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Commits on Mar 27, 2017
  1. ENH: Added labelmap and model export options to SH for segmentations

    pinter committed Mar 27, 2017
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25876 3bd1e089-480b-0410-8dfb-8563597acbee
  2. ENH: Display thumbnails in SampleData module

    lassoan committed Mar 27, 2017
    It makes the module nicer and the button easier to hit.
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25875 3bd1e089-480b-0410-8dfb-8563597acbee
  3. ENH: Indicate master volume in Segmentations module and make selections

    pinter committed Mar 27, 2017
    A label shows the master (reference) volume in the Segmentations module under the selected segmentation node, and the combobox of the reference volume for exporting to labelmap is populated
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25874 3bd1e089-480b-0410-8dfb-8563597acbee
  4. ENH: Added single snapshot option to ScreenCapture

    lassoan committed Mar 27, 2017
    If "single" toggle button is pressed then only a single image of the current state is captured (with filename auto-increment).
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25873 3bd1e089-480b-0410-8dfb-8563597acbee
Commits on Mar 25, 2017
  1. ENH: Reduced segmentations widget size

    lassoan committed Mar 25, 2017
    Hide effect options and masking section if no effect is selected.
    Paint options (sphere brush, color smudge, pixel mode) are laid out horizontally instead of vertically.
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25872 3bd1e089-480b-0410-8dfb-8563597acbee
  2. COMP: Move projects to correct folder in solution explorer

    lassoan committed Mar 25, 2017
    vtkSegmentationCoreCxxTests and qSlicerModulesCoreCxxTests projects were moved to the correct folders in solution explorer
    (now they are in the same folder as the projects that they test).
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25871 3bd1e089-480b-0410-8dfb-8563597acbee
Commits on Mar 24, 2017
  1. STYLE: Indentation related changes

    pinter committed Mar 24, 2017
    1. vtkMRMLNode::Indent member seemed unused in the core, except from the also unused ROI list node, so the member was removed
    
    2. In WriteXML functions, the increasing indentation was added between the XML attributes, which did not have major effect on the top level, but for example in the scene view section, where indentation was increased, it made the nodes look like this:
    
      <Selection
        id="vtkMRMLSelectionNodeSingleton"    name="Selection"    hideFromEditors="true"    selectable="true"    selected="false"    singletonTag="Singleton"
    
    As the purpose of indentation is to add space in front of the _lines_, adding that space between the XML attributes seems unnecessary. With these changes, the same entry now looks like this:
    
      <Selection
        id="vtkMRMLSelectionNodeSingleton" name="Selection" hideFromEditors="true" selectable="true" selected="false"
    
    History:
    
    In the first implementation of `WriteXML()`, the name of the node (e.g vtkMRMLModelNode.cxx) was explicitly serialized and indented in the function by explicitly using `nIndent`.
    See r40 (COMP: added vtkITK and MRML libs). Code like this was used:
    
        vtkIndent i1(nIndent);
        of << i1 << "<Model";
    
        of << " id='" << this->ID << "'";
        if (this->Name && strcmp(this->Name, ""))
        {
          of << " name='" << this->Name << "'";
        }
        [...]
        if (this->Color && strcmp(this->Color, ""))
        {
          of << " color='" << this->Color << "'";
        }
    
    Then, this approach was reviewed in r133 (ENH: more transform functionality) by systematically calling the base class implementation of WriteXML() function.
    
    Code above was then updated like this:
    
       Superclass::WriteXML(of, nIndent);
       vtkIndent indent(nIndent);
    
       if (this->Color && strcmp(this->Color, ""))
       {
         of << indent << " color='" << this->Color << "'";
       }
    
    This commit simplifies the XML serialization and explicitly mark `indent` parameter as deprecated.
    
