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Commits on Jul 30, 2014
  1. COMP: Fix VTK6 link error on MacOSX 10.6. Fixes #3741

    authored
    To reduce the number of libraries passed to the linker, this commit build
    VTK6 with the VTK_ENABLE_KITS option enabled.
    
    If building on MacOSX 10.6 without CMake 3.0, it also updated the build
    system to output a fatal error message explaining that a more recent
    version of CMake is required.
  2. COMP: Specify list VTK_MAKE_INSTANTIATOR3 input as list of cxx files …

    authored
    …only.
    
    This commit fixes a build error introduced by Kitware/VTK@5c3241b
    It ensures there are no duplicated entries in the instantiator files.
    
    The error (reported below) was first discovered when building Slicer
    on MacOSX 10.6 with the option VTK_ENABLE_KITS while working on issue
    #3741.
    
    // ------------------------
    $ make vtkSlicerTransformsModuleMRMLDisplayableManager/fast
    [ 59%] Building CXX object Modules/Loadable/Transforms/MRMLDM/CMakeFiles/vtkSlicerTransformsModuleMRMLDisplayableManager.dir/TransformsInstantiator.cxx.o
    /path/to/Slicer-build/Modules/Loadable/Transforms/MRMLDM/TransformsInstantiator.cxx: In function 'vtkObject* vtkInstantiatorvtkMRMLTransformsDisplayableManager2DNew()':
    /path/to/Slicer-build/Modules/Loadable/Transforms/MRMLDM/TransformsInstantiator.cxx:10: error: redefinition of 'vtkObject* vtkInstantiatorvtkMRMLTransformsDisplayableManager2DNew()'
    /path/to/Slicer-build/Modules/Loadable/Transforms/MRMLDM/TransformsInstantiator.cxx:9: error: 'vtkObject* vtkInstantiatorvtkMRMLTransformsDisplayableManager2DNew()' previously defined here
    /path/to/Slicer-build/Modules/Loadable/Transforms/MRMLDM/TransformsInstantiator.cxx: In function 'vtkObject* vtkInstantiatorvtkMRMLTransformsDisplayableManager3DNew()':
    /path/to/Slicer-build/Modules/Loadable/Transforms/MRMLDM/TransformsInstantiator.cxx:12: error: redefinition of 'vtkObject* vtkInstantiatorvtkMRMLTransformsDisplayableManager3DNew()'
    /path/to/Slicer-build/Modules/Loadable/Transforms/MRMLDM/TransformsInstantiator.cxx:11: error: 'vtkObject* vtkInstantiatorvtkMRMLTransformsDisplayableManager3DNew()' previously defined here
    make[1]: *** [Modules/Loadable/Transforms/MRMLDM/CMakeFiles/vtkSlicerTransformsModuleMRMLDisplayableManager.dir/TransformsInstantiator.cxx.o] Error 1
    make: *** [vtkSlicerTransformsModuleMRMLDisplayableManager/fast] Error 2
    // ------------------------
    
    The content of the associated instantiator file was:
    
    // ---------------
    $ cat Modules/Loadable/Transforms/MRMLDM/TransformsInstantiator.cxx
    
    [...]
    
    vtkInstantiatorNewMacro(vtkMRMLTransformsDisplayableManager2D)
    vtkInstantiatorNewMacro(vtkMRMLTransformsDisplayableManager2D)
    vtkInstantiatorNewMacro(vtkMRMLTransformsDisplayableManager3D)
    vtkInstantiatorNewMacro(vtkMRMLTransformsDisplayableManager3D)
    
    [...]
    // ---------------
    
    This commit avoid the duplicated entries in the instantiator file.
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23508 3bd1e089-480b-0410-8dfb-8563597acbee
  3. BUG: Partial fix for EMSegment/BRAINSFit integration. See #3561, #274…

    authored
    …1, #3779
    
    This commit is a follow up of EMSegment commit r23496. It updates BRAINSFit
    to integrate the fix done by Kent to specifically address the naming
    of .h5 transform files written by BRAINSFit.
    
    // ---------------------
    commit e46c99795cedd4c6aeec98e881af9c2b28dc5cf5
    Author: Kent Williams <norman-k-williams@uiowa.edu>
    Date:   Tue Jul 29 15:24:11 2014 -0500
    
    BUG: don't extend composite transform filenames needlessly.there was some deficient logic that
    was changing the filename of composit transforms to force them to hdf5 format, even if the filename
    given was already for an HDF5 file.
    // ---------------------
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23507 3bd1e089-480b-0410-8dfb-8563597acbee
Commits on Jul 29, 2014
  1. ENH: Added developer mode and base classes for scripted modules

    authored
    * Added "Enable developer mode" option in the application settings
    (Developer section, next to Enable QtTesting)
    
