ENH: add an event type for the end of a fiducial interaction

This can be used to trigger execution at the end of the interaction
instead of doing it on every mouse move.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23368 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: update to new LandmarkRegistration

Makes use of the new fiducial end moving event

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23369 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Two fixes in vtkSlicerSubjectHierarchyModuleLogicTest

Still fails due to transform hardening issue (investigating)

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23370 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Subject hierarchy study name now contains date

To facilitate easy differentiation between studies with same name

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23371 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Temporary fix for contour slice intersections

Based on today's discussions, a type check has been added to model displayable manager to facilitate proper contour display until the new segmentation node object is created and a new displayable manager is added.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23372 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Update (1) ITKv4 from v4.5.2 to v4.6rc01 and (2) update BRAINSTools

// ------------------------
BRAINSTools

 * Compliant with ITKv4 registration framework. This changes
the fundamental methods for registration to use the ITKv4 framework,
while maintaining both the API and the same results for all regression tests.

 * DWIConvert tool also add features for reading additional scanner types.
// ------------------------


// ------------------------
ITKv4 - New Features

* CMake improvements
 - Improved Remote Module support
 - Add ITK_FORBID_DOWNLOADS for package maintainers
 - ITK_USE_SYSTEM_EXPAT available

* Filtering Improvements
 - Moved TransformToDisplacementField out of Review
 - An entire noise image generation module
   - http://hdl.handle.net/10380/3158
 - Better pipeline support for ResampleImageFilter
 - Move MagnitudeAndPhaseToComplexImageFilter out of Review
 - Setters for LabelMap overlay filters
 - More consistent filter progress reporting

* ImageO improvements
 - Register the GE image formats by default
 - More IO modules are built as shared libraries
 - OpenFileForReading/Writing methods in ImageIO
 - Support for system tiff 4.0.0-4.0.2 (e.g. some Ubuntu versions)
 - Mangling to internal OpenJPEG
 - SCIFIO improvements

* Infrastructure improvements
 - MetaDataObject print specialization for common types
 - Improvements to ResourceProbe and RealTimeClock
 - More Solve methods for VNLSparseLUSolverTraits
 - Output stream operator for LightObject exposed
 - FFTW bump to 3.3.3

* New Remote Modules
 - Skull stripper
   - http://hdl.handle.net/10380/3353
 - Wiki examples
 - Sphinx examples
 - Variational registration
   - http://hdl.handle.net/10380/3460
 - AnalyzeObjectMapIO
   - http://hdl.handle.net/1926/593
 - FDFImageIO
 - SplitComponents
   - http://hdl.handle.net/10380/320

* Registrationv4 improvements
 - v4 regular step gradient descent optimizer
 - v4 amoeba optimizer
 - v4 exhaustive optimizer
 - v4 Powell optimizer
 - v4 one-plus-one-evolutionary optimizer
 - v4 LBFGS optimizer improvements
 - Use registration method classes as pipeline filters

* Performance improvements
 - Registrationv4
 - Histogram computation
 - Improved SmartPointer copy
 - CompositeTransform
 - Registration Jacobian re-use

* Wrapping improvements
 - pygccxml 1.0.0
 - .pth symlink usable in a virtualenv
 - Cleaner CMake configuration
 - SWIG and PCRE updated to 3.0.2, 8.34
 - Latest GCCXML, which works with GCC 4.9
 - Sweeping wrapping generation cleanup


* Many style improvements -- ITK gets more stylish with every release!

* Improved code coverage -- some measures put us over 85%!
// ------------------------

Co-authored-by: Hans Johnson <hans-johnson@uiowa.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23373 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Update BRAINSTools to include DWIConvert interface tweaks.

See #3693

$ git shortlog 8d870f0..ce609cb
Hans Johnson (2):
      ENH: Improve Slicer interface to DWIConvert
      ENH: Fine tuning the GUI for ease of use.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23374 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Fix sign-compare warning in vtkMRMLTransformStorageNode

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23375 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Fix unused variable warning in vtkOrientedGridTransform

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23376 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Update MultiVolumeExplorer project to fix unused-local-typedefs warnings

$ git shortlog 17a9095..d68663f --no-merges
Jean-Christophe Fillion-Robin (1):
      COMP: Fix unused-local-typedefs warnings

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23377 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: document string for markups event enum

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23378 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: update to latest LandmarkRegistration code

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23379 3bd1e089-480b-0410-8dfb-8563597acbee
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