Changesets: Slicer

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2145-support-for-installing-extension-from-file 5b9d1c40

2013-01-27 13:22:21

pieper

Details Diff 		BUG: fix dicom data bundle export/import

* Fix syntax of zip file size for dump2dcm call (use UL not IS)
* Fix UIDs by having dump2dcm generate new ones to overwrite reference
* Use app logic Zip/Unzip rather than python for consistency
* Fix some stylistic issues

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21642 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/DICOMLib/DICOMDataExchange.py Diff File
mod - Modules/Scripted/Scripts/DICOMPlugins/DICOMSlicerDataBundlePlugin.py Diff File

2145-support-for-installing-extension-from-file fd533b84

2013-01-27 13:22:19

pieper

Details Diff 		BUG: find dicom helper apps when DCMTK is build outside of CTK

Check in both CTK and DCMTK directories to find executables.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21641 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/DICOMLib/DICOMProcesses.py Diff File

2145-support-for-installing-extension-from-file 5916e3d8

2013-01-27 13:22:17

pieper

Details Diff 		BUG: fix calculation for snapping to center of slice (fixes 0002878)

When performing pixel level operations, as with the Editor module,
or even when rendering multiple layers, the result can be ambiguous
when the slice plane is exactly at the border between two pixels due
to rounding differences accumulated through transforms. This can lead
to inconsistent rendering or operations being applied in a differnt
location than expected.

A regression from 4.1 had crept in by which the slice plane was
being consistently adjusted to be exactly on the pixel boundary,
leading to the potential issues. This fix ensures that the plane
is adjusted to the middle of the pixel.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21640 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Logic/vtkMRMLSliceLogic.cxx Diff File

2145-support-for-installing-extension-from-file 65cc2b54

2013-01-25 17:05:05

jcfr

Details Diff 		COMP: Ensure optimized atlas, blas, mkl or lapack libraries are not discovered

When building NUMPY, it causes more harm than it helps to have the automatic
discovery of these libraries. Especially due to Fortran ABI mismatch [1].

It is also agree that compiling against an optimized version of these libraries
would probably make sens, it should be handled on a case by case basis by the
developer. A variable named NUMPY_ENABLE_OPTIMZED_LIBRARY or similar could
then be added.

[1] http://docs.scipy.org/doc/numpy/user/install.html#fortran-abi-mismatch

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21639 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/NUMPY_environment.cmake.in Diff File

2145-support-for-installing-extension-from-file 29939c84

2013-01-25 04:06:34

jcfr

Details Diff 		COMP: Remove WebGLExport module from Slicer core - Will be distributed as extension.

See https://github.com/xtk/SlicerWebGLExport/pull/2

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21638 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMakeLists.txt Diff File
mod - Modules/Scripted/CMakeLists.txt Diff File
mod - SuperBuild.cmake Diff File
rm - SuperBuild/External_SlicerWebGLExport.cmake Diff File

2145-support-for-installing-extension-from-file 1369a86b

2013-01-25 02:38:30

jcfr

Details Diff 		COMP: Simplify DICOM2FullBrainTractography CMakeLists.txt

Remove unused and obsolete extension related CMake code

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21637 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/Scripts/DICOM2FullBrainTractography/CMakeLists.txt Diff File

2145-support-for-installing-extension-from-file b1ea7c49

2013-01-25 02:38:25

jcfr

Details Diff 		COMP: Remove unused file

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21636 3bd1e089-480b-0410-8dfb-8563597acbee
rm - Modules/Scripted/Scripts/Resources/Icons/DICOM.png Diff File

2145-support-for-installing-extension-from-file f6a23941

2013-01-25 02:38:23

jcfr

Details Diff 		COMP: Add convenience macro "SlicerMacroBuildScriptedModule"

This will ease the maintenance and prevent developer from having to
update their CMakeLists.txt each time the process to build scripted
module change (for example value associated with parameter DESTINATION_DIR
and INSTALL_DIR of ctkMacroCompilePythonScript)

See http://www.na-mic.org/Bug/view.php?id=2647

Fixes 0002647

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21635 3bd1e089-480b-0410-8dfb-8563597acbee
add - CMake/SlicerMacroBuildScriptedModule.cmake Diff File
mod - CMake/UseSlicer.cmake.in Diff File
mod - Extensions/Testing/ScriptedLoadableExtensionTemplate/CMakeLists.txt Diff File
mod - Modules/Scripted/CMakeLists.txt Diff File
mod - Modules/Scripted/Scripts/CMakeLists.txt Diff File
mod - Modules/Scripted/Scripts/DICOM2FullBrainTractography/CMakeLists.txt Diff File
mod - Modules/Scripted/Scripts/DICOMPlugins/CMakeLists.txt Diff File

2145-support-for-installing-extension-from-file b575c637

2013-01-25 00:52:15

jcfr

Details Diff 		COMP: Add deprecated warning message to "slicerMacroBuildCLI"

