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master 594fe765

2014-12-12 13:20:51

pinter

Details Diff 		BUG: Subject hierarchy does not try to remove non-SH hierarchy nodes when data node is deleted

When a (non-SH) node is removed, the related subject hierarchy node is removed with it, so that it's not left dangling and become invalid. Previously the occasional other type hierarchy nodes were removed as well. This has caused problems when deleting the nodes in other modules handling hierarchies due to different handling of node deletion, so this feature has been removed.

Fixes 0003918

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23829 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyPluginLogic.cxx Diff File

master a7421fc9

2014-12-10 17:10:30

jcfr

Details Diff 		ENH: Use Python logging framework for scripted module logging

Use Python's built-in logging module to manage logging. A direct advantage is that line number, file name, method name can be logged, too. Also, it follows the convention of using qt-style logging in qt classes, vtk-style logging in vtk classes, etc.

Default behavior of log levels:
DEBUG: log to application log only, includes file name, line number, thread
INFO: log to stdout (appears in application log, too)
WARNING: log to stderr (appears in application log, too)
ERROR: log to stderr (appears in application log, too)

Usage:
import logging

[...]

logging.debug("this is a debug message")
logging.info("this is an info message")
logging.warning("this is a warning message")
logging.error("this is a error message")

From: Andras Lasso <lasso@queensu.ca>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23828 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/Python/CMakeLists.txt Diff File
mod - Base/Python/slicer/ScriptedLoadableModule.py Diff File
mod - Base/Python/slicer/__init__.py.in Diff File
rm - Base/Python/slicer/log.py Diff File
mod - Base/Python/slicer/util.py Diff File
mod - Extensions/Testing/ScriptedLoadableExtensionTemplate/ScriptedLoadableModuleTemplate/ScriptedLoadableModuleTemplate.py Diff File
mod - Utilities/Scripts/SlicerWizard/Utilities.py Diff File
mod - Utilities/Templates/Modules/Scripted/TemplateKey.py Diff File

master 0940a0a7

2014-12-10 16:29:20

jcfr

Details Diff 		ENH: Update OpenIGTLinkIF: Improve support for POINT and POLYDATA message

Fixes 0003875 and 0003907

$ git shortlog 2ffd26b..d56c985 --no-merges
Junichi Tokuda (10):
ENH: Use MarkupsFiducial node for POINT messages
STYLE: Rename vtkIGTLToMRMLPointMetaList to vtkIGTLToMRMLPoint
STYLE: Rename vtkIGTLToMRMLPoint to vtkIGTLToMRMLPoints.
ENH: Initial implementation of the PolyData converter.
ENH: Export PolyData through OpenIGTLink. Attributes are not exported.
ENH: Export attributes. All features for the POLYDATA converter are implemented.
ENH: Simplify vtkIGTLToMRMLPolyData::MRMLToIGTL() using vtkIGTLToMRMLPolyData::VTKToIGTLCellArray() function.
ENH: Simplify vtkIGTLToMRMLPolyData::MRMLToIGTL() using vtkIGTLToMRMLPolyData::VTKToIGTLAttribute() function.
ENH: Clean up the code.
STYLE: Remove debug code.

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23827 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File

master d0774029

2014-12-10 16:12:21

jcfr

Details Diff 		ENH: Added support for thin plate spline transforms

Added full support for thin plate spline transforms:
* save/load forward and inverse transform from ITK files
* verification that ITK and VTK thin plate spline transform computes exactly the same values
* basic storage and inversion tests

Thin plate spline transform is used by the Landmark Registration module, so now the computed transform can be saved to the scene or exported.

From: Andras Lasso <lasso@queensu.ca>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23826 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/Logic/vtkSlicerTransformLogic.cxx Diff File
mod - Base/Logic/vtkSlicerTransformLogic.h Diff File
mod - Libs/MRML/Core/Testing/CMakeLists.txt Diff File
mod - Libs/MRML/Core/Testing/NonLinearTransformScene.mrml Diff File
add - Libs/MRML/Core/Testing/TestData/TpsTransform.h5 Diff File
mod - Libs/MRML/Core/Testing/vtkMRMLNonlinearTransformNodeTest1.cxx Diff File
add - Libs/MRML/Core/Testing/vtkThinPlateSplineTransformTest1.cxx Diff File
mod - Libs/MRML/Core/vtkITKTransformConverter.h Diff File
mod - Libs/MRML/Core/vtkITKTransformInverse.h Diff File
mod - Libs/MRML/Core/vtkMRMLTransformNode.cxx Diff File

