1. 19 Dec, 2017 40 commits
    • jcfr's avatar
      ENH: Slicer 4.8.1 · 94a26e01
      jcfr authored
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26813 3bd1e089-480b-0410-8dfb-8563597acbee
      94a26e01
    • jcfr's avatar
      COMP: Fix macOS CMP0011 warning in SlicerExtensionCPackBundleFixup CMake module · 4e644ff7
      jcfr authored
      The following warning was reported when directly invoking the module
      from the command line.
      
      For example:
      
      $ cmake \
        -DCMAKE_INSTALL_PREFIX:PATH=/path/to/SlicerVMTK-build/inner-build/_CPack_Packages/Darwin/TGZ/26720-macosx-amd64-SlicerVMTK-git0efbf09-2017-12-18 \
        -P SlicerExtensionBundle/SlicerExtensionCPackBundleFixup.cmake
      
      CMake Warning (dev) in /path/to/Slicer/CMake/BundleUtilitiesWithRPath.cmake:
        Policy CMP0011 is not set: Included scripts do automatic cmake_policy PUSH
        and POP.  Run "cmake --help-policy CMP0011" for policy details.  Use the
        cmake_policy command to set the policy and suppress this warning.
      
        The included script
      
          /path/to/Slicer/CMake/BundleUtilitiesWithRPath.cmake
      
        affects policy settings.  CMake is implying the NO_POLICY_SCOPE option for
        compatibility, so the effects are applied to the including context.
      Call Stack (most recent call first):
        SlicerExtensionBundle/SlicerExtensionCPackBundleFixup.cmake:2 (include)
      This warning is for project developers.  Use -Wno-dev to suppress it.
      
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26812 3bd1e089-480b-0410-8dfb-8563597acbee
      4e644ff7
    • jcfr's avatar
      ENH: Made DICOM loading of scalar volume more configurable · 2fa90d6d
      jcfr authored
      Added options to application settings:
      
      - Acquisition geometry regularization: enable/disable adding regularization transform.
        A default option is added for those who don't know/don't care. For now, it is disabled by default.
        When an issue is found then Slicer displays a warning and the user may enable regularization.
        In the future we may add a "resample" option as well, to not just apply a transform but also use
        it to resample the volume.
      
      - Allow loading subseries by time: if disabled (default) then loadables are not offered by content or trigger time.
        This reduces clutter and increases chance that users try alternative loadables, grouped for example by image orientation.
      
      Minor improvements:
      - Simpler node names are generated for subseries. Instead of including actual image orientation and timestamps (which are long, cryptic
      strings), we use just indexes (imageOrientationPatient 1, imageOrientationPatient 2, ...).
      - Acquisition transform is added under the same subject hierarchy folder as the volume.
      
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26811 3bd1e089-480b-0410-8dfb-8563597acbee
      2fa90d6d
    • jcfr's avatar
      BUG: Fix import of vtk modules when building against VTKv9 and Qt5 · ff1186b8
      jcfr authored
      This commit updates the build system to ensure vtk can be imported from
      a build or an install tree.
      
      It fixes a regression introduced in r26697 where a newer version VTK9
      is used. The Slicer build system is updated to adapt to changes
      introduced the commit kitware/VTK@867d93c (Cleanup VTK's Python package.).
      
      It also updates VTK9 to include the following patch:
      
      $ git shortlog Slicer/VTK@27c57a1..Slicer/VTK@887c506 --no-merges
      Jean-Christophe Fillion-Robin (1):
            cmake: re-associate RuntimeLibraries component with python install rules
      
      also contributed upstream as vtk/vtk!3708
      
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26810 3bd1e089-480b-0410-8dfb-8563597acbee
      ff1186b8
    • jcfr's avatar
      STYLE: Update VTK external project removing obsolete Tcl options · 505ce0db
      jcfr authored
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26809 3bd1e089-480b-0410-8dfb-8563597acbee
      505ce0db
    • jcfr's avatar
      b3914999
    • jcfr's avatar
      STYLE: qSlicerSceneWriter: Remove unused variable · 3fe53c9d
      jcfr authored
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26807 3bd1e089-480b-0410-8dfb-8563597acbee
      3fe53c9d
    • jcfr's avatar
      ENH: Update vtkMRMLScene API adding "IsNodeClassRegistered" function · e57ffc42
      jcfr authored
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26806 3bd1e089-480b-0410-8dfb-8563597acbee
      e57ffc42
    • jcfr's avatar
      468d580f
    • jcfr's avatar
      COMP: Update CTK to fix DICOM/Widgets unused-variable warnings · 5384b608
      jcfr authored
      List of changes:
      
