GitLab

Merge remote-tracking branch 'remotes/spt/spt-4.4-2015-08-03-36efac4' into setup-spt-4.4-2015-08-03-36efac4

# Conflicts:
#	Applications/App/CMakeLists.txt
#	Applications/App/Main.cxx
#	Applications/App/Resources/App.qrc
#	Applications/App/Resources/Icons/Large/DesktopIcon.png
#	Applications/App/Resources/Icons/Medium/App.icns
#	Applications/App/Resources/Icons/Medium/DesktopIcon.png
#	Applications/App/Resources/Icons/Small/DesktopIcon.png
#	Applications/App/Resources/Icons/XLarge/DesktopIcon.icns
#	Applications/App/Resources/Icons/XLarge/DesktopIcon.png
#	Applications/App/Resources/Images/Logo.png
#	Applications/App/Resources/Images/SplashScreen.png
#	Applications/App/qAppAboutDialog.cxx
#	Applications/App/qAppAboutDialog.h
#	Applications/App/qAppMainWindow.cxx
#	Applications/App/qAppMainWindow.h
#	Applications/App/qAppMainWindow_p.h
#	Applications/CMakeLists.txt
#	CMake/ApplicationConfig.cmake.in
#	CMake/ConfigureFileMultipleTimes.cmake
#	CMake/DashboardTemplate.cmake
#	CMake/ExportLibrary.cmake
#	CMake/ExternalProjectDependency.cmake
#	CMake/External_Application.cmake.in
#	CMake/ExtractRepositoryInfo.cmake
#	CMake/FindGit.cmake
#	CMake/OSXVariables.cmake
#	CMake/QExport.h.in
#	CMake/SimpleTest.cmake
#	CMake/Superbuild/CMakeLists.txt
#	CMake/Superbuild/External_Slicer.cmake
#	CMake/UseApplication.cmake.in
#	CMake/qSlicerAppVersionConfigure.h.in
#	CMakeLists.txt
#	CTestConfig.cmake
#	Libs/CMakeLists.txt
#	Modules/CLI/CMakeLists.txt
#	Modules/CMakeLists.txt
#	Modules/Loadable/CMakeLists.txt
#	Modules/Scripted/CMakeLists.txt

Merge branch 'double-CLI-execution' of kwgitlab.kitware.com:PET-CT-Needle-Biopsy/SlicerPET into double-CLI-execution

# Conflicts:
#	Modules/Scripted/GuidedInterventionPETCT/Workflow/GuidedInterventionPETCTRegistrationStep.py

Conflicts:
	Modules/Scripted/GuidedInterventionPETCT/Resources/UI/GuidedInterventionPETCTRegistration.ui
	Modules/Scripted/GuidedInterventionPETCT/Workflow/GuidedInterventionPETCTRegistrationStep.py

*reduced number of registration parameters user needs to specify and are usually kept at default values

$ git shortlog 59dde2..b3aa069 --no-merges
alexy (5):
      BUG: 3983. Reverted to version 23690 that fixes the crash introduced in the JC's commits since that revision.
      BUG: 3857. Added support for Parallel and Perpendicular Diffusivity.
      ENH: added magnified slice view into DataProbe panel.
      BUG: 3857. Fixed scalar display on fibers.
      BUG: 3857. Fixed parallel/perpendicular diffusivity on glyphs, interactive seeding line display.

fedorov (9):
      BUG: ensure libvtkGUISupportQtOpenGL is packaged on mac
      BUG: added VTK libraries missing from the package
      ENH: update MultiVolumeImporter tag
      ENH: update MultiVolumeExplorer hash
      ENH: add echoscu DCMTK application
      BUG: update MultiVolumeExplorer SHA
      ENH: add support of DCMTK private dictionary
      BUG: Revert "ENH: add support of DCMTK private dictionary"
      BUG: Fix bug in vtkMRMLIGTLTrackingDataBundleNode::GetTransformNode() (See issue 4011)

