Changesets: Import 2017-06-07 23:51:09
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master 87c5055d 2015-09-09 23:29:28 Details Diff |
COMP: Facilitate build of FiberTractMeasurements as external module This commit (1) removes unused dependency to SlicerBaseCLI library and SlicerBaseLogic include directories and (2) specifies vtkSlicerTractographyDisplayModuleMRML include directories using variable exported in SlicerConfig. For more details, see http://slicer-devel.65872.n3.nabble.com/Fail-to-compile-FiberTractMeasurements-td4034841.html Reported-by: "Zhang, Fan" <FZHANG@bwh.harvard.edu> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24529 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/CLI/FiberTractMeasurements/CMakeLists.txt | Diff File | ||
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master b1bb1b7c 2015-09-09 15:41:11 naucoin Details Diff |
BUG: expand the Editor parameter node checking When an Editor parameter node is present in the current scene as well as in a MRML file about to be loaded, the check for the singleton node was failing (the singleton tag is not serialised to XML), this change expands the check so that the original singleton parameter node is found (the loaded one is not a singleton). Issue 0004006 git-svn-id: http://svn.slicer.org/Slicer4/trunk@24528 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Scripted/EditorLib/EditUtil.py | Diff File | ||
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master 4a3cf5ec 2015-09-09 13:58:55 Details Diff |
STYLE: fix typo in variable name and add some extra documentation git-svn-id: http://svn.slicer.org/Slicer4/trunk@24527 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Applications/SlicerApp/Testing/Python/RSNAQuantTutorial.py | Diff File | ||
| mod - Base/Python/slicer/ScriptedLoadableModule.py | Diff File | ||
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master 29328308 2015-09-09 10:20:24 Details Diff |
ENH: Upgrade to Python 2.7.10 This commit upgrades Slicer's Python from version 2.7.3 to version 2.7.10. The newer Python version fixes a number of build warnings seen when building Slicer with Python 2.7.3 in Visual Studio 2013, like: C:\Program Files (x86)\Microsoft Visual Studio 12.0\VC\include\xtgmath.h(190): warning C4273: '_hypot' : inconsistent dll linkage [C:\dev\SN\VTKv6-build\Wrapping\PythonCore\vtkWrappingPythonCore.vcxproj] C:\Program Files (x86)\Microsoft Visual Studio 12.0\VC\include\math.h(538) : see previous definition of '_hypot' and: C:\dev\SN\python-2.7.3\include\pymath.h(22): warning C4273: 'round' : inconsistent dll linkage [C:\dev\SN\python-build\CMakeBuild\libpython\libpython-shared.vcxproj] C:\Program Files (x86)\Microsoft Visual Studio 12.0\VC\include\math.h(516) : see previous definition of 'round' In addition to specifying the Python source directory with `SRC_DIR`, this commit makes the Python build more robust to default option changes by explicitly specifying `-DDOWNLOAD_SOURCES:BOOL=OFF` and `-DINSTALL_WINDOWS_TRADITIONAL:BOOL=OFF`. Also note that 'Lib/distutils/msvc9compiler.py' did not change between Python 2.7.3 and Python 2.7.10, so the patched version remains the same. This update has been manually tested on: - Windows (Visual Studio 2008, Release) - Windows (Visual Studio 2013, Debug) - Ubuntu 14.04.3 (Debug) - Mac OS X 10.6.8 (Release) Release builds show the following tests as failing: - vtkMRMLSceneImportIDModelHierarchyConflictTest - py_StandaloneEditorWidgetTest - py_DTINotReproducibleIssue3977 - qSlicerMultiVolumeExplorerModuleWidgetGenericTest Debug builds show the following additional test as failing: - vtkMRMLSceneImportTest_diffusionEditor.mrml From: Max Smolens <max.smolens@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24526 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild/External_python.cmake | Diff File | ||
| mod - SuperBuild/python_patch.cmake | Diff File | ||
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master 01a003a8 2015-09-09 10:20:16 Details Diff |