      $ git shortlog 4292fe0..1e13d98 --no-merges
      Jean-Christophe Fillion-Robin (1):
            COMP: Fix unused-variable warnings in DICOM/Widgets
      
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26804 3bd1e089-480b-0410-8dfb-8563597acbee
      5384b608
    • jcfr's avatar
      COMP: Fix in sign-compare warning in vtkITKTransformConverter · a4ec7d80
      jcfr authored
      This commit fixes the following warning:
      
      /home/kitware/Dashboards/Nightly/Slicer-0/Libs/MRML/Core/vtkITKTransformConverter.h: In static member function 'static bool vtkITKTransformConverter::SetITKImageFromVTKOrientedGridTransform(vtkObject*, itk::Image<itk::Vector<double, 3u>, 3u>::Pointer&, vtkOrientedGridTransform*)':
      /home/kitware/Dashboards/Nightly/Slicer-0/Libs/MRML/Core/vtkITKTransformConverter.h:1011:53: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26803 3bd1e089-480b-0410-8dfb-8563597acbee
      a4ec7d80
    • jcfr's avatar
      COMP: Fix unused variable warnings · 35d1c820
      jcfr authored
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26802 3bd1e089-480b-0410-8dfb-8563597acbee
      35d1c820
    • jcfr's avatar
      COMP: Update VTK project removing support for Slicer_VTK_VERSION_MAJOR=8 · fb155ed5
      jcfr authored
      Following this commit, the maintenance of VTK external project is streamlined.
      Only VTK7 and VTK9 will be checked out. Setting Slicer_VTK_VERSION_MAJOR to 8
      will report an error.
      
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26801 3bd1e089-480b-0410-8dfb-8563597acbee
      fb155ed5
    • jcfr's avatar
      COMP: Update vtkFSLookupTable to support changes integrated in previous commit · dcbd580c
      jcfr authored
      See r26708
      
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26800 3bd1e089-480b-0410-8dfb-8563597acbee
      dcbd580c
    • jcfr's avatar
      COMP: Update VTKv7 to fix build error · c8e8cee3
      jcfr authored
      
      Reported-by: Dženan Zukić's avatarDzenan Zukic <dzenan.zukic@kitware.com>
      
      List of changes:
      
      commit kitware/VTK@43f6ee3
      Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
      Date:   Tue Dec 12 18:07:48 2017 -0500
      
          Backport "Made vtkScalarsToColor::MapValue() return const"
      
          This commit backports https://github.com/Kitware/VTK/commit/ce5575e36aef609c125b8c3a577a9cccd9cdde30
      
          See https://discourse.slicer.org/t/vtkfslookuptable-mapvalue-signature-changed/1640/8
      
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26799 3bd1e089-480b-0410-8dfb-8563597acbee
      c8e8cee3
    • jcfr's avatar
      COMP: CTestCustom: Update exception list to ignore Python windows warnings · 062efe74
      jcfr authored
      Ignore warning like this one:
      
      c:\d\n\slicer-0-build\python-2.7.13\modules\socketmodule.h(26): warning C4005: 'HAVE_SOCKADDR_STORAGE' : macro redefinition [C:\D\N\Slicer-0-build\python-build\CMakeBuild\extensions\extension_socket\extension_socket.vcxproj] [C:\D\N\Slicer-0-build\python.vcxproj]
      C:\D\N\Slicer-0-build\Python-2.7.13\PC\bdist_wininst\install.c(2086): warning C4133: '=' : incompatible types - from 'BOOL (__cdecl *)(HWND,UINT,WPARAM,LPARAM)' to 'DLGPROC' [C:\D\N\Slicer-0-build\python-build\CMakeBuild\bdist_wininst\bdist_wininst.vcxproj] [C:\D\N\Slicer-0-build\python.vcxproj]
      
