Changesets: Import 2017-06-07 23:51:09
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master 09bacfcf 2015-11-11 19:00:57 Details Diff |
ENH: Slicer 4.5.0 git-svn-id: http://svn.slicer.org/Slicer4/trunk@24729 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - CMakeLists.txt | Diff File | ||
| mod - Utilities/Scripts/SlicerWizard/__version__.py | Diff File | ||
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master 0f74693c 2015-11-11 19:00:55 Details Diff |
BUG: ExtensionWizard: Fix configuration of __version__.py Output file associated with the "configure_file" has to be specified using an absolute path. Per CMake convention, placeholders in input file have to be of the form @VAR@. git-svn-id: http://svn.slicer.org/Slicer4/trunk@24728 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Utilities/Scripts/SlicerWizard/CMakeLists.txt | Diff File | ||
| mod - Utilities/Scripts/SlicerWizard/__version__.py.in | Diff File | ||
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master ae307a39 2015-11-11 17:32:00 Details Diff |
BUG: Do not show "Disable fiducial" popup when testing is enabled. See 0001690 This commit ensure the popup introduced in previous commit will not wait for user input when test are running. From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24727 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Widgets/qMRMLSliceControllerWidget.cxx | Diff File | ||
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master 0a7c91eb 2015-11-11 17:31:58 Details Diff |
BUG: Disable fiducials in light box mode. See 0001690 Fiducials are not being properly positioned when in light box mode, this change disables them and gives the user a warning that they are being disabled (new fiducials can still be placed, but will not be visible until you exit light box mode). This change fixes bugs that were left from the attempt to use the point handle widgets in 2D so that they can be properly hidden: fix the visibility setting on the point handles in light box mode, disable the point handles when invisible so that they don't become visible when the mouse is near it, updated a visibility check comparision to match return type from method. Also removed warning messages by casting the 3d handles before changing the picking state. Fixed a bug wherein if you had a mix of fiducials having been placed in lightbox and not light box mode, the seed widget would have a mix of 2d and 3d handles. This fix removes all the current handles so that they're properly recreated as the necessary type. Issue 0001690 From: Nicole Aucoin <nicole@bwh.harvard.edu> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24726 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Widgets/qMRMLSliceControllerWidget.cxx | Diff File | ||
| mod - Modules/Loadable/Markups/MRMLDM/vtkMRMLMarkupsDisplayableManager2D.cxx | Diff File | ||
| mod - Modules/Loadable/Markups/MRMLDM/vtkMRMLMarkupsFiducialDisplayableManager2D.cxx | Diff File | ||
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master 02b9c0eb 2015-11-11 17:31:56 Details Diff |
STYLE: Tweak debug message & fix indent in MarkupsFiducialDisplayableManager2D From: Nicole Aucoin <nicole@bwh.harvard.edu> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24725 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Loadable/Markups/MRMLDM/vtkMRMLMarkupsFiducialDisplayableManager2D.cxx | Diff File | ||
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master 832654c9 2015-11-11 16:12:13 Details Diff |
BUG: Fix 0002466, MRMLIDImageIO crashes with DWMRI volume http://www.na-mic.org/Bug/view.php?id=2466 Restore handling of b-values and gradients, and make code consistent with DWIConvert: use the `sqrt(b/b_max)` scaling factor as documented on the NA-MIC wiki page: http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format Reviewed-by: Francois Budin <fbudin@unc.edu> Reviewed-by: Lauren O'Donnell <odonnell@bwh.harvard.edu> Reviewed-by: Steve Pieper <pieper@isomics.com> Tested-by: Isaiah Norton <inorton@bwh.harvard.edu> From: Isaiah Norton <inorton@bwh.harvard.edu> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24724 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Core/vtkMRMLNRRDStorageNode.cxx | Diff File | ||
| mod - Libs/MRML/IDImageIO/itkMRMLIDImageIO.cxx | Diff File | ||
| mod - Libs/vtkTeem/vtkNRRDWriter.cxx | Diff File | ||
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master dd5c50f1 2015-11-11 15:04:19 Details Diff |
