 - Directory Listing
Modified Tue May 27 21:45:04 2014 UTC (3 years, 4 months ago) by jcfr
Original Path: trunk/Modules
COMP: Fixed Mac and Linux build error

Subject hierarchy widget designer plugins were deployed to Slicer_DIR/bin,
which broke the Linux and Mac build. This explicit output directory
setting has been removed.

From: Csaba Pinter <csaba.pinter@queensu.ca>

Revision 23242 - Directory Listing
Modified Tue May 27 21:45:01 2014 UTC (3 years, 4 months ago) by jcfr
Original Path: trunk/Modules
COMP: Moved subject hierarchy base plugin classes in widgets

In order to subject hierarchy plugins be accessible from extensions,
the include directories need to be exported. So that the current
infrastructure can be used, all subject hierarchy plugin
classes (abstract, handler, core plugins not related to modules) were
moved from Plugins to Widgets. Plugins subdirectory thus became
unnecessary and removed.

From: Csaba Pinter <csaba.pinter@queensu.ca>

Revision 23241 - Directory Listing
Modified Tue May 27 21:44:51 2014 UTC (3 years, 4 months ago) by jcfr
Original Path: trunk/Modules
ENH: Subject hierarchy python tests moved to SlicerApp

As the subject hierarchy tests cover multiple modules, they have been moved
from the SubjectHierarchy folder to Applications/SlicerApp/Testing/Python;
Occasional SlicerRT strings removed/replaced in subject hierarchy code
(mostly include dir comments)

From: Csaba Pinter <csaba.pinter@queensu.ca>

Revision 23239 - Directory Listing
Modified Tue May 27 21:44:45 2014 UTC (3 years, 4 months ago) by jcfr
Original Path: trunk/Modules
ENH: vtkMRMLHierarchyNode methods made virtual

Two methods in vtkMRMLHierarchyNode made virtual. GetAssociatedChildrendNodes contained
a typo so it is now called GetAssociatedChildrenNodes. Subject hierarchy volumes plugin
now can add volumes from potential list to tree

From: Csaba Pinter <csaba.pinter@queensu.ca>

Revision 23238 - Directory Listing
Modified Tue May 27 21:44:40 2014 UTC (3 years, 4 months ago) by jcfr
Original Path: trunk/Modules
ENH: Sank addSeriesInSubjectHierarchy function down to abstract DICOMPlugin

The addSeriesInSubjectHierarchy function (which was in DICOMScalarVolumePlugin so far) adds
the loaded node to subject hierarchy to the proper patient (subject) and study according to
the DICOM tags from the first file referenced in the associated loadable. This function is
now accessible from all the DICOM plugins. It needs to be called after the loaded object is
created in the load() function. Now it is called by DICOMDiffusionVolumePlugin too.

From: Csaba Pinter <csaba.pinter@queensu.ca>

Revision 23237 - Directory Listing
Modified Tue May 27 21:44:38 2014 UTC (3 years, 4 months ago) by jcfr
Original Path: trunk/Modules
ENH: Moved core module subject hierarchy plugins to related module

Subject hierarchy plugins project contained plugins for core modules
Markups, Models and Volumes. Those plugins are now in the
SubjectHierarchyPlugins subdirectory of those loadable modules.
Also the subject hierarchy support moved from
SlicerRT/DicomRtImport/DicomRtImportPlugin.py to
DICOMScalarVolumePlugin.py. Now the loaded DICOM scalar volumes are
automatically added to subject hierarchy.

From: Csaba Pinter <csaba.pinter@queensu.ca>

Revision 23236 - Directory Listing
Modified Tue May 27 21:39:47 2014 UTC (3 years, 4 months ago) by jcfr
Original Path: trunk/Modules
ENH: Node attribute table view and widget moved to MRMLWidgets

Now both Data and Subject hierarchy modules use qMRMLNodeAttributeTableView and
qMRMLNodeAttributeTableWidget, so they have been moved from Data module widgets to MRMLWidgets

From: Csaba Pinter <csaba.pinter@queensu.ca>

Revision 23235 - Directory Listing
Modified Tue May 27 20:09:22 2014 UTC (3 years, 4 months ago) by jcfr
Original Path: trunk/Modules
ENH: Subject hierarchy module added

This is the first step of integrating Subject hierarchy into Slicer core.
Next steps include moving subject hierarchy plugins to their related
modules and making DICOM import plugins add loaded objects in the
hierarchy.
More information: http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/SubjectHierarchy

From: Csaba Pinter <csaba.pinter@queensu.ca>

Revision 23234 - Directory Listing
Modified Sat May 24 05:46:58 2014 UTC (3 years, 4 months ago) by jcfr
Original Path: trunk/Modules
ENH: Allow users to acknowledge all DICOM loading errors with a single click

Problem: Each DICOM loading error was displayed in a separate popup, which
 required the user to click as many times as many series failed to load.
In some cases there are a large number of failures (for example,
experimental MRI sequences), which makes loading of a complete study very
frustrating (need to click 30 times, waiting several seconds between each).

Solution: Changed the error reporting to collect all errors and show it to the user at the end of the loading in a single error popup.

From: Andras Lasso <lasso@queensu.ca>

Revision 23233 - Directory Listing
Modified Sat May 24 05:41:46 2014 UTC (3 years, 4 months ago) by jcfr
Original Path: trunk/Modules
BUG: Fixed DICOM browser persistence

If the DICOM browser persistent option is enabled (usually when the DICOM browser is displayed on a second monitor) then the browser should be kept open when an image is loaded or the user opens another module.
The persistent flag was observed almost everywhere where it was needed, except at the end of the image loading step.

From: Andras Lasso <lasso@queensu.ca>

Revision 23225 - Directory Listing
Modified Wed May 21 21:21:14 2014 UTC (3 years, 5 months ago) by naucoin
Original Path: trunk/Modules
ENH: Update copy color icon

User feedback on the customisation of color tables suggested that
a more clear icon be used for the copy to edit functionality.

Issue #3573


Revision 23222 - Directory Listing
Modified Wed May 21 15:38:38 2014 UTC (3 years, 5 months ago) by finetjul
Original Path: trunk/Modules
BUG: Fix crash with vtkMRMLSelectionNode and vtkSlicerUnitsLogic

Since r23192, the GetUnitNodes() can return empty nodes.
This triggered asserts in vtkSlicerUnitsLogic.
vtkSlicerUnitLogic is only interested in unit quantities and IDs.

Revision 23221 - Directory Listing
Modified Wed May 21 15:02:26 2014 UTC (3 years, 5 months ago) by naucoin
Original Path: trunk/Modules
ENH: separate scene views with a line

Request from Ron, adding in a horizontal line between
scene views.

Issue #1299



Revision 23213 - Directory Listing
Modified Mon May 19 21:51:29 2014 UTC (3 years, 5 months ago) by naucoin
Original Path: trunk/Modules
BUG: fix crash when scene view added without screen shot

When saving a scene with the Scene Views module open, a null
pointer crash happened because the qSlicerSceneWriter was adding
the scene view node to the scene before capturing and setting
the screen shot. The mrml application logic does the same thing.
For now, avoid the crash by checking the pointer. The
thumbnail immage will appear on the next update, but since the
mrml scene isn't invoking an event when it's finished the
Commit call, the module will have to in future observe scene view
nodes for modified events to detect that a screen shot has been
added to the node (and if there have been other updates directly
to the node rather than via the GUI).

Issue #1299



Revision 23207 - Directory Listing
Modified Mon May 19 19:10:14 2014 UTC (3 years, 5 months ago) by finetjul
Original Path: trunk/Modules
ENH: Apply units to Transforms module

Revision 23206 - Directory Listing
Modified Mon May 19 19:10:03 2014 UTC (3 years, 5 months ago) by finetjul
Original Path: trunk/Modules
BUG: Fix unit scaling change

A scale of 0 could be generated when changing from one scale to another
(e.g. 0.1 to 1.)

Revision 23198 - Directory Listing
Modified Mon May 19 17:10:29 2014 UTC (3 years, 5 months ago) by millerjv
Original Path: trunk/Modules
BUG: #1696 LabelStatics regenerates plot on each SetParameter call

Added calls to StartModify()/EndModify() to limit the regeneration
of the plot until after the node is fully populated.

Revision 23197 - Directory Listing
Modified Mon May 19 16:15:26 2014 UTC (3 years, 5 months ago) by naucoin
Original Path: trunk/Modules
BUG: use Slicer system fonts in Scene Views

To bring the Scene Views module into alignment with
the Slicer system fonts, propagate the application
settings fonts to the QWebView used to display the
scene views.

Issue #1299



Revision 23178 - Directory Listing
Modified Wed May 14 21:05:01 2014 UTC (3 years, 5 months ago) by naucoin
Original Path: trunk/Modules
ENH: enable using the picking manager

Turn on the picking manager on the interactor when creating the first
fiducial, ruler, ROI.
Only for VTK6, solves the issue of picking fiducials in placed order
rather than 3d depth order.
Dragging fiducials near other ones will sometimes cause a jump, but now
the 3d glyph position and the MRML node location stay in synch.

Issue #3319

Revision 23176 - Directory Listing
Modified Wed May 14 05:01:02 2014 UTC (3 years, 5 months ago) by jcfr
Original Path: trunk/Modules
COMP: Fix unused variable / unused typdefs warnings.

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

Revision 23164 - Directory Listing
Modified Tue May 13 17:31:48 2014 UTC (3 years, 5 months ago) by mwoehlke
Original Path: trunk/Modules
COMP: Fix build errors with VTK6

Fix two minor compile errors in VTK6 conditional branch of
qSlicerSceneViewsModuleWidget, that were introduced in r23160.

Revision 23161 - Directory Listing
Modified Tue May 13 16:23:49 2014 UTC (3 years, 5 months ago) by naucoin
Original Path: trunk/Modules
COMP: remove unused variable warnings

Remove unused variables or mark as unused parameters
in the scene views module update.

Issue #1299



Revision 23160 - Directory Listing
Modified Tue May 13 15:30:42 2014 UTC (3 years, 5 months ago) by naucoin
Original Path: trunk/Modules
ENH: html facelift for SceneViews

Implemented a Qt web view and populated it with HTML to allow
viewing, editing, restoring, creating scene views with the
layout requested.

The scene view thumbnail is being written to disk in a temp dir.
To get the Edit, Delete, Restore and Capture funtionality I'm capturing the
clicks on the links and parsing specially formatted urls
(Edit/Restore/Delete mrmlNodeID/Create)

Clear out the temp files on scene close and clear the memory cache, now
don't have to write them out all the time. Resize the images before
writing to disk so that the web view doesn't have to handle resizing.
Added in support for VTK6
Created new MRML web view based on the qMRMLChartView.
It allows better resizing (returns an invalid size hint,
sets size policy to expanding/expanding) so that the web
view doesn't keep getting reset to width = 800.
Added a plug in for the designer.
Save and restore the scroll position so user goes back
to the scene view node that they were previously viewing after
adding a new scene view.

Running on a mac, you can't see the scroll bar
on the data store page nor on the scene views
module widget, but it is visible on a linux build.
You can scroll using the trackpad and it is consistent,
so only show the scroll bar as needed.
The dialog superclass disables capturing a new
thumbnail on review/edit so don't resave the thumbnail type nor the image data.

Issue #1299

Revision 23157 - Directory Listing
Modified Tue May 13 07:07:05 2014 UTC (3 years, 5 months ago) by jcfr
Original Path: trunk/Modules
ENH: Associate component with all install rules.

Related to #2397

Revision 23148 - Directory Listing
Modified Mon May 12 16:42:00 2014 UTC (3 years, 5 months ago) by lassoan
Original Path: trunk/Modules
ENH: Replaced vtkITKBSplineTransform by vtkOrientedBSplineTransform

Problem:
vtkITKBSplineTransform incorrectly computed the 1. forward derivatives, 2. inverse displacement when there was a bulk transform component and rotated bspline grid, 3. the inverse displacement.

Analysis:
In the ITK bspline transform no inverse computation is available and in the current ITK bspline version no additive bulk transform is supported (therefore it is not backward-compatible with the old ITK bspline transform), ITK's transform support is very limited (compared to the powerful transform pipelines in VTK), and Slicer already uses VTK transforms (vtkGridTransform), therefore the ITK bspline is not usable in Slicer as is.
A bspline transform implementation is available in VTK, which is is efficient and well-tested (and equivalence with ITK's bspline implementation can be proven by testing).

Solution:
Replaced vtkITKBSplineTransform it with a vtkBSplineTransform-based transform, vtkOrientedBSplineTransform, which extends the original VTK class to handle arbitrarily oriented b-spline grids and supports an additive bulk transform.
Added test that verifies the vtkOrientedBSplineTransform's equivalence with the ITK BSpline transform implementation in the whole bspline grid (the differences are less than 1e-10).
Added test that verifies the correctness of the inverse and derivative computation.

Fixes:
http://www.na-mic.org/Bug/view.php?id=3664
http://www.na-mic.org/Bug/view.php?id=3659
http://www.na-mic.org/Bug/view.php?id=3614


Revision 23142 - Directory Listing
Modified Thu May 8 17:28:15 2014 UTC (3 years, 5 months ago) by finetjul
Original Path: trunk/Modules
BUG: Fix volume rendering object factory on VTKv6

Issue #3514

Revision 23140 - Directory Listing
Modified Thu May 8 07:58:19 2014 UTC (3 years, 5 months ago) by jcfr
Original Path: trunk/Modules
COMP: Fix "unused-local"typedefs" warning and update ITKv4

Commit r23121 removed the addition of "-Wno-unused-local-typedefs",
this commit is an attempt to clean most of the warnings. It also
updates the ITKv4 external project so that it checks out the Slicer ITK
fork including the ITK patch currently in review. See [1], [2]

$ git shortlog 01661ccf99..184b1257ad
Jean-Christophe Fillion-Robin (3):
      COMP: Properly fix unused-local-typedefs warning using unused attribute.
      COMP: Fix "unused-local-typedefs" warnings
      COMP: Backport double conversion fix for "unused-local-typedefs" warning

[1] http://review.source.kitware.com/#/c/15379/
[2] http://review.source.kitware.com/#/c/15380/

Revision 23139 - Directory Listing
Modified Thu May 8 04:34:12 2014 UTC (3 years, 5 months ago) by jcfr
Original Path: trunk/Modules
COMP: Fix visibility warning in DiffusionTensor3DRead

Remove warning: ‘itk::DiffusionTensor3DRead<float>’ declared with greater
visibility than the type of its field ‘itk::DiffusionTensor3DRead<float>::m_Reader’

Due to the fact that itkDiffusionTensor3DRead was declaring a private
variable of type itkImageFileReader<DiffusionImageType>::Pointer and that
this class was declared with ITK_ABI_EXPORT, we had to add ITK_ABI_EXPORT
to the declaration of itkDiffusionTensor3DRead to remove the previously
described warning when ResampleDTIVolume was compiled (shared object).

From: Francois Budin <fbudin@unc.edu>

Revision 23138 - Directory Listing
Modified Thu May 8 04:34:09 2014 UTC (3 years, 5 months ago) by jcfr
Original Path: trunk/Modules
COMP: Fix unused-local-typedefs warnings

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

Revision 23137 - Directory Listing
Modified Wed May 7 18:16:22 2014 UTC (3 years, 5 months ago) by pieper
Original Path: trunk/Modules
ENH: Fixed 2498 and other ui enhancements for dicom browser.
This patch would fix
http://na-mic.org/Mantis/view.php?id=2498
and also fix the UI issues which Csaba reported on 2014-04-24 12:17 here:
http://na-mic.org/Mantis/view.php?id=3578
and fix a bug in saving the disabled plugins in Slicer application settings

From: Alireza Mehrtash <mehrtash@bwh.harvard.edu>

Revision 23122 - Directory Listing
Modified Fri May 2 21:55:04 2014 UTC (3 years, 5 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add VTK 6 support 2/2

Issue #3514

Revision 23121 - Directory Listing
Modified Fri May 2 21:49:48 2014 UTC (3 years, 5 months ago) by finetjul
Original Path: trunk/Modules
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 23120 - Directory Listing
Modified Fri May 2 21:49:01 2014 UTC (3 years, 5 months ago) by finetjul
Original Path: trunk/Modules
BUG: Fix VTK 4 backward compatibility removal

Issue #3485

Revision 23119 - Directory Listing
Modified Fri May 2 21:48:56 2014 UTC (3 years, 5 months ago) by finetjul
Original Path: trunk/Modules
ENH: Remove VTK 4 backwards compatibility

Removed vtkSource, vtkProcessObject and subclasses.
http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Overview#Removal_of_VTK_4_Backwards_Compatibility_Superclasses
http://www.vtk.org/Wiki/VTK/Tutorials/New_Pipeline#Converting_an_Existing_Filter_to_the_New_Pipeline

Closes #3485
From Yuzheng Zhou <yuzheng.zhou@kitware.com>

Revision 23117 - Directory Listing
Modified Thu May 1 21:14:01 2014 UTC (3 years, 5 months ago) by naucoin
Original Path: trunk/Modules
BUG: disable alternate color editors

The color module was just collapsing the color table and
continuous color transfer viewer/editors when the other type
of node was active. User feedback showed this to be confusing
as valid looking data was visible if the sections were
expanded. This change disables the invalid editor on
selection of a color node.

Issue #3573


Revision 23115 - Directory Listing
Modified Wed Apr 23 22:07:24 2014 UTC (3 years, 5 months ago) by naucoin
Original Path: trunk/Modules
COMP: remove compiler warnings

Remove unused variable, mark parameter as unused.

Issue #3632


Revision 23114 - Directory Listing
Modified Wed Apr 23 21:06:52 2014 UTC (3 years, 5 months ago) by naucoin
Original Path: trunk/Modules
BUG: fix behaviour of gui when markup inside transform

When editing the coordinates of a markup that's inside of a
transform, the pairing of getting the untransformed
coordinate and then saving it as transformed was leading to
incorrect values.
Added in a checkbox to select if the GUI table shows the
markup coordinates in transformed or untransformed versions.

Issue #3632

Revision 23113 - Directory Listing
Modified Wed Apr 23 21:06:48 2014 UTC (3 years, 5 months ago) by naucoin
Original Path: trunk/Modules
ENH: label change from XYZ to RAS

After discussion on Slicer Developer hangout, change the GUI
coordinate labels to RAS instead of XYZ.

Issue #3367

Revision 23112 - Directory Listing
Modified Wed Apr 23 21:06:44 2014 UTC (3 years, 5 months ago) by naucoin
Original Path: trunk/Modules
ENH: add check box to show/hide coordinate columns

When box is checked, hide the markup coordiante columns in the
table, when unchecked show them.

Issue #3667

Revision 23111 - Directory Listing
Modified Wed Apr 23 21:06:39 2014 UTC (3 years, 5 months ago) by naucoin
Original Path: trunk/Modules
ENH: add coordinates to right click menu

When select rows in the Markups table, right click will now add the
coordinate points to the top of the context menu. Works for
multi select, and will work for multiple points per markup.
Adds the label of the markup if there are multiple rows selected.
Adds a separator after the coordinates and before the command
actions.

Revision 23109 - Directory Listing
Modified Tue Apr 22 14:12:05 2014 UTC (3 years, 5 months ago) by pieper
Original Path: trunk/Modules
ENH: Store a list of disabled plugins when user disable plugins in
advanced mode. All plugins would be enabled by default (both in simple and
advanced mode).

From: Alireza Mehrtash <mehrtash@bwh.harvard.edu>

Revision 23108 - Directory Listing
Modified Fri Apr 18 22:25:06 2014 UTC (3 years, 6 months ago) by alexy
Original Path: trunk/Modules
BUG: 3660. Fixed faulty logic checking for coordinate changes in the vtkMRMLMarkupsFiducialDisplayableManager3D.cxx

Revision 23104 - Directory Listing
Modified Thu Apr 17 02:43:24 2014 UTC (3 years, 6 months ago) by lassoan
Original Path: trunk/Modules
BUG: Fixed transform info widget test name

Revision 23103 - Directory Listing
Modified Wed Apr 16 17:48:22 2014 UTC (3 years, 6 months ago) by jcfr
Original Path: trunk/Modules
BUG: ResampleDTIlog Euclidean was using the measurement frame to transform tensors from local coordinates to world coordinates

It should be using the space direction of the image instead. The measurement frame should only transform gradient vectors from DWI to world coordinates. To be backward compatible, if a measurement frame is detected in the MetaData of the image, the measurement frame is still used as the transform matrix from local to world coordinate unless --noMeasurementFrame is specified. If no measurement frame information is available in the image MetaData, the image space direction is used instead (as well as if --noMeasurementFrame is specified).

From: fbudin69500 <fbudin@unc.edu>

Revision 23102 - Directory Listing
Modified Wed Apr 16 17:40:24 2014 UTC (3 years, 6 months ago) by lassoan
Original Path: trunk/Modules
ENH: Added visualization of transforms

New features:
* Support non-linear transforms in the Transforms module: allow Apply, Harden, Invert transform
* Transform information displayed in the Transforms module (type of transform, basic properties)
* Transform visualization:
** Built into the Transforms module
** Three main modes: Glyphs (show an array of arrows, cones, spheres), Grid (show a deformed grid), or Contour (show isolines/isosurfaces for specified displacement magnitude values)
** All transform types are supported (chains of transforms as well)
** Visualization in the slice viewers
** Visualization in the 3D viewers, in the specified region (region can be a slice viewer, a volume, or a ROI widget)
** Real-time update: if the transform (or any visualization parameter) is changed then the visualization is updated immediately (interactive visualization while editing the transform)
** Built-in colormap editor
* MetaImage (mha), NIFTI (nii) vector volumes can be loaded as displacement field (grid) transform


Revision 23091 - Directory Listing
Modified Sat Apr 12 06:11:22 2014 UTC (3 years, 6 months ago) by jcfr
Original Path: trunk/Modules
COMP: Fix sign compararison warnings

Revision 23087 - Directory Listing
Modified Fri Apr 11 22:11:18 2014 UTC (3 years, 6 months ago) by naucoin
Original Path: trunk/Modules
ENH: add support for markups in different views

Added support in the displayable managers to check if
a markup is visible in a given view. Added testing.
Added a GUI drop down box to allow the user to
manipulate the view node settings (in the Advanced
Display group)

Resolves Issue #3216



Revision 23086 - Directory Listing
Modified Fri Apr 11 22:06:19 2014 UTC (3 years, 6 months ago) by naucoin
Original Path: trunk/Modules
ENH: expand the view combo box to work on abstract view nodes

Removed the limitation on the display node view combo box that
only allowed selecting 3D view nodes, now all subclasses of
abstract view nodes can be used. Slice nodes and chart view
nodes are now allowed. This fixes the issue that while a
display node could have a slice node added to it's list of
view nodes, this combo box would remove it as it wasn't a
3d view node.
Update the volume rendering module widget to use the new combo
box code, limiting the view nodes to 3d ones since volume
rendering can't be shown in slice views.

Issue #3216



Revision 23084 - Directory Listing
Modified Fri Apr 11 21:51:08 2014 UTC (3 years, 6 months ago) by naucoin
Original Path: trunk/Modules
ENH: Add procedural color storage node and GUI support

Add a new storage node, register it, test it.
Added support for copying procedural nodes so that users can copy
an existing one and then save it to disk.
LoadColorFile expanded to work with both color table and procedural
color node loading.
TBD: add support for .cxml
Added support in the Colors gui to display and edit color transfer
functions (Continuous frame, with a ctkVTKScalarsToColorsWidget).
As well as allowing the scalar bar widget to be set from a procedural
color node.

Issue #3573



Revision 23083 - Directory Listing
Modified Fri Apr 11 21:44:58 2014 UTC (3 years, 6 months ago) by naucoin
Original Path: trunk/Modules
ENH: Expand scalar range options

Add the ScalarRangeFlag on the display node, test it, use it in the Model
display node.
Provide a GUI interface for it in the Models Scalars GUI.
Use it in the model displayable manager.
Separate out the auto scalar range setting from updating the poly data
in the model display node.

This expands the options from just using the scalar range of the data
to allowing the user to select using the scalar range defined on the
display node, the range on the color node, or the range of the data
type (use this last with caution, TBD: readjusting the minimum and
maximum values allowed on the range slider). Keeps the default
behaviour of AutoScalarRange and Data. The interaction of Auto/Manual
and the range flags might need some tweaking.
Also keeps the deep copy of the color look up table in the model displayable
manager - monitor for performance issues.
Expands the model displayable manager to work with procedural color nodes,
this required copying the color transfer function to a look up table to
support setting the range. Using a table with 256 entries for now.
UI full change due to having to run dos2unix on it to get it commited
to git without whitespace errors.

Issue #3573



Revision 23081 - Directory Listing
Modified Fri Apr 11 20:33:22 2014 UTC (3 years, 6 months ago) by alexy
Original Path: trunk/Modules
BUG: 2346. Made default fiber solid color to white matter. 

Revision 23078 - Directory Listing
Modified Fri Apr 11 16:08:33 2014 UTC (3 years, 6 months ago) by alexy
Original Path: trunk/Modules
BUG: 3121. Added module wiki doc page link

Revision 23077 - Directory Listing
Modified Fri Apr 11 04:10:41 2014 UTC (3 years, 6 months ago) by jcfr
Original Path: trunk/Modules
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 23045 - Directory Listing
Modified Fri Apr 4 12:59:06 2014 UTC (3 years, 6 months ago) by alexy
Original Path: trunk/Modules
BUG: 3640. Added vtkMRMLFiberBundleDisplayNode::ProcessMRMLEvents () method to process modify events from vtkMRMLDiffusionTensorDisplayPropertiesNode referenced node

Revision 23032 - Directory Listing
Modified Tue Apr 1 18:03:12 2014 UTC (3 years, 6 months ago) by alexy
Original Path: trunk/Modules
BUG: 3609. fixed a left over property after conversion to QComboBox

Revision 23031 - Directory Listing
Modified Tue Apr 1 15:59:49 2014 UTC (3 years, 6 months ago) by alexy
Original Path: trunk/Modules
BUG: 3609. changed active tensor selector to use QComboBox

Revision 23026 - Directory Listing
Modified Wed Mar 26 21:11:04 2014 UTC (3 years, 6 months ago) by finetjul
Original Path: trunk/Modules
ENH: Remove unused Texture and NCI volume rendering mappers

Revision 23025 - Directory Listing
Modified Wed Mar 26 20:34:13 2014 UTC (3 years, 6 months ago) by jcfr
Original Path: trunk/Modules
BUG: Test data was missing since Slicer4 (test was still pointing where data
 was in Slicer3)

See bug report:
http://na-mic.org/Mantis/view.php?id=3341

The test that was not working does the following:
It runs ResampleDTIVolume and the result of this operation does not matter.
What is interesting is that the test makes sure that extending itkTestMainExtend
ed.h to work with DTI did not break the normal behavior of that file and that it
 still works with scalar images too.
Therefore, it compares a scalar image with itself and verifies that the test
 passes successfully

From: fbudin69500 <fbudin@unc.edu>

Revision 23023 - Directory Listing
Modified Wed Mar 26 17:56:24 2014 UTC (3 years, 6 months ago) by hjohnson
Original Path: trunk/Modules
BUG: Remove incorrect initialization

A compiler warning indicated incorrect initialization of
minimum value.

Slicer/Modules/CLI/RobustStatisticsSegmenter/SFLSRobustStatSegmentor3DLabelMap_single.h:133:
Slicer/Modules/CLI/RobustStatisticsSegmenter/SFLSRobustStatSegmentor3DLabelMap_single.txx:874:30: warning: implicit conversion
      from 'type' (aka 'unsigned int') to 'short' changes value from 4294967295 to -1 [-Wconstant-conversion]
  m_inputImageIntensityMin = std::numeric_limits<unsigned>::max(); // yes, it's twisted so easity to compute.

The numeric_limits type needed to be made consistent with the image.

Revision 23022 - Directory Listing
Modified Wed Mar 26 17:45:44 2014 UTC (3 years, 6 months ago) by hjohnson
Original Path: trunk/Modules
STYLE: Githook warnings about excessive line length

pre-commit hook failure
-----------------------
  in file 'Libs/MRML/Logic/vtkImageLinearReslice.cxx' is longer than 160 characters.
  in file 'Modules/Loadable/Annotations/MRML/vtkMRMLAnnotationControlPointsNode.cxx' is longer than 160 characters.
  in file 'Modules/Loadable/Annotations/MRML/vtkMRMLAnnotationControlPointsStorageNode.cxx' is longer than 160 characters.
  in file 'Modules/Loadable/Annotations/Testing/Cxx/vtkMRMLAnnotationControlPointsNodeTest1.cxx' is longer than 160 characters.

Revision 23021 - Directory Listing
Modified Wed Mar 26 17:45:15 2014 UTC (3 years, 6 months ago) by hjohnson
Original Path: trunk/Modules
STYLE: Remove end of line spaces

Spaces at the end of lines can cause noise in patch sets
when editors or git gobbles them up during other relatively
minor changes to files.

Removing end of line changes makes long term maintenance easier as
well.

When reviewing git histories or patch sets, the "--ignore-space-change"
option can be useful in filtering out changes due only to spacing.

i.e.
git diff HEAD~2 --ignore-space-change

Revision 23014 - Directory Listing
Modified Mon Mar 24 22:11:52 2014 UTC (3 years, 6 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Fix header copyright.

Revision 23013 - Directory Listing
Modified Mon Mar 24 22:11:46 2014 UTC (3 years, 6 months ago) by finetjul
Original Path: trunk/Modules
BUG: Fix crash in models logic when failing to read file

The returned node was deleted if not added into the scene.

Revision 23009 - Directory Listing
Modified Fri Mar 21 14:55:48 2014 UTC (3 years, 7 months ago) by alexy
Original Path: trunk/Modules
BUG: 3609. Added ability to select active tensor in the TractographyDisplay widgets

Revision 23008 - Directory Listing
Modified Wed Mar 19 17:41:09 2014 UTC (3 years, 7 months ago) by lassoan
Original Path: trunk/Modules
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 23005 - Directory Listing
Modified Fri Mar 14 21:08:41 2014 UTC (3 years, 7 months ago) by pieper
Original Path: trunk/Modules
ENH: 1. A basic mode added with auto-examine (only scalar plugin)

2. Advanced option added (using other plugings)
3. Tables orientation is not dynamic. Default is vertical, horizontal can
be toggled by a checkbox
4. tables are now expandable

STYLE: changed the metadata viewer name

From: Alireza Mehrtash <mehrtash@bwh.harvard.edu>

Revision 23003 - Directory Listing
Modified Thu Mar 13 21:12:49 2014 UTC (3 years, 7 months ago) by jcfr
Original Path: trunk/Modules
BUG: Enable numeric sorting in LabelStatistics table

Data is added as float in a QtVariant with Qt::DisplayRole, in stead of text. The
enable the columns to be numerically sorted.

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

Revision 23002 - Directory Listing
Modified Thu Mar 13 21:09:24 2014 UTC (3 years, 7 months ago) by jcfr
Original Path: trunk/Modules
COMP: Allow "external" compilation of TractographyLabelMapSeeding

Update CMakeLists.to reference variable also set in SlicerConfig.cmake

This should help to resolve the issue reported on the mailing list:
http://slicer-devel.65872.n3.nabble.com/Building-CLI-outside-of-the-Slicer-Build-tree-tt4031199.html

Revision 22944 - Directory Listing
Modified Tue Mar 11 19:52:21 2014 UTC (3 years, 7 months ago) by jcfr
Original Path: trunk/Modules
BUG: Update OtsuThresholdImageFilter test baseline

Following transition to ITKv4, the test started to fail because of the minor
different in the output. See [1]

This commit simply replaced the existing baseline with the current
output of the test.

[1] http://massmail.spl.harvard.edu/public-archives/slicer-devel/2013/011716.html

Revision 22931 - Directory Listing
Modified Fri Mar 7 23:28:20 2014 UTC (3 years, 7 months ago) by naucoin
Original Path: trunk/Modules
BUG: add missing .h file

Missed in svn 22930

Issue #3326


Revision 22930 - Directory Listing
Modified Fri Mar 7 21:02:31 2014 UTC (3 years, 7 months ago) by naucoin
Original Path: trunk/Modules
ENH: Add slice intersections toggle to Markups

Added a check box inside the jump slices group box. It's
available to toggle when jump slices is on. It updates
when entering the module, but isn't listening to the
slice composite nodes to update when the Navigation
menu and/or MRML updates happen.
Added test.

Issue #3326


Revision 22929 - Directory Listing
Modified Fri Mar 7 17:57:38 2014 UTC (3 years, 7 months ago) by naucoin
Original Path: trunk/Modules
ENH: save the last sceneview thumbnail type

Keep track of the last scene view and screen snapshot thumbnail type
and use it for the next one that's being captured.
For the scene views, base the next scene view name on the last
one instead of always going back to the default SceneView.

Issue #1760


Revision 22928 - Directory Listing
Modified Thu Mar 6 23:06:13 2014 UTC (3 years, 7 months ago) by naucoin
Original Path: trunk/Modules
STYLE: remove outdated documentation

Removed references to the Diffusion Editor since it
is not in Slicer4.

Issue #1875


Revision 22927 - Directory Listing
Modified Thu Mar 6 23:01:10 2014 UTC (3 years, 7 months ago) by pieper
Original Path: trunk/Modules
ENH: #2921 add summary dialog after running test

This was already being generated when running all tests, but
now do it even for a single test button click.

Revision 22926 - Directory Listing
Modified Thu Mar 6 23:01:05 2014 UTC (3 years, 7 months ago) by pieper
Original Path: trunk/Modules
BUG: avoid spurious python warning when a volume has no display node

Revision 22925 - Directory Listing
Modified Thu Mar 6 22:03:20 2014 UTC (3 years, 7 months ago) by naucoin
Original Path: trunk/Modules
STYLE: fix method documentation

Replace the \a with \arg to make a list with line breaks.

Issue #3512




Revision 22921 - Directory Listing
Modified Tue Mar 4 16:13:37 2014 UTC (3 years, 7 months ago) by naucoin
Original Path: trunk/Modules
BUG: disable selecting new fiducial if jump slices on

When new fiducials are added to a list, by default that row
in the GUI table was selected. If jump slices is checked,
that would result in the slices jumping to the coordinates
of the new fiducial, which is at the origin when it's first
added. The calculated coordinates are set by a second call
(and produce a second event) in the displayable manager
that was not triggering a second jump to the correct
coordinates. Disable jumping to the newly added
fiducial location when jump slices is on, this limits
the jumping to user clicks in the table.

Issue #3556


Revision 22919 - Directory Listing
Modified Mon Mar 3 23:26:58 2014 UTC (3 years, 7 months ago) by naucoin
Original Path: trunk/Modules
ENH: adjust the scale slider widgets to volume slice spacing

On entry to the Markups module, check for a background volume
in the red slice viewer, get the slice spacing and adjust
the scale slider maximum values by a scale factor times
the maximum slice spacing.
Round the max scale to the nearest 10 when resetting it from volume
spacing.
Also ensure that if the module is entered with scale values
on the display node that are larger than the slider maximums
that the sliders are adjusted.
Also works for the default settings being larger than slider
maximums.
Set the scale factor to 10 to allow for large markups on
widely spaced volumes.

Issue #3547



Revision 22915 - Directory Listing
Modified Mon Mar 3 00:08:33 2014 UTC (3 years, 7 months ago) by jcfr
Original Path: trunk/Modules
COMP: C++11 convertsion of types

error: no viable conversion from 'DiffusionTensor3DExtended<float>' to 'DiffusionTensor3DExtended<double>'

By preferring initialization to assignment this error is avoided.

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

Revision 22913 - Directory Listing
Modified Mon Mar 3 00:08:28 2014 UTC (3 years, 7 months ago) by jcfr
Original Path: trunk/Modules
COMP: C++11 conformance for static initialization

error: non-constant-expression cannot be narrowed from type 'unsigned long' to 'IndexValueType' (aka 'long') in initializer list [-Wc++11-narrowing]
as identifiied by the clang compiler.

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

Revision 22912 - Directory Listing
Modified Thu Feb 27 23:43:52 2014 UTC (3 years, 7 months ago) by naucoin
Original Path: trunk/Modules
BUG: reset table range for label map volumes

Label map volumes need to be mapped to colors in the color
look up table. For editing, don't allow procedurally defined
color nodes to be chosen.

Issue #3586



Revision 22907 - Directory Listing
Modified Wed Feb 26 19:25:38 2014 UTC (3 years, 7 months ago) by jcfr
Original Path: trunk/Modules
COMP: Simplify how BRAINSTools project options are specified

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

Revision 22905 - Directory Listing
Modified Wed Feb 26 19:25:35 2014 UTC (3 years, 7 months ago) by jcfr
Original Path: trunk/Modules
COMP: Do not force BRAINSTools options to ensure they can overwritten

Revision 22904 - Directory Listing
Modified Wed Feb 26 19:25:33 2014 UTC (3 years, 7 months ago) by jcfr
Original Path: trunk/Modules
COMP: Remove now obsolete patching of BRAINSTools ExternalData module

Considering both projects now use the same version of the module, it is
not required anymore to copy it.
See the associated BRAINStools issue for more details: https://github.com/BRAINSia/BRAINSTools/issues/3

Revision 22901 - Directory Listing
Modified Tue Feb 25 16:45:26 2014 UTC (3 years, 7 months ago) by alexy
Original Path: trunk/Modules
BUG: fixed qSlicerTransformModuleWidget::Invert method and qSlicerTransformModuleWidget test.

Revision 22893 - Directory Listing
Modified Fri Feb 21 01:36:25 2014 UTC (3 years, 7 months ago) by jcfr
Original Path: trunk/Modules
ENH: Implemented GetMarkupIndexByID and GetMarkupByID methods

From: Laurent Chauvin <lchauvin@bwh.harvard.edu>

Revision 22891 - Directory Listing
Modified Thu Feb 20 17:28:39 2014 UTC (3 years, 7 months ago) by inorton
Original Path: trunk/Modules
BUG: Fix #3585. Python bool('string') == True for any non-empty string

Revision 22885 - Directory Listing
Modified Sun Feb 16 20:51:57 2014 UTC (3 years, 8 months ago) by jcfr
Original Path: trunk/Modules
STYLE: Rename DiffusionTensorScalarMeasurements option name

The original option name was misleading, it has been renamed to better
guide the user.

Fixes #3591

Co-authored-by: Sonia Pujol <spujol@bwh.harvard.edu>

Revision 22884 - Directory Listing
Modified Sat Feb 15 21:47:25 2014 UTC (3 years, 8 months ago) by alexy
Original Path: trunk/Modules
BUG: Fixed usage of GetXYToIJKTransform in Editor tools

Revision 22880 - Directory Listing
Modified Fri Feb 14 23:44:04 2014 UTC (3 years, 8 months ago) by alexy
Original Path: trunk/Modules
BUG: Fixed usage of GetXYToIJKTransform in Editor tools

Revision 22879 - Directory Listing
Modified Fri Feb 14 22:40:40 2014 UTC (3 years, 8 months ago) by alexy
Original Path: trunk/Modules
BUG: Fixed usage of GetXYToIJKTransform in Editor PaintEffectTool

Revision 22877 - Directory Listing
Modified Fri Feb 14 16:11:06 2014 UTC (3 years, 8 months ago) by alexy
Original Path: trunk/Modules
BUG: fixed DataProbe module to work with non-linear transform

From: Alex Yarmarkovich <alexy@bwh.harvard.edu>

Revision 22876 - Directory Listing
Modified Fri Feb 14 16:10:58 2014 UTC (3 years, 8 months ago) by alexy
Original Path: trunk/Modules
ENH: rebased svn, fixed fiducials under nonlinear transform

From: Alex Yarmarkovich <alexy@bwh.harvard.edu>

Revision 22875 - Directory Listing
Modified Fri Feb 14 16:10:47 2014 UTC (3 years, 8 months ago) by alexy
Original Path: trunk/Modules
ENH: Made Markup and Annotation work with non-linear transforms

From: Alex Yarmarkovich <alexy@bwh.harvard.edu>

Revision 22874 - Directory Listing
Modified Fri Feb 14 16:10:27 2014 UTC (3 years, 8 months ago) by alexy
Original Path: trunk/Modules
ENH: changes to support non-linear transforms

From: Alex Yarmarkovich <alexy@bwh.harvard.edu>

Revision 22865 - Directory Listing
Modified Thu Feb 6 22:12:42 2014 UTC (3 years, 8 months ago) by jcfr
Original Path: trunk/Modules
BUG: Ensure label can be changed if it was been toggled.

Following commit r22862 fixing issue #3576 to ensure label is restored
after switching effect, the label couldn't be changed after it being
toggled.

This commit now ensures that label is reset when eraseLabel has been
enabled and effect is switched.

See #3576

Revision 22863 - Directory Listing
Modified Thu Feb 6 13:44:29 2014 UTC (3 years, 8 months ago) by jcfr
Original Path: trunk/Modules
COMP: Build 'DICOMDiffusionVolumePlugin' only if diffusion support is enabled

Revision 22862 - Directory Listing
Modified Wed Feb 5 22:36:13 2014 UTC (3 years, 8 months ago) by jcfr
Original Path: trunk/Modules
BUG: Restore stored label when selecting editor effect different from erase

Selecting the "EraseLabel" effect was storing the current label into
the 'storedLabel' parameter node attribute but this one was never restored
when selecting an other effect.

This commit fix the issue by ensuring the stored label is restored and also
introduce two new functions: 'backupLabel' and 'restoreLabel'

Fixes #3576

Revision 22859 - Directory Listing
Modified Tue Feb 4 20:17:03 2014 UTC (3 years, 8 months ago) by pieper
Original Path: trunk/Modules
BUG: #3568 Fix warning message about missing files

Revision 22858 - Directory Listing
Modified Tue Feb 4 15:17:20 2014 UTC (3 years, 8 months ago) by pieper
Original Path: trunk/Modules
BUG: avoid a warning dialog in Editor when scene is closed

The warning message was triggered because the validity of the
volume state is checked when nodes are added or removed from the
scene, but it doesn't make sense to warn about the missing master
volume if there is also no merge volume.

Thanks to Alexandra Prior for pointing this out.

http://slicer-users.65878.n3.nabble.com/Editor-td4027182.html

Revision 22850 - Directory Listing
Modified Fri Jan 24 09:03:31 2014 UTC (3 years, 8 months ago) by jcfr
Original Path: trunk/Modules
BUG: Fix "Reload and Test" function

While commit r22839 re-factored the code associated with "Reload" function,
it also made the "Reload and Test" function fails.

This commit fixes the issue by setting the "<moduleName>" key into
the global dictionary of the reloaded module so that it can be
referenced in the "onReloadAndTest()" function.

Note that the overall approach to reload modules could be revisited to
leverage either the "rollback importer" method or a more sophisticated one
like the "python-reloader" [2][3]

Thanks to "Csaba Pinter <csaba.pinter@queensu.ca>" for reporting the issue.

[1] http://pyunit.sourceforge.net/notes/reloading.html
[2] http://www.indelible.org/ink/python-reloading/
[3] https://github.com/jparise/python-reloader

Revision 22846 - Directory Listing
Modified Fri Jan 24 00:07:39 2014 UTC (3 years, 8 months ago) by finetjul
Original Path: trunk/Modules
COMP: Fix compilation error with ITKv3

MakeOutput expects a DataObjectPointerArraySizeType and not an integer.

Revision 22845 - Directory Listing
Modified Fri Jan 24 00:07:37 2014 UTC (3 years, 8 months ago) by finetjul
Original Path: trunk/Modules
BUG: Fix crash in vtkMRMLAnnotationDisplayableManager

Revision 22839 - Directory Listing
Modified Sun Jan 19 07:59:22 2014 UTC (3 years, 9 months ago) by jcfr
Original Path: trunk/Modules
ENH: Factor out scripted module reload function into 'slicer.util'

At least two versions of the code were used to reload a scripted module
were existing. This commit add the most recent version into
the function 'slicer.util.reloadScriptedModule' and update the
Slicer modules to use it.

Note that since not all module implements the 'cleanup' function,
an additional test has been added to check if the method is available.

Revision 22836 - Directory Listing
Modified Sun Jan 19 04:02:59 2014 UTC (3 years, 9 months ago) by jcfr
Original Path: trunk/Modules
COMP: Build test CLIs only if BUILD_TESTING is ON

Revision 22826 - Directory Listing
Modified Fri Jan 17 05:18:48 2014 UTC (3 years, 9 months ago) by jcfr
Original Path: trunk/Modules
COMP: Fix typo introduced in previous commit

Revision 22825 - Directory Listing
Modified Fri Jan 17 05:13:37 2014 UTC (3 years, 9 months ago) by jcfr
Original Path: trunk/Modules
COMP: Associate FiberBundleToLabelMap module with BUILD_DIFFUSION_SUPPORT

Revision 22823 - Directory Listing
Modified Tue Jan 14 23:10:56 2014 UTC (3 years, 9 months ago) by pieper
Original Path: trunk/Modules
BUG: avoid spurious warnings from DataProbe during startup

Make sure the frame member of the widget is set before
setting up observers to avoid a situation where the processEvents
is called before setup is complete.  This avoids some spurious
warning messages during startup.

Revision 22821 - Directory Listing
Modified Tue Jan 14 19:24:28 2014 UTC (3 years, 9 months ago) by jcfr
Original Path: trunk/Modules
COMP: Revert - vtkPichonFastMarching - Replace finite() with isfinite()"

This reverts commit r22819

isfinite() function is not available on windows 2008:

20>47>..\..\..\..\..\..\Slicer4\Modules\Scripted\EditorLib\Logic\vtkPichonFastMarchingPDF.cxx(193) : error C3861: 'isfinite': identifier not found

Revision 22819 - Directory Listing
Modified Tue Jan 14 18:58:22 2014 UTC (3 years, 9 months ago) by jcfr
Original Path: trunk/Modules
COMP: vtkPichonFastMarching - Replace finite() with isfinite()

finite() is not universally in the c standard.
isfinite is support in all c compilers since
c99.

As of Mac 10.9 under clang, finite() issues a
warning that it will be deprecated and that the
standards conforming isfinite() should be used.

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

Revision 22817 - Directory Listing
Modified Tue Jan 14 15:56:54 2014 UTC (3 years, 9 months ago) by jcfr
Original Path: trunk/Modules
BUG: BRAINSTools should not be built when CLIs are disabled

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

Revision 22809 - Directory Listing
Modified Thu Jan 9 00:38:29 2014 UTC (3 years, 9 months ago) by naucoin
Original Path: trunk/Modules
BUG: Allow assigning procedural color nodes to map scalars

Previously the GUI assumed that color table nodes only were used to
map scalars to colors onto model geometry. This change generalises
the color node selector to allow both color table nodes as well
as procedural color nodes.
Renamed the widget and methods to reflect the generalisation.
Only set the scalar widgets if they don't match the model
display node settings.
Added a label displaying the scalar range.



Revision 22805 - Directory Listing
Modified Tue Jan 7 18:13:10 2014 UTC (3 years, 9 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Add X,O,M and S documentation for VolumeRendering module

Revision 22804 - Directory Listing
Modified Tue Jan 7 18:12:49 2014 UTC (3 years, 9 months ago) by finetjul
Original Path: trunk/Modules
BUG: Cleanup ROI widget and representation

This reverts commit r22803 inadvertently pushed.

Revision 22803 - Directory Listing
Modified Tue Jan 7 18:09:37 2014 UTC (3 years, 9 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Cleanup ROI widget and representation

Add vtkMRMLDisplayNode::GetBounds() utility method.

Revision 22800 - Directory Listing
Modified Mon Jan 6 18:16:30 2014 UTC (3 years, 9 months ago) by naucoin
Original Path: trunk/Modules
BUG: fix updating fiducials after scene load

After loading a scene, changing the display properties of
a fiducial list was not being reflected in the 2d and 3d
views. There was a missing event observation in the
Markups displayable managers, adding in 
vtkMRMLDisplayableNode::DisplayModifiedEvent
to the list of events observed on a markups node
fixed the problem.

Issue #3480



Revision 22776 - Directory Listing
Modified Tue Dec 17 06:07:46 2013 UTC (3 years, 10 months ago) by jcfr
Original Path: trunk/Modules
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 22772 - Directory Listing
Modified Wed Dec 11 21:52:13 2013 UTC (3 years, 10 months ago) by pieper
Original Path: trunk/Modules
BUG: #3524 check for valid images in Editor

This generates a warning for situations that are thought to be
invalid.  Since some tools may still be workable, we let the user
go ahead, but include some suggestions in the warnings about how
to fix the volumes.

http://na-mic.org/Bug/view.php?id=3524

Revision 22763 - Directory Listing
Modified Wed Dec 4 22:26:21 2013 UTC (3 years, 10 months ago) by jcfr
Original Path: trunk/Modules
ENH: Consolidate qSlicerAppMainWindow

qSlicerAppMainWindowCore brings confusion to the code. It is now merged
with qSlicerAppMainWindow.
The custom macro is replaced by the automatic signal/slot connection of Qt
i.e. on_<SENDER_NAME>_<SENDER_SIGNAL>())
The objects had to be renamed to support the feature.

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

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

Revision 22762 - Directory Listing
Modified Wed Dec 4 20:29:48 2013 UTC (3 years, 10 months ago) by jcfr
Original Path: trunk/Modules
COMP: For consistency, rename qSlicer.*IO classes into qSlicer.*Reader

Since the classes derive from qSlicerFileReader, change their suffixes
into "Reader" to prevent confusion.

Revision 22759 - Directory Listing
Modified Tue Dec 3 23:03:32 2013 UTC (3 years, 10 months ago) by jcfr
Original Path: trunk/Modules
COMP: Remove unnecessary includes in vtkMRMLAbstractLogic header

This has the side effect of having a faster compilation

External module OpenIGTLinkIF and MultiVolumeExplorer have already been
updated according to change in vtkMRMLAbstractLogic header.
See #3493 / r22712  and  #3494 / r22693

On the other hand, no test build have been done for the extension. Issue
will be resolved on case by case following the dashboard results.

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

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

Revision 22754 - Directory Listing
Modified Tue Dec 3 00:13:02 2013 UTC (3 years, 10 months ago) by jcfr
Original Path: trunk/Modules
BUG: Fixed scene view node memory leak. Fixes #3515

From: Andras Lasso <lasso@queensu.ca>

Revision 22753 - Directory Listing
Modified Mon Dec 2 21:52:56 2013 UTC (3 years, 10 months ago) by jcfr
Original Path: trunk/Modules
BUG: Made file extension comparisons case-insensitive. Fixes #3511

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

From: Andras Lasso <lasso@queensu.ca>

Revision 22749 - Directory Listing
Modified Mon Dec 2 21:35:17 2013 UTC (3 years, 10 months ago) by naucoin
Original Path: trunk/Modules
ENH: bring Markups jump slices default in line with slice node

Jumping slices default reset to offset as per current vtkMRMLSliceNode
JumpMode.
Slice node and radio button settings are compared and updated on GUI
start up.