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26798 3bd1e089-480b-0410-8dfb-8563597acbee
      062efe74
    • jcfr's avatar
    • jcfr's avatar
      COMP: CTestCustom: Remove exception associated with Qt 4.6.2 · c826cd30
      jcfr authored
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26796 3bd1e089-480b-0410-8dfb-8563597acbee
      c826cd30
    • jcfr's avatar
      891a31f2
    • jcfr's avatar
      COMP: CTestCustom: Generalize warning exception associated with LNK4221 · d1208ca4
      jcfr authored
      This will address warnings like the following:
      
      vtkOpenGLVolumeTextureMapper3D.obj : warning LNK4221: This object file does not define any previously undefined public symbols, so it will not be used by any link operation that consumes this library [C:\D\N\Slicer-0-build\VTKv9-build\Rendering\VolumeOpenGL\vtkRenderingVolumeOpenGLObjects.vcxproj] [C:\D\N\Slicer-0-build\VTKv9.vcxproj]
      
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26794 3bd1e089-480b-0410-8dfb-8563597acbee
      d1208ca4
    • jcfr's avatar
      COMP: CTestCustom: Add Lua, PythonQtConversion and vtkkwiml warning exceptions · 22d2dabd
      jcfr authored
      This commit should suppress warnings like the following:
      
      Lua
      ---
      
      /Users/kitware/Dashboards/Nightly/Slicer-0-build/SimpleITK-build/Lua-prefix/src/Lua/src/lauxlib.c:577:61: warning: while loop has empty body [-Wempty-body]
         while ((c = getc(lf.f)) != EOF && c != LUA_SIGNATURE[0]) ;
                                                                  ^
      /Users/kitware/Dashboards/Nightly/Slicer-0-build/SimpleITK-build/Lua-prefix/src/Lua/src/lauxlib.c:577:61: note: put the semicolon on a separate line to silence this warning [-Wempty-body]
      1 warning generated.
      
      PythonQt
      --------
      
      /Users/kitware/Dashboards/Nightly/Slicer-0-build/CTK-build/CMakeExternals/Install/include/PythonQt/PythonQtConversion.h:485:23: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
          PyObject* items = PyMapping_Items(val);
                            ^
      /Users/kitware/Dashboards/Nightly/Slicer-0-build/python-install/include/python2.7/abstract.h:1354:50: note: expanded from macro 'PyMapping_Items'
      #define PyMapping_Items(O) PyObject_CallMethod(O,"items",NULL)
      
      
      /Users/kitware/Dashboards/Nightly/Slicer-0-build/CTK-build/PythonQt/src/PythonQtConversion.cpp:538:25: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
               if (ok && (val >= 0 && val <= UINT_MAX)) {
                          ~~~ ^  ~                                                 ^
      
      
      /Users/kitware/Dashboards/Nightly/Slicer-0-build/CTK-build/PythonQt/src/PythonQtSlot.cpp:399:19: warning: expression result unused [-Wunused-value]
          PyObject_INIT(op, &PythonQtSlotFunction_Type);
      
      
      /Users/kitware/Dashboards/Nightly/Slicer-0-build/CTK-build/PythonQt/src/PythonQtSignalReceiver.cpp:234:22: warning: '&&' within '||' [-Wlogical-op-parentheses]
        if ((foundCount>0) && (sigId == _destroyedSignal1Id) || (sigId == _destroyedSignal2Id)) {
            ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~
      
