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Commits on Dec 8, 2017
  1. ENH: Update LandmarkRegiration (save grid transform)

    pieper committed Dec 8, 2017
    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/trunk@26685 3bd1e089-480b-0410-8dfb-8563597acbee
Commits on Dec 7, 2017
  1. COMP: Update VisualStudioProject launcher option to always open Slice…

    jcfr committed Dec 7, 2017
    …r.sln
    
    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: Dzenan Zukic <dzenan.zukic@kitware.com>
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26684 3bd1e089-480b-0410-8dfb-8563597acbee
  2. COMP: Fix setting of Slicer_SUPERBUILD_DIR for Slicer Custom application

    jcfr committed Dec 7, 2017
    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: Dzenan Zukic <dzenan.zukic@kitware.com>
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26683 3bd1e089-480b-0410-8dfb-8563597acbee
  3. ENH: ExternalProjectForNonCMakeProject: Support disabling file capture

    jcfr committed Dec 7, 2017
    This commit teaches "ExternalProject_Execute" function to understand
    the variable EP_EXECUTE_DISABLE_CAPTURE_OUTPUTS. If set to 1, output
    is directly reported and not captured into files.
    
    This is particularly useful when debugging issue with building and installing
    of python packages.
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26682 3bd1e089-480b-0410-8dfb-8563597acbee
  4. COMP: ExternalProjectForNonCMakeProject: Fix ExternalProject_Execute

    jcfr committed Dec 7, 2017
    Remove incorrect "PYTHON_EXECUTABLE" argument. This has never been a
    problem because the variable was never set in the current scope.
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26681 3bd1e089-480b-0410-8dfb-8563597acbee
Commits on Dec 6, 2017
  1. BUG: Update cli.py, fix to runSync method

    lassoan committed Dec 6, 2017
    The call to run that is made in cli.runSync does not pass along the update_display parameter, even though runSync accepts it as a parameter. This fix passes the value of update_display to the run method.
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26680 3bd1e089-480b-0410-8dfb-8563597acbee
  2. BUG: Fixed using specified database in DICOMUtils function

    pinter committed Dec 6, 2017
    Also reduced an error message to debug in a recent subject hierarchy function
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26679 3bd1e089-480b-0410-8dfb-8563597acbee
  3. BUG: DICOMDetailsBase: Fix promptForDatabaseDirectory implementation …

    jcfr committed Dec 6, 2017
    …for Qt5
    
    This commit fixes the following error reported when loading the DICOM
    module:
    
    File "/path/to/Slicer-build/lib/Slicer-4.9/qt-scripted-modules/DICOMLib/DICOMWidgets.py", line 519, in promptForDatabaseDirectory
        documentsLocation = qt.QDesktopServices.DocumentsLocation
    AttributeError: QDesktopServices has no attribute named 'DocumentsLocation'
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26678 3bd1e089-480b-0410-8dfb-8563597acbee
  4. BUG: Fix Qt5 implementation of qSlicerCoreApplication::defaultScenePa…

    jcfr committed Dec 6, 2017
    …th()
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26677 3bd1e089-480b-0410-8dfb-8563597acbee
Commits on Dec 5, 2017
  1. BUG: Update BRAINSTools to integrate Nifti-related fixes

    jcfr committed Dec 5, 2017
    Thanks: Isaiah Norton <inorton@bwh.harvard.edu>
    
    References:
    * BRAINSia/BRAINSTools#356
    * https://discourse.slicer.org/t/dti-nifti-data-import-via-dwi-convert-module/1460/4
    
    List of changes:
    
    $ git shortlog 42ac3c3..c1289e6 --no-merges
    Hans J. Johnson (1):
          ENH: Need to add allowLossy for file types other than short.
    