BUG: Workaround MRML Scene import limitation. Fixes 0003462, 0002849 and 0004080 As documented in 0004081 [1], references to other nodes are not valid when the NodeAddedEvent is invoked during the import of a scene in an existing scene. This prevented the qMRMLSceneModel from working well when it is observing the scene and updating itself as new node are added during import. This commit workarounds the root issue by forcing all SceneModel to have "lazyUpdate" enabled. When lazyUpdate is enabled, the model ignores added node events when the scene is importing/restoring, but synchronize with the scene once its imported/restored. This affected a broad set of modules and was captured in the following issues: * 3462: ModelMaker functionality breaks display of Slice views * 2849: Hierachy not respected when loading the same scene multiples times * 4080: Transform module is not updated properly after importing a scene Reviewed-by: Andras Lasso <lasso@queensu.ca> Reviewed-by: Steve Pieper <pieper@isomics.com> Tested-by: Andras Lasso <lasso@queensu.ca> Tested-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24723 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Widgets/qMRMLSceneModel.cxx | Diff File | ||
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master 088b8182 2015-11-11 11:15:34 naucoin Details Diff |
BUG: Fix crash on saving node named with a single number A previous fix[1] to avoid crashes on windows when saving volumes named "1:xxxx" leads to a crash when a node name is just a single number (the first part of the check passes, but crashes when trying to get the second character in the name string). This fix adds a string length check so that valid node names like "1" or "2" will not cause a crash on save. [1] http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=24294 Issue 0003991 git-svn-id: http://svn.slicer.org/Slicer4/trunk@24722 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Base/QTGUI/qSlicerSaveDataDialog.cxx | Diff File | ||
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master 56f46785 2015-11-11 08:53:19 Details Diff |
STYLE: Ensure MergeModels tests run in order add dependency info. Since TestCompare test is checking the output of the TestVtp test, it should depend on it. This will ensure the test run in order when running tests in parallel. From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24721 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/CLI/MergeModels/Testing/CMakeLists.txt | Diff File | ||
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master 6061a14d 2015-11-11 08:53:17 Details Diff |
BUG: Add test & fix output for two-tensor tractography fiber selection. 0004042 Mantis ID: 0004042 1) For two-tensor tractography, FiberBundleLabelSelect outputs only one tensor. This change outputs all tensor information from the selected fibers of the input file. 2) A module test was added. Reviewed-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> From: zhangfanmark <fan@veggies.bwh.harvard.edu> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24720 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/CLI/FiberBundleLabelSelect/CMakeLists.txt | Diff File | ||
| add - Modules/CLI/FiberBundleLabelSelect/Data/Baseline/selectedfibersbaseline.vtk | Diff File | ||
| add - Modules/CLI/FiberBundleLabelSelect/Data/Input/mask.nrrd | Diff File | ||
| add - Modules/CLI/FiberBundleLabelSelect/Data/Input/tractography.vtk | Diff File | ||
| mod - Modules/CLI/FiberBundleLabelSelect/FiberBundleLabelSelect.cxx | Diff File | ||
| mod - Modules/CLI/FiberBundleLabelSelect/FiberBundleLabelSelect.xml | Diff File | ||
| add - Modules/CLI/FiberBundleLabelSelect/Testing/CMakeLists.txt | Diff File | ||
| add - Modules/CLI/FiberBundleLabelSelect/Testing/CompareTensorMeasure.cxx | Diff File | ||
| add - Modules/CLI/FiberBundleLabelSelect/Testing/FiberBundleLabelSelectTest.cxx | Diff File | ||
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master cb89f5ae 2015-11-10 15:04:35 Details Diff |
COMP: Fix CERTIFICATE_VERIFY_FAILED build error when SimpleITK is enabled. This commit is a follow-up of: * r24652 (BUG: ExtensionsWizard: Fix CERTIFICATE_VERIFY_FAILED publishing error) * r24662 (BUG: Fix CERTIFICATE_VERIFY_FAILED error using "urllib2.urlopen()" on MacOSX) It updates the SlicerPython launcher settings configuration script so that it copies the certificate file (Slicer.crt) where it is expected. It basically fixes the error reported below: 8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<--- Installed /path/to/Slicer/python-install/lib/python2.7/site-packages/SimpleITK-0.10.0.dev127-py2.7-macosx-10.11-x86_64.egg Processing dependencies for SimpleITK==0.10.0.dev127 Searching for SimpleITK==0.10.0.dev127 Reading