      
      In file included from /home/kitware/Dashboards/Nightly/Slicer-0-build/CTK-build/CMakeExternals/Install/include/PythonQt/PythonQt.h:47:0,
                       from /home/kitware/Dashboards/Nightly/Slicer-0-build/CTK-build/CTK-build/Libs/Core/generated_cpp/org_commontk_CTKCore/org_commontk_CTKCore_init.cpp:6:
      /home/kitware/Dashboards/Nightly/Slicer-0-build/CTK-build/CMakeExternals/Install/include/PythonQt/PythonQtInstanceWrapper.h: In member function 'PythonQtClassInfo* PythonQtInstanceWrapperStruct::classInfo()':
      /home/kitware/Dashboards/Nightly/Slicer-0-build/CTK-build/CMakeExternals/Install/include/PythonQt/PythonQtInstanceWrapper.h:68:37: warning: use of old-style cast [-Wold-style-cast]
      
      
      vtkkwiml
      --------
      
      /home/kitware/Dashboards/Nightly/Slicer-0-build/VTKv9/Utilities/KWIML/vtkkwiml/include/kwiml/abi.h:536:1: warning: use of old-style cast [-Wold-style-cast]
      
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26793 3bd1e089-480b-0410-8dfb-8563597acbee
      22d2dabd
    • jcfr's avatar
      2816cca0
    • jcfr's avatar
      COMP: CTestCustom: Remove obsolete Numpy warning exceptions · 5a67f2f7
      jcfr authored
      Since r23070 (ENH: Generalize NUMPY/SimpleITK build system), numpy
      configure/build/install outputs are captured in files, there is no
      need to use exceptions.
      
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26791 3bd1e089-480b-0410-8dfb-8563597acbee
      5a67f2f7
    • jcfr's avatar
      COMP: Fix macOS CMP0009 warning in SlicerCPackBundleFixup CMake module · 9cc406e2
      jcfr authored
      This commit should fix the following warning:
      
      CMake Warning (dev) at /Users/kitware/Dashboards/Nightly/Slicer-0/CMake/BundleUtilitiesWithRPath.cmake:857 (file):
        Policy CMP0009 is not set: FILE GLOB_RECURSE calls should not follow
        symlinks by default.  Run "cmake --help-policy CMP0009" for policy details.
        Use the cmake_policy command to set the policy and suppress this warning.
      Call Stack (most recent call first):
        /Users/kitware/Dashboards/Nightly/Slicer-0/CMake/BundleUtilitiesWithRPath.cmake:938 (verify_bundle_prerequisites)
        /Users/kitware/Dashboards/Nightly/Slicer-0/CMake/BundleUtilitiesWithRPath.cmake:835 (verify_app)
        /Users/kitware/Dashboards/Nightly/Slicer-0-build/Slicer-build/CMake/SlicerCPackBundleFixup/SlicerCPackBundleFixup.cmake:320 (fixup_bundle)
        /Users/kitware/Dashboards/Nightly/Slicer-0-build/Slicer-build/CMake/SlicerCPackBundleFixup/SlicerCPackBundleFixup.cmake:328 (fixup_bundle_with_plugins)
        /Users/kitware/Dashboards/Nightly/Slicer-0-build/Slicer-build/CMake/SlicerCPackBundleFixup-binary/cmake_install.cmake:31 (include)
        /Users/kitware/Dashboards/Nightly/Slicer-0-build/Slicer-build/CMake/LastConfigureStep/cmake_install.cmake:292 (include)
        /Users/kitware/Dashboards/Nightly/Slicer-0-build/Slicer-build/cmake_install.cmake:57 (include)
      This warning is for project developers.  Use -Wno-dev to suppress it
      
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26790 3bd1e089-480b-0410-8dfb-8563597acbee
      9cc406e2
    • jcfr's avatar
      COMP: Update CTK to fix compilation error when using Qt4 and C++98 · 854e05d3
      jcfr authored
      $ git shortlog 8c4bed5..4292fe0 --no-merges
      Jean-Christophe Fillion-Robin (1):
            COMP: Update ctkVTKDiscretizableColorTransferWidget to support C++98
      
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26789 3bd1e089-480b-0410-8dfb-8563597acbee
      854e05d3
    • jcfr's avatar
      ENH: Update VTK · 719357c5
      jcfr authored
      List of changes for VTK7:
      