Revision 22744 - Directory Listing
Modified Tue Nov 26 23:20:11 2013 UTC (3 years, 10 months ago) by jcfr
Original Path: trunk/Modules
COMP: Removed unused/unmaintained RemoteIO classes and FetchMI module logic

For future references, the corresponding code has been added to
the Slicer attic. See Slicer/Attic@53262c8

From discussion with Steve and Andras:

// --------------------
(1) Jc - Nov 26, 2013

I notice that the only reason we depend on curl is for existence
of RemoteIO library that has been "replaced" by SampleData
and DataStore.

I really like the concept of registering URI that could be
downloaded that is why we should keep the infrastructure in place.

That said, I was thinking to get remove the following classes:

vtkHIDHandler.h
vtkHIDTagTable.h
vtkSRBHandler.h
vtkXNATHandler.h
vtkXNDHandler.h
vtkXNDTagTable.h

Then, we could implement a Qt based  vtkHTTPHandler handler, that
way we could simply remove the curl dependency.

In the mean time, I would also remove the FetchMI logic which is
not maintained or used at that point.

Let me know what you think,

// --------------------
(2) Andras - Nov 26, 2013

It’s always a good idea to make the core smaller and simpler, so
I support the idea of getting rid of unused classes and unnecessary
dependencies.

We planned to use curl for uploading training results in a .zip
file to Moodle, but I guess we can add curl to our module then.

// --------------------
(3) Jc - Nov 26, 2013

Thanks for commenting.

If your module is a loadable or a scripted module, all "curl"
functionality can be provided by Qt. Would that work for you ?

// --------------------
(4) Andras - Nov 26, 2013

We would need quite complex curl functionalities for uploading data,
see the scripts below:

https://gist.github.com/Joshkunz/4516316

https://github.com/proyectoeduhub/moodle-cli/blob/master/moodle-file-upload-curl.sh

Would it be feasible to implement these?

// --------------------
(5) Jc - Nov 26, 2013

Good point. The plan would then be to:

  (1) remove dependency of Slicer core against curl

  (2) Only, build both the Curl library and the curl executable, keeping
 them in the package.

That way, it would provide great flexibility with minimum overhead.

// --------------------
(6) Steve - Nov 26, 2013

Sounds like an excellent plan.

Yes, I like the design of the remote IO support in MRML, but it's not
 being used and is great to simplify wherever possible.  FetchMI can
go away for now, with the hope that we'll reproduce and improve on
it in the future (someday).

Revision 22743 - Directory Listing
Modified Tue Nov 26 22:35:38 2013 UTC (3 years, 10 months ago) by naucoin
Original Path: trunk/Modules
BUG: adding a test for closing the scene with volume rendering + cropping

Crashes on linux.

Issue #3513



Revision 22724 - Directory Listing
Modified Sun Nov 24 08:09:34 2013 UTC (3 years, 10 months ago) by jcfr
Original Path: trunk/Modules
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 22713 - Directory Listing
Modified Mon Nov 18 20:37:20 2013 UTC (3 years, 11 months ago) by jcfr
Original Path: trunk/Modules
BUG: Fixed translation sliders in local coordinate reference mode.

In local coordinate reference mode the slider positions do not match
directly with the transformation matrix values.

Similarly to rotation sliders, only relative positions are set
with the sliders in local coordinate reference mode.

Fixes #3488

From: Andras Lasso <lasso@queensu.ca>

Revision 22705 - Directory Listing
Modified Thu Nov 14 23:26:45 2013 UTC (3 years, 11 months ago) by naucoin
Original Path: trunk/Modules
STYLE: updating docs for 4.3

Added description of including fiber bundles, scroll to, and show/hide all.



Revision 22697 - Directory Listing
Modified Wed Nov 13 22:55:42 2013 UTC (3 years, 11 months ago) by naucoin
Original Path: trunk/Modules
STYLE: minor edits for 4.3 documentation

Fix formatting errors, attributions, phrasing.



Revision 22695 - Directory Listing
Modified Wed Nov 13 14:11:33 2013 UTC (3 years, 11 months ago) by finetjul
Original Path: trunk/Modules
BUG: Support vtkStringArray as model field array

Closes #3344

Revision 22694 - Directory Listing
Modified Tue Nov 12 21:08:32 2013 UTC (3 years, 11 months ago) by pieper
Original Path: trunk/Modules
BUG: avoid python attribute error on dicom context menu

TODO: the elements are currently disabled since we don't have
corresponding implementations for the new dicom widget.

Revision 22689 - Directory Listing
Modified Thu Nov 7 16:54:34 2013 UTC (3 years, 11 months ago) by pieper
Original Path: trunk/Modules
ENH: dicom header viewer added to DICOMLib using ctkDICOMObjectListWidget

ENH: update DICOM module for Table View

New interface to support better searching and header display.

Now plugins are selectable to avoid wasting time on unneeded plugins.

Plugins are now evaluated on-demand, to simplify the workflow.

http://www.commontk.org/index.php/CTK-Hackfest-May-2013#DICOM_Database_and_Networking

https://github.com/commontk/CTK/pull/361

ENH: update to latest CTK for header widget

Also fix lingering rebase issue (stray variable).

BUG: Give header popup independent geometry setting

Also fix incorrect end of line character

ENH: examine button diabled until needed

STYLE: remove tabs in code

Revision 22687 - Directory Listing
Modified Thu Nov 7 15:33:04 2013 UTC (3 years, 11 months ago) by jcfr
Original Path: trunk/Modules
BUG: Properly support extension

Revert commit r22148 that was setting the path to saved MRB as MRMLScene URL.
The MRML scene URL knows remains associated with the mrml file after either
a read or save to mrml, or even export (MRB, Kiwi.zip, ...) operation.

To be able to properly switch between different available file formats
while supporting filename containing dots. The extension of a filename
needs to be removed based on a list of known extensions. For that purpose,
the following two functions have been introduced:
  - extractKnownExtension
  - stripKnownExtension

These functions rely on the existing IOManager function "fileWriterExtensions"
able to return a list of name filters associated with either a storage node
or a mrml scene.

For any fileName item, in order to get the associated storage node or mrml scene,
a new role named "UIDRole" has been introduced. For a given fileName item,
if a nodeID is set with the "UIDRole", it is understood that it will
be the nodeID of the corresponding storage node. If it is not set, it means
the fileName item is associated the scene.

See #2948

Revision 22683 - Directory Listing
Modified Tue Nov 5 14:24:15 2013 UTC (3 years, 11 months ago) by pieper
Original Path: trunk/Modules
ENH: clarify name of attribute (Markup not Seed)

There are different conventions in different parts of the code,
but Seed is consistently the vtk widget layer, and Markup is the
Slicer nomenclature.

Revision 22682 - Directory Listing
Modified Tue Nov 5 14:24:10 2013 UTC (3 years, 11 months ago) by pieper
Original Path: trunk/Modules
ENH: give Markups option to be visible only in selected views

Port change from r21740 from Annotations to Markups

    ENH: give annotations option to be visible only in selected views

    This uses the same convention used in dislay nodes for other
    displayable managers (e.g. VolumeRendering), except that it uses the
    sliceNode since it is the 2D analog to the 3D view Node (at some point
    perhaps there should be a generic superclass).  Here, since we are only
    using the ID string it doesn't matter what type the node it.

    This feature allows custom UIs, for example where some annotations only
    show up in one view while others show up everywher.  In particular, this
    is helpful for annotations representing volume-specific anatomical
    landmark locations.

    git-svn-id: http://svn.slicer.org/Slicer4/trunk@21740 3bd1e089-480b-0410-8dfb-8563597acbee

Revision 22677 - Directory Listing
Modified Sun Nov 3 23:07:51 2013 UTC (3 years, 11 months ago) by jcfr
Original Path: trunk/Modules
STYLE: Simplify vtkSlicerModelsLogic code using vtkNew

Revision 22676 - Directory Listing
Modified Sun Nov 3 23:07:48 2013 UTC (3 years, 11 months ago) by jcfr
Original Path: trunk/Modules
STYLE: Avoid confusion renaming SceneView API: "Nodes" into "StoredScene"

The following renaming have been done:
 - ivar Nodes -> StoredScene
 - method "UpdateSnapshotScene" -> "UpdateStoredScene"
 - method "GetNodes" -> "GetStoredScene"

Also remove the unused parameter from "UpdateStoredScene"

Revision 22671 - Directory Listing
Modified Thu Oct 31 17:03:51 2013 UTC (3 years, 11 months ago) by lassoan
Original Path: trunk/Modules
BUG: Prevent LevelTracingEffect crash when the user clicks on a pixel at the edge of the image (http://na-mic.org/Mantis/view.php?id=3470)

Revision 22669 - Directory Listing
Modified Thu Oct 31 04:51:11 2013 UTC (3 years, 11 months ago) by jcfr
Original Path: trunk/Modules
ENH: Optimized performance of observations management in vtkMRMLScene

Use a std::map< std::string, std::set<std::string> > instead of two
separate ReferencedIDs and ReferencingNodes vectors to make lookup,
insertion, and deletion much faster (especially scene close takes much
shorter time now).
Store both referenced and referring nodes by ID. It is simpler, safer,
and most of the time the node pointers were validated anyway using
scene->GetNodeFromID(node->GetID().

Also, use set instead of vector for storing unique IDs for improving
performance of scene loading (especially when the same scene is loaded
twice and a lot of IDs have to be generated).

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

From: Andras Lasso <lasso@queensu.ca>

Revision 22664 - Directory Listing
Modified Thu Oct 31 04:50:52 2013 UTC (3 years, 11 months ago) by jcfr
Original Path: trunk/Modules
BUG: Fixed references to nodes in qSlicerTractographyDisplayWidget

Crash happened at the end of SceneClose in py_test_tractography_display test because old (invalid) display node was still used.

From: Andras Lasso <lasso@queensu.ca>

Revision 22642 - Directory Listing
Modified Sun Oct 27 03:08:50 2013 UTC (3 years, 11 months ago) by jcfr
Original Path: trunk/Modules
BUG: Ensure ROI worked as expected. Fixes #3459

Fix bug introduced by r22539 when updating code to use vtkNew where
possible.

Revision 22637 - Directory Listing
Modified Mon Oct 21 21:28:04 2013 UTC (3 years, 11 months ago) by pieper
Original Path: trunk/Modules
ENH: add node attributes describing the currently active manipulation

Tell which slice viewer is manipulating which fiducial in the
markup node.

Markups.MovingInSliceView holds the LayoutName of the sliceNode associated
with the viewer where the widget is being manipulated.

Markups.MovingSeedNumber holds the seed number being manipulated.

Both are cleared when the seed is not being manipulated by a widget.

Revision 22635 - Directory Listing
Modified Mon Oct 21 20:40:48 2013 UTC (3 years, 11 months ago) by pieper
Original Path: trunk/Modules
ENH: Contribution from Albert Montillo to paint in 3D

Adds a Sphere option to the PaintEffect to make it quicker to segment
large anatomical regions that are somewhat spherical.

Powerful when used with ThresholdPaint.

Cleanup code.

Remove debug comments.

Clean up variable names.

STYLE: fix small typo

From: Jim Miller <millerjv@ge.com>

Revision 22617 - Directory Listing
Modified Fri Oct 18 16:35:49 2013 UTC (4 years ago) by alexy
Original Path: trunk/Modules
BUG: 3447. Added .nrrd extension to grid transform IO

Revision 22615 - Directory Listing
Modified Thu Oct 17 11:55:58 2013 UTC (4 years ago) by lassoan
Original Path: trunk/Modules
BUG: Fixed crash in Transform widget

When hardened transform or untransformed multiple transformed items (with multi-select) then Slicer crashed.
Applied the same fix as in http://www.na-mic.org/Bug/view.php?id=2578.

Revision 22613 - Directory Listing
Modified Tue Oct 15 20:10:36 2013 UTC (4 years ago) by finetjul
Original Path: trunk/Modules
STYLE: Improve Data module documentation

Add "MRML Node Inspector" section documentation.

Revision 22612 - Directory Listing
Modified Mon Oct 14 20:56:00 2013 UTC (4 years ago) by naucoin
Original Path: trunk/Modules
BUG: refactor code to remove unnecessary error message

There are two possible ways to obtain the results from PETStandardUptakeValueComputation,
having them written out to a .csv file or to a string parameter file that gets
parsed and loaded into the Slicer GUI. Only print out an error and fail if
neither parameter is specified. 
Checks for empty strings and doesn't try to open the files, so the unable
to open error messages will only occur if a non empty file name fails
to open.

Issue #3432


Revision 22609 - Directory Listing
Modified Wed Oct 9 21:11:54 2013 UTC (4 years ago) by naucoin
Original Path: trunk/Modules
STYLE: updated tool tip for markups table

Add a tool tip to hint at the right click context menu.

Issue #3397



Revision 22608 - Directory Listing
Modified Wed Oct 9 20:42:18 2013 UTC (4 years ago) by naucoin
Original Path: trunk/Modules
ENH: add copy to markups list right click option

Can now right click on a markup in the GUI and copy it
to another list, placing it at the end of the destination
list.
Updated the right click Move option to only offer at the
end of the list as that simplifies the UI and users can
move the markups with the move up/down buttons.
Updated test for logic copy.
Updated documentation for copy.

Issue #3397



Revision 22569 - Directory Listing
Modified Thu Oct 3 02:34:08 2013 UTC (4 years ago) by jcfr
Original Path: trunk/Modules
BUG: Fix vtkObserverManager warning happening after loading a file.

This commit ensured that the observer associated with MRMLNodesCallbackCommand
are removed also if the file is successfully loaded.

Warning: In /home/jchris/Projects/Slicer/Libs/MRML/Core/vtkObserverManager.cxx, line 59
vtkObserverManager (0x3b99ce0): The callback is not deleted because there
are still some observation. They seem to not have been registered into
the event broker.

Revision 22559 - Directory Listing
Modified Tue Oct 1 19:56:32 2013 UTC (4 years ago) by jcfr
Original Path: trunk/Modules
COMP: Fix [-Wunused-but-set-variable] in vtkSlicerVolumeRenderingLogic

After checking with the author of the class, it makes sense to remove the
code related to the unused "gradientRange" variable.

Revision 22539 - Directory Listing
Modified Tue Oct 1 19:25:00 2013 UTC (4 years ago) by jcfr
Original Path: trunk/Modules
ENH: Improve readability using vtkNew where possible

In addition to be shorter, it simply conveys the idea of locally
instantiating an object.

Indeed, vtkNew allow to instantiate an object on the heap and deleting it
when it goes out of scope if its reference count has been incremented by
either assigning the object to a smart pointer or calling Register.

Revision 22538 - Directory Listing
Modified Tue Oct 1 19:24:47 2013 UTC (4 years ago) by jcfr
Original Path: trunk/Modules
ENH: Improve readability of MRML tests using vtkNew where possible

Simplify code removing tests for null object already being done
in the helper macro "EXERCISE_BASIC_OBJECT_METHODS"

For example, the following should not be needed:

  vtkNew<vtkFoo> foo;
  if (foo.GetPointer() == 0)
  {
    std::cerr << "Failed to instantiate vtkFoo" << std::endl;
  }

Instead, the following should be used:

  EXERCISE_BASIC_OBJECT_METHODS(foo.GetPointer())

Remove use of unnecessary vtkSmartPointer to check return value. Indeed,
since the operator "==" of the vtkSmartPointer is overloaded to compare with
the pointed object, there is no need to used a smart pointer. [1]

// ---------
vtkSmartPointer<vtkMRMLDisplayableNode> pnode = node1->GetDisplayableNode();
std::cout << "GetDisplayableNode returned "
          << (pnode == NULL ? "null" : "not null")
          << std::endl;
// ---------

has been changed into

// ---------
vtkMRMLDisplayableNode* pnode = node1->GetDisplayableNode();
std::cout << "GetDisplayableNode returned "
          << (pnode == NULL ? "null" : "not null")
          << std::endl;
// ---------

[1] https://github.com/Kitware/VTK/blob/0e0674a3695fdeaf01ce87dfc04e32111b7402e0/Common/vtkSmartPointerBase.h#L104

Revision 22532 - Directory Listing
Modified Tue Oct 1 02:35:00 2013 UTC (4 years ago) by fedorov
Original Path: trunk/Modules
COMP: reverting previous change as it caused compile error on Win

Revision 22528 - Directory Listing
Modified Mon Sep 30 23:15:15 2013 UTC (4 years ago) by fedorov
Original Path: trunk/Modules
COMP: convert to integer explicitly to avoid ambiguity

Fixes #3420


Revision 22483 - Directory Listing
Modified Tue Sep 24 23:13:38 2013 UTC (4 years ago) by naucoin
Original Path: trunk/Modules
COMP: code clean up to unify setting the active place node

Added a utility function in the logic to set the active place node,
matching the get active place node id method. Call it where the
selection node was being accessed, and make sure that the testing
and setting of the ActivePlaceNodeClassName and ActivePlaceNodeID
are done only when there is a change and with the Reference call
so that events are triggered.
Added a test of the new SetActiveListID method.



Revision 22482 - Directory Listing
Modified Tue Sep 24 22:33:45 2013 UTC (4 years ago) by naucoin
Original Path: trunk/Modules
BUG: update the CLIs to create new Markup fiduicals from point node selector

The command line module GUI helper hadn't been updated to create Markups
Fiducial nodes by default when creating new nodes was enabled. It was still
set up to create Slicer3 vtkMRMLFiducialListNodes. 
Now by default a vtkMRMLMarkupsFiducialNode will be created when Create New is
selected.
Update the Markups module logic to detect node added events and add a display
node if not in batch processing, import or restore modes.
Updated the simple region growing segmentation help documentation to refer to the
Markups module.

Issue #3417



Revision 22481 - Directory Listing
Modified Tue Sep 24 21:42:13 2013 UTC (4 years ago) by naucoin
Original Path: trunk/Modules
STYLE: update Markups doxygen documentation

Moved sections so that they'll be visible on the generated pages.
Expanded documentation on the node level versus markup level settings.
Added separate comments for each documented method.



Revision 22480 - Directory Listing
Modified Tue Sep 24 19:46:29 2013 UTC (4 years ago) by naucoin
Original Path: trunk/Modules
STYLE: updated documentation on selection node

Updated doxygen comments to note that the PlaceNodeClassName
calls replace the AnnotationNodeID calls. 
Fixed a merge error on the enum, fixing the overwriting of event
numbers and moved the UnitModifiedEvent to be last.
Updated doxygen comments on the annotation fiducial node to
note it as deprecated moving the top level description so that
it shows up on the generated pages.



Revision 22475 - Directory Listing
Modified Mon Sep 23 14:43:02 2013 UTC (4 years ago) by jcfr
Original Path: trunk/Modules
ENH: Add user feedback section in Welcome module.

Added an offer for users to share their stories and feedback using the
google form created by Steve Pieper. See http://goo.gl/6BvcHm

Fixes #3229

Co-authored-by: Jean-Christophe Fillion-Robin <JChris.FillionR@kitware.com>

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

Revision 22467 - Directory Listing
Modified Sun Sep 22 02:52:34 2013 UTC (4 years ago) by pieper
Original Path: trunk/Modules
BUG: #3412 fix crash when no tensors on fiber label select

When the input fiber bundles have no tensors, we don't want to create
an output array.  When and empty tensor array was passed to the vtk
xml reader it crashed.

Now, don't create an output tensor array if there is not one on the input.

Revision 22462 - Directory Listing
Modified Fri Sep 20 23:42:39 2013 UTC (4 years, 1 month ago) by pieper
Original Path: trunk/Modules
BUG: avoid python error messages when path is not yet set in Endoscopy

This is triggered by some signals being emitted during the building
of the module widget.

Revision 22461 - Directory Listing
Modified Fri Sep 20 16:57:21 2013 UTC (4 years, 1 month ago) by alexy
Original Path: trunk/Modules
BUG: 3404. Check invalid label range in the Logic that seeds fibers rather than in the parameter node.

Revision 22460 - Directory Listing
Modified Fri Sep 20 14:01:27 2013 UTC (4 years, 1 month ago) by alexy
Original Path: trunk/Modules
BUG: 3403. Fixed logic for AND operation in FiberBundleLabelSelect module

Revision 22436 - Directory Listing
Modified Tue Sep 17 03:55:43 2013 UTC (4 years, 1 month ago) by jcfr
Original Path: trunk/Modules
BUG: Fix Slicer crash on DTIVolume reload after scene is closed.

Handle the case when newVolumeDispalyNode is NULL in setMRMLVolumeNode().
Fixes #3380

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

Revision 22433 - Directory Listing
Modified Mon Sep 16 20:18:14 2013 UTC (4 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: fix error on start up from SurfaceToolbox

Add in import string to fix start up error when 
trying to load the SurfaceToolbox scriptable module:

Traceback (most recent call last):
  File "/projects/birn/nicole/Slicer42/Slicer4-SuperBuild-Debug/Slicer-build/lib/Slicer-4.3/qt-scripted-modules/SurfaceToolbox.py", line 11, in __init__
    parent.helpText = string.Template("""
NameError: global name 'string' is not defined



Revision 22432 - Directory Listing
Modified Fri Sep 13 22:36:00 2013 UTC (4 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: finish steps for the Neurosurgical Planning Tutorial

Added the editor steps and label map seeding.
Added the screen capture functionality to the template file.

Issue #3328



Revision 22431 - Directory Listing
Modified Fri Sep 13 18:47:10 2013 UTC (4 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: add missing StartPlaceMode method

Laurent's extension was using the Annotation module logic
StartPlaceMode call and it wasn't working. Added it to
Markups logic and debugged it to work to set the mouse
mode to place Markup fiducials. Added a return boolean
to check success. Updated testing.



Revision 22424 - Directory Listing
Modified Tue Sep 10 20:19:28 2013 UTC (4 years, 1 month ago) by naucoin
Original Path: trunk/Modules
STYLE: update Annotatons module documentation for 4.3

Removed references to fiducials as they've been moved into the Markups module.



Revision 22423 - Directory Listing
Modified Tue Sep 10 16:18:02 2013 UTC (4 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: Fix missing conversion of fiducials in scene views

Annotation fiducials in scene view scenes were coming up as unsaved in the Save
data dialog when loaded from a scene with scene views where only the current
scene had had it's fiducials conerted to markups. This was due to the change
Alex made to save data that only appears in scene views, so added in
iterating over the current scene and scene views when converting fiducials. 
Added in looking for end scene restore events in the GUI so that it will
be updated properly even if there wasn't an active place node id in the saved scene view. 
Expanded the AddNewFiducialNode method to support adding to a passed in scene so
that the converted markups can be added to the scene view scenes.

Issue #3296



Revision 22421 - Directory Listing
Modified Tue Sep 10 15:51:47 2013 UTC (4 years, 1 month ago) by naucoin
Original Path: trunk/Modules
STYLE: print out widget projections

Revision 22414 - Directory Listing
Modified Fri Sep 6 20:16:32 2013 UTC (4 years, 1 month ago) by alexy
Original Path: trunk/Modules
ENH: 3379. Added a "Include Fibers" checkbox to the Models module to allow hierarchical grouping of Fiber Bundles

Revision 22412 - Directory Listing
Modified Thu Sep 5 02:58:49 2013 UTC (4 years, 1 month ago) by jcfr
Original Path: trunk/Modules
COMP: Do not build DWIConvert module if DICOM support is disabled

"DWIConvert.cxx" expects "itkDCMTKFileReader.h" header.
See https://github.com/BRAINSia/BRAINSTools/blob/ddf903b56fd6633945e1927b54393f7c65268dea/DWIConvert/DWIConvert.cxx#L47

Fixes #3370

Revision 22410 - Directory Listing
Modified Wed Sep 4 14:48:07 2013 UTC (4 years, 1 month ago) by naucoin
Original Path: trunk/Modules
COMP: fix compiling in debug mode

A variable was removed to fix a release mode unused variable warning,
in svn 22402, remove it from the vtkDebugMacro.



Revision 22407 - Directory Listing
Modified Wed Sep 4 10:48:34 2013 UTC (4 years, 1 month ago) by jcfr
Original Path: trunk/Modules
ENH: Update Documentation to 4.3

Revision 22402 - Directory Listing
Modified Wed Sep 4 09:27:53 2013 UTC (4 years, 1 month ago) by jcfr
Original Path: trunk/Modules
COMP: Fix unused variable warnings

Revision 22401 - Directory Listing
Modified Wed Sep 4 05:26:37 2013 UTC (4 years, 1 month ago) by jcfr
Original Path: trunk/Modules
BUG: Fix logic checking for readonly folder in writeToMRB method

Following r22395 "qSlicerSceneWriter::writeToMRB" has been updated to
check is the MRB file to be written was writable or not, the test was
always failing since the file itself wasn't existing.

This commit implement the appropriate logic by checking if the destination
folder where the MRB should be saved is writable.

This commit also fix the test "test_slicer_util_save.test_saveSceneAsMRB"

See #3242

Revision 22399 - Directory Listing
Modified Tue Sep 3 22:52:59 2013 UTC (4 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: fix failing test

Fix the write CLI test for the markpus node by adjusting the expected number
of arguments to be 2 times the number of points, as the flag is written
separately now.

Related to fixes for issue #1910


Revision 22396 - Directory Listing
Modified Tue Sep 3 21:47:50 2013 UTC (4 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: fix loading of double array files

The file extension didn't match that in the double array storage node.

Fixes issue #3289



Revision 22395 - Directory Listing
Modified Tue Sep 3 20:00:23 2013 UTC (4 years, 1 month ago) by jcfr
Original Path: trunk/Modules
BUG: Prevent crash when attempting to save a *.mrb in a readonly folder.

Fixes #3242

Revision 22393 - Directory Listing
Modified Tue Sep 3 18:29:42 2013 UTC (4 years, 1 month ago) by jcfr
Original Path: trunk/Modules
COMP: Fix "sign-compare" warning in vtkSlicerMarkupsLogic

vtkSlicerMarkupsLogic.cxx: In member function ‘void vtkSlicerMarkupsLogic::ConvertAnnotationFiducialsToMarkups()’:
vtkSlicerMarkupsLogic.cxx:882: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
vtkSlicerMarkupsLogic.cxx:954: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]

Revision 22392 - Directory Listing
Modified Tue Sep 3 18:29:40 2013 UTC (4 years, 1 month ago) by jcfr
Original Path: trunk/Modules
COMP: Fix unused variable warnings in vtkMRMLMarkupsStorageNode

Revision 22390 - Directory Listing
Modified Tue Sep 3 11:44:06 2013 UTC (4 years, 1 month ago) by fedorov
Original Path: trunk/Modules
BUG: fix the issue where warning field is editable

If non populated, warning is initialized to '', allowing to set item flags.
The solution was discussed with @pieper. Closes issue 3284.


Revision 22387 - Directory Listing
Modified Tue Sep 3 03:10:35 2013 UTC (4 years, 1 month ago) by jcfr
Original Path: trunk/Modules
COMP: Fix unused variable warning in qSlicerViewControllersModuleWidget

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

Revision 22381 - Directory Listing
Modified Mon Sep 2 17:14:16 2013 UTC (4 years, 1 month ago) by jcfr
Original Path: trunk/Modules
COMP: Remove obsolete comment in module CMakeLists.txt

Following r22038, the comment "# Do not use 'project()'" doesn't make
sense anymore.

Revision 22379 - Directory Listing
Modified Sat Aug 31 12:39:35 2013 UTC (4 years, 1 month ago) by alexy
Original Path: trunk/Modules
BUG: 3290. Fixed handling of ROIs and Annotation nodes in CLI modules. Added CLI_ROI_Test module.

Revision 22370 - Directory Listing
Modified Fri Aug 30 20:59:44 2013 UTC (4 years, 1 month ago) by jcfr
Original Path: trunk/Modules
COMP: Fix unused variable warning in vtkSlicerMarkupsLogicTest3

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

Revision 22369 - Directory Listing
Modified Fri Aug 30 18:41:01 2013 UTC (4 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: update WriteCLI to fill a vector of strings, honor mutiple = false

Because Markups define multiple markups (with potentially multiple points) in one node,
it was writting multiple instances of a string + coordinates to the string stream passed
in to WriteCLI. This causes a problem for the parsing of the arguments in CLIs such as
FiducialRegistration which needed a separate string for each point.
With this change, the markup points are writen into a vector of strings, one string
for each point in each Markup.
Added the multipleFlag to be passed to WriteCLI, and if it's false, only write the
first selected markup to the output vector. If that markup has multiple points, it will
write all of those points.
Updated the Annotation control point to use the new WriteCLI signature, but because
of the way the points are written, it will only write the first point in a multi point
annotation (such as a ruler) if multiple is false, so it ignores it and the
CLI module logic takes care of ensuring that only the first child in an
annotation hierachy is written out. Write out a warning message if this is the case.
Added a test for FiducialRegistration, updated the Markups node test 1 to test the single point flag.
Removed trailing white spaces.

Issue #1910 #3345 #3340



Revision 22364 - Directory Listing
Modified Fri Aug 30 01:23:58 2013 UTC (4 years, 1 month ago) by pieper
Original Path: trunk/Modules
STYLE: remove some trailing whitespace...

Revision 22363 - Directory Listing
Modified Fri Aug 30 01:23:56 2013 UTC (4 years, 1 month ago) by pieper
Original Path: trunk/Modules
BUG: #3323 turn of glyphs when tensor data not available

As described in but #3323, having a scalar (like FA) as the invariant
mode with the glyphs visible leads to a crash.  This appears to be
deep in the pipeline for glyphing. (TODO: fix the pipeline).
So the solution (workaround) here is to turn off any visible slice
glyphs when changing the invarient to anything other than color by
orientation and to disable the glyping panel.

Revision 22361 - Directory Listing
Modified Thu Aug 29 23:29:10 2013 UTC (4 years, 1 month ago) by jcfr
Original Path: trunk/Modules
BUG: Ensure EditColor widgets are all named

Naming widgets allows QtTesting to properly look up object and reply
actions.

See #2808

Co-authored-by: Chrystel Juan <chrystel.juan@kitware.com>

Revision 22360 - Directory Listing
Modified Thu Aug 29 22:22:55 2013 UTC (4 years, 1 month ago) by jcfr
Original Path: trunk/Modules
ENH: Ensure editor objects and widgets are all named

Doing so will make the debugging of QtTesting macro easier and less
confusing.

See #2808

Co-authored-by: Chrystel Juan <chrystel.juan@kitware.com>

Revision 22358 - Directory Listing
Modified Thu Aug 29 21:45:24 2013 UTC (4 years, 1 month ago) by naucoin
Original Path: trunk/Modules
STYLE: reduce levels of parameters

Rewrite the Markups documentation file to reduce the level
of nesting in the parameters. The wiki templates only show
3 levels, so go to a flatter description so all parameters
can be displayed on the wiki.



Revision 22357 - Directory Listing
Modified Thu Aug 29 16:37:40 2013 UTC (4 years, 1 month ago) by naucoin
Original Path: trunk/Modules
COMP: renable vtkMarkupsAnnotationSceneTest

Update from old theory of converting annotation fiducials
on scene read to a call on the Markups logic class. 



Revision 22354 - Directory Listing
Modified Wed Aug 28 22:20:46 2013 UTC (4 years, 1 month ago) by jcfr
Original Path: trunk/Modules
COMP: Simplify how Markups test inputs are specified

Revision 22353 - Directory Listing
Modified Wed Aug 28 21:57:40 2013 UTC (4 years, 1 month ago) by jcfr
Original Path: trunk/Modules
COMP: Simplify Markups module generic tests configuration

Simply passing option "WITH_GENERIC_TESTS" to the macro
"slicerMacroBuildLoadableModule" is enough.

Revision 22352 - Directory Listing
Modified Wed Aug 28 21:57:37 2013 UTC (4 years, 1 month ago) by jcfr
Original Path: trunk/Modules
STYLE: Consistently use MODULE_NAME var in Markups CMakeLists.txt

Revision 22351 - Directory Listing
Modified Wed Aug 28 21:11:19 2013 UTC (4 years, 1 month ago) by jcfr
Original Path: trunk/Modules
COMP: Disable configure time message mentioning some CLIs have NO tests

These messages (introduced by r20160 more than a year ago) didn't have
the intended effect. Despite the fact developer were systematically
looking at these warning message, they became "noise" and have been ignored.

This commit disables the warning message and reference a mantis issue
tracking the fact there is no test.

See #1619, #3333, #3334, #3335, #3336, #3337, #3338, #3339, #3340, #3341

Revision 22350 - Directory Listing
Modified Wed Aug 28 20:52:09 2013 UTC (4 years, 1 month ago) by demian
Original Path: trunk/Modules
BUG: Fixed bug #3272  http://www.na-mic.org/Bug/view.php?id=3272

Revision 22342 - Directory Listing
Modified Tue Aug 27 19:24:23 2013 UTC (4 years, 1 month ago) by jcfr
Original Path: trunk/Modules
COMP: Add macro "slicerMacroBuildLoadableModule"

Both macros "slicerMacroBuildQtModule" and "slicerMacroBuildLoadableModule"
can be used. At this point, no warning message is displayed if the
deprecated macro is used.

Fixes #2648

Revision 22340 - Directory Listing
Modified Tue Aug 27 18:51:25 2013 UTC (4 years, 1 month ago) by naucoin
Original Path: trunk/Modules
STYLE: remove debugging print out, fix doc category

Remove a qDebug call that is just informational about
the system settings for the markups.
Change the documentation category to Informatics.

Issue #2740



Revision 22339 - Directory Listing
Modified Tue Aug 27 18:43:26 2013 UTC (4 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: stop the dropping of fiducials dragged outside of 2d viewport

Check if the viewport coordinates have been restricted as well as if the display
coordinates were changed, as the second check wasn't fine grained enough
to detect when a restriction was made on a slow/small drag outside
of the viewport. This would lead to the fiducial being dropped
when it was outside the viewport.
Now the fiducial is stopped at the edge of the 2d viewport. When the
mouse comes back toward the view port, there is an offset between the
mouse position and the moving fiducial, but barring more user feedback,
we decided to leave this as is.

Issue #3318


Revision 22334 - Directory Listing
Modified Tue Aug 27 00:09:40 2013 UTC (4 years, 1 month ago) by pieper
Original Path: trunk/Modules
BUG: #3315 allow editor extensions to define custom cursor

The mechanism for editor extensions to declare their cursor had
already existed, but it was being ignored.

Revision 22333 - Directory Listing
Modified Mon Aug 26 23:46:19 2013 UTC (4 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: remove fiducial settings from the tutorial self test GUI

Remove left over code from copying the add many fiducials self test.
Replaced them with screen shot parameters to help with making the tutorial,
a check box to turn them on (off by default) and a slider to set the scale
(1 by default).
Tweaked the test: make sure that the fiducial list is named the same
as when a user would create one. Make the slices visible in 3D.

Issue #3328



Revision 22332 - Directory Listing
Modified Mon Aug 26 23:38:20 2013 UTC (4 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: confirm delete of markups

Add a message box to tell the user how many markups they
are about to delete and let them cancel. Option to
not show the message again.

COMP: cleaned up unused variable warnings

Fixes issue #3324



Revision 22330 - Directory Listing
Modified Mon Aug 26 16:18:24 2013 UTC (4 years, 1 month ago) by pieper
Original Path: trunk/Modules
ENH: #3284 don't let user edit some dicom fields

As of r22329 the name of the volume can be set via the table widget,
but editing the other fields makes no sense, so we disable it.

Revision 22329 - Directory Listing
Modified Mon Aug 26 16:05:37 2013 UTC (4 years, 1 month ago) by pieper
Original Path: trunk/Modules
ENH: Editing laodable names in DICOM widget can now lead to renaming of
the loaded loadables.

Closes #3284

From: Alireza Mehrtash <mehrtash@bwh.harvard.edu>

Revision 22324 - Directory Listing
Modified Fri Aug 23 14:52:46 2013 UTC (4 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: fix memory leak of vtkCollection

Clear and delete the node collection to remove a memory leak
from the snapshot dialog.

Fixes Issue #3314



Revision 22323 - Directory Listing
Modified Fri Aug 23 01:31:27 2013 UTC (4 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: Update Endoscopy module to support Markups

Added a backward compatibility call of GetNumberOfFiducials to the
Markups fiducial node.

See issue #2606

Revision 22322 - Directory Listing
Modified Fri Aug 23 01:31:24 2013 UTC (4 years, 1 month ago) by naucoin
Original Path: trunk/Modules
ENH: Update TractographyInteractiveSeeding module to support Markups

Allow usage of Markups fiducials or Annotations fiducials.

See issue #2606

Revision 22320 - Directory Listing
Modified Fri Aug 23 01:31:16 2013 UTC (4 years, 1 month ago) by naucoin
Original Path: trunk/Modules
ENH: Deprecating annotation fiducials

Edit properties in the Data module will go to the Markups module for
both Markups and Annotations fiducials, so that annotation fids
can be converted.

Unregister the Annotations fiducials IO, Markups can read .acsv files.
Add a label in the Annotations GUI that fiducials can be found in the Markups module.

See issue #2606

Revision 22317 - Directory Listing
Modified Fri Aug 23 01:24:56 2013 UTC (4 years, 1 month ago) by naucoin
Original Path: trunk/Modules
ENH: Add Markups module providing easy fiducials management.

Based on the Annotations module from Slicer 4.2 and the Fiducials
module from Slicer 3.6, add a new Markups module to provide
some missing functionality into Slicer4:
- one file per fiducial list
- added a unique id and orientation for each fiducial
- save/restore default display settings
- create list with current list display settings
- press p to add a fiducial
- possible to "jump" to a slice using either mouse click or right click menu
- move fids between lists
- split displayable managers into 2d and 3d versions
- pattern for names of new fiducials
- projection on 2d viewers
- add a right click menu option to delete highlighted markups
- support markups selection by mouse and keyboard arrow key
- %N can be used in the markups name format string
- possible to toggle visible/locked/selected state for a list of markups
- uniform scale for both markup text and glyph

Also added a compare view self test.

See issue #2606

Revision 22314 - Directory Listing
Modified Fri Aug 23 00:32:48 2013 UTC (4 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: Fix pan bug in annotation displayable manager

Comparison for valid viewpoint coordinates wasn't properly
checking the first coordinate.

Revision 22313 - Directory Listing
Modified Fri Aug 23 00:32:44 2013 UTC (4 years, 1 month ago) by naucoin
Original Path: trunk/Modules
ENH: Move the color conversion utility methods

Move the C++ color / Qt color conversion methods out of
Annotations and into qMRMLUtils.

Revision 22311 - Directory Listing
Modified Fri Aug 23 00:32:36 2013 UTC (4 years, 1 month ago) by naucoin
Original Path: trunk/Modules
ENH: Add support for the LPS coordinate system for CLIs

Add a coordinate system flag check, default to ras but support LPS.

Update the displayable nodes that use the WriteCLI method to
use the coordinate system flag.

TODO: IJK coordinate system - See issue #2979

Revision 22310 - Directory Listing
Modified Fri Aug 23 00:27:48 2013 UTC (4 years, 1 month ago) by naucoin
Original Path: trunk/Modules
ENH: Re-factor selection node

Use the class name so modules can register a node to place
via mouse more generally.

Use the new functionality in the mouse mode tool bar,
annotations, testing.

Revision 22309 - Directory Listing
Modified Thu Aug 22 23:16:43 2013 UTC (4 years, 1 month ago) by fedorov
Original Path: trunk/Modules
BUG: fix the crash on scene close, see issue #3313

Parameter node was referenced from a node selector event handler in the process
of scene close. Since parameter node was deleted before the the node selectors
were updated, this led to invalid reference.

The fix eliminates references to parameter node from node selector event handlers,
and does this only when user initiates the processing.



Revision 22306 - Directory Listing
Modified Thu Aug 22 00:34:39 2013 UTC (4 years, 1 month ago) by pieper
Original Path: trunk/Modules
ENH: #3309 add SurfaceToolbox module from Luca Antiga

Revision 22303 - Directory Listing
Modified Tue Aug 20 18:53:42 2013 UTC (4 years, 2 months ago) by jcfr
Original Path: trunk/Modules
BUG: Revert r22301 - Change ctkDirectoryButton into ctkPathLineEdit

This commit has been integrated by error

Revision 22301 - Directory Listing
Modified Tue Aug 20 18:50:03 2013 UTC (4 years, 2 months ago) by jcfr
Original Path: trunk/Modules
BUG: Change ctkDirectoryButton into ctkPathLineEdit

*DO NOT INTEGRATE*

Know issue: When updating the Cache directory in setting panel, each
key stroke leads to the creation of path.

Fixes #1672

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

Revision 22299 - Directory Listing
Modified Mon Aug 19 21:43:51 2013 UTC (4 years, 2 months ago) by pieper
Original Path: trunk/Modules
BUG: #2737, #2929 improve RemoveIslands tool

This adds a new "Morphological" island removal algorithm that has
been tested as useful on the brain mask that is output from the
diffusion tensor estimation module.  It may be useful for other
applications as well.

Revision 22297 - Directory Listing
Modified Mon Aug 19 19:53:38 2013 UTC (4 years, 2 months ago) by jcfr
Original Path: trunk/Modules
BUG: Fix "volume not marked as modified on save after harden transform".

Also, fix "annotations not marked as modified on save after they are changed" and "volume not marked as modified on save after volume origin or spacing is changed". Anytime a vtkMRMLStorableNode property that is saved in file is modified, the StorableModifiedTime time stamp must be modified.
Fixes #2980
Fixes #3246
Fixes #3260

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

Revision 22287 - Directory Listing
Modified Thu Aug 15 14:30:52 2013 UTC (4 years, 2 months ago) by pieper
Original Path: trunk/Modules
STYLE: fix compile warnings, unused variables, (un)signed, trailing spaces

Revision 22286 - Directory Listing
Modified Tue Aug 13 19:40:24 2013 UTC (4 years, 2 months ago) by alexy
Original Path: trunk/Modules
ENH: 3228. Added preset parameters to TractographyInteractiveSeeding module for compatibility with Slicer3 Fiducial Seeding and Slicer3 Labelmap Seeding. 

Revision 22284 - Directory Listing
Modified Tue Aug 13 16:05:47 2013 UTC (4 years, 2 months ago) by lassoan
Original Path: trunk/Modules
BUG: Fixed excessive memory consumption in the undo/redo buffer of the Editor module (http://www.na-mic.org/Bug/view.php?id=3283)

Revision 22280 - Directory Listing
Modified Fri Aug 9 19:50:49 2013 UTC (4 years, 2 months ago) by finetjul
Original Path: trunk/Modules
ENH: Apply units to Ruler node measurement labels

Issue #1694

Revision 22278 - Directory Listing
Modified Fri Aug 9 19:50:43 2013 UTC (4 years, 2 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add coefficient and offset support in unit's settings and widgets.

Issue #1694

Revision 22277 - Directory Listing
Modified Fri Aug 9 19:43:34 2013 UTC (4 years, 2 months ago) by alexy
Original Path: trunk/Modules
BUG: 1636. Log an Error on ROI rotation attempt (since current ROI implementation do not support local CS rotation). Propagate transform change events on ROI transform hardening.

Revision 22275 - Directory Listing
Modified Fri Aug 9 17:55:35 2013 UTC (4 years, 2 months ago) by fedorov
Original Path: trunk/Modules
BUG: modify the process of populating loadables table in DICOM widget to ensure that each loadable is added only once by selecting relevant loadables before adding them to the table; resolves issue #3282


Revision 22269 - Directory Listing
Modified Thu Aug 8 05:22:12 2013 UTC (4 years, 2 months ago) by finetjul
Original Path: trunk/Modules
ENH: Improve Dark style

Issue #3251

Revision 22268 - Directory Listing
Modified Wed Aug 7 21:00:18 2013 UTC (4 years, 2 months ago) by pieper
Original Path: trunk/Modules
BUG: fix size of paint cursor on rotated acquisitions

Make sure to use a column of the rasToXY matrix that is in the plane
of the zoom.  This is needed because the slice node's field of view
in Z does not reflect the in-plane zoom.

Revision 22261 - Directory Listing
Modified Tue Aug 6 16:39:56 2013 UTC (4 years, 2 months ago) by jcfr
Original Path: trunk/Modules
BUG: Name SampleData internal widget for easy referencing by QtTesting

See #2808

Revision 22258 - Directory Listing
Modified Mon Aug 5 17:18:09 2013 UTC (4 years, 2 months ago) by finetjul
Original Path: trunk/Modules
BUG: vtkGPURayCastVolumeMapper does not support image sample distance < 1.

Issue #1752

Revision 22253 - Directory Listing
Modified Thu Aug 1 20:09:31 2013 UTC (4 years, 2 months ago) by pieper
Original Path: trunk/Modules
BUG: #3262 update data probe on non-mouse-move events

Allow key strokes and other events that change the slice display
to trigger updates to the DataProbe window.  Only update the display
for the sliceView that matches the one most recently entered by
the mouse pointer.

Revision 22249 - Directory Listing
Modified Tue Jul 30 19:47:09 2013 UTC (4 years, 2 months ago) by alexy
Original Path: trunk/Modules
BUG: 3258. Fixed the case when the fiber is outside the label map volume extent and it caused the crash in FiberBundleSelect module. It will output a warning in this case now.

Revision 22245 - Directory Listing
Modified Mon Jul 29 18:10:46 2013 UTC (4 years, 2 months ago) by pieper
Original Path: trunk/Modules
BUG: avoid duplicated saveState when using applyScopedLabel in editor

Since the Chagne and Save island effects use the superclass's
applyScopedLabel method they don't need to explicitly save state
(it is done automatically).

Revision 22244 - Directory Listing
Modified Mon Jul 29 17:14:27 2013 UTC (4 years, 2 months ago) by pieper
Original Path: trunk/Modules
BUG: #3257 update color selection when color node changes in Editor

Be sure to use the up-to-date color node to display the names
and colors for the label layer.

Revision 22243 - Directory Listing
Modified Sat Jul 27 21:52:20 2013 UTC (4 years, 2 months ago) by alexy
Original Path: trunk/Modules
ENH: 3191. Added ability to select multiple ROI labels in the interactive seeding module

Revision 22233 - Directory Listing
Modified Tue Jul 23 18:07:29 2013 UTC (4 years, 2 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add support for MaximumQuality voluming rendering

High quality for CPU and GPU volume rendering mappers. Texture mapper
does not have quality control.
Issue #1752

Revision 22232 - Directory Listing
Modified Tue Jul 23 14:22:04 2013 UTC (4 years, 2 months ago) by alexy
Original Path: trunk/Modules
BUG: 3235. Fixed return statements.

Revision 22230 - Directory Listing
Modified Mon Jul 22 20:53:54 2013 UTC (4 years, 2 months ago) by jcfr
Original Path: trunk/Modules
ENH: Remove Qt Dependency from vtkMRMLAnnotationLogic

Following r22229, TemporaryPath can be accessible from MRML logics, the
Qt dependency code can now be removed from vtkMRMLAnnotationsLogic.

Fixes #1937

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

Revision 22229 - Directory Listing
Modified Mon Jul 22 20:39:04 2013 UTC (4 years, 2 months ago) by jcfr
Original Path: trunk/Modules
ENH: Allow temporary directory to be accessible in MRML logics.

TemporaryPath is added to vtkMRMLApplicationLogic, so that the temporary directory can be directly accessible from MRML logics.

Also add associated tests

Fixes #2416

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

Revision 22225 - Directory Listing
Modified Mon Jul 22 14:39:34 2013 UTC (4 years, 2 months ago) by pieper
Original Path: trunk/Modules
BUG: fix backward compatibility of sample data logic methods

Since the new generic API returns lists of loaded nodes, the
backward compatibility methods need to return the first element
rather than the list.

py_ThresholdThreadingTest
py_StandaloneEditorWidgetTest
py_sceneImport2428
py_ViewControllersSliceInterpolationBug1926

http://slicer.cdash.org/testDetails.php?test=4166721&build=129681
http://slicer.cdash.org/testDetails.php?test=4166722&build=129681
http://slicer.cdash.org/testDetails.php?test=4166791&build=129681
http://slicer.cdash.org/testDetails.php?test=4166797&build=129681

Revision 22222 - Directory Listing
Modified Mon Jul 22 01:59:16 2013 UTC (4 years, 3 months ago) by finetjul
Original Path: trunk/Modules
BUG: Fix units when reloading scenes

Restoring the selection node unit references shall not just be done when
closing scene, but also when loading or restoring a scene.
To simplify, it should be done anytime the selection node is modified.
When Clear() is called, singletons are reset, which means they loose their
node references. Which should trigger a ModifiedEvent (see next commit)
that is caught by the unit logic that can restore the unit references.

Fixes #3152

Revision 22221 - Directory Listing
Modified Sat Jul 20 15:09:18 2013 UTC (4 years, 3 months ago) by alexy
Original Path: trunk/Modules
ENH: 3235. Added And/Or logic for multiple label selection in FiberBundleLabelSelect

Revision 22218 - Directory Listing
Modified Fri Jul 19 21:54:00 2013 UTC (4 years, 3 months ago) by naucoin
Original Path: trunk/Modules
STYLE: update Model to Label Map xml file docs

More testing showed that the output volume will always be cast
to unsigned char, so limit the label value to 0-255 and
give the user some hints about good models to use.

Issue #3233



Revision 22217 - Directory Listing
Modified Fri Jul 19 20:04:05 2013 UTC (4 years, 3 months ago) by pieper
Original Path: trunk/Modules
BUG: #2326 Fix tests and ENH: refactor sample data

The bug refers to failures of the py_vtkITKArchetypeScalarReaderFile
and py_vtkITKArchetypeDiffusionTensorReaderFile tests after
commit [1].  These tests relied on a side-effect of downloading
the sample data in order to determine the file to load
data from, but this was not reliable since the data was in a temp
directory.   Now the tests request the download directly.

The enhancement is that the sample data module now supports the
concept of categories of sample data sources, such that modules
can register their sample data.  This way a version of slicer can
offer sample data appropriate for use with the particular extensions
that have been installed.

[1] http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=22162

Revision 22216 - Directory Listing
Modified Fri Jul 19 12:44:03 2013 UTC (4 years, 3 months ago) by finetjul
Original Path: trunk/Modules
ENH: Expose scrollTo() to qMRMLTreeView

So that other modules could conveniently use.

Revision 22215 - Directory Listing
Modified Fri Jul 19 05:27:46 2013 UTC (4 years, 3 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add search box in models module

Closes #1530

Revision 22211 - Directory Listing
Modified Thu Jul 18 20:46:51 2013 UTC (4 years, 3 months ago) by naucoin
Original Path: trunk/Modules
ENH: expose the label value for the model to label map CLI

Updated the documentation link and updated the wiki pages to 
include the new parameter.