    * Added base classes for scripted module, widget, logic, and test: they
    make scripted modules simpler and shorter and also more functions and
    helper methods can be added in the future without changing each scripted
    module
    ** Module handles selftest registration
    ** Widget handles reload&test (shown on GUI only in developer mode)
    ** Logic and Test contains delayDisplay utility function
    
    * As an example, updated ScriptedLoadableModuleTemplate and SurfaceToolbox to use the new base classes
    
    From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23506 3bd1e089-480b-0410-8dfb-8563597acbee
  2. BUG: Fixed SubjectHierarchyGenericSelfTest

    pinter authored
    Fixes #3754
    
    Additional minor fixes in handling potential nodes in the subject hierarchy tree (removed unavailable context menu items)
    Removed potential subject hierarchy node list and related classes (model, proxy model, designer plugin)
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23505 3bd1e089-480b-0410-8dfb-8563597acbee
  3. ENH: Implement installation of updates

    mwoehlke authored
    Implement installation of updates to extensions (consisting of first
    removing the old version, then installing the new version). Note that
    this will attempt to install new dependencies as well. Also, change
    handling of update downloads to additionally write the metadata for the
    update (in addition to the archive), as we'll want it when we install
    the update and need to persist it across a restart.
    
    Issue #2089
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23504 3bd1e089-480b-0410-8dfb-8563597acbee
  4. BUG: Improve UI update scheduling

    mwoehlke authored
    Improve update handling to enable 'restart' button when appropriate due
    to update-related actions. Disable updating of extensions scheduled to
    be uninstalled (the model already does this, but having the button
    enabled makes for a confusing user experience where clicking the update
    button does nothing).
    
    Issue #2089
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23503 3bd1e089-480b-0410-8dfb-8563597acbee
  5. ENH: Hook up UI for updating extensions

    mwoehlke authored
    Hook up update availability and download progress reporting in extension
    model. Add UI to extension manager to report update availability and
    allow requesting updates and canceling such requests. This brings update
    management almost to full functionality, missing only to actually
    install the update on restart.
    
    Issue #2089
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23502 3bd1e089-480b-0410-8dfb-8563597acbee
  6. ENH: Improve extension manager info icons

    mwoehlke authored
    Tweak the information icons used in the extension manager to have whiter
    glyphs, and a less muddy glyph for the 'i' (update available) icon.
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23501 3bd1e089-480b-0410-8dfb-8563597acbee
  7. ENH: Download updates

    mwoehlke authored
    Refactor update download logic, introducing a new 'task' class to
    manager downloads, rather than trying everything through the network
    manager's signals. Also, move the code to start such a task to a helper
    function. Leverage these to hook up downloading of updates, now that
    tasks can have different completion handlers assigned. Write update
    archive file and scheduling information on update download completion.
    
    Issue #2089
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23500 3bd1e089-480b-0410-8dfb-8563597acbee
  8. ENH: Start adding logic to check for updates

    mwoehlke authored
    Add logic to issue server API calls to check for updates to extensions,
    and to manage the same. This is still missing anything to actually
    download or apply said updates.
    
    Issue #2089
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23499 3bd1e089-480b-0410-8dfb-8563597acbee
  9. ENH: Adding API to check for extension updates

    mwoehlke authored
    Add some initial API to manage scheduling extensions for update, similar
    to how we schedule extensions for uninstall (as the implementation will
    necessarily be similar). For now, the settings management should be
    working; the rest (including a checkForUpdates() method) is mostly
    placeholder that is needed to start implementing UI and underlying
    logic.
    
    Issue #2089
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23498 3bd1e089-480b-0410-8dfb-8563597acbee
  10. ENH: Remember if updates are automatic

    mwoehlke authored
    Store if the user has enabled automatic extension updates in QSettings.
    
    Issue #2089
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23497 3bd1e089-480b-0410-8dfb-8563597acbee
  11. BUG: BRAINS can only now read in h5 files

    pohl authored
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23496 3bd1e089-480b-0410-8dfb-8563597acbee
  12. BUG: fix logic on showing slice intersections

    naucoin authored
    Added an attribute (and a name) for the volume slice
    model display nodes and check for it in a new slice
    logic static method. If it's not a volume slice model
    display node, use the visibility of the regular
    model to determine if should show the slice intersections,
    otherwise rely on the slice intersections visible flag.
    
    Issue #3718
    
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23495 3bd1e089-480b-0410-8dfb-8563597acbee
  13. BUG: check for valid transform pointers to avoid crash

    pieper authored
    On scene close and possibly other circumstances there can be transform
    nodes that don't have valid transforms, so check the pointers.
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23494 3bd1e089-480b-0410-8dfb-8563597acbee
  14. BUG: test for active camera before enabling fiducials

    naucoin authored
    Removes the error message that world to view and view to world
    can't compute result due to a missing active camera. Delaying
    setting the handles and widgets to be enabled if there's
    no active camera defined on their renderers seems to work well
    since the next time through the update code once the layout
    has stabilised and the renderers are updated, the seeds 
    will get positioned and enabled.
    
