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master af25b208

2016-01-29 13:27:12

jcfr

Details Diff 		ENH: Add infrastructure to support default MRML nodes

Allow modifying default node content: Scene can store "default" nodes. If
a default node is specified for a class then the content of that node will
be used to initialize new nodes and reset nodes.

Currently used only for 3D views but can be used for other purposes, too
(e.g., disable interpolation by default for volume nodes).

This is a backward incompatible change. Signature of

vtkMRMLNode::Reset()

has been changed into

vtkMRMLNode::Reset(vtkMRMLNode* defaultNode)

Co-authored-by: Csaba Pinter <csaba.pinter@queensu.ca>

From: Andras Lasso <lasso@queensu.ca>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24905 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTGUI/Resources/UI/qSlicerSettingsViewsPanel.ui Diff File
mod - Base/QTGUI/qSlicerSettingsViewsPanel.cxx Diff File
mod - Base/QTGUI/qSlicerSettingsViewsPanel.h Diff File
mod - Libs/MRML/Core/vtkMRMLAbstractViewNode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLAbstractViewNode.h Diff File
mod - Libs/MRML/Core/vtkMRMLColorNode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLColorNode.h Diff File
mod - Libs/MRML/Core/vtkMRMLColorTableNode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLColorTableNode.h Diff File
mod - Libs/MRML/Core/vtkMRMLCoreTestingUtilities.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLNode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLNode.h Diff File
mod - Libs/MRML/Core/vtkMRMLScene.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLScene.h Diff File
mod - Libs/MRML/Core/vtkMRMLSliceNode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLSliceNode.h Diff File
mod - Libs/MRML/Core/vtkMRMLUnitNode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLUnitNode.h Diff File
mod - Modules/Loadable/Annotations/Testing/Cxx/vtkMRMLAnnotationAngleNodeTest1.cxx Diff File
mod - Modules/Loadable/Annotations/Testing/Cxx/vtkMRMLAnnotationControlPointsNodeTest1.cxx Diff File
mod - Modules/Loadable/Annotations/Testing/Cxx/vtkMRMLAnnotationNodeTest1.cxx Diff File
mod - Modules/Loadable/Annotations/Testing/Cxx/vtkMRMLAnnotationROINodeTest1.cxx Diff File
mod - Modules/Loadable/Annotations/Testing/Cxx/vtkMRMLAnnotationRulerNodeTest1.cxx Diff File
mod - Modules/Loadable/ViewControllers/CMakeLists.txt Diff File
add - Modules/Loadable/ViewControllers/Logic/CMakeLists.txt Diff File
add - Modules/Loadable/ViewControllers/Logic/vtkSlicerViewControllersLogic.cxx Diff File
add - Modules/Loadable/ViewControllers/Logic/vtkSlicerViewControllersLogic.h Diff File
mod - Modules/Loadable/ViewControllers/qSlicerViewControllersModule.cxx Diff File
mod - Modules/Loadable/ViewControllers/qSlicerViewControllersModule.h Diff File

master 8fc57f44

2016-01-29 00:00:15

lassoan

Details Diff 		BUG: Prevent crash if ITK->VTK transform conversion fails

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24904 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/vtkMRMLTransformStorageNode.cxx Diff File

master 3e632781

2016-01-28 00:02:16

jcfr

Details Diff 		ENH: Update Python to 2.7.11

Also updates 'msvc9compiler' custom version backporting change from
python/cpython@1a2c95d (Issue 0004214: Remove ineffectual /pdb:none option
from msvc9compiler.py) - See https://bugs.python.org/issue4214

For the rational behind the introduction of a custom version of
msvc9compiler, see r23040 (COMP: Fix python_patched_msvc9compiler.py the
"right" way)


Reviewed-by: Max Smolens <max.smolens@kitware.com>
Suggested-by: Michael Powell <mwpowellhtx@gmail.com>

Associated python-cmake-buildsystem are listed below:

$ git shortlog ed5f9bc..b012e1e --no-merges
Chuck Atkins (3):
Create and use append_if_absent macro for constructing compiler options
Use the POSITION_INDEPENDENT_CODE target property instead of -fPIC
Adjust GCC-specific compiler options to work for Clang, Intel, and PGI

Jean-Christophe Fillion-Robin (6):
Create CONTRIBUTING.md
Add convenience macro "check_cmake_property_exists"
Fix distutils.sysconfig._python_build() on windows
Fix distutils.test_get_python_inc on windows copying headers into build dir
Fix test_get_config_h_filename in test_sysconfig.py
Add support for python 2.7.11rc1

Matt McCormick (4):
Add the ability to specify the Python version in the CMake configuration.
Update remark on supported Python versions.
Add Python 2.7.11 download support.
Make Python 2.7.11 the default.