"SEMMacroBuildCLI" should be used instead.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21634 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMake/SlicerMacroBuildCLI.cmake Diff File

2145-support-for-installing-extension-from-file 82ee88d7

2013-01-23 18:43:33

jcfr

Details Diff 		ENH: Add qMRMLTreeView::setSortFilterProxyModel function to be able to set custom proxy models to the tree view

Signed-off-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21633 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Widgets/qMRMLTreeView.cxx Diff File
mod - Libs/MRML/Widgets/qMRMLTreeView.h Diff File

2145-support-for-installing-extension-from-file cd92edf2

2013-01-23 17:58:14

jcfr

Details Diff 		STYLE: For consistency, rename "*[Ee]xtensionManager*" methods into "*[Ee]xtensionsManager*"

Note the extra "s" added to the word "Extension".

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21632 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Applications/SlicerApp/Resources/UI/qSlicerAppMainWindow.ui Diff File
mod - Applications/SlicerApp/qSlicerAppMainWindow.cxx Diff File
mod - Applications/SlicerApp/qSlicerAppMainWindow.h Diff File
mod - Base/QTCore/qSlicerCoreApplication.cxx Diff File
mod - Base/QTCore/qSlicerCoreApplication.h Diff File
mod - Base/QTGUI/Resources/UI/qSlicerSettingsExtensionsPanel.ui Diff File
mod - Base/QTGUI/qSlicerApplication.cxx Diff File
mod - Base/QTGUI/qSlicerApplication.h Diff File
mod - Base/QTGUI/qSlicerSettingsExtensionsPanel.cxx Diff File

2145-support-for-installing-extension-from-file 7fafce28

2013-01-23 17:58:11

jcfr

Details Diff 		ENH: Update ExtensionsManager webview when ExtensionsServer url is updated in the settings panel

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21631 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTGUI/qSlicerExtensionsInstallWidget.cxx Diff File
mod - Base/QTGUI/qSlicerExtensionsManagerDialog.cxx Diff File
mod - Base/QTGUI/qSlicerExtensionsManagerWidget.cxx Diff File
mod - Base/QTGUI/qSlicerExtensionsManagerWidget.h Diff File
mod - Base/QTGUI/qSlicerSettingsExtensionsPanel.cxx Diff File
mod - Base/QTGUI/qSlicerSettingsExtensionsPanel.h Diff File

2145-support-for-installing-extension-from-file e03a1ea0

2013-01-23 16:42:11

pieper

Details Diff 		PERF: handle boundary case when DICOM files have empty strings as tag values

When evaluating DICOM Plugins, and empty string triggered a reload
of the file, when if fact the empty string was valid, and not
an indication of uncached tag data.

https://github.com/commontk/CTK/commit/e96b581c23c7bf9cdb10a05ef35b22aca6bbc512

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21630 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_CTK.cmake Diff File

2145-support-for-installing-extension-from-file 0847b8a8

2013-01-22 18:37:17

pieper

Details Diff 		ENH: add hook for patient hierarchy testing (from Csaba)

This hook will allow testing but will later be refactored when
the patient hieararchy work is finalized.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21629 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/Scripts/DICOMPlugins/DICOMScalarVolumePlugin.py Diff File

2145-support-for-installing-extension-from-file 62eb5fe0

2013-01-22 16:15:59

pieper

Details Diff 		STYLE: fix coding style to match superclass (VTK)

Indentation and curly brace placement needs to match
the parent class!

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21628 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/vtkITK/vtkITKImageWriter.cxx Diff File

2145-support-for-installing-extension-from-file 44f7e333

2013-01-22 16:15:56

pieper

Details Diff 		BUG: handle fact that tensors input can come with either 6 or 9 components

Internally slicer (vtk) always represents tensors as 9 component, but
that conversion happens after the data is read in. So this optimization
needs to check for both cases.

Note that the py_SlicerMRBTest failed as a result of this optimization,
but nobody checked (it happened during the SLC project week, so
things were busy and other things broke as well).

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21627 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/vtkITK/vtkITKArchetypeDiffusionTensorImageReaderFile.cxx Diff File

2145-support-for-installing-extension-from-file 08d71ac1

2013-01-22 14:34:02

pieper

Details Diff 		BUG: avoid warning about point locator

Don't try to update the vtkPointLocator with null points or
it will generate a warning message.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21626 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/DisplayableManager/vtkMRMLModelSliceDisplayableManager.cxx Diff File

2145-support-for-installing-extension-from-file 2dd3c0a9

2013-01-21 13:33:39

finetjul

Details Diff 		ENH: Don't enforce un-necessary limitation on output signed image type

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21625 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/CLI/MaskScalarVolume/MaskScalarVolume.cxx Diff File
mod - Modules/CLI/MaskScalarVolume/MaskScalarVolume.xml Diff File

