Changesets: Import 2017-06-07 23:51:09
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master f5b48bbc 2016-07-04 17:53:51 Details Diff |
STYLE: Facilitate re-use of vtkImageFillROI relocating to Base/Logic Anticipating the re-use of the class by other C++ module, this commit moves the class to Base/Logic. From: Csaba Pinter <csaba.pinter@queensu.ca> git-svn-id: http://svn.slicer.org/Slicer4/trunk@25205 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Base/Logic/CMakeLists.txt | Diff File | ||
| mod - Modules/Scripted/EditorLib/Logic/CMakeLists.txt | Diff File | ||
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master 71152b18 2016-07-04 17:53:48 Details Diff |
STYLE: qSlicerDirectoryListView: Fix unused variable warning From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@25204 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Base/QTGUI/qSlicerDirectoryListView.cxx | Diff File | ||
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master 71a50496 2016-07-04 11:57:33 Details Diff |
BUG: Ignore user site python packages. This commit will fix error like the one reported below where PYTHONPATH was prepended with system locations because it found packages in user home folder. List of folders that will NOT be prepended after env. variable "PYTHONNOUSERSITE" is set to 1 are documented here: https://docs.python.org/2/library/site.html#site.USER_SITE Error: File "setup.py", line 19, in <module> exec(init_file.read(), command_ns) File "<string>", line 11, in <module> File "/home/lucas/Projects/Slicer/Slicer-superbuild/python-setuptools/setuptools/__init__.py", line 12, in <module> from setuptools.extension import Extension File "/home/lucas/Projects/Slicer/Slicer-superbuild/python-setuptools/setuptools/extension.py", line 7, in <module> from setuptools.dist import _get_unpatched File "/home/lucas/Projects/Slicer/Slicer-superbuild/python-setuptools/setuptools/dist.py", line 16, in <module> from setuptools.depends import Require File "/home/lucas/Projects/Slicer/Slicer-superbuild/python-setuptools/setuptools/depends.py", line 6, in <module> from setuptools import compat File "/home/lucas/Projects/Slicer/Slicer-superbuild/python-setuptools/setuptools/compat.py", line 19, in <module> import httplib File "/usr/lib/python2.7/httplib.py", line 71, in <module> import socket File "/usr/lib/python2.7/socket.py", line 68, in <module> from _ssl import \ ImportError: cannot import name RAND_egd Co-authored-by: Lucas Gandel <lucas.gandel@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@25203 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild/External_python.cmake | Diff File | ||
| mod - SuperBuild/python_customPythonLauncherSettings.ini.in | Diff File | ||
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master 71357481 2016-06-22 21:48:00 Details Diff |
ENH: Update BRAINSTools $ git shortlog 6763cdb..7859819 --no-merges Jean-Christophe Fillion-Robin (2): COMP: CMakeLists: Consistent name between top-level and inner-project. Fixes 0000287 COMP: BRAINSDemonWarpTemplates: Fix unknown SpatialObjectType error. git-svn-id: http://svn.slicer.org/Slicer4/trunk@25202 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild.cmake | Diff File | ||
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master 3ff21f91 2016-06-21 23:29:49 Details Diff |
COMP: Update BRAINSTools to avoid forcing configuration types This will avoid BRAINSTools to systematically force the configuration types to be "Release; Debug". Reported-by: Andras Lasso <lasso@queensu.ca> Reported-by: Kyle Sunderland <1krs1@queensu.ca> $ git shortlog 16526a5..eab1460 --no-merges Alexander Leinoff (3): COMP: Dont build the BRAINSABC Module by default BUG: Fixes CMake Dependencies in DWIConvert ENH: Throw IO Exception when reading/writing invalid landmarks file Ali Ghayoor (34): BUG: Fixed BRAINSFitTest_ROIBSpline by replacing the baseline ENH: Updated candidateRegionsThreshold value in BABC ENH: Make RC computation more stable BUG: Several modifications to identify bug in BCD BUG: Reliable computation of reflective correlation in BCD ENH: Add matlab companion to make a surface plot of metric ENH: print out CHM only in verbose mode ENH: Make BCD fail when we know results will be bad BUG: Move the physical origin to the center of the image BUG: Eyes ranges should be compared to aligned AC point BUG: Improved the input T1 test image by denoising BUG: Get MetaData dictionary from the reader output in BCD BUG: change the valid range for eye positions BUG: tuned valid range for eyes locations BUG: Generate ITK exception macro in the case of failure BUG: modify the threshold value for bad reflective correlation BUG: throw