Changesets: Import 2017-06-07 23:51:09

master 6690e56f

2013-11-14 21:56:47


Details Diff
COMP: Propagate cmake variable Slicer_QTSCRIPTEDMODULES_DISABLED

to the Slicer inner build configuration.

It originally was a typo: eq_superbuild_extra_args instead of
ep_superbuild_extra_args which was latter replaced into

git-svn-id: 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File

master 3e374d33

2013-11-14 18:26:45


Details Diff
STYLE: updating docs for 4.3

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

git-svn-id: 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Models/Documentation/Models.xml Diff File

master 8fd51029

2013-11-14 14:12:40


Details Diff
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: 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMakeLists.txt Diff File

master 17f51ad1

2013-11-14 13:26:46


Details Diff
ENH: Slicer 4.3.1-1

git-svn-id: 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMakeLists.txt Diff File

master 43e1d624

2013-11-14 11:12:56


Details Diff
ENH: Added test for MRML node reference serialization and parsing
Issue 0003416

From: Csaba Pinter <>

git-svn-id: 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/Testing/vtkMRMLNodeTest1.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLNode.cxx Diff File

master 2eac6a71

2013-11-13 17:55:42


Details Diff
STYLE: minor edits for 4.3 documentation

Fix formatting errors, attributions, phrasing.

git-svn-id: 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/CLI/ACPCTransform/ACPCTransform.xml Diff File
mod - Modules/CLI/MergeModels/MergeModels.xml Diff File
mod - Modules/CLI/ModelMaker/ModelMaker.xml Diff File
mod - Modules/CLI/ModelToLabelMap/ModelToLabelMap.xml Diff File

master 95f48d89

2013-11-13 09:11:33


Details Diff
BUG: Support vtkStringArray as model field array

Closes 0003344

git-svn-id: 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Models/Widgets/qMRMLModelDisplayNodeWidget.cxx Diff File
mod - SuperBuild/External_CTK.cmake Diff File

master 001f8e6b

2013-11-12 16:08:32


Details Diff
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: 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/DICOM/ Diff File

master 922bb212

2013-11-11 13:04:20


Details Diff
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 0003494

Co-authored-by: Jean-Christophe Fillion-Robin <>

From: Andrey Fedorov <>

git-svn-id: 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_MultiVolumeExplorer.cmake Diff File

master 5b46fd1a

2013-11-07 11:54:34


Details Diff
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.

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: 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Applications/SlicerApp/Testing/Python/ Diff File
mod - Applications/SlicerApp/Testing/Python/ Diff File
mod - Modules/Scripted/DICOM/ Diff File
mod - Modules/Scripted/DICOM/DICOMLib/ Diff File
mod - SuperBuild/External_CTK.cmake Diff File

master 544141a3

2013-11-07 10:33:06


Details Diff
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 0002948

git-svn-id: 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTGUI/qSlicerSaveDataDialog.cxx Diff File
mod - Base/QTGUI/qSlicerSaveDataDialog_p.h Diff File

master a4f50fef

2013-11-07 10:33:04


Details Diff
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,, ...) 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 0002948

git-svn-id: 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTGUI/qSlicerSaveDataDialog.cxx Diff File
mod - Base/QTGUI/qSlicerSaveDataDialog_p.h Diff File
mod - Modules/Loadable/Data/qSlicerSceneWriter.cxx Diff File

master d2a97a6d

2013-11-07 10:33:02


Details Diff
STYLE: Avoid confusion creating enum for custom SaveDataDialog role.

git-svn-id: 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTGUI/qSlicerSaveDataDialog.cxx Diff File
mod - Base/QTGUI/qSlicerSaveDataDialog_p.h Diff File

master 13099732

2013-11-06 14:56:48


Details Diff
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: 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Widgets/qMRMLSceneModel.cxx Diff File

master 2ef602d7

2013-11-06 14:43:35


Details Diff
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 0003253

Signed-off-by: Jean-Christophe Fillion-Robin <>

git-svn-id: 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMake/ Diff File

master 8ecf0edf

2013-11-05 09:24:15


Details Diff
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: 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Markups/MRMLDM/vtkMRMLMarkupsFiducialDisplayableManager2D.cxx Diff File

master a2f32ab8

2013-11-05 09:24:10


Details Diff
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: 3bd1e089-480b-0410-8dfb-8563597acbee

git-svn-id: 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Markups/MRMLDM/vtkMRMLMarkupsDisplayableManager2D.cxx Diff File

master 5ab938ef

2013-11-04 23:48:42


Details Diff
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 0000025.
STYLE: Increment the patch number.
COMP: Fix compiler warnings for Mac OS X Mavericks.
Merge pull request 0000027 from tokjun/25-missing-strnlen

Co-authored-by: Jean-Christophe Fillion-Robin <>

From: Junichi Tokuda <>

git-svn-id: 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_OpenIGTLink.cmake Diff File

master 9d2c53a1

2013-11-04 16:18:41


Details Diff
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.

