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

master edcd19fd

2014-07-29 18:11:12

pieper

Details Diff
ENH: Added a method in VolumesLogic class to resample volume node.

Also added a new CloneVolume method which does not clone the imageData. Changed the LabelStatistics.py to use the new resample logic to make labelmap same as input volume.

From: Kevin Wang <kevin.wang@rmp.uhn.ca>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23492 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Volumes/Logic/vtkSlicerVolumesLogic.cxx Diff File
mod - Modules/Loadable/Volumes/Logic/vtkSlicerVolumesLogic.h Diff File
mod - Modules/Scripted/LabelStatistics/LabelStatistics.py Diff File

master 067bd155

2014-07-29 18:11:10

pieper

Details Diff
ENH: Added a method in VolumesLogic class to resample volume node.

Also changed the LabelStatistics.py to use the new resample logic to make labelmap same as input volume.

From: Kevin Wang <kevin.wang@rmp.uhn.ca>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23491 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Volumes/Logic/vtkSlicerVolumesLogic.cxx Diff File
mod - Modules/Loadable/Volumes/Logic/vtkSlicerVolumesLogic.h Diff File
mod - Modules/Scripted/LabelStatistics/LabelStatistics.py Diff File

master 916b6e2f

2014-07-29 14:44:29

jcfr

Details Diff
COMP: Add HDF5 and Matlab TransformIO to ITKFactoryRegistration

This commit explicitly lists these transform to ensure the associated
files can be read/write.

This should help in fixing error related to the integration of
BRAINSFit and EMSegment.

Co-authored-by: Bradley Lowekamp <blowekamp@mail.nih.gov>
Co-authored-by: Steve Pieper <pieper@isomics.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23490 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/ITKFactoryRegistration/CMakeLists.txt Diff File

master 9e34b647

2014-07-28 18:06:04

pinter

Details Diff
BUG: Subject hierarchy UI update issues fixed
Fixes 0003714

- qMRMLSceneSubjectHierarchyModel::nodeIndex rewritten to generate correct indices, parentNode also fixed. Workarounds removed
- New subject hierarchy nodes get simpler names
- Setting icons is not so simple as it should be due to a bug in Qt (https://bugreports.qt-project.org/browse/QTBUG-20248), which raises the need to check if the icon to be set is the same as the current icon of an item. This introduces one more thing to remember to the developer. Thus, instead of having the plugins set icons on items, they just return it (or an empty one), and the model does the check. This way developing plugins is not harder than before.
- Changed copyright information in all subject hierarchy files
- Instead of having the potential nodes list on the bottom of the module, those nodes are shown in the subject hierarchy tree on the top-level without icons. They can be shown/hidden with a checkbox under the tree, and can be handled the same way as in the potential list before.