master 26d789cc

2014-12-10 14:56:40

pinter

Details Diff 		BUG: Fix backwards compatibility for DICOM plugins

Fixed issue discussed here:
http://slicer-devel.65872.n3.nabble.com/DICOM-plugins-are-not-called-td4033045.html
Now the DICOM plugins that don't use the new naming of the plugin functions (examine was renamed to examineForImport to avoid ambiguity due to adding examineForExport) work without any changes.


git-svn-id: http://svn.slicer.org/Slicer4/trunk@23825 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/DICOMLib/DICOMWidgets.py Diff File

master 3ceb1690

2014-12-10 14:33:06

pinter

Details Diff 		BUG: Fix subject hierarchy node creation bug and automatic tests

Bug reported in this thread
http://slicer-users.65878.n3.nabble.com/DICOM-RT-Export-td4028406.html
fixed, now subject hierarchy nodes are also created before the user visits the SH module (only if auto-generate is turned on, or if loaded from DICOM).

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23824 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Applications/SlicerApp/Testing/Python/SubjectHierarchyCorePluginsSelfTest.py Diff File
mod - Applications/SlicerApp/Testing/Python/SubjectHierarchyGenericSelfTest.py Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/CMakeLists.txt Diff File
add - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyPluginLogic.cxx Diff File
add - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyPluginLogic.h Diff File
mod - Modules/Loadable/SubjectHierarchy/qSlicerSubjectHierarchyModule.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/qSlicerSubjectHierarchyModule.h Diff File
mod - Modules/Loadable/SubjectHierarchy/qSlicerSubjectHierarchyModuleWidget.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/qSlicerSubjectHierarchyModuleWidget.h Diff File

master 8df30d81

2014-12-10 13:27:19

jcfr

Details Diff 		ENH: Update CTK to also wrap set/get for ctkErrorLogContext File attribute

$ git shortlog 0d2a634..cb53ac3a --no-merges
Jean-Christophe Fillion-Robin (1):
Update PythonQt decorator of ctkErrorLogContext to include set/get for file

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23823 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_CTK.cmake Diff File

master a842eab3

2014-12-09 17:52:07

jcfr

Details Diff 		ENH: Update CTK to ensure ctkErrorLogContext is available from python

From python, it is now possible to execute the following:

errorLogModel = slicer.app.errorLogModel()
errorLogModel.addEntry(qt.QDateTime.currentDateTime(), \
slicer.app.applicationPid(), \
ctk.ctkErrorLogLevel.Debug, \
"Python", \
ctk.ctkErrorLogContext("This is a message"), \
"This is a message")


$ git shortlog 42700cf..0d2a634 --no-merges
Jean-Christophe Fillion-Robin (1):
Add PythonQt decorator for ctkErrorLogContext

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23822 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_CTK.cmake Diff File

master b7d6ed07

2014-12-09 10:35:55

pinter

Details Diff 		BUG: Fix mixing subject hierarchy with other hierarchies

Two fixes have been applied. One is to enforce nested associations if there is a conflict of two hierarchy nodes associating to one data node.
Reminder: Nested associations prevent the scenario when two hierarchy nodes associate to the same data node, which leads to non-determinism if GetAssociatedHierarchyNode is called. In this case instead of the connections (SH --assoc--> Model <--assoc-- ModelHierarchy), this structure is created: SH --assoc--> ModelHierarchy --assoc--> Model
The other fix is to ensure reparenting to the same type of hierarchy nodes. If this proves to be too strict, then we may allow reparenting to base classes, or the alternative is to subclass the scene hierarchy model to the hierarchy types.

Also a subject hierarchy bug was fixed that occurred because the widget was created when instantiating the module (which is udesirable by itself), and this caused creation of context menu actions before external plugins had the chance to register. Now the widget is not created early, but the right connections are made at the right time.