Simon Su (1):
Expect BZIP2_INCLUDE_DIR when building bz2 module.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24903 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_python.cmake Diff File
mod - SuperBuild/python_patched_msvc9compiler.py Diff File

master 7e41e8af

2016-01-27 23:21:57

jcfr

Details Diff 		BUG: Fix registration addressing regression in vtkITKTransformConverter.

Fixes 0004139

This commit allows BRAINSFit registration to complete by addressing
a regression introduced in r24875 (BUG: Fix transform tests by not
using dynamic_cast in vtkITKTransformConverter)

It basically ensure the comparison of transform name includes
all derived type associated with itk::MatrixOffsetTransformBase

The python code allowing to reproduce the issue is reported below
and has been integrated into a self-test named "BRAINSFitRigidRegistrationCrashIssue4139"

8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---
import SampleData
from SampleData import SampleDataLogic
sampleDatalogic = SampleDataLogic()

fixed = sampleDatalogic.downloadMRBrainTumor1()
moving = sampleDatalogic.downloadMRBrainTumor2()

outputTransform = slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(outputTransform)

outputVolume = slicer.vtkMRMLScalarVolumeNode()
slicer.mrmlScene.AddNode(outputVolume)

parameters = {
'fixedVolume' : fixed,
'movingVolume' : moving,
'linearTransform' : outputTransform,
'outputVolume' : outputVolume,
'useRigid' : True
}
cmdLineNode = slicer.cli.runSync(slicer.modules.brainsfit, parameters=parameters)
8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---

Reported-by: Christian Herz <christian.herz@mevis.fraunhofer.de>
Suggested-by: Hans Johnson <hans-johnson@uiowa.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24902 3bd1e089-480b-0410-8dfb-8563597acbee
add - Applications/SlicerApp/Testing/Python/BRAINSFitRigidRegistrationCrashIssue4139.py Diff File
mod - Applications/SlicerApp/Testing/Python/CMakeLists.txt Diff File
mod - Libs/MRML/Core/vtkITKTransformConverter.h Diff File

master 90876ce0

2016-01-26 00:30:39

jcfr

Details Diff 		STYLE: Replace occurrences of QProgressDialog by slicer.util method calls

From: Christian Herz <christian.herz@mevis.fraunhofer.de>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24901 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/Python/slicer/util.py Diff File
mod - Modules/Scripted/DICOMLib/DICOMWidgets.py Diff File

master 53f7c53c

2016-01-26 00:30:37

jcfr

Details Diff 		STYLE: Replace manually created qMessageBox by slicer.util method calls.

From: Christian Herz <christian.herz@mevis.fraunhofer.de>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24900 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Applications/SlicerApp/Testing/Python/FiducialLayoutSwitchBug1914.py Diff File
mod - Applications/SlicerApp/Testing/Python/JRC2013Vis.py Diff File
mod - Modules/Loadable/Markups/Testing/Python/AddManyMarkupsFiducialTest.py Diff File
mod - Modules/Loadable/Markups/Testing/Python/MarkupsInCompareViewersSelfTest.py Diff File
mod - Modules/Loadable/Markups/Testing/Python/MarkupsInViewsSelfTest.py Diff File
mod - Modules/Loadable/Markups/Testing/Python/NeurosurgicalPlanningTutorialMarkupsSelfTest.py Diff File
mod - Modules/Loadable/VolumeRendering/Testing/Python/VolumeRenderingSceneClose.py Diff File
mod - Modules/Scripted/DICOMLib/DICOMProcesses.py Diff File
mod - Modules/Scripted/DICOMLib/DICOMWidgets.py Diff File
mod - Modules/Scripted/Editor/Editor.py Diff File
mod - Modules/Scripted/EditorLib/GrowCutEffect.py Diff File
mod - Modules/Scripted/EditorLib/LabelStructureListWidget.py Diff File
mod - Modules/Scripted/EditorLib/MakeModelEffect.py Diff File
mod - Modules/Scripted/ExtensionWizard/ExtensionWizard.py Diff File
mod - Modules/Scripted/ExtensionWizard/ExtensionWizardLib/CreateComponentDialog.py Diff File
mod - Modules/Scripted/ExtensionWizard/ExtensionWizardLib/EditExtensionMetadataDialog.py Diff File
mod - Modules/Scripted/LabelStatistics/LabelStatistics.py Diff File
mod - Modules/Scripted/PerformanceTests/PerformanceTests.py Diff File
mod - Modules/Scripted/SelfTests/SelfTests.py Diff File
mod - Modules/Scripted/VectorToScalarVolume/VectorToScalarVolume.py Diff File

