Changesets: Import 2017-06-07 23:51:09
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master 5784e418 2014-07-16 17:39:41 Details Diff |
BUG: fix method name difference between vtk 5 and 6 Fixes failing test on vtk 6. git-svn-id: http://svn.slicer.org/Slicer4/trunk@23442 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild.cmake | Diff File | ||
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master 63f6656f 2014-07-16 14:46:49 Details Diff |
ENH: LandmarkRegistration improvements (and fixed test on vtk5 and vtk6) git-svn-id: http://svn.slicer.org/Slicer4/trunk@23441 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild.cmake | Diff File | ||
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master dee8bfa3 2014-07-16 00:20:01 Details Diff |
BUG: Fix valgrind issues in vtkMRMLVolumeNodeTest1 This commit fixes regression introduced by commit r19917. Instead of re-implementing Get{I,J,K}ToRASDirection methods, the macro "TEST_SET_GET_VECTOR3_DOUBLE_RANDOM" has been updated to directly use the Set/Get method of the object. It then (1) avoids to return a pointer and (2) avoids to access possibly uninitialized value with the bracket operator. Valgrind errors like this one are fixed: [...] ==20657== Conditional jump or move depends on uninitialised value(s) ==20657== at 0x626297: vtkMRMLVolumeNodeTest1(int, char**) (vtkMRMLVolumeNodeTest1.cxx:114) ==20657== by 0x4717DC: main (MRMLCoreCxxTests.cxx:616) [...] git-svn-id: http://svn.slicer.org/Slicer4/trunk@23440 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Core/Testing/vtkMRMLVolumeNodeTest1.cxx | Diff File | ||
| mod - Libs/MRML/Core/vtkMRMLCoreTestingMacros.h | Diff File | ||
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master 5726de21 2014-07-16 00:19:58 Details Diff |
BUG: Fix "Deleting Unknown Object" warning in mrml node tests This commits (1) changes the helper node class name associated with the hierarchy node to be unique and (2) updates the helper node definitions to be consistent with the helper node declared in vtkMRMLNodeTest1. git-svn-id: http://svn.slicer.org/Slicer4/trunk@23439 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Core/Testing/vtkMRMLDisplayableHierarchyNodeTest1.cxx | Diff File | ||
| mod - Libs/MRML/Core/Testing/vtkMRMLDisplayableNodeTest1.cxx | Diff File | ||
| mod - Libs/MRML/Core/Testing/vtkMRMLVolumeNodeTest1.cxx | Diff File | ||
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master d673ed87 2014-07-16 00:19:55 Details Diff |
STYLE: Add vtkMRMLStorableNode method definition to cpp file. git-svn-id: http://svn.slicer.org/Slicer4/trunk@23438 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Core/vtkMRMLStorableNode.cxx | Diff File | ||
| mod - Libs/MRML/Core/vtkMRMLStorableNode.h | Diff File | ||
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master 63341b21 2014-07-16 00:19:53 Details Diff |
STYLE: Add vtkMRMLDisplayableNode method definition to cpp file. git-svn-id: http://svn.slicer.org/Slicer4/trunk@23437 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Core/vtkMRMLDisplayableNode.cxx | Diff File | ||
| mod - Libs/MRML/Core/vtkMRMLDisplayableNode.h | Diff File | ||
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master bc639c9f 2014-07-15 22:51:29 Details Diff |
BUG: Fix crash in vtkMRMLNode::UpdateNthNodeReference This commit fixes regression introduced in previous commit r23435. Interestingly the message in previous commit raised the question about the assignment ReferencingNode. It turns out that the method UpdateNthNodeReference was indirectly called after destroying the referencing node. The following pseudo stack trace illustrates the issue: (obtained while running the test "vtkMRMLVolumeNodeTest1" Destructor of vtkMRMLVolumeNode (referencing node) -> SetImageDataConnection(0) -> SetImageDataToDisplayNodes() -> GetNthDisplayNode(n) -> GetNthNodeReference() -> UpdateNthNodeReference(referenceRole, n) -> UpdateNthNodeReference(reference, n) this->ReferencingNode = this Since ReferencingNode is a weakpointer to the object represented by "this" and was indirectly called in the destructor of "this", this was causing a double free or corruption error. It was reported in valgrind as a "invalid read of size 8". The test is now passing. But valgrind is still reporting the error like this one: Generic Warning: In /home/jchris/Projects/Slicer-2-SuperBuild-Debug/VTKv6/Common/Core/vtkDebugLeaks.cxx, line 292 Deleting unknown object: vtkMRMLVolumeNodeTestHelper1 They will be fixed in follow-up commit. git-svn-id: http://svn.slicer.org/Slicer4/trunk@23436 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Core/vtkMRMLNode.cxx | Diff File | ||