Fixes 0003911

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23821 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Widgets/qMRMLSceneHierarchyModel.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qMRMLSubjectHierarchyTreeView.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qMRMLSubjectHierarchyTreeView.h Diff File
mod - Modules/Loadable/SubjectHierarchy/qSlicerSubjectHierarchyModule.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/qSlicerSubjectHierarchyModuleWidget.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/qSlicerSubjectHierarchyModuleWidget.h Diff File

master ce687194

2014-12-06 00:56:02

jcfr

Details Diff 		ENH: Improve scripted module templates

* Use "slicer.log" functionality

* Also update the scripted loadable module template to perform actual
image processing (thresholding, using a CLI) and not just
capture a screenshot, because this is much closer to what
most users would do.

From: Andras Lasso <lasso@cs.queensu.ca>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23820 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Extensions/Testing/ScriptedLoadableExtensionTemplate/ScriptedLoadableModuleTemplate/ScriptedLoadableModuleTemplate.py Diff File
mod - Utilities/Templates/Modules/Scripted/TemplateKey.py Diff File

master e76f062a

2014-12-06 00:55:58

jcfr

Details Diff 		ENH: Update scripted module base class to leverage "slicer.log" functionality

From: Andras Lasso <lasso@cs.queensu.ca>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23819 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/Python/slicer/ScriptedLoadableModule.py Diff File

master 80436d11

2014-12-06 00:55:56

jcfr

Details Diff 		ENH: Added logging functions for Python

Added info and error logging macros for Python modules.

Usage examples:

```
import slicer.log

slicer.log.info("This is an info message, logged as an INFO type message")
slicer.log.info("This is an info message, logged and also displayed in a popup for a short time", True)
slicer.log.info("This is an info message, logged and also displayed in a popup for 5 seconds", True, 5000)
slicer.log.info("This is an info message, logged and also displayed in a popup, the user has to click OK to continue", True, 0)

slicer.log.error("This is an error message, logged as an ERROR type message")
slicer.log.error("This is an error message, logged and also displayed in a popup, the user has to click OK to continue", True, 0)
```

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23818 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/Python/CMakeLists.txt Diff File
add - Base/Python/slicer/log.py Diff File

master 6cbc4839

2014-12-05 12:25:20

pinter

Details Diff 		ENH: Subject hierarchy nodes not auto-created by default

Subject hierarchy auto-creation has caused problems in other modules (like Models, see referred ticket), and some users won't use subject hierarchy, so the supported data nodes are not added to the hierarchy automatically.
Now when the user enters subject hierarchy, and there are supported nodes (i.e. there is an SH plugin that can handle the node) in the scene, a question pops up whether the user wants to create subject hierarchy. If they say no, the hierarchy remains empty and unusable, if they choose yes, then the hierarchy is created once, if they choose yes to all, then a setting is saved and auto-creation is turned on, which means every added node that is supported by SH is automatically added. The users who use subject hierarchy often, should choose this option.

Related to 0003911

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23817 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Logic/vtkMRMLModelHierarchyLogic.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/qSlicerSubjectHierarchyModule.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/qSlicerSubjectHierarchyModule.h Diff File
mod - Modules/Loadable/SubjectHierarchy/qSlicerSubjectHierarchyModuleWidget.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/qSlicerSubjectHierarchyModuleWidget.h Diff File

master b222a6ec

2014-12-03 17:12:27

pinter

Details Diff 		ENH: Make subject hierarchy plugin method addNodeToSubjectHierarchy non-virtual

Now that subject hierarchy nodes are automatically created when a supported data node (i.e. there exists an SH plugin that can add it to the tree) is added to the scene, the qSlicerSubjectHierarchyAbstractPlugin::addNodeToSubjectHierarchy method lost its purpose, so although it's still used as a convenience function, it cannot be overridden any more.
Minor fixes: comments, checks, typos

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23816 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Markups/SubjectHierarchyPlugins/qSlicerSubjectHierarchyMarkupsPlugin.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/MRML/vtkMRMLSubjectHierarchyNode.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyAbstractPlugin.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyAbstractPlugin.h Diff File
mod - Modules/Loadable/SubjectHierarchy/qSlicerSubjectHierarchyModule.h Diff File
mod - Modules/Loadable/Volumes/SubjectHierarchyPlugins/qSlicerSubjectHierarchyVolumesPlugin.cxx Diff File

master 8799bbeb

2014-12-03 14:06:21

jcfr

Details Diff 		BUG: Update CTK to ensure python error a written to stderr

$ git shortlog f341589..42700cf --no-merges
Andras Lasso (1):
BUG: Fixed issue of writing Python errors to stdout instead of stderr