jcfr (115):
      BUG: Address SimpleFilters FlipImageFilter
      BUG: Update extension build system to report packaging error on CDash.
      COMP: Fix missing "ctkcheckbox.h" compilation error on case-sensitive system
      STYLE: Fix unused variable warning in vtkMRMLSliceLayerLogic
      BUG: Update EMSegment to fix regression introduced in labelmap node support
      COMP: Fix packaging and upload for superbuild based extension
      COMP: Update Slicer, CTK and BRAINSTools to fix outdated builds on VS2012
      BUG: VTKObservationMixin: Fix removeObservers method and add unittests
      ENH: MRMLNodeComboBox - Support custom behavior for default action
      ENH: Expose qMRMLNodeComboBox::addMenuAction to python
      STYLE: Editor-helperBox: Refactor code introducing "mergeVolumePostfix" ivar
      BUG: Editor: Do not call virtual method "setMRMLDefaults" in constructor
      STYLE: Editor-Effect: Specify event using vtk.vtkCommand instead of string
      STYLE: Editor-helperBox: Remove unused code
      STYLE: Editor-helperBox: Remove unused "brushes" ivar
      STYLE: Editor-helperBox: Simplify code removing "items" ivar
      STYLE: Editor-helperBox: Simplify code reusing "slicer.util.errorDisplay()"
      STYLE: Editor-helperBox: Add "getNodeByName()" to slicer.util and rename it
      STYLE: Editor-helperBox: Move "propagateVolumeSelection" to EditUtil
      STYLE: Editor-helperBox: Rename "colorSelect" into "labelCreate"
      STYLE: Editor-helperBox: Refactor code introducing LabelCreateDialog
      STYLE: Editor-helperBox: Refactor code introducing LabelSelectDialog
      STYLE: Editor-helperBox: Rename ivar "mergeFrame" to "mergeSelectorFrame"
      ENH: Editor-helperBox: Simplify UI using node selector for merge volume
      STYLE: Editor-editUtil: Change EditUtil class method to be static
      STYLE: Update Editor effects and tests to directly use EditUtil
      STYLE: Editor-helperBox: Remove extraneous "applicationLogic" ivar
      STYLE: Editor-helperBox: Refactor code adding "EditUtil.setActiveVolumes()"
      STYLE: Editor-helperBox: Refactor and simplify code using VTKObservationMixin
      STYLE: Editor-helperBox: Refactor code adding LabelStructureListWidget
      BUG: Editor-helpBox: Maintain backward compatibility for structures widget
      STYLE: Editor-EditOptions: Use VTKObservationMixin for scene observation
      STYLE: Editor-EditColor: Use VTKObservationMixin for scene observation
      STYLE: Editor-Effect: Simplify updateMRMLFromGUI using NodeModify context
      BUG: EditorLib: Avoid circular dependency and optimize effect imports
      ENH: Backwards compatible FixedParameters
      BUG: Ensure effect FastGrowCut can use EditorLib.LabelEffectLogic
      BUG: String containing list of dependencies was not split. Fixes #4007
      BUG: Remove duplicate connection to node selector in Volumes module widget
      STYLE: Update volume info widget to track volume node using a weak pointer
      STYLE: Remove unused import statement from util.py
      BUG: Update BRAINSTools to fix loading of bspline transform
      BUG: sitkUtils: Add 'LabelMap' to list of volume types supported by SimpleITK
      ENH: Multiple node types can be created in qMRMLNodeComboBox
      ENH: Improve CLI image widget type handling
      ENH: Expose SH plugin "setDisplayVisibility()" method to python
      STYLE: Remove unused ivar from qSlicerSubjectHierarchyModuleWidget
      ENH: Update transforms module to support copy/paste of linear transforms.
      STYLE: Remove of Slicer_ITKV3_COMPATIBILITY build option
      ENH: Update to ITKv4.8rc2
      COMP: Update ITKv4 to fix MacOSX compilation issue.
      COMP: Fix windows transforms module build error related to sqrt()
      BUG: Update VTKv6 to include fix for vtkhdf5 libraries DLL manifest
      COMP: Fix compilation of Segment subject hierarchy plugin with python disabled
      COMP: Fix pcre package Linux download error relocating file on midas.
      ENH: Added copy-paste linear transform Icons
      ENH: Update ITK to v4.8
      ENH: Add option "Slicer_USE_ITKPython" to turn on ITK Python wrapping.
      COMP: Fix regression in ITKv4 external project properly setting INSTALL step
      STYLE: Simplify copy/paste code in transforms widget using QAction
      BUG: Fix display issue using explicit encoded byte sequence for unit name
      ENH: Organizing settings panel unit using a scroll area.
      ENH: Adding extra units support (frequency, velocity and intensity)
      ENH: Added node printself output to node inspector
      ENH: Extend IOManager to allow python script to invoke  "newFileLoaded" signal
      ENH: Update  DICOMWidgets to invoke "newFileLoaded()" signal.
      BUG: Fix test broken by addition of new units.
      ENH: Added orientation marker to slice view annotations.
      STYLE: Fix unused variable warning in qSlicerSubjectHierarchyVolumesPlugin
      STYLE: Add missing space in CLI help text.
      ENH: Extend core application API adding "isRelease" property.
      ENH: Extend qSlicerUtils API adding function to replace version in wiki urls
      ENH: Update wiki URLs in module panel to reference correct documentation.
      STYLE: Facilitate release process updating wiki URL with Nightly namespace
      STYLE: Remove version number from acknowledgment in Welcome module
      STYLE: Remove version string from loadable module xml description
      ENH: Add warning when GrowCut effect is attempted with unsupported image type
      STYLE: Refactor GrowCut effect logic moving popup outside of the logic
      BUG: Allow qSlicerSimpleMarkupsWidget to be instantiated without Slicer app
      ENH: Creating Qt designer plugin for qSlicerSimpleMarkupsWidget
      BUG: Update SimpleFilters with patches for LabelMapVolume node changes.
      BUG: Fix uninitialized value in vtkSlicerVolumesLogic.
      STYLE: Improve output of vtkMRMLColorLogicTest1 displaying line number
      BUG: Fix uninitialized value in vtkMRMLColorTableNode.
      BUG: Fix memory leak in vtkMRMLSubjectHierarchyNode
      BUG: Update CTK (include fix for memory leak in ctkDoubleSpinBox)
      BUG: Update VTK to include fix for memory leak in vtkSys SystemTools.
      BUG: Fix memory leak in vtkSlicerApplicationLogic
      BUG: Fix memory leak in vtkMRMLLayoutNode
      BUG: Fix memory leak in qMRMLThreeDView removing unused code
      BUG: Fix memory leak in qMRMLCheckableNodeComboBox
      BUG: Fix memory leaks in qSlicerAppMainWindow
      BUG: Fix memory leaks in SubjectHierarchy Register and Segment plugins
      BUG: Fix memory leak in vtkMRMLScene
      BUG: Fix memory leak in vtkMRMLDisplayNode
      BUG: Fix uninitialized value issue in vtkNRRDReader
      BUG: Fix uninitialized value issue in qMRMLTransformSliders
      BUG: Fix memory leak in vtkMRMLSubjectHierarchyNode
      BUG: Fix memory leak in vtkMRMLScene
      STYLE: Improve output of vtkMRMLColorTableNodeTest1 displaying line number
      BUG: Fix vtkMRMLColorTableNodeTest1
      BUG: Fix indentation issue in TemplateManager.py
      STYLE: Fix style in TemplateManager.py
      COMP: Fix narrowing warnings in qSlicerSimpleMarkupsWidget
      ENH: Update VTK to master (soon to be v6.3.0) and also update CTK
      STYLE: Remove Slicer macros used to build Qt plugins.
      BUG: Ensure Qt style plugin are fixed up.
      STYLE: Do not attempt to fixup windows matlab extension
      BUG: Ensure packaged Slicer.app MacOSX application find its Qt plugins
      STYLE: Remove obsolete fixup rule associated with iwidget tcl/tk library
      BUG: Ensure itcl library is fixed when packaging on MacOSX
      BUG: Ensure only one version of itcl library is built and packaged
      BUG: Ensure itcl library is fixed when packaging on MacOSX - Attempt #2
      BUG: Fix VTK library path configured into build tree launcher setting on unix
      ENH: Add support for DCMTK private dictionary

