Changesets: Import 2017-06-07 23:51:09
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master a299d916 2015-07-10 11:26:18 Details Diff |
ENH: Update ITK to v4.8 $ git shortlog 5f95aa6..3388d7b --no-merges Bradley Lowekamp (4): BUG: Remove reliance on exceptions in StringTools::ToData methods BUG: Remove reliance on exceptions in StringTools::ToData methods BUG: Fix WriteCellsAsBinary and valgrind defects COMP: Explicitly export SingleValuedNonLinearVnlOptimizerv4 Davis Vigneault (1): COMP: C++11 Warnings in thirdparty PNG module. Matthew McCormick (13): COMP: Address may bu used uninitialized in IdentityTransformTest. COMP: Address array subscript above bounds in VTKPolyDataReader. COMP: Work around GDCM test segfault with Clang 3.5+. BUG: Do not use pthreads with Emscripten. COMP: Fix unused parameter warnings in itkMultiThreaderNoThreads. BUG: Do not output CMake log files in itkSystemInformationTest. COMP: Work around segfaults with VS12 in RegionOfInterestImageFilter. DOC: Update Wiki Examples Remote to June 26, 2015. COMP: Update ParabolicMorphology to address doxygen warning. COMP: Add missing exports in the ITKFEM module. BUG: Use CMAKE_LIBRARY_OUTPUT_DIRECTORY for build tree WrapITK.pth. DOC: Document grafting the input image in composite filters. DOC: Bump SphinxExample remote module version to 2015-07-02. Michka Popoff (1): ENH: Update PyInit for Python 3 From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24404 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild/External_ITKv4.cmake | Diff File | ||
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master 672f7f3d 2015-07-10 11:26:06 Details Diff |
ENH: Added copy-paste linear transform Icons Also made the translation/rotation order selector smaller and simpler. From: Andras Lasso <lasso@queensu.ca> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24403 3bd1e089-480b-0410-8dfb-8563597acbee |
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| add - Modules/Loadable/Transforms/Resources/Icons/RotateFirst.png | Diff File | ||
| add - Modules/Loadable/Transforms/Resources/Icons/TranslateFirst.png | Diff File | ||
| mod - Modules/Loadable/Transforms/Resources/UI/qSlicerTransformsModuleWidget.ui | Diff File | ||
| mod - Modules/Loadable/Transforms/Resources/qSlicerTransformsModule.qrc | Diff File | ||
| mod - Modules/Loadable/Transforms/qSlicerTransformsModuleWidget.cxx | Diff File | ||
| mod - Modules/Loadable/Transforms/qSlicerTransformsModuleWidget.h | Diff File | ||
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master cfd202cb 2015-07-07 15:39:24 naucoin Details Diff |
BUG: fix regression introduced by adding storage nodes to scene views Update the test to check for the correct number of nodes, 3 to include the added storage node in the scene view. Issue 0003956 git-svn-id: http://svn.slicer.org/Slicer4/trunk@24402 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Core/Testing/vtkMRMLSceneViewNodeImportSceneTest.cxx | Diff File | ||
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master 399bc48a 2015-07-07 15:30:53 naucoin Details Diff |
BUG: update test to fix regression Update the scene view node store test to take into account the newly added storage nodes in scene view scenes. Issue 0003956 git-svn-id: http://svn.slicer.org/Slicer4/trunk@24401 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Core/Testing/vtkMRMLSceneViewNodeStoreSceneTest.cxx | Diff File | ||
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master f3783f07 2015-07-07 15:14:07 naucoin Details Diff |
BUG: add Scene null pointer check to copy Testing showed that Copy can be called when the node isn't in a scene, added a null pointer check to avoid crashing. Issue 0003965 git-svn-id: http://svn.slicer.org/Slicer4/trunk@24400 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Loadable/Markups/MRML/vtkMRMLMarkupsNode.cxx | Diff File | ||
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master ce8488e6 2015-07-07 13:55:01 naucoin Details Diff |