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25870 3bd1e089-480b-0410-8dfb-8563597acbee
  2. ENH: Terminology default contexts selection and validator link in mes…

    pinter committed Mar 24, 2017
    …sages
    
    1. Last terminology and anatomic context selections are now saved in application settings, and are selected in case terminology navigator is opened for a new segment. Thus the default segment terminology is now empty (instead of Tissue/Tissue), so that new segment can be detected.
    2. Link to the context validator web app is now included in the error message that is popped up when loading user terminology or anatomic context fails
    
    Related to QIICR/QuantitativeReporting#150
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25869 3bd1e089-480b-0410-8dfb-8563597acbee
  3. ENH: Updated to latest CTK version

    lassoan committed Mar 24, 2017
    New feature: ctkFittedTextBrowser has a collapsible option now. It allows showing a single-line message with a 'More...' link that the user can click to see the full message.
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25868 3bd1e089-480b-0410-8dfb-8563597acbee
  4. ENH: Added option in ScreenCapture module for capturing all views

    lassoan committed Mar 24, 2017
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25867 3bd1e089-480b-0410-8dfb-8563597acbee
Commits on Mar 23, 2017
  1. ENH: Improved and simplified volume and labelmap visibility from subj…

    pinter committed Mar 23, 2017
    …ect hierarchy
    
    Instead of the apparently hard-to-grasp way volumes and labelmaps were shown and hidden from subject hierarchy, a new and simplified way was implemented. Now if a non-labelmap volume is shown or hidden, then it is simply shown in the background layer of all slice views, replacing any background volume shown previously. Labelmaps work the same way, except on the label layer. This, besides the simplified and more robust operation, has a few advantages: 1) It doesn't use the selection node any more, meaning that its inconsistencies (http://www.na-mic.org/Bug/view.php?id=3551) are now irrelevant from this use case, 2) It was reported that show/hide changed the position of the slice views, which is now preserved, 3) Complete synchronization of actual volume visibility and visibility icon states in subject hierarchy is now achieved
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25866 3bd1e089-480b-0410-8dfb-8563597acbee
  2. ENH: Made screencapture rotation axis configurable

    lassoan committed Mar 23, 2017
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25865 3bd1e089-480b-0410-8dfb-8563597acbee
  3. BUG: Fixed segment visibility indicator bug in subject hierarchy

    pinter committed Mar 23, 2017
    When a segment was shown/hidden from somewhere else than SH, then the visibility icon in SH was not updated. By emitting modified event on the shown/hidden segment's SH item, the update is triggered.
    
    Also, minor issues were fixed in SHNode::GetDisplayVisibilityForBranch. The new implementation of GetDataNodesInBranch includes the given node's data node itself in the returned collection, so no need to add that explicitly. Also, the exception about segmentation nodes were removed, as it was a workaround in the past when segmentation node was not registered in the scene. Further, the warning about partial visibility for leaf nodes was removed, because it can happen if a data node has more than one display node (e.g. annotations, fiber bundles)
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25864 3bd1e089-480b-0410-8dfb-8563597acbee
  4. ENH: Added DTI volume subject hierarchy plugin

    pinter committed Mar 23, 2017
    Context menu action for interactive seeding allows users to start tractography from subject hierarchy. A second action for lablemap seeding also is created, but not shown until CLI support for segmentations is added.
    
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25863 3bd1e089-480b-0410-8dfb-8563597acbee
Commits on Mar 22, 2017
  1. ENH: Made segment editor effects list customizable

    lassoan committed Mar 22, 2017
    editorWidget.setEffectNameOrder defines the order of effects.
    If editorWidget.unorderedEffectsVisible is set to False then only those effects will be shown
    that are listed in editorWidget.setEffectNameOrder.
    
    editorWidget = slicer.modules.segmenteditor.widgetRepresentation().self().editor
    editorWidget.setEffectNameOrder(['Draw', 'Scissors', 'Islands'])
    editorWidget.unorderedEffectsVisible = False
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25862 3bd1e089-480b-0410-8dfb-8563597acbee
  2. ENH: Added option to load custom anatomical contexts for terminologies

    pinter committed Mar 22, 2017
    Schema information from the json files is now also used to determine the type of the loaded context. In case of an unrecognized or missing schema, loading fails and error is logged.
    Json files updated based on changes in the dcmqi repository.
    
    Fixes QIICR/QuantitativeReporting#150
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25861 3bd1e089-480b-0410-8dfb-8563597acbee
  3. STYLE: EditorExtensionTemplate: Fix docstring typo

    jcfr committed Mar 22, 2017
    Changed "be come" to "become".
    