master 89243fbc

2016-01-26 00:30:31

jcfr

Details Diff 		ENH: Add slicer.util.createProgressDialog method

From: Christian Herz <christian.herz@mevis.fraunhofer.de>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24899 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/Python/slicer/util.py Diff File

master a42f128f

2016-01-26 00:30:29

jcfr

Details Diff 		ENH: Add slicer.util display methods

In addition to the introducion of "messageBox()" method used to
refactore the existing "errorDisplay()" and "warningDisplay()"
methods, this commit also adds the following methods:
* confirmationDisplay
* confirmYesNoDisplay
* confirmRetryCloseDisplay
* infoDisplay

From: Christian Herz <christian.herz@mevis.fraunhofer.de>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24898 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/Python/slicer/util.py Diff File

master ed293512

2016-01-26 00:30:27

jcfr

Details Diff 		STYLE: Remove unused parameter from slicer.util display methods

From: Christian Herz <christian.herz@mevis.fraunhofer.de>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24897 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/Python/slicer/util.py Diff File

master efdfe959

2016-01-26 00:12:45

jcfr

Details Diff 		COMP: qSlicerApplication: Fix unused variable warning in release build

This commit fixes the following warning:

/path/to/Slicer/Base/QTGUI/qSlicerApplication.cxx: In member function ‘virtual void qSlicerApplication::handlePreApplicationCommandLineArguments()’:
/path/to/Slicer/Base/QTGUI/qSlicerApplication.cxx:451:30: warning: unused variable ‘options’ [-Wunused-variable]
qSlicerCoreCommandOptions* options = this->coreCommandOptions();
^

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24896 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTGUI/qSlicerApplication.cxx Diff File

master b6da8ad7

2016-01-26 00:12:44

jcfr

Details Diff 		ENH: ITKPython: Add support for optionally installing ITKPython Wrapping

This commit adds the option Slicer_INSTALL_ITKPython (default OFF) that
depends on Slicer_BUILD_ITKPython (also OFF by default).

When enabled, ITK Wrapping files will be installed and packaged along
side the Slicer application.

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

From: Johan Andruejol <johan.andruejol@kitware.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24895 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMake/SlicerBlockInstallCMakeProjects.cmake Diff File
mod - CMakeLists.txt Diff File
mod - SuperBuild/External_ITKv4.cmake Diff File

master 858d1a70

2016-01-26 00:12:42

jcfr

Details Diff 		STYLE: Fix indentation in SlicerBlockInstallCMakeProjects.cmake

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24894 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMake/SlicerBlockInstallCMakeProjects.cmake Diff File

master 3e8d89df

2016-01-26 00:12:40

jcfr

Details Diff 		STYLE: Rename Slicer_USE_ITKPython to Slicer_BUILD_ITKPython

From: Johan Andruejol <johan.andruejol@kitware.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24893 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMakeLists.txt Diff File
mod - SuperBuild/External_ITKv4.cmake Diff File

master 71bbf91b

2016-01-26 00:12:38

jcfr

Details Diff 		BUG: ITKPython: Add PYTHONPATH support to the launcher for ITK build tree.

This commit removes pythonpath detection script that was only
working when Slicer_USE_ITKPython was enabled with an existing
build tree. Indeed, when doing a clean build, it was failing
because Slicer python interpreter was not available at configure time.

To address this, this commit configures the PYTHONPATH launcher
settings for the build tree.