BUG: remove storable added after scene view message Testing showed that this was confusing, remove the observation on node added events from the capture toolbar as well as the pop up message. Leaves the popup timeout flag for future messages. TODO: move the test to on scene view about to be restored. Issue 0003956 git-svn-id: http://svn.slicer.org/Slicer4/trunk@24399 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Widgets/qMRMLCaptureToolBar.cxx | Diff File | ||
| mod - Libs/MRML/Widgets/qMRMLCaptureToolBar.h | Diff File | ||
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master 96d3e073 2015-07-07 13:54:52 naucoin Details Diff |
STYLE: add blank lines to warning message Make the message more readable by adding white space. Issue 0003956 git-svn-id: http://svn.slicer.org/Slicer4/trunk@24398 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Widgets/qMRMLCaptureToolBar.cxx | Diff File | ||
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master 1589f1c2 2015-07-07 13:54:49 naucoin Details Diff |
BUG: only time out extra storable message during testing The pop up window that gives the user feedback about how not to lose new storable data after creating a scene view was timing out before some testers could finish reading and understanding the information. Added a boolean property to the capture tool bar, popupsTimeOut, that the main window can set to true when the enable testing attribute has been turned on. Verified that the test AddStorableDataAfterSceneViewTest still passes and doesn't hang. Issue 0003956 git-svn-id: http://svn.slicer.org/Slicer4/trunk@24397 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Applications/SlicerApp/qSlicerAppMainWindow.cxx | Diff File | ||
| mod - Libs/MRML/Widgets/qMRMLCaptureToolBar.cxx | Diff File | ||
| mod - Libs/MRML/Widgets/qMRMLCaptureToolBar.h | Diff File | ||
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master bed28d5a 2015-07-07 13:54:45 naucoin Details Diff |
BUG: after MRB save, reset storables to modified When saving files into an MRB, the storable nodes are marked as not modified since the last save. This is a problem when new data was generated (for example via model maker) and the new files were only saved in the now deleted MRB directory. Reset all the storable nodes to modified since reads so that saving the scene as a .mrml file and data files will succeed. Will not affect multiple MRB savings. Issue 0003956 git-svn-id: http://svn.slicer.org/Slicer4/trunk@24396 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Loadable/Data/qSlicerSceneWriter.cxx | Diff File | ||
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master b29d28c9 2015-07-07 13:54:42 naucoin Details Diff |
BUG: update file list members, scene vars, update test Update the MRB save/restore test to use the slicer util delayDisplay method, as well as not counting file paths that point to the deleted bundle expansion directory. In scene view nodes make sure to also reset the file list Restore the url and root direcotry after saving a scene to the data bundle directory so that absolute paths can be calculatediproperly Issue 0003956 git-svn-id: http://svn.slicer.org/Slicer4/trunk@24395 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Applications/SlicerApp/Testing/Python/SlicerMRBSaveRestoreCheckPathsTest.py | Diff File | ||
| mod - Base/QTCore/qSlicerSceneBundleReader.cxx | Diff File | ||
| mod - Libs/MRML/Core/vtkMRMLSceneViewNode.cxx | Diff File | ||
| mod - Libs/MRML/Logic/vtkMRMLApplicationLogic.cxx | Diff File | ||
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master d34213e3 2015-07-07 13:54:36 naucoin Details Diff |
BUG: Add a test that checks file paths after MRML and MRB save/load Add a test that checks the paths in the scene with saving to mrml (have to force a write of a sample data node since the saveScene call only writes out the MRML file, no storage nodes are triggered to write) and MRB and reloading and saving to MRB. Remove skipping the master scene view as paths of storage nodes there do need to be updated. TBD: fix the paths after saving the MRB a second time (they get reset to the deleted bundle directory from the first MRB save). Issue 0003956 git-svn-id: http://svn.slicer.org/Slicer4/trunk@24394 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Applications/SlicerApp/Testing/Python/CMakeLists.txt | Diff File | ||