    From: Tammy DiPrima <tammy.diprima@stonybrook.edu>
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25860 3bd1e089-480b-0410-8dfb-8563597acbee
Commits on Mar 21, 2017
  1. ENH: Added scripted segment editor effect template

    lassoan committed Mar 21, 2017
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25859 3bd1e089-480b-0410-8dfb-8563597acbee
  2. STYLE: Removed unnecessary error messages that clutter the log

    pinter committed Mar 21, 2017
    These error messages appeared when creating charts and tables when the SH item was created, because it tried to get their visibility, but there was no chart or table view node, because no layout containing either has been used.
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25858 3bd1e089-480b-0410-8dfb-8563597acbee
  3. ENH: Added helper functions to vtkSlicerSegmentationsModuleLogic

    lassoan committed Mar 21, 2017
    CopyOrientedImageDataToVolumeNode: create volume node from oriented image data easily
    ImportLabelmapToSegmentationNode: update existing segments based on a labelmap node
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25857 3bd1e089-480b-0410-8dfb-8563597acbee
  4. BUG: Fixed SH node clone bug

    pinter committed Mar 21, 2017
    Some data role plugins rely on node attributes and/or place in branch to determine whether the data node can be claimed. In such cases, the SH item created by the SH plugin logic could be claimed by a more generic plugin (e.g. RTDose vs Volumes) when adding the cloned node to the scene, but before attributes were copied, or item was placed in branch. By requesting plugin search after these operations, the proper plugin claims the cloned data node
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25856 3bd1e089-480b-0410-8dfb-8563597acbee
  5. BUG: the sense of the test was inverted, leading to crash in Qt5

    pieper committed Mar 21, 2017
    This code is supposed to create a new quantity ui when
    a new one is discovered, but had a missing not operator
    so quantities weren't added until they later found via the
    selection node.  On Qt4 this was not a problem but did
    cause a crash in Qt5.
    
    From: Steve Pieper <pieper@isomics.com>
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25855 3bd1e089-480b-0410-8dfb-8563597acbee
  6. BUG: Fixed crash when setting root item to SH tree before showing it

    pinter committed Mar 21, 2017
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25854 3bd1e089-480b-0410-8dfb-8563597acbee
  7. BUG: Fixed scene views with subject hierarchy 2.0

    pinter committed Mar 21, 2017
    Some explanation besides the subject hierarchy node and scene view node changes:
    1. vtkMRMLScene.cxx:1140 and 1175:
    1/A) the ReferencedIDChanges map contained an invalid entry in every case, namely it associated the last created node's ID with empty string.
    1/B) In the case of loading a volume, the test scene created by vtkSlicerVolumesLogic::AddArchetypeVolume assigned ID with number 1 to the volume. Then, when adding it to the main MRML scene, the old ID with number 1 was found, and the ID change was stored always from 1 to the number of the last loaded volume. This is also an invalid ID change, as no ID was changed in the scene that stored this change. First approach was to clear node ID when removing from scene, but it caused tests failing in EMSegment (due to the specific way it creates sub-scenes), and it is expected to cause problems elsewhere too. So as an alternative solution, IDs are only added to ReferencedIDChanges, when a scene is being imported or a scene view restored. It seems to be reasonable, as these are the only two use cases where the IDs of other complete scenes need to be merged to the main Slicer scene.
    2. vtkMRMLSegmentationNode.cxx: This is basically reverting commit rev25625 that introduced display node copying and creation in the data node's copy. In the case of restoring the scene view, it caused a problem like this: if the segmentation node was before its display node in the snapshot scene, a new display node was created when copying the segmentation node, and so after restoring, two display nodes were present instead of one. So the segmentation was not visible. I checked other data nodes and none of the ones I looked at copy display properties in the copy function of the data node. I suggest taking care of this at the higher level, where the data node's copy is called (for example as it is done in the clone node SH plugin)
    
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25853 3bd1e089-480b-0410-8dfb-8563597acbee
Commits on Mar 20, 2017
  1. BUG: hide DMRIInstall properly, avoid assert in debug build

    ihnorton committed Mar 20, 2017
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25852 3bd1e089-480b-0410-8dfb-8563597acbee
  2. STYLE: rename functions to match slicer/pr/647 rework

    ihnorton committed Mar 20, 2017
    From: Isaiah Norton <inorton@bwh.harvard.edu>
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25851 3bd1e089-480b-0410-8dfb-8563597acbee
  3. ENH: change default DT glyph type to line, faster & clearer for norma…

    ihnorton committed Mar 20, 2017
    …l use
    
    From: Isaiah Norton <inorton@bwh.harvard.edu>
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25850 3bd1e089-480b-0410-8dfb-8563597acbee
  4. BUG: fix DT glyph display

    ihnorton committed Mar 20, 2017
    Fixes issues related to slicer/pr/647 changes in model display pipeline.
    - crash due to potential null node, needs null check.
    - rendering problems (inactive by default) due to missing pipeline update call after event propagation was changed
    