2145-support-for-installing-extension-from-file 2613be0c

2013-01-21 13:02:31

finetjul

Details Diff 		ENH: Add Negate property to Treshold Scalar Volume CLI

As of today, there is no easy mechanism in ITK to do so.
See ITK issues:
https://issues.itk.org/jira/browse/ITK-2991
https://issues.itk.org/jira/browse/ITK-2993

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21624 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/CLI/ThresholdScalarVolume/ThresholdScalarVolume.cxx Diff File
mod - Modules/CLI/ThresholdScalarVolume/ThresholdScalarVolume.xml Diff File

2145-support-for-installing-extension-from-file 7abe8eeb

2013-01-21 13:02:28

finetjul

Details Diff 		STYLE: Remove wrong signed/unsigned warning to ThresholdScalarVolume

As of r10439, the CLI doesn't force the output to be signed.
Update the documentation.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21623 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/CLI/ThresholdScalarVolume/ThresholdScalarVolume.cxx Diff File
mod - Modules/CLI/ThresholdScalarVolume/ThresholdScalarVolume.xml Diff File

2145-support-for-installing-extension-from-file 955a9e90

2013-01-18 18:21:28

finetjul

Details Diff 		BUG: Remote filter-end and filter-type from CLI output

Because filter-type was not removed, filter-end couldn't be removed.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21622 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTCLI/vtkSlicerCLIModuleLogic.cxx Diff File

2145-support-for-installing-extension-from-file c2582ecb

2013-01-18 18:13:00

naucoin

Details Diff 		ENH: add the ability to import multi level model hierarchies from CLIs

Added to support passing a template scene to the Model Maker
that contains a multi level model hierarchy.

TODO: decide the best practice when a hierarchy is imported twice (for
example, running the model maker on the same label map more than once)
right now this will make a new hierarchy rather than over writing
the old one.



git-svn-id: http://svn.slicer.org/Slicer4/trunk@21621 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/Logic/Testing/vtkSlicerApplicationLogicTest1.cxx Diff File
mod - Base/Logic/vtkSlicerApplicationLogic.cxx Diff File

2145-support-for-installing-extension-from-file 8d389969

2013-01-18 17:44:08

naucoin

Details Diff 		ENH: add a new test for importing model heirarchies.

Test that when a model hierarchy is imported that changes to model ids
are reflected in the parent node ids of child hierarchies.



git-svn-id: http://svn.slicer.org/Slicer4/trunk@21620 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/Testing/CMakeLists.txt Diff File
add - Libs/MRML/Core/Testing/vtkMRMLSceneImportIDModelHierarchyParentIDConflictTest.cxx Diff File

2145-support-for-installing-extension-from-file e15b1fad

2013-01-18 17:42:53

naucoin

Details Diff 		BUG: copy the correct model display node, fixing a copy/paste error

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21619 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/Logic/vtkSlicerApplicationLogic.cxx Diff File

2145-support-for-installing-extension-from-file 4e9e1bc4

2013-01-18 17:21:47

jcfr

Details Diff 		ENH: Associated icon with copy, cut and paste action

Icons are licensed under Creative Commons License (CC-BY-SA 3.0)
See http://creativecommons.org/licenses/by-sa/3.0/

They have respectivaly been downloaded from:
http://openiconlibrary.sourceforge.net/gallery2/?./Icons/actions/edit-copy-6.png
http://openiconlibrary.sourceforge.net/gallery2/?./Icons/actions/edit-cut-6.png
http://openiconlibrary.sourceforge.net/gallery2/?./Icons/actions/edit-paste-6.png

Before being uploaded on "openiconlibrary", the icons originally have
been obtained from http://www.oxygen-icons.org/

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21618 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Applications/SlicerApp/Resources/UI/qSlicerAppMainWindow.ui Diff File
add - Base/QTGUI/Resources/Icons/Large/SlicerEditCopy.png Diff File
add - Base/QTGUI/Resources/Icons/Large/SlicerEditCut.png Diff File
add - Base/QTGUI/Resources/Icons/Large/SlicerEditPaste.png Diff File
add - Base/QTGUI/Resources/Icons/Medium/SlicerEditCopy.png Diff File
add - Base/QTGUI/Resources/Icons/Medium/SlicerEditCut.png Diff File
add - Base/QTGUI/Resources/Icons/Medium/SlicerEditPaste.png Diff File
add - Base/QTGUI/Resources/Icons/Small/SlicerEditCopy.png Diff File
add - Base/QTGUI/Resources/Icons/Small/SlicerEditCut.png Diff File
add - Base/QTGUI/Resources/Icons/Small/SlicerEditPaste.png Diff File
add - Base/QTGUI/Resources/Icons/XLarge/SlicerEditCopy.png Diff File
add - Base/QTGUI/Resources/Icons/XLarge/SlicerEditCut.png Diff File
add - Base/QTGUI/Resources/Icons/XLarge/SlicerEditPaste.png Diff File
mod - Base/QTGUI/Resources/qSlicerBaseQTGUI.qrc Diff File
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