ENH: Update VTK - Add support for color lookup table annotation.

Kevin Wang (1):
      Update vtkScalarsToColors classes to support color lookup table annotation.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22678 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: OpenIGTLink - Fixes issue #3454 - could not receive LBMETA messages.

// -------------------------
OpenIGTLink updates:

Bonny Biswas (2):
      ENH: Added set/get methods for coordinate system in ImageMessage classes
      BUG: LPS coordinate system value in ImageMessage does not match protocol

Isaiah Norton (2):
      ENH: add StringEchoServer example
      ENH: add PointListServer example

Junichi Tokuda (41):
      ENH: start implementing session manager
      ENH: MessageHandler and SessionManager classes are implemented and now working. Template-based MessageHandler class has been removed.
      STYLE: adding comment in the source code for SessionManagerServer example program.
      ENH: implement session manager with pseudo non-blocking messaging (receive only)
      Merge pull request #3 from lchauvin/patch-1
      Merge pull request #4 from lchauvin/patch-1
      ENH: added the second argument for Process() in the message handler class to share data between the message handler class and other classes/functions outside the class.
      Solve conflict.
      ENH: Adding CapabilityMessage class
      ENH: Adding the capability message type and examples.
      ENH: Merging the fixes in the master branch to the development branch.
      BUG: Fixed the compile error caused by the last commit.
      STYLE: Merging the master repository with improved comments for Doxygen.
      STYLE: Merge changes in the master repository.
      STYLE: Merge updates in the master repository.
      STYLE: Merge master repository.
      ENH: Add igtlCreateDefaultQueryMessageClass() macro to help defining a class for query message.
      ENH: Create HeaderOnlyMessageBase as a base class for query message types.
      BUG: merge labonny's changes
      Merge pull request #13 from perim/master
      BUG: Fix Issue #14 Linker error in VS2012.
      STYLE: Fix wrong statement in help (coordinate -> string)
      Merge pull request #18 from ihnorton/add_pointlistserver_example
      ENH: Add a class for GET_STATUS message type.
      ENH: Add TrajectoryMessage example.
      ENH: Merge changes in master.
      STYLE: Fixed revision number
      COMP: Fix warning 'converting to non-pointer type int from NULL'.
      STYLE: Update version number.
      ENH: Merge github.com:tokjun/OpenIGTLink.git.
      BUG: Avoid * ((igtl_uint16 *) ptr) = <value> to address issue #20. Need testing.
      STYLE: Format README using Markdown
      STYLE: Rename README to README.md
      BUG: Address issue #21.. replace this->m_DefaultBodyType = this->DefaultBodyType() with this->m_DefaultBodyType = ""
      BUG: Reset changes in Example/Status/StatusClient
      BUG: Fixing Issue #20. 'signed' is explicitly specified for igtl_int8. Tested on Ubuntu + armv7l.
      STYLE: Use C-style comments in .c files.
      Merge pull request #22 from tokjun/master
      ENH: Add LBMETA message to ImageDatabaseServer example.
      BUG: Fixed bug in LabelMetaMessage. It could not extract owner image information from a LBMETA message.
      Merge pull request #24 from tokjun/23-LBMETA-example

Laurent Chauvin (3):
      Modified GetMode method
      Add igtlMessageHandlerMacro.h to the list of files
      ENH: Removed the sleep

Per Inge Mathisen (3):
      Fix wrong use of delete operator
      Fix wrong bitwise and operator
      Fix compile warnings under clang

// -------------------------
OpenIGTLinkIF updates:

Isaiah Norton (1):
      COMP: partially fix #9, and a leak

Junichi Tokuda (3):
      Merge pull request #10 from ihnorton/issue9_partial_fix
      ENH: Implement LableMetaList function. This commit requires OpenIGTLink library commit 661d4bd.
      Merge pull request #12 from tokjun/0003454-lbmeta

From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22679 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: vtkITK - Update GetJacobian() to make transform ITKv4 compliant

This patch is necessary to compile Slicer with a system ITKv4 library.

For more info see the ITKv4 migration guide.
http://itk.org/migrationv4/index.php?action=artikel&cat=3&id=110&artlang=en

Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

From: Dominique Belhachemi <domibel@debian.org>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22680 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: OpenIGTLink - Fix MacOSX build error related to missing strnlen()

$ git shortlog ee594372eb8c9a25da1dbff2bd081cb70ce9554a..3ac531115f55e74265e7de7ff508312dbfb16695
Junichi Tokuda (4):
      BUG: Implement igtl::Strnlen() for platforms that do not have strnlen. See issue #25.
      STYLE: Increment the patch number.
      COMP: Fix compiler warnings for Mac OS X Mavericks.
      Merge pull request #27 from tokjun/25-missing-strnlen

Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

From: Junichi Tokuda <tokuda@bwh.harvard.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22681 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: give Markups option to be visible only in selected views

Port change from r21740 from Annotations to Markups

    ENH: give annotations option to be visible only in selected views

    This uses the same convention used in dislay nodes for other
    displayable managers (e.g. VolumeRendering), except that it uses the
    sliceNode since it is the 2D analog to the 3D view Node (at some point
    perhaps there should be a generic superclass).  Here, since we are only
    using the ID string it doesn't matter what type the node it.