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23815 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_CTK.cmake Diff File

master 61909a7c

2014-12-03 00:21:05

fedorov

Details Diff 		ENH: enable parsing of Philips DWI datasets

Philips private tag added to allow parsing multi-b acquisitions as multivolumes by the plugin.


git-svn-id: http://svn.slicer.org/Slicer4/trunk@23814 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File

master d139dac6

2014-12-02 15:45:15

alexy

Details Diff 		BUG: 3911. Fixed crash on change of visibility of ModelHierarchy nodes introduced by making them part of SubjectHierarchy.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23813 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Logic/vtkMRMLModelHierarchyLogic.cxx Diff File
mod - Modules/Loadable/Models/Widgets/qMRMLModelDisplayNodeWidget.cxx Diff File

master 27cb942a

2014-12-02 14:06:17

pinter

Details Diff 		COMP: Fixed linux build warnings

Also fix Subject Hierarchy failing python self tests.

Fixes 0003910

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23812 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Applications/SlicerApp/Testing/Python/SubjectHierarchyCorePluginsSelfTest.py Diff File
mod - Applications/SlicerApp/Testing/Python/SubjectHierarchyGenericSelfTest.py Diff File
mod - Modules/Loadable/SubjectHierarchy/Logic/vtkSlicerSubjectHierarchyModuleLogic.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qMRMLSceneSubjectHierarchyModel.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyParseLocalDataPlugin.cxx Diff File
mod - Modules/Scripted/DICOMLib/Widgets/qSlicerDICOMExportDialog.cxx Diff File
mod - Modules/Scripted/DICOMLib/Widgets/qSlicerDICOMTagEditorWidget.cxx Diff File

master b4415c5f

2014-12-01 19:24:08

pinter

Details Diff 		COMP: Fixed export directive in DICOM subject hierarchy plugin

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23811 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/DICOMLib/SubjectHierarchyPlugins/qSlicerSubjectHierarchyDICOMPlugin.h Diff File

master f5e421f7

2014-12-01 19:09:44

pinter

Details Diff 		ENH: Add new DICOM export feature and scalar volume plugin

DICOM export dialog and tag editor widget are new widgets for DICOM export of all kinds of data in the new DICOMLib directory of the Scripted module folder. The existing DICOM plugin mechanism is used, but extended with an export function. Although the existing DICOMLoadable python object still works, C++ containers have been added to ensure C++ support of DICOM import/export. DICOMDataExchange.py was split into DICOMExportScalarVolume.py and DICOMExportScene.py.
See all details, including design considerations and usage information here:
http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/DICOMExport