https://pypi.python.org/simple/SimpleITK/ Scanning index of all packages (this may take a while) Reading https://pypi.python.org/simple/ warning: manifest_maker: standard file 'setup.py' not found zip_safe flag not set; analyzing archive contents... SimpleITK.SimpleITK: module references __file__ Download error on https://pypi.python.org/simple/SimpleITK/: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:590) -- Some packages may not be found! Couldn't find index page for 'SimpleITK' (maybe misspelled?) Download error on https://pypi.python.org/simple/: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:590) -- Some packages may not be found! No local packages or download links found for SimpleITK==0.10.0.dev127 error: Could not find suitable distribution for Requirement.parse('SimpleITK==0.10.0.dev127') CMake Error at /path/to/Slicer/CMake/ExternalProjectForNonCMakeProject.cmake:76 (message): SimpleITK: Error in install step. See /path/to/Slicer/SimpleITK_install_step_output.txt and /path/to/Slicer/SimpleITK_install_step_error.txt Call Stack (most recent call first): /path/to/Slicer/SimpleITK_install_step.cmake:3 (ExternalProject_Execute) make[2]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-install] Error 1 [...] 8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<--- Reported-by: Hans Johnson <hans-johnson@uiowa.edu> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24719 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild/python_customPython_configure.cmake.in | Diff File | ||
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master 4d20888b 2015-11-10 05:35:36 Details Diff |
STYLE: MRMLNodeTest1: Add test for CopyWithScene() node method. See 0003462 It allowed to identify the following unsupported case: Calling CopyWithScene after the copied node has been added to the scene will be problematic. In that case, (a) the source and copied node will end up having the same ID and (b) the scene cache and reference list won't be up-to-date either. This is explained because the method CopyWithScene systematically copy the nodeID from the source node without asking the scene to generate a new one if the scene is set. Issue 0004078 has been created to keep track of the problem. git-svn-id: http://svn.slicer.org/Slicer4/trunk@24718 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Core/Testing/vtkMRMLNodeTest1.cxx | Diff File | ||
| mod - Libs/MRML/Core/vtkMRMLNode.h | Diff File | ||
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master 3f7c7cc6 2015-11-10 05:35:35 Details Diff |
STYLE: MRMLCoreTestingUtilities: Improve output of CheckNodeInSceneByID This commit updates the method to also display the node IDs. git-svn-id: http://svn.slicer.org/Slicer4/trunk@24717 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Core/vtkMRMLCoreTestingUtilities.cxx | Diff File | ||
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master ec28f389 2015-11-09 22:32:03 Details Diff |
STYLE: Update ITK to backport fixes for optional ITK Python wrapping support. This update doesn't impact the regular build of Slicer where Slicer_USE_ITKPython is disabled by default. $ git shortlog 8989fda..0305504 Matthew McCormick (4): ENH: Install Python bindings into site-packages. ENH: Improve readability of Python site-packages path detection. BUG: Do install install wrapping development files. ENH: Add WRAP_ITK_INSTALL_COMPONENT_IDENTIFIER. Co-authored-by: Matt McCormick <matt.mccormick@kitware.com> Tested-by: Johan Andruejol <johan.andruejol@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24716 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild/External_ITKv4.cmake | Diff File | ||
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master 0374ab49 2015-11-09 20:25:00 Details Diff |
BUG: Update ITK to fix segmentation fault in 2 filters. Fixes 0004065 This commit integrates fixes backported from the ITK release branch: $ git shortlog 0f346bf7..8989fda --no-merges Bradley Lowekamp (1): BUG: Fix segfault when with empty IsolatedWatershed Threshold range Mikhail Isakov (1): BUG: DiffusionTensor3DReconstruction segfault if no baseline image Tested-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24715 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild/External_ITKv4.cmake | Diff File | ||
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master 43abdd5b 2015-11-09 16:20:47 Details Diff |
STYLE: Add TestImportSceneReferenceValidDuringImport node tests. See 0003462 This test ensures that import of scenes with regular nodes, hierarchy nodes and storable nodes work as expected. It will later be extended to test that references are valid after each NodeAddedEvent. git-svn-id: http://svn.slicer.org/Slicer4/trunk@24714 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Core/Testing/vtkMRMLNodeTest1.cxx | Diff File | ||