lassoan (19):
      ENH: Made disclaimer popup configurable
      BUG: Fixed application information logging
      BUG: Fixed MRHead sample data download in CropVolumeSelfTest
      BUG: Fixed qMRMLVolumeWidget crash on scene close
      BUG: Fixed failure of disabling slice view annotations from another module
      ENH: Use vtkMRMLLabelMapVolumeNode class for labelmap volumes
      BUG: Fixed  EMSegCL_Task_MRIHumanBrainFullParcellation_BRAINS_small test
      BUG: Attempt to fix py_nomainwindow_MRMLCreateNodeByClassWithSetReferenceCountToOne test
      BUG: Fixed FOV reset during volume selection propagation
      BUG: Fixed crash on scene close due to missing null-pointer check
      BUG: Fixed DataProbe startup error
      ENH: Added warning if obsolete LabelMap flag used in node selector
      STYLE: Removed remnants of non-existent qMRMLNodeSelector class
      BUG: Fixed node selector node type specification syntax
      ENH: Allow qMRMLNodeComboBox base name setting for each node type
      BUG: Fixed extension creation in version-controlled repository
      STYLE: Renamed qSlicerSimpleMarkupsWidget getCurrentNode() to currentNode()
      ENH: Fixed node observations in qSlicerSimpleMarkupsWidget
      STYLE: Replaced cout with vtkDebugMacro