    Isaiah Norton (2):
          BUG: ITK is row-major; fix NRRD output with mismatched (x,y) axis sizes
          BUG: FSL converter should check reader status
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26676 3bd1e089-480b-0410-8dfb-8563597acbee
  2. STYLE: vtkMRMLSegmentationStorageNode: Fix include order and remove d…

    jcfr committed Dec 5, 2017
    …uplicate
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26675 3bd1e089-480b-0410-8dfb-8563597acbee
Commits on Dec 4, 2017
  1. BUG: Fixed segmentation logic ExportAllSegmentsToModelHierarchy

    lassoan committed Dec 4, 2017
    ExportAllSegmentsToModelHierarchy returned with True but did not export anything as ExportSegmentsToModelHierarchy method did not export all segments when the received segment list was empty.
    
    Fixed it to work the same way as labelmap exporter: when segment list is empty then all segments are exported.
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26674 3bd1e089-480b-0410-8dfb-8563597acbee
Commits on Dec 2, 2017
  1. ENH: Improved ScreenCapture module looping options

    lassoan committed Dec 2, 2017
    It is now possible to export a video that is playing the animation forward and backwards.
    Also, the animation can be repeated multiple times, which allows playing short videos more conveniently on players where looped playback is restricted (e.g., YouTube and some media players).
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26673 3bd1e089-480b-0410-8dfb-8563597acbee
Commits on Nov 30, 2017
  1. ENH: Set unique name for image acquisition transforms

    lassoan committed Nov 30, 2017
    DICOM scalar volume importer creates acquisition transform to compensate missing slices or tilted acquisition plane.
    When multiple such volumes were loaded, it used the same node name "Acquisition Transform" for all of them, which caused all the nodes overwritten by the last one.
    
    Fixed by generating unique node names for each acquisition transform.
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26672 3bd1e089-480b-0410-8dfb-8563597acbee
  2. BUG: Fixed plotting using Y axis indices

    lassoan committed Nov 30, 2017
    Now it is possible to plot a single column of a table.
    Also fixed a couple of minor issues with getting/setting column names.
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26671 3bd1e089-480b-0410-8dfb-8563597acbee
  3. STYLE: vtkMRMLVolumeRenderingDM: Remove commented includes

    jcfr committed Nov 30, 2017
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26670 3bd1e089-480b-0410-8dfb-8563597acbee
  4. STYLE: Remove unused and obsolete ROI core module

    jcfr committed Nov 30, 2017
    This commit removes the ROi module originally disabled in 2011
    in r15893 (ENH: Disable ROI module as vtkMRMLROINode is obsolete)
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26669 3bd1e089-480b-0410-8dfb-8563597acbee
  5. COMP: BuildSystem: Exclude remote modules if dependent options are OFF

    jcfr committed Nov 30, 2017
    This commit ensures that remote modules are not included if associated
    options are disabled.
    
    For example, this will avoid re-build error if python support is
    disabled after CompareVolumes was first enabled and built.
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26668 3bd1e089-480b-0410-8dfb-8563597acbee
  6. STYLE: Improve comment in top-level CMakeLists

    jcfr committed Nov 30, 2017
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26667 3bd1e089-480b-0410-8dfb-8563597acbee
  7. ENH: Added slicer.util.arrayFromSegment helper function

    lassoan committed Nov 30, 2017
    The function provides easy access to voxels of a segment using numpy.
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26666 3bd1e089-480b-0410-8dfb-8563597acbee
Commits on Nov 29, 2017
  1. ENH: BuildSystem: Consolidate handling of remote module/extension dir…

    jcfr committed Nov 29, 2017
    …ectories
    
    This commit simplifies handling of remote module, remove extension and
    extension directories.
    
    It also updates BRAINSTools to the expected hash omitted in r26663:
    
    $ git shortlog 42ac3c3..4f25a8a --no-merges
    Jean-Christophe Fillion-Robin (1):
          COMP: Support integration with Slicer setting LAUNCH_EXE using SEM_LAUNCH_COMMAND
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26665 3bd1e089-480b-0410-8dfb-8563597acbee
  2. COMP: Fix build reverting OpenIGTLinkIF

    jcfr committed Nov 29, 2017
    It turns out that the version Slicer/OpenIGTLinkIF@fc16632 integrated in
    r26661 also required a newer version of OpenIGTLink the was only
    supporting C++11.
    