    From: Isaiah Norton <inorton@bwh.harvard.edu>
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25849 3bd1e089-480b-0410-8dfb-8563597acbee
  5. ENH: use wildcard filter in Data module

    ihnorton committed Mar 20, 2017
    This allows to match any part of the name rather than requiring to type
    exact phrase. So "Tens" matches "vtkMRMLDiffusionTensorVolumeNode" whereas
    currently it would not match.
    
    From: Isaiah Norton <inorton@bwh.harvard.edu>
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25848 3bd1e089-480b-0410-8dfb-8563597acbee
  6. ENH: Add external project step allowing to keep track of project vers…

    jcfr committed Mar 20, 2017
    …ion.
    
    This commit adds a module named "ExternalProjectGenerateProjectDescription"
    providing a convenient function allowing to add a step generating
    a project description file containing the name of the project and
    its version.
    
    For each project instrumented with this function, a file named
    "version-<projectnmame>.txt" is generated in ${CMAKE_BINARY_DIR}.
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25847 3bd1e089-480b-0410-8dfb-8563597acbee
  7. ENH: Support configuration of external project GIT tag and repository

    jcfr committed Mar 20, 2017
    For any given project checkout using Git, setting cache or environment
    variables of the form:
    
      Slicer_<proj>_GIT_REPOSITORY
      Slicer_<proj>_GIT_TAG
    
    allows to override the default values set within each External_* files.
    
    Fixes #4148
    
    Co-authored-by: "T.J. Corona" <tj.corona@kitware.com>
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25846 3bd1e089-480b-0410-8dfb-8563597acbee
  8. COMP: Update ExternalProjectDependency based on commontk/Artichoke@35…

    jcfr committed Mar 20, 2017
    …c64c7
    
    $ git shortlog  f3359ad..35c64c7 --no-merges
    Jean-Christophe Fillion-Robin (5):
          Add support for specifying a different CMAKE_GENERATOR for each project
          Add support for specifying different toolset/platform for each project
          Teach mark_as_superbuild how to handle variables with double-quotes
          Add ExternalProject_SetIfNotDefined macro
          ExternalProject_SetIfNotDefined: Add support for QUIET argument
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25845 3bd1e089-480b-0410-8dfb-8563597acbee
Commits on Mar 17, 2017
  1. BUG: Restored storable criteria in parse local data plugin

    pinter committed Mar 17, 2017
    The parse local data plugin by design can only work with storable nodes, because it builds the hierarchy based on the file locations found in the storage nodes. As non-storable nodes have no storage nodes, those nodes are not usable by the plugin
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25844 3bd1e089-480b-0410-8dfb-8563597acbee
  2. COMP: Update JsonCpp to fix GCC 6 build error. See #4268

    jcfr committed Mar 17, 2017
    See http://slicer-devel.65872.n3.nabble.com/Slicer-gcc-6-tt4038282.html
    and http://na-mic.org/Mantis/view.php?id=4268
    
    $ git shortlog f4afa75..73b8e17 --no-merges
    Gregory C. Sharp (1):
          COMP: Update json_(reader|writer).cpp to fix gcc6 build error
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25843 3bd1e089-480b-0410-8dfb-8563597acbee
Commits on Mar 16, 2017
  1. BUG: Update qRestAPI to fix regression causing extension installation…

    jcfr committed Mar 16, 2017
    … failure
    
    $ git shortlog 9d3cfb6..d1b07cc --no-merges
    Jean-Christophe Fillion-Robin (1):
          qMidasAPI: synchronousQuery: Fix regression and ensure query is sent
    
    Reported-by: Andriy Fedorov <fedorov@bwh.harvard.edu>
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@25842 3bd1e089-480b-0410-8dfb-8563597acbee