naucoin (42):
      BUG: use ruler end point scale and opacity
      BUG: fix translucency rendering of ruler
      BUG: revert to not showing tick labels on ruler by default
      BUG: expand null pointer checking
      BUG: expand null pointer checking
      ENH: add utility method to display node in only 1 view
      ENH: remove unused Resolution setting on ruler node
      ENH: signal end fiducial interaction in 3D
      BUG: adding a test to show MRB and scene view bug
      BUG: remove unreferenced storage node after loading sample data
      BUG: check for compressed file names
      BUG: update file list members when saving MRBs
      BUG: fix scene view storage leak on MRB save
      BUG: update test with more correct visibility toggles
      BUG: avoid overwriting markup information on scene view restore
      BUG: add missing storage nodes on scene view save
      BUG: use smart pointers for leaking storage node
      BUG: use smart pointers for new storage nodes
      BUG: implement a Slicer specific Qt file suffix
      BUG: function name clarification, add getting readable extensions
      BUG: warn the user when they add storable data after scene views
      BUG: use a mini scene for volume loading
      BUG: add support for remote IO
      ENH: factor out adding data io to the scene
      ENH: test adding storable data after a scene view is created
      COMP: fix test name for label
      BUG: double check for dot preceding file suffixes
      BUG: reduce message noise
      ENH: stress test saving and restoring MRBs, util methods added
      BUG: fix moving volume nodes from test to main scene
      BUG: redo observations for volume loading with mini scene
      BUG: remove node SceneRootDir, use RootDirectory on MRML scene
      BUG: Add a test that checks file paths after MRML and MRB save/load
      BUG: update file list members, scene vars, update test
      BUG: after MRB save, reset storables to modified
      BUG: only time out extra storable message during testing
      STYLE: add blank lines to warning message
      BUG: remove storable added after scene view message
      BUG: add Scene null pointer check to copy
      BUG: update test to fix regression
      BUG: fix regression introduced by adding storage nodes to scene views
      ENH: support fiducial file transfer between Slicer and CLIs

pieper (10):
      BUG: #3954 fixes slicer bundle scene import/export
      BUG: Avoid error on shutdown
      ENH: #3996 accept broader range of DICOM transfers
      BUG: #3993 fix update of render window when transform changes
      ENH: only update Bg and Lb layers when switching editor volumes
      BUG: #3994 fix issue switching between master volumes
      ENH: Editor - Ensure a related merge volume is selected after a structure delete
      ENH: update CompareVolumes to support label map nodes
      ENH: update volume rendering descriptions, remove out of date info
      ENH: reset editor interface when scene is closing

pinter (14):
      BUG: Handle layout manager deletion in slice view annotations
      STYLE: Added doxygen comments to simple markups widget header
      BUG: Instantiate DICOM exportables with a parent to avoid deconstruction
      BUG: Better solution for previous quick fix for DICOM exportables
      BUG: Fixed crash when SH node dropped onto scene
      COMP: Reverting faulty fix
      STYLE: Indentation fixes
      ENH: Added labelmap node support to subject hierarchy
      BUG: Fixed save data dialog cras in case of certain node names
      ENH: Read and apply window/level found in DICOM volumes
      COMP: Fixed subject hierarchy build issue with CLI disabled
      ENH: Added removeAttribute function to MRML node comboboxes and proxy model
      STYLE: Removed unnecessary developer mode setting from self tests
      ENH: DICOM reference name made checkable

Changes copied from Slicer r23859

Setting the OSX_DEPLOYMENT_TARGET implicitly controls which C++
standard library is used libstdc++ vs libc++. Mixing the two in
binaries can result in unstable behavior.