ENH: Update python-cmake-buildsystem to support building Python 2.7.10 $ git shortlog 0838470ec2a0d20909571793ebb4ccc8a3292ac5..ed5f9bcee540e47f82fa17f8360b820591aa6d66 --no-merges Chuck Atkins (9): Accomodate the various configurations of nbdm.h Use proper assembler support instead of manually assembling .S files. Use list(APPEND ...) to build lists avoiding excessive ";"s Use target_compile_definitions so defs get appended instead of replaced Remove dlmalloc.c from libffi's source list Use BUILD_EXTENSIONS_AS_BUILTIN as default but let BUILTIN_FOO override Mark BUILTIN_FOO and ENABLE_FOO as advanced if they use default values. Add additional locations to check for python source Fix `exec_prefix` error occurring when no extension are built shared Gaëtan Lehmann (1): Automatically download the python sources Jean-Christophe Fillion-Robin (42): Use official tar.gz source archive for both windows and unix Check MD5 of downloaded source archive Document DOWNLOAD_SOURCES CMake option Display source download messages with first letter upper-cased Download source archive in the parent directory travis: Add initial configuration appveyor: Add initial configuration pyconfig: Re-locate HAVE_UINTPTR_T macro to match position in official source Issue #18747: Re-seed OpenSSL's pseudo-random number generator after fork. Issue #20494: mmap obmalloc arenas so that they may be immediately returned to the system when unused pyconfig: Better comment associated with HAVE_DEV_PTMX and HAVE_DEV_PTC Fix for r84195: add HAVE_ALLOCA_H to configure and only include alloca.h if it's available Read version from python source Generate pybuilddir.txt and _sysconfigdata.py if python >= 2.7.5 is used Update default python version from 2.7.3 to 2.7.8 Install _sysconfigdata.py Fix md5 used with Python-2.7.8.tgz Disable ctypes extension when using "Visual Studio 2008 Win64" generator. Disable ctypes extension when using CMake < 2.8.12 with VS2010 generators. Fix typo in ConfigureChecks.cmake Add build matrix for appveyor and travis. Use target_compile_definitions only if available Rename "append_list_in_cache" CMake macro into "_append_list_in_cache" Fix undeclared PyDateTimeAPI error when building _testcapi module as builtin Update Extensions module to support conditional requirements Fix link / undefined symbol error associated with "_curses_panel" extension Fix "pyexpat" import error when "_sqlite3" and "pyexpat" where "builtin" Never build '_ctypes_test' as builtin extension Add option BUILD_EXTENSIONS_AS_BUILTIN Hide BUILTIN_FOO option if FOO is disabled Tweak check required to conditionally exclude ctypes extensions Fix build of ctypes as builtin extension with Visual Studio 10 Relocate CMake checks into its own module Fix error message displaying python source searched locations. UpdateSysconfig: Fix typo Fix regular dashboard removing version from project name set in CTestConfig Fix value of CMAKE_SYSTEM_PROCESSOR on windows when using CMake < 2.8.11 Add support for building the windows installer Enable travis-ci OSX builds setting-up multi-os support README: Fix repository URL in clone instruction Speed-up travis CI build using contained-based infrastructure Fix openssl_md_meth_names error reported on travis John Cary (2): Add option INSTALL_WINDOWS_TRADITIONAL Allow configuration providing the patch version. Fixes 0000057 John R. Cary (3): Fix undefined _PyTime_FloatTime symbol linker error Add Crypt32 library to _ssl_LIBRARIES to fix shared link. Exclude timemodule.c when building datemodule extension on windows. Marcel Metz (1): Escape PYTHONPATH macro value separator for NMake Matt McCormick (4): Expose ffi headers only for _ctypes module compiled on unix Add _ctypes support for x86, MSVC. Add support for 64-bit _ctypes with MSVC. Improve README overview text. Max Smolens (4): Fix building on windows Fix failing tests on Windows by making more modules built-in Hide CMake policy CMP0042 warnings Fix Unix build when CMAKE_BUILD_WITH_INSTALL_RPATH is enabled From: Max Smolens <max.smolens@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24525 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild/External_python.cmake | Diff File | ||
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master dd51ff1f 2015-09-09 10:20:07 Details Diff |
ENH: Update CTK to include PythonQt cleanup fixes $ git shortlog 35a187ff5ae15f1c590a2ac317cd102c5746a81b..3884436e0e089360c900e786513f821281a00805 --no-merges Julien Finet (1): Fix compilation on Visual Studio Max Smolens (3): Update PythonQt to patched-6 ctkAbstractPythonManager: Clean up PythonQt before finalizing the Python interpreter Update PythonQt to patched-5, which now includes selected updates from patched-6 From: Max Smolens <max.smolens@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24524 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild/External_CTK.cmake | Diff File | ||
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master dc914981 2015-09-08 18:43:22 Details Diff |