Resolves issue #3233



Revision 22207 - Directory Listing
Modified Wed Jul 17 20:02:53 2013 UTC (4 years, 3 months ago) by naucoin
Original Path: trunk/Modules
STYLE: update clipping documentation

Use the text strings from the MRML clip node widget.

Issue #2560



Revision 22205 - Directory Listing
Modified Wed Jul 17 19:45:27 2013 UTC (4 years, 3 months ago) by naucoin
Original Path: trunk/Modules
ENH: add a utility method to add a new fiducial

Prevents memory leaks and error messages from adding a fiducial
and a display node. 

For access from python, use:
fidID = slicer.modules.annotations.logic().AddFiducial(10.0, -50.0, 8.8, 'P1')
fidNode = getNode(fidID)

Resolves issue #3138



Revision 22201 - Directory Listing
Modified Tue Jul 16 19:52:28 2013 UTC (4 years, 3 months ago) by jcfr
Original Path: trunk/Modules
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 22199 - Directory Listing
Modified Tue Jul 16 13:22:09 2013 UTC (4 years, 3 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Initialize logics in ObserveMRMLScene instead of SetMRMLSceneInternal

Revision 22193 - Directory Listing
Modified Mon Jul 15 15:24:47 2013 UTC (4 years, 3 months ago) by finetjul
Original Path: trunk/Modules
BUG: Fix Volumes module decimals behavior

* make sure qMRMLVolumeInfoWidget gets setMRMLScene called before
the current volume node combobox. This is important because
qMRMLSliderWidget can change the number of decimals from the units node.
Such decimal number should be overwritten by the value of the spacing (or
origin).

Revision 22192 - Directory Listing
Modified Mon Jul 15 15:24:37 2013 UTC (4 years, 3 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add vtkMRMLUnitNode::GetDisplayStringFromValue

Revision 22191 - Directory Listing
Modified Mon Jul 15 15:24:29 2013 UTC (4 years, 3 months ago) by finetjul
Original Path: trunk/Modules
BUG: Fix modules depending on units

Revision 22190 - Directory Listing
Modified Mon Jul 15 15:24:21 2013 UTC (4 years, 3 months ago) by finetjul
Original Path: trunk/Modules
ENH: Improve qMRMLUnitWidget interface

QFlags were added to this widget so one can choose what properties are
visible or not. This is what is done in the qSlicerUnitsSettingsPanel to
hide the advanced properties of the unit to the user. By default, the user
can only modify the precision property.
If he choose to show more properties, a warning stating that only display
values are changed when modifying an unit is shown along with the other
properties.

Style wise, the groupbox title now has its first letter in uppercase to
follow the GUI conventions and a horizontale line in the
qMRMLUnitNodeWidget between the precision and the rest of the properties.

See Issue #3137

From: Johan Andruejohl <johan.andruejohl@kitware.com>

Revision 22189 - Directory Listing
Modified Mon Jul 15 15:24:11 2013 UTC (4 years, 3 months ago) by finetjul
Original Path: trunk/Modules
BUG: Restore the selection node units on scene close

Re-enable Units module.
Closes #3176, #3152

Revision 22185 - Directory Listing
Modified Sat Jul 13 19:46:46 2013 UTC (4 years, 3 months ago) by jcfr
Original Path: trunk/Modules
COMP: Ensure external module can directly find Slicer

Following commit r22063, extensions bundled using Slicer_EXTENSION_SOURCE_DIRS
didn't have to use the "if(NOT Slicer_SOURCE_DIR)" safeguard.

This commit move inclusion of external modules from the CLI, Loadable
and Scripted sub-directories into a single "Modules/Remote" folder
included after Slicer_DIR so that external module can also directly call
"find_package(Slicer)"

Thanks to Brad Lowekamp for reporting the issue.

Revision 22182 - Directory Listing
Modified Sat Jul 13 07:55:59 2013 UTC (4 years, 3 months ago) by jcfr
Original Path: trunk/Modules
BUG: Turn off projections when annotations are not visible

Projections of annotations were not "hidden" with annotation.

This fix ensure the widget representing an annotation's projection
is "hidden" when an annotation visibility is turned off.

This commit is a follow-up of r22176 ensuring projections are deleted
when an annotation is deleted.

Fixes #3214

From: Laurent Chauvin <lchauvin@bwh.harvard.edu>

Revision 22180 - Directory Listing
Modified Sat Jul 13 05:36:57 2013 UTC (4 years, 3 months ago) by jcfr
Original Path: trunk/Modules
COMP: Fix unused variable warnings

Revision 22177 - Directory Listing
Modified Sat Jul 13 04:54:23 2013 UTC (4 years, 3 months ago) by jcfr
Original Path: trunk/Modules
BUG: Ensure projections do not appear as selectable

Projections are not selectable and shouldn't be, however they
were displayed as if they were selectable, so it could be confusing
for the user. This fix ensure projections are properly displayed to
not look like selectable.

Fixes #3222

From: Laurent Chauvin <lchauvin@bwh.harvard.edu>

Revision 22176 - Directory Listing
Modified Sat Jul 13 04:39:41 2013 UTC (4 years, 3 months ago) by jcfr
Original Path: trunk/Modules
BUG: Turn off projections when annotations are deleted

Projections of annotations were not deleted with annotation.
This fix ensure the widget representing an annotation's projection is
deleted when the corresponding annotation is deleted.

Partially fixes #3214

From: Laurent Chauvin <lchauvin@bwh.harvard.edu>

Revision 22168 - Directory Listing
Modified Thu Jul 11 12:17:09 2013 UTC (4 years, 3 months ago) by finetjul
Original Path: trunk/Modules
ENH: Make volume property file reading more robust

* nextHigher does no longer produce denormalized values, it's error prone
* ensure values are are unique when reading from file
Issue #3220

Revision 22167 - Directory Listing
Modified Thu Jul 11 12:17:06 2013 UTC (4 years, 3 months ago) by finetjul
Original Path: trunk/Modules
BUG: Fix VolumeProperty file reading with gcc < 4.2.2

http://gcc.gnu.org/bugzilla/show_bug.cgi?id=35397
Closes #3220

Revision 22162 - Directory Listing
Modified Tue Jul 9 23:00:39 2013 UTC (4 years, 3 months ago) by pieper
Original Path: trunk/Modules
BUG: #2326 remove storage nodes for sample data downloads

Since the download is in a temp directory, make sure the user
is prompted to save when saving the scene.

Revision 22158 - Directory Listing
Modified Tue Jul 9 12:42:05 2013 UTC (4 years, 3 months ago) by fedorov
Original Path: trunk/Modules
BUG: setting inputs to NULL when selectors not initialized; attempt to fix 3117


Revision 22155 - Directory Listing
Modified Mon Jul 8 22:41:31 2013 UTC (4 years, 3 months ago) by fedorov
Original Path: trunk/Modules
BUG: adding self-test in an attempt to reproduce the crash in issue 3117


Revision 22152 - Directory Listing
Modified Mon Jul 8 20:29:05 2013 UTC (4 years, 3 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add control over decimals in Transforms module

Closes #2480, #2579

Revision 22150 - Directory Listing
Modified Mon Jul 8 19:39:40 2013 UTC (4 years, 3 months ago) by pieper
Original Path: trunk/Modules
BUG: #2203  better instructions for Endoscopy module

The module's help and wiki page have been updated to better
describe the use of the module.

Revision 22149 - Directory Listing
Modified Mon Jul 8 19:02:38 2013 UTC (4 years, 3 months ago) by pieper
Original Path: trunk/Modules
ENH: #1419 show scene path in DataProbe

We could consider someday moving this information
to the mainWindow with the setWindowTitle method.

Revision 22148 - Directory Listing
Modified Mon Jul 8 17:02:45 2013 UTC (4 years, 3 months ago) by pieper
Original Path: trunk/Modules
BUG: #2948 save updated MRB file name for next save step

The URL instance variable of the scene is used to store
the source / destination of the scene, so it needs to be
set for use as the default for the next save operation.

Revision 22147 - Directory Listing
Modified Mon Jul 8 17:02:43 2013 UTC (4 years, 3 months ago) by pieper
Original Path: trunk/Modules
ENH: #2543 small changes to documentation for FiberBundleToLabelMap

Clean up the documentation and improve the display of the name.

Revision 22141 - Directory Listing
Modified Thu Jul 4 22:22:43 2013 UTC (4 years, 3 months ago) by pieper
Original Path: trunk/Modules
ENH: put a space between the number and suffix in sample data status

e.g. use 411.0 bytes instead of 411.0bytes.  It just looks better.

From: Steve Pieper <pieper@isomics.com>

Revision 22140 - Directory Listing
Modified Thu Jul 4 22:22:41 2013 UTC (4 years, 3 months ago) by pieper
Original Path: trunk/Modules
BUG: fixed issue in SampleData's logging.

Before, when downloaded file's size was larger than the transfer block size, the logger would report being >100% done. This has been fixed.

From: Luis G. Torres <lgtorres42@gmail.com>

Revision 22139 - Directory Listing
Modified Thu Jul 4 22:20:40 2013 UTC (4 years, 3 months ago) by finetjul
Original Path: trunk/Modules
ENH: Disable scrolling everywhere there is an active scrollarea

Don't do it only for comboboxes.
Closes #1820, #1462

Revision 22138 - Directory Listing
Modified Thu Jul 4 21:32:11 2013 UTC (4 years, 3 months ago) by pieper
Original Path: trunk/Modules
BUG: #2749 fix undo/redo for change label effect

The logic superclass handles undo/redo, but the instance of the undoRedo
needs to be explicitly set.

Revision 22135 - Directory Listing
Modified Thu Jul 4 13:22:07 2013 UTC (4 years, 3 months ago) by finetjul
Original Path: trunk/Modules
ENH: Don't scroll comboboxes that are inside a scroll area

Using the mouse in a scroll area could inadvertently change combobox
current index (on mouse over).
For conveniency, all the qMRMLNodeComboBoxes won't scroll in scrollarea by
default.
Closes #1820, #1462

Revision 22132 - Directory Listing
Modified Wed Jul 3 21:43:46 2013 UTC (4 years, 3 months ago) by jcfr
Original Path: trunk/Modules
STYLE: ITK_EXPORT had no use

The defintion of ITK_EXPORT was empty in all cases

This has been identified since 2003 as not being necessary
for builds. see https://issues.itk.org/jira/browse/ITK-3110

On Windows builds that need exports, they must
be unique per library, and that is not controlled by CMake now.

The PrintSelfCheck.tcl was the only remenant need for
This patch, and that is no longer being used, so that
file as been removed.

The ITK_EXPORT define was set to nothing and had no
known remaining purpose.  It was removed to make the
over all code easier to understand.  There was,
understandably, a bit of confusion about the
need for this being pervasive in the code.

It is currently backwards compatible to have
this in code, but at some future point it will
be removed.

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

Revision 22131 - Directory Listing
Modified Wed Jul 3 01:14:26 2013 UTC (4 years, 3 months ago) by alexy
Original Path: trunk/Modules
BUG: 3203. Fixed no pass label specified case. XML change is a workaround the bug 3202.

Revision 22128 - Directory Listing
Modified Fri Jun 28 22:49:43 2013 UTC (4 years, 3 months ago) by finetjul
Original Path: trunk/Modules
COMP: Propagate CTK renaming: ctkSpinBox to ctkDoubleSpinBox

Revision 22124 - Directory Listing
Modified Thu Jun 27 17:14:40 2013 UTC (4 years, 3 months ago) by pieper
Original Path: trunk/Modules
BUG: cast output to int16_t after watershed

Previously the output was being casted to uint16. Some editor effects,
such as the SaveIslandEffect don't behave correctly with this
unexpected image type. The output of the watershed effect is now
converted to int16 if needed.

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

Revision 22123 - Directory Listing
Modified Thu Jun 27 17:14:38 2013 UTC (4 years, 3 months ago) by pieper
Original Path: trunk/Modules
PERF: try to import SimpleITK at file scope

Repeatedly importing a library at function scope is less efficient
then  at the module level.

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

Revision 22121 - Directory Listing
Modified Sun Jun 23 23:05:34 2013 UTC (4 years, 3 months ago) by fedorov
Original Path: trunk/Modules
BUG: refer to mandatory parameters by index, no with flags (fixes 3184)


Revision 22120 - Directory Listing
Modified Fri Jun 21 21:40:55 2013 UTC (4 years, 3 months ago) by pieper
Original Path: trunk/Modules
BUG: gracefully handle case where SimpleITK is not available

On continuous builds and local developer builds SimpleITK is not
enabled by default, so we need to test for it and avoid raising
an error that prevents the module from loading.

Revision 22119 - Directory Listing
Modified Fri Jun 21 18:45:05 2013 UTC (4 years, 4 months ago) by pieper
Original Path: trunk/Modules
ENH: Adding new editor effect to perform WatershedFromMarker

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

Revision 22112 - Directory Listing
Modified Wed Jun 19 20:27:48 2013 UTC (4 years, 4 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add vtkSlicerVolumesLogic::CenterVolume()

Note that the code is from qMRMLVolumeInfoWidget

Revision 22111 - Directory Listing
Modified Wed Jun 19 20:27:40 2013 UTC (4 years, 4 months ago) by finetjul
Original Path: trunk/Modules
BUG: Zombie display node when turning a volume into labelmap

When the current display node was removed, the slicer layer logic was
creating a new node and adding it into the scene.
Such node was not being removed of the scene when the new display node
was set.

Revision 22103 - Directory Listing
Modified Tue Jun 18 13:02:59 2013 UTC (4 years, 4 months ago) by aylward
Original Path: trunk/Modules
COMP: Removed warning of no tests, because there are in expertregistration...


Revision 22102 - Directory Listing
Modified Tue Jun 18 12:52:06 2013 UTC (4 years, 4 months ago) by aylward
Original Path: trunk/Modules
COMP: Removed warning of unused parameter via itkNotUsed macro


Revision 22094 - Directory Listing
Modified Mon Jun 10 15:36:22 2013 UTC (4 years, 4 months ago) by jcfr
Original Path: trunk/Modules
STYLE: RobustStatisticsSegmenter - Better default parameters

See #3149 - http://na-mic.org/Mantis/view.php?id=3149

From: Yi Gao <yi.gao@gatech.edu>

Revision 22091 - Directory Listing
Modified Fri Jun 7 21:53:45 2013 UTC (4 years, 4 months ago) by pieper
Original Path: trunk/Modules
BUG: fix fiducials display to preserve screenspace size

This change compensates for the size of the slice view
when displaying fiducial glyphs and text.  Without this change,
switching to a layout showing only a single slice would lead
to humerously large fiducials being displayed.  The base size can
still be controlled via the display nodes.

Revision 22090 - Directory Listing
Modified Fri Jun 7 18:18:32 2013 UTC (4 years, 4 months ago) by alexy
Original Path: trunk/Modules
BUG: fixed module labels

Revision 22087 - Directory Listing
Modified Fri Jun 7 14:56:35 2013 UTC (4 years, 4 months ago) by pieper
Original Path: trunk/Modules
ENH: #3081 support drag-and-drop of dicom directories

Use Julien's nice scripted file dialog code to support adding
directories to the dicom database.

Revision 22086 - Directory Listing
Modified Thu Jun 6 20:59:58 2013 UTC (4 years, 4 months ago) by pieper
Original Path: trunk/Modules
BUG: RSS label image type bug fixed

previously char pixel type is used for input/output label images.
but that is not enough for larger label values. this causes crash.
I changed it to short type to hold more label values.
Tested on previous fail cases and works now. Linux 64

From: Yi Gao <yi.gao@gatech.edu>

Revision 22081 - Directory Listing
Modified Wed Jun 5 21:14:16 2013 UTC (4 years, 4 months ago) by pieper
Original Path: trunk/Modules
BUG: check in a new baseline for Multiresolution Affine cli test

This result is based on the module running with ITKv4 and shows
a slight shift compared to the old baseline, which is probably
due to improved subpixel indexing in the newer version of ITK.

Revision 22079 - Directory Listing
Modified Wed Jun 5 20:26:52 2013 UTC (4 years, 4 months ago) by pieper
Original Path: trunk/Modules
ENH: add example of manipulating contents of web view

In this example the qt qpi is used to manipulate the DOM of a loaded
web page.  In this case, we add a search string into a form, but the
concept could be generalized to allow exchange of data between slicer
and any web-based system that doesn't expose a clean web services api.

Revision 22076 - Directory Listing
Modified Tue Jun 4 19:56:28 2013 UTC (4 years, 4 months ago) by alexy
Original Path: trunk/Modules
BUG: Fixed crash on missed fiber selection

Revision 22070 - Directory Listing
Modified Fri May 31 16:46:45 2013 UTC (4 years, 4 months ago) by alexy
Original Path: trunk/Modules
ENH: moved Enable Tracks button to the top

Revision 22069 - Directory Listing
Modified Fri May 31 16:26:47 2013 UTC (4 years, 4 months ago) by alexy
Original Path: trunk/Modules
ENH: put more checks into fiber editing

Revision 22068 - Directory Listing
Modified Fri May 31 12:15:30 2013 UTC (4 years, 4 months ago) by alexy
Original Path: trunk/Modules
BUG: fixed fiber editing for multiple bundles

Revision 22062 - Directory Listing
Modified Wed May 29 21:44:45 2013 UTC (4 years, 4 months ago) by johan.andruejol
Original Path: trunk/Modules
BUG: Fix annotation logic build error

Two things here:
1 - Unused variable warning:
  Slicer4/Modules/Loadable/Annotations/Logic/vtkSlicerAnnotationModuleLogic.cxx:1998: warning: unused variable 'lengthUnit' [-Wunused-variable]

This is fixed by deleting the unused pointer

2 - ostringstream error:
  /Slicer4/Modules/Loadable/Annotations/Logic/vtkSlicerAnnotationModuleLogic.cxx:2018: error: no matching function for call to 'std::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::basic_ostringstream(double)'
  /Developer/SDKs/MacOSX10.6.sdk/usr/include/c++/4.2.1/sstream:433: note: candidates are: std::basic_ostringstream<_CharT, _Traits, _Alloc>::basic_ostringstream(const std::basic_string<_CharT, _Traits, _Alloc>&, std::_Ios_Openmode) [with _CharT = char, _Traits = std::char_traits<char>, _Alloc = std::allocator<char>]
  /Developer/SDKs/MacOSX10.6.sdk/usr/include/c++/4.2.1/sstream:412: note:                 std::basic_ostringstream<_CharT, _Traits, _Alloc>::basic_ostringstream(std::_Ios_Openmode) [with _CharT = char, _Traits = std::char_traits<char>, _Alloc = std::allocator<char>]
  /Developer/SDKs/MacOSX10.6.sdk/usr/include/c++/4.2.1/iosfwd:79: note:                 std::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::basic_ostringstream(const std::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >&)
  /Slicer4/Modules/Loadable/Annotations/Logic/vtkSlicerAnnotationModuleLogic.cxx:2107: error: no matching function for call to 'vtkMRMLUnitNode::WrapValueWithPrefixAndSuffix(std::string)'
  /Slicer4/Libs/MRML/Core/vtkMRMLUnitNode.h:73: note: candidates are: std::string vtkMRMLUnitNode::WrapValueWithPrefixAndSuffix(std::string&)
  /Slicer4/Modules/Loadable/Annotations/Logic/vtkSlicerAnnotationModuleLogic.cxx:2128: error: no matching function for call to 'vtkMRMLUnitNode::WrapValueWithPrefixAndSuffix(std::string)'
  /Slicer4/Libs/MRML/Core/vtkMRMLUnitNode.h:73: note: candidates are: std::string vtkMRMLUnitNode::WrapValueWithPrefixAndSuffix(std::string&)

This is fized by using the ostringstream more properly.

See Issue #1694

Revision 22061 - Directory Listing
Modified Wed May 29 21:44:39 2013 UTC (4 years, 4 months ago) by johan.andruejol
Original Path: trunk/Modules
BUG: vtkMRMLUnitNodeTest1 use size_t instead of int

This fixes the warnings for linux brought by r22053

  /Slicer-TR/Libs/MRML/Core/Testing/vtkMRMLUnitNodeTest1.cxx: In function ‘bool TestScenesUnitNodeID(vtkMRMLScene*)’:
  /Slicer-TR/Libs/MRML/Core/Testing/vtkMRMLUnitNodeTest1.cxx:86: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  /Slicer-TR/Libs/MRML/Core/Testing/vtkMRMLUnitNodeTest1.cxx:92: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  /Slicer-TR/Libs/MRML/Core/Testing/vtkMRMLUnitNodeTest1.cxx: In function ‘bool TestUnitNodeAttribute(vtkMRMLScene*)’:
  /Slicer-TR/Libs/MRML/Core/Testing/vtkMRMLUnitNodeTest1.cxx:121: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]

And the same kind of warning in the logic test.

See Issue #1694

Revision 22057 - Directory Listing
Modified Wed May 29 17:38:01 2013 UTC (4 years, 4 months ago) by johan.andruejol
Original Path: trunk/Modules
BUG: Rename forgotten currentNodeId to currentNodeID

Following Revision 22052, the signal was renamed currentNodeID. Fixing
forgotten python script.

See Issue #1694

Revision 22056 - Directory Listing
Modified Wed May 29 16:53:59 2013 UTC (4 years, 4 months ago) by johan.andruejol
Original Path: trunk/Modules
ENH: Only one unit per quantity accessible to the user

Now only one unit per quantity is accessible to the user. This unit can
be customized and it's logged in the settings so it can be restored
when opening the application.
On the implementation side of things:
- Add access method to all the referenced unit nodes in the selection node
- Remove the unit widget
- Hide module
- Create the unit widget to easily customize units (add the plugins with
it)
- Create the unit settings widget using the unit widget. This widget
is tailored to be used in the setting panel (no plugin)
- Refactorize the setting panel to use the setting unit widget and
log the unit node properties
- Create only node for each quantity exposed to the user. The preset nodes
are kept in a special scene in the logic.

See Issue #1694

Revision 22055 - Directory Listing
Modified Wed May 29 16:53:44 2013 UTC (4 years, 4 months ago) by johan.andruejol
Original Path: trunk/Modules
ENH: Apply units widget to slicer

Modified:
- Volume info widget: Made it a qMRMLWidget so it can propagate the
mrml scene.
- Annotations: Add to vtk widget and GUI
- Tractography Interactive seeding: Add units to GUI
- Slice controller: add units in spinboxes
- Volumes: add units to GUI
- Editor: add units to paint and island effects

See Issue #1694

Revision 22053 - Directory Listing
Modified Wed May 29 16:53:18 2013 UTC (4 years, 4 months ago) by johan.andruejol
Original Path: trunk/Modules
ENH: Add Units module

The unit module handle the unit in slicer. The units are singleton in the
scene that belong to a quantity. So far the only quantity available are
length and time. The units are settings saved with the application.

See Issue #1694

Revision 22052 - Directory Listing
Modified Wed May 29 16:53:05 2013 UTC (4 years, 4 months ago) by johan.andruejol
Original Path: trunk/Modules
ENH: Harmonize qMRMLNodeComboBox properties

Previously, the property currentNodeId of the node combobox was set with an
id (QString) and sent a signal with a node (vtkMRMLNode*) which can be
confusing in the widgets using it. Now, the node combobox as an id
property or a node property.

See Issue #1694

Revision 22042 - Directory Listing
Modified Mon May 27 19:31:57 2013 UTC (4 years, 4 months ago) by alexy
Original Path: trunk/Modules
ENH: moved label to tool tip

Revision 22040 - Directory Listing
Modified Sat May 25 16:52:54 2013 UTC (4 years, 4 months ago) by alexy
Original Path: trunk/Modules
BUG: 3054. Added dimensions check in ImageLabelCombine module

Revision 22039 - Directory Listing
Modified Sat May 25 12:15:15 2013 UTC (4 years, 4 months ago) by alexy
Original Path: trunk/Modules
ENH: Added help text for the edit fibers checkbox

Revision 22037 - Directory Listing
Modified Fri May 24 20:37:58 2013 UTC (4 years, 4 months ago) by jcfr
Original Path: trunk/Modules
COMP: ExtractSkeleton - Fix clang -Wparentheses-equality warning

Detailed output from Clang:

 warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
        if( (result[i] == OBJ) )
             ~~~~~~~~~~^~~~~~
 note: remove extraneous parentheses around the comparison to silence this warning

Revision 22035 - Directory Listing
Modified Fri May 24 15:32:03 2013 UTC (4 years, 4 months ago) by alexy
Original Path: trunk/Modules
ENH: Added selection, de-selection, deleting-of-selected fibers.

Revision 22027 - Directory Listing
Modified Mon May 20 22:53:42 2013 UTC (4 years, 5 months ago) by jcfr
Original Path: trunk/Modules
STYLE: Reference private member using "this->"

Revision 22024 - Directory Listing
Modified Sat May 18 12:15:34 2013 UTC (4 years, 5 months ago) by pieper
Original Path: trunk/Modules
BUG: Remove check of spacing in LabelStatistics

Because small differences in spacing can be introduced by rounding
or the way floating point numbers are handled, the check of exact
equality caused false negatives.  Removing this check will allow
valid use cases to succeed, while the other checks still prevent
incorrect calculations (where the grids to not actually align in
pixel space).

Revision 22011 - Directory Listing
Modified Fri May 17 13:34:19 2013 UTC (4 years, 5 months ago) by pieper
Original Path: trunk/Modules
ENH: add an attribute indicating the layout name of the view of anno manip

When a widget is actively moving a fiducial, the viewer should not
be modified by external commands, such as chaning the slice node
since that will reset the widget.  To avoid this, the added attribute
allows other code to know which view is the one in which the widget
is active, and can thereby keep it out of any other updates.

(See Landmark registration project for an example
gitub.com/pieper/LandmarkRegistration)

Revision 22010 - Directory Listing
Modified Fri May 17 12:46:50 2013 UTC (4 years, 5 months ago) by alexy
Original Path: trunk/Modules
ENH: added mode for enabling/disabling Fiber editing in TractographyDisplay module and vtkMRMLTractographyDisplayDisplayableManager

Revision 22006 - Directory Listing
Modified Thu May 16 19:02:54 2013 UTC (4 years, 5 months ago) by alexy
Original Path: trunk/Modules
BUG: 2528. Fixed the cause of the crash because of invalid LUT in vtkMRMLDiffusionTensorDisplayPropertiesNode

Revision 22005 - Directory Listing
Modified Thu May 16 18:37:18 2013 UTC (4 years, 5 months ago) by naucoin
Original Path: trunk/Modules
BUG: Calculate ruler distance so it's up to date

When adding a ruler node programatically to the scene, with initialised
end point coordinates, the distance wasn't getting updated. Removed the 
local variable that saved the distance and changed GetDistanceMeasurement
to calculate it when called. Still writes out the distance to MRML
but does not read it back in as it will be re-calculated.

Issue #3123



Revision 22000 - Directory Listing
Modified Wed May 15 22:25:07 2013 UTC (4 years, 5 months ago) by jcfr
Original Path: trunk/Modules
BUG: Fix OtsuThresholdImageFilterTest

Based on discussion during May 14 Slicer developer hangout, the test
failure was due to the transition to ITKv4.

The update of the baseline has been done with the following command:

cp /home/jchris/Projects/Slicer-TR-Superbuild-Release/Slicer-build/Testing/Temporary/OtsuThresholdImageFilterTest.raw.gz /home/jchris/Projects/Slicer-TR/Modules/CLI/OtsuThresholdImageFilter/Data/Baseline/

Revision 21999 - Directory Listing
Modified Wed May 15 19:29:15 2013 UTC (4 years, 5 months ago) by naucoin
Original Path: trunk/Modules
BUG: set LUT range widget to trigger setting range on LUT

Updating the GUI element will trigger a signal to update the look up table
on the color node.
Renamed a method from setNumberOfColors to updateNumberOfColors as it wasn't
taking an argument.
TODO: set up an observation on the look up table on the color node

Issue #3115



Revision 21993 - Directory Listing
Modified Tue May 14 21:36:03 2013 UTC (4 years, 5 months ago) by naucoin
Original Path: trunk/Modules
BUG: Set the color range when changing number of colors

When copying a color table node and reducing the number
of colors in it, the color table range wasn't updated.
This led to problems in the Editor module when the selected
drawing integer wasn't matched up to the expected color.
Now when the number of colors is set on a user editable
color node, the range is set on the color look up table
and on the GUI slider at the same time.
Also updated the number of colors spin box to only trigger
a reset of the number of colors on the node on the editingFinished signal
as othewise cutting down a table from 300 to 50 colors could
empty out the table and refill it with black rather than 
creating a subset of the original table.

Issue #3115



Revision 21987 - Directory Listing
Modified Tue May 14 17:03:28 2013 UTC (4 years, 5 months ago) by jcfr
Original Path: trunk/Modules
COMP: Prevent windows build error shortening DisplayableManager directory

"MRMLDisplayableManager" sub directory associated with module has been
changed into "MRMLDM" to prevent issue related to path length limitation.

See http://slicer-devel.65872.n3.nabble.com/No-Windows-nightly-package-since-May-2-tp4028642p4028646.html

Revision 21986 - Directory Listing
Modified Tue May 14 15:18:05 2013 UTC (4 years, 5 months ago) by alexy
Original Path: trunk/Modules
ENH: added ability to interactively remove fiber lines.

Revision 21978 - Directory Listing
Modified Thu May 9 20:15:14 2013 UTC (4 years, 5 months ago) by pieper
Original Path: trunk/Modules
BUG: avoid overtaxing the system when many studies retrieved

Avoid having too many insert processings active at once
by ensuring that each one completes before the next one is
processed (with storescp --exec-sync option).

http://massmail.spl.harvard.edu/public-archives/slicer-users/2013/006324.html

Might also fix #1978.

Revision 21977 - Directory Listing
Modified Thu May 9 13:52:03 2013 UTC (4 years, 5 months ago) by pieper
Original Path: trunk/Modules
BUG: #3012 eraser no longer cancels active editor effect

Also undo/redo.  Now you can either use the keyboard
shortcuts or the buttons to perform these actions
and the currently active tool will not be canceled.

Revision 21975 - Directory Listing
Modified Thu May 9 12:30:49 2013 UTC (4 years, 5 months ago) by pieper
Original Path: trunk/Modules
BUG: #3104 allow floating point thresholds for ThresholdScalarVolume

Since everything internally is tempalted this only required
changing the data type in the xml file.

Revision 21974 - Directory Listing
Modified Thu May 9 12:21:11 2013 UTC (4 years, 5 months ago) by pieper
Original Path: trunk/Modules
BUG: #3090 Support painting on transformed volumes

Take into account any parent (linear) transforms applied to the
volume when doing painting.  Unify some logic between paint
and other label effects.

Revision 21972 - Directory Listing
Modified Tue May 7 22:23:28 2013 UTC (4 years, 5 months ago) by pieper
Original Path: trunk/Modules
BUG: fix some misc. issues with the editor identified by PNL

Thanks to Eli, Zora and all for finding these!

* 'e' key now toggles between zero and last color
* 'h' key now does not modify the Navigation mode of the crosshair
* there are now 100 undo/redo steps in the editor
* the tool palette re-docks when exiting the editor so it
will be back in place when re-entering the editor (if it had
been left undocked while editing -- space bar).

Revision 21971 - Directory Listing
Modified Tue May 7 18:34:57 2013 UTC (4 years, 5 months ago) by alexy
Original Path: trunk/Modules
ENH: Added TractographyDisplay MRMLDisplayableManager and supporting changes to make possible interactive editing of fibers.

Revision 21970 - Directory Listing
Modified Tue May 7 18:21:52 2013 UTC (4 years, 5 months ago) by alexy
Original Path: trunk/Modules
ENH: Added TractographyDisplay MRMLDisplayableManager and supporting changes to make possible interactive editing of fibers.

Revision 21959 - Directory Listing
Modified Tue Apr 30 19:53:11 2013 UTC (4 years, 5 months ago) by alexy
Original Path: trunk/Modules
BUG: 3094. Update ROI selection widget after an ROI is selected


Revision 21958 - Directory Listing
Modified Tue Apr 30 19:49:39 2013 UTC (4 years, 5 months ago) by pieper
Original Path: trunk/Modules
ENH: add more keyboard shortcuts in Editor

Per request from Sonia, give shortcuts for paint, draw, wand, and
rectangle effects.

See full list here:

http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Editor#Editor_Wide_Keystrokes

Also STYLE: some dead code removal and end-of-line space removal.

Revision 21952 - Directory Listing
Modified Mon Apr 29 15:02:53 2013 UTC (4 years, 5 months ago) by pieper
Original Path: trunk/Modules
ENH: #2761 Add CTCTDentalSurgery example

One click to get pre- and post- surgery scans, but the
logic API allows access to individual scans if desired.

http://na-mic.org/Bug/view.php?id=2761

Revision 21941 - Directory Listing
Modified Fri Apr 26 17:09:16 2013 UTC (4 years, 5 months ago) by alexy
Original Path: trunk/Modules
BUG: Fixed update problem on selecting different Tensor Property in TractographyDisplay module

Revision 21940 - Directory Listing
Modified Thu Apr 25 21:55:25 2013 UTC (4 years, 5 months ago) by pieper
Original Path: trunk/Modules
ENH: prevent incorrect calculations when volumes don't match

As pointered out by Yanling Liu on the slicer-users list [1] the
statistics values will be incorrect if the pixels do not match
in the grayscale and label volumes.  Now we detect this and
generate a dialog box to prevent miscalculations.

Also minor style adjustments with trailing whitespace.

[1] http://massmail.spl.harvard.edu/public-archives/slicer-users/2013/006487.html

Revision 21939 - Directory Listing
Modified Thu Apr 25 15:13:44 2013 UTC (4 years, 5 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add vtkMRMLCommandLineModuleNode::Completing

* Add vtkMRMLCommandLineModuleNode::Completing: state before the outputs
are loaded into the scene
* Add vtkMRMLCommandLineModuleNode::StatusModifiedEvent: event invoked when
status is changed.
* Remove unused wait_for_module(module, time_pause=5): should use the
Completing/Completed mechanism instead.

Revision 21937 - Directory Listing
Modified Thu Apr 25 15:13:39 2013 UTC (4 years, 5 months ago) by finetjul
Original Path: trunk/Modules
BUG: Color/Opacity transfer functions must be "sharp" for labelmaps

Revision 21919 - Directory Listing
Modified Thu Apr 25 15:13:01 2013 UTC (4 years, 5 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add convenient function vtkSlicerVolumesLogic::SetVolumeAsLabelMap

Revision 21918 - Directory Listing
Modified Thu Apr 25 15:12:58 2013 UTC (4 years, 5 months ago) by finetjul
Original Path: trunk/Modules
BUG: Fix volume rendering of lut

A slight offset was added to labels in Volume Rendering.
This was visible when having lots of labels.

Revision 21915 - Directory Listing
Modified Wed Apr 24 22:11:52 2013 UTC (4 years, 5 months ago) by pieper
Original Path: trunk/Modules
BUG: fix typo and warning in diffusion tensor scalars

One of the command line argument parsing options was misspelled.

Also there was an extra SetInput that caused a warning message.

Thanks to Vadim vadmalis@gmail.com for pointing this out.

Revision 21908 - Directory Listing
Modified Tue Apr 23 20:06:29 2013 UTC (4 years, 5 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Update Models documentation

Add documentation for ctkVTKPropertyWidget properties.

Revision 21907 - Directory Listing
Modified Tue Apr 23 19:05:29 2013 UTC (4 years, 5 months ago) by alexy
Original Path: trunk/Modules
BUG: 3084. Fixed multiple usability issues in ROI selection in Tractography Display module.
1. Changing Percentage Fibers Shown does not update display
2. Percentage Fibers Shown should update on mouse release not on drag
3. The ROI selection controls should be inactive until Fiber and ROI are selected to prompt users to select
4. Better name for ROI nodes needed
5. Tube slices do not show up on the newly created Fibers 

Revision 21906 - Directory Listing
Modified Mon Apr 22 20:52:09 2013 UTC (4 years, 5 months ago) by hjohnson
Original Path: trunk/Modules
ENH: Reset BRAINSTools to build without the ITK_FUTURE_LEGACY_REMOVE

The inconsistent use of ITK_FUTURE_LEGACY_REMOVE was causing major runtime
errors with regards to virtual functions being located in different places
in the object files between compilation units.

This update also turns off many new tools that are not ready for
distribution with Slicer.

Revision 21903 - Directory Listing
Modified Sat Apr 20 22:06:15 2013 UTC (4 years, 6 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Reorder CLI description XML elements

Revision 21902 - Directory Listing
Modified Fri Apr 19 22:56:32 2013 UTC (4 years, 6 months ago) by johan.andruejol
Original Path: trunk/Modules
BUG: Fix lost on focus when modifying spinbox

Previously, the spinbox would lose focus when modifying the value due to
an update by the node. Using the new ctkSpinBox that actually checks
if the values are the same before updating fixes this.

See Issue #2986

Revision 21899 - Directory Listing
Modified Fri Apr 19 15:37:30 2013 UTC (4 years, 6 months ago) by alexy
Original Path: trunk/Modules
BUG: 2916. Moved vtkSlicerModelsLogicAutoRemoveTest into the data module testing directory and use a datamodule logic instead of a models logic. Removed unused AutoRemoveDisplayAndStorageNodes  property of vtkSlicerModelsModuleLogic.

Revision 21892 - Directory Listing
Modified Wed Apr 17 14:19:28 2013 UTC (4 years, 6 months ago) by pieper
Original Path: trunk/Modules
BUG: #3076 make sure scalar range is updated after edit operations.

This new method unifies the updating of the image data and volume
node to trigger rendering.  By calling modified on the point scalars,
this GetScalarRange call returns the correct data.

http://na-mic.org/Bug/view.php?id=3076

This is confirmed by looking at the results of the call after
editing in new colors as shown below.

>>> l = getNode('*label')
>>> l
(vtkMRMLScalarVolumeNode)0x131766ba8
>>> l.GetImageData().GetScalarRange()
(0.0, 15.0)
>>> l.GetImageData().GetScalarRange()
(0.0, 18.0)
>>>

Revision 21882 - Directory Listing
Modified Tue Apr 9 19:34:33 2013 UTC (4 years, 6 months ago) by naucoin
Original Path: trunk/Modules
ENH: Implement feature #2918, fiducial projection on 2D slice plane

From: Laurent Chauvin <lchauvin@bwh.harvard.edu>

Revision 21878 - Directory Listing
Modified Mon Apr 8 15:50:03 2013 UTC (4 years, 6 months ago) by fedorov
Original Path: trunk/Modules
ENH: updated baseline, removed unnecessary files, updated CMakeLists.txt to
use the compressed baseline. See #3034.


Revision 21877 - Directory Listing
Modified Sat Apr 6 16:09:34 2013 UTC (4 years, 6 months ago) by alexy
Original Path: trunk/Modules
ENH: Enhancement to Tractography Display and ROI selection: Fiber selected by default, ROI interactive mode and visibility exposed, other minor UI improvements 

Revision 21876 - Directory Listing
Modified Sat Apr 6 00:40:18 2013 UTC (4 years, 6 months ago) by pieper
Original Path: trunk/Modules
BUG: fix spurious warning message

If there had been no study added in the past month, a string format
operation would fail and generate a warning.

Revision 21875 - Directory Listing
Modified Sat Apr 6 00:23:32 2013 UTC (4 years, 6 months ago) by pieper
Original Path: trunk/Modules
ENH: for issue #3002 fix eyedropper

Make sure all label effects have an instance of their logic class
and that the allow the superclass to optionally process keystrokes
and other events (this allows the eyedropper operation to work).

See keystroke list here:
http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Editor#Keystrokes

Revision 21874 - Directory Listing
Modified Fri Apr 5 22:32:16 2013 UTC (4 years, 6 months ago) by pieper
Original Path: trunk/Modules
BUG: #2932, #3001, #3002 Several improvements to the editor.

#2932 - new Pixel Mode in Paint tool allows precise control when zoomed
in close to the image.

Add a set of hotkeys per #3002 for editor-wide functions, also
new +/- control on the paint brush to adjust size while it is active.

Per #3002 if a master and merge volumes already have been selected,
don't reset them when entering the editor.

Revision 21870 - Directory Listing
Modified Fri Apr 5 17:48:44 2013 UTC (4 years, 6 months ago) by pieper
Original Path: trunk/Modules
BUG: fix paths for DICOM executable searches

Since the helper executables are not in the slicer bin directory
for a local build of slicer, be sure to also check in the DCMTK-build
bin directory to find the actual executable.

Revision 21862 - Directory Listing
Modified Thu Apr 4 18:40:07 2013 UTC (4 years, 6 months ago) by pieper
Original Path: trunk/Modules
BUG: fix DWI loading in DICOM module by using DWIConvert module

Adapt to updates in DWIConvert by creating a target DWI volume
to store the output.

Revision 21845 - Directory Listing
Modified Thu Mar 28 01:53:55 2013 UTC (4 years, 6 months ago) by fedorov
Original Path: trunk/Modules
STYLE: rearrange parameters to make the interface more user-friendly, see #3034


Revision 21834 - Directory Listing
Modified Fri Mar 22 22:55:02 2013 UTC (4 years, 6 months ago) by naucoin
Original Path: trunk/Modules
BUG: adding the dir in svn not working with git svn dcommit, removing it

Issue #2919



Revision 21833 - Directory Listing
Modified Fri Mar 22 22:47:05 2013 UTC (4 years, 6 months ago) by naucoin
Original Path: trunk/Modules
BUG: add a dir in SVN for the git svn commit from kevin wang

Kevin is adding a scalar bar actor with extra features, it
will go in the VTKRendering subdir

Issue #2919



Revision 21829 - Directory Listing
Modified Fri Mar 22 13:52:55 2013 UTC (4 years, 7 months ago) by mccormic
Original Path: trunk/Modules
BUG: itkImageToImageRegistrationHelper not using defaultPixelValue throughout. 3024

The defaultPixelValue was not being set on all ResampleImageFilter's.

Suggested-by: Roland Kwitt <roland.kwitt@kitware.com>

Revision 21828 - Directory Listing
Modified Tue Mar 19 21:30:21 2013 UTC (4 years, 7 months ago) by pieper
Original Path: trunk/Modules
ENH: Improve efficiency of PaintOver mode in WandEffect of Editor

Use a numpy array of booleans to store the visit status for
faster lookup.
Thanks to Andras for the contribution!

Revision 21827 - Directory Listing
Modified Tue Mar 19 21:27:43 2013 UTC (4 years, 7 months ago) by pieper
Original Path: trunk/Modules
STYLE: change category of Performance Tests per developer discussion

Now is Testing not Developer Tools.

Revision 21824 - Directory Listing
Modified Mon Mar 18 20:31:20 2013 UTC (4 years, 7 months ago) by pieper
Original Path: trunk/Modules
ENH: enable the editor cursor for the wand effect

Revision 21823 - Directory Listing
Modified Mon Mar 18 19:16:28 2013 UTC (4 years, 7 months ago) by pieper
Original Path: trunk/Modules
ENH: Add WandEffect to segmentation editor

This tool was a demonstration for creating an editor extension, but
some users found it to be a valuable addition, so Andras suggested
adding it to the core of slicer.  This version exposes additional options,
such as segmenting in 3D and also using a fixed threshold for better
precision when segmenting.

Revision 21820 - Directory Listing
Modified Sat Mar 16 22:34:29 2013 UTC (4 years, 7 months ago) by pieper
Original Path: trunk/Modules
ENH: editor eyedropper, eraser toggle, and related (issue #2928)

This adds the framework for other requested hotkeys.

Revision 21819 - Directory Listing
Modified Sat Mar 16 22:34:27 2013 UTC (4 years, 7 months ago) by pieper
Original Path: trunk/Modules
STYLE: make a comment into a docstring

Revision 21816 - Directory Listing
Modified Sat Mar 16 16:59:33 2013 UTC (4 years, 7 months ago) by demian
Original Path: trunk/Modules
COMP: Fixed compatibility with VS problems in my previous commit

Revision 21815 - Directory Listing
Modified Sat Mar 16 14:16:31 2013 UTC (4 years, 7 months ago) by demian
Original Path: trunk/Modules
ENH: Made naming of new modules more coherent

Revision 21814 - Directory Listing
Modified Sat Mar 16 13:07:17 2013 UTC (4 years, 7 months ago) by demian
Original Path: trunk/Modules
ENH: Moved the FiberBundleToLabelMap module to Diffusion->Tractography

Revision 21813 - Directory Listing
Modified Sat Mar 16 12:55:23 2013 UTC (4 years, 7 months ago) by demian
Original Path: trunk/Modules
ENH: Moved the DTIimport/export modules to the legacy menu as the support for Nifti is now in the main slicer code

Revision 21812 - Directory Listing
Modified Sat Mar 16 12:35:20 2013 UTC (4 years, 7 months ago) by demian
Original Path: trunk/Modules
BUG: Corrected bug introduced due to interface change

Revision 21811 - Directory Listing
Modified Sat Mar 16 12:35:16 2013 UTC (4 years, 7 months ago) by demian
Original Path: trunk/Modules
ENH: Added a module to select tracts using labelmaps

Revision 21806 - Directory Listing
Modified Wed Mar 13 05:24:57 2013 UTC (4 years, 7 months ago) by jcfr
Original Path: trunk/Modules
COMP: Ensure BRAINSTools uses Slicer ExternalData by replacing it.

This is obviously a hack allowing to use ExternalData withing Slicer while
building BRAINSTools. An issue has been reported upstream.
See https://github.com/BRAINSia/BRAINSTools/issues/3

Revision 21787 - Directory Listing
Modified Tue Mar 5 23:46:16 2013 UTC (4 years, 7 months ago) by jcfr
Original Path: trunk/Modules
STYLE: Rename "GradientAnisotropicDiffusion" baselines to be explicit

Naming files/functions/classes something1, something2, something3 .. is
not helpful to understand what the files/functions/classes are used for.

This commit rename baselines and test to be explicit and also remove
the comment in the CMakeLists (now unnecessary and redundant).

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

Revision 21786 - Directory Listing
Modified Tue Mar 5 23:46:12 2013 UTC (4 years, 7 months ago) by jcfr
Original Path: trunk/Modules
BUG: UseImageSpacing defaults for GradientAnisotropicDiffusion

When Slicer4 was switched from ITKv3 to ITKv4, the
GradientAnisotropicDiffusionImageFilterTest started failing.  This is
because the default for the parameter "UseImageSpacing" changed from
"off" to "on" between these versions of ITK.  This patch adds an
advanced option to the CLI to enable the user to choose whether to use
image spacing, and the default is "on" in accordance with the new ITK
behavior. Tests are added that test turning this variable both on and
off, and a new regression test image is included to test the case when
the parameter is on.  With these changes, the tests should pass when
both ITKv3 and ITKv4 are used.

From: Dirk Padfield <padfield@ge.com>

Revision 21784 - Directory Listing
Modified Tue Mar 5 23:18:50 2013 UTC (4 years, 7 months ago) by jcfr
Original Path: trunk/Modules
BUG: Fix ResampleDTIVolumeBSplineInterpolationTest

Based on discussion with module maintainer, the test failure was
due to the transition to ITKv4. There were other improvements to
the BSpline code.
See http://slicer-devel.65872.n3.nabble.com/Slicer-baselines-need-to-be-updated-due-to-ITKv4-integration-tp4027636p4027789.html

The update of the baseline has been done with the following command:
cp /home/jchris/Projects/Slicer-AHM-Superbuild-Debug/Slicer-build/Testing/Temporary/dt-helix-transformed4.nrrd /home/jchris/Projects/Slicer-AHM/Modules/CLI/ResampleDTIVolume/Testing/../Data/Baseline/dt-helix-ref-BSInterpolation.nrrd

Revision 21782 - Directory Listing
Modified Thu Feb 28 21:18:39 2013 UTC (4 years, 7 months ago) by pieper
Original Path: trunk/Modules
BUG: #2983 and #2206 fix position of the dicom popup

Detect when the window is already open so it doesn't get repositioned
more than once.  Also keep track of when you have applied the
settings geometry and then don't apply the standard placement
in that case.

Revision 21780 - Directory Listing
Modified Wed Feb 27 21:02:35 2013 UTC (4 years, 7 months ago) by pieper
Original Path: trunk/Modules
BUG: #2831 - allow loading of secondary capture dicom files

Sometimes people create 'secondary capture' (SC) dicom types as a byproduct
of anonymization or other data processing.  While is really meant
to be a 2D screen capture, when you have a stack of them it is
sometime desirable to load them as a volume.  So with this change
we allow loading with a warning, and with a low confidence so that
some other plugin can precome the default selection if it is better
able to load this data.

Revision 21779 - Directory Listing
Modified Wed Feb 27 21:02:33 2013 UTC (4 years, 7 months ago) by pieper
Original Path: trunk/Modules
ENH: print a stack trace when a dicom plugin fails to execute

Revision 21778 - Directory Listing
Modified Wed Feb 27 16:01:04 2013 UTC (4 years, 7 months ago) by pieper
Original Path: trunk/Modules
BUG: fix a warning message when dicom file has been deleted

The Recent Activity widget now gracefully handles the case where
files have been deleted that are referenced in the database.

Revision 21777 - Directory Listing
Modified Wed Feb 27 16:01:01 2013 UTC (4 years, 7 months ago) by pieper
Original Path: trunk/Modules
ENH: implement #2206 and #2983

Since the browser is raised when the module is entered, people
naturally think that pressing the button that enters the module
will also open the browser; but when the module is already active,
selecting the module is a no-op and the browser is closed.

With this change, the action will also raise the browser when
the module is active, so it conforms with expectations.

Revision 21773 - Directory Listing
Modified Sun Feb 24 20:17:38 2013 UTC (4 years, 7 months ago) by pieper
Original Path: trunk/Modules
ENH: allow LabelEffect subclasses to selectively disable some features

Paint Over and Threshold options may not be possible to implement
for some label effects, so make it possible for the subclass to disable
display of the widgets.

Revision 21771 - Directory Listing
Modified Sun Feb 24 02:08:32 2013 UTC (4 years, 7 months ago) by fedorov
Original Path: trunk/Modules
BUG: account for the new location of the FM filter


Revision 21770 - Directory Listing
Modified Fri Feb 22 07:53:39 2013 UTC (4 years, 7 months ago) by jcfr
Original Path: trunk/Modules
COMP: Update modules to use WITH_GENERIC_TESTS and SlicerMacroConfigureModuleCxxTestDriver

Overall simplification of the CMakeLists related to Testing.

Revision 21767 - Directory Listing
Modified Fri Feb 22 04:44:46 2013 UTC (4 years, 7 months ago) by jcfr
Original Path: trunk/Modules
COMP: Move Editor logic Cpp classes from "Base/Logic" to "EditorLib/Logic"

These classes implementing the logic associated with editor effects, it
make sens to move them along side the EditorLib module.

