BUG: 3416. Added generic mechanism for persisting node references in .mrml files. 
References stored in the form: references="role1:id1 id2 iid3;role2:id3;". Note that for backwards compatibility the  reference nodes such as displayable, transformable etc. still read/write their references the old way. Only custom references will use new syntax.


git-svn-id: http://svn.slicer.org/Slicer4/trunk@22610 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: fix typo in AdditionalInitializeStep method name

Fixing a mis spelling in the additional initialize step method name.
In vtkMRMLAbstractDisplayableManager it's defined as:
AdditionalInitializeStep
but vtkMRMLCameraDisplayableManager was using:
AdditionnalInitializeStep
with an extra n. Using that signature, it was never getting called
so when new layout windows were being created, the active camera
was not getting set on the renderer.

Issue #1690



git-svn-id: http://svn.slicer.org/Slicer4/trunk@22611 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: refactor code to remove unnecessary error message

There are two possible ways to obtain the results from PETStandardUptakeValueComputation,
having them written out to a .csv file or to a string parameter file that gets
parsed and loaded into the Slicer GUI. Only print out an error and fail if
neither parameter is specified. 
Checks for empty strings and doesn't try to open the files, so the unable
to open error messages will only occur if a non empty file name fails
to open.

Issue #3432


git-svn-id: http://svn.slicer.org/Slicer4/trunk@22612 3bd1e089-480b-0410-8dfb-8563597acbee
STYLE: Improve Data module documentation

Add "MRML Node Inspector" section documentation.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22613 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Added string length check in vtkMRMLNode::GetReferenceRoleFromMRMLAttributeName to fix Slicer crash when loading a scene

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22614 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fixed crash in Transform widget

When hardened transform or untransformed multiple transformed items (with multi-select) then Slicer crashed.
Applied the same fix as in http://www.na-mic.org/Bug/view.php?id=2578.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22615 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: see comments of r17039 in Slicer 3 trunk

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22616 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: 3447. Added .nrrd extension to grid transform IO

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22617 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Changed type of mrb file loading log messages from error to debug

The messages were logged as errors, while they are actually debug messages.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22618 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Revert r22484 - Fix already integrated in ITK release branch.

Corresponding fixes in ITK release branch is InsightSoftwareConsortium/ITK@35000ead738c6

Fixes #3421

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22633 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Contribution from Albert Montillo to paint in 3D

Adds a Sphere option to the PaintEffect to make it quicker to segment
large anatomical regions that are somewhat spherical.

Powerful when used with ThresholdPaint.

Cleanup code.

Remove debug comments.

Clean up variable names.

STYLE: fix small typo

From: Jim Miller <millerjv@ge.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22635 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Do not install teem development files.

Fixes #2397

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22636 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: add node attributes describing the currently active manipulation

Tell which slice viewer is manipulating which fiducial in the
markup node.

Markups.MovingInSliceView holds the LayoutName of the sliceNode associated
with the viewer where the widget is being manipulated.

Markups.MovingSeedNumber holds the seed number being manipulated.

Both are cleared when the seed is not being manipulated by a widget.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22637 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Update ITKv4.

Bump ITKv4 this fixes some MetaIO issues:

Stephen Aylward (3):
   BUG: Fixed bugs in Form and hidden virtual funcs in Image
   COMP: Fixed unused variable warnings in tests
   COMP: Disable tests since paths are set wrong in VTK

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22638 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Fix check in midas_api_upload_extension macro

Since the variable ${var} were defined in the parent scope, no warning
were displayed.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22639 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Tweak midas_api_upload_extension macro test case

Add link to existing screenshot and also add a svn example.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22640 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Attempt to fix font issue related to webkit performance on MacOSX 10.9

Associated message in the system log:
CoreText performance note: Client called CTFontCreateWithName() using name "Lucida Grande" and got font with PostScript name "LucidaGrande". For best performance, only use PostScript names when calling this API.

See https://bugreports.qt-project.org/browse/QTBUG-32789 and
http://successfulsoftware.net/2013/10/23/fixing-qt-4-for-mac-os-x-10-9-mavericks/

Fixes #3460

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22641 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Ensure ROI worked as expected. Fixes #3459

Fix bug introduced by r22539 when updating code to use vtkNew where
possible.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22642 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: UpdateITKv4 - Fix unused typedefs warnings specific to gcc >= 4.8

$ git shortlog 4c1d191ceac136b920dbb13564c419fc821dd848..ee6472628dcbb12d2723f04dbf3b14764de2b4ff
Matthew McCormick (1):
      COMP: Do not warn about unused typedefs

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22651 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fix "No LookupTable" error in qMRMLSliceWidget test

Full name of the test is: qMRMLSliceWidgetEventTranslatorPlayerTest1

The following error was reported:

//----------------------
ERROR: In /path/to/VTK/Imaging/vtkImageMapToColors.cxx, line 153
vtkImageMapToColors (0x268f190): RequestInformation: No LookupTable was set but number of components in input doesn't match OutputFormat, therefore input can't be passed through!

ERROR: In /path/to/VTK/Imaging/vtkImageExtractComponents.cxx, line 239
vtkImageExtractComponents (0x26947e0): Execute: Component 1 is not in input.

ERROR: In /path/to/VTK/Imaging/vtkImageExtractComponents.cxx, line 239
vtkImageExtractComponents (0x26947e0): Execute: Component 1 is not in input.
//----------------------

It is fixed by adding colorNodeRef attribute to VolumeDisplay element.

Also documented in the FAQ: http://wiki.slicer.org/slicerWiki/index.php?title=Documentation/Nightly/Developers/FAQ#Developer_FAQ:_MRML

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22654 3bd1e089-480b-0410-8dfb-8563597acbee