git-svn-id: http://svn.slicer.org/Slicer4/trunk@23489 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Markups/SubjectHierarchyPlugins/qSlicerSubjectHierarchyMarkupsPlugin.cxx Diff File
mod - Modules/Loadable/Markups/SubjectHierarchyPlugins/qSlicerSubjectHierarchyMarkupsPlugin.h Diff File
mod - Modules/Loadable/Models/SubjectHierarchyPlugins/qSlicerSubjectHierarchyModelsPlugin.cxx Diff File
mod - Modules/Loadable/Models/SubjectHierarchyPlugins/qSlicerSubjectHierarchyModelsPlugin.h 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/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/DesignerPlugins/qMRMLPotentialSubjectHierarchyListViewPlugin.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/DesignerPlugins/qMRMLPotentialSubjectHierarchyListViewPlugin.h Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/DesignerPlugins/qMRMLSubjectHierarchyTreeViewPlugin.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/DesignerPlugins/qMRMLSubjectHierarchyTreeViewPlugin.h Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/DesignerPlugins/qSlicerSubjectHierarchyModuleWidgetsAbstractPlugin.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/DesignerPlugins/qSlicerSubjectHierarchyModuleWidgetsAbstractPlugin.h Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/DesignerPlugins/qSlicerSubjectHierarchyModuleWidgetsPlugin.h Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qMRMLPotentialSubjectHierarchyListView.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qMRMLPotentialSubjectHierarchyListView.h Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qMRMLScenePotentialSubjectHierarchyModel.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qMRMLScenePotentialSubjectHierarchyModel.h Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qMRMLScenePotentialSubjectHierarchyModel_p.h Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qMRMLSceneSubjectHierarchyModel.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qMRMLSceneSubjectHierarchyModel.h Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qMRMLSceneSubjectHierarchyModel_p.h Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qMRMLSortFilterPotentialSubjectHierarchyProxyModel.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qMRMLSortFilterPotentialSubjectHierarchyProxyModel.h Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qMRMLSortFilterSubjectHierarchyProxyModel.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qMRMLSortFilterSubjectHierarchyProxyModel.h 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/qMRMLTransformItemDelegate.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qMRMLTransformItemDelegate.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/qSlicerSubjectHierarchyChartsPlugin.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyChartsPlugin.h Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyCloneNodePlugin.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyCloneNodePlugin.h Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyDICOMPlugin.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyDICOMPlugin.h Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyDefaultPlugin.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyDefaultPlugin.h Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyParseLocalDataPlugin.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyParseLocalDataPlugin.h Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyPluginHandler.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyPluginHandler.h Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyRegisterPlugin.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyRegisterPlugin.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
mod - Modules/Loadable/Volumes/SubjectHierarchyPlugins/qSlicerSubjectHierarchyVolumesPlugin.cxx Diff File
mod - Modules/Loadable/Volumes/SubjectHierarchyPlugins/qSlicerSubjectHierarchyVolumesPlugin.h Diff File

master 41ee3bdf

2014-07-28 09:56:08

jcfr

Details Diff
BUG: Fix CheckForLabelVolumeValidity warning. Fixes 0003776

This commit fixes a regression introduced in r23406 [1]
where calling CheckForLabelVolumeValidity with two volumes that have
the same dimension was returning a wrong warning, e.g. "IJKToRAS mismatch
at [0, 3] (-89.6207 != -89.6207)", "IJKToRAS mismatch
at [1, 1] (0.000542851 != 0.000542851)", and "IJKToRAS mismatch
at [2, 0] (4.32616e-09 != 4.32616e-09) IJKToRAS mismatch
at [2, 2] (0.0752821 != 0.0752821)", and "IJKToRAS mismatch
at [2, 3] (176.197 != 176.197)".

Thanks to "safir" for reporting the problem and suggesting a solution.

[1] http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=23406

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23488 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Volumes/Logic/vtkSlicerVolumesLogic.cxx Diff File

master 6b2a3a94

2014-07-27 17:57:16

finetjul

Details Diff
BUG: Fix IconEngine and d&d of QStandardItems with icons

When doing drag&drop, the mime data failed to stream the QIcon because
qSlicerIconEnginePlugin was not a subclass of QIconEngineV2.
Regression when adding Qt5 support in CTK.
Closes 0003778

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23487 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_CTK.cmake Diff File

master 5ef43180

2014-07-26 00:10:03

pohl

Details Diff
BUG: cli-modules were not included in PATH of installed version of MAC so added it to search path

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23486 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File

master 36407933

2014-07-25 17:28:37

pohl

Details Diff
BUG: Fixed error with intensity sampling; removed code not used under Slicer4

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23485 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File

master 47a00b26

2014-07-24 10:20:37

pinter

Details Diff
STYLE: Removed testing code from previous commit

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23484 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/DICOM/DICOMLib/DICOMPlugin.py Diff File

master 7f862f31

2014-07-24 10:18:44

pinter

Details Diff
BUG: Fixed accented character display of series and studies in subject hierarchy

Fixes 0003688

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23483 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/DICOM/DICOMLib/DICOMPlugin.py Diff File

master d4d57047

2014-07-24 02:16:04

jcfr

Details Diff
BUG: Properly serialize python paths when installing extension. Fixes 0003772

Following r23036 environment variable specifying list of path were
handled differently. This commit ensures that python paths associated
with extension are also serialized into the settings by following the
new convention introduced in r23036.