| add - Applications/SlicerApp/Testing/Python/SlicerMRBSaveRestoreCheckPathsTest.py | Diff File | ||
| mod - Libs/MRML/Core/vtkMRMLSceneViewNode.cxx | Diff File | ||
| mod - Libs/MRML/Logic/vtkMRMLApplicationLogic.cxx | Diff File | ||
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master e6477abb 2015-07-07 13:54:31 naucoin Details Diff |
BUG: remove node SceneRootDir, use RootDirectory on MRML scene The node ivar scene root directory wasn't staying updated when the root directory was changing on the scene. Updated the code to refer to the scene for the root directory. One important change is that in the XML parser, the scene has to be set on a storage node before reading/writing it so that the absolute path can be determined. Also set the scene root dir more consistently Updated the fiber bundle node test to use the testing macros since it was reproducing code. Issue 0003956 git-svn-id: http://svn.slicer.org/Slicer4/trunk@24393 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Core/Testing/vtkMRMLFiberBundleNodeTest1.cxx | Diff File | ||
| mod - Libs/MRML/Core/vtkMRMLCoreTestingMacros.h | Diff File | ||
| mod - Libs/MRML/Core/vtkMRMLNode.cxx | Diff File | ||
| mod - Libs/MRML/Core/vtkMRMLNode.h | Diff File | ||
| mod - Libs/MRML/Core/vtkMRMLParser.cxx | Diff File | ||
| mod - Libs/MRML/Core/vtkMRMLScene.cxx | Diff File | ||
| mod - Libs/MRML/Core/vtkMRMLStorageNode.cxx | Diff File | ||
| mod - Modules/Loadable/Data/qSlicerSceneWriter.cxx | Diff File | ||
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master ad493e38 2015-07-07 13:54:25 naucoin Details Diff |
BUG: redo observations for volume loading with mini scene Found during stress testing MRBs with file paths, the final correct set of nodes used to load the volume need the storage and display node observations reset after moving from the mini scene to the main scene. The SampleData module wasn't finding the extra storage node to remove it. Issue 0003956 git-svn-id: http://svn.slicer.org/Slicer4/trunk@24392 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Loadable/Volumes/Logic/vtkSlicerVolumesLogic.cxx | Diff File | ||
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master 5a954215 2015-07-07 13:54:22 naucoin Details Diff |
BUG: fix moving volume nodes from test to main scene In testing the Reporting extension, a bug was found where error messages were being printed and the volume node had it's IJK to RAS matrix reset to identity. Removing the nodes from the test scene before adding them to the main scene seems to have fixed this, all relevant tests are passing now. This change removes the following error messages: GetNodeByID: Node is in the scene, but its ID is missing from the NodeIDs cache: vtkMRMLScalarVolumeNode3 ditto for vtkMRMLScalarVolumeDisplayNode2 and vtkMRMLVolumeArchetypeStorageNode2 and fixes the test py_ReportingRoundTripTest Issue 0003956 git-svn-id: http://svn.slicer.org/Slicer4/trunk@24391 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Loadable/Volumes/Logic/vtkSlicerVolumesLogic.cxx | Diff File | ||
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master 1721c0ef 2015-07-07 13:54:03 naucoin Details Diff |
ENH: stress test saving and restoring MRBs, util methods added Add a test to save and restore MRBs in a loop, fixing the bug note in the save restore test as well. Clean up the testing of saving and loading MRBs by exposing the core io manager loadScene method to Python, and adding a saveScene one. This will simplify testing since it uses detects that it needs to use the scene writer which will use the application logic save to MRB bundle directory + zip calls, so from python you won't need to make the two calls with attendant managing of temporary directories. Added a note to the application logic header file pointing to saveScene for general use. Issue 0003956 git-svn-id: http://svn.slicer.org/Slicer4/trunk@24390 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Applications/SlicerApp/Testing/Python/CMakeLists.txt | Diff File | ||
| add - Applications/SlicerApp/Testing/Python/SlicerMRBMultipleSaveRestoreLoopTest.py | Diff File | ||
| mod - Applications/SlicerApp/Testing/Python/SlicerMRBMultipleSaveRestoreTest.py | Diff File | ||