Revision 21765 - Directory Listing
Modified Fri Feb 22 02:20:57 2013 UTC (4 years, 7 months ago) by jcfr
Original Path: trunk/Modules
COMP: Move Editor icons from "Base/Logic" into "EditorLib/Resources/Icons"

Also introduced the python constant EditorLib.ICON_DIR allowing
to easily resolve icon filepaths.

The variable is set using the __file__ attribute of EditorLib module.

Since the file/directory organization of either (1) source code, (2) file copied
into the build dir or (3) installed files is the same, the ICON_DIR
variable will allow to resolve the icon file paths successfully.

Revision 21764 - Directory Listing
Modified Fri Feb 22 00:46:12 2013 UTC (4 years, 7 months ago) by jcfr
Original Path: trunk/Modules
COMP: Re-organize Scripted module directories

* Built-in scripted module are now organize like the extension. One folder
per module.

* Macro "slicerMacroBuildScriptedModule" is now used consistently.

* Generic tests are now added auto-magically with the help of the new
parameter "WITH_GENERIC_TESTS".

* Remove unused ChangeTracker tests and created an issue
on the extension tracker. See https://github.com/fedorov/ChangeTrackerPy/issues/13

Revision 21758 - Directory Listing
Modified Thu Feb 21 18:49:53 2013 UTC (4 years, 7 months ago) by fedorov
Original Path: trunk/Modules
ENH: adding FastMarching effect to Editor; see issue #2454


Revision 21756 - Directory Listing
Modified Wed Feb 20 20:58:51 2013 UTC (4 years, 7 months ago) by mccormic
Original Path: trunk/Modules
STYLE: Fix include style for ITK headers.

Slicer style is to use < > instead of " for ITK headers.

Revision 21755 - Directory Listing
Modified Wed Feb 20 20:42:22 2013 UTC (4 years, 7 months ago) by mccormic
Original Path: trunk/Modules
STYLE: Include itkConfigure.h to show where macro originates.

Also, move include with the rest of the ITK headers.

Revision 21752 - Directory Listing
Modified Wed Feb 20 15:49:47 2013 UTC (4 years, 7 months ago) by mccormic
Original Path: trunk/Modules
COMP: Link GenerateExpertAutomatedRegistrationTestData with ITKFactoryRegistration.

Needed for TubeTK to link.

Revision 21751 - Directory Listing
Modified Wed Feb 20 05:06:17 2013 UTC (4 years, 7 months ago) by mccormic
Original Path: trunk/Modules
BUG: GenerateExpertAutomatedRegistrationTestData FactoryRegistration.

The executable needs to call the ITK FactoryRegistration function to
get the ImageIO factories registered hen in Slicer.

Revision 21742 - Directory Listing
Modified Tue Feb 19 22:43:45 2013 UTC (4 years, 8 months ago) by mccormic
Original Path: trunk/Modules
COMP: Fix ExpertAutomatedRegistration shadowing typedef.

Revision 21741 - Directory Listing
Modified Tue Feb 19 18:42:05 2013 UTC (4 years, 8 months ago) by pieper
Original Path: trunk/Modules
ENH: update dataprobe even when mousing over annotation

Increase the priority to get all events, even if they will later
be used by another observer.  Also be sure to observe the interactor
rather than the interactor style so the priority will work with
respect to widgets which observe the interactor itself.  The
interactor style is observing the interactor so this is the same
for the purposes of the data probe.

Revision 21740 - Directory Listing
Modified Tue Feb 19 18:42:03 2013 UTC (4 years, 8 months ago) by pieper
Original Path: trunk/Modules
ENH: give annotations option to be visible only in selected views

This uses the same convention used in dislay nodes for other
displayable managers (e.g. VolumeRendering), except that it uses the
sliceNode since it is the 2D analog to the 3D view Node (at some point
perhaps there should be a generic superclass).  Here, since we are only
using the ID string it doesn't matter what type the node it.

This feature allows custom UIs, for example where some annotations only
show up in one view while others show up everywher.  In particular, this
is helpful for annotations representing volume-specific anatomical
landmark locations.

Revision 21738 - Directory Listing
Modified Tue Feb 19 02:30:50 2013 UTC (4 years, 8 months ago) by jcfr
Original Path: trunk/Modules
STYLE: Simplify CMakeLists associated with Annotations, Models and Volumes testing

Revision 21737 - Directory Listing
Modified Tue Feb 19 01:47:58 2013 UTC (4 years, 8 months ago) by jcfr
Original Path: trunk/Modules
STYLE: Change CLI test launch command to "SEM_LAUNCH_COMMAND"

Since the idea is to decouple the CLI build code from Slicer related
variables so that module could easily be built outside of Slicer, let's
use "SEM_LAUNCH_COMMAND" instead of "Slicer_LAUNCH_COMMAND"

Revision 21736 - Directory Listing
Modified Tue Feb 19 01:12:17 2013 UTC (4 years, 8 months ago) by jcfr
Original Path: trunk/Modules
COMP: Remove unneeded "SlicerBaseLogic" dependency from "ProbeVolumeWithModel" module

Revision 21735 - Directory Listing
Modified Tue Feb 19 01:12:15 2013 UTC (4 years, 8 months ago) by jcfr
Original Path: trunk/Modules
STYLE: Fix indent and re-organize includes in "DiffusionWeightedVolumeMasking" module

Revision 21734 - Directory Listing
Modified Tue Feb 19 01:12:13 2013 UTC (4 years, 8 months ago) by jcfr
Original Path: trunk/Modules
COMP: Remove unneeded "SlicerBaseLogic" dependency from "DiffusionTensorScalarMeasurements" module

Revision 21733 - Directory Listing
Modified Tue Feb 19 01:12:11 2013 UTC (4 years, 8 months ago) by jcfr
Original Path: trunk/Modules
COMP: Remove unneeded "SlicerBaseLogic" dependency from DWIToDTIEstimation module

Revision 21732 - Directory Listing
Modified Tue Feb 19 01:12:09 2013 UTC (4 years, 8 months ago) by jcfr
Original Path: trunk/Modules
COMP: Remove now optional LINK_DIRECTORIES param passed to SEMMacroBuildCLI

Within a same CMake project, a CMake target embeds information like
the link directory and it is not required to explicitly set the link
directories.

From the CMake documentation [1], "this command is rarely necessary.
Library locations returned by find_package() and find_library() are
absolute paths. Pass these absolute library file paths directly to
the target_link_libraries() command. CMake will ensure the linker
finds them."

The same apply for dependening project like SlicerExecutionModel.
Indeed, since SlicerExecutionModel commit fdb7e28b, targets are exported
and it is not required to explicitly specify the link directories to link
against ModuleDescriptionParser library.

Same explanation apply for vtkTeem and MRML Libraries. The associated
targets are exported since Slicer r16490 and the library are already CMake
targets.

Also remove reference to an unset variable "MRML_LIB_DIR" originally
introduced by r3886 where it was used without being set.

[1] http://www.cmake.org/cmake/help/v2.8.10/cmake.html#command:link_directories

Revision 21730 - Directory Listing
Modified Mon Feb 18 21:48:07 2013 UTC (4 years, 8 months ago) by mccormic
Original Path: trunk/Modules
ENH: Remove OPTIMIZED warnings from ExpertAutomatedRegistration.

The optimized version were merged in from review as the default
for ITKv4.

Revision 21722 - Directory Listing
Modified Sat Feb 16 02:38:39 2013 UTC (4 years, 8 months ago) by jcfr
Original Path: trunk/Modules
COMP: Remove build system option related to ChangeTracker

Follow up of commit r21716

Revision 21721 - Directory Listing
Modified Sat Feb 16 02:38:34 2013 UTC (4 years, 8 months ago) by jcfr
Original Path: trunk/Modules
BUG: Ensure ITKv4 IO Factory are registered within tests

* Include directories associated with ITKFactoryRegistration are also
appended to ITK_INLCUDE_DIRS to ensure that the method itk::itkFactoryRegistration
could be called.

* Code allowing to register the factory has been manually added to the
tests.

* Would it make sens to have this library ITKFactoryIORegistration
being built/provided by ITKv4 proper ?

See #2813 - http://www.na-mic.org/Bug/view.php?id=2813
See #2951 - http://www.na-mic.org/Bug/view.php?id=2951

Revision 21720 - Directory Listing
Modified Sat Feb 16 02:38:18 2013 UTC (4 years, 8 months ago) by jcfr
Original Path: trunk/Modules
STYLE: Fix indent

Revision 21718 - Directory Listing
Modified Sat Feb 16 02:38:07 2013 UTC (4 years, 8 months ago) by jcfr
Original Path: trunk/Modules
STYLE: Remove unnecessary extra quotes used with "slicerMacroBuildScriptedModule"

The way list are passed when using "slicerMacroBuildScriptedModule" is now
consistent with the other build macros.

Revision 21712 - Directory Listing
Modified Fri Feb 15 20:28:28 2013 UTC (4 years, 8 months ago) by naucoin
Original Path: trunk/Modules
BUG: update tracts when scene views are restored.

Have the logic respond to scene view restored events and update
any tracts that are seeded from the first parameter node.

Issue #2949


Revision 21708 - Directory Listing
Modified Fri Feb 15 00:42:06 2013 UTC (4 years, 8 months ago) by jcfr
Original Path: trunk/Modules
BUG: Register ITKv4 IO factory in itkTestMainExtended

Revision 21707 - Directory Listing
Modified Fri Feb 15 00:42:04 2013 UTC (4 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Enable floating point exceptions in itkTestMainExtended

Revision 21706 - Directory Listing
Modified Fri Feb 15 00:42:02 2013 UTC (4 years, 8 months ago) by jcfr
Original Path: trunk/Modules
COMP: Update itkTestMainExtended to use GetImageType function from itkPluginUtilities.h

Revision 21705 - Directory Listing
Modified Fri Feb 15 00:42:00 2013 UTC (4 years, 8 months ago) by jcfr
Original Path: trunk/Modules
STYLE: Consistent style between itkTestMainExtended and itkTestMain

Revision 21704 - Directory Listing
Modified Thu Feb 14 22:05:23 2013 UTC (4 years, 8 months ago) by jcfr
Original Path: trunk/Modules
STYLE: For consistency, change CMake macro from "SIMPLE_TEST" to "simple_test"

Use of lower case CMake function/macro when including underscore has been
first introduced with r17191.

See http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=17191

Revision 21700 - Directory Listing
Modified Thu Feb 14 16:31:17 2013 UTC (4 years, 8 months ago) by mccormic
Original Path: trunk/Modules
COMP: Fix ExpertAutomatedRegistration TEMP directory.

Make it also work if built outside the Slicer source tree.

Revision 21698 - Directory Listing
Modified Wed Feb 13 23:20:11 2013 UTC (4 years, 8 months ago) by mccormic
Original Path: trunk/Modules
ENH: Generate ExpertAutomatedRegistration test data.

The code to generate test data was already.  It was fixed
up and re-enabled.

Revision 21697 - Directory Listing
Modified Wed Feb 13 23:20:10 2013 UTC (4 years, 8 months ago) by mccormic
Original Path: trunk/Modules
STYLE: Remove extra ITK_LIBRARIES in GaussianBlurImageFilter CMake config.

Revision 21696 - Directory Listing
Modified Wed Feb 13 04:34:15 2013 UTC (4 years, 8 months ago) by mccormic
Original Path: trunk/Modules
COMP: itkImageToImageRegistrationMethod: shadowed method.

Warning occurs with switch to ITKv4.

Revision 21695 - Directory Listing
Modified Wed Feb 13 04:34:13 2013 UTC (4 years, 8 months ago) by mccormic
Original Path: trunk/Modules
COMP: itkBSplineImageToImageRegistrationMethod unused variable.

Revision 21694 - Directory Listing
Modified Wed Feb 13 04:34:11 2013 UTC (4 years, 8 months ago) by mccormic
Original Path: trunk/Modules
STYLE: Improvements to ExpertAutomatedRegistration.

Revision 21689 - Directory Listing
Modified Tue Feb 12 00:38:18 2013 UTC (4 years, 8 months ago) by jcfr
Original Path: trunk/Modules
COMP: Exclude Slicer test involving GPU to prevent dashboard client issue.

Running GPU based tests simultaneously from multiple VM is not recommended.
Time we exclude the test by updating the dashboard script, let's simply
disable the test within the code base itself.

This will prevent the dashboard from failing while checking that the transition
to ITKv4 is working as expected.

Re-enabling of GPU based tests is captured by issue #2939
See http://www.na-mic.org/Bug/view.php?id=2939

Revision 21687 - Directory Listing
Modified Mon Feb 11 22:31:01 2013 UTC (4 years, 8 months ago) by naucoin
Original Path: trunk/Modules
BUG: clean up the model node logic for toggling visibility.

Model slice nodes are distinguished by name rather than class, make that a more easily set string.
Don't toggle annotations or fiber bundle nodes or any other sub classes of 
model nodes.

Issue #2576



Revision 21683 - Directory Listing
Modified Mon Feb 11 02:40:50 2013 UTC (4 years, 8 months ago) by jcfr
Original Path: trunk/Modules
STYLE: Remove extra include and properly name variables in Reformat module

See #2926 - http://www.na-mic.org/Bug/view.php?id=2926

Revision 21678 - Directory Listing
Modified Sun Feb 10 05:04:48 2013 UTC (4 years, 8 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Add doc to new Harden Transform button

Revision 21677 - Directory Listing
Modified Sun Feb 10 04:53:24 2013 UTC (4 years, 8 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add Harden transform into Transforms module

+ Change "Transformed nodes" collapsible groupbox title.

Closes #2909

Revision 21673 - Directory Listing
Modified Fri Feb 8 18:40:51 2013 UTC (4 years, 8 months ago) by naucoin
Original Path: trunk/Modules
BUG: fix the detection of models with extensions orig and inflated.

The concatenated string list was mushing the two extensions together and
they were not being detected on loading data. 

Issue #2924


Revision 21672 - Directory Listing
Modified Fri Feb 8 17:38:22 2013 UTC (4 years, 8 months ago) by pieper
Original Path: trunk/Modules
BUG: prevent crash reported in #2925 - missing annotation point

The fiducials did not load correctly so no coordinate exists.

The underling question of why the fiducials do not correctly
load from that scene is not resolved.

Revision 21670 - Directory Listing
Modified Thu Feb 7 21:39:12 2013 UTC (4 years, 8 months ago) by naucoin
Original Path: trunk/Modules
ENH: add buttons to show/hide all models. Issue #2576

Revision 21666 - Directory Listing
Modified Wed Feb 6 19:57:01 2013 UTC (4 years, 8 months ago) by naucoin
Original Path: trunk/Modules
COMP: use boolean operator rather than bitwise to remove a windows build warning

Revision 21665 - Directory Listing
Modified Tue Feb 5 22:49:20 2013 UTC (4 years, 8 months ago) by naucoin
Original Path: trunk/Modules
ENH: extend the model maker to take a template model hierarchy as an argument.

Also added a test, and adjusted the testing to use different mrml files 
per test as the new test is going to modify the mrml file.

If the model maker is passed a template model hierarchy scene file that
has model hierarchies with the same names as the colors used in the
input label map volume color node, the output models are placed in the 
hierarchy as associated nodes. The 1:1 hierarchy nodes are set hidden 
as it will be easier for a user to create a template hierarchy in the Models
GUI with all the nodes not hidden from editors.

Leaving this an an advanced option hidden under the Debug panel until further 
user testing can be done and more templates provided. To use this feature, one
currently needs to craft hierarchies by hand in the Models GUI, save the scene,
then edit the mrml file to remove scene views and other unneccessary 
mrml nodes. The plan is to provide templates for the most used color
tables that Slicer provides in the Base/Logic/Resources/ColorFiles 
directory.


From work at the 2013 winter project week
http://wiki.na-mic.org/Wiki/index.php/2013_Project_Week:ColorHierarchies



Revision 21657 - Directory Listing
Modified Fri Feb 1 23:32:24 2013 UTC (4 years, 8 months ago) by naucoin
Original Path: trunk/Modules
BUG: adjust hidden flag on model hierarchy nodes to get back to previous behaviour

Libs/MRML/Core/vtkMRMLModelHierarchyNode.cxx - set hide from editors to false as a default
Modules/Loadable/Models/Resources/UI/qSlicerModelsModuleWidget.ui - set showHidden to false
Modules/Loadable/Models/qSlicerModelsModuleWidget.cxx - take out call to setShowHiddenForTypes
Libs/MRML/Widgets/qMRMLSceneHierarchyModel.cxx - set hidden true on new 1:1 hierarchy nodes
Modules/CLI/ModelMaker/ModelMaker.cxx - ditto
Base/QTCLI/qSlicerCLIModuleUIHelper.cxx - set show hidden to false and setting the node type by directly checking multiple and aggregate.

Issue #2906



Revision 21656 - Directory Listing
Modified Thu Jan 31 20:33:22 2013 UTC (4 years, 8 months ago) by naucoin
Original Path: trunk/Modules
COMP: removing compiler warnings for release builds as well as unused vars

Revision 21655 - Directory Listing
Modified Thu Jan 31 20:19:30 2013 UTC (4 years, 8 months ago) by naucoin
Original Path: trunk/Modules
COMP: remove signed unsigned comparison compiler warning

Revision 21654 - Directory Listing
Modified Thu Jan 31 20:08:24 2013 UTC (4 years, 8 months ago) by naucoin
Original Path: trunk/Modules
COMP: remove compiler warning of signed unsigned comparison

Revision 21650 - Directory Listing
Modified Wed Jan 30 19:40:44 2013 UTC (4 years, 8 months ago) by pieper
Original Path: trunk/Modules
STYLE: remove debugging statement

Revision 21649 - Directory Listing
Modified Tue Jan 29 21:45:40 2013 UTC (4 years, 8 months ago) by naucoin
Original Path: trunk/Modules
ENH: Implement feature 2885, display ruler projection on 2D viewers.

Add options to display the projection of a ruler on the 2D slices.

Code from Laurent Chauvin 
https://github.com/lchauvin/Slicer/commit/203b44301c0421d619d68e2ccd3a13dee0047cf0

Issue #2885


Revision 21648 - Directory Listing
Modified Tue Jan 29 20:48:14 2013 UTC (4 years, 8 months ago) by pieper
Original Path: trunk/Modules
BUG: fix crash detected by RSNA2012Quant SelfTest

When nodes are removed from the scene, do it as part of a batch
process rather than removing them as the are discovered.

Revision 21646 - Directory Listing
Modified Mon Jan 28 20:37:42 2013 UTC (4 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Remove "Load & Add Scenes Or Individual Datasets" section from Data module.

Minimize confusion by having on way of loading data.
See http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/SlicerApplication/LoadingData

See http://www.na-mic.org/Bug/view.php?id=2892

Fixes #2892

Revision 21643 - Directory Listing
Modified Sun Jan 27 18:22:24 2013 UTC (4 years, 8 months ago) by pieper
Original Path: trunk/Modules
STYLE: some improvements in comments and naming for debug of DICOM export

TODO: write tests to identify and debug boundary cases.

Revision 21642 - Directory Listing
Modified Sun Jan 27 18:22:21 2013 UTC (4 years, 8 months ago) by pieper
Original Path: trunk/Modules
BUG: fix dicom data bundle export/import

* Fix syntax of zip file size for dump2dcm call (use UL not IS)
* Fix UIDs by having dump2dcm generate new ones to overwrite reference
* Use app logic Zip/Unzip rather than python for consistency
* Fix some stylistic issues

Revision 21641 - Directory Listing
Modified Sun Jan 27 18:22:19 2013 UTC (4 years, 8 months ago) by pieper
Original Path: trunk/Modules
BUG: find dicom helper apps when DCMTK is build outside of CTK

Check in both CTK and DCMTK directories to find executables.

Revision 21638 - Directory Listing
Modified Fri Jan 25 09:06:34 2013 UTC (4 years, 8 months ago) by jcfr
Original Path: trunk/Modules
COMP: Remove WebGLExport module from Slicer core - Will be distributed as extension.

See https://github.com/xtk/SlicerWebGLExport/pull/2

Revision 21637 - Directory Listing
Modified Fri Jan 25 07:38:30 2013 UTC (4 years, 8 months ago) by jcfr
Original Path: trunk/Modules
COMP: Simplify DICOM2FullBrainTractography CMakeLists.txt

Remove unused and obsolete extension related CMake code

Revision 21636 - Directory Listing
Modified Fri Jan 25 07:38:25 2013 UTC (4 years, 8 months ago) by jcfr
Original Path: trunk/Modules
COMP: Remove unused file

Revision 21635 - Directory Listing
Modified Fri Jan 25 07:38:23 2013 UTC (4 years, 8 months ago) by jcfr
Original Path: trunk/Modules
COMP: Add convenience macro "SlicerMacroBuildScriptedModule"

This will ease the maintenance and prevent developer from having to
update their CMakeLists.txt each time the process to build scripted
module change (for example value associated with parameter DESTINATION_DIR
and INSTALL_DIR of ctkMacroCompilePythonScript)

See http://www.na-mic.org/Bug/view.php?id=2647

Fixes #2647

Revision 21629 - Directory Listing
Modified Tue Jan 22 23:37:17 2013 UTC (4 years, 8 months ago) by pieper
Original Path: trunk/Modules
ENH: add hook for patient hierarchy testing (from Csaba)

This hook will allow testing but will later be refactored when
the patient hieararchy work is finalized.

Revision 21625 - Directory Listing
Modified Mon Jan 21 18:33:39 2013 UTC (4 years, 8 months ago) by finetjul
Original Path: trunk/Modules
ENH: Don't enforce un-necessary limitation on output signed image type

Revision 21624 - Directory Listing
Modified Mon Jan 21 18:02:31 2013 UTC (4 years, 8 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add Negate property to Treshold Scalar Volume CLI

As of today, there is no easy mechanism in ITK to do so.
See ITK issues:
https://issues.itk.org/jira/browse/ITK-2991
https://issues.itk.org/jira/browse/ITK-2993

Revision 21623 - Directory Listing
Modified Mon Jan 21 18:02:28 2013 UTC (4 years, 8 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Remove wrong signed/unsigned warning to ThresholdScalarVolume

As of r10439, the CLI doesn't force the output to be signed.
Update the documentation.

Revision 21617 - Directory Listing
Modified Fri Jan 18 21:38:57 2013 UTC (4 years, 9 months ago) by jcfr
Original Path: trunk/Modules
BUG: Update QtTesting XML files to reference the appropriate module widget

This is a follow-up on commit r21613 where the xml files haven't been
updated as expected.

See #2247

Revision 21616 - Directory Listing
Modified Fri Jan 18 21:27:36 2013 UTC (4 years, 9 months ago) by jcfr
Original Path: trunk/Modules
BUG: Remove redundant connections from qSlicerWelcomeModuleWidget

Fix warning:

Object::connect: No such slot qSlicerWelcomeModuleWidget::loadData() in /home/jchris/Projects/Slicer-AHM-Superbuild-Debug/Slicer-build/Modules/Loadable/SlicerWelcome/ui_qSlicerWelcomeModuleWidget.h:293
Object::connect: (sender name: 'LoadNonDicomDataButton')
Object::connect: (receiver name: 'qSlicerWelcomeModuleWidget')


See #2247

Revision 21615 - Directory Listing
Modified Fri Jan 18 21:27:34 2013 UTC (4 years, 9 months ago) by jcfr
Original Path: trunk/Modules
BUG: Ensure module widget listen to mrmlSceneChanged signal

This is a follow-up on commit r21613 where the connections haven't been
updated as expected.

Fixes #2247

Revision 21614 - Directory Listing
Modified Fri Jan 18 20:32:17 2013 UTC (4 years, 9 months ago) by pieper
Original Path: trunk/Modules
ENH: add FiberBundleToLabelMap module and test

Per request from Ron, this was added as a core diffusion module
rather than as an extension.

Revision 21613 - Directory Listing
Modified Fri Jan 18 16:37:03 2013 UTC (4 years, 9 months ago) by christopher.mullins
Original Path: trunk/Modules
STYLE: Renamed qSlicer{MODULE_NAME}Module.ui into qSlicer{MODULE_NAME}ModuleWidget.ui

See na-mic.org/Mantis/view.php?id=2247

Fixes #2247

Revision 21608 - Directory Listing
Modified Thu Jan 17 19:14:12 2013 UTC (4 years, 9 months ago) by naucoin
Original Path: trunk/Modules
BUG: fix a crash caused by an overlay file with unassigned labels.

When loading some FreeSurfer scalar overlay files, the reader 
returns a warning that some labels were unassigned. This was being
treated as an error, but a valid node was being returned from the
Models logic instead of NULL, causing a crash in the IO file. 
Fixed that issue then changed the response to that warning
to return valid nodes and color tables and that seemed to 
fix the issue.

Issue #2851



Revision 21607 - Directory Listing
Modified Tue Jan 15 21:19:59 2013 UTC (4 years, 9 months ago) by pieper
Original Path: trunk/Modules
BUG: restructure the event collapsing timers so they only run once

Before, a singleshot would be triggered once each time the timer
ran out.  Now, the timer interval is extended so that one a single
invocation occcurs even if a large number of events come, as long as
no two events are separated by more than half a second.

Revision 21604 - Directory Listing
Modified Fri Jan 11 21:31:03 2013 UTC (4 years, 9 months ago) by jcfr
Original Path: trunk/Modules
COMP: Make sure itkTestMain.h is available when building extension

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

Revision 21599 - Directory Listing
Modified Fri Jan 11 21:30:39 2013 UTC (4 years, 9 months ago) by jcfr
Original Path: trunk/Modules
ENH: Update python script to use DWIConvert module instead of DicomToNrrd with DWIConvert

The new DWIConvert is much more flexible and complete
in it's handling of DWI data.

Contributed by Hans Johnson

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

Revision 21598 - Directory Listing
Modified Fri Jan 11 21:30:30 2013 UTC (4 years, 9 months ago) by jcfr
Original Path: trunk/Modules
ENH: Update ITK and DCMTK to support DWIConvert provided by BRAINSTools

By adding DWIConvert to BRAINSTools, the logic necessary to support
this tool becames much simpler.  It will also reduce the burden
of maintainance.

The DWIConvert program was originally building a private version
of the ITKv4 DCMTK interface.

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

Revision 21596 - Directory Listing
Modified Fri Jan 11 21:30:18 2013 UTC (4 years, 9 months ago) by jcfr
Original Path: trunk/Modules
COMP: Properly link SFLSRobustStat3DTestConsole CLI executable

Contributed by Matt McCormick

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

Revision 21594 - Directory Listing
Modified Fri Jan 11 21:30:04 2013 UTC (4 years, 9 months ago) by jcfr
Original Path: trunk/Modules
COMP: ConstBoundaryCondition header was missing.

Previously the ConstBoundaryCondition header was implicitly included
from other headers.  It now must be explicitly specified if used.

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

Revision 21586 - Directory Listing
Modified Thu Jan 10 23:38:02 2013 UTC (4 years, 9 months ago) by finetjul
Original Path: trunk/Modules
ENH: Speed-up qMRMLSceneModel node observation

Don't listen to nodes that are filtered out by the sort&filter proxy model.
Issue #2642

Example of performance on MacBookPro laptop:
AddData (BrainAtlas2012.mrb) took 22741 msecs -10000msecs
CloseScene () took 11827 msecs  -10000msecs
AddData (BrainAtlas2012.mrb) took 20909 msecs
ModifyNode (vtkMRMLScalarVolumeNode1) took 4 msecs
ModifyNode (vtkMRMLScalarVolumeNode2) took 24 msecs
ModifyNode (vtkMRMLScalarVolumeDisplayNode2) took 22 msecs
ModifyNode (vtkMRMLScalarVolumeNode3) took 15 msecs
ModifyNode (vtkMRMLModelHierarchyNode2) took 10 msecs
ModifyNode (vtkMRMLModelNode4) took 0 msecs
ModifyNode (vtkMRMLModelDisplayNode5) took 11 msecs
ModifyNode (vtkMRMLModelHierarchyNode3) took 10 msecs
ModifyNode (vtkMRMLModelStorageNode1) took 0 msecs
AddNode (vtkMRMLModelNode302) took 20 msecs
Layout (3) took 51 msecs
Layout (2) took 24 msecs
RestoreSceneView (vtkMRMLSceneViewNode15) took 865 msecs  -1000msecs
RestoreSceneView (vtkMRMLSceneViewNode15) took 622 msecs

Revision 21584 - Directory Listing
Modified Thu Jan 10 18:14:31 2013 UTC (4 years, 9 months ago) by demian
Original Path: trunk/Modules
ENH: colortable now is not possible to select when not appropriate

Revision 21578 - Directory Listing
Modified Thu Jan 10 17:09:51 2013 UTC (4 years, 9 months ago) by demian
Original Path: trunk/Modules
BUG: Fixed bug 2824 Perpendicular diffusivity now works

Revision 21577 - Directory Listing
Modified Thu Jan 10 17:00:51 2013 UTC (4 years, 9 months ago) by demian
Original Path: trunk/Modules
BUG: Corrected bug 2381 the DTI volume glyphs now use the correct color map when in color by orientation mode

Revision 21576 - Directory Listing
Modified Thu Jan 10 17:00:44 2013 UTC (4 years, 9 months ago) by demian
Original Path: trunk/Modules
ENH: Changed the label fo the fiber bundle ROI editing buttons to make the more clear

Revision 21573 - Directory Listing
Modified Wed Jan 9 23:39:20 2013 UTC (4 years, 9 months ago) by demian
Original Path: trunk/Modules
ENH: Added W/L controls for fiber bundles (mantis ID: 0002789)

Revision 21569 - Directory Listing
Modified Tue Jan 8 22:42:44 2013 UTC (4 years, 9 months ago) by demian
Original Path: trunk/Modules
BUG: Solved part of bug 2577, color fibers by segment and mean orientation works

Revision 21568 - Directory Listing
Modified Tue Jan 8 22:42:39 2013 UTC (4 years, 9 months ago) by demian
Original Path: trunk/Modules
BUG: Corrected bug 2577, now there is always a fiber bundle selected if there is one in the scene

Revision 21562 - Directory Listing
Modified Fri Jan 4 17:51:54 2013 UTC (4 years, 9 months ago) by naucoin
Original Path: trunk/Modules
BUG: don't add hierarchy nodes if the scene is importing/restoring. Issue #2849

Revision 21561 - Directory Listing
Modified Fri Jan 4 00:46:32 2013 UTC (4 years, 9 months ago) by finetjul
Original Path: trunk/Modules
BUG: Fix import of hierarchy node with existing ID

Note that it does not fix the import of annotation hierarchies.
For some reasons (see vtkSlicerAnnotationModuleLogic::OnSceneNodeAdded),
the hierarchies are automatically loaded into the wrong hierarchy node
parent.
Issue #2849

Revision 21552 - Directory Listing
Modified Mon Dec 31 12:49:02 2012 UTC (4 years, 9 months ago) by finetjul
Original Path: trunk/Modules
BUG: Add validity check

In case where the mrml node passed is null, this code crashes.

Revision 21549 - Directory Listing
Modified Mon Dec 31 12:48:38 2012 UTC (4 years, 9 months ago) by finetjul
Original Path: trunk/Modules
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 21547 - Directory Listing
Modified Mon Dec 31 12:48:20 2012 UTC (4 years, 9 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add vtkMRMLAnnotationClickCounter::Click

HasEnoughClicks doesn't provide enough flexibility when dealing with
annotations.

Revision 21546 - Directory Listing
Modified Mon Dec 31 12:48:12 2012 UTC (4 years, 9 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Minor indentation and factorization changes in Annotations module

Revision 21545 - Directory Listing
Modified Mon Dec 31 12:48:03 2012 UTC (4 years, 9 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add qMRMLTreeView::setCurrentNode()

Similarly to qMRMLTreeView::currentNode(), setCurrentNode abstracts
setCurrentIndex().

Revision 21544 - Directory Listing
Modified Mon Dec 31 12:47:51 2012 UTC (4 years, 9 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add support for parentable annotations

Sometimes we want the annotations to be parent of other annotations.

Revision 21542 - Directory Listing
Modified Mon Dec 31 11:54:49 2012 UTC (4 years, 9 months ago) by finetjul
Original Path: trunk/Modules
BUG: Delete unnecessary re-declaration of signal

Revision 21541 - Directory Listing
Modified Mon Dec 31 11:54:41 2012 UTC (4 years, 9 months ago) by finetjul
Original Path: trunk/Modules
ENH: Make qMRMLSceneAnnotationModel columns configurable

Note: Annotation hierarchies have an unclickable visibility icon

Issue #2606

Revision 21540 - Directory Listing
Modified Mon Dec 31 11:54:29 2012 UTC (4 years, 9 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add support for parent/child annotations

Some annotations (e.g. bones) can have direct parent/child relationship
in the tree view.
It shouldn't impact the existing annotations.

Revision 21539 - Directory Listing
Modified Mon Dec 31 11:54:21 2012 UTC (4 years, 9 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add methods to derive Annotations displayable manager

Revision 21538 - Directory Listing
Modified Mon Dec 31 11:54:11 2012 UTC (4 years, 9 months ago) by finetjul
Original Path: trunk/Modules
ENH: Speedup Annotations: remove unnecessary scene browsing

Checking if there is at least 1 node of type m_Focus in the scene is
costly.
When there is at least 1 node, the scene was getting browsed twice, once
in that step and once again later in the code.

Revision 21536 - Directory Listing
Modified Mon Dec 31 11:53:55 2012 UTC (4 years, 9 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add qMRMLTreeView::showScene and qMRMLTreeView::showRootNode

Give more flexibility to decide what item is root.
A root index for QTreeView is the invisible index that is the parent of all
the top level indexes.
showScene or showRootNode give the option to decide if the root scene/node
is visible, which implies that its parent becomes the root index for QTreeView.

Revision 21534 - Directory Listing
Modified Mon Dec 31 11:53:35 2012 UTC (4 years, 9 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Minor style changes in qSlicerMouseModeToolBar

Improve readability.

Revision 21532 - Directory Listing
Modified Fri Dec 28 20:53:29 2012 UTC (4 years, 9 months ago) by pieper
Original Path: trunk/Modules
ENH: track/restore DICOM popup geometry

Revision 21531 - Directory Listing
Modified Wed Dec 26 22:13:04 2012 UTC (4 years, 9 months ago) by naucoin
Original Path: trunk/Modules
BUG: stop the annotation tree view from auto expanding lists 

Don't use calling setMRMLScene on the tree view to refresh the tree, 
as it resets the expand level on the tree view, only call it when 
the scene is different.
This stopped the auto added top level all annotations list and the fiducials/ruler
list nodes from expanding, so invoke an event from the logic when those default
hierarchy nodes are added to trigger the tree to expand them (using the
Expanded value on the hierarchy node).
Also expand the hierarchy node when it's added by the user via the add
hierarchy button.

Fixes issue #1735


Revision 21530 - Directory Listing
Modified Wed Dec 26 16:33:34 2012 UTC (4 years, 9 months ago) by sankhesh
Original Path: trunk/Modules
BUG: Inserting new hierarchy causes parent to lose expansion state

Fixes issue 2840

Revision 21528 - Directory Listing
Modified Sat Dec 22 18:26:42 2012 UTC (4 years, 9 months ago) by alexy
Original Path: trunk/Modules
BUG 2639. Added logic to remove display and storage nodes when displayable node is removed.

Revision 21526 - Directory Listing
Modified Fri Dec 21 21:43:15 2012 UTC (4 years, 9 months ago) by pieper
Original Path: trunk/Modules
BUG: make sure precache tags are set for database instances

Since the precache tags are specific to the ctkDICOMDatabase,
be sure to set the correct values to both slicer.app.dicomDatabase
and the database that is internal to the ctkDICOMAppWidget.

Need to use a timer here, because we want to ensure that all plugins
(which are modules) have been discovered before we set the precache
tags.

Revision 21525 - Directory Listing
Modified Fri Dec 21 21:43:12 2012 UTC (4 years, 9 months ago) by pieper
Original Path: trunk/Modules
BUG: use correct signal for QAction

Since this is a QAction not a QPushButton, use
triggered instead of clicked.

Revision 21524 - Directory Listing
Modified Thu Dec 20 22:02:21 2012 UTC (4 years, 10 months ago) by pieper
Original Path: trunk/Modules
BUG: #2812 start with default database directory

Use Qt to specify default location in a platform-appropriate
manner.

Also some minor style cleanups or trailing spaces.

Revision 21520 - Directory Listing
Modified Tue Dec 18 22:36:29 2012 UTC (4 years, 10 months ago) by alexy
Original Path: trunk/Modules
BUG 2759. Fixed camera and camera node observers, made unique node names.

Revision 21518 - Directory Listing
Modified Fri Dec 14 19:02:35 2012 UTC (4 years, 10 months ago) by alexy
Original Path: trunk/Modules
BUG 1916. Added reading of ROI annotation data files

Revision 21515 - Directory Listing
Modified Mon Dec 10 14:02:08 2012 UTC (4 years, 10 months ago) by pieper
Original Path: trunk/Modules
ENH: add web instpector option to web view example

Supports better introspection html/css/javascript internals.

Thanks for finding this Luca!

Revision 21500 - Directory Listing
Modified Sat Dec 8 00:14:29 2012 UTC (4 years, 10 months ago) by lorensen
Original Path: trunk/Modules
ENH: Remove unnecessary qDebug

While using the Volume Rendering module, qDebug reports many lines containing
Default: "" on stdout.
This polluted the console with unnecessary lines.



Revision 21494 - Directory Listing
Modified Fri Dec 7 19:53:01 2012 UTC (4 years, 10 months ago) by naucoin
Original Path: trunk/Modules
BUG: fix fiducial display in light box mode.

Use the renderer from the light box proxy manager if it's defined
When in light box mode, switch to using 2d point handles for fiducials.
Avoid seed widget and representation having different renderers on creation.
Unify light box index calculation.
Fix the annotations showing up in the 0th light box when the annotation
should be in the -1th. 
Take into account volume spacing, calculate the distance between the fiducial
and the slice at this light box index using distance from the fiducial point and the slice plane.
Reset the glyph type when changing in and out of lightbox mode.

Issue #1690


Revision 21482 - Directory Listing
Modified Fri Dec 7 00:23:59 2012 UTC (4 years, 10 months ago) by jcfr
Original Path: trunk/Modules
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 21478 - Directory Listing
Modified Thu Dec 6 22:50:11 2012 UTC (4 years, 10 months ago) by pieper
Original Path: trunk/Modules
BUG: Issue #2821 fiducial moves on mouse over

Only respond to InteractionEvents from the widget when the
seed widget is in MovingSeed mode.

Revision 21477 - Directory Listing
Modified Thu Dec 6 18:54:18 2012 UTC (4 years, 10 months ago) by naucoin
Original Path: trunk/Modules
BUG: fix loading of ruler files from Add Data dialogue.

Needed to call Initialize on the ruler to add the needed display nodes.

Issue #1406



Revision 21475 - Directory Listing
Modified Tue Dec 4 20:48:28 2012 UTC (4 years, 10 months ago) by pieper
Original Path: trunk/Modules
BUG: fix typo in iterator loop

See issue #2811

Revision 21466 - Directory Listing
Modified Thu Nov 29 20:51:28 2012 UTC (4 years, 10 months ago) by finetjul
Original Path: trunk/Modules
BUG: VolumeRendering: Support short scalar range volumes

Closes #2797

Revision 21456 - Directory Listing
Modified Wed Nov 21 12:40:33 2012 UTC (4 years, 10 months ago) by hjohnson
Original Path: trunk/Modules
BUG: Remove non-ascii characters

Non-ASCII characters make compilation difficult on issue
compiler warnings.  In addition, the non-ascii characters confuse
some code generation tools (i.e. autogenerating python wrappings for
nipype).

Revision 21442 - Directory Listing
Modified Mon Nov 19 00:00:39 2012 UTC (4 years, 11 months ago) by hjohnson
Original Path: trunk/Modules
ENH: Add ITKv4 PETStandardUptakeValueComputation

Extracting DICOM header values needed updating
for compatibility with API in ITKv4

Revision 21427 - Directory Listing
Modified Fri Nov 16 16:02:44 2012 UTC (4 years, 11 months ago) by finetjul
Original Path: trunk/Modules
BUG: Apply redesign to glyphable volume slice display nodes

In r20910, model display nodes had a demand driven pipeline redesign.
However, this redesign wasn't applied to glyphable volume slice display
nodes.
Issue #2374

Revision 21425 - Directory Listing
Modified Fri Nov 16 03:48:20 2012 UTC (4 years, 11 months ago) by jcfr
Original Path: trunk/Modules
BUG: Add method to streamline loading of scalar volumes

* Update DICOM scalar volume plugin to use the new method name.

Adapted from topic proposed by Andriy Fedorov
Credit: Andriy Fedorov, Julien Finet and Steve Pieper

See http://na-mic.org/Bug/view.php?id=2748

Fixes #2748

Revision 21417 - Directory Listing
Modified Thu Nov 15 15:50:38 2012 UTC (4 years, 11 months ago) by jcfr
Original Path: trunk/Modules
BUG: Remove SWidget related code from Performance test

This is a follow up of commit r21404

See http://na-mic.org/Mantis/view.php?id=2735
Fixes #2735

Revision 21406 - Directory Listing
Modified Wed Nov 14 16:24:35 2012 UTC (4 years, 11 months ago) by naucoin
Original Path: trunk/Modules
STYLE: Provide more output to the user when missing parameter values issue #2517

Revision 21362 - Directory Listing
Modified Wed Nov 14 15:20:21 2012 UTC (4 years, 11 months ago) by pieper
Original Path: trunk/Modules
STYLE: avoid using Error macro on when behavior is not unexpected

Since the null node message can be triggered during a scene load
or scene view change, don't print messages to the error log unless
specifically placed in debug mode.

Revision 21353 - Directory Listing
Modified Wed Nov 14 14:32:48 2012 UTC (4 years, 11 months ago) by pieper
Original Path: trunk/Modules
STYLE: remove unused script (performance test cleanup)

Revision 21352 - Directory Listing
Modified Wed Nov 14 03:07:12 2012 UTC (4 years, 11 months ago) by hjohnson
Original Path: trunk/Modules
ENH; Update ITKv4, SimpleITK, BRAINSTools

Revision 21349 - Directory Listing
Modified Tue Nov 13 23:16:49 2012 UTC (4 years, 11 months ago) by pieper
Original Path: trunk/Modules
ENH: add reloadable self test for DataProbe module

Note: not yet fully implemented.  Requires additional refactoring
of gui into logic, and reloadable code should replace widget in
main gui (not just module gui).

Revision 21348 - Directory Listing
Modified Tue Nov 13 23:16:46 2012 UTC (4 years, 11 months ago) by pieper
Original Path: trunk/Modules
ENH: show self test buttons in alphabetical order

Revision 21339 - Directory Listing
Modified Sun Nov 11 15:57:01 2012 UTC (4 years, 11 months ago) by hjohnson
Original Path: trunk/Modules
ENH: Make inclusion of .hxx/.txx files consistent.

A long oustanding inconsistentcy in ITKv4 has been made
consistent.  This patch syncronizes all the code
to use the consistent and preferred mechanisms.

Revision 21327 - Directory Listing
Modified Thu Nov 8 02:45:33 2012 UTC (4 years, 11 months ago) by jcfr
Original Path: trunk/Modules
COMP: Remove unused *.tcl files from Base/Tcl

Also verified that non of these tcl modules were used in EMSegment using the
following one-liner:

cd /home/jchris/Projects/Slicer4-Superbuild-Debug/EMSegment
$ for i in `ls -1 ~/Projects/Slicer4/Base/GUI/Tcl/*.tcl`; do bn=`basename $i`; ack --no-mrml  "[^A-Za-z0-9]${bn%.tcl}"; done

See http://na-mic.org/Bug/view.php?id=2735

Fixes #2735

Revision 21322 - Directory Listing
Modified Wed Nov 7 20:52:56 2012 UTC (4 years, 11 months ago) by pieper
Original Path: trunk/Modules
BUG: more useful error messages when dicom database cannot be used

Provide diagnostic info about missing or non-readable/non-writable
directories and files.  Also point user to directory selection button
in the dicom browser dialog to indicate where to make the fix.

Fixes issue #2715.

Revision 21312 - Directory Listing
Modified Fri Nov 2 21:31:34 2012 UTC (4 years, 11 months ago) by naucoin
Original Path: trunk/Modules
BUG: working on lightbox mode, reduce widget flashing, ignore extra renderers

Issue #1690



Revision 21310 - Directory Listing
Modified Fri Nov 2 18:42:37 2012 UTC (4 years, 11 months ago) by naucoin
Original Path: trunk/Modules
BUG: Working on getting lightbox mode working for annotations.

Reduce code duplication, use IsWidgetDisplayable.
Check for the lightbox index changing when comparing display coordinates.

Issue #1690


Revision 21309 - Directory Listing
Modified Fri Nov 2 18:39:56 2012 UTC (4 years, 11 months ago) by naucoin
Original Path: trunk/Modules
BUG: make sure fiducial display coordinates are zeroed out.

Initialise fiducial display coordinates before getting widget and mrml locations.

Issue #1690



Revision 21308 - Directory Listing
Modified Fri Nov 2 18:19:22 2012 UTC (4 years, 11 months ago) by naucoin
Original Path: trunk/Modules
BUG: issue #2716 add more error checking when responding to an annotation display node modified event


Revision 21306 - Directory Listing
Modified Fri Nov 2 17:01:54 2012 UTC (4 years, 11 months ago) by alexy
Original Path: trunk/Modules
BUG 2528. Exclude derived ColorTable nodes (such as vtkMRMLDiffusionTensorDisplayPropertiesNode) from the LUT selection

Revision 21305 - Directory Listing
Modified Fri Nov 2 16:27:37 2012 UTC (4 years, 11 months ago) by lorensen
Original Path: trunk/Modules
BUG: Fixed missing library for GrayscaleModelMaker

During Slicer4 startup on a Fedora 13 system, gcc 4.4.5,
GrayscaleModelMaker was not registered because it could not resolve
symbols in vtkInfovis. The GrayscalModelmaker module was using an old
style list in TARGET_LIBRARIES. This patch uses a proper list for
TARGET_LIBRARIES and INCLUDE_DIRECTORIES.
 


Revision 21304 - Directory Listing
Modified Fri Nov 2 15:36:28 2012 UTC (4 years, 11 months ago) by pieper
Original Path: trunk/Modules
BUG: (from Nicole) fix reload of annotations from mrml Issue #2716

Observe display modified event rather than the display nodes
directly.

http://na-mic.org/Bug/view.php?id=2716

Revision 21302 - Directory Listing
Modified Fri Nov 2 15:19:15 2012 UTC (4 years, 11 months ago) by jcfr
Original Path: trunk/Modules
STYLE: Fix indent in CMakeLists.txt

Revision 21301 - Directory Listing
Modified Thu Nov 1 16:59:54 2012 UTC (4 years, 11 months ago) by naucoin
Original Path: trunk/Modules
BUG: issue #2716 detect annotation nodes that have been added to the scene without display nodes

Revision 21294 - Directory Listing
Modified Wed Oct 31 12:58:40 2012 UTC (4 years, 11 months ago) by pieper
Original Path: trunk/Modules
STYLE: avoid DeprecationWarning messages from vtk wrapping

When passing a float to a vtk method that expects int, a
DeprecationWarning is issued, but it does not provide any
diagnositic information about the method or class that caused
the issue. To get the information, you need to issue the following
python commands before the warning is triggered:

 import warnings
 warnings.simplefilter('error')

This generates a stack trace that can be used to find the issue.

Revision 21293 - Directory Listing
Modified Wed Oct 31 12:12:15 2012 UTC (4 years, 11 months ago) by pieper
Original Path: trunk/Modules
BUG: fix for SlicerRT Issue #153 (hang when dicom plugins fail)

A python error in a dicom plugin (e.g. an extension like rt or pet/ct)
could cause the dicom module to be unresponsive.  Now there is a warning
dialog with the name of the failing plugin.

https://www.assembla.com/spaces/slicerrt/tickets/153#/activity/ticket:

Revision 21287 - Directory Listing
Modified Tue Oct 30 22:17:02 2012 UTC (4 years, 11 months ago) by finetjul
Original Path: trunk/Modules
BUG: Delete display nodes returned from CreateXXX() functions

Revision 21285 - Directory Listing
Modified Tue Oct 30 13:11:04 2012 UTC (4 years, 11 months ago) by finetjul
Original Path: trunk/Modules
BUG: Restore and fix commits r21277 and r21278 with invalid VTK external project reference

Revision 21284 - Directory Listing
Modified Tue Oct 30 05:33:23 2012 UTC (4 years, 11 months ago) by jcfr
Original Path: trunk/Modules
COMP: Revert commits r21282 and r21283 due to invalid VTK external project reference

Obtained the following message:

 "fatal: reference is not a tree: 9355f2d8b2d8c62a4e352176832576a3a0ecd37d
 CMake Error at VTK-prefix/tmp/VTK-gitclone.cmake:28 (message):
   Failed to checkout tag: '9355f2d8b2d8c62a4e352176832576a3a0ecd37d'"

Revision 21283 - Directory Listing
Modified Tue Oct 30 03:55:09 2012 UTC (4 years, 11 months ago) by finetjul
Original Path: trunk/Modules
BUG: Restore and fix commit r21278 with invalid CTK external project reference

This reverts commit r21279

Revision 21282 - Directory Listing
Modified Tue Oct 30 03:55:06 2012 UTC (4 years, 11 months ago) by finetjul
Original Path: trunk/Modules
BUG: Restore and fix commit r21277 with invalid CTK external project reference

This reverts commit r21289

Revision 21280 - Directory Listing
Modified Tue Oct 30 02:58:59 2012 UTC (4 years, 11 months ago) by jcfr
Original Path: trunk/Modules
COMP: Revert commit r21277 due to invalid CTK external project reference

This reverts commit 011e6d4772267f0a8a6ca62649a304c00b1b1471.

Revision 21279 - Directory Listing
Modified Tue Oct 30 02:56:34 2012 UTC (4 years, 11 months ago) by jcfr
Original Path: trunk/Modules
COMP: Revert commit r21278 due to invalid CTK external project reference

This reverts commit 6e89f699aab211f04e176b262a1febd69c94236e.

Revision 21278 - Directory Listing
Modified Tue Oct 30 00:08:50 2012 UTC (4 years, 11 months ago) by finetjul
Original Path: trunk/Modules
ENH: Speed up VR module initialization

When having a color node with a lot of colors > 1000, deep copying
vtkPiecewiseFunction fires lots of Modified events that are propagated by
the volume property node. This significantly slows down the
initialization of the volume rendering module (20secs in release mode).
The core problem is that a modified volume property node triggers
unnecessary updates. But it will be fixed later on.