Co-authored-by: Johan Andruejol <johan.andruejol@kitware.com>
Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionR@kitware.com>

From: Matt McCormick <matt.mccormick@kitware.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24892 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_ITKv4.cmake Diff File

master 7ea8c508

2016-01-25 23:59:20

jcfr

Details Diff 		ENH: Moved up vtkMRMLStorableNode in the MRML node hierarchy.

vtkMRMLStorableNode is not a children of vtkMRMLTransformable node anymore,
but directly a children of vtkMRMLNode.

This allows making a node storable without requiring it to be also
transformable. It is important for several node types (color maps, tables,
etc), which require separate storage node but are not transformable.

From: Andras Lasso <lasso@queensu.ca>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24891 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTGUI/qSlicerSaveDataDialog.cxx Diff File
mod - Libs/MRML/Core/Testing/vtkMRMLSceneViewNodeImportSceneTest.cxx Diff File
mod - Libs/MRML/Core/Testing/vtkMRMLSceneViewNodeRestoreSceneTest.cxx Diff File
mod - Libs/MRML/Core/Testing/vtkMRMLSceneViewNodeStoreSceneTest.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLCoreTestingMacros.h Diff File
mod - Libs/MRML/Core/vtkMRMLCoreTestingUtilities.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLCoreTestingUtilities.h Diff File
mod - Libs/MRML/Core/vtkMRMLDisplayableNode.h Diff File
mod - Libs/MRML/Core/vtkMRMLFiducialListNode.h Diff File
mod - Libs/MRML/Core/vtkMRMLSceneViewNode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLStorableNode.h Diff File
mod - Libs/MRML/Core/vtkMRMLTransformableNode.h Diff File
mod - Libs/MRML/DisplayableManager/Testing/Data/vtkMRMLCameraDisplayableManagerTest1.mrml Diff File
mod - Libs/MRML/Logic/vtkMRMLApplicationLogic.cxx Diff File

master 68bdb844

2016-01-25 23:17:57

jcfr

Details Diff 		ENH: Add test for CloneVolume in vtkSlicerVolumesLogicTest1

This new test checks :
(1) That a cloned volume has no storage node
(2) That a cloned volume has display nodes not referencing
the original volume (fixed in commit 2525fc2 by copying only
the first display node and removing the others)
(3) That a cloned volume has the same imageData than the
original volume.

Also updates the other tests to use the testing macros
introduced in commit d58ba3b.

From: Alexis Girault <alexis.girault@kitware.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24890 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Volumes/Testing/Cxx/vtkSlicerVolumesLogicTest1.cxx Diff File

master 163e1c78

2016-01-23 05:21:31

jcfr

Details Diff 		COMP: Update BRAINSTools to fix MacOSX and Linux packaging.

This commit fixes a regression originally introduced in r24881 (BUG: Update
BRAINSTools to include fixes for BRAINSFit and BRAINSResample.)

Fixes 0004135

//---------------------------------------------
commit Slicer/BRAINSTools@1a8e84b
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date: Sat Jan 23 05:06:52 2016 -0500

COMP: Force CMAKE_CONFIGURATION_TYPES only when using multi-config generator

This commit fixes a regression first introduced in BRAINSia/BRAINSTools@831eab6 (ENH: Allow
selecting C++11 from CMAKE_CXX_STANDARD) and incorrectly fixed
in BRAINSia/BRAINSTools@8987b5d (BUG: Do not dereference a variable when checking for existance.)

CMAKE_CONFIGURATION_TYPES variable is now forced to a value only
if it has been defined by CMake. This ensures that project (e.g Slicer)
directly adding BRAINSTools source tree can still rely on the
assumption CMAKE_CONFIGURATION_TYPES is set only when multi-configuration
generator are used.
//---------------------------------------------

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24889 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File

master 51c746b7

2016-01-23 03:44:30

jcfr

Details Diff 		COMP: Fix windows packaging. Fixes 0004131

This commit addresses regression introduced in r24855 (ENH: Add SlicerDMRI
remote module) where the build folder became too long.

This commit introduces the concept of "REMOTE_EXTENSION" allowing to
add source directory to an extension containing multiple modules. Since
the build directory associated with remote extensions is 13 characters
shorter, it should address the windows packaging problem.