exception where needed BUG: Choose a reasonable search radius for mid-brain lmks BUG: new baselines for BCD search radius tests BUG: new baselines for BCD rescale intensity tests BUG: Fixed BCDTest_inputLandmarksEMSP BUG: Fixed twelve BCD test failures BUG: Fixed BCD forced lmks tests BUG: Fixed BCD lmks compare tests ENH: throw exception when error happens BUG: Fixed BRAINSTrimForeground test BUG: center of head mass must be passed to reflectionFunctor BUG: Fixed BRAINSAlignMSPTest ENH: RC computation is robust now, no need for repeated computation ENH: Consider a different threshold for RC metric ENH: Add correctionType to dtiestim in DWI pipeline ENH: Print a more informative error message in DWIConvert COMP: Added GTRACT as an option in cmake COMP: List the applications that need VTK in cmake build Hans J. Johnson (70): PERF: Optimize cluster density usage BUG: Test for CenterOfROI had many bugs ENH: Make error checking robust for T1 image PERF: Allow running BCD with multiple cores ENH: Modernizing vcl_ to std:: ENH: Update base code for fixing BAW features. COMP: Update for VTK 7.1 compilation ENH: Cleanup python code for snapshot writing. COMP: Remove compiler warning about unused variable. ENH: Update ANTs and ITK trying to resolve denoise issue ENH: Add ConvertBetweenFileFormats as a default build. ENH: RemoveVTKDependance. ENH: Allow building of BRAINSTools without VTK. COMP: Prefer _REQUIRES_VTK to BRAINSTools_REQUIRES_VTK COMP: Fix setting Mac OSX vars for build. ENH: Remove Compiler Warnings For clang c++11 ENH: Const correctness and prefer initialization COMP: Compilation bug for mismatch signature. ENH: Update ITK to latest version. ENH: Hack hardcode to one file for speed. ENH: Added timing to computations. ENH: Instrument of heirarchial testing. ENH: Fine tune heuristic PERF: Use heirarcial heuristic for exhausitve search BUG: Replace std::__1::cout with std::cout ENH: Reorganize variables for readability. ENH: Update to new version of itkTestDriver*.inc files STYLE: Put all old unused code at end of file. ENH: ITK, DCMTK, ANTs updated in hopes of addressing denoise empty images. ENH: Update version number of BRAINSTools. BUG: Update ANTS to fix Denoise. ENH: Update ITK and SlicerExecutionModel looking for linker warning resolution STYLE: Consolidate common typedef in one location COMP: Improve compilation by avoiding rebuilds of GenerateCLP COMP: KWSYS removed support for pre-C++98 in 2015 COMP: Update to latest to remove compiler warnings COMP: CMP0063 Honor visibility properties for all target types ENH: Update ANTs to latest version. ENH: Update ITK version. PERF: Remove redundant assignment ENH: Remove shadowed typedefs ENH: Prefer const functions COMP: Address CPPCHECK warnings ENH: Allow specifying crash dump dir in config file. COMP: Incorrectly removed necessary function. COMP: Remove warnings about shadowed typedefs. ENH: Force T1 only processing for ANTS JointFusion. BUG: Only the first element was passing ENH: Update ITKv4. ENH: Change build for SlicerExecutionModel for visibility COMP: Conditionally turn off tests that require VTK COMP: Fix issues with SEM Hidden Symbols. DOC: Improve documentation for DWIConvert ENH: Fix regresion with respect to ITK 4.10 ENH: Start of a test program for LinearRegression. BUG: Numerics for optimal averaging of images fixed ENH: Improve the unwrapping function ENH: Remove unnecessary outputs to reduce disk usage. ENH: Enable NIPYPE Provenance COMP: Remove incomplete test ENH: Partial additon of resampling code for all images ENH: Fine tune autoworkup for unwrapping and BABC candiate region thresholds. STYLE: Keep naming consistent with Slicer conventions. COMP: Silence compiler warnings ENH: Improve CSF and VB joint fusion results by cleanup BUG: Missing outputs when maxBiasOrder=0 ENH: Improve true/false processing logic ENH: Use registration masks from template when available STYLE: Make the node name match the actual behavior ENH: Do not do BFC for BABC Isaiah Norton (1): ENH: throw (overridable) error when attempting lossy NIFTI conversion. Jean-Christophe Fillion-Robin (7): STYLE: Common.cmake: Group CMake include together and remove dead code. BUG: SuperBuild.cmake: Ensure calls to mark_as_superbuild are processed ENH: Superbuild.cmake: Simplify passing of build option to inner project. STYLE: CMakeLists.txt / Common.cmake: Remove commented code STYLE: Common.cmake: Remove unused variable ${PROJECT_NAME}_BUILD_FFTWF_SUPPORT BUG: Common.cmake: Do not force variable CTEST_CONFIGURATION_TYPE COMP: Update ExternalProjectDependency to support cache args with dbl quote Juan Carlos Prieto (3): BUG: Linking error due to missing ITK libraries STYLE: Remove ITK version from find package Revert "STYLE: Remove ITK version from find package" Regina Kim (10): ENH: ScreenShot script ENH: BCD user selected landmark option BUG: EMSP file error fix in BAW ENH: compute label volume ENH: Remove unused variables ENH: T2 is only excluded to Joint Fusion ENH: Stage5 Resgistration BUG: simpleITK BinaryThreshold BUG: save_state was not being used BUG: template and longitudinal pipeline fix git-svn-id: http://svn.slicer.org/Slicer4/trunk@25201 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild.cmake | Diff File | ||