We now implicitly configure the OSX_SYSROOT to the latest SDK, but
require the user to explicitly set the OSX_DEPLOYMENT_TARGET to ensure
compatibility with the build environment.
Co-authored-by: Hans Johnson <hans-johnson@uiowa.edu>
Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

From: Bradley Lowekamp <blowekamp@mail.nih.gov>

Major changes:
* Update to ITK v4.7.2
* Update to SimpleITK 0.0.9
* Update to recent BRAINSTools
* Update CTK to include PythonQt C++/Python ownership tracking feature
* Fixes for DWIToDTIEstimation module. See #3977
* Added reusable simple markups widget
* Fixes layout manager issues

$ git shortlog 4d1f5ba..59dde26 --no-merges
jcfr (28):
      BUG: Fix crash in qMRMLMatrixWidget::setMRMLTransformNode
      STYLE: Remove redundant and unused vtkMRMLSliceLogicTest.cxx file
      STYLE: Add TEST_GET_OBJECT_* macros to vtkMRMLCoreTestingMacros.h file
      BUG: Fix RSNA2012ProstateDemoTest
      BUG: Fix RSNA2012ProstateDemo (attempt #2)
      ENH: Associated docstring with "slicer.(modules,moduleName)" python modules
      ENH: Simplify DICOM subject hierarchy plugin registration
      ENH: Update CTK to include new PythonQt C++/Python ownership tracking feature
      ENH: Fix ownership management for subject hierarchy plugin registration
      ENH: Ensure slicer.(modules|moduleNames) is updated when a module is unloaded
      ENH: Introduce qSlicerScriptedUtils::setModuleAttribute()
      ENH: Refactor addVTKObjectToPythonMain to use setModuleAttribute()
      ENH: Refactor scripted module classes to use setModuleAttribute()
      STYLE: Facilitate debugging associating ObjectName with qSlicerPythonCppAPI
      BUG: Fix leaks in qSlicerScriptedLoadableModule[Widget]::setPythonSource()
      BUG: Fix potential leaks in qSlicerPythonCppAPI using PythonQtObjectPtr
      STYLE: Simplify SliceViewAnnotations using VTKObservationMixin
      BUG: Fix SliceViewAnnotations AttributeError happening on closing Slicer
      BUG: Ensure scripted module are deleted when exiting Slicer
      BUG: Resolve multithread issue that caused errors with multiple b values.
      BUG: Do not reset slice node "layout color" and "layout label". Fixes #1770
      BUG: Update SimpleFilters to fix failing py_SimpleFiltersModuleTest
      ENH: Update ITK to v4.7.2
      ENH: Update SimpleITK to v0.9.0
      ENH: Add self test DTINotReproducibleIssue3977. See issue #3977
      ENH: Update BRAINSTools to include DWIConvert bug fixes
      COMP: Update BRAINSTools - fix configure warning with Slicer SVN source tree
      COMP: Update BRAINSTools to fix windows build error

lassoan (3):
      BUG: Fixed crash when currently shown linear transform is set
      BUG: Fixed transform setting failure
      ENH: Made default startup and favorite module configurable

naucoin (1):
      BUG: update fiducial layout test to check RAS

pieper (8):
      ENH: Adding ability to delete only the selected structure.
      BUG: fix tooltips on editor effect buttons
      BUG: fix variable name typo
      BUG: switching merge volumes was broken
      BUG: use file name match, not regular expression #3994
      BUG: #2267 image label outline incorrect
      BUG: #2267 - remove mask code from vtkImageLabelOutline
      BUG: #2267 fix symmetry of label outline thickness

pinter (4):
      BUG: Fixed DICOM export crash
      BUG: Fix python errors when examining empty file lists
      ENH: Added reusable simple markups widget
      ENH: Enable slice view annotations to work on external layouts