Here is an example of path before and after this change:

C:\path\to\Slicer-Release\Slicer-build\Modules\Remote\SlicerDMRI\Modules\Loadable\TractographyDisplay
C:\path\to\Slicer-Release\Slicer-build\E\SlicerDMRI\Modules\Loadable\TractographyDisplay


Notes:

To avoid doing a clean build and ensure incremental build
are successful, developers should update file:

C:\path\to\Slicer-Release\Slicer-build\CMakeCache.txt

and remove variables of the form

"... :INTERNAL= ... Modules\Remote\SlicerDMRI ...".

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24888 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMakeLists.txt Diff File
mod - SuperBuild.cmake Diff File

master 51c9e67b

2016-01-22 13:22:22

pieper

Details Diff 		BUG: 0004128 python ValueError on scene close after visiting Editor

Accessing the state of the parameter node during scene close
was causing an access to an incompletely build parameter node.

Important to note that node events can be invoked on singletons
during scene operations.

From: Steve Pieper <pieper@isomics.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24887 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/EditorLib/EditBox.py Diff File
mod - Modules/Scripted/EditorLib/EditUtil.py Diff File

master f7bcba3d

2016-01-21 16:27:16

pinter

Details Diff 		STYLE: Removed unnecessary friend class declaration

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24886 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyPluginHandler.h Diff File

master 6bd2588b

2016-01-21 10:11:24

pinter

Details Diff 		BUG: Prevent clash of subject hierarchy and other hierarchies

When a model not in a model hierarchy was deleted, then the associated subject hierarchy was found (if SH was enabled, which is by default disabled) due to using the generic vtkMRMLHierarchyNode, and the model node was deleted twice, causing a crash. By downcasting to the expected hierarchy type the crash does not occur.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24885 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Logic/vtkMRMLDisplayableHierarchyLogic.cxx Diff File
mod - Modules/Loadable/Models/qSlicerModelsModuleWidget.cxx Diff File

master daac6091

2016-01-19 21:50:36

lassoan

Details Diff 		ENH: Added RemoveAllColumns convenience function to vtkMRMLTableNode

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24884 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/Testing/vtkMRMLTableNodeTest1.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLTableNode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLTableNode.h Diff File

master 5c34f8c2

2016-01-19 12:34:50

jcfr

Details Diff 		BUG: Update ITKv4 to fix issue with N4ITKBiasFieldCorrection. Fixes 0004130

More specifically, commit InsightSoftwareConsortium/ITK@be66cfa will fix
the following tests:
EMSeg_SlicerCommonInterfaceTestGeneral
EMSegCL_Task_MRIHumanBrain_2CH

It basically prevents the following error:

//---------------
itk::ExceptionObject (0x2a4c110)
Location: "void itk::MultiThreader::SingleMethodExecute()"
File: /home/jcfr/Projects/Slicer-Debug/ITKv4/Modules/Core/Common/src/itkMultiThreader.cxx
Line: 417
Description: itk::ERROR: MultiThreader(0x2a8d3b0): Exception occurred during SingleMethodExecute
/home/jcfr/Projects/Slicer-Debug/ITKv4/Modules/Filtering/ImageGrid/include/itkBSplineScatteredDataPointSetToImageFilter.hxx:621:

itk::ERROR: PointSetToImageFilter(0x2a81400): The reparameterized point component -1.97373e-16 is outside
the corresponding parametric domain of [0, 1).
//---------------


Associated ITK updates:

$ git shortlog 619f991..615607f --no-merges
Bradley Lowekamp (1):
BUG: Fix precision with accumulation and scaling in AdaptiveHistogram

Hans Johnson (5):
COMP: BSD command lines do not have --version
COMP: Respect CMAKE_CXX_STANDARD during config
COMP: Clang Override warnings removed
BUG: Download URL was wrong for macosx
COMP: The ComputeUpdate function is needed

Hyun Jae Kang (1):
BUG: Exclude a test code of ITKLabelMapTestDriver on OSX 10.6

Isaiah Norton (1):
COMP: fix build with -std=c++11 when ITK/VXL initially configured without

Jean-Christophe Fillion-Robin (1):
COMP: Fix Slicer MacOSX extension packaging setting CMP0042 policy to OLD

Matthew McCormick (10):
DOC: Update the location of the GNUPlot Software Guide scripts.
DOC: Update the Software Guide repo location in Examples/README.txt.
COMP: Add export specification for itk::ResourceProbe.
COMP: Require NO_MODULE with DCMTK find_package.
COMP: Update CastXML revision for C++14 VS 2015.
BUG: Fix PythonTransformCoverage test for Python 3.4.
BUG: Fix PythonExtras test with Python 3.
BUG: Fix PythonTypemaps tests with Python 3.
ENH: Do not force shared libraries when wrapping.
ENH: Allow ITKVideoBridgeOpenCV to be built externally.