BUG: Fix constructor of ScriptedLoadableModuleTest This commit fixes a regression introduced in r24514 (ENH: allow self tests to set a default message display) where the constructor of the ScriptedLoadableModuleTest test case was specialized to set a default value for messageDelay ivar. Since the original constructor of a unittest.TestCase accept both regular arguments and keyword arguments, constructor in derived class have to use the form "*args, **kwargs". This commit fixes the following tests: py_DTINotReproducibleIssue3977 py_ColorsScalarBarSelfTest Associated error was of the form: //---------------- Traceback (most recent call last): File "/home/kitware/Dashboards/Nightly/Slicer-0-build/Slicer-build/lib/Slicer-4.4/qt-scripted-modules/ColorsScalarBarSelfTest.py", line 120, in runTest self.test_ColorsScalarBarSelfTest1() File "/home/kitware/Dashboards/Nightly/Slicer-0-build/Slicer-build/lib/Slicer-4.4/qt-scripted-modules/ColorsScalarBarSelfTest.py", line 124, in test_ColorsScalarBarSelfTest1 self.delayDisplay("Starting the scalarbar test") File "/home/kitware/Dashboards/Nightly/Slicer-0-build/Slicer-build/bin/Python/slicer/ScriptedLoadableModule.py", line 269, in delayDisplay slicer.util.delayDisplay(message, msec) File "/home/kitware/Dashboards/Nightly/Slicer-0-build/Slicer-build/bin/Python/slicer/util.py", line 637, in delayDisplay qt.QTimer.singleShot(autoCloseMsec, messagePopup.close) File "/home/kitware/Dashboards/Nightly/Slicer-0-build/Slicer-build/bin/Python/slicer/slicerqt.py", line 74, in _singleShot timer.start( msec ) ValueError: Could not find matching overload for given arguments: ('test_ColorsScalarBarSelfTest1',) The following slots are available: start(int msec) start() //---------------- git-svn-id: http://svn.slicer.org/Slicer4/trunk@24523 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Base/Python/slicer/ScriptedLoadableModule.py | Diff File | ||
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master 2e54ee9c 2015-09-08 16:58:00 Details Diff |
COMP: Update ITKv4 to maintain support for CMake >= v2.8.9 and <= v3 // ----------------- Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> Date: Tue Sep 8 16:11:02 2015 -0400 COMP: Set policy CMP0042 only if CMake version support it. Thanks: Bradley Lowekamp <blowekamp@mail.nih.gov> // ----------------- git-svn-id: http://svn.slicer.org/Slicer4/trunk@24522 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild/External_ITKv4.cmake | Diff File | ||
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master 1f134eca 2015-09-08 16:49:49 Details Diff |
ENH: Add test for DCMTK private dictionary. See issue 0004013 Philips phantom DWI dataset is included. The test runs dcmdump command, and looks for the description of tag (2001,1003), which should be DiffusionBFactor, and can only be recognized when private dictionary support is enabled in DCMTK. Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> Tested-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> From: Andrey Fedorov <fedorov@bwh.harvard.edu> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24521 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Applications/SlicerApp/Testing/Python/CMakeLists.txt | Diff File | ||
| add - Applications/SlicerApp/Testing/Python/DCMTKPrivateDictTest.py | Diff File | ||
| add - Testing/Data/Input/philips_ingenia_4_1_3_dwi.dcm | Diff File | ||
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master eabe277c 2015-09-04 16:43:11 naucoin Details Diff |
BUG: fix add storable after scene view test Move to using just the slicer.util.delayDisplay as using the self.delayDisplay was causing a conflict. git-svn-id: http://svn.slicer.org/Slicer4/trunk@24520 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Loadable/SceneViews/Testing/Python/AddStorableDataAfterSceneViewTest.py | Diff File | ||
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master 135f5c12 2015-09-04 14:16:51 Details Diff |
ENH: add extra DCMTK apps * dsr2html can be useful for creating human-readable representations of DICOM structured reports * xml2dcm and xml2dsr are reverse operations for existing converters to XML, which is using DCMTK-specific schema git-svn-id: http://svn.slicer.org/Slicer4/trunk@24519 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - CMake/SlicerBlockInstallDCMTKApps.cmake | Diff File | ||
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master aaa58166 2015-09-03 10:28:50 cpinter Details Diff |
BUG: Fixed python module tests by calling base constructor for ScriptedLoadableModuleTest git-svn-id: http://svn.slicer.org/Slicer4/trunk@24518 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Base/Python/slicer/ScriptedLoadableModule.py | Diff File | ||