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master 5e2bea68 2016-06-21 14:03:00 Details Diff |
ENH: 4217. Added presets for DTI scalar volumes (like FA etc.). Did it for both Volumes and VolumeRendering modules. git-svn-id: http://svn.slicer.org/Slicer4/trunk@25200 3bd1e089-480b-0410-8dfb-8563597acbee |
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| add - Modules/Loadable/VolumeRendering/Resources/Icons/DTI-FA-Brain.png | Diff File | ||
| mod - Modules/Loadable/VolumeRendering/Resources/presets.xml | Diff File | ||
| mod - Modules/Loadable/VolumeRendering/Resources/qSlicerVolumeRenderingModule.qrc | Diff File | ||
| add - Modules/Loadable/Volumes/Widgets/Resources/Icons/WindowLevelPreset-DTI.png | Diff File | ||
| mod - Modules/Loadable/Volumes/Widgets/Resources/UI/qSlicerScalarVolumeDisplayWidget.ui | Diff File | ||
| mod - Modules/Loadable/Volumes/Widgets/Resources/qSlicerVolumesWidgetsModule.qrc | Diff File | ||
| mod - Modules/Loadable/Volumes/Widgets/qSlicerScalarVolumeDisplayWidget.cxx | Diff File | ||
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master 029ee221 2016-06-19 01:57:13 Details Diff |
BUG: Removed crashing vtkMRMLSliceNode::SetSliceToRAS method Using vtkCxxSetObjectMacro on a vtkSmartPointer-based variable always crashes. There was an option to either change SliceToRAS to a simple pointer and still allow users to set the pointer from outside, but object ownership would not have been very clear, several NULL-pointer checks should have been included; and already ->GetSliceToRAS()->DeepCopy(...) us used in Slicer core to modify the variable everywhere in the Slicer core and it is better not to have different mechanisms for the same purpose. git-svn-id: http://svn.slicer.org/Slicer4/trunk@25199 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Core/Testing/vtkMRMLSliceNodeTest1.cxx | Diff File | ||
| mod - Libs/MRML/Core/vtkMRMLSliceNode.cxx | Diff File | ||
| mod - Libs/MRML/Core/vtkMRMLSliceNode.h | Diff File | ||
| mod - Libs/MRML/Logic/vtkMRMLSliceLinkLogic.cxx | Diff File | ||
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master f4ae105a 2016-06-17 17:00:17 Details Diff |
ENH: Update ITK to include newer version of ITK-Minimal-Path remote module $ git shortlog 7db7b60..16df9b6 --no-merges Sumedha Singla (1): ENH: Updated the git tag for the ITK-Minimal-Path external module. From: Sumedha Singla <sumedha.singla@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@25198 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild/External_ITKv4.cmake | Diff File | ||
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master 33488dbc 2016-06-16 22:39:21 Details Diff |
BUG: Update EMSegment to fix python module import on windows This commit updates EMSegment to fix a regression introduced in r25128 (STYLE: Simplify import of Logic/MRML/DisplayableManager python modules). It ensures python modules built on system (e.g Visual Studio) using intermediate directories (e.g Release, Debug, ...) can be imported. All EMSegment tests are now expected to pass on Windows. From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@25197 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild.cmake | Diff File | ||
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master f27a777e 2016-06-16 22:39:19 Details Diff |
ENH: Update EMSegment to include Python wrapping fixes for VTK 7.1 This commit updates EMSegment to include Python wrapping fixes for the current VTK master (upcoming VTK 7.1). From: Max Smolens <max.smolens@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@25196 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild.cmake | Diff File | ||
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master 9ce9e318 2016-06-16 18:54:59 Details Diff |
BUG: vtkMRMLSliceLogic: Correct slice offset when fit to volume is called. Fixes 0003350 From: Thomas Greer <hastings.greer@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@25195 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Logic/vtkMRMLSliceLogic.cxx | Diff File | ||