    Waiting the Slicer trunk transition to C++11, this commit reverts to an
    older version of OpenIGTLinkIF including the following new changes:
    
    $ git shortlog 06379c2..0266aa2 --no-merges
    Jean-Christophe Fillion-Robin (2):
          COMP: Update minimum required CMake version to match Slicer requirements
          COMP: Improve support for building as a "Slicer Remote module"
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26664 3bd1e089-480b-0410-8dfb-8563597acbee
  3. ENH: Update BRAINSTools

    jcfr committed Nov 29, 2017
    List of changes:
    
    git shortlog 66db91f..4f25a8a --no-merges
    Hans J. Johnson (5):
          Moved documentation to the public wiki page
          DOC:  Added usecase documentation for super resolution.
          ENH: Add the ability to deface using BAW results.
          ENH: Improve cmake to force new behaviors with CMake 3.5
          COMP: Improve compilation behaviors for CMake > 3.8.2
    
    Isaiah Norton (1):
          BUG: fix FSLToNrrd mode from Slicer
    
    Jean-Christophe Fillion-Robin (3):
          COMP: Export BRAINSCommonLib target for build tree
          COMP: Consistently exclude test if BRAINSTools_DISABLE_TESTING is ON
          COMP: Support integration with Slicer setting LAUNCH_EXE using SEM_LAUNCH_COMMAND
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26663 3bd1e089-480b-0410-8dfb-8563597acbee
  4. ENH: Move edited segmentation to the study of the master volume

    pinter committed Nov 29, 2017
    In addition, a feature is added to warn the user about issues with DICOM export. Many users have asked why they could not export a segmentation, and the answer always was that because it was not under a patient+study. A check is now done when clicking Export to DICOM in subject hierarchy, and a question is shown asking whether default patient and study should be created and referenced datasets (by DICOM or MRML) moved in it for export. If the user chooses yes then those defaults are created, unless a referenced item is in a study, because then the exported node and all other references are moved under that.
    
    With MRML references involved in SH, in addition to DICOM references, MRML references are also highlighted.
    Highlight added also for referencing items with a slightly different color.
    
    Fixes https://issues.slicer.org/view.php?id=4313
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26662 3bd1e089-480b-0410-8dfb-8563597acbee
  5. ENH: Update OpenIGTLinkIF

    jcfr committed Nov 29, 2017
    List of changes:
    
    $ git shortlog 06379c2..fc16632 --no-merges
    Hina Shah (1):
          COMP Adding VTK_OVERRIDE keyword to the overrident functions
    
    Jean-Christophe Fillion-Robin (6):
          COMP: vtkIGTLToMRMLTrajectory: Fix deprecated declaration warning
          COMP: vtkMRMLIGTLConnectorNode: Fix sign compare warning
          STYLE: Fix unused variable warnings
          ENH: Add support for Qt5
          COMP: Update minimum required CMake version to match Slicer requirements
          COMP: Improve support for building as a "Slicer Remote module"
    
    Longquan Chen (7):
          EHN: Extend the module to use meta info to specify the mrmlnode.
          EHN: 1: Image message working now regarding the user specified mrmlnode from meta info. 2: GUI element improved
          EHN: Refactoring in progress
          EHN: Sending version2 openigtlink message in progress
          EHN: 1.Converters are created for each connector. simultaneously IGTLToMRML convension for two  devices with the same types is now possible.2. A converter factory class is added to make the code cleaner.
          EHN: improving the handling of version 2 igtlmessage without meta information
          EHN: Updated according to the new API of polydatamessage
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26661 3bd1e089-480b-0410-8dfb-8563597acbee
  6. COMP: Update CTK external project to ensure Python wrapping option ar…

    jcfr committed Nov 29, 2017
    …e passed
    
    This commit ensures that disabling Python wrapping in an existing build of
    Slicer will properly reconfigure CTK.
    
    $ git shortlog b5c41ca..cb6f57a --no-merges
    Jean-Christophe Fillion-Robin (1):
          Update ExternalProjectDependency based on commontk/Artichoke@0437a6d
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26660 3bd1e089-480b-0410-8dfb-8563597acbee
  7. COMP: Fix "install_tree_cleanup" python-GitPython build step error

    jcfr committed Nov 29, 2017
    This commit ensures "import git" succeeds on platform where git is not
    added to the path (e.g windows with Git Bash installed).
    