| mod - Base/QTCore/qSlicerCoreIOManager.cxx | Diff File | ||
| mod - Base/QTCore/qSlicerCoreIOManager.h | Diff File | ||
| mod - Libs/MRML/Logic/vtkMRMLApplicationLogic.h | Diff File | ||
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master 904f2c42 2015-07-07 13:53:56 naucoin Details Diff |
BUG: reduce message noise When adding a storable node to the scene after a scene view has been added, make sure that only nodes that are saved with the scene generate the warning. Cleaned up debugging messages by changing warning to debug macros. Issue 0003956 git-svn-id: http://svn.slicer.org/Slicer4/trunk@24389 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Logic/vtkMRMLApplicationLogic.cxx | Diff File | ||
| mod - Libs/MRML/Widgets/qMRMLCaptureToolBar.cxx | Diff File | ||
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master c8b12d80 2015-07-07 13:53:52 naucoin Details Diff |
BUG: double check for dot preceding file suffixes GUI testing showed that renaming a node could lead to a file name of label..nrrd, this fix only adds the leading dot if the complete Slicer writable suffix call doesn't start with it. Issue# 3956 git-svn-id: http://svn.slicer.org/Slicer4/trunk@24388 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Base/QTGUI/qSlicerSaveDataDialog.cxx | Diff File | ||
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master b651869b 2015-07-07 13:53:49 naucoin Details Diff |
COMP: fix test name for label Configuration was failing with the previous name for the new scripted self test. Issue 0003956 git-svn-id: http://svn.slicer.org/Slicer4/trunk@24387 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Loadable/SceneViews/Testing/Python/CMakeLists.txt | Diff File | ||
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master 9d69cc06 2015-07-07 13:53:45 naucoin Details Diff |
ENH: test adding storable data after a scene view is created Add a fiducial, store a scene view, add a volume, restore the scene view. To conform with the current implmentation, the new storable node should not be present after the scene view is restored. The test pops up an info window which times out after 15s (needed during run time to let the user read it). Issue 0003956 git-svn-id: http://svn.slicer.org/Slicer4/trunk@24386 3bd1e089-480b-0410-8dfb-8563597acbee |
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| add - Modules/Loadable/SceneViews/Testing/Python/AddStorableDataAfterSceneViewTest.py | Diff File | ||
| mod - Modules/Loadable/SceneViews/Testing/Python/CMakeLists.txt | Diff File | ||
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master ab2676a1 2015-07-07 13:53:41 naucoin Details Diff |
ENH: factor out adding data io to the scene Encapsulated setting up the remote IO logic and the data manager IO in the application so that it can work as an example template. Moved the hooking up of the data logic to the scene to the application logic so that it can be called by classes with access to the application logic, and use it in the volumes logic for the mini scene. Added some comments to direct developers to the places they need to look to hook up a mini scene that can do data management both locally and remotely. Issue 0003956 git-svn-id: http://svn.slicer.org/Slicer4/trunk@24385 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Base/Logic/vtkSlicerApplicationLogic.cxx | Diff File | ||
| mod - Base/Logic/vtkSlicerApplicationLogic.h | Diff File | ||
| mod - Base/QTCore/qSlicerCoreApplication.cxx | Diff File | ||
| mod - Base/QTCore/qSlicerCoreApplication.h | Diff File | ||
| mod - Base/QTCore/qSlicerCoreApplication_p.h | Diff File | ||
| mod - Libs/MRML/Logic/vtkMRMLRemoteIOLogic.cxx | Diff File | ||
| mod - Modules/Loadable/Volumes/Logic/vtkSlicerVolumesLogic.cxx | Diff File | ||
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master cc0cc610 2015-07-07 13:53:34 naucoin Details Diff |
BUG: add support for remote IO The crop volume module self test uses remote data, it was failing with the mini scene in volumes logic until all the pieces were added in to support remote IO. TBD: update the infrastructure to make this more modular, test without batch processing flags. Issue 0003956 git-svn-id: http://svn.slicer.org/Slicer4/trunk@24384 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Loadable/Volumes/Logic/vtkSlicerVolumesLogic.cxx | Diff File | ||