For example, before this commit, after installing an extension named
"Foo", the settings contained:

// ----------------------
[Modules]
AdditionalPaths=/home/jchris/.config/NA-MIC/Extensions-23473/Foo/lib/Slicer-4.3/qt-scripted-modules

[...]

[EnvironmentVariables]
PYTHONPATH=/home/jchris/.config/NA-MIC/Extensions-23473/Foo/lib/Slicer-4.3/qt-scripted-modules
// ----------------------

whereas the following is now written:

// ----------------------
[Modules]
AdditionalPaths=/home/jchris/.config/NA-MIC/Extensions-23473/Foo/lib/Slicer-4.3/qt-scripted-modules

[...]

[PYTHONPATH]
1\path=/home/jchris/.config/NA-MIC/Extensions-23473/Foo/lib/Slicer-4.3/qt-scripted-modules
size=1
// ----------------------

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23482 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTCore/Testing/Cxx/qSlicerExtensionsManagerModelTest.cxx Diff File
mod - Base/QTCore/qSlicerExtensionsManagerModel.cxx Diff File

master 74070c4e

2014-07-23 22:57:52

jcfr

Details Diff
BUG: Ensure extension wizard can find git executable provided by Git Bash

This commit explicit set the environment variable "GIT_PYTHON_GIT_EXECUTABLE"
to ensure GitPython finds and uses the git executable provided by Git Bash.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23481 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Utilities/Scripts/CMakeLists.txt Diff File
mod - Utilities/Scripts/slicerExtensionWizard-install.sh.in Diff File
mod - Utilities/Scripts/slicerExtensionWizard.sh.in Diff File

master a8a01aa2

2014-07-23 12:59:10

jcfr

Details Diff
BUG: Ensure MultiVolume modules work with VTK 5 and 6

This commit updates the modules to check for the version
of VTK (using `vtk.VTK_MAJOR_VERSION`). This is required
because the MacOSX factory is still building against VTK5.

For more details see:

fedorov/MultiVolumeExplorer@1053c40
fedorov/MultiVolumeImporter@351226a

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23480 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File

master 060d2d1e

2014-07-23 12:38:13

mwoehlke

Details Diff
BUG: Fix missing icons in extension manager

Update qSlicerBaseQTGUI.qrc[1] to include icons for new tool menu in
extension manager. This fixes the button for the same having no icon on
systems that lack the themed icon, as the non-themed icon was being
specified and exists in the source tree, but was missing from the
aforementioned .qrc.

(1: http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Build_system/Qt_resource_files)

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23479 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTGUI/Resources/qSlicerBaseQTGUI.qrc Diff File

master 9c4fc29a

2014-07-23 02:51:17

jcfr

Details Diff
BUG: Update SlicerExecutionModel - Fixes 0002712

This commit updates SlicerExecutionModel to include an updated version
of ModuleDescription::ReadParameterFile function that support string
parameter without value. The Slicer/SlicerExecutionModel@05af78d also
adds corresponding test checking that parameter file with and without
value can still be read.

$ git shortlog feef59e..a6616b52 --no-merges
Jean-Christophe Fillion-Robin (1):
BUG: Support parameter file with empty value

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23478 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_SlicerExecutionModel.cmake Diff File

master bff80397

2014-07-22 23:01:25

jcfr

Details Diff
STYLE: Add "python-" prefix to GitPython, Github and pydicom module

Consistently name python package.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23477 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File

master 2d4084b2

2014-07-22 22:42:01

jcfr

Details Diff
COMP: Wrap setuptools module installation to avoid false-positive error.