      $ git shortlog 57d826c..c19ce17 --no-merges
      Andras Lasso (1):
            Fix interactionState computation in SeedWidget
      
      List of changes for VTK8:
      
      $ git shortlog 71cf316..b796f88 --no-merges
      Andras Lasso (1):
            Fix interactionState computation in SeedWidget
      
      List of changes for VTK9:
      
      $ git shortlog e3f97b0..27c57a1 --no-merges
      Allison Vacanti (8):
            Restore Timing functionality for D3/PkTree.
            Replaced std::set with std::vector/sort/unique in vtkExtractCells.
            Optimize the PointMap lookup in vtkExtractCells (12.8% speedup in D3).
            Use a batch copy for points/pointdata in vtkExtractCells.
            Add a minimum ghost level option to D3.
            Fix MSVC warning C4512 in KdTree and D3 classes.
            Deprecate vtkHyperOctreeFractalSource.
            Deprecate everything that touches vtkHyperOctree.
      
      Alvaro Sanchez (1):
            Fix various build issues of vtkRenderingOptiX.
      
      Andras Lasso (1):
            Fix interactionState computation in SeedWidget
      
      Andrew Bauer (4):
            Fixing vtkExodusIIReader issue with QA record name length
            Cleanup and improvements for vtkPUnstructuredGridGhostCellsGenerator
            Pre-incrementing stl iterators instead of post-incrementing
            Fixing using EGL when kits are enabled
      
      Ben Boeckel (48):
            utf8: remove old import
            utf8: add an update script
            utf8: add module infrastructure
            cmake: use the vtkutf8 module
            vtkMakeInstantiator: remove support
            cmake: remove usage of the ABSTRACT property
            tcl: deprecate for 8.1
            vtkJavaUtil: support converting constant arrays to Java
            vtkOpenGLBufferObject: include missing <string> header
            vtkOpenGLGL2PSHelperImpl: also don't wrap in Python
            vtkWrapJava: make empty files for unwrappable classes
            Common/Core: fix source file property settings
            Java: follow Python
            Java: vtkRenderWindowPanel needs vtkCanvas
            Java: remove `-sourcepath` arguments
            Utilities/Rpm: remove
            TclTk: remove old versions
            vtkPythonInteractiveInterpreter: remove const casting
            vtkEncodeString: add a module to write a C string for content
            vtkEncodeString: replace the executable with a CMake script
            Utilities/EncodeString: deprecate for the vtkEncodeString module
            vtkX3DExporterXMLWriter: include <string>
            Testing/External: include vtkEncodeString
            wrapping: use WRAP_EXCLUDE_PYTHON for the hierarchy
            wrapping: support creating hierarchy files independently
            wrapping: remove support for SIP wrapping
            vtkDataArrayIteratorMacro: don't comment line continuations
            vtkGenericDataArrayLookupHelper: don't use C++11 initializer lists
            vtkOStreamWrapper: hide from the wrappers
            vtkTestDataArray: include vtkObjectFactory.h
            vtkVariant: include vtkObject.h
            Common/Core: install the vtkSMPTools header
            Rendering/GL2PSOpenGL2: set properties consistently
            qt4: remove support
            Examples/HyperTree: remove unused example
            modules: update modules for OpenGL1 removal
            opengl1: remove OpenGL1-backend modules and examples
            Maintenance: remove backend switching support
            opengl1: remove conditional code for the OpenGL1 backend
            cmake: simplify VTK_RENDERING_BACKEND conditionals
            vtkXRenderWindowTclInteractor: remove unused class
            tcl: remove Tcl tests
            examples: remove Tcl code
            cmake: remove support for Tcl wrapping
            tcl: remove support from helper scripts and tools
            tcl: remove references from comments
            Rendering/Tk: fix for post-Tcl world
            Accelerators/Vtkm: don't overwite other job pools
      
      Bill Lorensen (13):
            ENH: More baselines and examples
            Update WikiExamples.remote.cmake
            Update WikiExamples.remote.cmake
            Update WikiExamples.remote.cmake
            ENH: Fixed baselines ans added new examples.
            ENH: Bump VTKExamples version
            ENH: Enable git lfs
            ENH: Bump VTKExamples version
            Update WikiExamples.remote.cmake
            Update WikiExamples.remote.cmake
            ENH: Bump VTKExamples
            Update WikiExamples.remote.cmake
            Update WikiExamples.remote.cmake
      
