BUG: 3241 Fix transform not applied to volume when scene is read from a file

When a scene is loaded, vtkMRMLScene::UpdateNodeReferences doesn't handle event registration.
Except for vtkCommand::ModifiedEvent, any other events need to be registered via OnNodeReferenceAdded API.
Fixes #3241

From: Yuzheng Zhou <yuzheng.zhou@kitware.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22343 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: remove color table entries from mrml file

Rely on the file written to disk by the storage node, 
reduces the size of the mrml file.
Keep the number of colors in the mrml file so that the
table is properly initialised.

Issue #2486


git-svn-id: http://svn.slicer.org/Slicer4/trunk@22344 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Hide initialization info when running Slicer as python interpreter.

Add method "qSlicerCoreCommandOptions::verbos" currently returning false
only  if slicer runs a python script directly passed as a command line
argument.

Later on, the system could be extended so that all initialization
information are hidden by default. They would be displayed
only if --verbose is explicitly passed.

Fixes #3285

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22345 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: fix extent check to accommodate single-slice data

No plots were shown correctly when extent range was 0 in one of the dimensions


git-svn-id: http://svn.slicer.org/Slicer4/trunk@22346 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fix opening of link in extension manager

Opening of links different from slicer.kitware.com host into regular
browser has been initially introduced by r21897. Then, when commit r22220
introduced qSlicerWebWidget, the management of external links has been
broken.

This commit fixes the issue by ensuring the qSlicerWebWidget always open
link within its associated webview. The slot "onLinkClicked" from
"qSlicerExtensionsInstallWidget" will check what is the host and open
into a regular browser if needed.

See #3045

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22347 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Add back/forward button to extension manager

Fixes #2191

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22348 3bd1e089-480b-0410-8dfb-8563597acbee
STYLE: Tweak comment in SlicerConfig.cmake

See #3247

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22349 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fixed bug #3272  http://www.na-mic.org/Bug/view.php?id=3272

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22350 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Disable configure time message mentioning some CLIs have NO tests

These messages (introduced by r20160 more than a year ago) didn't have
the intended effect. Despite the fact developer were systematically
looking at these warning message, they became "noise" and have been ignored.

This commit disables the warning message and reference a mantis issue
tracking the fact there is no test.

See #1619, #3333, #3334, #3335, #3336, #3337, #3338, #3339, #3340, #3341

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22351 3bd1e089-480b-0410-8dfb-8563597acbee
STYLE: Consistently use MODULE_NAME var in Markups CMakeLists.txt

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22352 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Simplify Markups module generic tests configuration

Simply passing option "WITH_GENERIC_TESTS" to the macro
"slicerMacroBuildLoadableModule" is enough.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22353 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Simplify how Markups test inputs are specified

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22354 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Ensure tilted volumes keeps correct orientation on DICOM export

This commit update the ITKv4 tag associated with the ITK release branch
so that at least the following commit is included:

 cf0bd26 - BUG: GDCMImageIO ignore image orienations from MetaDataDictionary

The other notable ITKv4 commits that are now included are the following:

 f2b19f0 - BUG: Need to set 3rd dir cosine for DICOM images
 e966e36 - DOC: Rename DCMTKException DCMTKExceptionOrErrorReturn
 449c71b - ENH: Accomodate Philips 4D Multiframe DICOM files
 1c09982 - COMP: Avoid MetaIO config conflict with USE_SYSTEM_GDCM.
 268bb25 - COMP: New baseline image for MultiResImageRegistrationTest.
 ab3d00c - BUG: A fix for using sys installed GDCM.
 6954fa3 - ENH: Exclude ITKGDCM module when system GDCM is ON.
 2c00ca5 - BUG: itkSingleLevelSetsv4WhitakerImage2DTest output clobber.
 b24c9f0 - COMP: Do not try to include float.h for MinGW.
 376aeec - BUG: Row/Column assignment into ImageDimensions was wrong
 34deb5c - BUG: Guard against Divide by Zero
 0f27099 - BUG: {Opening,Closing}ByReconstructionImageFilter information propagation
 ed3538f - BUG: Two tests were writing to same filename.
 424c76f - BUG: ConstPointer assigned to non-const raw pointer
 e8dfc74 - BUG: Fix failure in InteractivePause test
 e218909 - BUG: Check that region for thread is not empty
 0f0c163 - COMP: Fixed compiler error in C++11

For a complete list, see https://github.com/Kitware/ITK/compare/35b90133a793ffd884820e499175db19366fe627...237932867d8491db6a7745e6b4cc2b25f8e4470c

Fixes #3254

Co-authored-by: Jim Miller <millerjv@ge.com>
Co-authored-by: Matt McCormick <matt.mccormick@kitware.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22355 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: DirectoryListView - Allow path with same root to be added

Before this commit, if two existing paths with the same root were added, the
second one wasn't considered.

For example, after successively calling "addDirectory" with the
following paths:

 "/tmp/foo"
 "/tmp"

, the second path "/tmp" wasn't added.

This commit fixes the "hasDirectory()" method so that it uses an "Exact"
match instead of "StartWith" match.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22356 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: renable vtkMarkupsAnnotationSceneTest

Update from old theory of converting annotation fiducials
on scene read to a call on the Markups logic class. 



git-svn-id: http://svn.slicer.org/Slicer4/trunk@22357 3bd1e089-480b-0410-8dfb-8563597acbee
STYLE: reduce levels of parameters

Rewrite the Markups documentation file to reduce the level
of nesting in the parameters. The wiki templates only show
3 levels, so go to a flatter description so all parameters
can be displayed on the wiki.



git-svn-id: http://svn.slicer.org/Slicer4/trunk@22358 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Ensure scripted module and scripted module widget are named.

Naming object is helpful when both introspecting/debugging the application
or when recording QtTesting macros.

See #2808

Co-authored-by: Chrystel Juan <chrystel.juan@kitware.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22359 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Ensure editor objects and widgets are all named

Doing so will make the debugging of QtTesting macro easier and less
confusing.

See #2808

Co-authored-by: Chrystel Juan <chrystel.juan@kitware.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22360 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Ensure EditColor widgets are all named

Naming widgets allows QtTesting to properly look up object and reply
actions.

See #2808

Co-authored-by: Chrystel Juan <chrystel.juan@kitware.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22361 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Ensure objectName is set for all type of modules and moduleWidgets

This commit revert r22359

ObjectName associated with ...

  ... module is now "<ModuleName>Module"

  ... module widget is now "<ModuleName>ModuleWidget"

The objectName will always be set by set externally by ...

  ... qSlicerAbstractModuleFactoryManager for the module

  ... qSlicerAbstractModuleWidget::setup() method for the module widget

See #2808

Co-authored-by: Chrystel Juan <chrystel.juan@kitware.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22362 3bd1e089-480b-0410-8dfb-8563597acbee