$ git shortlog 0d758d2..4d1f5ba --no-merges
jcfr (6):
      STYLE: Improve vtkMRMLScene apidox
      STYLE: Improve vtkMRMLNode apidox
      BUG: Fix vtkMRMLCameraDisplayableManagerTest1
      BUG: Fix "orphan view" issue in layout manager
      BUG: Fix qMRMLLayoutManagerTest2 - Setting new scene reset view node factories
      STYLE: Explicitly identify layout node arrangements

naucoin (1):
      STYLE: update Volumes documentation to include outline thickness

pieper (1):
      ENH: Add function to explicitly set label outline state on all nodes

As of bb9a5625, similar settings is already set in DefaultSettings.ini

Among other things, it consolidates how application vendor and domain
are passed around. The corresponding value can simply be set in the top
level CMakeLists.txt

Within Slicer, only the variables Slicer_ORGANIZATION_DOMAIN
and Slicer_ORGANIZATION_NAME are expected. There are no need to
pass NameOfYourApp_ORGANIZATION_DOMAIN and NameOfYourApp_ORGANIZATION_NAME.


$ git shortlog 36eaeaf..0d758d2
alexy (2):
      BUG: 3857. Fixed displaying of Tensor properties and their ranges in Tractography display module for lines/tubes/glyphs
      ENH: reverted the order of adding scalars and normals so the scalars added first. Some modules take the first component.

fedorov (6):
      BUG: Replaced re with fnmatch
      ENH: Updated revision number for MultiVolumeImporter
      ENH: update MultiVolumeImporter
      BUG: fix unresolved os module
      ENH: update MultiVolumeImporter
      ENH: add more DCMTK applications