    This feature allows custom UIs, for example where some annotations only
    show up in one view while others show up everywher.  In particular, this
    is helpful for annotations representing volume-specific anatomical
    landmark locations.

    git-svn-id: http://svn.slicer.org/Slicer4/trunk@21740 3bd1e089-480b-0410-8dfb-8563597acbee

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22682 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: clarify name of attribute (Markup not Seed)

There are different conventions in different parts of the code,
but Seed is consistently the vtk widget layer, and Markup is the
Slicer nomenclature.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22683 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Ensure custom qt style plugins are fixed-up on MacOSX

This is a follow-up of commit r22238 ensuring the style plugins
are considered as candidate by the fixup script.

See #3253

Signed-off-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22684 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fixed volume rendering presets issue (presets were not displayed)

The scene model RowCache was temporarily outdated during node insertion. If the cache was accessed during node insertion, the qMRMLSceneModel::indexFromNode method indicated that the node doesn't exist yet.
Fixed by adding an entry to the cache with the node-to-be-added, which results in not using the cache to determine if the node exists or not but uses the traditional way of iterating through all the items.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22685 3bd1e089-480b-0410-8dfb-8563597acbee
STYLE: Avoid confusion creating enum for custom SaveDataDialog role.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22686 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Properly support extension

Revert commit r22148 that was setting the path to saved MRB as MRMLScene URL.
The MRML scene URL knows remains associated with the mrml file after either
a read or save to mrml, or even export (MRB, Kiwi.zip, ...) operation.

To be able to properly switch between different available file formats
while supporting filename containing dots. The extension of a filename
needs to be removed based on a list of known extensions. For that purpose,
the following two functions have been introduced:
  - extractKnownExtension
  - stripKnownExtension

These functions rely on the existing IOManager function "fileWriterExtensions"
able to return a list of name filters associated with either a storage node
or a mrml scene.

For any fileName item, in order to get the associated storage node or mrml scene,
a new role named "UIDRole" has been introduced. For a given fileName item,
if a nodeID is set with the "UIDRole", it is understood that it will
be the nodeID of the corresponding storage node. If it is not set, it means
the fileName item is associated the scene.

See #2948

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22687 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: In Slicer session, keep track of Scene file format used to save

Within a given a Slicer session, the selected Scene file format will
be remembered if the scene could be successfully saved/exported.
Note that the corresponding value won't be saved into the settings.

See #2948

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22688 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: dicom header viewer added to DICOMLib using ctkDICOMObjectListWidget

ENH: update DICOM module for Table View

New interface to support better searching and header display.

Now plugins are selectable to avoid wasting time on unneeded plugins.

Plugins are now evaluated on-demand, to simplify the workflow.

http://www.commontk.org/index.php/CTK-Hackfest-May-2013#DICOM_Database_and_Networking

https://github.com/commontk/CTK/pull/361

ENH: update to latest CTK for header widget

Also fix lingering rebase issue (stray variable).

BUG: Give header popup independent geometry setting

Also fix incorrect end of line character

ENH: examine button diabled until needed

STYLE: remove tabs in code

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22689 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: MultiVolumeExplorer - Anticipate logic headers reorganization.

Soon, as a compilation speedup, the base class "vtkMRMLAbstractLogic"
will forward declared classes in its definition file.

This commit fix compilation issue that would have occurred following
integration of the topic "finetjul/Slicer@vtkmrmlabstractlogic-clean-includes-trunk"

Fixes #3494

Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

From: Andrey Fedorov <fedorov@bwh.harvard.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22693 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: avoid python attribute error on dicom context menu

TODO: the elements are currently disabled since we don't have
corresponding implementations for the new dicom widget.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22694 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Support vtkStringArray as model field array

Closes #3344

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22695 3bd1e089-480b-0410-8dfb-8563597acbee
STYLE: minor edits for 4.3 documentation

Fix formatting errors, attributions, phrasing.



git-svn-id: http://svn.slicer.org/Slicer4/trunk@22697 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Added test for MRML node reference serialization and parsing
Issue #3416

From: Csaba Pinter <csaba.pinter@queensu.ca>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22700 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Slicer 4.3.1-1

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22702 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Revert  tweak release 4.3.1-1 commit done on trunk

This commit revert the previous commit r22702. This commit should be
done on the Slicer-4-3-1-1 branch instead of the trunk.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22703 3bd1e089-480b-0410-8dfb-8563597acbee
STYLE: updating docs for 4.3

Added description of including fiber bundles, scroll to, and show/hide all.



git-svn-id: http://svn.slicer.org/Slicer4/trunk@22705 3bd1e089-480b-0410-8dfb-8563597acbee