      Bjoern Thiel (1):
            debug name for python modules on windows
      
      Boonthanome Nouanesengsy (1):
            Improving vtkPUnstructuredGridGhostCellsGenerator filter
      
      Cory Quammen (4):
            Fixed MPI tests specified with custom names
            Add guards for null XAxis and YAxis.
            Added parallel connectivity filter
            Added documentation on parallel connectivity algorithm
      
      David E. DeMarle (1):
            add a quick and dirty material reader
      
      GitSetup Upstream (2):
            GitSetup 2017-10-26 (1639317d)
            GitSetup 2017-12-01 (91813607)
      
      H. Cole Wiley (4):
            added check for GL_POINT_SPRTIE define
            using cmakedefine for ANDROID since its not being defined else where
            applied fixes that allow Android to bind to current EGL context
            commneted out vtkRegressionTestImage
      
      Joachim Pouderoux (1):
            Add support for vtkMolecule I/O in Programmable Filter & Source.
      
      Ken Martin (8):
            suppress a gcc/boost warning
            fix issues with the array calc and string arrays
            fixed case where the array name differed from
            add an executable to do opengl detection
            Remove vtkProbeOpebGLSupport executable from Mobile
            patch from Kathleen S. Biagas fixing opacity
            update shadow maps to use exponential functions
            just catching some more places with NULL in them
      
      Kenneth Moreland (4):
            Fix errors with variable names with hyphen in git setup scripts
            Remove VTK-m includes and libs from test compile
            Remove references to VTK-m header files from VTK filters
            Remove direct usage of VTK-m in LOD test
      
      Mathieu Westphal (6):
            Adding opacity support in vtkDiscretizableColorTransferFunction
            Fix a bug when opening composite table files
            fix DiscretizableColorTransferFunction legacy typos
            Adding a vector array parameter to the transform method
            Fix a missing include of <string>
            Remove breaks that were genrating warnings
      
      Max Smolens (1):
            COMP: WIP: Fix inconsistent-missing-override warning
      
      Menno Deij - van Rijswijk (8):
            fixed a corner-case out-of-memory crash in polygon builder
            don't use vtkNew, but do free up unused vtkIdList
            pre-emptive style guide conformation
            pre-emptive style guide conformation
            merge changes
            don't use vtkNew, but do free up unused vtkIdList
            pre-emptive style guide conformation
            pre-emptive style guide conformation
      
      Michael Migliore (6):
            Add quaternion support in vtkOpenGLGlyph3DMapper
            Fix mapper and create test
            Fix quaternion glyphs on OpenGL1
            Add include to fix build
            Cosmetic changes
            Fix OpenGL1 test
      
      Mmanu Chaturvedi (1):
            Fix memory leakage in vtkWrapHierarchy.c
      
      Philippe P. Pébaÿ (1):
            Fixed an initialized-yet-unused-variable warning on Windows
      
      Philippe Pébaÿ (3):
            Fixed issues with the computation of material interfaces in HTG
            Modified non-regression test for interface reconstruction.
            Fix two HTG examples and some annoying typos in the documentation.
      
      Robert Maynard (3):
            Correct bugs that the new VTK-m dispatcher type checking has found.
            Update the VTK-m submodule to get the improved dispatcher code.
            VTK-m: When building with ninja use job pools to reduce memory usage
      
      Sankhesh Jhaveri (12):
            Provide access to the shader program in UpdateShaderEvent callback
            Added test that demonstrates ability to set shader uniforms from python
            Invoke UpdateShaderEvent from volume mapper
            Fix clear shader replacement issue
            API to clear all shader replacements
            Provide access to the shader program in UpdateShaderEvent callback
            Added test that demonstrates ability to set shader uniforms from python
            Invoke UpdateShaderEvent from volume mapper
            Clear all custom shader code in clear shader API
            Create a default render window for the QVTKOpenGLWidget
            Port the TestQtSwapWindows test to use modern QVTKOpenGLWidget
            Add MTime check to rebuild shaders when user replacements change
      