Closes 0003163

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23810 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Applications/SlicerApp/Testing/Python/SubjectHierarchyCorePluginsSelfTest.py Diff File
mod - Applications/SlicerApp/Testing/Python/SubjectHierarchyGenericSelfTest.py Diff File
mod - Modules/Loadable/SubjectHierarchy/Logic/vtkSlicerSubjectHierarchyModuleLogic.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Logic/vtkSlicerSubjectHierarchyModuleLogic.h Diff File
mod - Modules/Loadable/SubjectHierarchy/MRML/CMakeLists.txt Diff File
rm - Modules/Loadable/SubjectHierarchy/MRML/vtkMRMLSubjectHierarchyConstants.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/MRML/vtkMRMLSubjectHierarchyConstants.h Diff File
mod - Modules/Loadable/SubjectHierarchy/MRML/vtkMRMLSubjectHierarchyNode.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/MRML/vtkMRMLSubjectHierarchyNode.h Diff File
mod - Modules/Loadable/SubjectHierarchy/Resources/UI/qSlicerSubjectHierarchyModule.ui Diff File
mod - Modules/Loadable/SubjectHierarchy/Testing/Cxx/vtkSlicerSubjectHierarchyModuleLogicTest.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/CMakeLists.txt Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/DesignerPlugins/qSlicerSubjectHierarchyModuleWidgetsAbstractPlugin.h Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qMRMLSceneSubjectHierarchyModel.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qMRMLSortFilterSubjectHierarchyProxyModel.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qMRMLSubjectHierarchyTreeView.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qMRMLSubjectHierarchyTreeView.h Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyAbstractPlugin.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyAbstractPlugin.h Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyCloneNodePlugin.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyFolderPlugin.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyParseLocalDataPlugin.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyPluginHandler.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyPluginHandler.h Diff File
mod - Modules/Loadable/SubjectHierarchy/qSlicerSubjectHierarchyModule.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/qSlicerSubjectHierarchyModuleWidget.cxx Diff File
mod - Modules/Loadable/Volumes/SubjectHierarchyPlugins/qSlicerSubjectHierarchyVolumesPlugin.cxx Diff File
mod - Modules/Scripted/CMakeLists.txt Diff File
mod - Modules/Scripted/DICOM/CMakeLists.txt Diff File
mod - Modules/Scripted/DICOM/DICOM.py Diff File
rm - Modules/Scripted/DICOM/DICOMLib/DICOMDataExchange.py Diff File
add - Modules/Scripted/DICOMLib/CMakeLists.txt Diff File
add - Modules/Scripted/DICOMLib/DICOMExportScalarVolume.py Diff File
add - Modules/Scripted/DICOMLib/DICOMExportScene.py Diff File
add - Modules/Scripted/DICOMLib/Logic/CMakeLists.txt Diff File
add - Modules/Scripted/DICOMLib/Logic/vtkSlicerDICOMExportable.cxx Diff File
add - Modules/Scripted/DICOMLib/Logic/vtkSlicerDICOMExportable.h Diff File
add - Modules/Scripted/DICOMLib/Logic/vtkSlicerDICOMLoadable.cxx Diff File
add - Modules/Scripted/DICOMLib/Logic/vtkSlicerDICOMLoadable.h Diff File
add - Modules/Scripted/DICOMLib/SubjectHierarchyPlugins/CMakeLists.txt Diff File
add - Modules/Scripted/DICOMLib/Widgets/CMakeLists.txt Diff File
add - Modules/Scripted/DICOMLib/Widgets/DesignerPlugins/CMakeLists.txt Diff File
add - Modules/Scripted/DICOMLib/Widgets/DesignerPlugins/qSlicerDICOMLibModuleWidgetsAbstractPlugin.cxx Diff File
add - Modules/Scripted/DICOMLib/Widgets/DesignerPlugins/qSlicerDICOMLibModuleWidgetsAbstractPlugin.h Diff File
add - Modules/Scripted/DICOMLib/Widgets/DesignerPlugins/qSlicerDICOMLibModuleWidgetsPlugin.cxx Diff File
add - Modules/Scripted/DICOMLib/Widgets/DesignerPlugins/qSlicerDICOMLibModuleWidgetsPlugin.h Diff File
add - Modules/Scripted/DICOMLib/Widgets/DesignerPlugins/qSlicerDICOMTagEditorWidgetPlugin.cxx Diff File
add - Modules/Scripted/DICOMLib/Widgets/DesignerPlugins/qSlicerDICOMTagEditorWidgetPlugin.h Diff File
add - Modules/Scripted/DICOMLib/Widgets/Resources/UI/qSlicerDICOMExportDialog.ui Diff File
add - Modules/Scripted/DICOMLib/Widgets/Resources/qSlicerDICOMLibModuleWidgets.qrc Diff File
add - Modules/Scripted/DICOMLib/Widgets/qSlicerDICOMExportDialog.cxx Diff File
add - Modules/Scripted/DICOMLib/Widgets/qSlicerDICOMExportDialog.h Diff File
add - Modules/Scripted/DICOMLib/Widgets/qSlicerDICOMExportable.cxx Diff File
add - Modules/Scripted/DICOMLib/Widgets/qSlicerDICOMExportable.h Diff File
add - Modules/Scripted/DICOMLib/Widgets/qSlicerDICOMLoadable.cxx Diff File
add - Modules/Scripted/DICOMLib/Widgets/qSlicerDICOMLoadable.h Diff File
add - Modules/Scripted/DICOMLib/Widgets/qSlicerDICOMTagEditorWidget.cxx Diff File
add - Modules/Scripted/DICOMLib/Widgets/qSlicerDICOMTagEditorWidget.h Diff File
mod - Modules/Scripted/DICOMPlugins/DICOMDiffusionVolumePlugin.py Diff File
mod - Modules/Scripted/DICOMPlugins/DICOMScalarVolumePlugin.py Diff File
mod - Modules/Scripted/DICOMPlugins/DICOMSlicerDataBundlePlugin.py Diff File
mod - Modules/Scripted/EditorLib/CMakeLists.txt Diff File
mod - Modules/Scripted/EditorLib/Logic/CMakeLists.txt Diff File

master 236c03fd

2014-12-01 14:12:14

jcfr

Details Diff 		BUG: Ensure RemoveAllMarkups also invoke MarkupRemovedEvent

This commit improve the API consistency by ensuring the event will
be sent also if RemoveAllMarkups is called.