    Issue #3761
    
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23493 3bd1e089-480b-0410-8dfb-8563597acbee
  15. ENH: Added a method in VolumesLogic class to resample volume node.

    pieper authored
    Also added a new CloneVolume method which does not clone the imageData. Changed the LabelStatistics.py to use the new resample logic to make labelmap same as input volume.
    
    From: Kevin Wang <kevin.wang@rmp.uhn.ca>
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23492 3bd1e089-480b-0410-8dfb-8563597acbee
  16. ENH: Added a method in VolumesLogic class to resample volume node.

    pieper authored
    Also changed the LabelStatistics.py to use the new resample logic to make labelmap same as input volume.
    
    From: Kevin Wang <kevin.wang@rmp.uhn.ca>
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23491 3bd1e089-480b-0410-8dfb-8563597acbee
  17. COMP: Add HDF5 and Matlab TransformIO to ITKFactoryRegistration

    authored
    This commit explicitly lists these transform to ensure the associated
    files can be read/write.
    
    This should help in fixing error related to the integration of
    BRAINSFit and EMSegment.
    
    Co-authored-by: Bradley Lowekamp <blowekamp@mail.nih.gov>
    Co-authored-by: Steve Pieper <pieper@isomics.com>
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23490 3bd1e089-480b-0410-8dfb-8563597acbee
Commits on Jul 28, 2014
  1. BUG: Subject hierarchy UI update issues fixed

    pinter authored
    Fixes #3714
    
    - qMRMLSceneSubjectHierarchyModel::nodeIndex rewritten to generate correct indices, parentNode also fixed. Workarounds removed
    - New subject hierarchy nodes get simpler names
    - Setting icons is not so simple as it should be due to a bug in Qt (https://bugreports.qt-project.org/browse/QTBUG-20248), which raises the need to check if the icon to be set is the same as the current icon of an item. This introduces one more thing to remember to the developer. Thus, instead of having the plugins set icons on items, they just return it (or an empty one), and the model does the check. This way developing plugins is not harder than before.
    - Changed copyright information in all subject hierarchy files
    - Instead of having the potential nodes list on the bottom of the module, those nodes are shown in the subject hierarchy tree on the top-level without icons. They can be shown/hidden with a checkbox under the tree, and can be handled the same way as in the potential list before.
    
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23489 3bd1e089-480b-0410-8dfb-8563597acbee
  2. BUG: Fix CheckForLabelVolumeValidity warning. Fixes #3776

    authored
    This commit fixes a regression introduced in r23406 [1]
    where calling CheckForLabelVolumeValidity with two volumes that have
    the same dimension was returning a wrong warning, e.g. "IJKToRAS mismatch
    at [0, 3] (-89.6207 != -89.6207)", "IJKToRAS mismatch
    at [1, 1] (0.000542851 != 0.000542851)", and "IJKToRAS mismatch
    at [2, 0] (4.32616e-09 != 4.32616e-09) IJKToRAS mismatch
    at [2, 2] (0.0752821 != 0.0752821)", and "IJKToRAS mismatch
    at [2, 3] (176.197 != 176.197)".
    
    Thanks to "safir" for reporting the problem and suggesting a solution.
    
    [1] http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=23406
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23488 3bd1e089-480b-0410-8dfb-8563597acbee
Commits on Jul 27, 2014
  1. @finetjul

    BUG: Fix IconEngine and d&d of QStandardItems with icons

    finetjul authored
    When doing drag&drop, the mime data failed to stream the QIcon because
    qSlicerIconEnginePlugin was not a subclass of QIconEngineV2.
    Regression when adding Qt5 support in CTK.
    Closes #3778
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23487 3bd1e089-480b-0410-8dfb-8563597acbee
Commits on Jul 26, 2014
  1. BUG: cli-modules were not included in PATH of installed version of MA…

    pohl authored
    …C so added it to search path
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23486 3bd1e089-480b-0410-8dfb-8563597acbee
Commits on Jul 25, 2014
  1. BUG: Fixed error with intensity sampling; removed code not used under…

    pohl authored
    … Slicer4
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23485 3bd1e089-480b-0410-8dfb-8563597acbee
Commits on Jul 24, 2014
  1. STYLE: Removed testing code from previous commit

    pinter authored
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23484 3bd1e089-480b-0410-8dfb-8563597acbee
  2. BUG: Fixed accented character display of series and studies in subjec…

    pinter authored
    …t hierarchy
    
    Fixes #3688
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23483 3bd1e089-480b-0410-8dfb-8563597acbee
  3. BUG: Properly serialize python paths when installing extension. Fixes…

    authored
    … #3772
    
    Following r23036 environment variable specifying list of path were
    handled differently. This commit ensures that python paths associated
    with extension are also serialized into the settings by following the
    new convention introduced in r23036.
    