      Sean McBride (3):
            Fixed, again, a slightly incorrect assert
            Made vtkScalarsToColor::MapValue() return const
            Replaced many int with vtkTypeBool
      
      Shawn Waldon (1):
            Treat signed and unsigned char data as integers when labeling
      
      Steve Pieper (1):
            BUG: WIP: fix vtkPickingManager interaction with widgets
      
      Tiff Upstream (1):
            tiff 2017-12-05 (818c6fed)
      
      Utkarsh Ayachit (33):
            Fix install/build paths for mpi4py.
            Add vtkPythonInterpreter to vtkWrappingPythonCore.
            Python < 2.4 is no longer supported. Remove related code.
            Cleanup VTK's Python package.
            Clean Python related CMake variables.
            Python interpreter fixes.
            Help static builds find vtk modules.
            fix VTK module import.
            another attemp to fix kit build/run issues.
            Handle VS generator.
            Help Windows builds find PythonD dlls.
            Add target for `vtk` python package.
            Fix path setup when in an App on OsX.
            Default program name in Python 3 is `python3`.
            Use default library search order to locate syms.
            Adding vtkResourceFileLocator
            Update vtkPythonInterpreter to use vtkResourceFileLocator.
            Fix importing of VTK Python modules.
            Don't copy *Python.so files during installation.
            Improve support for multi-config generators.
            Don't use deprecated `<CONFIGURATION>`.
            Fix vtkBuildPath to reflect new Python package locations.
            Fix incorrect warning message.
            Plot3D wasn't supporting bigendian. Fixed it.
            Add missing override.
            Use relative imports in `vtk` package.
            Use vtkIdType in vtkMergeCells for indices.
            Handle long string in vtkDataWriter.
            Handle spaces in path.
            Support Python with frozen modules.
            Make vtkOutputWindow::New create a new instance.
            Make `vtkpython` output messages to stderr/stdout.
            Use std::unordered_map & std::unordered_set.
      
      Will Schroeder (1):
            Remove compilation warnings
      
      luzpaz (1):
            Misc. typo fixes
      
      utf8cpp Upstream (3):
            utf8 2017-11-14 (4e3d1c17)
            utf8 2017-11-15 (f2a3fced)
            utf8 2017-11-22 (e8de6037)
      
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26788 3bd1e089-480b-0410-8dfb-8563597acbee
      719357c5
    • jcfr's avatar
      COMP: CTestCustom: Update warning exceptions · 26b569d6
      jcfr authored
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26787 3bd1e089-480b-0410-8dfb-8563597acbee
      26b569d6
    • jcfr's avatar
      COMP: ensure copied items writable in cpack staging dir · f0575c36
      jcfr authored
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26786 3bd1e089-480b-0410-8dfb-8563597acbee
      f0575c36
    • jcfr's avatar
      ENH: Update CTK to include python console fix · 5d22bd5d
      jcfr authored
      See https://github.com/commontk/CTK/issues/736
      
      List of changes:
      
      $ git shortlog cb6f57a..8c4bed5 --no-merges
      Csaba Pitner (1):
            BUG: Fixed console paste bug
      
      Tristan (2):
            Improve color table widget
            Improve ctkSliderWidget and ctkVTKDiscretizableColorTransferWidget
      
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26785 3bd1e089-480b-0410-8dfb-8563597acbee
      5d22bd5d
    • jcfr's avatar
      COMP: Improve support for <projectName>_USE_GIT_PROTOCOL option · e51b6cab
      jcfr authored
      * Use "https" instead of "http"
      * Remove ITKv3 deprecated setting
      
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26784 3bd1e089-480b-0410-8dfb-8563597acbee
      e51b6cab
    • jcfr's avatar
      COMP: don't exclude Qt as system library when packaging · bb745aca
      jcfr authored
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26783 3bd1e089-480b-0410-8dfb-8563597acbee
      bb745aca
    • jcfr's avatar
      COMP: Fix setting of EXTERNAL_PROJECT_DIR · 824e3ed4
      jcfr authored
      Since Slicer project is not yet added when setting the variable, use
      CMAKE_CURRENT_SOURCE_DIR instead.
      