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master 552ec3eb 2015-09-02 23:28:21 Details Diff |
COMP: Allow building EMSegment with C++11 EMSegment/CommandLineApplication/EMSegmentAPIHelper.h:112:21: error: invalid suffix on literal; C++11 requires a space between literal and identifier [-Wreserved-user-defined-literal] cout << "Setting "Slicer_HOME_ENVVAR_NAME" ..." << endl; From: Hans Johnson <hans-johnson@uiowa.edu> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24517 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild.cmake | Diff File | ||
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master 91acaa06 2015-09-02 08:25:15 Details Diff |
BUG: Fixed transform translation slider instability in rotate first mode How to reproduce the problem: 1. Create a new Transform 2. Switch to 'rotate first' mode (pushbutton pressed) 3. Drag the LR translation slider to 200 4. Drag the AP slider to 1 and back to 0 5. Drag the LR translation slider to the rightmost position => ERROR: the translation jumps to tens of thousands (instead of the expected 400) Fix: Don't update the translation slider range if in 'rotate first' mode. Set the matrix range to a fixed large value to allow larger translation values in the matrix than the slider range. git-svn-id: http://svn.slicer.org/Slicer4/trunk@24516 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Widgets/qMRMLLinearTransformSlider.cxx | Diff File | ||
| mod - Libs/MRML/Widgets/qMRMLTransformSliders.cxx | Diff File | ||
| mod - Libs/MRML/Widgets/qMRMLTransformSliders.h | Diff File | ||
| mod - Modules/Loadable/Transforms/qSlicerTransformsModuleWidget.cxx | Diff File | ||
| mod - Modules/Loadable/Transforms/qSlicerTransformsModuleWidget.h | Diff File | ||
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master 3dd75da5 2015-09-01 14:00:04 Details Diff |
BUG: qSlicerNodeWriter: Default parameters allowed incorrect usage This commit fixes the following warning obtained when compiling using clang and c++11. Slicer/Modules/Loadable/Models/qSlicerModelsModule.cxx:165:44: warning: 'this' pointer cannot be null in well-defined C++ code; pointer may be assumed to always convert to true [-Wundefined-bool-conversion] QStringList() << "vtkMRMLModelNode", this)); ^~~~ The 'this' pointer was interpreted as boolean. To ensure complete proper usage, the default parameters were removed, thus forcing compiler errors that were easy to identify and fix. From: Hans Johnson <hans-johnson@uiowa.edu> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24515 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Base/QTGUI/qSlicerNodeWriter.h | Diff File | ||
| mod - Modules/Loadable/Annotations/qSlicerAnnotationsModule.cxx | Diff File | ||
| mod - Modules/Loadable/Colors/qSlicerColorsModule.cxx | Diff File | ||
| mod - Modules/Loadable/DoubleArrays/qSlicerDoubleArraysModule.cxx | Diff File | ||
| mod - Modules/Loadable/Markups/qSlicerMarkupsModule.cxx | Diff File | ||
| mod - Modules/Loadable/Models/qSlicerModelsModule.cxx | Diff File | ||
| mod - Modules/Loadable/SceneViews/qSlicerSceneViewsModule.cxx | Diff File | ||
| mod - Modules/Loadable/TractographyDisplay/qSlicerTractographyDisplayModule.cxx | Diff File | ||
| mod - Modules/Loadable/Transforms/qSlicerTransformsModule.cxx | Diff File | ||
| mod - Modules/Loadable/VolumeRendering/qSlicerVolumeRenderingModule.cxx | Diff File | ||
| mod - Modules/Loadable/Volumes/qSlicerVolumesModule.cxx | Diff File | ||
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master 03d93916 2015-08-31 11:43:23 Details Diff |
ENH: allow self tests to set a default message display The default message delay for self.delayDisplay for a scripted module test is still 1 second, but can be set to a smaller value to speed up testing. It's still possible to override the delay time on a per-call basis, for example to highlight transitions between test sections by giving a longer timeout. git-svn-id: http://svn.slicer.org/Slicer4/trunk@24514 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Base/Python/slicer/ScriptedLoadableModule.py | Diff File | ||
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master ee3954a2 2015-08-28 14:03:59 Details Diff |
ENH: update MultiVolumeExplorer reorganization of the code git-svn-id: http://svn.slicer.org/Slicer4/trunk@24513 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild.cmake | Diff File | ||
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master 6976c394 2015-08-28 11:38:58 Details Diff |
STYLE: Improve readability of code in vtkReformatLogic::SetSliceNormal() git-svn-id: http://svn.slicer.org/Slicer4/trunk@24512 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Loadable/Reformat/Logic/vtkSlicerReformatLogic.cxx | Diff File | ||