Issue #2642 (0006854)

Revision 21277 - Directory Listing
Modified Tue Oct 30 00:08:40 2012 UTC (4 years, 11 months ago) by finetjul
Original Path: trunk/Modules
BUG: Volume rendering now support labelmaps with more than 1024 colors

Closes #2165, #2527

Revision 21275 - Directory Listing
Modified Mon Oct 29 19:17:57 2012 UTC (4 years, 11 months ago) by naucoin
Original Path: trunk/Modules
BUG: issue #2700 update doxygen comments to make use of ROI node more clear

Revision 21272 - Directory Listing
Modified Mon Oct 29 17:45:16 2012 UTC (4 years, 11 months ago) by jcfr
Original Path: trunk/Modules
BUG: Display message when sample data download fails

See http://www.na-mic.org/Bug/view.php?id=1226

Fixes #1226

Revision 21268 - Directory Listing
Modified Sun Oct 28 15:28:02 2012 UTC (4 years, 11 months ago) by demian
Original Path: trunk/Modules
BUG: Fixed bug 0002383: setting line color to FA does not work http://www.na-mic.org/Bug/view.php?id=2383

Revision 21266 - Directory Listing
Modified Sat Oct 27 19:35:25 2012 UTC (4 years, 11 months ago) by jcfr
Original Path: trunk/Modules
BUG: Ensure vtkMRMLAnnotationDisplayableManager can be instantiated by name

This will fix vtkMRMLAnnotationDisplayableManagerTest1. Indeed, this test
attempt to instantiate the base vtkMRMLAnnotationDisplayableManager.

Revision 21264 - Directory Listing
Modified Sat Oct 27 16:56:16 2012 UTC (4 years, 11 months ago) by alexy
Original Path: trunk/Modules
BUG 2656. Create line/tube/glyph FiberBundleDisplayNode while adding a FiberBundleNode

Revision 21263 - Directory Listing
Modified Sat Oct 27 01:56:32 2012 UTC (4 years, 11 months ago) by naucoin
Original Path: trunk/Modules
BUG: issue #1690 disable fiducials and rulers in lightbox mode to avoid showing them in the wrong place

Revision 21258 - Directory Listing
Modified Fri Oct 26 19:27:57 2012 UTC (4 years, 11 months ago) by naucoin
Original Path: trunk/Modules
BUG: Fixes issue #2473, fiducials now don't appear in all slices if visibility is toggled.

The UpdateVisible check was failing in the case that the annotation was generally 
visible but was not close enough to the current slice being shown in this viewer.


Revision 21255 - Directory Listing
Modified Fri Oct 26 15:59:46 2012 UTC (4 years, 11 months ago) by naucoin
Original Path: trunk/Modules
BUG: issue #1690 get the right RAS coordinate when click on a 2d slice in lightbox mode. Use the slice view displayable manager methods to calculate device to xyz to ras coordinates

Revision 21243 - Directory Listing
Modified Thu Oct 25 18:26:13 2012 UTC (4 years, 11 months ago) by naucoin
Original Path: trunk/Modules
COMP: use unsigned int to index nodes

Revision 21233 - Directory Listing
Modified Tue Oct 23 21:16:10 2012 UTC (4 years, 11 months ago) by alexy
Original Path: trunk/Modules
BUG 2653. Prevent fibers from switching to solid color when polydata for tracts has no points. 

Revision 21227 - Directory Listing
Modified Tue Oct 23 18:00:05 2012 UTC (4 years, 11 months ago) by jcfr
Original Path: trunk/Modules
ENH: Update Documentation to 4.2

Revision 21226 - Directory Listing
Modified Tue Oct 23 16:15:39 2012 UTC (4 years, 11 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Include VR displayable manager instantiator to properly link

Make VR consistent with Annotations module.
See r21224.

Revision 21225 - Directory Listing
Modified Tue Oct 23 15:46:24 2012 UTC (4 years, 11 months ago) by naucoin
Original Path: trunk/Modules
BUG: issue #2665 cropping is disabled by default, but the ROI visibility is enabled by default, so need to turn the ROI off after it's been initialised and it's display nodes have been added

Revision 21224 - Directory Listing
Modified Tue Oct 23 14:56:30 2012 UTC (4 years, 11 months ago) by jcfr
Original Path: trunk/Modules
BUG: Ensure Annotations displayable manager instantiators are registered

For explanation: http://www.vtk.org/doc/nightly/html/classvtkInstantiator.html#details

See http://www.na-mic.org/Bug/view.php?id=2663

Fixes #2663

Revision 21220 - Directory Listing
Modified Mon Oct 22 16:06:13 2012 UTC (4 years, 11 months ago) by naucoin
Original Path: trunk/Modules
BUG: hook up the line width widget

Revision 21217 - Directory Listing
Modified Fri Oct 19 18:16:46 2012 UTC (5 years ago) by jcfr
Original Path: trunk/Modules
STYLE: Simplify vtkAnnotationRulerWidget::CreateDefaultRepresentation

Based on suggestion of Julien

See #2664 / http://www.na-mic.org/Bug/view.php?id=2664

Revision 21214 - Directory Listing
Modified Fri Oct 19 00:21:06 2012 UTC (5 years ago) by jcfr
Original Path: trunk/Modules
BUG: Update vtkAnnotationRulerWidget to adequately distinguish 2D and 3D case

Add functions "GetIs2Widget" and "SetIs2DWidget" allowing to build
the appropriate representation.

Note that calling "SetIs2DWidget" after a representation has been built
as a no-op.

See http://www.na-mic.org/Bug/view.php?id=2664

Fixes #2664

Revision 21213 - Directory Listing
Modified Thu Oct 18 22:36:02 2012 UTC (5 years ago) by jcfr
Original Path: trunk/Modules
BUG: Use "GetMRMLDisplayableNode" instead of using redundant member m_SliceNode

See #2664 / http://www.na-mic.org/Bug/view.php?id=2664

Revision 21212 - Directory Listing
Modified Thu Oct 18 22:16:18 2012 UTC (5 years ago) by naucoin
Original Path: trunk/Modules
BUG: issue #2664 avoid a crash stemming from the wrong 2d/3d check for the ruler widget. Use the superclass to avoid a null pointer on safe down cast

Revision 21207 - Directory Listing
Modified Wed Oct 17 18:41:12 2012 UTC (5 years ago) by jcfr
Original Path: trunk/Modules
COMP: Remove empty directory

Revision 21206 - Directory Listing
Modified Wed Oct 17 18:38:58 2012 UTC (5 years ago) by jcfr
Original Path: trunk/Modules
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 21202 - Directory Listing
Modified Tue Oct 16 23:12:20 2012 UTC (5 years ago) by sankhesh
Original Path: trunk/Modules
ENH: 2592 Renamed TractographyFiducialSeedingModule

Renamed the module directory as well as all references to the module

Revision 21200 - Directory Listing
Modified Tue Oct 16 19:39:23 2012 UTC (5 years ago) by jcfr
Original Path: trunk/Modules
BUG: Fix windows assert associated with extension tests

To ensure existing tests pass, the Cxx folder has been added to the list
of sub dirs to consider when looking up IntDir.

That said, the recommended solution is to set the target property
RUNTIME_OUTPUT_DIRECTORY for the test executable. The value of this property
should be ${CMAKE_BINARY_DIR}/${Slicer_BIN_DIR}

See http://na-mic.org/Mantis/view.php?id=2348

Fixes #2348

Revision 21198 - Directory Listing
Modified Tue Oct 16 16:56:05 2012 UTC (5 years ago) by sankhesh
Original Path: trunk/Modules
BUG: 2584 Rotation sliders not affected by node change

Fixed range of rotation sliders to -180,180.
Range of rotation sliders not affected by OnMRMLTransformNodeModified
event.

Revision 21197 - Directory Listing
Modified Tue Oct 16 15:22:49 2012 UTC (5 years ago) by jcfr
Original Path: trunk/Modules
COMP: Fix NUMBER_HANDLES macro redefinition error adding "static const int" member

Revision 21192 - Directory Listing
Modified Mon Oct 15 22:35:55 2012 UTC (5 years ago) by jcfr
Original Path: trunk/Modules
COMP: Waiting the support of Java based module is updated. Disable it.

It prevent Slicer from being built on some linux system.

See http://www.na-mic.org/Bug/view.php?id=2633

Fixes #2633

Revision 21183 - Directory Listing
Modified Mon Oct 15 04:27:21 2012 UTC (5 years ago) by finetjul
Original Path: trunk/Modules
COMP: Annotations displayable manager depends on annotation logic

Revision 21181 - Directory Listing
Modified Sun Oct 14 17:11:05 2012 UTC (5 years ago) by finetjul
Original Path: trunk/Modules
ENH: Expose Annotations displayable managers to other modules

By moving the displayable managers into their own library,
it is then possible for modules to use and link to it.
The Annotations VTKWidgets had to be moved as well.

Issue #2606

Conflicts:
	Modules/Loadable/Annotations/CMakeLists.txt

Revision 21179 - Directory Listing
Modified Sun Oct 14 17:10:15 2012 UTC (5 years ago) by finetjul
Original Path: trunk/Modules
ENH: Add qMRMLAnnotationTreeView into Qt designer plugin

It can then be used when designing your module with Qt Designer

Revision 21175 - Directory Listing
Modified Sat Oct 13 20:32:24 2012 UTC (5 years ago) by alexy
Original Path: trunk/Modules
ENH: reduced number of Modified events in Interactive Tractography module

Revision 21173 - Directory Listing
Modified Sat Oct 13 14:03:09 2012 UTC (5 years ago) by pieper
Original Path: trunk/Modules
ENH: provide feedback during the editor test

Make sure qt has had time to process events before teardown of the
userinterface - otherwise pythonqt may hold references to QStandardItem
instances (and perhaps other objects) that Qt has destroyed.

Revision 21172 - Directory Listing
Modified Sat Oct 13 14:03:06 2012 UTC (5 years ago) by pieper
Original Path: trunk/Modules
ENH: avoid updating Qt while scene is batch processing

Revision 21171 - Directory Listing
Modified Sat Oct 13 13:34:19 2012 UTC (5 years ago) by pieper
Original Path: trunk/Modules
BUG: avoid over-responding to mrml scene changes in per-structure volumes

Use the specific methods for node added and remove events rather
than the generic modified events. This avoids creating/destroying
Qt classes while the scene is being torn down and avoids a
crash in the ThresholdThreading test.

Revision 21166 - Directory Listing
Modified Fri Oct 12 17:21:35 2012 UTC (5 years ago) by pieper
Original Path: trunk/Modules
BUG: include entire scalar range in threshold

Because the ctk range widget rounds the values for display, it
can have the effect of truncating the values such that the
selected range does not include the highest
value(s) in the volume.  Adding 1 to the max value avoids this
problem with no anticipated downsides.

Revision 21161 - Directory Listing
Modified Fri Oct 12 12:57:04 2012 UTC (5 years ago) by alexy
Original Path: trunk/Modules
BUG: 1574. Fixed crash on deleting FiberBundleNode

Revision 21159 - Directory Listing
Modified Thu Oct 11 18:49:27 2012 UTC (5 years ago) by naucoin
Original Path: trunk/Modules
BUG: mantis issue #2473 unify the visibility setting on the annotation nodes. Needed to have the data module displayable tree show the correct visibility flag and for calculating widget visibility in the displayable managers

Revision 21157 - Directory Listing
Modified Thu Oct 11 15:12:28 2012 UTC (5 years ago) by jcfr
Original Path: trunk/Modules
COMP: Annotations/Logic should be build before Annotations/Widgets library

As a side note, logic should NOT depend on any Widget/UI related code.
Additionally, by doing so a dependency cycle will be introduced.

Revision 21153 - Directory Listing
Modified Wed Oct 10 20:57:28 2012 UTC (5 years ago) by sankhesh
Original Path: trunk/Modules
ENH: Added volume rendering module tutorial test for abdomen dataset

Second test without VTK GPU Ray Casting on Apple as it fails to render

Revision 21152 - Directory Listing
Modified Wed Oct 10 20:43:06 2012 UTC (5 years ago) by jcfr
Original Path: trunk/Modules
COMP: Revert commit r21150 integrated by mistake.

Note for myself, always do a "git log" before doing "git svn dcommit"

This reverts commit daf274c85e8c7e46440e48f76b7c3f0dfb17000e.

Revision 21150 - Directory Listing
Modified Wed Oct 10 20:34:59 2012 UTC (5 years ago) by jcfr
Original Path: trunk/Modules
ENH: Added volume rendering module tutorial test for abdomen dataset

Second test without VTK GPU Ray Casting on Apple as it fails to render

Revision 21146 - Directory Listing
Modified Tue Oct 9 16:01:25 2012 UTC (5 years ago) by finetjul
Original Path: trunk/Modules
BUG: Correctly initialize ROI node in VR module

Closes #2620

Revision 21145 - Directory Listing
Modified Tue Oct 9 15:18:30 2012 UTC (5 years ago) by finetjul
Original Path: trunk/Modules
COMP: Missing returning node in vtkSlicerVolumesLogic::CreateLabelVolume

Add warning message for deprecated function.
Issue #2626

Revision 21141 - Directory Listing
Modified Tue Oct 9 13:56:16 2012 UTC (5 years ago) by finetjul
Original Path: trunk/Modules
BUG: Add more cheks and tests in VR logic methods for robustness

Crashed was happening if the VR display node was not in the scene.
Issue #2622

Revision 21140 - Directory Listing
Modified Tue Oct 9 13:55:04 2012 UTC (5 years ago) by fedorov
Original Path: trunk/Modules
BUG: fix memory leaks

GetNodesByClass() requires manual dereferencing, as described in
http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Developers/Tutorials/MemoryManagement


Revision 21139 - Directory Listing
Modified Tue Oct 9 13:23:07 2012 UTC (5 years ago) by finetjul
Original Path: trunk/Modules
BUG: Add backward compatible functions CreateLabelVolume

Issue #2626

Revision 21137 - Directory Listing
Modified Tue Oct 9 05:04:33 2012 UTC (5 years ago) by finetjul
Original Path: trunk/Modules
STYLE: Volume logic CreateLabelVolume should not add node to scene

Only CreateAndAddLabelVolume() can add a node to the scene.
Closes #2626

Revision 21136 - Directory Listing
Modified Tue Oct 9 05:04:19 2012 UTC (5 years ago) by finetjul
Original Path: trunk/Modules
STYLE: VR logic CreateVolumeRenderingDisplayNode should not add node to scene

Because the method name has the format "CreateXXX", it is implied that the
method does not add the instantiated node into the scene. It is instead the
caller's responsability.
vtkSlicerVolumesLogic::CreateLabelVolume() should also be changed (maybe
add utility CreateAndAddLabelVolume())
Issue #2626

Revision 21135 - Directory Listing
Modified Mon Oct 8 22:22:53 2012 UTC (5 years ago) by finetjul
Original Path: trunk/Modules
ENH: Expose qMRMLAnnotationTreeView and qMRMLSceneAnnotationModel

to other modules. Those classes can be handy when modules implement their
own annotation nodes.
To be "public", classes must be in subdirectories such as MRML, Logic or Widgets.

Issue #2606

Revision 21120 - Directory Listing
Modified Fri Oct 5 21:13:47 2012 UTC (5 years ago) by pieper
Original Path: trunk/Modules
BUG: better managment of startup conditions for dicom database

In particular for self testing on systems where dicom module
has not previously been run.

Revision 21108 - Directory Listing
Modified Thu Oct 4 20:39:31 2012 UTC (5 years ago) by naucoin
Original Path: trunk/Modules
STYLE: change debugging print out to a debug macro

Revision 21093 - Directory Listing
Modified Tue Oct 2 21:21:32 2012 UTC (5 years ago) by fedorov
Original Path: trunk/Modules
STYLE: cleanup console output


Revision 21088 - Directory Listing
Modified Mon Oct 1 20:31:36 2012 UTC (5 years ago) by finetjul
Original Path: trunk/Modules
ENH: Add qMRMLDisplayNodeViewComboBox

Combobox of display node view nodes.
Observe the view nodes of a display node and mark them as checked in the
scene view node list.

Move it from qSlicerVolumeRenderingModuleWidget.
Fix a small bug with the display views when a VR display node was
created.

Revision 21086 - Directory Listing
Modified Mon Oct 1 18:14:06 2012 UTC (5 years ago) by pieper
Original Path: trunk/Modules
BUG: files with no PixelData tag should be ignored

Some series come with extra files which are of Modality MR, but have
no PixelData - for example the vegetable scans here:
http://www.insight-journal.org/midas/collection/view/194

So we skip these and process only the multiframe pixel data.

Revision 21084 - Directory Listing
Modified Sun Sep 30 19:24:48 2012 UTC (5 years ago) by finetjul
Original Path: trunk/Modules
BUG: Fix Data module tree view auto size

Setting the minimumSize on the widget prevents the minimumSizeHint from
being used.
Use instead minSizeHint to enforce a minimum size of the widget.
Closes #2582

Revision 21080 - Directory Listing
Modified Sun Sep 30 02:52:56 2012 UTC (5 years ago) by finetjul
Original Path: trunk/Modules
BUG: Crash when applying transform on multiple selection

When transform is applied on first model index,
the model is update which invalidates other selected model indexes.
Closes #2578

Revision 21078 - Directory Listing
Modified Sat Sep 29 16:12:03 2012 UTC (5 years ago) by pieper
Original Path: trunk/Modules
ENH: improve printing of sample data downloads for readability

Revision 21077 - Directory Listing
Modified Sat Sep 29 05:49:50 2012 UTC (5 years ago) by finetjul
Original Path: trunk/Modules
ENH: Add resize grip into Models module tree view

It allows the user to decide the size of the tree view.
Issue #2433 (and related)

Revision 21074 - Directory Listing
Modified Fri Sep 28 18:46:55 2012 UTC (5 years ago) by pieper
Original Path: trunk/Modules
BUG: update to new display node API - fixes 2575

Use SetInputPolyData rather than SetPolyData

(TODO: this module needs a self test)

Revision 21056 - Directory Listing
Modified Wed Sep 26 17:16:29 2012 UTC (5 years ago) by finetjul
Original Path: trunk/Modules
ENH: Add backward compatibility support for Volume Rendering nodes

VR nodes used to have the tag VolumeRenderingParameters.
vtkMRMLVolumeRenderingDisplayNode is not an instantiable node.

Revision 21055 - Directory Listing
Modified Wed Sep 26 17:16:23 2012 UTC (5 years ago) by finetjul
Original Path: trunk/Modules
STYLE: Consolidate scene backward compatibility

Following r21032, ensure that MRML consistently use the same mechanism
for backward compatibility.

ROI -> AnnotationROI
SceneSnapshot -> SceneView

Revision 21054 - Directory Listing
Modified Wed Sep 26 17:03:02 2012 UTC (5 years ago) by jcfr
Original Path: trunk/Modules
COMP: Simplify how dependencies in generic Cxx module tests are handled

Based on suggestion of Julien Finet

See #2251 / http://www.na-mic.org/Bug/view.php?id=2251

Revision 21052 - Directory Listing
Modified Wed Sep 26 14:25:02 2012 UTC (5 years ago) by jcfr
Original Path: trunk/Modules
COMP: Ensure QTApp library can use Module/Core headers

See #2251 / http://www.na-mic.org/Bug/view.php?id=2251

Revision 21048 - Directory Listing
Modified Wed Sep 26 02:27:46 2012 UTC (5 years ago) by finetjul
Original Path: trunk/Modules
BUG: Write vtkMRMLVolumePropertyNode functions with highest precision

The point precision can be very important. Especially when have a
threshold like transfer function:
      _____
     |     |
_____|     |____
0   1,2   3,4   5
in that case, the points 1 and 2 have almost the same 'x'. But it is a
different 'x' otherwise the points would be merged.
A difference of std::numeric_limits<double>::epsilon() can be used.
Issue #2485

Revision 21047 - Directory Listing
Modified Wed Sep 26 02:27:40 2012 UTC (5 years ago) by finetjul
Original Path: trunk/Modules
STYLE: Cleanup vtkMRMLVolumePropertyNode

Revision 21046 - Directory Listing
Modified Tue Sep 25 22:20:26 2012 UTC (5 years ago) by jcfr
Original Path: trunk/Modules
BUG: Update module cxx generic test to load dependent modules

See http://www.na-mic.org/Bug/view.php?id=2251

Fixes #2251

Revision 21043 - Directory Listing
Modified Tue Sep 25 22:20:18 2012 UTC (5 years ago) by jcfr
Original Path: trunk/Modules
BUG: Editor.py - Handle case when layoutManager hasn't been intantiated

This will allow generic test associated with module depending on Editor
to pass. The following error will be avoided:

File "/home/jchris/Projects/Reporting-build/lib/Slicer-4.1/qt-loadable-modules/Python/qSlicerReportingModuleWidget.py", line 274, in enter
2:     self.__editorWidget.enter()
2:   File "/home/jchris/Projects/Slicer4-Superbuild-Debug/Slicer-build/lib/Slicer-4.1/qt-scripted-modules/Editor.py", line 79, in enter
2:     sliceLogics = slicer.app.layoutManager().mrmlSliceLogics()
2: AttributeError: 'NoneType' object has no attribute 'mrmlSliceLogics'

See http://www.na-mic.org/Bug/view.php?id=2251

Partial fix for #2251

Revision 21042 - Directory Listing
Modified Tue Sep 25 22:20:16 2012 UTC (5 years ago) by jcfr
Original Path: trunk/Modules
BUG: EditColor.py - Only "destroyed()" signal is exposed in PythonQt

This commit will fix the following error:

   PythonQt: QObject::connect() signal 'destroyed(QObject)' does not exist on QFrame

See http://www.na-mic.org/Bug/view.php?id=2251

Partial fix for #2251

Revision 21038 - Directory Listing
Modified Mon Sep 24 02:59:59 2012 UTC (5 years ago) by finetjul
Original Path: trunk/Modules
BUG: Concatenated transforms didn't fire modified events

The problem was that the created transform was observing the parent
transform too early (before the scene was set). It observed the node ID
but not the events of the node.
Closes #2530

Revision 21036 - Directory Listing
Modified Sun Sep 23 16:15:33 2012 UTC (5 years ago) by demian
Original Path: trunk/Modules
BUG: Corrected #0002544: ROI does not update fiber bundle

Revision 21034 - Directory Listing
Modified Sun Sep 23 04:07:04 2012 UTC (5 years ago) by finetjul
Original Path: trunk/Modules
STYLE: Add abstract class for all view nodes

vtkMRMLViewNode, vbtkMRMLSliceNode and vtkMRMLChartViewNode share some
common properties: they are views of a layout.

Revision 21031 - Directory Listing
Modified Sat Sep 22 17:11:48 2012 UTC (5 years ago) by demian
Original Path: trunk/Modules
BUG: Corrected #0002544: ROI does not crop fiber bundle

Revision 21029 - Directory Listing
Modified Fri Sep 21 21:33:57 2012 UTC (5 years ago) by finetjul
Original Path: trunk/Modules
ENH: Add Print utility menu command in Data module

It can be useful to print in the console the contents of the selected
node or scene.

Revision 21027 - Directory Listing
Modified Fri Sep 21 21:33:46 2012 UTC (5 years ago) by finetjul
Original Path: trunk/Modules
BUG: SceneView was not re-ID-ing some MRML nodes

When importing a scene view, if there are conflicts with the current
scene, it updates the ID of its nodes (see
vtkMRMLSceneViewNode::UpdateScene).
But when changing the ID of a node, one needs to update the nodes that
reference to these ID. This is done by
vtkMRMLSceneViewNode::UpdateNodeReferences. But some nodes (e.g.
vtkMRMLVolumeRenderingDisplayNode) were not propagating the id change to
subclasses.
This was the case of the view node ID being changed that wasn't applied
to the volume rendering display node in a scene view node.
Issue #1744

Revision 21023 - Directory Listing
Modified Fri Sep 21 12:57:31 2012 UTC (5 years ago) by finetjul
Original Path: trunk/Modules
BUG: Don't volume render when no mapper is set

This can happen when having multiple
vtkMRMLVolumeRenderingDisplayableManager in 1 view (eg.
CUDAVolumeRenderingDisplayableManager).
If the VR fails for one, it will make it fail for the other.

Revision 21022 - Directory Listing
Modified Fri Sep 21 12:57:24 2012 UTC (5 years ago) by finetjul
Original Path: trunk/Modules
STYLE: Create qMRMLSliceView

Consistent with qMRMLThreeDView/Widget
Issue #2540

Revision 21013 - Directory Listing
Modified Wed Sep 19 14:31:04 2012 UTC (5 years, 1 month ago) by sankhesh
Original Path: trunk/Modules
BUG: Issue 2380 - Listen to transform node changes

Fixes issue 2380.
qMRMLTransformSliders is the only class that needs to listen to
transform node changes. Removed redundant code where multiple
classes were listening to transform node changes.

Revision 21012 - Directory Listing
Modified Wed Sep 19 14:31:03 2012 UTC (5 years, 1 month ago) by sankhesh
Original Path: trunk/Modules
BUG: Handle range of matrix widget and slider widget for new matrix

Fixes issue 2380 completely.
Loading a new transform node from a file makes sure the range of the
sliders and matrix are set correctly. If the matrix is changed
externally using python, etc. the min-max values are set again based on
the new matrix value. A buffer of 30% of the range is applied to the
min-max values allowing the user to set values outside of current range.

Revision 20999 - Directory Listing
Modified Mon Sep 17 23:32:38 2012 UTC (5 years, 1 month ago) by finetjul
Original Path: trunk/Modules
ENH: Move model expand column into its own column

Issue #2163

Revision 20997 - Directory Listing
Modified Mon Sep 17 23:32:25 2012 UTC (5 years, 1 month ago) by finetjul
Original Path: trunk/Modules
STYLE: Add comments in vtkSlicerVolumeRenderingLogic

Revision 20995 - Directory Listing
Modified Sat Sep 15 21:52:26 2012 UTC (5 years, 1 month ago) by finetjul
Original Path: trunk/Modules
ENH: Add video card information in Volume Rendering logic

Issue #2522

Revision 20992 - Directory Listing
Modified Sat Sep 15 19:27:38 2012 UTC (5 years, 1 month ago) by finetjul
Original Path: trunk/Modules
BUG: VolumeRendering refreshes 3D view when preset and ROI are changed

Closes #2472

Revision 20991 - Directory Listing
Modified Sat Sep 15 19:27:33 2012 UTC (5 years, 1 month ago) by finetjul
Original Path: trunk/Modules
ENH: Move Color Expand/Collapse checkbox in the color column

Issue #2163

Revision 20988 - Directory Listing
Modified Thu Sep 13 20:48:43 2012 UTC (5 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: take out the dash from the label file name regexp, add in optional s for label, add optional capital first letter for label and seg

Revision 20985 - Directory Listing
Modified Thu Sep 13 17:13:15 2012 UTC (5 years, 1 month ago) by finetjul
Original Path: trunk/Modules
ENH: Add support for color name in qMRMLColorPickerWidget

Issue #2497

Revision 20983 - Directory Listing
Modified Wed Sep 12 23:38:16 2012 UTC (5 years, 1 month ago) by fedorov
Original Path: trunk/Modules
BUG: if multiple parameter nodes were present in the scene, the first one was always returned


Revision 20981 - Directory Listing
Modified Wed Sep 12 20:46:03 2012 UTC (5 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: when a scene view node doesn't have an screen shot, create a black thumbnail

Revision 20980 - Directory Listing
Modified Wed Sep 12 20:45:23 2012 UTC (5 years, 1 month ago) by naucoin
Original Path: trunk/Modules
STYLE: update message, hierarchies are deleted

Revision 20979 - Directory Listing
Modified Wed Sep 12 19:45:02 2012 UTC (5 years, 1 month ago) by pieper
Original Path: trunk/Modules
BUG: fix test timeout prompting for database

When in testing mode, don't block for user selection and instead
just use a temp directory.

Revision 20967 - Directory Listing
Modified Tue Sep 11 09:32:54 2012 UTC (5 years, 1 month ago) by finetjul
Original Path: trunk/Modules
BUG: Reformat module doesn't enforce entered value

Closes #2463

Revision 20966 - Directory Listing
Modified Tue Sep 11 09:32:48 2012 UTC (5 years, 1 month ago) by finetjul
Original Path: trunk/Modules
BUG: Reformat widget doesn't resize to whole volume

If the view has only its labelmap set, the volume was not considered.
Closes #2462

Revision 20963 - Directory Listing
Modified Mon Sep 10 22:42:36 2012 UTC (5 years, 1 month ago) by pieper
Original Path: trunk/Modules
BUG: be sure to return correct parameter node

When a fresh singleton is added to the scene it is copied
rather than added.  So we need to get a pointer to the node
in the scene rather than returning the node we added.

Revision 20961 - Directory Listing
Modified Mon Sep 10 19:01:10 2012 UTC (5 years, 1 month ago) by sankhesh
Original Path: trunk/Modules
BUG: Range of translation sliders set based on loaded file

Fixes issue 2380
When a file is loaded the matrix widget is populated first. Since
the widget observes the range of the translation sliders, the range of
the matrix was limited by the range of translation sliders.

The node is now added to the sliders first, which makes sure the range of
the sliders is set. The matrix widget is populated after this, making
sure the range is based on the file loaded.

Revision 20953 - Directory Listing
Modified Fri Sep 7 16:33:02 2012 UTC (5 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: issue 2030 unifty how screen shots are taken, using the ctk::grabVTKWidget and passing QImages to the scene writer. Fixes white background screen shots in saving mrml and mrb

Revision 20950 - Directory Listing
Modified Fri Sep 7 14:40:49 2012 UTC (5 years, 1 month ago) by pieper
Original Path: trunk/Modules
BUG: fix test crash due to incorrect template

Explicitly make the itk::Image be three dimensional, or else
the test overwrites the end of the size array.

Revision 20947 - Directory Listing
Modified Fri Sep 7 12:54:40 2012 UTC (5 years, 1 month ago) by lassoan
Original Path: trunk/Modules
BUG: Fixed BSplineToDeformationField module GUI (no image selectors appeared)

Revision 20943 - Directory Listing
Modified Thu Sep 6 19:56:20 2012 UTC (5 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: issue 2030 but also addressing slow scene loading: don't call read data on storage nodes when parsing xml files, rely on UpdateScene to read the data. Removed ProcessParentNode since only the storage nodes were calling it and only calling ReadData in it

Revision 20941 - Directory Listing
Modified Thu Sep 6 18:06:46 2012 UTC (5 years, 1 month ago) by naucoin
Original Path: trunk/Modules
COMP: fix python exception syntax, test should be able to pass now

Revision 20937 - Directory Listing
Modified Thu Sep 6 14:53:48 2012 UTC (5 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: mark editor created label map volumes as label maps on loading

Revision 20933 - Directory Listing
Modified Wed Sep 5 22:31:23 2012 UTC (5 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: issue 2379 and 2120 reset the root of the scene view tree in the GUI on end batch process rather than on end restore, otherwise it doesn't update properly

Revision 20932 - Directory Listing
Modified Wed Sep 5 22:29:53 2012 UTC (5 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: issue 2120 and 2379 do some more checking on scene view load/save/restore to detect bad file paths, vtkImageData wrangling in that case, and nodes that shouldn't be in the scene view. Scene view mrml hierarchy nodes now have an attribute to distinguish them rather than relying on a name, but keep backward compatibilty by also checking for the old names

Revision 20928 - Directory Listing
Modified Wed Sep 5 01:02:31 2012 UTC (5 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: issue 2379 on scene view restore, make sure reset the root and flatten the hierarchy. Still problems setting the root node but seem to not be losing nodes now

Revision 20926 - Directory Listing
Modified Tue Sep 4 22:22:46 2012 UTC (5 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: issue 2112: hide the visibility button for hierarchy nodes as support for using hierarchy display nodes is not currently fully implemented

Revision 20921 - Directory Listing
Modified Tue Sep 4 17:42:15 2012 UTC (5 years, 1 month ago) by pieper
Original Path: trunk/Modules
BUG: Check for valid polydata before updating fiber selection

Revision 20919 - Directory Listing
Modified Tue Sep 4 12:55:47 2012 UTC (5 years, 1 month ago) by inorton
Original Path: trunk/Modules
COMP: fix header file name

Revision 20916 - Directory Listing
Modified Mon Sep 3 18:18:12 2012 UTC (5 years, 1 month ago) by fedorov
Original Path: trunk/Modules
BUG: fixed cropping for the non-scalar volumes; before this commit, the output volume would always be initialized to scalar volume, independent of the input
ENH: added voxel-based cropping: this mode of operation does not need interpolation and preserves the original data; this functionality was contributed by Paul Mercea, pmercea@gmx.net


Revision 20913 - Directory Listing
Modified Sat Sep 1 14:21:33 2012 UTC (5 years, 1 month ago) by pieper
Original Path: trunk/Modules
BUG: avoid crash when refreshing dicom activity widget

Happened only on linux build (not mac) and appears to be a
management problem with pythonqt and Qt model items.  Using
the addItem API leaves all the item memory management to Qt.

Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0x7f49d71d17c0 (LWP 26275)]
0x0000000000000041 in ?? ()
(gdb) where
#0  0x0000000000000041 in ?? ()
#1  0x00007f49cf77352a in PythonQtWrapper_QListWidgetItem::delete_QListWidgetItem (this=0x622a360, obj=0x6105a90) at /usr/include/qt4/QtCore/qbytearray.h:383
#2  0x00007f49cf7709b6 in PythonQtWrapper_QListWidgetItem::qt_metacall (
    this=0x622a360, _c=QMetaObject::InvokeMetaMethod, _id=9, _a=0x7fff80b40cf0)
    at /usr/include/qt4/QtCore/qbytearray.h:383
#3  0x00007f49cf3356a4 in PythonQtInstanceWrapper_deleteObject (
    self=0x4d3e9b0, force=false) at /usr/include/qt4/QtCore/qbytearray.h:383
#4  0x00007f49cf335805 in PythonQtInstanceWrapper_dealloc (self=0x4d3e9b0)
    at /usr/include/qt4/QtCore/qbytearray.h:383
#5  0x00007f49cfe77155 in subtype_dealloc (self=0x4d3e9b0)
    at Objects/typeobject.c:2675
#6  0x0000000002b47130 in ?? ()
#7  0x0000000000000000 in ?? ()
(gdb) q
The program is running.  Quit anyway (and detach it)? (y or n) y
Detaching from program: /home/pieper/slicer4/latest/Slicer-superbuild/Slicer-build/bin/SlicerApp-real, process 26275

Revision 20912 - Directory Listing
Modified Sat Sep 1 13:15:28 2012 UTC (5 years, 1 month ago) by pieper
Original Path: trunk/Modules
BUG: show status message only if there are recent DICOM series

Avoids python warning

Revision 20911 - Directory Listing
Modified Sat Sep 1 01:49:06 2012 UTC (5 years, 1 month ago) by finetjul
Original Path: trunk/Modules
BUG: Reset clipping range of camera when loading scene

Clipping range is not a saved camera node property, so it needs to be
recomputed when being loaded.
This is particularly true when the camera position is far (>1000) from the
 focal point as the default clipping range is 0.1 -> 1000

Closes #1744

Revision 20910 - Directory Listing
Modified Fri Aug 31 22:35:41 2012 UTC (5 years, 1 month ago) by finetjul
Original Path: trunk/Modules
ENH: Add VTK demand driven pipeline to Model display nodes

Similar to what is done in the volume display nodes, it is now supported
to have a pipeline of VTK filters in the model display nodes.

Revision 20909 - Directory Listing
Modified Fri Aug 31 22:35:32 2012 UTC (5 years, 1 month ago) by finetjul
Original Path: trunk/Modules
ENH: Move PolyData from vtkMRMLDisplayableNode to vtkMRMLModelNode

vtkMRMLDisplayableNode is the base class of Model and Volume nodes, it
shouldn't have a reference to specialization of the Model node.

Revision 20908 - Directory Listing
Modified Fri Aug 31 22:31:01 2012 UTC (5 years, 1 month ago) by pieper
Original Path: trunk/Modules
ENH: implement feature for request #1876 - DICOM notification

Now series are shown in the dicom module in order of their
insertion date, so if you are receiving data periodically from
a scanner the most recent studies will be listed first.

Clicking on a series will give the option to load it.

Also a status message is displayed in the application main
window indicating when the most recent database insertion
happened.  This will be visible when new data is received, for
example via a network transaction, even when you are working
in a different module.

Revision 20903 - Directory Listing
Modified Fri Aug 31 16:15:53 2012 UTC (5 years, 1 month ago) by pieper
Original Path: trunk/Modules
ENH: fix implementation of Slicer Data Bundle writing

Rather than make a new temp scene, we update the paths
of the existing scene and restore them afterwards.  Creating
the temp scene caused problems with IDs not matching references
and this was not correctable since nodes were shared between
scene views and the original nodes (that is, remapping all the
nodes inside scene views to have the nodes they needed to
have for the databundle save caused problems for the original scene).

Fixes #2120

Revision 20897 - Directory Listing
Modified Fri Aug 31 14:10:21 2012 UTC (5 years, 1 month ago) by alexy
Original Path: trunk/Modules
BUG 2444. Renamed in UI Tractography Fiducial Seeding to Tractography Interactive Seeding

Revision 20896 - Directory Listing
Modified Fri Aug 31 00:33:58 2012 UTC (5 years, 1 month ago) by fedorov
Original Path: trunk/Modules
BUG: initilize the maximum value for spin box to a large number to address the
use case when one EditColor widget is initialized with a color node, and the
color selection needs to be propagated to a different EditColor widget that is
not aware of the color node.


Revision 20895 - Directory Listing
Modified Thu Aug 30 22:10:39 2012 UTC (5 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: issue 2379 this should fix the importing of a scene with scene views while there are scene views already in the scene - use a singleton top level scene views hiearchy node, use lazy update on the tree, respond to scene end import events. ENH: do a sanity check and reparent scene view nodes to the top level if necessary

Revision 20894 - Directory Listing
Modified Wed Aug 29 20:30:14 2012 UTC (5 years, 1 month ago) by pieper
Original Path: trunk/Modules
ENH: minimize status update during sample data download

Only report in 10% increments....

Revision 20892 - Directory Listing
Modified Wed Aug 29 17:25:25 2012 UTC (5 years, 1 month ago) by pieper
Original Path: trunk/Modules
ENH: Don't redownload the volume if there is a non-empty file in cache

TODO: would be good to compare hash of file so we could
confirm correct download.

Revision 20887 - Directory Listing
Modified Tue Aug 28 17:18:20 2012 UTC (5 years, 1 month ago) by pieper
Original Path: trunk/Modules
BUG: clear pointer before calling set macro

Still need to investigate options to avoid manual pointer
management, but for now just avoid crash.

Revision 20884 - Directory Listing
Modified Mon Aug 27 22:24:21 2012 UTC (5 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: issue 1184: don't allow dropping onto annotation nodes that are associated with a heirarchy node that doesn't allow children, this should stop nodes from disappearing because they're under hidden nodes

Revision 20883 - Directory Listing
Modified Mon Aug 27 22:16:10 2012 UTC (5 years, 1 month ago) by pieper
Original Path: trunk/Modules
BUG: fix progress dialog during dicom loads

Revision 20882 - Directory Listing
Modified Mon Aug 27 22:07:22 2012 UTC (5 years, 1 month ago) by pieper
Original Path: trunk/Modules
ENH: add an Uncheck All option to the DICOM browser

per request from Ron, Paul & Andrey

Revision 20880 - Directory Listing
Modified Mon Aug 27 21:54:15 2012 UTC (5 years, 1 month ago) by pieper
Original Path: trunk/Modules
ENH: clean up dead code in DICOM module

Remove some older optional modes (like the dicom app widget
inside the module panel) and the pre-plugin load options.

Revision 20879 - Directory Listing
Modified Mon Aug 27 21:21:30 2012 UTC (5 years, 1 month ago) by pieper
Original Path: trunk/Modules
BUG: compress dicom model reset events

Since some operations can generate huge numbers of datbaseChanged
signals, we want to ignore most of them.  This is done by scheduling
a future reset of the model and not adding any new requests if
there is one pending.

Revision 20878 - Directory Listing
Modified Mon Aug 27 20:58:54 2012 UTC (5 years, 1 month ago) by pieper
Original Path: trunk/Modules
BUG: update the name of the DICOMToNRRD converter module

This issue prevented DWI scans from loading properly.

Revision 20869 - Directory Listing
Modified Mon Aug 27 17:29:27 2012 UTC (5 years, 1 month ago) by pieper
Original Path: trunk/Modules
COMP: multivolume relies on DICOM, so disable if no DICOM

Revision 20865 - Directory Listing
Modified Mon Aug 27 14:23:18 2012 UTC (5 years, 1 month ago) by pieper
Original Path: trunk/Modules
ENH: improved SampleData progress message

Revision 20864 - Directory Listing
Modified Mon Aug 27 14:19:02 2012 UTC (5 years, 1 month ago) by pieper
Original Path: trunk/Modules
ENH: provide download feedback in SampleData

Use the report hook in urllib.

Revision 20863 - Directory Listing
Modified Mon Aug 27 01:58:56 2012 UTC (5 years, 1 month ago) by pieper
Original Path: trunk/Modules
BUG: fix for cursor management between annoation and Editor

Turn off the Interaction Mode before changing cursor so
that custom cursor is not disabled by annotation.
Note that similar change should be made to annotation
code.

Revision 20862 - Directory Listing
Modified Mon Aug 27 01:52:41 2012 UTC (5 years, 1 month ago) by pieper
Original Path: trunk/Modules
ENH: implementation of feature 2432 custom cursors in Editor

With this, there is an auto-generated cursor for each mouse tool
to remind the user what mode they are in.  This update also
allows tools to turn off the cursor during interaction so it
is easier to see the background.

Revision 20861 - Directory Listing
Modified Mon Aug 27 01:52:38 2012 UTC (5 years, 1 month ago) by pieper
Original Path: trunk/Modules
ENH: #2432 Custom cursors for editor effects

Still WIP because the background is not being painted correctly, and
the toggle erase effect does not behave right.  Otherwise the basics
are in place.

Revision 20860 - Directory Listing
Modified Fri Aug 24 22:42:23 2012 UTC (5 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: closes issue 1090 and related by adding in some widgets in the hierarchy node annotation properites widget, iterating over annotations in heirarchies to set text and glyph scale, and glyph type

Revision 20858 - Directory Listing
Modified Fri Aug 24 15:07:41 2012 UTC (5 years, 1 month ago) by fedorov
Original Path: trunk/Modules
STYLE: use 'not var' instead of 'var == None', per Steve's stylistic recommendation :)


Revision 20855 - Directory Listing
Modified Fri Aug 24 00:12:27 2012 UTC (5 years, 1 month ago) by fedorov
Original Path: trunk/Modules
ENH: added an option to specify color node, which is useful in situations when EditColor is used outside Editor


Revision 20854 - Directory Listing
Modified Thu Aug 23 23:40:08 2012 UTC (5 years, 1 month ago) by finetjul
Original Path: trunk/Modules
STYLE: Make utility function a Volumes logic method

Revision 20853 - Directory Listing
Modified Thu Aug 23 23:40:00 2012 UTC (5 years, 1 month ago) by finetjul
Original Path: trunk/Modules
BUG: VolumeRendering was broken with doing ditor split and merge

Volume Rendering display nodes have the particularity to reference
displayable nodes. This is because the Bg/Fg display node needs to
reference 2 volumes at a time.
When a volume node is copied(Editor split and merge), it copies the
reference of the display nodes which make them to be used by 2 displayable
nodes at the same time. Volume Rendering display nodes don't support it.
And it seems unlikely that any display node will ever totally support it.

Closes #2135

Revision 20848 - Directory Listing
Modified Thu Aug 23 22:44:25 2012 UTC (5 years, 1 month ago) by fedorov
Original Path: trunk/Modules
BUG: more fixes to make sure editor widget can be used outside Editor: import vtk and check for existence of helper before accessing it


Revision 20839 - Directory Listing
Modified Thu Aug 23 16:50:35 2012 UTC (5 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: issue 1811, don't lock the name and visibility entries as they can me modified from elsewhere in the module when the annotation is locked

Revision 20838 - Directory Listing
Modified Thu Aug 23 15:20:07 2012 UTC (5 years, 1 month ago) by pieper
Original Path: trunk/Modules
BUG: fix for 2414 - support 3 or 4 component vector volumes

Revision 20833 - Directory Listing
Modified Thu Aug 23 12:40:44 2012 UTC (5 years, 1 month ago) by pieper
Original Path: trunk/Modules
ENH: ensure that dicom tree matches changes in the database (#2418)

Revision 20832 - Directory Listing
Modified Thu Aug 23 12:40:42 2012 UTC (5 years, 1 month ago) by pieper
Original Path: trunk/Modules
BUG: #2418 - manage python and C++ access to the dicom database

It might be possible to remove slicer.dicomDatabase and change
all code to use slicer.app.dicomDatabase() as done in the branch
linked below.  However it's not clear how to manage reference counts.
When a ctkDICOMDatabase is instanced in python and then set in the
core application with setDICOMDatabase things are fine.  But calling
setDICOMDatabase(None) destroys the ctkDICOMDatabase even though
the PythonQt wrapper still exists.  Calling methods on the PythonQt
wrapper gracefully refuses to operate on a destroyed instance.  Until
this issue is cleared up, it's better for python to retain an instance
of the database and pass it down to the core application only when it
is known to be valid.

https://github.com/pieper/Slicer/tree/2418-dicomdb-in-core-app-remove-slicer.dicomDatabase

Revision 20830 - Directory Listing
Modified Wed Aug 22 22:06:29 2012 UTC (5 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: working on issue 2428, check return from poly data writer

Revision 20829 - Directory Listing
Modified Wed Aug 22 21:21:45 2012 UTC (5 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: issue 1600 hide the selected checkbox and label in the models module

Revision 20827 - Directory Listing
Modified Wed Aug 22 19:36:33 2012 UTC (5 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: issue 1249 use the lazy update call on the scene model, it updates the tree after a scene is loaded (some color editors were missing if loaded the knee atlas scene while in the Models module and this seems to fix it)

Revision 20824 - Directory Listing
Modified Wed Aug 22 16:45:43 2012 UTC (5 years, 1 month ago) by finetjul
Original Path: trunk/Modules
BUG: Remove assert in Volume Rendering settings panel

It's fine if the new memory can't be found in the list,
it just means the user manually typed a value

Closes #2359

Revision 20823 - Directory Listing
Modified Wed Aug 22 16:16:15 2012 UTC (5 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: expand delete and rename to work on hierarchy nodes, issue 2108

Revision 20820 - Directory Listing
Modified Wed Aug 22 15:10:37 2012 UTC (5 years, 1 month ago) by pieper
Original Path: trunk/Modules
BUG: issue 2420 - turn off editor effect when in Place mode

Track the state of the InteractionNode and respond accordingly.
Also set the state of the InteractionNode when the Editor
effect is actively using the mouse.

Revision 20817 - Directory Listing
Modified Wed Aug 22 13:18:30 2012 UTC (5 years, 1 month ago) by pieper
Original Path: trunk/Modules
BUG: better startup behavior for dicom if database does not exist

Better fix for 1969.  Now if the database directory does not exist or
cannot be opened, we prompt the user for a valid one.

Revision 20816 - Directory Listing
Modified Wed Aug 22 12:59:34 2012 UTC (5 years, 1 month ago) by pieper
Original Path: trunk/Modules
BUG: fix slicer.org hyperlink in dicom acknowledgements

Revision 20815 - Directory Listing
Modified Wed Aug 22 12:53:56 2012 UTC (5 years, 1 month ago) by pieper
Original Path: trunk/Modules
BUG: 2118 fix documentation link for Editor

Also tweak the dicom links.

Revision 20814 - Directory Listing
Modified Wed Aug 22 03:43:16 2012 UTC (5 years, 1 month ago) by finetjul
Original Path: trunk/Modules
BUG: One click activates items in color picker dialog

This makes it easier for the QtTesting to record actions.

Closes #2187

Revision 20813 - Directory Listing
Modified Tue Aug 21 21:07:40 2012 UTC (5 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: issue 1759 found that loading an old scene version with the a node with id vtkMRMLSelectionNode1 will cause an assert crash in GetNodeByID

Revision 20810 - Directory Listing
Modified Tue Aug 21 20:14:50 2012 UTC (5 years, 1 month ago) by pieper
Original Path: trunk/Modules
BUG: fixes for 2406 - DICOM initialization sequence when no settings exist

Revision 20809 - Directory Listing
Modified Tue Aug 21 20:11:25 2012 UTC (5 years, 1 month ago) by naucoin
Original Path: trunk/Modules
STYLE: add a tool tip to make case sensitive filter a bit more user friendly

Revision 20807 - Directory Listing
Modified Tue Aug 21 19:47:33 2012 UTC (5 years, 1 month ago) by fedorov
Original Path: trunk/Modules
BUG: lower the confidence if the geometry information is not available


Revision 20806 - Directory Listing
Modified Tue Aug 21 19:18:31 2012 UTC (5 years, 1 month ago) by naucoin
Original Path: trunk/Modules
BUG: working on bug issue 2375, disable ruler intersections until rewrite in Markups module

Revision 20805 - Directory Listing
Modified Tue Aug 21 15:34:01 2012 UTC (5 years, 2 months ago) by Michael.jeulinl
Original Path: trunk/Modules
ENH: Make the file type support mode more flexible

Remove the IOFileType enum and use instead a QString.

Revision 20804 - Directory Listing
Modified Mon Aug 20 23:11:49 2012 UTC (5 years, 2 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add DoubleArrays module to add DoubleArray IO support

Closes #2410

Revision 20802 - Directory Listing
Modified Mon Aug 20 23:11:43 2012 UTC (5 years, 2 months ago) by finetjul
Original Path: trunk/Modules
BUG: Fixup vtkSlicerModelsLogicAddFileTest::testAddEmptyFile

Revision 20798 - Directory Listing
Modified Mon Aug 20 22:28:29 2012 UTC (5 years, 2 months ago) by finetjul
Original Path: trunk/Modules
ENH: Make annotation point coordinates as Double QVariant and not QString

Todo: use more than 2 decimals for numbers that require it
(tweak qMRMLItemDelegate)

Closes #1810

Revision 20794 - Directory Listing
Modified Mon Aug 20 20:56:46 2012 UTC (5 years, 2 months ago) by finetjul
Original Path: trunk/Modules
BUG: Annotations file types where not set

Still not working correctly for the ROI and Ruler

Issue #1406

Revision 20792 - Directory Listing
Modified Mon Aug 20 17:46:48 2012 UTC (5 years, 2 months ago) by naucoin
Original Path: trunk/Modules
BUG: issue 1302 add mm to size label for points

Revision 20790 - Directory Listing
Modified Mon Aug 20 16:28:01 2012 UTC (5 years, 2 months ago) by finetjul
Original Path: trunk/Modules
BUG: Colors module was chaning LUT range if wider than -1024 -> 3071

The range of the spinbox widget should be updated to make sure it can
contain the new values.
Restore the module that was hidden until the issue was fixed.