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26782 3bd1e089-480b-0410-8dfb-8563597acbee
      824e3ed4
    • jcfr's avatar
      764f4ee5
    • jcfr's avatar
      COMP: ExternalProjectForNonCMakeProject: Only re-use CMAKE_(C|CXX)_FLAGS_INIT · 92d1179b
      jcfr authored
      This allows use of the module in extension building python packages.
      
      Indeed, since regular CMAKE_(C|CXX)_FLAGS can contain flags incompatible
      with python packages (e.g "-Wl,--no-undefined"), this commit removes
      usage of the variable to initialize CFLAGS and CXXFLAGS variables.
      
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26780 3bd1e089-480b-0410-8dfb-8563597acbee
      92d1179b
    • jcfr's avatar
      BUG: Ensure user site-packages are not imported by PythonQt · 81de94c2
      jcfr authored
      This commit ensures that packages installed in directory like "~/.local/"
      are not imported before Slicer own packages.
      
      References:
      * https://docs.python.org/2/library/site.html#site.getusersitepackages
      * https://www.python.org/dev/peps/pep-0370/
      
      Reported-by: Dženan Zukić's avatarDzenan Zukic <dzenan.zukic@kitware.com>
      Reported-by: Forrest Li's avatarForrest Li <forrest.li@kitware.com>
      
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26779 3bd1e089-480b-0410-8dfb-8563597acbee
      81de94c2
    • jcfr's avatar
      BUG: Added Latin1 encoding specification to saved MRML file · c35dbb4b
      jcfr authored
      In case special characters (e.g. in the patient name) ended up being saved in the MRML file, loading the MRML failed due to an XML reading error. These special characters were valid in Slicer, as they were produced by slicer.util.toVTKString. If the character set is specified in the MRML file, then loading is successful.
      
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26778 3bd1e089-480b-0410-8dfb-8563597acbee
      c35dbb4b
    • jcfr's avatar
      ENH: Do not reset view when Segmentation master node selected · 7e097b14
      jcfr authored
      User may have carefully set up view, so resetting it when switching to Segment Editor module would cause inconvenience.
      
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26777 3bd1e089-480b-0410-8dfb-8563597acbee
      7e097b14
    • jcfr's avatar
      ENH: Update LandmarkRegiration (save grid transform) · 17b41545
      jcfr authored
      This change includes a fix so that exported grid
      transforms are vtkOrientedGridTransform and can
      be saved in .h5 format.
      
      From: Steve Pieper <pieper@isomics.com>
      
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26776 3bd1e089-480b-0410-8dfb-8563597acbee
      17b41545
    • jcfr's avatar
      COMP: Update VisualStudioProject launcher option to always open Slicer.sln · f53d6447
      jcfr authored
      
      
      Since the top-level solution file is always named "Slicer.sln", this commit
      removes the use of Slicer_MAIN_PROJECT_APPLICATION_NAME variable.
      Suggested-by: Dženan Zukić's avatarDzenan Zukic <dzenan.zukic@kitware.com>
      
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26775 3bd1e089-480b-0410-8dfb-8563597acbee
      f53d6447
    • jcfr's avatar
      COMP: Fix setting of Slicer_SUPERBUILD_DIR for Slicer Custom application · 768fdd5b
      jcfr authored
      
      
      This commit updates the build system so that it:
      * ensures that python files are packaged
      * an error is reported if "PYTHON_DIR" variable is not set in SlicerBlockInstallPython
      
      Symptom leading to this fix was the following error reported when
      starting the application:
      
        ImportError: No module named site
      Co-authored-by: Dženan Zukić's avatarDzenan Zukic <dzenan.zukic@kitware.com>
      
      git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26774 3bd1e089-480b-0410-8dfb-8563597acbee
      768fdd5b