Michka Popoff (2):
COMP: Re-enable review module for python 3 and older VTK's
ENH: Use importlib for python 3.4 instead of imp

Nick Tustison (1):
ENH: Accommodate epsilon error on left side.

Sean McBride (1):
DOC: Update some woefully out-of-date GDCM comments, and typos

Seun Odutola (1):
BUG: Improved itkAnalyzeImageIO to handle case insensitive extensions

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24883 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_ITKv4.cmake Diff File

master deedcdfd

2016-01-19 12:34:48

jcfr

Details Diff 		STYLE: Remove unused SlicerITKv3BSplineControlPointImageFilter

This commit removes the class SlicerITKv3BSplineControlPointImageFilter
that originally became obsolete following r23077 (ENH: Remove ITKv3
support).

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24882 3bd1e089-480b-0410-8dfb-8563597acbee
rm - Modules/CLI/N4ITKBiasFieldCorrection/SlicerITKv3BSplineControlPointImageFilter.h Diff File
rm - Modules/CLI/N4ITKBiasFieldCorrection/SlicerITKv3BSplineControlPointImageFilter.txx Diff File

master 6a4e5263

2016-01-19 12:34:46

jcfr

Details Diff 		BUG: Update BRAINSTools to include fixes for BRAINSFit and BRAINSResample.

This commit fixes a regression introduced
by InsightSoftwareConsortium/ITK@d1e9fe2 (BUG: Ensure Transform IO
factories are registered once.) and integrated in r24836 (ENH: Update
ITKv4 to v4.9.0 release branch).

Following this ITK commit, the ITKIO transform libraries are build as
shared and dynamic_cast can NOT be used with templated classes that are
instantiated in a translation unit different than the one where they are
defined. It will work only if the classes are explicitly instantiated
and exported.

To workaround the issue, code that was relying on dynamic_cast is updated
to (1) ensure the objects are of the right type doing string comparison
and (2) then use static_cast instead of dynamic_cast.

This patch fixes the following EMSegment test (internally using
BRAINSFit) when compiled using gcc 4.4.3 and executed on Ubuntu 10.04:

EMSegCL_Task_BRAINS_MRIHumanBrain_scalartype_float_very_small
EMSegCL_Task_BRAINS_MRIHumanBrain_scalartype_uint_very_small
EMSegCL_Task_HumanEye_BRAINS_small
EMSegCL_Task_MRIHumanBrain_BRAINS_small
EMSegCL_Task_MRIHumanBrainExp_BRAINS_small
EMSegCL_Task_MRIHumanBrainFullParcellation_BRAINS_small
EMSegCL_Task_MRIHumanBrainParcellation_BRAINS_small
EMSegCL_Task_NonHumanPrimate_BRAINS_small

It fixes runtime error like the following:

//-----------------
Read ITK transform from file: /tmp/EMSegmentCommandLine/EMS282744605229D1c.h5
HACK: 0 VersorRigid3DTransform
Caught an ITK exception:

itk::ExceptionObject (0x18ef450)
Location: "unknown"
File: /path/to/Slicer-0-build/BRAINSTools/BRAINSCommonLib/GenericTransformImage.cxx
Line: 346
Description: itk::ERROR: Error in type conversion
//-----------------

Complete list of BRAINSTools updates:

$ git shortlog c658c75..e257e62 --no-merges
Alexander Leinoff (18):
DOC: Updates build instructions for OS X
COMP: Updates ITK dependency and Removes Python from build system
COMP: Allows Top-level cmake options to be passed down to BRAINSTools
COMP: Fixes data dependency for BRAINSCommonLib test
COMP: Fixes build errors on debain8
COMP: Fixes some CMake dependency issues with the FindVTKUtil module
COMP: Fixes Unused parameter warning on Linux in BRAINSCut
COMP: Fixes sign compare warning on linux
BUG: Fix failing BCD tests by adjusting image compare tolerences
BUG: Fixes failing test BCDTest_rescaleIntensity
BUG: Adds multiple baselines to BCD tests
BUG: Adds new baseline fcsv files so BCD tests pass on ubuntu
BUG: Fixes BCDTest_rescaleIntensity on Debian
BUG: Adds baseline for chk_BCDTest_ForcePCPoint
ENH: Updates compareTwoCVSFiels.py.in to work with python3
BUG: Adds null check to string assignment in BRAINSMeasureSurface.cxx
BUG: Fixes ctest dependencies for BRAINSTransformConvert
BUG: TBB should only be requested when building BRAINSABC

Ali Ghayoor (18):
ENH: Added two more tests to gtract
ENH: Remove most calls to EncapsulateMetaData in GTRACT
ENH: Compute seedsPerVoxel for UKF in DWI pipeline
BUG: Fixed a bug in DWI pipeline tractography workflow
BUG: now ANTs returns composite transform not as a list
BUG: import necessary module from python
BUG: Added proper python module inside the function
BUG: Unnecessary computation of ListOfClassStatistics
ENH: Convert a 4D image to a series of 3D images
ENH: Change internal pixel type to float
ENH: Increased dilate size in AtlasToSubject registration
ENH: run multiresolution AtlasToSubject SyN registration
ENH: NO atlasToSubject registration if transform filename exist
ENH: Make sure there are anough samples for KNN training
ENH: A samrter way to set the feature space values of KNN
ENH: Generate pure plugs mask and its incorporation in BABC
DOC: Added more detailed explanations for atlasVolume flag in BCD
ENH: A confusing print statement was modified for BABC

Csaba Pinter (1):
STYLE: Reconcile orphan module categories for DWICleanup and LabelStatistics

Hans J. Johnson (68):
BUG: Update path change for neuromorphometric data.
BUG: activate_this is not available in anaconda.
ENH: New version of NIPYPE ants interface
STYLE: Fixed spelling error.
BUG: Failure multi-modal BABC is run without a T2
BUG: Need to verify that dependant submodules are specified.
BUG: Indexing for MALF was off
ENH: Update ITK, ANTs
BUG: Now that ANTs composite transform is not a list, fix code
ENH: Improve cluster performance tuning.
BUG: Revised MALF indexing to work both for single and multi-modal cases.
ENH: Prepare code base for Python version 3
ENH: Stage 2 futurize
BUG: Remove incorrect use of relative import from non-package
ENH: Improve fall through with sentinal values
COMP: Fixe linkage failures with ITK changes
COMP: Fix new linkage issues with ITK
BUG: Force string from path
BUG: BrainStem cleanup bug when non-identity image was used.
BUG: MALF_SNAPSHOT_WRITER fails on non-identity images
ENH: Zeropad output images for easier sorting.
COMP: Remove shadow typedef warning.
BUG: Incorrect library specification
STYLE: Remove errant xcode build files.
COMP: Remove compiler warnings
ENH: Update Superbuild packages.
ENH: Remove dependance on Boost.
COMP: Add ITK_OVERRIDE for ICCDEF
COMP: Improve compatibility with VTK 6.1
COMP: Remove compiler warning.
COMP: Fix VTK-6.3 compilation issues.
BUG: DCMTK APPs don't build with intel compiler.
ENH: Updated Superbuild for later C++11 support.
ENH: Newest version of ITK.
ENH: Updated ITKv4 for build.
COMP: make vcl_pow command non-ambiguous
BUG: Updated DCMTK requires new CMAKE settings
COMP: Remove unnecessary cmake config message.
ENH: Merged PREDICT logic for Freesurfer script wiht main tree.
ENH: Improve python 3 compatibility.
ENH: Update DCMTK, ITK and ANTs
ENH: TrackOn Freesurfer Processing.
COMP: Remove unnecessary typedef
COMP: Add ITK_OVERRIDE to functions
BUG: BCD post landmark ACPC to atlas only when atlas is from same subject.
ENH: Only allow QT 4.8 or higher.
ENH: VTK, ITK and ANTS Updated.
PERF: Do not use hyperthreads for ITK
ENH: Allow selecting C++11 from CMAKE_CXX_STANDARD
ENH: This is an initial implementation of tbb
BUG: Fix TBB propagations to BRAINSTools
ENH: Update BABC build only with C++11
PERF: Replace OPEN_MP with TBB
BUG: Need to ensure that TBB is respecting num threads specified.
STYLE: Modernize to C++11 style conformance
ENH: Update version of BRAINSTools to 4.6.0
ENH: Enable the new feature for BRAINSABC
BUG: Do not dereference a variable when checking for existance.
COMP: Remove unused programs unless BUILD_FOR_DASHBOARD is set
ENH: Improve logic checking for ANTs external tool
COMP: Make ANTs integration more robust.
COMP: Only require VTK when requested.
BUG: Incorrect block_range3d extents
ENH: Add grainsize explicitly for blocked_ranges
ENH: Parallelize preparation for KNN measurements
PERF: Prefer pass by const reference to pass by value
ENH: Instrument reductions with CompensatedSummationType
ENH: Instrument std::vector reductions with CompensatedSummationType