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master 82a6a18e 2014-07-15 17:56:02 Details Diff |
BUG: Fix infinite loop when opening or closing a scene This commit fixes a regression introduced by commit r23191. Commit r23191 simplified the code introducing smart pointer, typedefs and also updated "SetNthNodeReferenceID" and "SetAndObserveNthNodeReferenceID" so that they have have similar code. It turns out that after this update new reference where systematically created with an ID being an empty string instead of being a NULL string. Commits following r23191 also updated the MRML reference system and attempted to fix what was most likely an issue with the "SetNth" methods. See r23192, r23196]. These commits fixes the behavior of the SetNth methods so that setting a reference N was always returning the associated reference if the reference n-1 was removed. It turned out that these changes caused more trouble than expected and to fully support the new behavior, major and backward incompatible changes in the displayable and storable nodes and also in the scene serialization would have occur. For that reason, commit r23395 and r23414 have been integrated to revert all commit updating the behavior but keeping the "smart pointer" and "typedefs" updates around. It is only by "reverting" these last commit that the issue fixed by this commit was revealed. Note for later: * In method almost doing the same thing, do not comment code without clearly mentioning the reason. * If very similar functions are doing almost the same thing, re-factoring the code is key to reduce the maintenance burden. Finally, this commit also update method "UpdateNthNodeReference" to set the ReferencingNode (it was done before the commit introducing smart pointers), the questions are "Why is this needed ?" and "What is causing the reference to be dissociated from a referencing node?" Fixes 0003754 Fixes 0003768 git-svn-id: http://svn.slicer.org/Slicer4/trunk@23435 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Core/vtkMRMLNode.cxx | Diff File | ||
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master f3550312 2014-07-15 11:21:33 Details Diff |
BUG: fix type of argument to SetGridExtent for LandmarkRegistration Exposed by vtk v5 vs v6 testing. git-svn-id: http://svn.slicer.org/Slicer4/trunk@23434 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild.cmake | Diff File | ||
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master cfe09bc7 2014-07-14 20:01:37 Details Diff |
ENH: update to new LandmarkRegistration Now with interactive ThinPlate registration! - uses real-time nonlinear transform updates - compatible with transform visualization Other improvments and upgrades, like VTKv6 support and generalization of the plugin architecture. git-svn-id: http://svn.slicer.org/Slicer4/trunk@23433 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild.cmake | Diff File | ||
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master f362f542 2014-07-14 18:00:31 Details Diff |
STYLE: Consistently use "referencedNodeID" parameter name To make maintenance of the code easier, the same parameter name is used across all MRML node reference functions. git-svn-id: http://svn.slicer.org/Slicer4/trunk@23432 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Core/vtkMRMLNode.cxx | Diff File | ||
| mod - Libs/MRML/Core/vtkMRMLNode.h | Diff File | ||
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master 7a0f02f6 2014-07-14 17:32:32 Details Diff |
