ENH: Generate tarball of SlicerWizard doc

Create a new build target to generate a tarball of the SlicerWizard
documentation. This is meant to be used similar to the existing Doxygen
tarball, to be scp'd or otherwise transferred from a build machine to
another machine which will serve the pages publicly.

Issue #3601

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23209 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Refactor documentation targets

Replace generate_userdoc.cmake script with direct build commands,
separating creation of the doc and creation of the tarball thereof into
separate targets, for consistency with how the SlicerWizard doc build
rules are set up. Also modify the latter to explicitly remove the old
tarball first for consistency with (the historic and retained behavior
of) the former.

The old rules depended on the output index.html, which would cause them
to do nothing once the doc had been created (ever). The new rules, like
the rules for the SlicerWizard doc, have no dependencies and so the doc
is always regenerated when the target is traversed. As doxygen
unfortunately does not implement its own dependency tracking (sphinx
does), this is very inefficient, but more correct, which is more
important for this case.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23210 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fix cpp documentation names

The C++ documentation covers all of Slicer, not just Base. Therefore,
fix the tarball name and target names (the latter of which have been
"wrong" since a while back).

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23211 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Install extension dependencies

When installing an extension, also query the extension's internal
description file for its list of dependencies, and prompt to install
them as well.

Issue #2912

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23212 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: fix crash when scene view added without screen shot

When saving a scene with the Scene Views module open, a null
pointer crash happened because the qSlicerSceneWriter was adding
the scene view node to the scene before capturing and setting
the screen shot. The mrml application logic does the same thing.
For now, avoid the crash by checking the pointer. The
thumbnail immage will appear on the next update, but since the
mrml scene isn't invoking an event when it's finished the
Commit call, the module will have to in future observe scene view
nodes for modified events to detect that a screen shot has been
added to the node (and if there have been other updates directly
to the node rather than via the GUI).

Issue #1299



git-svn-id: http://svn.slicer.org/Slicer4/trunk@23213 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Expanded vtkSlicerCommonInterfaceTest1.cxx to expose bug that makes multiple tests fail of EMSegmenter

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23214 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Updating SimpleITK to 0.9.0.dev171

This update contains minor fixes in the 0.8 release branch along with
the addition of many ITK RLE LabelMap filters. Additionally it
contains a major refactoring of Statistics filters. Which includes the
removal of the MeasurementMap structure and the statistic procedural
methods.

The LabelMap functionality and new Statistics filters will form the
foundation of several planned projects during project week.

Dashboard:
http://open.cdash.org/index.php?project=SimpleITK&date=20140509

One failing test related to deleting command, during a command, prior
behavior was to call std::terminate. A patch in ITK fixes this issue.

This commit also contains an initial implementation of the
ImageRegistrationMethod which is still under development and unstable.

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23215 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: 3615. Enable Non-linear transforms in ModelSliceDisplayableManager

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23216 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Fix install location of VTKv6

Update External_VTKv6.cmake to reflect upstream changes to the name(s)
of the variables that control the install locations of the libraries.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23217 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: In Selection node, get unit node only for valid MRML node references.

This fixes the issue discussed in [1]

[1] http://slicer-devel.65872.n3.nabble.com/stack-trace-for-failing-self-test-tt4031667.html

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23218 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Fix SlicerWizard/Utilities.py for Python 2.6

Use tuples instead of set literals for checking for a supported VCS
tool, as set literals are only supported in Python 2.7.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23219 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Update CTK project to fix windows build and dicom repair msg box issue.

$ git shortlog 1b2973d58..3aaa591 --no-merges
Alireza Mehrtash (1):
      Fixed a bug in repair message box

Jean-Christophe Fillion-Robin (1):
      Fix typo introduced by commit 8d376ed

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23220 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: separate scene views with a line

Request from Ron, adding in a horizontal line between
scene views.

Issue #1299



git-svn-id: http://svn.slicer.org/Slicer4/trunk@23221 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fix crash with vtkMRMLSelectionNode and vtkSlicerUnitsLogic

Since r23192, the GetUnitNodes() can return empty nodes.
This triggered asserts in vtkSlicerUnitsLogic.
vtkSlicerUnitLogic is only interested in unit quantities and IDs.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23222 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: #3694 check for valid image data before running pipeline

Since the display node is observing the image data directly it
may receive Modified events on image data that is not yet
completely constructed, in particular, during a DeepCopy, the scalar
fields may not yet have been copied when a ModifiedEvent is triggered
by one of the Set methods.

This change prevents a spurious vtkErrorMessage from being generated,
and so it allows the EMSegment test to pass.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23223 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Update qMRMLSliderWidget single step when range changes

The single step can depend on the range of the slider, update it when
needed.

Issues #3657, #3700
$ git shortlog 3aaa591..daaf705 --no-merges
Julien Finet (1):
      Virtualize ctkRangeWidget and ctkSliderWidget public API

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23224 3bd1e089-480b-0410-8dfb-8563597acbee
Merge branch 'master' of https://github.com/cpinter/Slicer into subject-hierarchy-integration
Merge branch 'subject-hierarchy-integration' of https://github.com/cpinter/Slicer into subject-hierarchy-integration