STYLE: Simplify qMRMLScene canBeAChild/canBeAParent implementation

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23380 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Expose qMRMLSceneModel mrml/setMRMLScene methods to python.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23381 3bd1e089-480b-0410-8dfb-8563597acbee
STYLE: Elaborate doxygen documentation of qMMRLSCeneModel::nodeIndex

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23382 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Expose vtkMRMLSceneViewNode::GetNodesByClass to python

Since std::vector<vtkMRMLNode *> is not "wrapped" by PythonQt, this commit
add an alternative method returning the nodes as a vtkCollection.

From: Nicole Aucoin <nicole@bwh.harvard.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23383 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Add prostate MR-Ultrasound to sample data

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23384 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: set main app shortcut context to allow unambiguous QActions handlers in child widgets

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23385 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Update ITKv4 project to backport fix related to GDCMIO

// --------
BUG: Do not ENABLED_SHARED for GDCMIO

With shared libraries on windows and export specification with gcc,
memory leaking is being detected by valgrind. This should be
re-enabled when GDCM it self is enabled as shared with export
specifications.
// --------

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23386 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Added mouse cursor position to vtkMRMLCrosshairNode.

Now cursor (now only mouse position in 2D Slice view, but later also
other pointing devices can be supported) position can be obtained by
observing the vtkMRMLCrosshairNode singleton node.

The feature is used in:
* DataProbe window
* Transform info window (showing the transform displacement vector value
  at the current mouse position in real-time)

After the integration into the Slicer core is done, it will be also used
in MultiVolume, Multidimensional data for live 3D graphing.

Also separated SetCursorPositionRAS and SetCursorPositionXYZ methods to
allow 3D-only positioning devices to specify the cursor position
(when no 2D slice position is available)

From: Andras Lasso <lasso@queensu.ca>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23387 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Update SimpleFilters

This commit updates both SimpleFilters documentation strings
presented in the help section, and json description used to described the
filters.

b27cdf6 Remove statistics only filters
148d863 Update help and acknowledgment text
bcdabde Fix json syntax issue StatisticsImageFilter
c62f9a8 Removing Filters which produce labelmaps as outputs
77fb3ac SimpleITK cd897256 Filter descriptions (reduced)
85d1ab2 Add utility script to generate Wiki table of filter

From: Bradley Lowekamp <blowekamp@mail.nih.gov>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23388 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Update ITKv4 - Attempt to fix ResampleDTI tests

This commit is an attempt to fix a regression introduced by previous
ITKv4 update (r23373) that is causing the following tests to fail:

  py_vtkITKArchetypeDiffusionTensorReaderFile
  ResampleDTIVolumeRotationNNTest
  ResampleDTIVolume2RigidTransformsLinearTest
  ResampleDTIVolumeBSplineInterpolationTest
  ResampleDTIVolumeHFieldTest
  ResampleDTIVolumeBSplineWSInterpolationTest

It updates ITKv4 integrating a "work-in-progress" patch
proposed by Bradley Lowekamp:

//-------
WIP: Add additional MetaDataObject explicit instantiation.

The MetaDataObject  of std::vector<std::vector<double> > > use by
Slicer's ResampleDTI module. This needed to be explicitly instantiated
and exported to enable dynamic_casts to correctly work.

Additionally other related types have been added that may be used in
other applications.

See http://review.source.kitware.com/#/c/15945/
//-------

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23389 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fix slicerExtensionWizard in MacOSX package. Fixes #3750

This commit fixes the following error:

//-----
 /Volumes/Slicer-4.3.1-2014-06-26-macosx-amd64/Slicer.app/Contents/bin/slicerExtensionWizard: line 11: /Volumes/Slicer-4.3.1-2014-06-26-macosx-amd64/Slicer.app/Contents/bin/../Slicer: No such file or directory
Traceback (most recent call last):
 File "/Volumes/Slicer-4.3.1-2014-06-26-macosx-amd64/Slicer.app/Contents/bin/../libexec/Slicer-4.3/ExtensionWizard.py", line 6, in <module>
   from SlicerWizard import ExtensionWizard
ImportError: No module named SlicerWizard
//-----

Instead of relying on Slicer launcher that is not available on MacOSX,
the SlicerPython launcher available on all platform is configured with
the path to the SlicerWizard module and the slicerExtensionWizard script
is updated to use it.

