ENH: Update the BRAINSTools Suite.

The BRAINSTools suite has moved to a new repository
to better reflect a consistent and meaningful name.
During this move, a significant amount of code and git
cleanup was done to reduce the size of the git repository.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21788 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: load() now returns the loaded node

This behavior is consistent with the other plugins.


git-svn-id: http://svn.slicer.org/Slicer4/trunk@21789 3bd1e089-480b-0410-8dfb-8563597acbee
COMP:  DoubleConvert needs to be included

In order to build BRAINSTools, the External_DoubleConvert.cmake needs
to be built prior to building the BRAINSTools.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21790 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Fix double-convert external project so that it works as intended

1) The previous version was working because the double-conversion project
was exporting its build tree in the cmake package registry.

See http://www.cmake.org/cmake/help/v2.8.10/cmake.html#command:export

Since the package was exported, the find_package(double-conversion ..) within
BRAINSTools was working. Line like the following weren't not used at all:

  list(APPEND ${CMAKE_PROJECT_NAME}_SUPERBUILD_EP_VARS ${extProjName}_DIR:PATH)

2) Remove dependency to DCMTK. See https://github.com/BRAINSia/BRAINSTools/issues/5

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21791 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Fix "-fPIC" DWIConvert build error related to DoubleConvert project

See also https://github.com/BRAINSia/BRAINSTools/issues/3

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21792 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Update ExternalData module to version 1fd8d01 available in recent CMake

It includes the following fixes:

2013-02-04	Brad King	ExternalData: Attach download rules to content links...
2013-01-30	Brad King	ExternalData: Collapse ../ components in DATA{} paths
2013-01-30	Brad King	ExternalData: Add support for SHA 1 and 2 hash algorithms
2013-01-30	Brad King	ExternalData: Generalize hash algo/ext handling
2013-01-30	Brad King	ExternalData: Allow DATA{} syntax to reference directories
2013-01-30	Brad King	ExternalData: Allow ()-groups in series match regex
2013-01-29	Brad King	ExternalData: Improve series matching using an explicit...
2013-01-28	Brad King	ExternalData: Remove unused private interface
2013-01-28	Brad King	ExternalData: Cleanup stray TODO and typo in comments
2013-01-28	Brad King	ExternalData: Do not match directory names when resolvi...
2013-01-24	Brad King	ExternalData: Remove compatibility with CMake < 2.8.5
2013-01-24	Brad King	Add ExternalData module

See here for details: http://cmake.org/gitweb?p=cmake.git;a=history;f=Modules/ExternalData.cmake;h=9d84f8d135ae8b4e86d78a2e3b570a3b520445a1;hb=HEAD

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21793 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Update Slicer test macros to support ExternalData

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21794 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Clean code and add command line option "--temporary-path"

Remove unused headers

Remove tempDirectory initially added with r11985,
qSlicerCoreApplication::temporaryPath  (added with r15424) should be used
instead.

Calling slicer with both --testing and --temporary-path options returns
the directory associated with testing.

$ ./Slicer --temporary-path
/tmp/Slicer

$ ./Slicer --testing --temporary-path
/tmp/Slicer-tmp

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21795 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Add saveNode and saveScene to python API

Example:

  n = slicer.util.GetNode('MRHead')
  slicer.util.saveNode(n, '/tmp/foo.nrrd')  # Save node data

  slicer.util.saveScene('/tmp/currentscene.mrml') # Save scene as MRML file

  slicer.util.saveScene('/tmp/currentscene.mrb') # Save scene as MRB file

  slicer.util.saveScene('/tmp/currentscene') # Save scene as directory

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21796 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Add python unitTest testing slicer.util.{saveNode, saveScene} methods

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21797 3bd1e089-480b-0410-8dfb-8563597acbee
STYLE: Fix typo and remove "Qt" from message associated with slicerMacroBuildQtModule

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21798 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Added first cut of vtkMRMLNode reference API

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21799 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: implementation of vtkMRMLNode reference API

Implemented Get/Set/SetAndObserve methods in vtkMRMLNode class

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21800 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Bump SlicerExecutionModel ExternalProject to be11bda829.

Include improvements to GenerateCLP.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21801 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Reverted erroneously commit from github


git-svn-id: http://svn.slicer.org/Slicer4/trunk@21802 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Update DoubleConvert tag and remove hack to manually add "-fPIC"

This reverts commit r21792 and also update DoubleConvert external project.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21803 3bd1e089-480b-0410-8dfb-8563597acbee
STYLE: Update BRAINSTools project to remove extra message debug statement

See https://github.com/BRAINSia/BRAINSTools/pull/8

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21804 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Update ExternalData and remove hack in SLICER_ADD_PYTHON_UNITTEST

ExternalData module has been updated to preserve escaped semicolons during
argument expansion.

Details: http://cmake.org/gitweb?p=cmake.git;a=commit;h=1823ab4d76d8efe79bed85328a3f8c74c7d625bd

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21805 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Ensure BRAINSTools uses Slicer ExternalData by replacing it.

This is obviously a hack allowing to use ExternalData withing Slicer while
building BRAINSTools. An issue has been reported upstream.
See https://github.com/BRAINSia/BRAINSTools/issues/3

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21806 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: figured out why transitioning to SpatialAtlas Step takes so long when loading the FullParcellation task and removed bug when setting atlas or subparcellation to None - it was not saved in mrml

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21807 3bd1e089-480b-0410-8dfb-8563597acbee