Closes #2141

Revision 20789 - Directory Listing
Modified Mon Aug 20 14:45:54 2012 UTC (5 years, 2 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Update http links to 4.1 documentation

Revision 20787 - Directory Listing
Modified Mon Aug 20 13:29:18 2012 UTC (5 years, 2 months ago) by pieper
Original Path: trunk/Modules
BUG: 2408 - avoid scientific notation in DataProbe

Use approach suggested in one of the posts here:

http://stackoverflow.com/questions/2440692/formatting-floats-in-python-without-superfluous-zeros

Revision 20777 - Directory Listing
Modified Thu Aug 16 17:52:15 2012 UTC (5 years, 2 months ago) by naucoin
Original Path: trunk/Modules
COMP: remove copy/paste string error

Revision 20776 - Directory Listing
Modified Thu Aug 16 15:46:19 2012 UTC (5 years, 2 months ago) by naucoin
Original Path: trunk/Modules
STYLE: remove commented out ref to hierarchy storage node

Revision 20775 - Directory Listing
Modified Thu Aug 16 15:03:44 2012 UTC (5 years, 2 months ago) by naucoin
Original Path: trunk/Modules
COMP: clean up storage nodes to remove compilation warnings about hidden methods. 
Only the top level storage node implements WriteDataInternal, the subclasses use the home brew WriteAnnotationDataInternal. 
ENH: add return value and checking
BUG: removed the last traces of the hierarchy storage node



Revision 20774 - Directory Listing
Modified Wed Aug 15 21:47:16 2012 UTC (5 years, 2 months ago) by demian
Original Path: trunk/Modules
BUG: corrected the use of ITK space representation into the slicer on for the tractography seeding module

Revision 20771 - Directory Listing
Modified Wed Aug 15 21:07:39 2012 UTC (5 years, 2 months ago) by pieper
Original Path: trunk/Modules
BUG: gracefully handle missing dicom converter

Avoids a dialog box that doesn't go away.

Revision 20768 - Directory Listing
Modified Wed Aug 15 18:39:05 2012 UTC (5 years, 2 months ago) by finetjul
Original Path: trunk/Modules
ENH: Use checkbox to control the "Expanded" hierarchy node property

The "Expanded" property is a property of the model and not of the view.
This is why the "Collapsed/Expanded" tree view visual feedback can't be
used to control the model, it was linked to the view, not the underlying
model.

Note that the Visibility of models is still not correctly working.

Issue #2163

Revision 20764 - Directory Listing
Modified Wed Aug 15 15:10:25 2012 UTC (5 years, 2 months ago) by demian
Original Path: trunk/Modules
ENH: Changing the tractography defaults for the DICOM2FullBrainTractography workflow

Revision 20763 - Directory Listing
Modified Tue Aug 14 18:57:38 2012 UTC (5 years, 2 months ago) by millerjv
Original Path: trunk/Modules
COMP: warning on type comparison

Revision 20760 - Directory Listing
Modified Tue Aug 14 12:52:23 2012 UTC (5 years, 2 months ago) by demian
Original Path: trunk/Modules
BUG: Clarifies the use of the storable node pipeline solving bug 0002394 ( http://www.na-mic.org/Bug/view.php?id=2394 )

Revision 20756 - Directory Listing
Modified Fri Aug 10 23:18:44 2012 UTC (5 years, 2 months ago) by pieper
Original Path: trunk/Modules
ENH: re-enable full test

Revision 20755 - Directory Listing
Modified Fri Aug 10 23:11:13 2012 UTC (5 years, 2 months ago) by pieper
Original Path: trunk/Modules
ENH: Make the Editor ThresholdThreadingTest work as a module

Revision 20754 - Directory Listing
Modified Fri Aug 10 23:11:01 2012 UTC (5 years, 2 months ago) by pieper
Original Path: trunk/Modules
BUG: the loadVolume API was returning wrong type

The method is supposed to return the volumeNode, but a recent
change caused it to return a boolean instead, breaking the
API.

Revision 20753 - Directory Listing
Modified Fri Aug 10 23:10:50 2012 UTC (5 years, 2 months ago) by pieper
Original Path: trunk/Modules
ENH: add infrastructure to make editor lib test a self test

Revision 20752 - Directory Listing
Modified Fri Aug 10 23:10:38 2012 UTC (5 years, 2 months ago) by pieper
Original Path: trunk/Modules
ENH: improve reporting of test results

Use a custom string formatter and a qt information
message box for now - later we can have a better
table view of results (or something).

Revision 20751 - Directory Listing
Modified Fri Aug 10 23:10:31 2012 UTC (5 years, 2 months ago) by pieper
Original Path: trunk/Modules
ENH: improved self test skeleton

Some build-tin tests and a logic class to collect and
report test results.

Revision 20750 - Directory Listing
Modified Fri Aug 10 23:10:27 2012 UTC (5 years, 2 months ago) by pieper
Original Path: trunk/Modules
ENH: add a skeleton template for BIST (see bug 1922)

Revision 20748 - Directory Listing
Modified Fri Aug 10 17:54:26 2012 UTC (5 years, 2 months ago) by fedorov
Original Path: trunk/Modules
PERF: speed up scalar volume loading by using scalar volume storage node directly; addresses #2389


Revision 20744 - Directory Listing
Modified Fri Aug 10 13:16:34 2012 UTC (5 years, 2 months ago) by vrnova
Original Path: trunk/Modules
ENH: remove BlobDetection and other CLI modules as requested

Revision 20743 - Directory Listing
Modified Fri Aug 10 12:42:03 2012 UTC (5 years, 2 months ago) by pieper
Original Path: trunk/Modules
BUG: shorten volume names in dataprobe as needed

Addresses 1463.

Revision 20739 - Directory Listing
Modified Thu Aug 9 18:56:48 2012 UTC (5 years, 2 months ago) by pieper
Original Path: trunk/Modules
BUG: fix to fix for 2184

Fix crash due to edits being in wrong order
in previous commit. (fixes revision 20738)

Revision 20738 - Directory Listing
Modified Thu Aug 9 18:40:48 2012 UTC (5 years, 2 months ago) by pieper
Original Path: trunk/Modules
BUG: 2184 crash after multiple editor steps

It turns out that even after the python objects
go out of scope they do not get deleted if their
pipeline is still connected to the output vtkobject.
With this change we explicitly disconnect the pipeline.

Revision 20736 - Directory Listing
Modified Wed Aug 8 18:03:59 2012 UTC (5 years, 2 months ago) by pieper
Original Path: trunk/Modules
BUG: fix missing load option in dicom loadables

Account for tristate nature of checkboxes so that
the selected (boolean) value of a loadable can
be updated from the tristate value of a checkState
of a checkbox.

Revision 20735 - Directory Listing
Modified Wed Aug 8 13:55:33 2012 UTC (5 years, 2 months ago) by vrnova
Original Path: trunk/Modules
ENH: updated Decimate parameter description to match with the definition in the corresponding VTK class.

Revision 20733 - Directory Listing
Modified Wed Aug 8 13:20:39 2012 UTC (5 years, 2 months ago) by millerjv
Original Path: trunk/Modules
COMP: missing include <algorithm>

Revision 20730 - Directory Listing
Modified Tue Aug 7 23:35:10 2012 UTC (5 years, 2 months ago) by fedorov
Original Path: trunk/Modules
BUG: fix the issue when EditorWidget could not be instantiated outside Editor GUI; add a test to exercise the fixed functionality; this addressed bug #2329


Revision 20728 - Directory Listing
Modified Tue Aug 7 16:01:08 2012 UTC (5 years, 2 months ago) by millerjv
Original Path: trunk/Modules
ENH: Removed unused methods for Scalar and Headerless volumes.

Archetype method is entry point.

Revision 20727 - Directory Listing
Modified Tue Aug 7 16:00:31 2012 UTC (5 years, 2 months ago) by millerjv
Original Path: trunk/Modules
ENH: using factory methods for configuring objects for IO

Factory methods create and configure a triple of a Volume node,
a Display node, and a Storage node.

Revision 20723 - Directory Listing
Modified Fri Aug 3 21:34:36 2012 UTC (5 years, 2 months ago) by pieper
Original Path: trunk/Modules
ENH: provide better feedback about which plugin is being checked

It seems that each change to the progress dialog (text
and progress value) needs to be followed by a call to
process events or else the dialog falls behind the actual
processing and provides misleading information.

Revision 20721 - Directory Listing
Modified Wed Aug 1 22:57:06 2012 UTC (5 years, 2 months ago) by pieper
Original Path: trunk/Modules
ENH: Add support for ctkDICOMDatabase tag precaching

Squashed commit of the following:

commit 1c1e8d7de393ba8c766b219c4b5af163026b99d3
Author: Steve Pieper <pieper@isomics.com>
Date:   Wed Aug 1 18:50:13 2012 -0400

    ENH: support CTK DICOM datbase tag precaching

    Make sure both the slicer instance and the dicomAppWidget
    instance of the database have the correct tag list
    for precaching on import.

commit ba8f75f7e738efd39be223dd721b6c5cec0ada52
Author: Steve Pieper <pieper@isomics.com>
Date:   Wed Aug 1 14:40:37 2012 -0400

    ENH: adapt DICOM plugins to use pre-caching

    By exposing the tags they use, plugins can get
    better performance.

commit 359d99bd4b5cca9ac924bb34b02b39e6e949a49c
Author: Steve Pieper <pieper@isomics.com>
Date:   Tue Jul 31 14:42:41 2012 -0400

    ENH: make use of the precache feature of the dicom database

    Now each dicom plugin has the option to declare tags that will
    be of use when interpreting the dicom instances.  The database
    offers the option of pre-caching these tags during a
    database insert operation to speed up subsequent accesses.

commit 8f770c69885378bbb0b5aa4b997fd4be58a2ec5a
Author: Steve Pieper <pieper@isomics.com>
Date:   Tue Jul 31 14:39:50 2012 -0400

    BUG: fix superclass reference

    The 'super' method requires that you repeat the name
    of your class, not use the name of the superclass itself.

commit e54ee04fdfb34c145712265dc26a35e047c7b2f7
Author: Steve Pieper <pieper@isomics.com>
Date:   Mon Jul 30 16:10:12 2012 -0400

    BUG: typos and misplaced variables in dicom plugin tags

    Small debugging issues.

commit 3b7e6aa8b40333d7172e0507b97beba940299812
Author: Steve Pieper <pieper@isomics.com>
Date:   Mon Jul 30 16:04:13 2012 -0400

    ENH: Define symbolic tags in the plugin class for precaching

    Allow each DICOM plugin subclass to expose the list of
    tags that it needs to have access to for performing
    its calculations.  The application may be able to
    speed up access.

commit c5c30bb650f739e66f9f31d2d5820c91de8a8a4e
Author: Steve Pieper <pieper@isomics.com>
Date:   Sat Jul 28 11:36:46 2012 -0400

    WIP: restructuring for tag precache feature of ctkDICOMDatabase

Revision 20720 - Directory Listing
Modified Wed Aug 1 17:02:59 2012 UTC (5 years, 2 months ago) by ungi
Original Path: trunk/Modules
ENH: Compute RMS error value in the target coordinate system, not the source. Since result will be observed in the target system, it is more informative about quality.

Revision 20719 - Directory Listing
Modified Wed Aug 1 13:47:44 2012 UTC (5 years, 2 months ago) by ungi
Original Path: trunk/Modules
BUG: Fixed RMS computation.

Revision 20718 - Directory Listing
Modified Tue Jul 31 15:57:42 2012 UTC (5 years, 2 months ago) by pieper
Original Path: trunk/Modules
BUG: use the blocking form of dialog for warning message

Avoid having the dicom browser pop up in front of the warning
dialog (Qt's exec method is masked by python's exec keyword,
so use exec_).

Revision 20716 - Directory Listing
Modified Mon Jul 30 18:12:05 2012 UTC (5 years, 2 months ago) by vrnova
Original Path: trunk/Modules
ENH: added the new blob detection module

Revision 20715 - Directory Listing
Modified Mon Jul 30 18:11:46 2012 UTC (5 years, 2 months ago) by vrnova
Original Path: trunk/Modules
ENH: a blob detection CLI module. the module can be used as basis for segmentation.

Revision 20713 - Directory Listing
Modified Mon Jul 30 13:02:58 2012 UTC (5 years, 2 months ago) by pieper
Original Path: trunk/Modules
BUG: fix modality of initial dicom database prompt

Address #1969 - previously, the dicom browser would
appear in front of the dialog prompting for selection
of the database directory.  Now, user must first select
database which then gets used by browser.

Revision 20712 - Directory Listing
Modified Mon Jul 30 13:02:56 2012 UTC (5 years, 2 months ago) by pieper
Original Path: trunk/Modules
STYLE: remove experimental code from dicom data exchange

Revision 20705 - Directory Listing
Modified Fri Jul 27 15:56:07 2012 UTC (5 years, 2 months ago) by ungi
Original Path: trunk/Modules
BUG: RMS error computation fixed in case of similarity transform.

Revision 20702 - Directory Listing
Modified Fri Jul 27 15:05:24 2012 UTC (5 years, 2 months ago) by demian
Original Path: trunk/Modules
BUG: Fixed bug #0002245

Revision 20701 - Directory Listing
Modified Thu Jul 26 22:10:55 2012 UTC (5 years, 2 months ago) by pieper
Original Path: trunk/Modules
BUG: fix for 2106 level tracing crash

Check volume dimensions before creating preview polydata.

Revision 20693 - Directory Listing
Modified Wed Jul 25 09:30:04 2012 UTC (5 years, 2 months ago) by jcfr
Original Path: trunk/Modules
COMP: Fix "delete-non-virtual-dtor" warning in RayCastVolumeRenderingPropertiesWidget

Revision 20692 - Directory Listing
Modified Wed Jul 25 09:18:28 2012 UTC (5 years, 2 months ago) by jcfr
Original Path: trunk/Modules
COMP: Fix "signed/unsigned" warning in qSlicerVolumeRenderingSettingsPanel

Revision 20691 - Directory Listing
Modified Wed Jul 25 09:15:47 2012 UTC (5 years, 2 months ago) by jcfr
Original Path: trunk/Modules
COMP: Fix "delete-non-virtual-dtor" warning in qMRMLVolumePropertyNodeWidgetPrivate

Revision 20690 - Directory Listing
Modified Wed Jul 25 08:43:45 2012 UTC (5 years, 2 months ago) by jcfr
Original Path: trunk/Modules
COMP: Fix "unused-but-set-variable" warning in vtkSlicerGPURayCastMultiVolumeMapper

Revision 20689 - Directory Listing
Modified Wed Jul 25 08:37:08 2012 UTC (5 years, 2 months ago) by jcfr
Original Path: trunk/Modules
COMP: Fix "delete-non-virtual-dtor" warning in qSlicerVolumeRenderingModuleWidgetPrivate

Revision 20688 - Directory Listing
Modified Wed Jul 25 08:01:36 2012 UTC (5 years, 2 months ago) by jcfr
Original Path: trunk/Modules
COMP: Fix "unused-but-set-variable" warning in vtkSlicerGPURayCastVolumeMapper

Revision 20686 - Directory Listing
Modified Wed Jul 25 07:30:39 2012 UTC (5 years, 2 months ago) by jcfr
Original Path: trunk/Modules
ENH: Update SampleData module to work with "Recent Loaded" menu

See issue #1669 / http://na-mic.org/Mantis/view.php?id=1669

Revision 20683 - Directory Listing
Modified Tue Jul 24 22:16:19 2012 UTC (5 years, 2 months ago) by alexy
Original Path: trunk/Modules
BUG: Reverted back to rev. 20516. The changes made it worse.

Revision 20682 - Directory Listing
Modified Tue Jul 24 21:37:55 2012 UTC (5 years, 2 months ago) by alexy
Original Path: trunk/Modules
BUG: Dont recreate polydata in the tractography if it exists

Revision 20681 - Directory Listing
Modified Tue Jul 24 21:16:01 2012 UTC (5 years, 2 months ago) by alexy
Original Path: trunk/Modules
ENH: Dont recreate polydata in the tractography if it exists

Revision 20669 - Directory Listing
Modified Tue Jul 24 10:12:19 2012 UTC (5 years, 2 months ago) by jcfr
Original Path: trunk/Modules
COMP: Fix "unused-but-set-variable" warning in vtkFetchMILogic

Revision 20656 - Directory Listing
Modified Mon Jul 23 23:32:25 2012 UTC (5 years, 2 months ago) by hjohnson
Original Path: trunk/Modules
COMP: Change StartRegistration to Update

In 2006 the StartRegistration method was made unnecessary.  Since then
the recommended member function call has been Update to match the
standard ITK ProcessObject paradigm.

Revision 20653 - Directory Listing
Modified Mon Jul 23 20:20:10 2012 UTC (5 years, 2 months ago) by pieper
Original Path: trunk/Modules
ENH: implement a confidence option for dicom loadables

Since multiple plugins may be able to load a give dicom series,
plugins now have the option of specifying their confidence that
they are the 'right' plugin.  For example, an RTDOSE series may
be readable as either a scalar volume or an RTDOSE object.  If the
modality is RTDOSE, then that plugin can set the confidence to 1.0,
where the scalar volume will have the default 0.5.  Only the plugins
with the hightest confidence values will be selected by default
for the user.

Revision 20652 - Directory Listing
Modified Mon Jul 23 20:20:08 2012 UTC (5 years, 2 months ago) by pieper
Original Path: trunk/Modules
BUG: show all checked loadables at top of list

Loop was reversed so that checked state of loadables
was only sorted within a plugin rather than accross plugins.

Revision 20646 - Directory Listing
Modified Fri Jul 20 04:31:09 2012 UTC (5 years, 3 months ago) by jcfr
Original Path: trunk/Modules
STYLE: Fix indent and remove extra unused CMake code

Revision 20638 - Directory Listing
Modified Thu Jul 19 18:32:25 2012 UTC (5 years, 3 months ago) by jcfr
Original Path: trunk/Modules
COMP: Fix compile of SlicerITKv3BSplineControlPointImageFilter on MacOSX/llvm

The problem occurred on "Mac OSX 10.7.4 / llvm-g++-4.2.1"

Thanks for Stephen Aylward for contributing this patch :)


Details of the errors:

/Users/aylward/src/Slicer-Release/ITKv3/Testing/Code/Common/itkMeshSourceGraftOutputTest.cxx:153:3:
error:
      use of undeclared identifier 'GraftOutput'
  GraftOutput( filter->GetOutput() );
  ^
  this->
/Users/aylward/src/Slicer-Release/ITKv3/Testing/Code/Common/itkMeshSourceGraftOutputTest.cxx:280:11:
note:
      in instantiation of member function
      'itk::MeshSourceGraftOutputFilter<itk::Mesh<int, 3,
      itk::DefaultStaticMeshTraits<int, 3, 3, float, float, int> >,
      itk::Mesh<int, 3, itk::DefaultStaticMeshTraits<int, 3, 3, float, float,
      int> >, itk::AffineTransform<float, 3> >::GenerateData' requested here
  filter->SetTransform( affineTransform );
          ^
/Users/aylward/src/Slicer-Release/ITKv3/Code/Common/itkMeshSource.h:106:16:
note:
      must qualify identifier to find this declaration in dependent base class
  virtual void GraftOutput(DataObject *output);
               ^
27 warnings and 1 error generated.
make[2]: *** [Testing/Code/Common/CMakeFiles/itkCommonTests2.dir/itkMeshSourceGraftOutputTest.o]
Error 1
make[1]: *** [Testing/Code/Common/CMakeFiles/itkCommonTests2.dir/all] Error 2
make: *** [all] Error 2

Revision 20631 - Directory Listing
Modified Wed Jul 18 19:41:41 2012 UTC (5 years, 3 months ago) by naucoin
Original Path: trunk/Modules
BUG: fixing issue # 2079, the calculation of the widget visibility in the Helper class wasn't taking into account the slice viewer visibility calculation that the manager class was making and so over rode it

Revision 20626 - Directory Listing
Modified Sun Jul 15 20:37:23 2012 UTC (5 years, 3 months ago) by fedorov
Original Path: trunk/Modules
STYLE: correct module description


Revision 20618 - Directory Listing
Modified Fri Jul 13 12:10:01 2012 UTC (5 years, 3 months ago) by demian
Original Path: trunk/Modules
BUG: Fixed bugs when loading scenes where tracts where filtered with annotation nodes

Revision 20617 - Directory Listing
Modified Fri Jul 13 12:09:57 2012 UTC (5 years, 3 months ago) by demian
Original Path: trunk/Modules
BUG: Fixed possible crash introduced in r20538

Revision 20616 - Directory Listing
Modified Fri Jul 13 12:09:53 2012 UTC (5 years, 3 months ago) by demian
Original Path: trunk/Modules
ENH: Changed the granularity of tractography parameters in the DICOM 2 full brain tractography wizard

Revision 20614 - Directory Listing
Modified Fri Jul 13 06:27:01 2012 UTC (5 years, 3 months ago) by jcfr
Original Path: trunk/Modules
COMP: Exclude Volume module python tests if Slicer_USE_PYTHONQT is OFF

Revision 20599 - Directory Listing
Modified Tue Jul 10 23:39:09 2012 UTC (5 years, 3 months ago) by pieper
Original Path: trunk/Modules
ENH: upgrade plugins to use new ctkDICOM value access code

Centralizes access to data elements and cleans up syntax
for extracting values.

Currently CTK caches the last accessed file, but may still
thrash when depending on the order of access into the files
(iterating by elements in a file should be fast, but getting
the same element from a list of files would be slow).

Profiling will indicate where time is being spent.

Revision 20594 - Directory Listing
Modified Tue Jul 10 13:47:12 2012 UTC (5 years, 3 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Cleanup ResampleScalarVolume XML description to respect XML Schema

Revision 20592 - Directory Listing
Modified Mon Jul 9 11:38:37 2012 UTC (5 years, 3 months ago) by pieper
Original Path: trunk/Modules
BUG: fix missing icons when there is more than one editor extension

Thanks for fixing this Brad!

Missing indentation meant that only the last value
of the effect variable was being used.

Revision 20591 - Directory Listing
Modified Sun Jul 8 20:14:15 2012 UTC (5 years, 3 months ago) by pieper
Original Path: trunk/Modules
ENH: features contributed by the SlicerRT team

(Thanks Andras and all!)

Most fixes listed below were accepted as-is, however the
'Generic DICOM' reader concept requires more discussion so
it was not included in this update.

#105: Integrate DICOM import fixes into Slicer trunk
Created on: Thu, Jul 05
Reported by: lassoan
Assigned to: lassoan
Milestone: Release for AAPM2012
	Status: New
Priority: Normal (3)
Component:

Comment:
We’ve modified 3 DICOM loading related files in SlicerRT (git@github.com:SlicerRt/Slicer.git).

DICOMWidgets.py
• if any custom loader recognizes an item then uncheck the item provided by the default “Scalar Volume” loader plugin and move it to the end of the loadable list
• have a “Reader” column in the loadable list that tells the user plugin provides the item
DICOMScalarVolumePlugin.py
• prevent recognizing a DICOM file without pixel data as a valid “Scalar Volume” item (because the loading would fail anyway and we would get an error message)
• show the first file in the tooltip
DICOMPlugin.py
• there is a small bug when initializing class members

Revision 20579 - Directory Listing
Modified Fri Jul 6 01:42:04 2012 UTC (5 years, 3 months ago) by inorton
Original Path: trunk/Modules
COMP: fix compilation with ITK4

ITKV3_COMPATIBILITY is not defined until other ITK4 header is included,
therefore compilation fails at line 262 because itkAnalyzeImageIOFactory.h
is IFDEF'd out. Move to end of includes.

Revision 20578 - Directory Listing
Modified Thu Jul 5 23:15:54 2012 UTC (5 years, 3 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Cleanup ModelToLabelMap and avoid memory leak

The early return in DoIt was not deleting the vtk readers.

Revision 20569 - Directory Listing
Modified Wed Jul 4 21:45:02 2012 UTC (5 years, 3 months ago) by jcfr
Original Path: trunk/Modules
BUG: Ensure Editor module can be loaded by preventing "EditUtil" import error

Thanks to "Andras Lasso" for contributing this patch :)

See http://www.na-mic.org/Bug/view.php?id=2299

Fixes #2299

Revision 20567 - Directory Listing
Modified Wed Jul 4 15:27:34 2012 UTC (5 years, 3 months ago) by alexy
Original Path: trunk/Modules
BUG: fixed crash in tract display, better fiber node display defaults

Revision 20566 - Directory Listing
Modified Tue Jul 3 23:49:07 2012 UTC (5 years, 3 months ago) by jcfr
Original Path: trunk/Modules
ENH: Display volume loading error only when it makes sens

Created  a class named "vtkSlicerErrorSink" allowing to keep track
of error messages. These messages are either discarded if the volume
was successfully loaded. If the volume could not be loaded using the
available reader, error will be displayed.

It will probably make sens to either move that class into MRML/Core or
VTK proper vtkSlicerErrorSink. Before doing so, few iteration will be
needed to improve the associated API.

See http://www.na-mic.org/Bug/view.php?id=2268

Fixes #2268

Revision 20565 - Directory Listing
Modified Tue Jul 3 23:49:05 2012 UTC (5 years, 3 months ago) by jcfr
Original Path: trunk/Modules
ENH: Remove extra call to Modified() function in SetActiveVolumeNode

Macro "vtkSetMRMLNodeMacro" already takes care of calling "Modified()"
if required.

Revision 20564 - Directory Listing
Modified Tue Jul 3 23:49:02 2012 UTC (5 years, 3 months ago) by jcfr
Original Path: trunk/Modules
ENH: Add convenient function CreateLabelVolume that use the current scene

Revision 20563 - Directory Listing
Modified Tue Jul 3 23:49:00 2012 UTC (5 years, 3 months ago) by jcfr
Original Path: trunk/Modules
ENH: Add convenient function FillLabelVolumeFromTemplate that use the current scene

Revision 20562 - Directory Listing
Modified Tue Jul 3 23:48:58 2012 UTC (5 years, 3 months ago) by jcfr
Original Path: trunk/Modules
ENH: Add convenient function CloneVolume that use the current scene

Revision 20561 - Directory Listing
Modified Tue Jul 3 23:48:56 2012 UTC (5 years, 3 months ago) by jcfr
Original Path: trunk/Modules
STYLE: Update doxygen comment of vtkSlicerVolumesLogic to new style

Revision 20560 - Directory Listing
Modified Tue Jul 3 23:48:54 2012 UTC (5 years, 3 months ago) by jcfr
Original Path: trunk/Modules
ENH: Simplify vtkSlicerVolumesLogic::CreateLabelVolume using smart pointer

Also ensure that input parameters are all valid

See #2268 / http://www.na-mic.org/Bug/view.php?id=2268

Revision 20559 - Directory Listing
Modified Tue Jul 3 23:48:52 2012 UTC (5 years, 3 months ago) by jcfr
Original Path: trunk/Modules
ENH: Simplify vtkSlicerVolumesLogic::FillLabelVolumeFromTemplate using smart pointer

See #2268 / http://www.na-mic.org/Bug/view.php?id=2268

Revision 20558 - Directory Listing
Modified Tue Jul 3 23:48:51 2012 UTC (5 years, 3 months ago) by jcfr
Original Path: trunk/Modules
ENH: Simplify vtkSlicerVolumesLogic::CloneVolume using smart pointer

Revision 20557 - Directory Listing
Modified Tue Jul 3 23:48:48 2012 UTC (5 years, 3 months ago) by jcfr
Original Path: trunk/Modules
ENH: Simplify TranslateFreeSurferRegistrationMatrixIntoSlicerRASTo by using vtkNew

See #2268 / http://www.na-mic.org/Bug/view.php?id=2268

Revision 20556 - Directory Listing
Modified Tue Jul 3 23:48:46 2012 UTC (5 years, 3 months ago) by jcfr
Original Path: trunk/Modules
ENH: More robust vtkSlicerVolumesLogic::IsFreeSurferVolume

Check for NULL filename

See #2268 / http://www.na-mic.org/Bug/view.php?id=2268

Revision 20555 - Directory Listing
Modified Tue Jul 3 23:48:44 2012 UTC (5 years, 3 months ago) by jcfr
Original Path: trunk/Modules
ENH: Simplify and refactor code in vtkSlicerVolumesLogic::AddArchetypeVolume

Create the struct ArchetypeVolumeNodeSet having pointers to
a Node, a DisplayNode and a Scene.

Code in charge of setting up the different nodes has been factored
out into function like:
  SetupDiffusionWeightedVolumeNodeSet
  SetupDiffusionTensorVolumeNodeSet
  [...]
  SetupScalarVolumeNodeSet

The function AddArchetypeVolume will now try to read data iterating
through a vector of NodeSetsItem. A node nodeSetsItem is a composed
of both a pointer to a storage node and a ArchetypeVolumeNodeSet.

The different steps associated with the AddArchetypeVolume function can
now be clearly identified:
 1) Process loading options
 2) Initialization of the I/O mechanisms
 3) Compute volume name
 4) Initialize NodeSetsItem vector
 5) Iterate over NodeSetsItem and try to read data
 6) Remove unused data
 7) Set and observe color node

See #2268 / http://www.na-mic.org/Bug/view.php?id=2268

Revision 20554 - Directory Listing
Modified Tue Jul 3 23:48:42 2012 UTC (5 years, 3 months ago) by jcfr
Original Path: trunk/Modules
STYLE: Simplify code - vtkSmartPointer do not have to be explicitly set to NULL

From VTK documentation:

  vtkSmartPointer() => Initialize smart pointer to NULL.

Revision 20552 - Directory Listing
Modified Tue Jul 3 21:56:39 2012 UTC (5 years, 3 months ago) by pieper
Original Path: trunk/Modules
ENH: remove tcl code from main Editor module

Some singleton bookkeeping is not needed in the python
version.

Edit util can be used to access parameter node.

Revision 20551 - Directory Listing
Modified Tue Jul 3 21:56:35 2012 UTC (5 years, 3 months ago) by pieper
Original Path: trunk/Modules
ENH: remove last tcl dependencies in Editor

Corresponding methods in EditUtil are now used.

Also remove unused EditOptions classes that were in use
prior to the creation of per-effect Options classes in the
effect files themselves.

Revision 20550 - Directory Listing
Modified Tue Jul 3 17:07:23 2012 UTC (5 years, 3 months ago) by christopher.mullins
Original Path: trunk/Modules
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 - Directory Listing
Modified Mon Jul 2 21:28:10 2012 UTC (5 years, 3 months ago) by christopher.mullins
Original Path: trunk/Modules
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 20545 - Directory Listing
Modified Mon Jul 2 16:08:02 2012 UTC (5 years, 3 months ago) by alexy
Original Path: trunk/Modules
ENH: Select the tab for the only visible display out of tube/line/glyph in Advanced Tractography Display

Revision 20544 - Directory Listing
Modified Mon Jul 2 15:00:15 2012 UTC (5 years, 3 months ago) by jcfr
Original Path: trunk/Modules
BUG: Fix test condition in vtkSlicerVolumeRenderingLogicTest

The test should fail if displayNode class is different from
"vtkMRMLCPURayCastVolumeRenderingDisplayNode" or "vtkMRMLGPURayCastVolumeRenderingDisplayNode",
initially it was testing if the node class was equal to these values.

Additionally, to avoid confusion, the format of the error message should
start with:

"Line XXX - Problem with ..."

The previous format was:

"vtkSlicerVolumeRenderingLogic::CreateVolumeRenderingDisplayNode():74 failed:
0x1cac0a0 vtkMRMLCPURayCastVolumeRenderingDisplayNode"

and it leads to think that the line number was associated with the code within
vtkSlicerVolumeRenderingLogic class.

Revision 20543 - Directory Listing
Modified Mon Jul 2 15:00:13 2012 UTC (5 years, 3 months ago) by jcfr
Original Path: trunk/Modules
BUG: Ensure vtkSlicerVolumeRenderingLogicTest can find "presets.xml"

Revision 20542 - Directory Listing
Modified Mon Jul 2 05:24:32 2012 UTC (5 years, 3 months ago) by demian
Original Path: trunk/Modules
ENH: Interface improvement in the tractography display module: consistent selection of the fiber selection behaviour with the tract list

Revision 20541 - Directory Listing
Modified Mon Jul 2 04:06:53 2012 UTC (5 years, 3 months ago) by jcfr
Original Path: trunk/Modules
COMP: Fix promoted widget headers in qSlicerTractographyDisplayWidget.ui

Promoted headers are now specified using the proper case. For
example: "ctkcollapsiblegroupBox.h" instead of "ctkCollapsibleGroupBox.h"

This will fix the following compilation issue on case sensitive file system:

In file included from /home/jchris/Projects/Slicer4/Modules/Loadable/TractographyDisplay/Widgets/qSlicerTractographyDisplayWidget.cxx:5:
/path/to/Modules/Loadable/TractographyDisplay/Widgets/ui_qSlicerTractographyDisplayWidget.h:27:36: error: ctkcollapsiblegroupbox.h: No such file or directory
/path/to/Modules/Loadable/TractographyDisplay/Widgets/ui_qSlicerTractographyDisplayWidget.h:28:39: error: ctkmaterialpropertywidget.h: No such file or directory

Revision 20538 - Directory Listing
Modified Mon Jul 2 00:53:02 2012 UTC (5 years, 3 months ago) by demian
Original Path: trunk/Modules
ENH: Interface improvement in the tractography display module: consistent selection of the nodes

Revision 20537 - Directory Listing
Modified Sun Jul 1 19:48:20 2012 UTC (5 years, 3 months ago) by alexy
Original Path: trunk/Modules
ENH: Added ctk material properties widget to TractographyDisplayWidget

Revision 20536 - Directory Listing
Modified Sun Jul 1 16:35:39 2012 UTC (5 years, 3 months ago) by alexy
Original Path: trunk/Modules
ENH:Code cleanup

Revision 20535 - Directory Listing
Modified Sat Jun 30 18:17:18 2012 UTC (5 years, 3 months ago) by alexy
Original Path: trunk/Modules
ENH:Code cleanup

Revision 20532 - Directory Listing
Modified Sat Jun 30 02:59:14 2012 UTC (5 years, 3 months ago) by jcfr
Original Path: trunk/Modules
STYLE: For sake of consistency, specify module files using MODULE_NAME variables

See #2260 / http://na-mic.org/Bug/view.php?id=2260

Revision 20530 - Directory Listing
Modified Sat Jun 30 01:36:03 2012 UTC (5 years, 3 months ago) by jcfr
Original Path: trunk/Modules
STYLE: Simplify header includes in "Annotation MRMLDisplayableManager"

See #2260 / http://na-mic.org/Bug/view.php?id=2260

Revision 20529 - Directory Listing
Modified Sat Jun 30 01:35:59 2012 UTC (5 years, 3 months ago) by jcfr
Original Path: trunk/Modules
COMP: Remove ModuleTemplate and use LoadableExtensionTemplate instead

See #2260 / http://na-mic.org/Bug/view.php?id=2260

Revision 20519 - Directory Listing
Modified Fri Jun 29 15:17:33 2012 UTC (5 years, 3 months ago) by alexy
Original Path: trunk/Modules
ENH 1778. Added Simple Display widget to Tractography Display module. Fixed other classes to make it possible to inherit model and tree view.


Revision 20516 - Directory Listing
Modified Thu Jun 28 21:17:35 2012 UTC (5 years, 3 months ago) by jcfr
Original Path: trunk/Modules
BUG: Fix memory leaks associated with tractographyFiducialSeeding using vtkNew

See http://na-mic.org/Mantis/view.php?id=2162

Fixes #2162

Revision 20515 - Directory Listing
Modified Thu Jun 28 21:17:33 2012 UTC (5 years, 3 months ago) by jcfr
Original Path: trunk/Modules
STYLE: Fix indentation in qSlicerTractographyFiducialSeedingModuleWidget

See #2162 / http://na-mic.org/Mantis/view.php?id=2162

Revision 20514 - Directory Listing
Modified Thu Jun 28 20:40:21 2012 UTC (5 years, 3 months ago) by benjamin.long
Original Path: trunk/Modules
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 20511 - Directory Listing
Modified Thu Jun 28 18:16:50 2012 UTC (5 years, 3 months ago) by demian
Original Path: trunk/Modules
BUG: Fixed bug in labelmap seeding introduced in previous modification

Revision 20507 - Directory Listing
Modified Thu Jun 28 04:40:07 2012 UTC (5 years, 3 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add PLY file reader/writer for models

Revision 20505 - Directory Listing
Modified Wed Jun 27 23:05:24 2012 UTC (5 years, 3 months ago) by jcfr
Original Path: trunk/Modules
COMP: Add option Slicer_BUILD_DICOM_SUPPORT

See http://na-mic.org/Mantis/view.php?id=2271

Fixes #2271

Revision 20496 - Directory Listing
Modified Wed Jun 27 14:54:26 2012 UTC (5 years, 3 months ago) by pinter
Original Path: trunk/Modules
BUG: adding new attribute in Node inspector widget of Data module when another attribute name is selected does not overwrite the selected attribute any more; Test added for this scenario. Fixes #2258

Revision 20495 - Directory Listing
Modified Wed Jun 27 03:54:43 2012 UTC (5 years, 3 months ago) by finetjul
Original Path: trunk/Modules
BUG: Failed to restore Volume Rendering method setting

The Volume Rendering method setting was registered before the QSettings
were set to the panel, this has the drawback to not restore the value
from the settings but keep the default value.

Closes #2265

Revision 20494 - Directory Listing
Modified Wed Jun 27 00:30:52 2012 UTC (5 years, 3 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add property to qMRMLTreeView to hide "Rename" and "Delete" menu entries

In the case of the Models module, there was duplication of entries:
 - Rename
 - Delete
 - Delete Model(s)
 - Rename Multiple Models

Revision 20490 - Directory Listing
Modified Tue Jun 26 21:32:25 2012 UTC (5 years, 3 months ago) by finetjul
Original Path: trunk/Modules
BUG: ModelMaker failed with labels names containing '/'

As the model maker uses the label name (vtkMRMLColorNode::GetColorName) for
saving temporary results, when the name contained a '/' it failed to write
the model as the part before '/' was considered as a directory and not a
file name.

Revision 20489 - Directory Listing
Modified Tue Jun 26 20:10:53 2012 UTC (5 years, 3 months ago) by fedorov
Original Path: trunk/Modules
STYLE: clean up console output


Revision 20485 - Directory Listing
Modified Mon Jun 25 22:32:17 2012 UTC (5 years, 3 months ago) by jcfr
Original Path: trunk/Modules
COMP: Ensure loadable module widget are exposed to python

See http://www.na-mic.org/Bug/view.php?id=2198

Fixes #2198

Revision 20474 - Directory Listing
Modified Sun Jun 24 20:09:15 2012 UTC (5 years, 3 months ago) by finetjul
Original Path: trunk/Modules
ENH: Redesign Volume Rendering module to support additional mappers

To add a volume rendering:
 create a new vtkMRMLVolumeRenderingDisplayNode
 create a new vtkMRMLVolumeRenderingDisplayableManager
 register your display node into vtkSlicerVolumeRenderingLogic
 register your optional widget into qSlicerVolumeRenderingModuleWidget

Revision 20473 - Directory Listing
Modified Sun Jun 24 14:33:10 2012 UTC (5 years, 3 months ago) by fedorov
Original Path: trunk/Modules
BUG: make sure test fails if volume or image is invalid


Revision 20472 - Directory Listing
Modified Sun Jun 24 14:25:08 2012 UTC (5 years, 3 months ago) by fedorov
Original Path: trunk/Modules
BUG: pass first file name, not path


Revision 20471 - Directory Listing
Modified Sun Jun 24 03:22:26 2012 UTC (5 years, 3 months ago) by fedorov
Original Path: trunk/Modules
ENH: adding test for AddArchetypeVolume()


Revision 20463 - Directory Listing
Modified Fri Jun 22 15:32:04 2012 UTC (5 years, 3 months ago) by hjohnson
Original Path: trunk/Modules
COMP: Remove deprecated functions from use

In ITKv4 the itkLegacyMacro allows deprecated
functions to be easily identified.  These functions
have been replaced with their modern equivalents.

Revision 20461 - Directory Listing
Modified Fri Jun 22 15:31:58 2012 UTC (5 years, 3 months ago) by hjohnson
Original Path: trunk/Modules
COMP: Turn off the BRAINSSurface tools

The BRAINSSurface Tools are not yet ready for
public deployment.  They are currently turned
off by default.

Revision 20419 - Directory Listing
Modified Wed Jun 20 14:44:10 2012 UTC (5 years, 4 months ago) by vrnova
Original Path: trunk/Modules
ENH: new multi-volume rendering module

Revision 20406 - Directory Listing
Modified Tue Jun 19 17:53:37 2012 UTC (5 years, 4 months ago) by lorensen
Original Path: trunk/Modules
COMP: Missing NRRD_SPACE_MAX on some platform

For ITKv4, some platforms require NrrdIO.h to define
NRRD_SPACE_MAX. This patch includes NrrdIO.h if NRRD_SPACE_MAX. The
ifndef is required since NrrdIO.h does not have include blockers.



Revision 20405 - Directory Listing
Modified Tue Jun 19 17:39:03 2012 UTC (5 years, 4 months ago) by hjohnson
Original Path: trunk/Modules
COMP: Better ITKv4 and ITKv3 NRRD enumeration type

ITKv4 and ITKv3 version of team for NRRD are different
versions that require different includes.

Revision 20402 - Directory Listing
Modified Tue Jun 19 17:02:42 2012 UTC (5 years, 4 months ago) by hjohnson
Original Path: trunk/Modules
COMP: Floating point exceptions should be active

Floating point exceptions should be addressed
through algorithm modification.

Revision 20396 - Directory Listing
Modified Mon Jun 18 17:27:54 2012 UTC (5 years, 4 months ago) by jcfr
Original Path: trunk/Modules
COMP: Ensure TractographyLabelMapSeeding CLI compiles against ITKv4

Including "itkConfigure.h" ensures the macro ITK_VERSION_MAJOR is
available and prevents the following compile error from occurring:

/home/jchris/Projects/Slicer4/Modules/CLI/TractographyLabelMapSeeding/TractographyLabelMapSeeding.cxx: In function ‘int ModuleEntryPoint(int, char**)’:
/home/jchris/Projects/Slicer4/Modules/CLI/TractographyLabelMapSeeding/TractographyLabelMapSeeding.cxx:29: error: ‘itk::FloatingPointExceptions’ has not been declared

Revision 20394 - Directory Listing
Modified Mon Jun 18 07:40:41 2012 UTC (5 years, 4 months ago) by jcfr
Original Path: trunk/Modules
COMP: Update built-in CLIs to use SEMMacroBuildCLI macro

Revision 20390 - Directory Listing
Modified Mon Jun 18 06:31:36 2012 UTC (5 years, 4 months ago) by demian
Original Path: trunk/Modules
STYLE: Incorporating Julien's suggestions regarding code quality

Revision 20388 - Directory Listing
Modified Mon Jun 18 03:51:37 2012 UTC (5 years, 4 months ago) by demian
Original Path: trunk/Modules
ENH: Fixed ProveVolumeWithModel so it can read .vtk as well as .vtp model files

Revision 20387 - Directory Listing
Modified Mon Jun 18 03:20:12 2012 UTC (5 years, 4 months ago) by demian
Original Path: trunk/Modules
ENH: Updated Tractography Labelmap Seeding to be able to output VTK as well as VTP files

Revision 20386 - Directory Listing
Modified Mon Jun 18 03:19:58 2012 UTC (5 years, 4 months ago) by demian
Original Path: trunk/Modules
STYLE: Reorganized the interface of the Tractography Labelmap Seeding to make it simpler

Revision 20384 - Directory Listing
Modified Mon Jun 18 02:31:06 2012 UTC (5 years, 4 months ago) by demian
Original Path: trunk/Modules
ENH: changed TractographyLabelMapSeeding so it uses vtkITK instead of NRRD reader for the input files

Revision 20383 - Directory Listing
Modified Sun Jun 17 17:24:20 2012 UTC (5 years, 4 months ago) by demian
Original Path: trunk/Modules
ENH: Use ITK to read Tensor files enabling the reading of Nifti and all ITK supported formats

Revision 20378 - Directory Listing
Modified Sat Jun 16 21:05:03 2012 UTC (5 years, 4 months ago) by finetjul
Original Path: trunk/Modules
COMP: Fix multiple inheritance compilation error with gcc

In file included from
/home/gsharp/build/slicer-4/Slicer4/Base/QTGUI/qSlicerFileDialog.cxx:32:0:
/home/gsharp/build/slicer-4/Slicer4/Base/QTGUI/qSlicerIOOptionsWidget.h: In
member function ‘qSlicerIOOptionsPrivate* qSlicerIOOptionsWidget::d_func()’:
/home/gsharp/build/slicer-4/Slicer4/Base/QTGUI/qSlicerIOOptionsWidget.h:52:3:
error: reference to ‘d_ptr’ is ambiguous

Revision 20375 - Directory Listing
Modified Sat Jun 16 05:56:41 2012 UTC (5 years, 4 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add "Compress" option for saving MRML nodes

Some nodes might not support the "Compress" option.

Closes #986

Revision 20374 - Directory Listing
Modified Sat Jun 16 01:25:39 2012 UTC (5 years, 4 months ago) by demian
Original Path: trunk/Modules
ENH: Changed vtkWarningMacro for vtkDebugMacro in Tractographies

Revision 20371 - Directory Listing
Modified Fri Jun 15 15:24:13 2012 UTC (5 years, 4 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Fix doxygen comments with \code \endcode blocks

Revision 20368 - Directory Listing
Modified Thu Jun 14 21:26:00 2012 UTC (5 years, 4 months ago) by finetjul
Original Path: trunk/Modules
COMP: Propagate obsolete SetModifiedSinceRead to Scripts

Issue #2082

Revision 20365 - Directory Listing
Modified Thu Jun 14 20:02:17 2012 UTC (5 years, 4 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Update vtkSlicerVolumeRenderingLogic documentation

Revision 20364 - Directory Listing
Modified Thu Jun 14 19:57:47 2012 UTC (5 years, 4 months ago) by benjamin.long
Original Path: trunk/Modules
BUG: Restore previous behavior with signal "clicked" in the Editor module

Now we use the signal "currentChanged" of the selection model.

Close #2187

Revision 20360 - Directory Listing
Modified Thu Jun 14 16:15:20 2012 UTC (5 years, 4 months ago) by finetjul
Original Path: trunk/Modules
ENH: Redesign ModifiedSinceRead

ModifiedSinceRead can no longer be set externally, it's the nodes themselves that computes it based on the last time the data was stored and on the modifications.
ModifiedSinceRead is no longer a vtkMRMLNode property but a vtkMRMLStorableNode property.
The storage nodes have been cleaned-up (factorized) in the process.
At exit time, the scene is checked to see if it has been modified or if its storable nodes have been modified since read/write.

Some other changes:
Removed vtkMRMLModelNode::GetDefaultWriteFileExtension() it is a duplicate from vtkMRMLModelStorageNdoe::GetDefaultWriteFileExtension()
Removed vtkMRMLColorNode::AddColorName() as it is not used and increase code complexity
Removed vtkMRMLAnnotation*StorageNode::WriteData(vtkMRMLNode* refNode) as it was doing the same than vtkMRMLAnnotationStorageNode::WriteData(vtkMRMLNode* refNode)

Remaining issues:
The check on the modified scene is not perfect and can be fine tuned.
The loading of annotations are marking the nodes as ModifiedSinceRead but it shouldn't.
The loading of a vtkMRMLVolumePropertyNode from within a scene load incorrectly marks the node as ModifiedSinceRead


Revision 20357 - Directory Listing
Modified Wed Jun 13 23:32:47 2012 UTC (5 years, 4 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Rename "Add DICOM" menu entry into "DICOM"

Closes #1740

Revision 20355 - Directory Listing
Modified Wed Jun 13 22:39:39 2012 UTC (5 years, 4 months ago) by naucoin
Original Path: trunk/Modules
BUG: adding a test that illustrates hitting the assert at qMRMLSceneModel.cxx, line 1271: load volume, close scene will in a module that has a displayable scene model for a tree view

Revision 20352 - Directory Listing
Modified Wed Jun 13 19:10:59 2012 UTC (5 years, 4 months ago) by naucoin
Original Path: trunk/Modules
BUG: allow dragging models past the end of the tree, turn on extended selection to allow multiple models to be operated on at once.
ENH: add menu items to delete and rename multiple models at once.
To do: get dropping of multiple models working.

Related to Issue #2163


Revision 20350 - Directory Listing
Modified Tue Jun 12 23:50:49 2012 UTC (5 years, 4 months ago) by ungi
Original Path: trunk/Modules
ENH: Additional output to Fiducial Registration. RMS Error and message if input is not appropriate.

Revision 20348 - Directory Listing
Modified Mon Jun 11 19:07:49 2012 UTC (5 years, 4 months ago) by Michael.jeulinl
Original Path: trunk/Modules
BUG: 0002094. Move 3DSlicer icons into appropriate subdirectories.

Revision 20340 - Directory Listing
Modified Fri Jun 8 22:38:03 2012 UTC (5 years, 4 months ago) by hjohnson
Original Path: trunk/Modules
COMP: ITKv3 ITKv4 compilation fix.

Revision 20338 - Directory Listing
Modified Fri Jun 8 19:56:25 2012 UTC (5 years, 4 months ago) by hjohnson
Original Path: trunk/Modules
COMP:  Missing include files for teem

The files were missing, and caused compilation errors.
\#include <teem/nrrdEnums.h>
\#include <teem/ten.h>

Revision 20334 - Directory Listing
Modified Fri Jun 8 05:23:27 2012 UTC (5 years, 4 months ago) by finetjul
Original Path: trunk/Modules
ENH: Cosmetics and update for the file menu

Closes #1740

Revision 20333 - Directory Listing
Modified Fri Jun 8 04:51:13 2012 UTC (5 years, 4 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add option to save scene as Data Bundle in Save Data dialog

+ minor bugs due to previous commits
Closes #2097

Revision 20331 - Directory Listing
Modified Thu Jun 7 20:14:10 2012 UTC (5 years, 4 months ago) by finetjul
Original Path: trunk/Modules
ENH: SaveData dialog uses qSlicerFileWriters for improved scalability

Custom file writers can easily be added for each node or scene.
Options specific to scene/nodes could easily be added via the qSlicerFileWriters::options

Issue #2098

Revision 20330 - Directory Listing
Modified Thu Jun 7 20:04:51 2012 UTC (5 years, 4 months ago) by finetjul
Original Path: trunk/Modules
ENH: Split qSlicerIO into qSlicerFileReader

qSlicerFileReader is too different from qSlicerFileWriter to have their methods shared in qSlicerIO.
Add qSlicerNodeWriter, a utility class to simplify file writers

Revision 20317 - Directory Listing
Modified Mon Jun 4 15:34:18 2012 UTC (5 years, 4 months ago) by finetjul
Original Path: trunk/Modules
BUG: Disable Colors module GUI

Issue #2141

Revision 20306 - Directory Listing
Modified Fri Jun 1 17:24:04 2012 UTC (5 years, 4 months ago) by finetjul
Original Path: trunk/Modules
BUG: Fix vtkMRMLModelNode::SetAndObservePolyData when display node is not yet set and observed

Depending on when the display node was added into the scene/model, the polydata was not necessarily propagated to the display node.
vtkMRMLModelNode::UpdateScene() was removed because the polydata is now set to the display nodes by vtkMRMLModelNode::OnDisplayNodeAdded whenever a display node is added/retrieved
vtkMRMLModelNode::ProcessMRMLEvents is modified because there was a side effect in vtkMRMLModelNode::SetAndObservePolyData: the polydata was first set to the display nodes that fired a modified event observed by the model node which was resetting the polydata to its own old value (not yet set in SetAndObservePolyData) cancelling the first set.
Add utility method vtkSlicerModelsLogic::AddModel(vtkPolyData*) to shorten the creation of model node and display node.