Co-authored-by: Peter Savadjiev <petersv@bwh.harvard.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23390 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: 3751. Fixed typo in the vtkMRMLModelNode::ApplyTransform code that broke hardening.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23391 3bd1e089-480b-0410-8dfb-8563597acbee
STYLE: Add .gitignore file

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23392 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Update ITKv4 - Fix "unused-local-typedefs" warning

This commit fixes the following warning in FiducialRegistration:

// -------
In file included from /path/to/ITKv4/Modules/Core/Transform/include/itkLandmarkBasedTransformInitializer.h:188:0,
                 from /path/to/Slicer/Modules/CLI/FiducialRegistration/FiducialRegistration.cxx:7:
/path/to/ITKv4/Modules/Core/Transform/include/itkLandmarkBasedTransformInitializer.hxx: In member function ‘void itk::LandmarkBasedTransformInitializer<TTransform, TFixedImage, TMovingImage>::InternalInitializeTransform(itk::LandmarkBasedTransformInitializer<TTransform, TFixedImage, TMovingImage>::VersorRigid3DTransformType*)’:
/path/to/ITKv4/Modules/Core/Transform/include/itkLandmarkBasedTransformInitializer.hxx:252:65: warning: typedef ‘RotationCenterType’ locally defined but not used [-Wunused-local-typedefs]
   typedef typename VersorRigid3DTransformType::CenterType       RotationCenterType;
// -------


$ git shortlog 79ec70b..3307a27
Jean-Christophe Fillion-Robin (1):
      COMP: Fix "unused-local-typedefs" warning in LandmarkBasedTransformInitializer

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23393 3bd1e089-480b-0410-8dfb-8563597acbee
STYLE: Add *.pyc files to .gitignore

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23394 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Restore original behavior of "Set(AndObserve)NthNodeReference" functions

This commit fixes test vtkSlicerUnitsLogicTest1 by partially reverting
commit r23192.

It restores the original behavior of the "Set(AndObserve)NthNodeReference"
functions. Instead of ensuring reference can be set and get at position
n, if n is larger than the number of reference nodes, the node ID
is added at the end of the list. If nodeReferenceID is 0, the node ID is
removed from the list.

Fixes #3708

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23395 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Remove unused CLIs MIDASApplications and BatchMakeApplications

See #3401

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23396 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Fix test to work with restored "Set(AndObserve)NthNodeReference" funcs

This commit integrates the remaining of the test updates required for
commit r23395.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23397 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Initial refactoring of extension manager UI

Refactor right corner area of extension manager into a .ui file, similar
to how the left corner area (navigation buttons) is already handled.
This allows us to have separate search widgets per tab (allowing for
independent search states, if/when support for searching installed
extensions is added), and also to add a 'configure' button (which we do)
that provides independent menus per tab.

The menus are created, but not yet functional. Icons (from the Public
Domain Tango theme) are also added. (The 'check for updates' icon uses
the theme pixmaps. Tango does not provide a 'configure' icon as such, so
the modified svg from which the pixmaps were generated is also being
committed.)

Issue #2089
Issue #2145

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23398 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Add function to list archives

Add a function to vtkArchive.cxx to obtain the list of files in an
archive without extracting the archive. Also, fix parameter name in
(misnamed) extract_tar to make at least some kind of sense.
("archiveFileName", as in list_archive(), would be better, since
extract_tar likewise works on non-tar archives, but for now leaving it
consistent with the function name.)

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23399 3bd1e089-480b-0410-8dfb-8563597acbee