Isaiah Norton (4):
ENH: FSLToNrrd should default to transposed bvecs
ENH: refactor SiemensDWIConverter::ExtractDWIData
BUG: fix segfault when reading single-file dataset
ENH: SiemensDWI: add support for fallback to non-CSA diffusion tags

Jean-Christophe Fillion-Robin (17):
ENH: Allow testing to be optionally enabled in Slicer build.
BUG: Ensure IO factory are registered.
BUG: BRAINSResample: Fix tests removing usage of dynamic_cast with transform
BUG: BRAINSFitHelperTemplate: Add missing static_cast
STYLE: BRAINSResample: Remove now uneeded check.
STYLE: VTKITKVectorReader: Remove now unneeded itkFactoryRegistration code
BUG: BRAINSFit: Fix tests removing usage of dynamic_cast with transform
STYLE: BRAINSFit: Remove now uneeded check.
STYLE: Remove git merge conflict resolution artifacts
COMP: Update ITKVtkGlue requirements to fix build with default option.
BUG: BRAINSFitHelperTemplate: Add missing static_cast
STYLE: BRAINSResample: Remove now uneeded check.
STYLE: VTKITKVectorReader: Remove now unneeded itkFactoryRegistration code
BUG: BRAINSFit: Fix tests removing usage of dynamic_cast with transform
STYLE: BRAINSFit: Remove now uneeded check.
STYLE: Remove git merge conflict resolution artifacts
COMP: Update ITKVtkGlue requirements to fix build with default option.

Jessica Forbes (18):
ENH: Splits atlas list into lists with lengths of n_modality
ENH: Makes target_image into a list of list
ENH: Adds atlasSmallIslandCleanup.py for pipeline
ENH: Initial commit for WorkupAtlasDustCleanup.py
ENH: Moves import command inside the function
ENH: Sets inFN2/T2 input as optional/None if only T1 session
ENH: Sets the T2 file as an optional arg for the dust cleanup script
ENH: Removed unused BASE_DATA_GRABBER_DIR function parameter
ENH: Adds dust cleanup workflow to baseline.py after MALF
ENH: Specifies input params for dust cleaning workflow
ENH: Added option to not dilate in dust cleanup script
ENH: Includes new dilation arg for dust cleanup in pipeline
ENH: Adds suspicious dust cleaning node before other cleaning node
BUG: Sets includeList to str not int
ENH: Removes unused input arg in CreateDustCleanupWorkflow
ENH: Updates output naming schema for WorkupAtlasDustCleanup.py
ENH: Moves dustCleanup node within Malf after injectSurfaceCSFandVBIntoLabelMap
BUG: Fixes typo conflict left in CreateFreeSufereScripts.py

Regina Kim (20):
COMP: Remove Unused variable
WIP: Update interface for antsJointFusion
BUG: ants Joint Fusion requires search_radius option
ENH: Closes 0000221
BUG: outputs should be returned with fullpath
Update README.md
Update README.md
Update README.md
ENH: BRAINSTools AutoWorkup Tutorial
Update README.md
Update README.md
Update README.md
Update README.md
Update README.md
Update README.md
ENH: ITK version 4.9 Update
ENH: ANTs Version upgrade
ENH: ants Denoise for Auto Workup
BUG: Denoise interface fix
BUG: Resample T2 after BRAINSABC

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24881 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File
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