    For example, before this commit, after installing an extension named
    "Foo", the settings contained:
    
    // ----------------------
    [Modules]
    AdditionalPaths=/home/jchris/.config/NA-MIC/Extensions-23473/Foo/lib/Slicer-4.3/qt-scripted-modules
    
    [...]
    
    [EnvironmentVariables]
    PYTHONPATH=/home/jchris/.config/NA-MIC/Extensions-23473/Foo/lib/Slicer-4.3/qt-scripted-modules
    // ----------------------
    
    whereas the following is now written:
    
    // ----------------------
    [Modules]
    AdditionalPaths=/home/jchris/.config/NA-MIC/Extensions-23473/Foo/lib/Slicer-4.3/qt-scripted-modules
    
    [...]
    
    [PYTHONPATH]
    1\path=/home/jchris/.config/NA-MIC/Extensions-23473/Foo/lib/Slicer-4.3/qt-scripted-modules
    size=1
    // ----------------------
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23482 3bd1e089-480b-0410-8dfb-8563597acbee
  4. BUG: Ensure extension wizard can find git executable provided by Git …

    authored
    …Bash
    
    This commit explicit set the environment variable "GIT_PYTHON_GIT_EXECUTABLE"
    to ensure GitPython finds and uses the git executable provided by Git Bash.
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23481 3bd1e089-480b-0410-8dfb-8563597acbee
Commits on Jul 23, 2014
  1. BUG: Ensure MultiVolume modules work with VTK 5 and 6

    authored
    This commit updates the modules to check for the version
    of VTK (using `vtk.VTK_MAJOR_VERSION`). This is required
    because the MacOSX factory is still building against VTK5.
    
    For more details see:
    
      fedorov/MultiVolumeExplorer@1053c40
      fedorov/MultiVolumeImporter@351226a
    
    From: Andrey Fedorov <fedorov@bwh.harvard.edu>
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23480 3bd1e089-480b-0410-8dfb-8563597acbee
  2. BUG: Fix missing icons in extension manager

    mwoehlke authored
    Update qSlicerBaseQTGUI.qrc[1] to include icons for new tool menu in
    extension manager. This fixes the button for the same having no icon on
    systems that lack the themed icon, as the non-themed icon was being
    specified and exists in the source tree, but was missing from the
    aforementioned .qrc.
    
    (1: http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Build_system/Qt_resource_files)
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23479 3bd1e089-480b-0410-8dfb-8563597acbee
  3. BUG: Update SlicerExecutionModel - Fixes #2712

    authored
    This commit updates SlicerExecutionModel to include an updated version
    of ModuleDescription::ReadParameterFile function that support string
    parameter without value. The Slicer/SlicerExecutionModel@05af78d also
    adds corresponding test checking that parameter file with and without
    value can still be read.
    
    $ git shortlog feef59e..a6616b52 --no-merges
    Jean-Christophe Fillion-Robin (1):
          BUG: Support parameter file with empty value
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23478 3bd1e089-480b-0410-8dfb-8563597acbee
  4. STYLE: Add "python-" prefix to GitPython, Github and pydicom module

    authored
    Consistently name python package.
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23477 3bd1e089-480b-0410-8dfb-8563597acbee
  5. COMP: Wrap setuptools module installation to avoid false-positive error.

    authored
    This commit ensure the build and install output of setuptools module is
    redirected into files to avoid warning like the following one to be
    falsely categorized as error:
    
    15>removing 'build\bdist.win-amd64\egg' (and everything under it)
    15>C:\D\C\Slicer-1-build\python-setuptools\setuptools\command\easy_install.py:316: UserWarning: Unbuilt egg for setuptools [unknown version] (c:\d\c\slicer-1-build\python-setuptools)
    15>  self.local_index = Environment(self.shadow_path + sys.path)
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23476 3bd1e089-480b-0410-8dfb-8563597acbee
Commits on Jul 22, 2014
  1. BUG: Update launcher to version 0.1.14. Fixes #3771

    authored
    // -------------------
    Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
    Date:   Tue Jul 22 18:19:04 2014 -0400
    
        Ensure 'additionalPathVariables' is not overridden. Fixes #56
    
        Commit 714981 generalized how environment variables dealing with paths
        were managed. This commit fixes a regression where environment variables
        set in the main settings file where not considered is additional settings
        where found.
    // -------------------
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@23475 3bd1e089-480b-0410-8dfb-8563597acbee
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