Similarly, the function "SetLocked" is called instead of directly
setting the ivar, doing so will ensure that the LockModifiedEvent
is also invoked.

Note that the pair StartModify/EndModify is used to ensure the ModifedEvent
associated with the markups node is invoked at the end if it applies.

For sake of consistency, the function RemoveAllTexts() has been added.
Since no text is added/removed when function Add/RemoveMarkup are called,
it doesn't make sense to clear the text when removing markups.

Running the test py_AddManyMarkupsFiducialTest doesn't show any decrease
in time with/without this patch. (Ubuntu 13.10 / debug build)

With: 24.17 sec, 26.65 sec, 24.01 sec (3 runs)
Without: 26.59 sec, 27.04 sec, 24.72 sec (3 runs)

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23809 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Markups/MRML/vtkMRMLMarkupsNode.cxx Diff File
mod - Modules/Loadable/Markups/MRML/vtkMRMLMarkupsNode.h Diff File

master 5ebec949

2014-11-27 10:38:21

alexy

Details Diff 		BUG: 3905. Fixed visibility control logic for model hierarchy nodes.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23808 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Widgets/qMRMLTreeView.cxx Diff File

master b2f186cb

2014-11-26 22:39:59

lassoan

Details Diff 		BUG: Fixed composite transform problems

By hardening a non-linear transform on a vtkMRMLLinearTransformNode makes the contents of the linear transform node non-linear. This causes errors in many places in the code where linearity of the transform is tested by checking the class type instead of calling transform->IsLinear() or transform->IsTransformToParentLinear().

In the long term all specific transform nodes (linear, bspline, grid) should be removed and only the generic vtkMRMLTransformNode should be used everywhere. The specific classes are already “empty”, they do not contain any useful functionality, but they are be used in extensions (and still have not removed from everywhere in the Slicer core), so they have to be phased out gradually.

Specific problems:
* If affine transform is applied to bspline then bspline component is ignored
* If affine transform is applied to bspline and affine is hardened then the bspline component is lost.
* Hardening multiple nonlinear transforms on a transform sometimes results in incorrect composite transform

Fixes:
* Instead of casting to vtkMRMLLinearTransform IsLinear or IsTransformToWorldLinear has to be called to decide if a transform is linear (checking the class type does not work correctly for composite transforms)
* Fixed vtkMRMLTransformNode::ApplyTransform
* Moved full implementation of get/set transform matrix functions in vtkMRMLTransformNode (it further prepares removal of obsolete linear/bspline/grid transform node classes)

Enhancements:
* Allow splitting of composite transforms to its components (Transforms module: Split button – only displayed for composite transforms)