Revision 20292 - Directory Listing
Modified Wed May 30 18:45:10 2012 UTC (5 years, 4 months ago) by benjamin.long
Original Path: trunk/Modules
ENH: Added first 2 tests using Qttesting framework

- Added new Sample Datas, used by QtTesting framework tests
- Named all buttons in SampleData module, and added function to download
files from Midas

Revision 20291 - Directory Listing
Modified Wed May 30 18:45:06 2012 UTC (5 years, 4 months ago) by benjamin.long
Original Path: trunk/Modules
ENH: Changed signal "clicked" to "activated" in Editor Module (HelperBox)

Signal "activated" is needed, by QtTesting, to avoid a faulty play back.
Updated CTK tag to update QtTesting version
 - QtTesting emits a "activated" signal even for a setCurrentIndex.

Revision 20290 - Directory Listing
Modified Wed May 30 16:13:53 2012 UTC (5 years, 4 months ago) by finetjul
Original Path: trunk/Modules
BUG: Fix sizing issue in Tractography Fiducial Seeding module

Also remove unnecessary margin around stack widget.
Closes #2093

Revision 20270 - Directory Listing
Modified Mon May 28 21:52:03 2012 UTC (5 years, 4 months ago) by jcfr
Original Path: trunk/Modules
COMP: Update code and remove VTK legacy code

This commit is a follow up of r17510. It basically include header vtkDataArray
where it needed after building VTK with VTK_LEGACY_REMOVE ON

See http://www.na-mic.org/Bug/view.php?id=2129
and http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=17510

Revision 20164 - Directory Listing
Modified Sun May 27 16:27:30 2012 UTC (5 years, 4 months ago) by jcfr
Original Path: trunk/Modules
COMP: Ensure ${cli_module}_SOURCE_DIR variable is set

Since 'project()' statement is not used anymore within CMakeLists of module,
it's important to define ${cli_module}_SOURCE_DIR so that module can reference
the source of their dependent module.

This should fix compilation error associated with module "ResampleScalarVectorDWIVolume"

See also r20160

Revision 20160 - Directory Listing
Modified Sun May 27 01:47:47 2012 UTC (5 years, 4 months ago) by jcfr
Original Path: trunk/Modules
STYLE: Module CMakeLists are now written using consistent and simple convention

MODULE_NAME_UPPER variable used systematically to define the export directive

MODULE_TITLE always specified

Module variable names now have the form "MODULE_*"

Variable build within a module are now specified using "${KIT}_*"

Extensions template and built-in module now follow the same style.

Revision 20159 - Directory Listing
Modified Sat May 26 00:33:53 2012 UTC (5 years, 4 months ago) by demian
Original Path: trunk/Modules
ENH: Added the feature to color tracts by mean orienation and by the orientation of each segment (which does not need tensor information now)

Revision 20153 - Directory Listing
Modified Fri May 25 13:15:40 2012 UTC (5 years, 4 months ago) by alexy
Original Path: trunk/Modules
BUG: 2099. Changed local variable name conflicting with member variable.

Revision 20152 - Directory Listing
Modified Thu May 24 22:49:38 2012 UTC (5 years, 4 months ago) by demian
Original Path: trunk/Modules
ENH: Improved efficiency of the modules outputting DWI images by using uncompressed images for the output by default

Revision 20151 - Directory Listing
Modified Thu May 24 22:49:33 2012 UTC (5 years, 4 months ago) by demian
Original Path: trunk/Modules
BUG: Fixed 0002062, 0001781: problem when loading and saving DWI files: 2nd part CLIs reading and writing DWI files can not be libraries

Revision 20149 - Directory Listing
Modified Thu May 24 17:30:38 2012 UTC (5 years, 4 months ago) by demian
Original Path: trunk/Modules
BUG: Guarantee that some tracts will always be displayed when loading a new tractography, even with large tractography files (typo corrected)

Revision 20148 - Directory Listing
Modified Thu May 24 16:09:07 2012 UTC (5 years, 4 months ago) by demian
Original Path: trunk/Modules
BUG: Guarantee that some tracts will always be displayed when loading a new tractography, even with large tractography files

Revision 20147 - Directory Listing
Modified Thu May 24 16:09:02 2012 UTC (5 years, 4 months ago) by demian
Original Path: trunk/Modules
ENH: Added projections of the eigenvector corresponding to the maximal eigenvalue to the main axes

Revision 20145 - Directory Listing
Modified Wed May 23 18:47:01 2012 UTC (5 years, 4 months ago) by pinter
Original Path: trunk/Modules
ENH: Fix testRename test case in qMRMLNodeAttributeTableViewTest; Fix typo; Fixes #2065

Revision 20144 - Directory Listing
Modified Wed May 23 05:51:01 2012 UTC (5 years, 4 months ago) by finetjul
Original Path: trunk/Modules
BUG: Fix qMRMLNodeAttributeTableViewTest committed by mistake in r20142

However, it now fails in testRename

Revision 20142 - Directory Listing
Modified Wed May 23 04:30:34 2012 UTC (5 years, 4 months ago) by finetjul
Original Path: trunk/Modules
ENH: Save Data dialog: Move Change Diretory for all selected in button box

It saves screen real estate to move the button in the dialog button box
Change the text of the directory button as the directory path is not important.

Issue #2098

Revision 20140 - Directory Listing
Modified Tue May 22 23:00:37 2012 UTC (5 years, 4 months ago) by pinter
Original Path: trunk/Modules
ENH: Use the concept of "_data" in every test of qMRMLNodeAttributeTableViewTest. Fixes #2065

Revision 20135 - Directory Listing
Modified Mon May 21 22:39:34 2012 UTC (5 years, 5 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add loading options to MRML Scene file

Option to clear the scene (equivalent to Load Scene) or not (equivalent to Import).
If the scene is imported, then the option Copy Cameras (enabled by default) copy the properties of the scene-to-import camera nodes into the existing nodes with the same name.
Move qSlicerSceneIO into the Data module to add an OptionsWidget to control the options.

Closes #1952

Revision 20134 - Directory Listing
Modified Mon May 21 19:30:22 2012 UTC (5 years, 5 months ago) by finetjul
Original Path: trunk/Modules
BUG: Fix unit tests following Cameras module move to be a loadable module

Revision 20132 - Directory Listing
Modified Mon May 21 19:15:21 2012 UTC (5 years, 5 months ago) by pieper
Original Path: trunk/Modules
ENH: allow bigger paint brushes

Previously the maximum paint brush size was set on the min volume
dimension (times spacing) but this was problematic for thin volumes.
Now make the max size be dependent on the max dimension.


Revision 20131 - Directory Listing
Modified Mon May 21 18:58:35 2012 UTC (5 years, 5 months ago) by finetjul
Original Path: trunk/Modules
ENH: Move Cameras module from core module to loadable module

That way it can expose a cameras logic.

Revision 20126 - Directory Listing
Modified Sun May 20 19:45:23 2012 UTC (5 years, 5 months ago) by finetjul
Original Path: trunk/Modules
BUG: vtkSlicerVolumesLogicTest1 requires a volume as 1st argument

Revision 20125 - Directory Listing
Modified Sun May 20 19:19:04 2012 UTC (5 years, 5 months ago) by finetjul
Original Path: trunk/Modules
BUG: Restore unit tests for Volumes and VolumeRendering modules

Revision 20123 - Directory Listing
Modified Sun May 20 19:16:36 2012 UTC (5 years, 5 months ago) by finetjul
Original Path: trunk/Modules
BUG: Transforms module Identity and Invert were rotating too much

Expose identity and invert for unit testing.
Closes #1980

Revision 20122 - Directory Listing
Modified Sun May 20 15:13:33 2012 UTC (5 years, 5 months ago) by alexy
Original Path: trunk/Modules
BUG: 20292. Added label map input option and UI to Fiducial Seeding Module.

Revision 20114 - Directory Listing
Modified Fri May 18 17:29:51 2012 UTC (5 years, 5 months ago) by finetjul
Original Path: trunk/Modules
COMP: Missing cassert include in vtkMRMLVolumeRenderingMultiVolumeTest

Revision 20111 - Directory Listing
Modified Fri May 18 04:30:41 2012 UTC (5 years, 5 months ago) by finetjul
Original Path: trunk/Modules
BUG: Volume IgnoreOrientation load option was unused

Different property name was given by qSlicerVolumesIOOptionsWidget.
Closes #2038

Revision 20110 - Directory Listing
Modified Fri May 18 04:08:19 2012 UTC (5 years, 5 months ago) by finetjul
Original Path: trunk/Modules
COMP: Fix compilation warnings in vtkMRMLVolumeRenderingMultiVolumeTest

Closes #2066

Revision 20109 - Directory Listing
Modified Fri May 18 00:53:45 2012 UTC (5 years, 5 months ago) by finetjul
Original Path: trunk/Modules
BUG: Revert qMRMLNodeAttributeTableViewTest::testSetAttribute original behavior

Original behavior passes since r20108

Revision 20108 - Directory Listing
Modified Fri May 18 00:37:13 2012 UTC (5 years, 5 months ago) by finetjul
Original Path: trunk/Modules
BUG: Cleanup vtkMRMLNode::SetAttribute behavior

Since r20104, ill formed tests were failing.
vtkMRMLNode::SetAttribute behavior is now better defined and tested.

Revision 20105 - Directory Listing
Modified Thu May 17 18:59:05 2012 UTC (5 years, 5 months ago) by pinter
Original Path: trunk/Modules
STYLE 2070: Using QString instead of std::string in qMRMLNodeAttributeTableView

Revision 20104 - Directory Listing
Modified Thu May 17 18:40:51 2012 UTC (5 years, 5 months ago) by pinter
Original Path: trunk/Modules
BUG 2065. Fixed qMRMLNodeAttributeTableViewTest to pass

Revision 20103 - Directory Listing
Modified Thu May 17 17:12:47 2012 UTC (5 years, 5 months ago) by pinter
Original Path: trunk/Modules
BUG: 2067. Fixed wrong merging

Revision 20102 - Directory Listing
Modified Thu May 17 15:33:26 2012 UTC (5 years, 5 months ago) by pinter
Original Path: trunk/Modules
BUG: 2063. Build warning due to unused parameter 'previousItem' fixed

Revision 20101 - Directory Listing
Modified Thu May 17 15:22:50 2012 UTC (5 years, 5 months ago) by pinter
Original Path: trunk/Modules
BUG: 2067. Fixed crash when clicking "Add" button when no node is selected

Revision 20099 - Directory Listing
Modified Thu May 17 00:26:53 2012 UTC (5 years, 5 months ago) by jcfr
Original Path: trunk/Modules
COMP: Fix qMRMLNodeAttributeTableViewTester::testSetAttribute. See #2064

The initial intent of the test is to set a null string. QByteArray(0) being
equivalent to an empty string (with the '\0'), the test has been fixed
to deal with "const char*".

See http://www.na-mic.org/Bug/view.php?id=2064

Revision 20096 - Directory Listing
Modified Wed May 16 21:30:10 2012 UTC (5 years, 5 months ago) by jcfr
Original Path: trunk/Modules
COMP: qMRMLNodeAttributeTableViewTest::testRemove  now uses "_data". Fixes #2065, #2064

See http://www.na-mic.org/Bug/view.php?id=2064
See http://www.na-mic.org/Bug/view.php?id=2065

Revision 20095 - Directory Listing
Modified Wed May 16 21:30:08 2012 UTC (5 years, 5 months ago) by jcfr
Original Path: trunk/Modules
COMP: Fix compilation error associated to qMRMLNodeAttributeTableViewTester::testSetAttribute. Fixes #2065

See http://www.na-mic.org/Bug/view.php?id=2065

Revision 20093 - Directory Listing
Modified Wed May 16 20:22:21 2012 UTC (5 years, 5 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add exhaustive test for setting attributes in qMRMLNodeAttributeTableView

The added tests are failing.

Revision 20092 - Directory Listing
Modified Wed May 16 20:20:24 2012 UTC (5 years, 5 months ago) by jcfr
Original Path: trunk/Modules
STYLE: qMRMLNodeAttributeTableViewTest - Use vtkNew and remove extra code. See #2065

See http://www.na-mic.org/Bug/view.php?id=2065

Revision 20091 - Directory Listing
Modified Wed May 16 19:27:15 2012 UTC (5 years, 5 months ago) by jcfr
Original Path: trunk/Modules
COMP: Ensure qMRMLNodeAttributeTableView can be build on Linux

Use function "QString::toStdString()" to explicitly convert to std::string

Revision 20090 - Directory Listing
Modified Wed May 16 18:58:24 2012 UTC (5 years, 5 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Cleanup vtkMRMLVolumeRenderingMultiVolumeTest

Remove unnecessary code

Revision 20089 - Directory Listing
Modified Wed May 16 17:26:02 2012 UTC (5 years, 5 months ago) by pinter
Original Path: trunk/Modules
ENH: Node attribute table added in Data module

Revision 20088 - Directory Listing
Modified Wed May 16 17:13:17 2012 UTC (5 years, 5 months ago) by jcfr
Original Path: trunk/Modules
COMP: SkullStripper being an extension, remove code to build it as built-in module.

Revision 20086 - Directory Listing
Modified Wed May 16 02:59:52 2012 UTC (5 years, 5 months ago) by finetjul
Original Path: trunk/Modules
BUG: Volume Rendering: Refresh view when a new image data is set to the volume node

When an imageData is set and observed by the volume node, ImageDataModifiedEvent is fired which is observed by the displayable manager that reconfigures the mapper and request a render.

Revision 20082 - Directory Listing
Modified Tue May 15 17:27:28 2012 UTC (5 years, 5 months ago) by finetjul
Original Path: trunk/Modules
COMP: vtkSlicerFiberBundleLogic::MaxNumberOfFibersToShowByDefault was missing

Restore r19614 overwritten by r20080

Revision 20080 - Directory Listing
Modified Tue May 15 13:32:55 2012 UTC (5 years, 5 months ago) by joe.snyder
Original Path: trunk/Modules
ENH: Merge TractographyDisplay and Tractography Modules.

Move the RegisterNodes() function from vtkSlicerTractographyLogic to vtkSlicerFiberBundleLogic
Move MRML folder from Tractography Module to TractographyDisplay
Delete the Tractography Module

Revision 20072 - Directory Listing
Modified Sat May 12 04:59:06 2012 UTC (5 years, 5 months ago) by finetjul
Original Path: trunk/Modules
ENH: Volume Rendering module now supports vtkColorTransferFunction labelmap volumes

Revision 20065 - Directory Listing
Modified Fri May 11 15:32:47 2012 UTC (5 years, 5 months ago) by pieper
Original Path: trunk/Modules
BUG: fix pathname for windows (avoid backslash)

For filePaths destined for code like ITK where backslash means
escape character, be sure to avoid using os.path.join since it
tries to be 'native' and adds backslashes.

In the modern era there is *no* commonly used computer system
that does not accept forward slashes as directory component
separater so there is no reason to use os.path.join.

Revision 20064 - Directory Listing
Modified Fri May 11 15:10:36 2012 UTC (5 years, 5 months ago) by pieper
Original Path: trunk/Modules
BUG: explicitly set the output directory for DWI conversion

Revision 20061 - Directory Listing
Modified Thu May 10 18:51:20 2012 UTC (5 years, 5 months ago) by pieper
Original Path: trunk/Modules
STYLE: fix typo in xml file (Directtory)

Revision 20058 - Directory Listing
Modified Wed May 9 22:32:46 2012 UTC (5 years, 5 months ago) by pieper
Original Path: trunk/Modules
ENH: make threshold test work as unit test subclass

Revision 20056 - Directory Listing
Modified Wed May 9 22:32:38 2012 UTC (5 years, 5 months ago) by pieper
Original Path: trunk/Modules
ENH: turn ThresholdThreading into unittest and add to ctest

Revision 20055 - Directory Listing
Modified Wed May 9 22:32:33 2012 UTC (5 years, 5 months ago) by pieper
Original Path: trunk/Modules
ENH: cleanup after test and check result values

Revision 20054 - Directory Listing
Modified Wed May 9 22:32:28 2012 UTC (5 years, 5 months ago) by pieper
Original Path: trunk/Modules
ENH: add a run-time test to replicate bug 1822

Revision 20053 - Directory Listing
Modified Wed May 9 22:32:24 2012 UTC (5 years, 5 months ago) by pieper
Original Path: trunk/Modules
ENH: refactor SampleData code for easier re-use

The logic class now allows access to download methods

Revision 20052 - Directory Listing
Modified Wed May 9 22:32:20 2012 UTC (5 years, 5 months ago) by pieper
Original Path: trunk/Modules
BUG: fix status text message

Revision 20051 - Directory Listing
Modified Wed May 9 22:32:16 2012 UTC (5 years, 5 months ago) by pieper
Original Path: trunk/Modules
STYLE: remove unneeded code

Revision 20050 - Directory Listing
Modified Wed May 9 22:32:12 2012 UTC (5 years, 5 months ago) by pieper
Original Path: trunk/Modules
BUG: set default value for label in editor parameter node

Revision 20049 - Directory Listing
Modified Wed May 9 22:32:08 2012 UTC (5 years, 5 months ago) by pieper
Original Path: trunk/Modules
ENH: add skeleton of test

Revision 20033 - Directory Listing
Modified Tue May 8 03:02:14 2012 UTC (5 years, 5 months ago) by finetjul
Original Path: trunk/Modules
BUG: Ensure nodes to remove are still valid when Restoring scene

When removing nodes one by one in vtkMRMLSceneViewNode::RestoreScene, it is
possible that the removal of a node removes another node. If that other
node is later removed by RestoreScene it must stay valid (not destructed)
to query if it has already been removed from the scene. In that case, the
node is not removed from the scene.

Revision 20026 - Directory Listing
Modified Fri May 4 18:13:16 2012 UTC (5 years, 5 months ago) by pieper
Original Path: trunk/Modules
ENH: add Vector to Scalar volume converter

Allow users to easily switch convert data loaded as stacks of bmp or
jpg files into scalar volumes for use with the Editor, VolumeRenderer
and other modules

Revision 20005 - Directory Listing
Modified Fri May 4 00:06:35 2012 UTC (5 years, 5 months ago) by pieper
Original Path: trunk/Modules
ENH: add scene bundle load option

Integrates with file dialog structure for loading or
importing

Revision 19994 - Directory Listing
Modified Thu May 3 22:48:46 2012 UTC (5 years, 5 months ago) by finetjul
Original Path: trunk/Modules
COMP: Fix signed unsigned mismatch warning in vtkSlicerModelsLogic

Revision 19993 - Directory Listing
Modified Thu May 3 22:46:59 2012 UTC (5 years, 5 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Fix typo in Transforms module documentation

Revision 19988 - Directory Listing
Modified Thu May 3 14:59:00 2012 UTC (5 years, 5 months ago) by finetjul
Original Path: trunk/Modules
ENH: Further refine the behavior of vtkMRMLDisplayableNode

When a displayable node is removed from the scene, its display nodes shall be 0 as they can't be found from the scene which is 0.

Revision 19978 - Directory Listing
Modified Wed May 2 18:31:59 2012 UTC (5 years, 5 months ago) by vrnova
Original Path: trunk/Modules
ENH: Adding test for the module

Revision 19959 - Directory Listing
Modified Mon Apr 30 23:11:21 2012 UTC (5 years, 5 months ago) by benjamin.long
Original Path: trunk/Modules
ENH: Add Qt Testing support

Expose signals/slots on some widget APIs for qttesting recording/replay

Revision 19958 - Directory Listing
Modified Mon Apr 30 21:40:57 2012 UTC (5 years, 5 months ago) by Michael.jeulinl
Original Path: trunk/Modules
ENH: Rename Slicer application classes

- Use to make distinction between inner and outer files.
- Make it more generic to be able to derive SlicerApp.
- Decouple resource usage between core and application.

Revision 19955 - Directory Listing
Modified Mon Apr 30 21:06:19 2012 UTC (5 years, 5 months ago) by pieper
Original Path: trunk/Modules
BUG: avoid turning filling label map under one remove islands case

When no islands is below the minimum size, just return from the 
tool because otherwise the thresholding code will set the entire
label map to the label value, which is not really what the user
would want in this case



Revision 19954 - Directory Listing
Modified Mon Apr 30 20:59:53 2012 UTC (5 years, 5 months ago) by pieper
Original Path: trunk/Modules
BUG: fix the RemoveIslandsEffect

Some code to was not properly ported from slicer3 to slicer4.  The
code is used to identify the 'land mass' within which the 'lake' that
has the 'islands' is located.  Now the 'islands' in the 'lake' are
removed if they are below the specified minimum size.


Revision 19951 - Directory Listing
Modified Fri Apr 27 15:08:07 2012 UTC (5 years, 5 months ago) by pieper
Original Path: trunk/Modules
ENH: save the foreground volume ID so it will remain constant as different volumes are selected for editing

Revision 19950 - Directory Listing
Modified Fri Apr 27 14:25:31 2012 UTC (5 years, 5 months ago) by pieper
Original Path: trunk/Modules
ENH: enable display of recently selected colors in editor color picker

Revision 19941 - Directory Listing
Modified Wed Apr 25 16:46:39 2012 UTC (5 years, 5 months ago) by demian
Original Path: trunk/Modules
BUG: Fixed bug introduced by weak reference handling in the DWI to Full brain tractography module and refactoring of it

Revision 19939 - Directory Listing
Modified Tue Apr 24 21:14:05 2012 UTC (5 years, 5 months ago) by naucoin
Original Path: trunk/Modules
BUG: update the visibility of the annotation in PropagateMRMLToWidget as loading invisible fiducials from a mrml file was resulting in them being visible

Revision 19937 - Directory Listing
Modified Tue Apr 24 18:23:16 2012 UTC (5 years, 5 months ago) by finetjul
Original Path: trunk/Modules
COMP: Annotations logic depends on Qt and BaseQtCore

This is a dangerous dependency. It needs more care to remove all Qt use
in vtkMRMLAnnotationsLogic.
It is not sure what is the reason why it was compiling fine before, it is
failing on a build with Slicer_USE_PYTHONQT off.

Revision 19935 - Directory Listing
Modified Tue Apr 24 16:33:44 2012 UTC (5 years, 5 months ago) by hjohnson
Original Path: trunk/Modules
ENH: Added BRAINSTransformConvert to Slicer.

Revision 19928 - Directory Listing
Modified Mon Apr 23 17:47:04 2012 UTC (5 years, 5 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Fix DTIImport and DTIExport documentation. 

Remove newlines.
Closes #1923

Revision 19926 - Directory Listing
Modified Mon Apr 23 14:45:11 2012 UTC (5 years, 5 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Remove empty CLI modules

The CLI module cleanup has been done with GIT-SVN which doesn't remove properly empty directories.

Revision 19915 - Directory Listing
Modified Fri Apr 20 17:47:06 2012 UTC (5 years, 6 months ago) by vrnova
Original Path: trunk/Modules
ENH: new CLI module wrapping itk connected component filter for segmentation work

Revision 19914 - Directory Listing
Modified Fri Apr 20 17:36:56 2012 UTC (5 years, 6 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Clean doc DTIExport XML description

Online wiki documentation (www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/DTIExport) seems to have issues with the newlines and spacings of the XML.

Revision 19913 - Directory Listing
Modified Fri Apr 20 14:08:30 2012 UTC (5 years, 6 months ago) by pieper
Original Path: trunk/Modules
BUG: don't build editor module gui when there is no main window - fix for 1895

Revision 19912 - Directory Listing
Modified Fri Apr 20 13:20:09 2012 UTC (5 years, 6 months ago) by pieper
Original Path: trunk/Modules
ENH: turn off effect when switching volumes

Avoid a condition where old values (like min/max of
radius controls or the slice node plane rotation to
acquisition spacing) will get reset when the user
re-selects the effect.

Revision 19911 - Directory Listing
Modified Fri Apr 20 13:20:07 2012 UTC (5 years, 6 months ago) by pieper
Original Path: trunk/Modules
ENH: set min radius to half pixel

Per suggestion from Brad for better per-pixel
control

Revision 19910 - Directory Listing
Modified Fri Apr 20 13:20:04 2012 UTC (5 years, 6 months ago) by pieper
Original Path: trunk/Modules
ENH: make the paint brush radius "spacing aware" (bug 1853)

Add some reasonable default behavior for adapting the size range
and default size of the paint brush based on the pixel
spacing and volume dimensions

Revision 19907 - Directory Listing
Modified Thu Apr 19 15:36:28 2012 UTC (5 years, 6 months ago) by finetjul
Original Path: trunk/Modules
ENH: Update Module Template to use a vertical spacer by default

Revision 19906 - Directory Listing
Modified Thu Apr 19 00:13:45 2012 UTC (5 years, 6 months ago) by jcfr
Original Path: trunk/Modules
COMP: Include Editor tests only if Slicer_USE_PYTHONQT_WITH_TCL is ON

This is related to commit r19879 - See http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=19879

Fixes #1919 - See http://www.na-mic.org/Bug/view.php?id=1919

Revision 19905 - Directory Listing
Modified Wed Apr 18 15:11:16 2012 UTC (5 years, 6 months ago) by demian
Original Path: trunk/Modules
BUG: Solved non-appearance of the widget in the DICOM to Full brain tractography wizard

Revision 19904 - Directory Listing
Modified Tue Apr 17 15:32:05 2012 UTC (5 years, 6 months ago) by vrnova
Original Path: trunk/Modules
STYLE: specified smaller step length for Multiplier (for segmenting small animal images).

Revision 19903 - Directory Listing
Modified Tue Apr 17 14:55:25 2012 UTC (5 years, 6 months ago) by pieper
Original Path: trunk/Modules
BUG: fix DICOM documentation

Revision 19902 - Directory Listing
Modified Tue Apr 17 14:52:41 2012 UTC (5 years, 6 months ago) by pieper
Original Path: trunk/Modules
ENH: update xml documentation for 4.1 release

Revision 19899 - Directory Listing
Modified Mon Apr 16 19:30:57 2012 UTC (5 years, 6 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Remove &amp; from Transforms module documentation 

Revision 19898 - Directory Listing
Modified Mon Apr 16 19:09:16 2012 UTC (5 years, 6 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Wrap Transforms module description with CDATA

Revision 19897 - Directory Listing
Modified Mon Apr 16 18:51:05 2012 UTC (5 years, 6 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Fix ampersand sign in Transforms module documentation

Revision 19896 - Directory Listing
Modified Mon Apr 16 18:45:07 2012 UTC (5 years, 6 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Add online documentation to Transforms module

Revision 19892 - Directory Listing
Modified Thu Apr 12 23:02:21 2012 UTC (5 years, 6 months ago) by naucoin
Original Path: trunk/Modules
STYLE: updating UI to match docs (unselect and visible were swapped at one point), update xml to match code (color box not shown in tree)

Revision 19891 - Directory Listing
Modified Thu Apr 12 22:20:54 2012 UTC (5 years, 6 months ago) by naucoin
Original Path: trunk/Modules
STYLE: point to 4.1 documentation

Revision 19879 - Directory Listing
Modified Wed Apr 11 22:27:41 2012 UTC (5 years, 6 months ago) by jcfr
Original Path: trunk/Modules
COMP: Include Editor(Lib) only if Slicer_USE_PYTHONQT_WITH_TCL is ON

* This is xplained by the Editor.py, EditOptions.py, EditColor.py,
LabelEffect.py and HelperBox.py all have dependency on 'tcl' module.

* It could also probably make sens to exclude/include just part of the
module with TCL is disabled/enabled. Such task will be left to the
maintainer of the module.

* Let's also note that having a test suite associated with the
different EditorEffect would make sens.

Revision 19811 - Directory Listing
Modified Sat Apr 7 08:41:32 2012 UTC (5 years, 6 months ago) by jcfr
Original Path: trunk/Modules
BUG: Address memory leaks associated with SlicerDICOM2FullBrainTractographyModuleGenericTest

* The first issue was related to the presence of a "circular reference"
which was preventing the ctkWorkflow from being properly garbage
collected.

By using the newly introduced module 'saferef', the call back declared
in 'full_tractography_workflow' and associated with a step can be referenced
using a weak reference and resolved when needed.

* The second issue came after the problem of circular reference has been
addressed. During python finalization, the workflow widget was dealing
with a dangling pointer to the ctkWorkflow. This was causing a crash.
By making use of QWeakPointer within the workflow widget, we can now make
sure the pointer to the workflow is in a good state.

Revision 19810 - Directory Listing
Modified Sat Apr 7 08:41:29 2012 UTC (5 years, 6 months ago) by jcfr
Original Path: trunk/Modules
COMP: Avoid confusion by removing duplicated code

* Slicelet class was declared at two locations

* Note that all the code related to Slicelet should really be factored out
and tested. May be decorators could be created.

Revision 19796 - Directory Listing
Modified Thu Apr 5 21:50:51 2012 UTC (5 years, 6 months ago) by naucoin
Original Path: trunk/Modules
BUG: when loading in Slicer3 fiducial list files, batch processing was on and it prevented the widget from being created in the assumed order. PropagateMRMLToWidget was used to set up the new widget and it wasn't setting the lock flag.

Revision 19795 - Directory Listing
Modified Thu Apr 5 21:36:44 2012 UTC (5 years, 6 months ago) by demian
Original Path: trunk/Modules
ENH: Coordinating the defaults of the tractography labelmap seeding and the fiducial seeding

Revision 19794 - Directory Listing
Modified Thu Apr 5 21:32:59 2012 UTC (5 years, 6 months ago) by demian
Original Path: trunk/Modules
BUG: Fixed bugs in the Full brain tractography workflow and added the possibility of starting from a DWI node

Revision 19790 - Directory Listing
Modified Thu Apr 5 00:46:14 2012 UTC (5 years, 6 months ago) by jcfr
Original Path: trunk/Modules
COMP: Disable "MRIBiasFieldCorrection" CLI until tests are fixed.

It resumes the windows 64-bit test associated with MRIBiasFieldCorrection are
failing for now quite some time.

The incriminated test are the following:

  MRIBiasFieldCorrection_N3_Brain2D_1 http://slicer.cdash.org/testDetails.php?test=1284620&build=13977

and

   MRIBiasFieldCorrection_N4_Brain2D: http://slicer.cdash.org/testDetails.php?test=1284621&build=13977

From mailing list archive [1]:

  MRIBiasFieldCorrection -- Probably just remove this one N4ITKBiasFieldCorrection does a much better job.

[1] http://massmail.spl.harvard.edu/public-archives/slicer-devel/2011/006988.html

Revision 19789 - Directory Listing
Modified Thu Apr 5 00:20:37 2012 UTC (5 years, 6 months ago) by jcfr
Original Path: trunk/Modules
COMP: Remove empty directory. Using git-svn option --rmdir would avoid this commit.

Revision 19788 - Directory Listing
Modified Thu Apr 5 00:17:47 2012 UTC (5 years, 6 months ago) by jcfr
Original Path: trunk/Modules
COMP: Remove "MeshContourSegmentation" CLI until tests are fixed.

* As discussed, considering the output of the module isn't reliably tested
on the different platforms, while working on the coming 4.1 release,
it has been decided to disable the module.

* Not willing to keep code that's note compiled and tested in the
repository, this one has been *removed*. Before doing so, note that
the corresponding code has been extracted and pushed into
a repository on Slicer github organization accessible using the
following URL:

  http://github.com/Slicer/MeshContourSegmentation

* When the issue will be fixed. There are two options:
  - Create an extension
  - Revert that commit and apply the bug fixes.

* It's important to consider that at some point in time the code
of the module has been moved from:

      Applications/CLI/SparseFieldLevelSetContour  (a)

   into

      Modules/CLI/SparseFieldLevelSetContour       (b)

   and then renamed into

      Modules/CLI/MeshContourSegmentation          (c)


  The current extraction will only consider the history following (c).

* Here are the step executed to be able to extract the code from the
main repository:

 1) Install git subtree module.
      - Clone https://github.com/apenwarr/git-subtree
      - Run install.sh
      - See also http://ruleant.blogspot.com/2011/04/git-subtree-module.html

 2) Create locally a bare repo that will host the extracted code
    cd ~/Projects
    mkdir MeshContourSegmentation && cd MeshContourSegmentation && git init --bare && cd..


 3) Proceed to the extraction

     git checkout master
     git subtree split --prefix=Modules/CLI/MeshContourSegmentation/ -b MeshContourSegmentation


  5) Push topic into bare repo previously created

    git remote add local-MeshContourSegmentation file:///home/jchris/Projects/MeshContourSegmentation
    git push local-MeshContourSegmentation MeshContourSegmentation:refs/heads/master

  5) After you created a project on github, push.

    cd ~/Projects/MeshContourSegmentation
    git remote add origin git@github.com:Slicer/MeshContourSegmentation.git
    git push origin master

Revision 19786 - Directory Listing
Modified Wed Apr 4 16:08:40 2012 UTC (5 years, 6 months ago) by naucoin
Original Path: trunk/Modules
BUG: disable compiling and testing the MeshContourSegmentation module until we can develop an appropriate test that can pass on all platforms, and probably turn it into an extension

Revision 19782 - Directory Listing
Modified Tue Apr 3 17:26:22 2012 UTC (5 years, 6 months ago) by pieper
Original Path: trunk/Modules
BUG: avoid unneeded warning message

Processing events that aren't explicitly handled by 
the code could lead to misleading 
messages about missing actor attributes


Revision 19781 - Directory Listing
Modified Tue Apr 3 16:39:23 2012 UTC (5 years, 6 months ago) by demian
Original Path: trunk/Modules
BUG: Fix test for qSlicerDTISliceDisplayWidget1

Revision 19775 - Directory Listing
Modified Tue Apr 3 01:18:01 2012 UTC (5 years, 6 months ago) by jcfr
Original Path: trunk/Modules
STYLE: Prevent future issue related to refactoring by referencing all MRML node from 'slicer' module.

* Doing so allow to instantiate MRML nodes specific to a
module without knowing they are associated to a given module.

* Instead of having namespace like 'modulemrml' or 'modulewidget', it could
probably make more sens to keep the classes provided by each module into
a python module named after the name of the module associated with the
considered classes.

Revision 19773 - Directory Listing
Modified Mon Apr 2 06:54:42 2012 UTC (5 years, 6 months ago) by jcfr
Original Path: trunk/Modules
BUG: Prevent crashes by not using vtkMRMLScene::CreateNodeByClass in python

As explained in commit r19772, using CreateNodeByClass could easily lead
to bugs and crashes.

See http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=19772

Revision 19767 - Directory Listing
Modified Mon Apr 2 06:30:07 2012 UTC (5 years, 6 months ago) by jcfr
Original Path: trunk/Modules
ENH: Update python tests to use new "exit" mechanism

* To indicate an error, regular python Exception can be used.

* For more details refer to r19581.
See http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=19581

Revision 19747 - Directory Listing
Modified Thu Mar 29 15:10:05 2012 UTC (5 years, 6 months ago) by pieper
Original Path: trunk/Modules
ENH: refactor IJK plane calculation for easier re-use


Revision 19746 - Directory Listing
Modified Thu Mar 29 14:47:44 2012 UTC (5 years, 6 months ago) by pieper
Original Path: trunk/Modules
BUG: handle evaluation of DICOM file with invalid position information

In some sample DICOM RT datasets from the SlicerRt project files
contain ImagePositionPatient tags that are empty.  I believe this
is invalid according to the DICOM spec, but we catch that case anyway
and provide a warning to the user.



Revision 19745 - Directory Listing
Modified Thu Mar 29 14:12:28 2012 UTC (5 years, 6 months ago) by demian
Original Path: trunk/Modules
BUG: Fixed behaviour not allowing to select color by a scalar in tractographies when there is no tensor data

Revision 19724 - Directory Listing
Modified Wed Mar 28 16:05:25 2012 UTC (5 years, 6 months ago) by naucoin
Original Path: trunk/Modules
BUG: Smooth parameter was missing an upper limit, slider extended to 32k. DOC: expanded tool tip to define what Smooth parameter means depending on filter type

Revision 19716 - Directory Listing
Modified Tue Mar 27 18:58:37 2012 UTC (5 years, 6 months ago) by pieper
Original Path: trunk/Modules
BUG: detect and warn user if dicom files in database do not exist on disk

Revision 19710 - Directory Listing
Modified Mon Mar 26 22:11:47 2012 UTC (5 years, 6 months ago) by naucoin
Original Path: trunk/Modules
BUG: working on bug 1812, but point to the 4.0 pages as the 4.1 pages aren't ready yet

Revision 19697 - Directory Listing
Modified Sat Mar 24 18:54:43 2012 UTC (5 years, 6 months ago) by pieper
Original Path: trunk/Modules
ENH:  change radius calculation mode for paint quickset

Per feedback from Ron radius is now set based on
the min spacing dimension.

Also added some tool tips describing the behavior

Revision 19691 - Directory Listing
Modified Fri Mar 23 23:16:14 2012 UTC (5 years, 6 months ago) by finetjul
Original Path: trunk/Modules
ENH: restore change to enum from string of ModifiedEvent for vtk 5.10 compatibility

This reverts commit r19679 which was reverting r19670.

Revision 19684 - Directory Listing
Modified Thu Mar 22 08:13:30 2012 UTC (5 years, 7 months ago) by jcfr
Original Path: trunk/Modules
COMP: Allow extension to include testing macros.

* Split CMake/TestingMacros.h into MRML/Core/{vtkMRMLCoreTestingMacros, vtkMRMLDebugLeaksMacro}

* MRML/Core being a directory already included, when building extension
the header providing the testing macro will be found.

* Also split the macro allowing to consider leaks as error into "vtkMRMLDebugLeaksMacro.h"

Revision 19679 - Directory Listing
Modified Wed Mar 21 22:14:16 2012 UTC (5 years, 7 months ago) by pieper
Original Path: trunk/Modules
BUG: revert change to enum from string of ModifiedEvent for vtk 5.10 compatibility

Revision 19677 - Directory Listing
Modified Wed Mar 21 21:16:23 2012 UTC (5 years, 7 months ago) by jcfr
Original Path: trunk/Modules
COMP: Minimize confusion by using the shared library wrapper provided by SlicerExecutionModel

Revision 19676 - Directory Listing
Modified Wed Mar 21 19:24:41 2012 UTC (5 years, 7 months ago) by pieper
Original Path: trunk/Modules
BUG: turn of threading in threshold until bug 1822 is resolved

Revision 19674 - Directory Listing
Modified Wed Mar 21 18:40:58 2012 UTC (5 years, 7 months ago) by pieper
Original Path: trunk/Modules
BUG: fix for issue 1818 (clear modified-since-read flag on newly read data

Revision 19672 - Directory Listing
Modified Wed Mar 21 13:29:09 2012 UTC (5 years, 7 months ago) by pieper
Original Path: trunk/Modules
BUG: fix for bug 1757 (radius consistency in Paint)

Need to check the parameter node when first setting up
the paint cursor (not just when node changes)

Revision 19670 - Directory Listing
Modified Wed Mar 21 08:42:53 2012 UTC (5 years, 7 months ago) by jcfr
Original Path: trunk/Modules
COMP: Improve robustness of the code by using vtk.vtkCommand.ModifiedEvent instead of string "ModifiedEvent"

* Assuming the code is tested, doing so will allow to enforce
valid event are used by avoiding misspelled  error associated to event
specified as string.

Revision 19668 - Directory Listing
Modified Tue Mar 20 20:48:58 2012 UTC (5 years, 7 months ago) by naucoin
Original Path: trunk/Modules
STYLE: removing status message printing out temp dir

Revision 19667 - Directory Listing
Modified Tue Mar 20 20:39:46 2012 UTC (5 years, 7 months ago) by naucoin
Original Path: trunk/Modules
BUG: update the baseline model for the mesh contour segmentation test, MeshContourSegmentationTestCompare passing locally now

Revision 19665 - Directory Listing
Modified Tue Mar 20 15:51:00 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
BUG: Potential crash in Volume Rendering module

Revision 19662 - Directory Listing
Modified Tue Mar 20 08:15:28 2012 UTC (5 years, 7 months ago) by jcfr
Original Path: trunk/Modules
COMP: Minimize confusion and improve readability by consistently using ".toLatin1()"

* There were occurrences of:
   .toLatin1().data()
   .toStdString().c_str()
   .toAscii().data()

these ones have been replaced with the shorter and equivalent form ".toLatin1()"

* The function qPrintable() is also used to print a QString within a std stream.

Revision 19655 - Directory Listing
Modified Mon Mar 19 07:02:07 2012 UTC (5 years, 7 months ago) by jcfr
Original Path: trunk/Modules
COMP: Avoid confusion by defining SIMPLE_TEST macro only once.

* Consistently set the variable KIT within the Testing/Cxx/CMakeLists.txt of
each library.

* Fix name inconsistency. See #1615

Revision 19641 - Directory Listing
Modified Sun Mar 18 13:39:32 2012 UTC (5 years, 7 months ago) by pieper
Original Path: trunk/Modules
BUG: add file omitted from last commit - fix dicom browser issue reported by Andrey

Revision 19639 - Directory Listing
Modified Sat Mar 17 22:02:27 2012 UTC (5 years, 7 months ago) by pieper
Original Path: trunk/Modules
BUG: make window smaller and resizable to fit on laptop screen

Based on feedback from Andras, make window resizable to fit
on target screen size.  Remove extra thumbnail preview
window to save space and avoid redundancy.  Give other
widgets smaller default size.



Revision 19638 - Directory Listing
Modified Sat Mar 17 21:48:06 2012 UTC (5 years, 7 months ago) by pieper
Original Path: trunk/Modules
BUG: fix case where dicom dialog gets stuck behind main window

Since the DICOM window was a dialog of the mainWindow and progress
dialogs from ctk and slicer are/were parented to the dicomApp
or mainWindow they there could be a race condition when the 
progress dialog was dismissed.  Also, users (Andras) did not like
the modal behavior of the dialog.  To fix these the window
is not a toplevel and slicer progress dialogs are relative to 
this.  This also allows the window to be kept open during 
other operations.



Revision 19633 - Directory Listing
Modified Fri Mar 16 22:32:34 2012 UTC (5 years, 7 months ago) by demian
Original Path: trunk/Modules
BUG: badly commited file

Revision 19632 - Directory Listing
Modified Fri Mar 16 22:28:13 2012 UTC (5 years, 7 months ago) by demian
Original Path: trunk/Modules
BUG: Fixed SEGFAULT when assigning and empty vtkPolyData to a FiberBundleNode

Revision 19630 - Directory Listing
Modified Fri Mar 16 20:19:57 2012 UTC (5 years, 7 months ago) by demian
Original Path: trunk/Modules
BUG: The data probe widget can handle NaNs now

Revision 19625 - Directory Listing
Modified Fri Mar 16 00:46:05 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
COMP: Fix unused variable warnings in ExtractSkeleton

Revision 19622 - Directory Listing
Modified Thu Mar 15 23:34:51 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
BUG: Crash in DicomToNrrdConverter when trying to access DiffusionVectors line 1995

Revision 19620 - Directory Listing
Modified Thu Mar 15 22:33:12 2012 UTC (5 years, 7 months ago) by pieper
Original Path: trunk/Modules
STYLE: remove print statements

Revision 19618 - Directory Listing
Modified Thu Mar 15 18:59:42 2012 UTC (5 years, 7 months ago) by pieper
Original Path: trunk/Modules
BUG: fix min size option of RemoveIslands (reported by Matt Jolley)

Revision 19617 - Directory Listing
Modified Thu Mar 15 16:58:22 2012 UTC (5 years, 7 months ago) by naucoin
Original Path: trunk/Modules
BUG: resolving bug 1810, the column numbers were off by one so the points table wasn't updating the correct coordinates

Revision 19616 - Directory Listing
Modified Thu Mar 15 16:25:11 2012 UTC (5 years, 7 months ago) by naucoin
Original Path: trunk/Modules
BUG: closing bug 1811, unify the property dialog lock/unlock to enable/disable on enter depending on lock state of annotation, and on toggle of lock

Revision 19614 - Directory Listing
Modified Wed Mar 14 22:37:33 2012 UTC (5 years, 7 months ago) by demian
Original Path: trunk/Modules
ENH: Improving the tractography subsampling

Revision 19613 - Directory Listing
Modified Wed Mar 14 22:37:27 2012 UTC (5 years, 7 months ago) by demian
Original Path: trunk/Modules
ENH: Fixing the color orientation problem from the interface and not the display node, window/level issue now (bug 0001679)

Revision 19612 - Directory Listing
Modified Wed Mar 14 19:34:48 2012 UTC (5 years, 7 months ago) by pieper
Original Path: trunk/Modules
ENH: add callback on mouse over to chart view

Revision 19611 - Directory Listing
Modified Wed Mar 14 18:58:12 2012 UTC (5 years, 7 months ago) by demian
Original Path: trunk/Modules
COMP: Fixed uninitialized variable warnings

Revision 19608 - Directory Listing
Modified Wed Mar 14 18:45:50 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
ENH: Upgrade documentation to 4.1

Revision 19607 - Directory Listing
Modified Wed Mar 14 18:24:42 2012 UTC (5 years, 7 months ago) by demian
Original Path: trunk/Modules
ENH: Got rid of the workaround used in r19085 as now the
ctkVTKDataSetArrayComboBox allows to select which kinds of attributes
are permitted to use

Revision 19606 - Directory Listing
Modified Wed Mar 14 18:05:40 2012 UTC (5 years, 7 months ago) by demian
Original Path: trunk/Modules
ENH: Fixing the color orientation problem from the interface and not the display node (bug 0001679)

Revision 19604 - Directory Listing
Modified Wed Mar 14 18:05:29 2012 UTC (5 years, 7 months ago) by demian
Original Path: trunk/Modules
STYLE: Unifying DT scalar invariant combo box population for fibers and DT volumes

Revision 19599 - Directory Listing
Modified Wed Mar 14 03:42:42 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Fix order of header inclusion in TractographyLabelMapSeeding

Headers must be grouped by toolkit and listed in alphabetical order

Revision 19595 - Directory Listing
Modified Wed Mar 14 01:14:31 2012 UTC (5 years, 7 months ago) by jcfr
Original Path: trunk/Modules
COMP: Headers referenced in qSlicerTractographyFiducialSeedingModule.ui are case-sensitive

* Working on windows where the filesystem is case insensitive doesn't make
it easy to avoid such issue ... some interesting reading:
http://support.microsoft.com/?scid=kb%3Ben-us%3B817921&x=9&y=4

Revision 19591 - Directory Listing
Modified Tue Mar 13 22:10:36 2012 UTC (5 years, 7 months ago) by pieper
Original Path: trunk/Modules
BUG: remove legacy code - remove EffectSWidget default creation that casused mac crash

Revision 19589 - Directory Listing
Modified Tue Mar 13 21:40:37 2012 UTC (5 years, 7 months ago) by alexy
Original Path: trunk/Modules
ENH 1684. Updated UI and defaults for Fiducial and Label Seeding so they look similar

Revision 19588 - Directory Listing
Modified Tue Mar 13 19:58:06 2012 UTC (5 years, 7 months ago) by naucoin
Original Path: trunk/Modules
BUG: annotation nodes in a scene view were having their control points modified when the main scene annotations were modified, since the Copy call didn't copy the vtkPolyData. ReleaseData is commented out since it caused the new poly data to be invalid. Added a test that I wrote that passes with this change (with leaks).

Revision 19587 - Directory Listing
Modified Tue Mar 13 18:34:26 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
BUG: Volume Rendering: Synchronize with Volumes is on toggled signal, not on checkstate changed

There is nothing wrong with the checkBoxToggled signal, but there was a
problem when unchecking the button, the volume was still synchronized because
it didn't uncheck the checkbox.

Revision 19586 - Directory Listing
Modified Tue Mar 13 18:34:24 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Add comments on the popup double slider in Volumes module

Revision 19584 - Directory Listing
Modified Tue Mar 13 16:17:54 2012 UTC (5 years, 7 months ago) by demian
Original Path: trunk/Modules
ENH: Changed the labelmap seeding to use vtkSmartPointers

Revision 19577 - Directory Listing
Modified Tue Mar 13 01:43:36 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
COMP: Initialize A,B,C,D,E,F,G,H before use in Volume Rendering

Warning at compile time:
vtkSlicerFixedPointVolumeRayCastCompositeGOHelper.cxx:492:3: warning: 'A[0]' may be used uninitialized in this function [-Wuninitialized]
vtkSlicerFixedPointVolumeRayCastCompositeGOHelper.cxx:492:3: warning: 'B[0]' may be used uninitialized in this function [-Wuninitialized]
...

Revision 19576 - Directory Listing
Modified Tue Mar 13 00:15:40 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
BUG: DicomToNrrdConverter crashes when nStride > 1

With SIEMENS image, the bValues array is of size nSlice/nStride bvalues.
Crash in DicomToNrrdConverter test.
Still some errors remaining:
In .../Slicer4-Debug/ITKv3/Utilities/gdcm/src/gdcmSerieHelper.cxx, line 663, function bool gdcm::SerieHelper::ImagePositionPatientOrdering(gdcm::FileList*)
File: .../Slicer4/Testing/Data/Input/DWIDicom/MR_0004_1621.dcm Distance: 29.4915 position is not unique

Revision 19575 - Directory Listing
Modified Mon Mar 12 21:17:16 2012 UTC (5 years, 7 months ago) by pieper
Original Path: trunk/Modules
ENH: pure-python implementation of editor module

ENH: add stub of draw effect

More work in progress for conversion of core
editor functionality from tcl to python

ENH: further migration of editor effects to new design

Make a functioning paint effect as an editor builtin

BUG: disconnect pipeline when making label volume

This allows modified events on the label map to trigger
render without pulling original pipeline.