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master 859dafe5 2016-06-16 18:49:55 Details Diff |
STYLE: vtkMRMLViewDisplayableManager: Remove dead code. See mantis 0002341 From: Thomas Greer <hastings.greer@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@25194 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/DisplayableManager/vtkMRMLViewDisplayableManager.cxx | Diff File | ||
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master 34ca8e58 2016-06-14 08:10:29 Details Diff |
ENH: Update OpenIGTLinkIF to include compilation fixes for VTK 7.1 OpenIGTLink updates: $ git shortlog 9271ec5..f3ebcbd --no-merges Max Smolens (1): Fix compilation with VTK 7.1 git-svn-id: http://svn.slicer.org/Slicer4/trunk@25193 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild.cmake | Diff File | ||
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master b2952023 2016-06-13 20:12:06 Details Diff |
STYLE: Add vtkSlicerVersionConfigureTest1 git-svn-id: http://svn.slicer.org/Slicer4/trunk@25192 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Base/Logic/Testing/CMakeLists.txt | Diff File | ||
| add - Base/Logic/Testing/vtkSlicerVersionConfigureTest1.cxx | Diff File | ||
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master be0d9ec6 2016-06-13 20:12:05 Details Diff |
STYLE: Simplify SlicerConfigureVersionHeader target This commit introduces vtkSlicerVersionConfigureInternal.h header containing static information not expected to change between source updates. This commit also adds doxygen documentation. Suggested-by: Francois Budin <francois.budin@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@25191 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - CMake/SlicerConfigureVersionHeaderTarget.cmake | Diff File | ||
| mod - CMake/vtkSlicerVersionConfigure.h.in | Diff File | ||
| add - CMake/vtkSlicerVersionConfigureInternal.h.in | Diff File | ||
| mod - CMakeLists.txt | Diff File | ||
| mod - Utilities/Doxygen/Doxyfile.txt.in | Diff File | ||
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master 2a57053e 2016-06-13 20:12:03 Details Diff |
BUG: Ensure vtkSlicerConfigureVersion header is always up-to-date. Fixes 0002087 Since vtkSlicerVersionConfigure.h was only updated at configure time, a source code update that wasn't triggering a reconfigured was causing the content of the header to be out of sync with the current build date and revision. This commit adds the target 'SlicerConfigureVersionHeader' ensuring the version header is always up-to-date. To ensure the file is generated when first needed, a dependency between qSlicerBaseQTCore and SlicerConfigureVersionHeader is added. Co-authored-by: Francois Budin <francois.budin@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@25190 3bd1e089-480b-0410-8dfb-8563597acbee |
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| add - CMake/SlicerConfigureVersionHeaderTarget.cmake | Diff File | ||
| mod - CMakeLists.txt | Diff File | ||
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master 417ff0eb 2016-06-13 20:12:02 Details Diff |
STYLE: CMakeLists: Move setting of Slicer version into its own file git-svn-id: http://svn.slicer.org/Slicer4/trunk@25189 3bd1e089-480b-0410-8dfb-8563597acbee |
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| add - CMake/SlicerVersion.cmake | Diff File | ||
| mod - CMakeLists.txt | Diff File | ||
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master a469c504 2016-06-13 15:46:01 Details Diff |
ENH: Update EMSegment to include compilation fixes for VTK 7.1 This commit updates EMSegment to include compilation fixes for the current VTK master (upcoming VTK 7.1). git-svn-id: http://svn.slicer.org/Slicer4/trunk@25188 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild.cmake | Diff File | ||
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master 55731d6c 2016-06-13 12:57:22 Details Diff |
COMP: Remove usage of #include <vtksys/stl/*> VTK no longer requires this compatibility layer and instead directly includes the STL headers. In preparation for upgrading the version of VTK that Slicer uses, directly include the STL headers in Slicer as well. See https://github.com/Kitware/VTK/commit/eaf0f6a. From: Max Smolens <max.smolens@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@25187 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Loadable/VolumeRendering/MRML/vtkMRMLVolumePropertyNode.h | Diff File | ||
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master 375e69d3 2016-06-13 12:57:19 Details Diff |