ENH: Add test checking reference set to null or empty string are removed. git-svn-id: http://svn.slicer.org/Slicer4/trunk@23431 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Core/Testing/vtkMRMLNodeTest1.cxx | Diff File | ||
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master e14d0c5f 2014-07-14 14:52:10 Details Diff |
COMP: Ensure DCMTK libraries are packaged. This commit fixes a regression introduced in r23413 where call to "find_package(DCMTK ..)" have been moved in the sub-project where it was explicitly needed. By calling, "find_package(DCMTK ..)", it now ensures that the variable "DCMTK_LIBRARIES" will be set. Note that ideally DCMTK libraries could be installed leveraging the fact the project is cmake'ified by installing the expected components. git-svn-id: http://svn.slicer.org/Slicer4/trunk@23430 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - CMake/SlicerBlockInstallDCMTKLibs.cmake | Diff File | ||
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master 33621409 2014-07-14 13:21:06 Details Diff |
ENH: Update OpenIGTLinkIF - Add new message converters. Fixes 0003548 & 0003738 Also update GUI to allow users to push MRML nodes (0003738) From: Junichi Tokuda <tokuda@bwh.harvard.edu> git-svn-id: http://svn.slicer.org/Slicer4/trunk@23429 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild.cmake | Diff File | ||
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master 4ee0623a 2014-07-11 17:39:56 Details Diff |
BUG: Fixed crash on scene close when the Transforms module is active Units module triggered an update in the Transforms module GUI after the current transform node has been already deleted. Use a weak pointer to make sure no dangling pointers are accidentally used. git-svn-id: http://svn.slicer.org/Slicer4/trunk@23428 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Widgets/qMRMLLinearTransformSlider.cxx | Diff File | ||
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master 69067fa6 2014-07-11 17:34:09 Details Diff |
BUG: Fixed saving of inverted linear transforms (conversion to ITK sense was missed for inverse transforms) git-svn-id: http://svn.slicer.org/Slicer4/trunk@23427 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Core/vtkMRMLTransformStorageNode.cxx | Diff File | ||
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master db2b3b70 2014-07-09 23:48:59 Details Diff |
BUG: Extesions did not look in right directory - in addition CMTK could pass even if CMTK was not installed as EMSegmenter automatically switches to Brains git-svn-id: http://svn.slicer.org/Slicer4/trunk@23426 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild.cmake | Diff File | ||
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master 83d1f998 2014-07-09 04:17:39 Details Diff |
BUG: vtkNRRDReader filename ambiguity. Fixes 0003766 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> git-svn-id: http://svn.slicer.org/Slicer4/trunk@23425 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/CLI/DWIToDTIEstimation/CMakeLists.txt | Diff File | ||
| mod - Modules/CLI/DiffusionTensorScalarMeasurements/CMakeLists.txt | Diff File | ||
| mod - Modules/CLI/DiffusionWeightedVolumeMasking/CMakeLists.txt | Diff File | ||
| mod - Modules/CLI/ProbeVolumeWithModel/CMakeLists.txt | Diff File | ||
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master 8cfc8f48 2014-07-08 23:34:30 Details Diff |
BUG: Fixed VTK 6 incompatibility in LabelStatistics git-svn-id: http://svn.slicer.org/Slicer4/trunk@23424 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Scripted/LabelStatistics/LabelStatistics.py | Diff File | ||
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master d77217bd 2014-07-08 12:37:40 Details Diff |
BUG: depreciated flag of BRAINS was changed git-svn-id: http://svn.slicer.org/Slicer4/trunk@23423 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild.cmake | Diff File | ||
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master 4c6623d0 2014-07-04 18:02:11 Details Diff |