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master d4c68cff 2015-08-27 12:35:13 Details Diff |
COMP: Update CTK to include QtTesting fixes $ git shortlog a1751e0..35a187f --no-merges Jean-Christophe Fillion-Robin (4): ctkAbstractPythonManagerTest: Fix typo ctkAbstractPythonManagerTest: Improve testExecuteString to check for error ctkAbstractPythonManagerTest: Update testExecuteString to check function call QtTesting: Update Git repository URL to fix invalid cert issues. Laurenn Lam (1): Fix ctkFileDialogEventTranslator bottom widget events recording git-svn-id: http://svn.slicer.org/Slicer4/trunk@24511 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild/External_CTK.cmake | Diff File | ||
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master cdf257d0 2015-08-27 12:10:59 Details Diff |
BUG: handle missing parameter for propagationMode for legacy mrml files Ron reported that the editor did not display correctly when loading an old mrml file (the SPL brain atlas from the DataStore). The issue was that the editor parameter node in the file did not contain a value for the propagationMode field and so the editor interface could not be constructed. This fix ensures that a valid propagation mode is selected in this case. TODO: it would be good to have a sanity check on the node to confirm that all needed values exist and if not they should be set to the application default. git-svn-id: http://svn.slicer.org/Slicer4/trunk@24510 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Scripted/EditorLib/EditBox.py | Diff File | ||
| mod - Modules/Scripted/EditorLib/EditUtil.py | Diff File | ||
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master fcef008b 2015-08-26 16:36:46 naucoin Details Diff |
BUG: remove extra node added event When switching to using a mini scene to try various ways of loading volumes, the final node added event wasn't removed when I switched to using AddNode to move the final set of nodes into the main scene. This change removes the extra node added event triggered by adding a volume. Issue 0004033 git-svn-id: http://svn.slicer.org/Slicer4/trunk@24509 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Loadable/Volumes/Logic/vtkSlicerVolumesLogic.cxx | Diff File | ||
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master d20e98ac 2015-08-26 15:50:05 Details Diff |
ENH: update MultiVolumeExplorer Enhancements in code organization, make the chart detachable. git-svn-id: http://svn.slicer.org/Slicer4/trunk@24508 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild.cmake | Diff File | ||
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master 4e54d1fc 2015-08-26 08:31:42 Details Diff |
BUG: env variable was incorrectly initialized DCMDICTPATH should be used, not DCMDICTHOME. Thanks to @jcfr for catching this. git-svn-id: http://svn.slicer.org/Slicer4/trunk@24507 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild/External_DCMTK.cmake | Diff File | ||
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master a4129c45 2015-08-25 16:13:54 Details Diff |
BUG: Make sure display nodes are observed before adding model to scene This caused a subtle bug reported by Beatriz Paniagua. Sequence to reproduce before this change: * start fresh slicer * make green slice visible (it appears) * close scene * make green slice visible (BUG: it does not appear) * perform any other operation that changes the 3D view, green slice appears Note that the issue only happened with the green slice model, which importantly is the last one on the list. Issue was because all slice models where observing their display nodes *after* being added to the scene, meaning that the displayable manager saw no display node on the model nodes when it got the node added event for the model node and therefore did not observe the node. Other slice model nodes did not exhibit this issue because they were being refreshed when other nodes were added to the scene. git-svn-id: http://svn.slicer.org/Slicer4/trunk@24506 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Logic/vtkMRMLSliceLogic.cxx | Diff File | ||
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master ba983891 2015-08-25 16:13:52 Details Diff |
STYLE: remove out of date comment Global hotkeys for 'e' and backslash have been moved to qt and are no longer handled as vtk events. git-svn-id: http://svn.slicer.org/Slicer4/trunk@24505 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Scripted/EditorLib/Effect.py | Diff File | ||