jcfr (136):
      BUG: Remove obsolete NeurosurgicalPlanningTutorial QtTesting based test
      STYLE: Add inclusion to guard to vtkAddon.h
      BUG: Update CTK to include fix for VTK log message parsing regexp
      BUG: Update EMSegment to fix "EMSeg_MRML_DiffReadWriteNodes" test
      BUG: Fix py_nomainwindow_qSlicerDICOMModuleGenericTest
      BUG: Set scene to MRB directory instead of temp
      ENH: Add scene static method to set storable nodes modified since read
      ENH: Update VTK to v6.2.0
      STYLE: Fix typo in comment
      ENH: Display module loading stats only if verbose module discovery is set.
      ENH: Add convenience function to append text to current log file.
      ENH: Append module loading stats to log file.
      STYLE: Fix help message layout removing logging of application name
      BUG: Do not expect log file to exist to try to append text for the first time
      STYLE: Remove commented / unused code from Main.cxx
      BUG: Fix slicer_nomainwindow_DisableModulesCommandLineOptionsTest
      BUG: Fix regression introduced when adding VTKv5 ViewAnnotation support
      BUG: Support loading of SliceViewAnnotation if loadable module are disabled
      STYLE: Display module loading stats only once
      STYLE: Fix typo in qSlicerCoreCommandOptions.cxx
      BUG: Fix MRML warning "Setting the same object should be a no-op."
      ENH: Update SetAndObserveObjectEvents to match SetAndObserveObject
      ENH: Update SetAndObserveObject to display a warning if setting same object
      BUG: Fix py_RSNA2012ProstateDemo test
      STYLE: Remove unused code
      BUG: Support restoring of a sceneview not having a camera
      COMP: Ensure vtkMRMLScene can be compiled with MRMLSCENE_VERBOSE set to 1
      BUG: Keep NodeIDs cache up-to-date when importing Singleton node
      STYLE: Tweak SlicerBlockFindQtAndCheckVersion to display main project name
      ENH: Check if organization and domain name are not already defined
      ENH: Check if Slicer major/minor/patch version are not already defined
      ENH: Check if SlicerApp application name is not already defined
      COMP: SlicerCPack: Find additional dependencies quietly
      ENH: Pass organization domain and name to Slicer inner build
      STYLE: Fix typo in configuration message displaying organization domain/name
      STYLE: Remove unused Slicer png files from top-level Resources folder
      STYLE: Rename SlicerApp icon files to match application name "Slicer"
      STYLE: Move and rename "Slicer3.png" to "Slicer-ModulePanelLogo.png"
      STYLE: Remove duplicated "Slicer.icns" file
      ENH: Improve error message associated with 'slicer_cpack_set' macro
      STYLE: Set "desc. summary" property in slicerMacroBuildAppLibrary macro
      STYLE: Set "desc. file" property in slicerMacroBuildAppLibrary macro
      STYLE: Remove commented code from qSlicerAppMainWindow
      BUG: Fix DataProbe loading error when NumPy is not available
      STYLE: Remove commented code from DICOMWidget
      STYLE: Remove redundant code from DICOM module
      STYLE: Update DICOM to use 'logging' python module
      STYLE: Rename DICOM ivar from 'showBrowser' to 'showBrowserButton'
      STYLE: Remove obsolete code from DICOM module
      STYLE: Move dicom series selection code into DICOMDetailsPopup
      STYLE: Removed unused DICOMTest / DICOMDemo classes from DICOM module
      STYLE: Remove unused function question() and okayCancel() from DICOM module
      STYLE: Update DICOM module to use slicer.util.warningDisplay
      STYLE: Remove code associated with broken "Send" action
      STYLE: Remove code associated with broken "Send" action
      STYLE: Remove commented code from "DICOMDetailsPopup"
      STYLE: Remove dead code related to DICOMDetailsPopup close button
      ENH: Refactor DICOM module to allow DICOMDetailsPopup standalone instantiation
      BUG: Fix py_SubjectHierarchyGenericSelfTest
      ENH: Add option to control the PropagateVolumeSelection behavior
      ENH: Update SimpleITK to v0.9b01 with few patches
      BUG: Fixed editor behaviour in restoring correct label.
      BUG: Update CTK to include DICOMTableView fixes
      COMP: Update VTKv6 to include fix for vs2013 compilation
      ENH: Extend slicer.util API introducing 'settingsValue' and 'toBool'
      ENH: Support for hiding most of DICOM Browser controls through settings
      ENH: Add support for default settings
      ENH: Lookup launcher and default settings files based on application name
      BUG: Update CTK to include logger fixes
      ENH: Added support in vtkMRMLNode for multiple references to the same node
      COMP: Fix "unused-but-set-variable" warning in vtkMRMLNode
      COMP: slicerFunctionAddPythonQtResources - Fix unknown argument warning
      BUG: Fix missing DLL for extensions that use OpenMP (requires CMake 3.1)
      BUG: Update SliceViewAnnotation to avoid error when restoring scene view
      ENH: Generalize Editor "propagationMode" to support arbitrary set of layers
      STYLE: Refactor qMRMLLayoutManager introducing "setLayoutManager()"
      ENH: Added option for setting the layoutManager in the main application
      STYLE: itkMGHImageIO - Remove usage of reserved "__" prefix in header guard
      BUG: Fix py_mainwindow_RestoreSceneViewWithoutCamera test failing on windows
      ENH: Update CTK to fix warning and include ctkButtonGroup tweaks
      STYLE: Update CTK to fix warning related to wrapping of CTKDICOM module
      STYLE: Fix doxygen warning in vtkMRMLSubjectHierarchyNode
      STYLE: Fix compilation warnings
      STYLE: Fix compilation warnings
      ENH: Adding label type column in Label Statistics
      BUG: Update LandmarkRegistration to fix failing generic test
      STYLE: Refactor code introducing qSlicerScriptedUtils::executeFile
      STYLE: Simplify scripted module introducing SlicerPythonCppAPI
      STYLE: VectorToScalarVolume - Make sure all required object are imported
      BUG: Ensure "qSlicerScriptedUtils::executeFile()" set "__file__" property.
      BUG: Fix qSlicerScriptedLoadableModuleWidgetTest broken by previous commit
      STYLE: List attribute to export in ScriptedLoadableModule
      ENH: Extend module API with "widgetRepresentationCreationEnabled" property
      ENH: Simplify DICOM plugin removing unneeded widget class.
      ENH: Add test illustrating issue #3549 related to scripted module import
      ENH: Fixes #3549. Import scripted module as python module
      BUG: Update CTK to fix python interactor keyboard shortcuts
      BUG: Update CTK to fix qMRMLSliceControllerWidgetEventTranslatorPlayerTest1
      BUG: Update CTK to fix python interactor regression
      ENH: Extend ModulePanel API to control if Help&Ack section is visible
      STYLE: Remove unused forward declarations from qSlicerAppMainWindow
      STYLE: Fix position of DataProbe display using monospace font and fixed width
      ENH: Update LandmarkRegistration to show warning if plugin failed to be loaded
      STYLE: Fix typo in qSlicerVolumeRenderingModuleWidget
      STYLE: Fix typos in qSlicerLoadableModule doxygen comments
      COMP: Fix build of tcl on Windows 32-bit (See #3984)
      STYLE: Fix indentation in vtkSlicerApplicationLogic
      STYLE: Fix comment in vtkMRMLLabelMapVolumeDisplayNode
      STYLE: Simplify code in vtkMRMLVolumeArchetypeStorageNode
      STYLE: Simplify memory management in vtkSlicerApplicationLogic
      BUG: Prevent crash in vtkSlicerApplicationLogic checking pointer validity
      BUG: Fix generation of additional launcher settings
      STYLE: Fix indent in qSlicerApplication
      STYLE: Nicely pad information logged at startup.
      STYLE: Mark qSlicerCommandOptions readonly Qt properties as CONSTANT
      STYLE: Fix doxygen comment associated with displayTemporaryPathAndExit()
      STYLE: Simplify code introducing displayMessageAndExit()
      ENH: Display application information only if starting the application.
      ENH: Update teem
      COMP: Update teem to fix windows build error
      STYLE: Fix doxygen in qMRMLChartView
      ENH: Update SimpleITK
      ENH: Update CTK
      BUG: Consider output image orientation when using "noMeasurementFrame" option
      STYLE: Remove obsolete comment in ResampleDTIVolume
      ENH: Extension Wizard: Substitute CMake variable reference if possible.
      BUG: Ensure qMRMLLayoutManager::viewWidget can return custom widget
      ENH: Make color selector search box case-insensitive
      STYLE: Add test for vtkMRMLScene::GetFirstNode
      ENH: Extend vtkMRMLScene::GetFirstNode API adding exactNameMatch parameter
      BUG: Pattern matching for label volume does not account for underscore
      ENH: Update CTK
      BUG: Fixed SlicerApp-real.exe.exe filename on Windows
      BUG: Editor: Ensure label map is updated each time a master volume is selected
      BUG: Change default value for vtkMRMLAbstractViewNode Visibility property
      ENH: Update layout view factory to consider view node visibility property