STYLE: Improve comment associated with lock variable. This commit updates the text illustrating why a lock variable should be used. For reference, the lock variable has been introduced in r23409. git-svn-id: http://svn.slicer.org/Slicer4/trunk@23422 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild.cmake | Diff File | ||
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master 83dc5d5e 2014-07-04 18:02:10 Details Diff |
COMP: Prevent windows build freeze when downloading setuptools 2.2 Updates setuptools from version 1.4.2 to 5.3 This commit fixes 0003763 by ensuring a recent version of setuptools is used by all projects. Having a recent version of setuptools in the python path will prevent SimpleITK (and other project) from trying to download older setuptools will avoid the possible freeze. This commit also patches the "setup.py" provided by pydicom to avoid downloading an old version of distribute. This is done by removing the first 3 lines of setup.py that were using an ancient distribute_setup.py. Finally, after some testing recent version of setuptools (5.3 in the present case) does NOT prevent incorrect update of "easy-install.pth" in case of concurrent installs. The issue distribute issue 389 [1] also mentioned in Slicer issue 0003757 [2] is still current. [1] https://bitbucket.org/tarek/distribute/issue/389/concurrent-installations-can-lose-updates [2] http://www.na-mic.org/Bug/view.php?id=3757 git-svn-id: http://svn.slicer.org/Slicer4/trunk@23421 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild/External_pydicom.cmake | Diff File | ||
| mod - SuperBuild/External_python-setuptools.cmake | Diff File | ||
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master cc02e50f 2014-07-04 18:02:08 Details Diff |
BUG: Fix typo in PyGithub and python-smmap projects. This commit properly sets the SETUPTOOLS lock variable introduced in r23409 and addressing issue 0003757. git-svn-id: http://svn.slicer.org/Slicer4/trunk@23420 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild/External_PyGithub.cmake | Diff File | ||
| mod - SuperBuild/External_python-smmap.cmake | Diff File | ||
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master 020a08d9 2014-07-04 09:36:15 Details Diff |
COMP: Ensure executable are excluded from fixup process. While GP_IS_FILE_EXECUTABLE_EXCLUDE_REGEX is convenient to speed-up the function 'get_bundle_all_executables', when set if prevent file with '.exe' extension from being excluded on non windows platform. This commit will help fixing the following packaging error: 609 - fixing item /Users/kitware/Dashboards/Nightly/Slicer-build-64bits-QT4.8.5-PythonQt-With-Tcl-CLI-Release-nightly/Slicer-build/bin/libqSlicerApp.dylib with @rpath/lib/Slicer-4.3 install_name_tool: input file: /Users/kitware/Dashboards/Nightly/Slicer-build-64bits-QT4.8.5-PythonQt-With-Tcl-CLI-Release-nightly/Slicer-build/_CPack_Packages/macosx-amd64/DragNDrop/Slicer-4.3.1-2014-07-03-macosx-amd64/Slicer.app/Contents/lib/Python/lib/python2.7/site-packages/distribute-0.6.17-py2.7.egg/setuptools/cli.exe is not a Mach-O file install_name_tool: input file: /Users/kitware/Dashboards/Nightly/Slicer-build-64bits-QT4.8.5-PythonQt-With-Tcl-CLI-Release-nightly/Slicer-build/_CPack_Packages/macosx-amd64/DragNDrop/Slicer-4.3.1-2014-07-03-macosx-amd64/Slicer.app/Contents/lib/Python/lib/python2.7/site-packages/distribute-0.6.17-py2.7.egg/setuptools/gui.exe is not a Mach-O file CPack Error: Error when generating package: Slicer make: *** [package] Error 1 git-svn-id: http://svn.slicer.org/Slicer4/trunk@23419 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - CMake/SlicerCPackBundleFixup.cmake.in | Diff File | ||
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master db842871 2014-07-04 03:26:47 Details Diff |
STYLE: dashboarddriver: Update macro setOnlyIfNotDefined to display info This commit updates the macro "setOnlyIfNotDefined" to display the environment variable value (introduced in r23417) if it has been set. git-svn-id: http://svn.slicer.org/Slicer4/trunk@23418 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - CMake/SlicerDashboardDriverScript.cmake | Diff File | ||