    Co-authored-by: Dženan Zukić <dzenan.zukic@kitware.com>
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26659 3bd1e089-480b-0410-8dfb-8563597acbee
  8. COMP: Extension build system: Do not recursively collect description …

    jcfr committed Nov 29, 2017
    …files
    
    This commit fixes build of the Extension build system with default options:
    
    $ cmake -DSlicer_DIR:PATH=/path/to/Slicer-build /path/to/src/Slicer/Extensions/CMake/
    [...]
    -- Configuring extension: CLIExtensionTemplate
    -- Configuring extension: EditorExtensionTemplate
    -- Configuring extension: LoadableExtensionTemplate
    -- Configuring extension: ScriptedLoadableExtensionTemplate
    -- Configuring extension: ScriptedSegmentEditorEffectExtensionTemplate
    -- Configuring extension: SuperBuildExtensionTemplate
    -- Configuring done
    -- Generating done
    -- Build files have been written to: /path/to/ExtensionsIndex-Release
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26658 3bd1e089-480b-0410-8dfb-8563597acbee
  9. STYLE: Update Extension Build System to use SlicerInitializeBuildType

    jcfr committed Nov 29, 2017
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26657 3bd1e089-480b-0410-8dfb-8563597acbee
Commits on Nov 28, 2017
  1. BUG: Fixed DICOM browser not visible for usernames having special cha…

    lassoan committed Nov 28, 2017
    …racters
    
    Error occurred during displaying unicode characters in the information window (https://discourse.slicer.org/t/dicom-browser-could-not-pop-up/1528).
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26656 3bd1e089-480b-0410-8dfb-8563597acbee
  2. BUG: Fixed crash on scene close caused by annotation ROI node

    lassoan committed Nov 28, 2017
    When an annotation ROI node was added to the scene and then Initialize() method was called then the node got added to the scene twice.
    
    This caused crash on scene close, because on instance of the node was still present in the scene but was partially invalid (its scene member was NULL and vtkMRMLAnnotationNode::SaveView() was called).
    
    Fixed crash by adding a check in vtkMRMLAnnotationNode::SaveView(). Also made ROI node initialization more robust by only adding the node to the scene if it is not added already.
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26655 3bd1e089-480b-0410-8dfb-8563597acbee
Commits on Nov 23, 2017
  1. BUG: Fixed new segment color after last segment has been removed

    pinter committed Nov 23, 2017
    If the last segment has been removed (and it was Segment_1), then the display node still contains the properties of Segment_1 until an update is triggered (for example by slice controller widget, but it depends on what the user does). But the segment ID generator index in vtkSegmentation is also reset to 0, so the new segment will be Segment_1, which simply "claims" those display properties. However, a new segment color is then not generated, so it will be gray. The implemented solution explicitly calls the update function when a segment is removed or added. The number of generated colors is also reset in the display node so that the colors for the subsequent segments are the same.
    
    An unnecessary modified was removed from subject hierarchy node that resulted in an error message when there was no error.
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26654 3bd1e089-480b-0410-8dfb-8563597acbee
Commits on Nov 21, 2017
  1. ENH: BuildSystem: Introduce Slicer_BUILD_DOCUMENTATION option

    jcfr committed Nov 21, 2017
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26653 3bd1e089-480b-0410-8dfb-8563597acbee
  2. ENH: BuildSystem: Refactor adding CMake modules to initialize build/r…

    jcfr committed Nov 21, 2017
    …elease types
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26652 3bd1e089-480b-0410-8dfb-8563597acbee
  3. COMP: Update python external project to ensure it is built in release

    jcfr committed Nov 21, 2017
    This fixes build error when Slicer is configured with
    
      -DCMAKE_CONFIGURATION_TYPES:STRING=RelWithDebInfo
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26651 3bd1e089-480b-0410-8dfb-8563597acbee