EHN: more porting of Paint Effect

Fix LabelEffect options gui and parameter node
settings for threshold paint, etc.

Hook up undo/redo for paint effect.

ENH: remove 'embedded' mode and clean up code

Per discussion with Danielle at 2012 Winter
Project Week, embedded mode is no longer needed and
we can accomplish our goals with editor extensions
and other methods.

Also remove some other dead code and comments.

EHN: work in progress for new editor

ENH: further editor porting and helper methods

ENH: code refactor and porting for DrawEffect in Editor

Porting to python and better distinction between tool and
logic classes with better abstraction of LabelEffect superclass
to handle rasterization tasks.

BUG: minor porting syntax differences

Tcl to python issues and naming convention change from
EditOptions to Options/Tool/Logic effect convention.

BUG: fixes to Label and Draw effects

better allocation of work between superclass and subclass
and new it actually works.

BUG: fix draw effect

- button release detected
- visibility fixed on enter/leave
- delete with 'x' key fixed

BUG: avoid crash in threaded routine

Make sure the thread is terminated before allowing
destructor to complete

BUG: fix smudge mode in new paint tool

ENH: remove workaround for updating other slice views

After paint, a call to labelNode.Modified() is enough
to trigger a scheduleRender in all other slice views

BUG: Fix typos in util methods

also clean up style of arg list

ENH: port editor's threshold effect to python

BUG: fixes for undo/redo buttons and gui creation

BUG: fix logic of undo/redo to store only specified number of steps

BUG: fix setting threshold paint from thresholdeffect

ENH: port rectangle effect to python

ENH: add level tracing python port

(still some debugging to do)

BUG: fix level tracing preview and apply

Add scheduleRender and transform correct points

BUG: fix crash in level tracing

Avoid case where one pixel difference in xy space
mapped to same ijk pixel leading to abmiguity in
the definition of extraction plane.

Use an offset value that is the max size of screen space,
but catch the case where we map back to the same
pixel.

ENH: fix pan/zoom while level trace is active

BUG: observe middle mouse button for pan in level tracing

ENH: add a scope option for all effects

If the effect defines a custom list of scopeOptions from
the Effect's list of availableScopeOptions then
a combobox will be displayed to give the user the option
of scope contexts.  This controls the input and output volume
behavior for the effect (still being ported)

EHN: Port of Erode effect and related fixes to class hierarchy

ENH: add dilate effect and fix up morphology

Now erode and dilate working as expected with mrml,
undoRedo, etc.

ENH: add ChangeLabelEffect

ENH: add MakeModelEffect

BUG: restrict morphology operations to scope of 'All'

Really no convenient way to have the operation apply only
to the visible region since it does not get applied
with respect to a slice.

Real solution for these would be to give a scope option of
'Window' in which case the EffectOptions would present a
combo box of the current views and the user could select
the one to apply the operation in - add this to the TODO list.

BUG: use the class name in the parameter node

ENH: add new effects

Add to the __init__.py, the CMakeLists.txt and to the
EditBox.

ENH: adopt explicit declaration of connections for guis

By adding the connections list to each class instance it is
possible for users of the class to explicitly turn off the connection
before updating the widget values.  This avoids having
updateMRMLFromGUI calls interfering with the updating
of the gui itself.

Label and Paint have been updated with this behavior, other
effects to follow.

ENH: switch more effects to use the connections list

Includes other minor debugging fixes too

STYLE: better method names: now (dis)connectWidgets

was (dis)connectConnections

ENH: add RemoveIslands and IdentifyIslands effects

STYLE: better comment

ENH: add converted save island effect

ENH: remove unused widgets and fix undo/redo for save island

ENH: add ChangeIslandEffect

Finishes out porting of core effects

ENH: detect missing model maker module and provide error dialog

ENH: port GrowCut to new effect architecture

GrowCut no longer inherits from PaintEffect - instead
users will use ordinary tools to draw gestures and
then invoke the grow cut.  If they want to edit the
gestures they can use Undo.

Note: Still needs some debugging in the apply logic
of growCut

STYLE: remove some dead code (pauseEffect)

BUG: fix status message call

ENH: improve label name and set default step for range

Per feedback from Sonia, the step size now adapts to the
scalar range of the background data

BUG: turn off effect when leaving the module

BUG: avoid crash in GrowCut by ensuring segmentated data is valid

BUG: fix grow cut effect

Now all effects have been ported and the editor invokes
only the pure-python versions of the code.

ENH: reorganize icons for better flow

Now growcut is near erode and dilate, which it is somehow
similar to.  Make Model is at the end, since it is often
the final step.

Revision 19574 - Directory Listing
Modified Mon Mar 12 21:11:00 2012 UTC (5 years, 7 months ago) by pieper
Original Path: trunk/Modules
ENH: new undo/redo implementation

Create a dedicated util class to oganize and manage
the undo and redo lists.

Revision 19573 - Directory Listing
Modified Mon Mar 12 20:52:36 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add option for synchronization mode in Volume Rendering

There are 2 ways to synchronize the volume rendering transfer functions
with the Volumes module: Using the threshold information or not.
When not using the threshold information, use the window level range and
don't ramp down after the upper limit is reached, stay with an opaque
opacity instead.

Closes #1612

Revision 19572 - Directory Listing
Modified Mon Mar 12 20:01:24 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
BUG: Crash when untransforming a non transformable node in Transforms module

When a transform is loaded from disk, the order of initialization in the Transforms module prevented the RootNode of the loaded transforms node to be set because the MRML scene wasn't set at the time the transform node was made current (when the node selector was getting its scene set). The fix here is to set the mrml scene of the transformable and transformed scene tree views before the node selector.
Closes #1803

Revision 19571 - Directory Listing
Modified Mon Mar 12 18:40:33 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
BUG: Transforms module: rename "Revert" button into "Invert"

Revert is confusing as it implies that it "cancel" last actions, it doesn't mean matrix inversion.
Closes #1802

Revision 19569 - Directory Listing
Modified Mon Mar 12 16:21:36 2012 UTC (5 years, 7 months ago) by demian
Original Path: trunk/Modules
BUG: Fix window and level problems in DTI scalar visualization when
coloring by orientation

Revision 19568 - Directory Listing
Modified Mon Mar 12 16:21:31 2012 UTC (5 years, 7 months ago) by demian
Original Path: trunk/Modules
ENH: Added DTI import/export tools

Revision 19567 - Directory Listing
Modified Mon Mar 12 16:21:27 2012 UTC (5 years, 7 months ago) by demian
Original Path: trunk/Modules
ENH: Reorganized the diffusion menu

Revision 19561 - Directory Listing
Modified Sat Mar 10 16:59:35 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Remove useless code in qSlicerPresetComboBox and vtkMRMLVolumeArchetypeStorageNode

Revision 19560 - Directory Listing
Modified Sat Mar 10 16:58:32 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
COMP: Remove various warnings

Unused variable
Third party warnings
Doxygen warnings

Revision 19559 - Directory Listing
Modified Sat Mar 10 06:25:12 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
COMP: BSplineToDeformationField, CLIs and Brainstools must be ON for EMSegment to work

By depending on Slicer_BUILD_BRAINSTOOLS, it indirectly depends on Slicer_BUILD_CLI and Slicer_BUILD_CLI_SUPPORT.

Revision 19558 - Directory Listing
Modified Sat Mar 10 00:05:21 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
BUG: Don't delete last annotation node twice

Bug was already there but got active as a side effect of r19555
Closes #1799

Revision 19556 - Directory Listing
Modified Fri Mar 9 23:13:20 2012 UTC (5 years, 7 months ago) by jcfr
Original Path: trunk/Modules
STYLE: Improve readability by consistently using "virtual" qualifier

* This particular commit applies to "dependencies()" method associated to modules

Revision 19555 - Directory Listing
Modified Fri Mar 9 22:22:41 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
ENH: Extract annotations logic into separate library: vtkSlicerAnnotationModuleLogic

This allows other modules to depends on it. Module's communication is only done via logics, not Qt widgets.

Revision 19548 - Directory Listing
Modified Fri Mar 9 00:41:02 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
BUG: Be smarter about "Single File" auto check beahvior.

Some dicom files contain . in their name (e.g. 1.12.1233.234325234.12313213132121.dcm)
Their base name should then be: 1.12.1233.234325234.12313213132121.

Revision 19547 - Directory Listing
Modified Thu Mar 8 23:15:53 2012 UTC (5 years, 7 months ago) by naucoin
Original Path: trunk/Modules
BUG: needs to call superclass enter to set flag so doesn't hit assert on exit

Revision 19546 - Directory Listing
Modified Thu Mar 8 22:03:43 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
BUG: Display new volume rendering when changing current volume to an existing volume

When the display node doesn't exist, it is created and made current.
But if the display node already exists, the displayable manager doesn't know it's the new current volume, call modified on it to trigger its display.
Closes #1790

Revision 19545 - Directory Listing
Modified Thu Mar 8 22:00:30 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
ENH: Don't fire unnecessary Modified event when creating display node

Regroup StartModify()/EndModify() to call Modified only once.


Revision 19543 - Directory Listing
Modified Thu Mar 8 19:35:15 2012 UTC (5 years, 7 months ago) by pieper
Original Path: trunk/Modules
BUG: fix crash reported by Sonia - setting color on a fiber node with missing display nodes

Revision 19533 - Directory Listing
Modified Wed Mar 7 19:55:01 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
BUG: Assert when leaving Tractography Fiducial Seeding

For each qSlicerAbstractModuleWidget::enter() must match one
 qSlicerAbstractModuleWidget::exit. Here qSlicerAbstractModuleWidget::enter()
was never called, but qSlicerAbstractModuleWidget::exit() was called.
Closes #1793

Revision 19530 - Directory Listing
Modified Wed Mar 7 00:15:36 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
COMP: Fix compilation warnings, loss of precision

Revision 19529 - Directory Listing
Modified Wed Mar 7 00:15:01 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
BUG: Inconsistent DLL linkage in MeshContourSegmentation

When the module has been renamed (r19175), the EXPORT variable hasn't been renamed accordingly.

Revision 19521 - Directory Listing
Modified Tue Mar 6 16:56:50 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
COMP: Some Qt versions don't expose their private headers (part 2)

Revision 19520 - Directory Listing
Modified Tue Mar 6 16:51:24 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
COMP: Some Qt versions don't expose their private headers

Qt that are "installed" not "build" don't come with private headers.
This makes the preset tooltip preview don't work on Qt <4.7

Revision 19519 - Directory Listing
Modified Tue Mar 6 16:10:31 2012 UTC (5 years, 7 months ago) by naucoin
Original Path: trunk/Modules
BUG: don't remove nodes if the node removed event comes when the scene is closing, as the scene is handling removal of all nodes

Revision 19517 - Directory Listing
Modified Tue Mar 6 05:55:44 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
COMP: Fix typo in qSlicerPresetComboBoxTest1

Revision 19516 - Directory Listing
Modified Tue Mar 6 04:30:27 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
BUG: Display base64 preview of presets in Volume Rendering module

With Qt 4.6.3 (Windows 64bits), the base64 previews didn't show up in tool tips.

Revision 19515 - Directory Listing
Modified Tue Mar 6 04:28:49 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add unit test for qSlicerPresetComboBox

Revision 19514 - Directory Listing
Modified Mon Mar 5 21:48:14 2012 UTC (5 years, 7 months ago) by pieper
Original Path: trunk/Modules
BUG: partial fix for #1788 - raise the color select window when clicking on the button

Revision 19508 - Directory Listing
Modified Mon Mar 5 03:29:40 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
BUG: DICOM2FullBrainTractography was failing because it couldn't call DiffusionWeightedVolumeMasking CLI

DiffusionWeightedMasking was renamed in r19189 into DiffusionWeightedVolumeMasking.
Closes #1786

Revision 19507 - Directory Listing
Modified Sun Mar 4 16:16:04 2012 UTC (5 years, 7 months ago) by pieper
Original Path: trunk/Modules
ENH: don't select DWI option by default

Since there is ambiguity in the heuristic to detect DICOM series
that may be DWI, don't select the option by default and instead
make the user select it explicitly.

For example, a GE SPRG (T1 scalar scan) contains all the tags
associated with DWI, even though it is not a DWI series.
0x0043, 0x1039,
0x0019, 0x10bb,
0x0019, 0x10bc,
0x0019, 0x10bd,

Revision 19506 - Directory Listing
Modified Sun Mar 4 15:11:17 2012 UTC (5 years, 7 months ago) by pieper
Original Path: trunk/Modules
ENH: move persistence checkbox into dialog

Makes more sense this way (Ron's suggestion)

Revision 19504 - Directory Listing
Modified Sat Mar 3 21:33:27 2012 UTC (5 years, 7 months ago) by naucoin
Original Path: trunk/Modules
BUG: backing out changes to make hierarchy nodes storable (bug 1717) as it's not stable enough for the release

Revision 19502 - Directory Listing
Modified Sat Mar 3 19:19:32 2012 UTC (5 years, 7 months ago) by naucoin
Original Path: trunk/Modules
STYLE: fix copy/paste and typo errors in comments

Revision 19492 - Directory Listing
Modified Fri Mar 2 01:54:10 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
ENH: Set minimum height to scene view in Data module

Revision 19490 - Directory Listing
Modified Fri Mar 2 00:15:27 2012 UTC (5 years, 7 months ago) by pieper
Original Path: trunk/Modules
ENH: improvements to dicom based on user feedback (Andras)

Option to keep dicom browser persistent across modules

Updated CTK to include progress dialog for import

Cache to avoid re-parsing dicom files to display load options



Revision 19488 - Directory Listing
Modified Thu Mar 1 15:33:54 2012 UTC (5 years, 7 months ago) by pieper
Original Path: trunk/Modules
ENH: reorganize dicom dialog based on user feedback

Move the tree widget and other tools all into the same 
top level window so they are more logically grouped while
still giving more real estate for browsing.  Also make this 
able to be opened and closed from within the dicom module.



Revision 19482 - Directory Listing
Modified Thu Mar 1 02:33:58 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
BUG: Memory leak in the scene views module dialog

Revision 19481 - Directory Listing
Modified Thu Mar 1 02:33:56 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
ENH: Avoid "flickering" when scene view dialog is opened to edit node

The dialog was first opened as if it is "taking a scene view" then it
it set to edit the node. It leaves enough time to see the change of state
by the user.
Fix is to setup the panel before it is shown.

Side fix: make the dialog modeless (block the user interactions until the
dialog is accepted/rejected). There is no reason to keep it on (or it needs
more feature.)
rejected() and accepted() already hide() the dialog automatically, no need
to manually do it.

Revision 19478 - Directory Listing
Modified Thu Mar 1 01:22:48 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add vtkSlicerModelsLogicTest, a test for vtkSlicerModelsLogic

Revision 19477 - Directory Listing
Modified Thu Mar 1 01:20:35 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
BUG: Assert when model failed to load

The qMRMLSceneModel was complaining that a node was removed twice.
Because the models logic automatically removes the display/storage nodes
when the model is removed from the scene  (r16764, issue #1170)
When the model fails to be loaded, don't remove the display and storage
nodes as they will be automatically be removed in OnMRMLSceneNodeRemoved

Remove the IsBatchProcessing() test: if it skips the auto removal, it
would need to keep track to which display nodes to remove when the batch
processing is over.

Closes #1769

Revision 19474 - Directory Listing
Modified Wed Feb 29 22:45:49 2012 UTC (5 years, 7 months ago) by fedorov
Original Path: trunk/Modules
BUG: change API to enable setting of parameters from python


Revision 19473 - Directory Listing
Modified Wed Feb 29 22:30:33 2012 UTC (5 years, 7 months ago) by fedorov
Original Path: trunk/Modules
BUG: fixing bug 1764

The problem was caused by the following. When the scene closes, parameter node
used by CropVolume is removed. The new node has never been created, since it
is done in setMRMLScene(). To resolve this, I added observer for SceneEndClose
event, where I initialize a new parameter node. In the process of fixing this,
the API of the parameter node has been simplified so that only IDs, not
pointers to the actual nodes are kept. ChangeTracker module needs to be
updated to account for this change.


Revision 19466 - Directory Listing
Modified Wed Feb 29 16:56:51 2012 UTC (5 years, 7 months ago) by naucoin
Original Path: trunk/Modules
BUG: get rid of the qt error on exit since the widget destructor was called before the event observation was removed

Revision 19465 - Directory Listing
Modified Wed Feb 29 16:12:47 2012 UTC (5 years, 7 months ago) by naucoin
Original Path: trunk/Modules
BUG: fixing bug 1758 so that the tree displays properly when loading a scene while in the models module

Revision 19463 - Directory Listing
Modified Wed Feb 29 00:09:58 2012 UTC (5 years, 7 months ago) by jcfr
Original Path: trunk/Modules
STYLE: Help string associated with loadable and scripted module will match slicer version.

* This has been done by relying on Slicer_VERSION_MAJOR and Slicer_VERSION_MINOR
within the loadable module and using 'slicer.app.majorVersion' and 'slicer.app.minorVersion'
within the scripted module.

* Ideally, we could define a small meta langage including special string
like: '<WIKIURL>" "<VERSION>" "<MODULENAME>", "<CONTRIBUTOR1>", ... that could
be used. the module manager would take of the substituation so that
the correct is rendered.

Revision 19462 - Directory Listing
Modified Tue Feb 28 21:38:59 2012 UTC (5 years, 7 months ago) by naucoin
Original Path: trunk/Modules
BUG: add missing test for the annotation hierarchy storage nodes

Revision 19461 - Directory Listing
Modified Tue Feb 28 21:38:22 2012 UTC (5 years, 7 months ago) by naucoin
Original Path: trunk/Modules
BUG: when reading in a list of annotations, make sure it's not hidden and is in the annotations hierarchy correctly

Revision 19460 - Directory Listing
Modified Tue Feb 28 21:37:37 2012 UTC (5 years, 7 months ago) by naucoin
Original Path: trunk/Modules
BUG: disable ruler nodes in a list file until get it reading properly

Revision 19458 - Directory Listing
Modified Tue Feb 28 20:21:50 2012 UTC (5 years, 7 months ago) by pieper
Original Path: trunk/Modules
ENH: workaround for mac, where dialogs don't stay on top of the main window so we explicitly call raise_() when needed

Revision 19454 - Directory Listing
Modified Tue Feb 28 03:28:12 2012 UTC (5 years, 7 months ago) by pieper
Original Path: trunk/Modules
ENH: improvements to DICOM Module

ENH: Enable export to study option with context menu in data tree:
- supports export of volumes and whole scene (new feature - not well tested)
- support re-import of scenes from DICOM files using (also could be buggy)
  plugin mechanism
- TODO: enable plugins to provide custom export behavior

ENH: popup is now a more normal dialog that can be moved
and does not go away when you move your mouse out of it

ENH: made lodables list wider for readability

TODO: add back an option to look at dicom headers

ENH: volume names now include series number as prefix

ENH: loadable options are now sorted numerically

ENH: new progress dialog when organizing series
TODO: organized data should be cached for efficiency

TODO: this commit includes some code for an experimental Study Browser

BUG: fix for changed dicom writing module name



Revision 19451 - Directory Listing
Modified Tue Feb 28 01:47:00 2012 UTC (5 years, 7 months ago) by naucoin
Original Path: trunk/Modules
COMP: not using the transform just yet, so remove the warning

Revision 19450 - Directory Listing
Modified Tue Feb 28 01:40:38 2012 UTC (5 years, 7 months ago) by naucoin
Original Path: trunk/Modules
ENH: Support reading a list of annotations from a single file, bug 1717

* Make the hierarchy nodes storable (storable and transformable methods need to be tested further! ApplyTransform TBD)
* Add the annotation hierarchy storage node to the IO widget
* Skip Read/Write in the storage nodes if the nodes are in a hierarchy
* Wrote utility methods to read from an open file



Revision 19445 - Directory Listing
Modified Mon Feb 27 19:15:01 2012 UTC (5 years, 7 months ago) by pieper
Original Path: trunk/Modules
BUG: fix attribute error warning when wrong widget type is detected

Revision 19444 - Directory Listing
Modified Mon Feb 27 17:35:44 2012 UTC (5 years, 7 months ago) by lorensen
Original Path: trunk/Modules
BUG: Test that uses vtkNRRDReader fails with floating point exception

ITKv4 enables floating point exception testing. Tests that use
vtkNRRDReader must disable floating point exceptions to avoid floating
point overflow.



Revision 19406 - Directory Listing
Modified Sun Feb 26 22:21:44 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add icon to the DICOM module

Icon designed by Wendy.
Ideally, it should use the icon in Scripts/Resources/Icons/DICOM.png

Revision 19405 - Directory Listing
Modified Sun Feb 26 22:21:32 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add icon to the View Controllers module

Icon designed by Wendy

Revision 19404 - Directory Listing
Modified Sun Feb 26 22:21:20 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add icon to the Slicer Welcome module

Icon designed by Wendy.

Revision 19401 - Directory Listing
Modified Sun Feb 26 20:35:13 2012 UTC (5 years, 7 months ago) by jcfr
Original Path: trunk/Modules
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 19400 - Directory Listing
Modified Sun Feb 26 19:21:22 2012 UTC (5 years, 7 months ago) by haehn
Original Path: trunk/Modules
ENH: Add the WebGLExport.py module as work-in-progress.

Revision 19390 - Directory Listing
Modified Sat Feb 25 22:05:28 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
BUG: Crash in Volume Rendering when changing layout

Don't observe vtkObjects with vtkSetAndObserveMRMLNodeEventsMacro. Only
vtkMRMLNodes are supported (see vtkMRMLAbstractLogic::OnMRMLNodes...)
Bug introduced in r19350

It's ok to comment the observations because they are not yet being used.
Will have to be fixed when the new event observation mechanism is in place.

Closes #1641

Revision 19382 - Directory Listing
Modified Sat Feb 25 06:29:12 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
BUG: Crash at scene view restore of Volume Rendering

The rule is: "Don't use AddObserver with a callback command."
Closes #1744

Revision 19377 - Directory Listing
Modified Fri Feb 24 22:36:20 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add --testing launcher argument

By being in testing mode, it uses different settings than user settings.

Revision 19375 - Directory Listing
Modified Fri Feb 24 20:42:08 2012 UTC (5 years, 7 months ago) by pieper
Original Path: trunk/Modules
BUG: add callback to turn off dicom model for listener

The onListenerToAddFile callback was being added if
the listener was started by the button, but not when
started automatically on startup

Revision 19374 - Directory Listing
Modified Fri Feb 24 20:42:04 2012 UTC (5 years, 7 months ago) by pieper
Original Path: trunk/Modules
BUG: handle space in dicom directory name for listener

Revision 19370 - Directory Listing
Modified Fri Feb 24 17:53:24 2012 UTC (5 years, 7 months ago) by naucoin
Original Path: trunk/Modules
ENH: add a test to load a scene containing a ruler, trying to track down a crash on mac

Revision 19364 - Directory Listing
Modified Fri Feb 24 04:52:31 2012 UTC (5 years, 7 months ago) by jcfr
Original Path: trunk/Modules
COMP: qSlicerCropVolumeModule.cxx - Add missing semicolon

Revision 19363 - Directory Listing
Modified Fri Feb 24 04:28:59 2012 UTC (5 years, 7 months ago) by jcfr
Original Path: trunk/Modules
ENH: Contributor field of XML module description and *Module.cxx are now consistent.

* The list of contributor should be specified using the following syntax:

  Firstname1 Lastname1 ([SubOrg1, ] Org1), Firstname2 Lastname2 ([SubOrg2, ]Org2)


* Organization should be referenced without the "Inc.", "Kitware" instead of "Kitware Inc.",
"Isomics" instead of "Isomics Inc."

* By using a consistent syntax, it will be possible to retrieve/associate
 the logo of the organization easily.

Revision 19355 - Directory Listing
Modified Thu Feb 23 19:31:34 2012 UTC (5 years, 7 months ago) by joe.snyder
Original Path: trunk/Modules
ENH: Update documentation strings to 4.0 Links

Change the helptext/documentation url to point to the 4.0 module help rather than the 3.6

Revision 19353 - Directory Listing
Modified Thu Feb 23 19:04:05 2012 UTC (5 years, 7 months ago) by jcfr
Original Path: trunk/Modules
COMP: Remove empty directory.

Revision 19352 - Directory Listing
Modified Thu Feb 23 19:01:53 2012 UTC (5 years, 7 months ago) by jcfr
Original Path: trunk/Modules
COMP: Remoce unnused code associated to ZeroCrossingBasedEdgeDetectionImageFilter

Ron: If I remember correctly, its ok to remove.

Lauren O'Donnell: Yes it's okay to delete entirely. It was the project
of a student at a programming week and was never fully completed.
That said, it may work to some extent... But much cleaner to just
remove it entirely.

Revision 19351 - Directory Listing
Modified Thu Feb 23 15:34:58 2012 UTC (5 years, 7 months ago) by vrnova
Original Path: trunk/Modules
STYLE: updated template function calling style

Revision 19345 - Directory Listing
Modified Thu Feb 23 01:54:07 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
ENH: Enable cropping in VolumeRendering module when displaying crop ROI

Revision 19343 - Directory Listing
Modified Wed Feb 22 22:26:47 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
ENH: Initial volume rendering scalar opacity transfer function shall be a linear ramp

Add UseLinearRamp to control the shape of the scalar opacity function when
copying the Volumes display threshold into the volume rendering display node.

Closes #1612,

Revision 19340 - Directory Listing
Modified Wed Feb 22 20:22:56 2012 UTC (5 years, 7 months ago) by jcfr
Original Path: trunk/Modules
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 19339 - Directory Listing
Modified Wed Feb 22 20:20:55 2012 UTC (5 years, 7 months ago) by vrnova
Original Path: trunk/Modules
ENH: added output type selection with short type as default

Revision 19338 - Directory Listing
Modified Wed Feb 22 19:34:55 2012 UTC (5 years, 7 months ago) by vrnova
Original Path: trunk/Modules
BUG: use int instead of float for DICOM writing

Revision 19335 - Directory Listing
Modified Wed Feb 22 18:37:58 2012 UTC (5 years, 7 months ago) by vrnova
Original Path: trunk/Modules
BUGFIX: added missing dependencies() function

Revision 19334 - Directory Listing
Modified Wed Feb 22 18:13:00 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
ENH: Register factories and scan directories only once.

Only module names (QString) can be used as method/slot parameters. No module
pointer directly.

Move module registration/instantiation/loading in a unique factory manager class.
qSlicerModuleManager is a placeholder for module specific actions with the scene
and the application: "Edit properties...", setCurrentModule, ...

Add modulesToIgnore property to prevent modules from being loaded for
performance (and clarity) reasons.

Revision 19332 - Directory Listing
Modified Wed Feb 22 17:40:14 2012 UTC (5 years, 7 months ago) by vrnova
Original Path: trunk/Modules
ENH: new multi-volume rendering module

Revision 19328 - Directory Listing
Modified Wed Feb 22 16:00:34 2012 UTC (5 years, 7 months ago) by vrnova
Original Path: trunk/Modules
BUGFIX: change data type from short to float for bright MRI images

Revision 19322 - Directory Listing
Modified Tue Feb 21 18:03:09 2012 UTC (5 years, 7 months ago) by millerjv
Original Path: trunk/Modules
ENH: commenting out debug statements

Revision 19318 - Directory Listing
Modified Tue Feb 21 15:59:56 2012 UTC (5 years, 7 months ago) by finetjul
Original Path: trunk/Modules
BUG: Fix CLI ExtractSkeleton and MeshContourSegmentation

When their XML description was asked, noise was printing before the xml.
It produced error for the XML parser that tries to read the output

Revision 19313 - Directory Listing
Modified Sun Feb 19 03:05:01 2012 UTC (5 years, 8 months ago) by finetjul
Original Path: trunk/Modules
ENH: Collapse by default the display section in the Models module

per Ron's request during SLC AHM 2012

Revision 19312 - Directory Listing
Modified Sun Feb 19 03:04:58 2012 UTC (5 years, 8 months ago) by finetjul
Original Path: trunk/Modules
BUG: Shrink the required width for the Models module

Module widgets can't have a width larger than 500px.

Revision 19308 - Directory Listing
Modified Sat Feb 18 20:27:38 2012 UTC (5 years, 8 months ago) by pieper
Original Path: trunk/Modules
ENH: add a memory tracking window

Simple window to periodically check the physical and
virtual memory status of the system.

Revision 19306 - Directory Listing
Modified Fri Feb 17 23:13:04 2012 UTC (5 years, 8 months ago) by naucoin
Original Path: trunk/Modules
ENH: some speed improvements for when deleting lots of fiducials: use batch processing state on the scene, check for batch processing state before requesting a render, remove the remove node event from the logic's list of events as it doesn't do anything with it

Revision 19305 - Directory Listing
Modified Fri Feb 17 23:07:11 2012 UTC (5 years, 8 months ago) by fedorov
Original Path: trunk/Modules
BUG: fix from J2, see context here:
http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/007770.html


Revision 19303 - Directory Listing
Modified Fri Feb 17 19:45:28 2012 UTC (5 years, 8 months ago) by millerjv
Original Path: trunk/Modules
ENH: new color tables for charts based on paper by Stephen Few

Revision 19302 - Directory Listing
Modified Fri Feb 17 17:50:19 2012 UTC (5 years, 8 months ago) by pieper
Original Path: trunk/Modules
BUG: native mac dialog isn't working on mac

Use the qt provided dialog box to avoid issue with save mode
not working correctly on mac.

This sequence does not show any dialog on Lion and Qt 4.7.4
(and probably other mac platforms)

>>> d = qt.QFileDialog()
>>> d.acceptMode = 1
>>> d.show()

Revision 19301 - Directory Listing
Modified Thu Feb 16 23:40:35 2012 UTC (5 years, 8 months ago) by naucoin
Original Path: trunk/Modules
BUG: bug 1713, get rid of the hard coding of comparing selected count against the number of columns, as it tends to change and so break being able to delete hierarchies

Revision 19300 - Directory Listing
Modified Thu Feb 16 23:19:28 2012 UTC (5 years, 8 months ago) by alexy
Original Path: trunk/Modules
BUG 1684. Set parameters of the Tractography Label Map Seeding module to be similar to Tractography Fiducial Seeding

Revision 19297 - Directory Listing
Modified Thu Feb 16 17:57:50 2012 UTC (5 years, 8 months ago) by alexy
Original Path: trunk/Modules
BUG 1685. Re-added event processing from annotation nodes that was removed in rev 18435

Revision 19293 - Directory Listing
Modified Wed Feb 15 19:17:05 2012 UTC (5 years, 8 months ago) by finetjul
Original Path: trunk/Modules
BUG: qSlicerColorsModule shall not crash without Application logic

Revision 19291 - Directory Listing
Modified Tue Feb 14 22:25:53 2012 UTC (5 years, 8 months ago) by naucoin
Original Path: trunk/Modules
BUG: for now, turn off fitSizeToVisibleIndexes on the hierarchy tree view so that can drag and drop past the visible fiducials

Revision 19286 - Directory Listing
Modified Tue Feb 14 20:02:04 2012 UTC (5 years, 8 months ago) by naucoin
Original Path: trunk/Modules
ENH: Add imported fiducial list files to their own hierarchy, named from the fiducial list storage node name line, bug report 1715.

Revision 19285 - Directory Listing
Modified Tue Feb 14 18:24:41 2012 UTC (5 years, 8 months ago) by finetjul
Original Path: trunk/Modules
BUG: Revert accidental commit in Volume Rendering module widget

Revert commit r19263
Closes #1721

Revision 19284 - Directory Listing
Modified Tue Feb 14 18:23:28 2012 UTC (5 years, 8 months ago) by naucoin
Original Path: trunk/Modules
ENH: associate label volumes with the scalar volume from which they're created. Print out the attributes in PrintSelf

Revision 19282 - Directory Listing
Modified Tue Feb 14 17:13:21 2012 UTC (5 years, 8 months ago) by naucoin
Original Path: trunk/Modules
ENH: add measurement unit to label

Revision 19279 - Directory Listing
Modified Mon Feb 13 20:53:39 2012 UTC (5 years, 8 months ago) by finetjul
Original Path: trunk/Modules
BUG: Set vtkSlicerColorLogic to vtkSlicerApplicationLogic

vtkSlicerColorLogic was not propagated to chart views because the logic
was not set to the vtkMRMLApplicationLogic which wasn't notifying
qSlicerApplication that the logic was changed which wasn't setting the
new color logic to the chart widgets via qMRMLLayoutManager.

Revision 19276 - Directory Listing
Modified Mon Feb 13 16:50:28 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
STYLE: In CLI description, 'description' and 'acknowledgment' tags are wrapped using CData

* Doing so allow to embed HTML tag within the XML description.

* Using the previously escaped version where '<p>' was written like '&lt;p&gt;'
was also valid but less easy to read and maintain.

* See https://en.wikipedia.org/wiki/CDATA#CDATA_sections_in_XML

Revision 19273 - Directory Listing
Modified Sun Feb 12 21:56:12 2012 UTC (5 years, 8 months ago) by finetjul
Original Path: trunk/Modules
STYLE: vtkMRMLColorLogic can't reference file color nodes

Those files are only known by vtkSlicerColorLogic
(in Base/Logic/Resources).

Revision 19272 - Directory Listing
Modified Sun Feb 12 21:56:07 2012 UTC (5 years, 8 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add vtkMRMLColorLogic::GetDefaultChartNodeID

Revision 19268 - Directory Listing
Modified Thu Feb 9 23:55:40 2012 UTC (5 years, 8 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Move Slicer color logic into Colors module

Revision 19264 - Directory Listing
Modified Thu Feb 9 01:22:35 2012 UTC (5 years, 8 months ago) by finetjul
Original Path: trunk/Modules
BUG: Don't resize force Volumes module panel to be as wide as volume name

The a volume has a very long name, it was enforcing the active volume
node selector to be very wide which was forcing the module panel to be
very wide as well.

Closes #1649

Revision 19263 - Directory Listing
Modified Wed Feb 8 22:37:31 2012 UTC (5 years, 8 months ago) by Michael.jeulinl
Original Path: trunk/Modules
ENH: Add controls to the reformat module

- Lock Normal to Camera menu action
- Change SetLockNormalToCamera PushButton to a ctkCheckBoxPushButton
- Normalize the normal from the node
- Change Reformat module icon

Revision 19262 - Directory Listing
Modified Wed Feb 8 21:31:22 2012 UTC (5 years, 8 months ago) by pieper
Original Path: trunk/Modules
BUG: remove scripted observer that caused crash on exit

This observer wasn't being triggered anyway so there was no way to
know when to remove it.  To really fix this issue we need to have the 
storage nodes and the remote IO code generate start/end/progress events
that can be tracked.



Revision 19261 - Directory Listing
Modified Wed Feb 8 21:06:23 2012 UTC (5 years, 8 months ago) by millerjv
Original Path: trunk/Modules
ENH: use label names for x-axis on bar charts with lookup tables and categorical data

Rotate label text if there are more than 6 label names being used.

Turned off the legend on the LabelStatistics module.

Revision 19260 - Directory Listing
Modified Wed Feb 8 20:42:45 2012 UTC (5 years, 8 months ago) by pieper
Original Path: trunk/Modules
BUG: explicit setting of the label name is no longer needed since the auto-naming of new nodes has been fixed

Revision 19256 - Directory Listing
Modified Wed Feb 8 00:07:27 2012 UTC (5 years, 8 months ago) by pieper
Original Path: trunk/Modules
ENH: new features for LabelStatistics

* Column in table view showing the color of the index
* Tool tips with the name of the structure
* Option to chart different values from the table
* Option to ignore the background value when creating the chart 
  (since it is often so large as to dominate the other values)



Revision 19253 - Directory Listing
Modified Tue Feb 7 22:03:13 2012 UTC (5 years, 8 months ago) by millerjv
Original Path: trunk/Modules
ENH: allow a ColorNode to be assigned to a Chart or to an Array

Added a default color table for Slicer Charts, GenericChartColors.txt

ColorNodes can be assigned to a chart which will assign the colors for
each series.

ColorNodes can be assigned to an array which for bar charts (and perhaps
someday pie charts) will allow each bar to be colored differently.

Revision 19250 - Directory Listing
Modified Tue Feb 7 18:31:29 2012 UTC (5 years, 8 months ago) by pieper
Original Path: trunk/Modules
STYLE: minor cleanups

Revision 19249 - Directory Listing
Modified Tue Feb 7 16:09:12 2012 UTC (5 years, 8 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Rename qSlicerModuleTest1.py.in into qSlicerModuleGenericTest.py.in
 (part 2)

SVN doesn't support a file move and edit in the same commit

Revision 19248 - Directory Listing
Modified Tue Feb 7 16:08:05 2012 UTC (5 years, 8 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Rename qSlicerModuleTest1.py.in into qSlicerModuleGenericTest.py.in

Move testing of Modules/Scripted/Scripts into a Python subdirectory

Revision 19247 - Directory Listing
Modified Tue Feb 7 15:40:00 2012 UTC (5 years, 8 months ago) by pieper
Original Path: trunk/Modules
BUG: another contributor/contributors issue

Revision 19245 - Directory Listing
Modified Tue Feb 7 15:29:56 2012 UTC (5 years, 8 months ago) by fedorov
Original Path: trunk/Modules
ENH: update contributors`


Revision 19243 - Directory Listing
Modified Tue Feb 7 15:17:45 2012 UTC (5 years, 8 months ago) by pieper
Original Path: trunk/Modules
BUG: fix renaming typo

Revision 19242 - Directory Listing
Modified Tue Feb 7 05:25:32 2012 UTC (5 years, 8 months ago) by finetjul
Original Path: trunk/Modules
COMP: Fix transforms module testing

qSlicerTransformsModuleTest1 was missing.

Revision 19241 - Directory Listing
Modified Tue Feb 7 05:20:58 2012 UTC (5 years, 8 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Rename qSlicerAbstractCoreModule::contributor to contributors

Revision 19239 - Directory Listing
Modified Tue Feb 7 04:01:16 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
COMP: Use "std" version of vector, string and sstream.

* This class are now consistenly used accross the code base. There is no
more mix of both vtksys and std headers.

* See http://www.vtk.org/pipermail/vtk-developers/2012-February/010806.html

* Details of the updates:

 #include <vtksys/ios/sstream> -> #include <sstream>
 vtksys_ios::ostringstream     -> std::ostringstream

 #include <vtksys/stl/string> -> #include <string>
 vtksys_stl::string           -> std::string


 #include <vtkstd/vector> -> #include <vector>
 vtksys_stl::vector       -> std::vector

Revision 19238 - Directory Listing
Modified Tue Feb 7 03:42:35 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Clean XML description file

* Remove empty lines

* Fix indent

* See https://github.com/jcfr/Scriptacular/blob/master/trimxml.py
and https://github.com/jcfr/Scriptacular/blob/master/trimxml.sh

Revision 19235 - Directory Listing
Modified Mon Feb 6 23:31:44 2012 UTC (5 years, 8 months ago) by finetjul
Original Path: trunk/Modules
ENH: Reduce the minimumSizeHint width of the loadable modules

to be under 500px. Ideally it should be under 400px.

Revision 19234 - Directory Listing
Modified Mon Feb 6 23:31:40 2012 UTC (5 years, 8 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add contributor to loadable modules

contributor is now a mandatory field

Revision 19233 - Directory Listing
Modified Mon Feb 6 23:31:35 2012 UTC (5 years, 8 months ago) by finetjul
Original Path: trunk/Modules
ENH: Add ctkFlowLayout::replaceLayout

Revision 19232 - Directory Listing
Modified Mon Feb 6 23:28:14 2012 UTC (5 years, 8 months ago) by finetjul
Original Path: trunk/Modules
ENH: Improve generic module tests

qSlicerAbstractCoreModule::categories() and contributor() are mandatory
minimumSizeHint width is 500px

Revision 19231 - Directory Listing
Modified Mon Feb 6 23:20:42 2012 UTC (5 years, 8 months ago) by finetjul
Original Path: trunk/Modules
STYLE: Fix minimumSizeHint of the transforms module

The matrix widget and tree views were taking too much horizontal space.

Revision 19218 - Directory Listing
Modified Mon Feb 6 19:59:23 2012 UTC (5 years, 8 months ago) by pieper
Original Path: trunk/Modules
BUG: enable plugin modules, fix to handle different cmake versions, and remove some debug info

Revision 19217 - Directory Listing
Modified Mon Feb 6 19:50:30 2012 UTC (5 years, 8 months ago) by pieper
Original Path: trunk/Modules
ENH: initial checkin of new DICOM plugin interface 

Example plugins for Scalar and Diffusion volumes provided.  New interface
will allow separation of DICOM module from the details of different
volume parsing and loading.

Next steps are to flesh out different DICOM datatypes and also to 
support exporting of slicer data to DICOM.  In addition, effiency of the
DICOM header examination process needs to be addressed (to avoid
duplicated parsing in different plugins).  Some of this will need to
happen at the ctkDICOM level.



Revision 19215 - Directory Listing
Modified Mon Feb 6 15:31:12 2012 UTC (5 years, 8 months ago) by fedorov
Original Path: trunk/Modules
BUG: update to account for CLI renaming


Revision 19211 - Directory Listing
Modified Mon Feb 6 14:03:29 2012 UTC (5 years, 8 months ago) by pieper
Original Path: trunk/Modules
BUG: set the x axis of the label statistics bar chart to correspond to the row of the table shown in the module panel and fix the axis label accordingly

Revision 19210 - Directory Listing
Modified Sat Feb 4 14:31:10 2012 UTC (5 years, 8 months ago) by pieper
Original Path: trunk/Modules
BUG: account for label indices with 0 pixel count

Revision 19209 - Directory Listing
Modified Fri Feb 3 23:01:11 2012 UTC (5 years, 8 months ago) by pieper
Original Path: trunk/Modules
ENH: put sample charting functionality into Label Statistics module

Revision 19207 - Directory Listing
Modified Fri Feb 3 15:31:51 2012 UTC (5 years, 8 months ago) by hjohnson
Original Path: trunk/Modules
COMP: Changed to match new naming of autogenerated header.

Revision 19204 - Directory Listing
Modified Thu Feb 2 14:46:50 2012 UTC (5 years, 8 months ago) by pieper
Original Path: trunk/Modules
ENH: add Jim's new features to demo, including click signal

Revision 19203 - Directory Listing
Modified Thu Feb 2 09:30:02 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
BUG: Set Category in DICOM.xml

Revision 19202 - Directory Listing
Modified Thu Feb 2 07:13:34 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
COMP: Remove empty directory

Revision 19201 - Directory Listing
Modified Thu Feb 2 06:53:21 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Rename "DiffusionTensorEstimation" module into "DWIToDTIEstimation"

* Use a more meaningful module name

See http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/007599.html

Revision 19200 - Directory Listing
Modified Thu Feb 2 06:53:18 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Do not install "DiffusionTensorTest" and "TestGridTransformRegistration" module

Revision 19199 - Directory Listing
Modified Thu Feb 2 06:53:16 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Remove legacy module "MultipleModelsExample"

* ModelMaker already allows to create models from segmented data

* See http://massmail.spl.harvard.edu/public-archives/slicer-devel/2010/005814.html

Revision 19198 - Directory Listing
Modified Thu Feb 2 06:53:06 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Rename "RobustStatSegmenter" module into "RobustStatisticsSegmenter"

* Remove unused source code

* Move test data into Data/Input folder

* Create Testing directory

* Module name and module title are now consistent

See http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/007599.html

Revision 19197 - Directory Listing
Modified Thu Feb 2 06:52:52 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Move modules located into DiffusionApplications into main CLI folder

Revision 19196 - Directory Listing
Modified Thu Feb 2 06:52:27 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Remove duplicated headers

* Reorganize header includes in main cxx files

Revision 19195 - Directory Listing
Modified Thu Feb 2 06:52:24 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Rename "jointLMMSE" module into "DWIJointRicianLMMSEFilter"

* Module name and module title are now consistent

See http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/007599.html

Revision 19194 - Directory Listing
Modified Thu Feb 2 06:52:19 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Update module title in CLI XML description

* Module name and module title are now consistent

* Fix indent

See http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/007599.html

Revision 19193 - Directory Listing
Modified Thu Feb 2 06:52:12 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Rename "OrientImage" module into "OrientScalarVolume"

* Module name and module title are now consistent

See http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/007599.html

Revision 19192 - Directory Listing
Modified Thu Feb 2 06:52:08 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
COMP: Clean CMakeLists associated to "DicomToNrrdConverter"

Revision 19191 - Directory Listing
Modified Thu Feb 2 06:52:06 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Remove legacy code "DiffusionWeightedTest"

* The cope wasn;t compiled

Revision 19190 - Directory Listing
Modified Thu Feb 2 06:52:03 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Rename "ComputeSUVBodyWeight" module into "PETStandardUptakeValueComputation"

* Module name and module title are now consistent

See http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/007599.html

Revision 19189 - Directory Listing
Modified Thu Feb 2 06:52:00 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Rename "DiffusionWeightedMasking" module into "DiffusionWeightedVolumeMasking"

* Module name and module title are now consistent

See http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/007599.html

Revision 19188 - Directory Listing
Modified Thu Feb 2 06:51:57 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Rename "define.h" into "itkDiffusionTensor3DConstants.h"

Choosing generic name like "define.h" for header file is very base idea.
Indeed, it doesn't provide any information about the scope of the file and
won't prevent name collision.

Revision 19187 - Directory Listing
Modified Thu Feb 2 06:51:43 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Rename "ResampleDTI" module into "ResampleDTIVolume"

* Clean CMakeLists.txt and re-organized testing data. There is not an
Data/Input and Data/Baseline folder

* Module name and module title are now consistent

See http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/007599.html

Revision 19186 - Directory Listing
Modified Thu Feb 2 06:51:27 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Rename "ResampleVolume2" module into "ResampleScalarVectorDWIVolume"

* Module name and module title are now consistent

See http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/007599.html

Revision 19185 - Directory Listing
Modified Thu Feb 2 06:51:23 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Rename "ResampleScalarVolume" module into "ResampleVolume"

* Module name and module title are now consistent

See http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/007599.html

Revision 19184 - Directory Listing
Modified Thu Feb 2 06:51:18 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Rename "dwiNoiseFilter" module into "DWIRicianLMMSEFilter"

* Module name and module title are now consistent

See http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/007599.html

Revision 19183 - Directory Listing
Modified Thu Feb 2 06:51:13 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Rename "dwiUNLM" module into "DWIUnbiasedNonLocalMeansFilter"

* Module name and module title are now consistent

See http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/007599.html

Revision 19182 - Directory Listing
Modified Thu Feb 2 06:51:08 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Rename "Seeding" module into "TractographyLabelMapSeeding"

* Module name and module title are now consistent

See http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/007599.html

Revision 19181 - Directory Listing
Modified Thu Feb 2 06:50:50 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Rename "PolyDataToLabelmap" module into "ModelToLabelMap"

* Move input data into CLI specific directory

* Module name and module title are now consistent

See http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/007599.html

Revision 19180 - Directory Listing
Modified Thu Feb 2 06:50:44 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Rename "ConfidenceConnected" module into "SimpleRegionGrowingSegmentation"

* Module name and module title are now consistent

See http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/007599.html

Revision 19179 - Directory Listing
Modified Thu Feb 2 06:50:39 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Rename "Subtract" module into "SubtractScalarVolumes"

* Module name and module title are now consistent

See http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/007599.html

Revision 19178 - Directory Listing
Modified Thu Feb 2 06:50:34 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Rename "Threshold" module into "ThresholdScalarVolume"

* Module name and module title are now consistent

See http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/007599.html

Revision 19177 - Directory Listing
Modified Thu Feb 2 06:50:29 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Rename "Multiply" module into "MultiplyScalarVolumes"

* Module name and module title are now consistent

See http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/007599.html

Revision 19176 - Directory Listing
Modified Thu Feb 2 06:50:24 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Remove extra parameter passed to run_MergeModelsTest.cmake

Revision 19175 - Directory Listing
Modified Thu Feb 2 06:50:18 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Rename "SparseFieldLevelSetContour" module into "MeshContourSegmentation", restore appropriate test.

* Restore compare test. The test is now failing probably because compare to
the baseline, the output model seems to contain additional information:
 - ActiveContourVertexIndices
 - SurfaceMeanCurvature
This difference can be observed after loading the data using Paraview 3.8.0

* Module name and module title are now consistent

See http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/007599.html

Revision 19174 - Directory Listing
Modified Thu Feb 2 06:50:09 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Rename "Mask" module into "MaskScalarVolume"

* Module name and module title are now consistent

See http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/007599.html

Revision 19173 - Directory Listing
Modified Thu Feb 2 06:50:03 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Split "RegisterImageModule" folder into "ExpertAutomatedRegistration", "MultiResolutionAffineRegistration" and "FiducialRegistration"

* Module name and module title are now consistent

* One directory for one module

* Clean CMakeLists and use slicerMacroBuildCLI

See http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/007599.html

Revision 19172 - Directory Listing
Modified Thu Feb 2 06:49:45 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Rename "DiffusionTensorMathematics" module into "DiffusionTensorScalarMeasurements"

* Module name and module title are now consistent

See http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/007599.html

Revision 19171 - Directory Listing
Modified Thu Feb 2 06:49:42 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Rename "ImageReadDicomWrite" module into "CreateDICOMSeries"

* Module name and module title are now consistent

See http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/007599.html

Revision 19170 - Directory Listing
Modified Thu Feb 2 06:49:37 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Rename "CheckBoard" module into "CheckBoardFilter"

* Module name and module title are now consistent

See http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/007599.html

Revision 19169 - Directory Listing
Modified Thu Feb 2 06:49:33 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Rename "Cast" module into "CastScalarVolume"

* Module name and module title are now consistent

See http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/007599.html

Revision 19168 - Directory Listing
Modified Thu Feb 2 06:49:23 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Rename "Add" module into "AddScalarVolumes"

* Module name and module title are now consistent

See http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/007599.html

Revision 19167 - Directory Listing
Modified Thu Feb 2 06:49:17 2012 UTC (5 years, 8 months ago) by jcfr
Original Path: trunk/Modules
ENH: Rename "Realign" module into "ACPCTransform"

* Module name and module title are now consistent

See http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/007599.html

Revision 19165 - Directory Listing
Modified Wed Feb 1 20:10:44 2012 UTC (5 years, 8 months ago) by Michael.jeulinl
Original Path: trunk/Modules
STYLE: Change namming variable for Reformat module and update the documentation

Revision 19162 - Directory Listing
Modified Wed Feb 1 18:25:06 2012 UTC (5 years, 8 months ago) by Michael.jeulinl
Original Path: trunk/Modules
BUG: & in the Reformat module documation file

Revision 19161 - Directory Listing
Modified Wed Feb 1 16:59:48 2012 UTC (5 years, 8 months ago) by Michael.jeulinl <