lassoan (22):
      ENH: Added vtkInfoMacro
      COMP: Added missing file to source control
      ENH: Write all info to the log file as formatted log messages
      ENH: Improve performance of node delete
      ENH: Added VTK output window class for capturing VTK errors/warnings during testing
      BUG: Fixed silently failing qSlicerWidgetTest2
      BUG: Log warnings instead of throw exception from vtkITKArchetypeImageSeriesReader
      BUG: Fixed more silsntly failing tests
      BUG: Added back ITK image IO factory registration to qMRMLSliceWidgetTest2
      ENH: Enabled output VTK error and warning testing for all qMRMLWidgetCxxTests
      BUG: Updated OpenIGTLinkIF
      BUG: Fixed 0003876: All python modules fail after uninstalling an extension
      ENH: Allow slicelets and Slicer tests to handle log messages
      STYLE: Added comment explaining FD message handler usage
      ENH: Do not build doc in VisualStudio when F7 is pressed
      ENH: Added logging of Python console user input
      ENH: Make ExtensionWizard available without SSL support
      BUG: Fixed orphaned views displayed in secondary layout widgets
      ENH: Improve reslicing speed of quasi-axis-aligned slices
      ENH: Removed unnecessary UpdateExtent hack from vtkMRMLSliceLayerLogic
      BUG: Fixed sample data loading in PerformanceTests, errors in VR tests
      ENH: Improved vtkMRMLTransformNode::ApplyTransform

naucoin (1):
      BUG: add outline thickness for label map outlines

pieper (3):
      COMP: update LandmarkRegistration to include landmark refinement
      ENH: include updated LandmarkRegistration
      ENH: fix Diffusion dicom plugin; add utility function

pohl (1):
      BUG: took out class 10 as the structure shown inside the probability atlas was very thin and so caused issue for whene executing tests involved _Human-Eye.mrml - all EMSegment  tests pass now on ubuntu

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