git-svn-id: http://svn.slicer.org/Slicer4/trunk@23807 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/Logic/vtkSlicerApplicationLogic.cxx Diff File
mod - Base/Logic/vtkSlicerFiducialsLogic.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLFiducialListNode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLLinearTransformNode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLLinearTransformNode.h Diff File
mod - Libs/MRML/Core/vtkMRMLROINode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLTransformNode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLTransformNode.h Diff File
mod - Libs/MRML/Core/vtkMRMLTransformableNode.cxx Diff File
mod - Libs/MRML/DisplayableManager/vtkMRMLModelDisplayableManager.cxx Diff File
mod - Libs/MRML/Logic/Testing/Cxx/vtkMRMLSliceLogicTest.cxx Diff File
mod - Libs/MRML/Logic/vtkMRMLSliceLayerLogic.cxx Diff File
mod - Libs/MRML/Widgets/qMRMLLinearTransformSlider.cxx Diff File
mod - Libs/MRML/Widgets/qMRMLLinearTransformSlider.h Diff File
mod - Libs/MRML/Widgets/qMRMLMatrixWidget.cxx Diff File
mod - Libs/MRML/Widgets/qMRMLMatrixWidget.h Diff File
mod - Libs/MRML/Widgets/qMRMLSceneTransformModel.cxx Diff File
mod - Libs/MRML/Widgets/qMRMLTransformSliders.cxx Diff File
mod - Libs/MRML/Widgets/qMRMLTransformSliders.h Diff File
mod - Libs/MRML/Widgets/qMRMLUtils.cxx Diff File
mod - Libs/MRML/Widgets/qMRMLUtils.h Diff File
mod - Modules/Loadable/Annotations/MRML/vtkMRMLAnnotationROINode.cxx Diff File
mod - Modules/Loadable/Annotations/MRMLDM/vtkMRMLAnnotationDisplayableManager.cxx Diff File
mod - Modules/Loadable/Annotations/MRMLDM/vtkMRMLAnnotationROIDisplayableManager.cxx Diff File
mod - Modules/Loadable/CropVolume/Logic/vtkSlicerCropVolumeLogic.cxx Diff File
mod - Modules/Loadable/CropVolume/qSlicerCropVolumeModuleWidget.cxx Diff File
mod - Modules/Loadable/Markups/MRML/vtkMRMLMarkupsNode.cxx Diff File
mod - Modules/Loadable/Markups/MRMLDM/vtkMRMLMarkupsDisplayableManager2D.cxx Diff File
mod - Modules/Loadable/Markups/MRMLDM/vtkMRMLMarkupsDisplayableManager3D.cxx Diff File
mod - Modules/Loadable/Reformat/qSlicerReformatModuleWidget.cxx Diff File
mod - Modules/Loadable/Transforms/MRMLDM/vtkMRMLTransformsDisplayableManager2D.cxx Diff File
mod - Modules/Loadable/Transforms/Resources/UI/qSlicerTransformsModuleWidget.ui Diff File
mod - Modules/Loadable/Transforms/SubjectHierarchyPlugins/qSlicerSubjectHierarchyTransformsPlugin.cxx Diff File
mod - Modules/Loadable/Transforms/Testing/Cxx/qSlicerTransformsModuleWidgetTest.cxx Diff File
mod - Modules/Loadable/Transforms/qSlicerTransformsModuleWidget.cxx Diff File
mod - Modules/Loadable/Transforms/qSlicerTransformsModuleWidget.h Diff File

master 112cb916

2014-11-26 17:02:25

jcfr

Details Diff 		COMP: Update python - Fix configuration error on 32-bit system of type i686

The commit fixes the following error:

// ---------------
CMAKE_SYSTEM_PROCESSOR:i686

/home/thiele/Slicer-SuperBuild-Debug/python-build/../Python-2.7.3/Modules/_ctypes/libffi/src/i686/ffi.c

Tried extensions .c .C .c++ .cc .cpp .cxx .m .M .mm .h .hh .h++ .hm .hpp
.hxx .in .txx
Call Stack (most recent call first):
cmake/extensions/CMakeLists.txt:183 (add_python_extension)

// ---------------

[python]

$ git shortlog 47845c5..ee53f79 --no-merges
Jean-Christophe Fillion-Robin (1):
Fix configuration of ctypes extension in case system processor is i686



Thanks to "Thiele Kobus <TKOBUS@partners.org>" for his help identifying
the issue.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23806 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_python.cmake Diff File

master c6d96397

2014-11-26 17:02:23

jcfr

Details Diff 		ENH: Update build system to more robustly check bitness using void ptr size

This commit update the build system so that void pointer size is used
instead of system process name.

[CTK]

$ git shortlog 9e8f66f..f34158 --no-merges
Jean-Christophe Fillion-Robin (1):
Check bitness using void ptr size instead of system processor name

[DMCTK]

$ git shortlog f461865..042de27 --no-merges
Jean-Christophe Fillion-Robin (1):
Update CMake build system to more robustly check bitness using void pointer size

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23805 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_CTK.cmake Diff File
mod - SuperBuild/External_DCMTK.cmake Diff File
mod - SuperBuild/External_curl.cmake Diff File
mod - SuperBuild/External_tcl.cmake Diff File
mod - SuperBuild/External_tk.cmake Diff File
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