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master 1cd45a8b 2015-11-09 16:20:46 Details Diff |
STYLE: MRMLScene: Improve readability of "UpdateNodeReferences" function This commit simply adds the intermediate ivars oldID and newID git-svn-id: http://svn.slicer.org/Slicer4/trunk@24713 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Core/vtkMRMLScene.cxx | Diff File | ||
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master 7ed9da6d 2015-11-09 16:20:44 Details Diff |
STYLE: Improve SceneImportIDModelHierarchyParentIDConflictTest error reporting By having every tests explicitly specifying the line, current and expected values. It is easier and faster to identify the test that failed. git-svn-id: http://svn.slicer.org/Slicer4/trunk@24712 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Core/Testing/vtkMRMLSceneImportIDModelHierarchyParentIDConflictTest.cxx | Diff File | ||
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master aba4a16c 2015-11-09 16:20:42 Details Diff |
STYLE: Improve SceneImportIDModelHierarchyConflictTest error reporting By having every tests explicitly specifying the line, current and expected values. It is easier and faster to identify the test that failed. git-svn-id: http://svn.slicer.org/Slicer4/trunk@24711 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Core/Testing/vtkMRMLSceneImportIDModelHierarchyConflictTest.cxx | Diff File | ||
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master ae856fa2 2015-11-09 16:20:41 Details Diff |
STYLE: Improve vtkMRMLSceneImportIDConflictTest error reporting By having every tests explicitly specifying the line, current and expected values. It is easier and faster to identify the test that failed. git-svn-id: http://svn.slicer.org/Slicer4/trunk@24710 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Core/Testing/vtkMRMLSceneImportIDConflictTest.cxx | Diff File | ||
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master f4c6bf01 2015-11-09 16:20:39 Details Diff |
STYLE: MRMLNodeTest1: Refactor TestNodeReferenceSerialization This commit introduces the convenience function "CheckNotNull()" and re-organize the test to facilitate interpretation of a failure. It will now clearly display which function call failed and what are the current and expected values. git-svn-id: http://svn.slicer.org/Slicer4/trunk@24709 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Core/Testing/vtkMRMLNodeTest1.cxx | Diff File | ||
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master 5d977e53 2015-11-09 16:20:38 Details Diff |
STYLE: Refactor tests introducing vtkMRMLCoreTestingUtilities This module provides functions to facilitate writing tests. The module itself is tested to ensure the utilities function detect failing condition correctly. git-svn-id: http://svn.slicer.org/Slicer4/trunk@24708 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Core/CMakeLists.txt | Diff File | ||
| mod - Libs/MRML/Core/Testing/CMakeLists.txt | Diff File | ||
| mod - Libs/MRML/Core/Testing/vtkMRMLColorTableNodeTest1.cxx | Diff File | ||
| add - Libs/MRML/Core/Testing/vtkMRMLCoreTestingUtilitiesTest.cxx | Diff File | ||
| mod - Libs/MRML/Core/Testing/vtkMRMLNodeTest1.cxx | Diff File | ||
| add - Libs/MRML/Core/vtkMRMLCoreTestingUtilities.cxx | Diff File | ||
| add - Libs/MRML/Core/vtkMRMLCoreTestingUtilities.h | Diff File | ||
| add - Libs/MRML/Core/vtkMRMLCoreTestingUtilities.txx | Diff File | ||
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master 72221667 2015-11-09 12:43:39 Details Diff |
BUG: Could not load atlas in command line without it being centered git-svn-id: http://svn.slicer.org/Slicer4/trunk@24707 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild.cmake | Diff File | ||
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master dd9576cd 2015-11-07 11:11:48 Details Diff |
BUG: 3648. Fixed scalar display on fibers. git-svn-id: http://svn.slicer.org/Slicer4/trunk@24706 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Loadable/TractographyDisplay/Widgets/qSlicerTractographyDisplayWidget.cxx | Diff File | ||
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master 53b63e71 2015-11-06 23:36:26 Details Diff |
STYLE: MRMLScene: Refactor to use existing "AddNodeID()" function git-svn-id: http://svn.slicer.org/Slicer4/trunk@24705 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Core/vtkMRMLScene.cxx | Diff File | ||