COMP: Update usage of legacy vtkMatrix4x4 method VTK has deprecated the vtkMatrix4x4::operator[] method. In preparation for upgrading the version of VTK that Slicer uses, update code that uses that method to use GetElement()/SetElement() instead. See https://github.com/Kitware/VTK/commit/d9c5ca0. From: Max Smolens <max.smolens@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@25186 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Core/vtkITKTransformConverter.h | Diff File | ||
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master a78fa0dc 2016-06-13 12:57:13 Details Diff |
COMP: Update #include of deprecated vtkStreamer.h VTK has deprecated the vtkStreamer class hierarchy. In preparation for upgrading the version of VTK that Slicer uses, update usage of the deprecated classes. This preemptively fixes errors like: C:\path\to\Slicer\Libs\vtkTeem\vtkHyperPointandArray.cxx(52) : error C2065: 'VTK_INTEGRATE_FORWARD' : undeclared identifier See https://github.com/Kitware/VTK/commit/c9f7a5e. From: Max Smolens <max.smolens@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@25185 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/vtkTeem/vtkHyperPointandArray.h | Diff File | ||
| mod - Libs/vtkTeem/vtkTractographyPointAndArray.h | Diff File | ||
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master 60ffd59d 2016-06-13 00:40:57 Details Diff |
STYLE: EMSegment: Fix 'Tag already registered' warnings. This commit updates EMSegment and vtkMRMLScene::CopyRegisteredNodesToScene to avoid warnings like this one: //-------- Warning: In /home/jcfr/Projects/Slicer/Libs/MRML/Core/vtkMRMLScene.cxx, line 517 vtkMRMLScene (0x2590e90): Tag LinearTransform has already been registered, unregistering previous node class vtkMRMLLinearTransformNode to register vtkMRMLLinearTransformNode //-------- Note that calling "GetClassNameByTag" in "CopyRegisteredNodesToScene" changes "CopyRegisteredNodesToScene" complexity from O(n) to O(n^2). Considering that (1) "CopyRegisteredNodesToScene" is only called from "GetReferencedSubScene", itself used only in EMSegment, and (2) testing times associated with EMSegment tests does not increase .. removing the warning to facilitate the understanding of the test outputs justifies the added complexity. git-svn-id: http://svn.slicer.org/Slicer4/trunk@25184 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Core/vtkMRMLScene.cxx | Diff File | ||
| mod - SuperBuild.cmake | Diff File | ||
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master ab86159d 2016-06-11 02:36:23 Details Diff |
BUG: Extension packaging: Fix regression for regular extension This commit re-adds code that was inadvertently removed in r25181 (BUG: Extension packaging: For SuperBuild extension, ensure fixup happens last) git-svn-id: http://svn.slicer.org/Slicer4/trunk@25183 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - CMake/SlicerExtensionCPack.cmake | Diff File | ||
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master 74737cf5 2016-06-10 19:55:16 Details Diff |
BUG: Extension packaging: Support fixup of 3rd-party (external proj) libs Introduces "Slicer_THIRDPARTY_(BIN|LIB|SHARE)_DIR" and "Slicer_INSTALL_THIRDPARTY_(BIN|LIB|SHARE)_DIR" variables providing a well defined interface for configuring the build and install directories of external projects. This commit also updates the extension fixup script to consider libraries associated with thirdparty libraries. See SBU-BMI/SlicerOpenCV#30 git-svn-id: http://svn.slicer.org/Slicer4/trunk@25182 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - CMake/SlicerConfig.cmake.in | Diff File | ||
| mod - CMake/SlicerExtensionCPackBundleFixup.cmake.in | Diff File | ||
| mod - CMake/UseSlicer.cmake.in | Diff File | ||
| mod - Extensions/Testing/SuperBuildExtensionTemplate/SuperBuild/External_Foo.cmake | Diff File | ||
| mod - Utilities/Templates/Extensions/SuperBuild/SuperBuild/External_Foo.cmake | Diff File | ||
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master 195c0d55 2016-06-10 19:55:14 Details Diff |
BUG: Extension packaging: For SuperBuild extension, ensure fixup happens last For extension of type "SuperBuild", the external projects to install are specified by appending build directories to the variable "CPACK_INSTALL_CMAKE_PROJECTS", then this variable is processed at packaging time by "CPack". This means that simply ensuring the fixup script is executed last during the install of the current project was not sufficient. Instead, this commit creates a minimal CMake project named "<ExtensionName>-Fixup" that is including the fixup script. Then, this project is appending last to the variable "CPACK_INSTALL_CMAKE_PROJECTS". See SBU-BMI/SlicerOpenCV#30 git-svn-id: http://svn.slicer.org/Slicer4/trunk@25181 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - CMake/SlicerExtensionCPack.cmake | Diff File | ||