Co-authored-by: Jean-Christophe Fillion-Robin <>

From: Dominique Belhachemi <>

git-svn-id: 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/vtkITK/vtkITKBSplineTransform.cxx Diff File

master 29a04b80

2013-11-04 16:04:45


Details Diff
BUG: OpenIGTLink - Fixes issue 0003454 - 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 0000003 from lchauvin/patch-1
Merge pull request 0000004 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 0000013 from perim/master
BUG: Fix Issue 0000014 Linker error in VS2012.
STYLE: Fix wrong statement in help (coordinate -> string)
Merge pull request 0000018 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
BUG: Avoid * ((igtl_uint16 *) ptr) = <value> to address issue 0000020. Need testing.
STYLE: Format README using Markdown
BUG: Address issue 0000021.. replace this->m_DefaultBodyType = this->DefaultBodyType() with this->m_DefaultBodyType = ""
BUG: Reset changes in Example/Status/StatusClient
BUG: Fixing Issue 0000020. 'signed' is explicitly specified for igtl_int8. Tested on Ubuntu + armv7l.
STYLE: Use C-style comments in .c files.
Merge pull request 0000022 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 0000024 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 0000009, and a leak

Junichi Tokuda (3):
Merge pull request 0000010 from ihnorton/issue9_partial_fix
ENH: Implement LableMetaList function. This commit requires OpenIGTLink library commit 661d4bd.
Merge pull request 0000012 from tokjun/0003454-lbmeta

From: Jean-Christophe Fillion-Robin <>

git-svn-id: 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_OpenIGTLink.cmake Diff File
mod - SuperBuild/External_OpenIGTLinkIF.cmake Diff File

master 63a1a0e6

2013-11-04 15:43:07


Details Diff
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: 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_VTK.cmake Diff File

master 72406d08

2013-11-03 18:07:51


Details Diff
STYLE: Simplify vtkSlicerModelsLogic code using vtkNew

git-svn-id: 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Models/Logic/vtkSlicerModelsLogic.cxx Diff File

master 598f1038

2013-11-03 18:07:48


Details Diff
STYLE: Avoid confusion renaming SceneView API: "Nodes" into "StoredScene"

The following renaming have been done:
- ivar Nodes -> StoredScene
- method "UpdateSnapshotScene" -> "UpdateStoredScene"
- method "GetNodes" -> "GetStoredScene"

Also remove the unused parameter from "UpdateStoredScene"

git-svn-id: 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Applications/SlicerApp/Testing/Python/ Diff File
mod - Base/QTGUI/qSlicerSaveDataDialog.cxx Diff File
mod - Libs/MRML/Core/Testing/vtkMRMLSceneAddSingletonTest.cxx Diff File
mod - Libs/MRML/Core/Testing/vtkMRMLSceneViewNodeImportSceneTest.cxx Diff File
mod - Libs/MRML/Core/Testing/vtkMRMLSceneViewNodeStoreSceneTest.cxx Diff File
mod - Libs/MRML/Core/Testing/vtkMRMLSceneViewNodeTest1.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLSceneViewNode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLSceneViewNode.h Diff File
mod - Modules/Loadable/Markups/Logic/vtkSlicerMarkupsLogic.cxx Diff File

master f3b94810

2013-11-03 18:07:42


Details Diff
COMP: MRML Scene ivar "ActiveScene" is not unused anymore.

git-svn-id: 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/vtkMRMLScene.h Diff File

master 681693d6

2013-11-03 18:07:39


Details Diff
COMP: Remove redundant Scene methods: GetClassNameList, GetNodeClasses

The method "GetNodeClassesList" fulfills the same goal.

git-svn-id: 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/Logic/Testing/volumes.tcl Diff File
mod - Libs/MRML/Core/Testing/testVolume.tcl Diff File
mod - Libs/MRML/Core/Testing/vtkMRMLSceneTest1.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLScene.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLScene.h Diff File
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