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master 785b4454 2015-07-07 13:53:31 naucoin Details Diff |
BUG: use a mini scene for volume loading The volumes logic was adding in multiple volume, display, storage nodes as it tries to load a file. This generated lots of node added/removed events so it was placed inside of a batch processing state for the scene. This leads to no node added event after the batch processing end event so the warning about adding new storable nodes to the scene after a scene view is already present wasn't getting triggered. This change uses a mini test scene to try loading data (borrowing the main scene cache manager in case the data is remote) and then adding the successful set of volume nodes to the main scene, with an extra node added event after batch processing ends. Issue 0003956 git-svn-id: http://svn.slicer.org/Slicer4/trunk@24383 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Loadable/Volumes/Logic/vtkSlicerVolumesLogic.cxx | Diff File | ||
| mod - Modules/Loadable/Volumes/Logic/vtkSlicerVolumesLogic.h | Diff File | ||
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master 68a6db7c 2015-07-07 13:53:24 naucoin Details Diff |
BUG: warn the user when they add storable data after scene views When a storable node is added to the scene after scene views, warn the user that restoring a scene view will lose the newly added data. To avoid too many pop ups, don't warn during batch processing. Issue 0003956 git-svn-id: http://svn.slicer.org/Slicer4/trunk@24382 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Widgets/qMRMLCaptureToolBar.cxx | Diff File | ||
| mod - Libs/MRML/Widgets/qMRMLCaptureToolBar.h | Diff File | ||
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master 7666fb8a 2015-07-07 13:53:20 naucoin Details Diff |
BUG: function name clarification, add getting readable extensions Thanks to comments from JC: Renamed completeSlicerSuffix to ompleteSlicerWritableFileNameSuffix in order to make it explicit that this was only checking writable extensions. Renamed allFileExtensions to allWritableFileExtensions to be more clear as well as adding the equivalent call for readable extensions, allReadableFileExtensions Issue 0003956 git-svn-id: http://svn.slicer.org/Slicer4/trunk@24381 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Base/QTCore/Testing/Cxx/qSlicerCoreIOManagerTest1.cxx | Diff File | ||
| mod - Base/QTCore/qSlicerCoreIOManager.cxx | Diff File | ||
| mod - Base/QTCore/qSlicerCoreIOManager.h | Diff File | ||
| mod - Base/QTGUI/qSlicerNodeWriter.cxx | Diff File | ||
| mod - Base/QTGUI/qSlicerSaveDataDialog.cxx | Diff File | ||
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master c6d6ec14 2015-07-07 13:53:15 naucoin Details Diff |
BUG: implement a Slicer specific Qt file suffix In the MRML storage node it is dealing correctly with tricky file names like brain.1.nii.gz to return the proper suffix. In Qt we were relying on completeSuffix but that was returning everything after the first dot in the file name and would fail on that example case. This change leverages the storage nodes to gather a list of valid file suffixes and compares them against the file name endings and returns a matching one. Special case included if .* is a valid Slicer suffix, that goes back to Qt's completeSuffix call. Note: tried calling fileWriterExtensions and ran into a crash as it was trying to add new storage nodes to the scene. Use the new suffix in the save data dialog and node writer. Added testing, more file name cases can be added easily. Issue 0003956 git-svn-id: http://svn.slicer.org/Slicer4/trunk@24380 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Base/QTCore/Testing/Cxx/qSlicerCoreIOManagerTest1.cxx | Diff File | ||
| mod - Base/QTCore/qSlicerCoreIOManager.cxx | Diff File | ||
| mod - Base/QTCore/qSlicerCoreIOManager.h | Diff File | ||
| mod - Base/QTGUI/qSlicerNodeWriter.cxx | Diff File | ||
| mod - Base/QTGUI/qSlicerSaveDataDialog.cxx | Diff File | ||