This commit ensure the build and install output of setuptools module is
redirected into files to avoid warning like the following one to be
falsely categorized as error:

15>removing 'build\bdist.win-amd64\egg' (and everything under it)
15>C:\D\C\Slicer-1-build\python-setuptools\setuptools\command\easy_install.py:316: UserWarning: Unbuilt egg for setuptools [unknown version] (c:\d\c\slicer-1-build\python-setuptools)
15> self.local_index = Environment(self.shadow_path + sys.path)

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23476 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_python-setuptools.cmake Diff File

master 03d7657f

2014-07-22 18:35:10

jcfr

Details Diff
BUG: Update launcher to version 0.1.14. Fixes 0003771

// -------------------
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date: Tue Jul 22 18:19:04 2014 -0400

Ensure 'additionalPathVariables' is not overridden. Fixes 0000056

Commit 714981 generalized how environment variables dealing with paths
were managed. This commit fixes a regression where environment variables
set in the main settings file where not considered is additional settings
where found.
// -------------------

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23475 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_CTKAPPLAUNCHER.cmake Diff File

master 78709fe7

2014-07-22 05:54:34

jcfr

Details Diff
COMP: Update setuptools to support parallel install. See 0003757

This commit removes the complex and un-maintainable "lock" mechanism
first introduced in r23465. Instead it updates the version of setuptools
to use a patched version able to support parallel build.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23474 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File
mod - SuperBuild/External_GitPython.cmake Diff File
mod - SuperBuild/External_PyGithub.cmake Diff File
mod - SuperBuild/External_SimpleITK.cmake Diff File
mod - SuperBuild/External_pydicom.cmake Diff File
mod - SuperBuild/External_python-chardet.cmake Diff File
mod - SuperBuild/External_python-setuptools.cmake Diff File
mod - SuperBuild/External_python-smmap.cmake Diff File

master 07924c33

2014-07-21 16:51:00

pieper

Details Diff
BUG: unicodeify date to fix subject hierarchy

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23473 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/DICOM/DICOMLib/DICOMPlugin.py Diff File

master 60583219

2014-07-21 16:50:56

pieper

Details Diff
BUG: 3688 unicode characters from dicom

Add a utility to handle unicode conversion. It works in the
ScalarVolume plugin but not in the Subject Hiearchy
code. I want to run this by @pinter for help.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23472 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/Python/slicer/util.py Diff File
mod - Modules/Scripted/DICOM/DICOMLib/DICOMPlugin.py Diff File
mod - Modules/Scripted/DICOMPlugins/DICOMScalarVolumePlugin.py Diff File

master 140b36b5

2014-07-20 23:36:54

jcfr

Details Diff
COMP: Update SlicerExecutionModel to fix issue with find_package(ITK)

Associated issues:
https://issues.itk.org/jira/browse/ITK-3294
https://github.com/Slicer/SlicerExecutionModel/issues/35

Thanks to "Hans Johnson <hans-johnson@uiowa.edu>" for tracking down
and identifying the problem and thanks to "Matt McCormick <matt.mccormick@kitware.com>"
for submitting a fix.

//---------------
$ git shortlog 4e61f6..feef59e --no-merges
Matt McCormick (1):
BUG: Allow projects to specify their own list of ITK COMPONENTS. 0000035
//---------------

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23471 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_SlicerExecutionModel.cmake Diff File

master c392b074

2014-07-20 18:29:51

alexy

Details Diff
BUG: Fixed crash on reading DWI volume in CLI modules, they assumed DWI had Tensors not Vectors which was wrong.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23470 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/IDImageIO/itkMRMLIDImageIO.cxx Diff File

master b46fe001

2014-07-20 16:07:28

jcfr

Details Diff
ENH: Update SimpleITK to be in sync with ITK

Recent additions for registration framework API changes
have been incorporated into recent versions of SimpleITK

Since ITK was updated, we should update SimpleITK to be
in sync with that version.

From: Hans Johnson <hans-johnson@uiowa.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23469 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_SimpleITK.cmake Diff File

master b1359c77

2014-07-20 16:07:26

jcfr

Details Diff
COMP: Provide Updates to BRAINSFit and DWIConvert

After the NAMIC meeting, several changes were made to address issues
with BRIANSFit and DWIConvert (Fixes 0003736).

Reference atlas is a new module and is not needed by Slicer.

From: Hans Johnson <hans-johnson@uiowa.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23468 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File
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