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

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master c860108c

2017-01-23 10:44:17

johan.andruejol

Details Diff 		STYLE: Fix constness of methods in qMRMLSliceView

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25647 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Widgets/qMRMLSliceView.cxx Diff File
mod - Libs/MRML/Widgets/qMRMLSliceView.h Diff File
mod - Libs/MRML/Widgets/qMRMLSliceWidget.h Diff File

master 9e7de725

2017-01-21 18:04:24

lassoan

Details Diff 		ENH: Added CLI output display to module widget

Problem:
It is often difficult to find out why a CLI failed or get detailed output.
(user would need to open the log window and find the messages in the log,
but most users don't even know that there is a log window).

Solution:

Expand button is added next to the status message.
User can click there to show/hide all details.
Error output is displayed in red, at the top. Standard output is displayed black.
Window is automatically sized to show all content with minimal need for scrolling.

If CLI completes with errors, error output is displayed regardless of show/hide details choice.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25646 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTCLI/qSlicerCLIProgressBar.cxx Diff File
mod - Base/QTCLI/qSlicerCLIProgressBar.h Diff File
mod - Base/QTCLI/vtkSlicerCLIModuleLogic.cxx Diff File
mod - Libs/MRML/CLI/vtkMRMLCommandLineModuleNode.cxx Diff File
mod - Libs/MRML/CLI/vtkMRMLCommandLineModuleNode.h Diff File

master 4d38cdcc

2017-01-21 13:34:41

lassoan

Details Diff 		COMP: Fixed vtkSlicerCLIModuleLogic build error on linux

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25645 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Terminologies/Logic/vtkSlicerTerminologiesModuleLogic.cxx Diff File

master dd6c15cf

2017-01-19 23:18:47

lassoan

Details Diff 		ENH: Use RapidJSON instead of JsonCPP in Terminologies module logic

RapidJSON is magnitudes faster than JsonCPP (https://github.com/miloyip/nativejson-benchmark).
This is important, because when terminologies (rather large json documents) are parsed/searched/modified then each operation may take hundreds of milliseconds
with JsonCPP. Multiple calls easily accumulate to user-perceivable delays (magnitude of seconds). By keep using JsonCPP we would constantly have to
optimize number of logic calls to make sure only json access is minimized. Also, JsonCPP was unbearably slow in debug mode in Windows (simple operations took
tens of seconds).

To minimize development time and optimize speed we switch to RapidJSON instead. RapidJSON's advantages compared to jsoncpp (https://github.com/miloyip/nativejson-benchmark):
* Magnitudes faster, also, its API facilitates writing efficient application code
* CMake-ified
* Header-only (no need to install DLLs, ...)
* More conform to json standard
* Library is much smaller (31k vs 243k)

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25644 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMake/SlicerGenerateSlicerConfig.cmake Diff File
mod - CMakeLists.txt Diff File
mod - Modules/Loadable/Terminologies/Logic/CMakeLists.txt Diff File
mod - Modules/Loadable/Terminologies/Logic/vtkSlicerTerminologiesModuleLogic.cxx Diff File
mod - SuperBuild.cmake Diff File
add - SuperBuild/External_RapidJSON.cmake Diff File

master c1f6ec16

2017-01-19 15:30:43

johan.andruejol

Details Diff 		COMP: Update smmap to 2.0.1

After the update of GitPython in r25526, the smmap required version for
pythond-gdb changed to >=2.0.0.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25643 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_python-smmap.cmake Diff File

master 15b748b0

2017-01-19 12:21:14

lassoan

Details Diff 		BUG: Fix ITK transform conversion crash

Lack of ITK dynamic_cast requires yet another workaround.

Problem: When a CLI returned a transform with dimension != 3 it made Slicer crash.
Solution: Verify transform dimension before static_cast (not just scalar type and transform type).

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25642 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/vtkITKTransformConverter.h Diff File

master 42630e64

2017-01-18 08:40:39

lassoan

Details Diff 		ENH: Add further rules to DICOM patcher module

Added a rule to change DCMTK's private storage SOP class UID to CT storage,
because files with unknown (private) class UID are rejected by ITK's GDCM DICOM reader.

It is now possible to force patient name and IDs to be the same for all files in a directory
(disabled by default).


git-svn-id: http://svn.slicer.org/Slicer4/trunk@25641 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/DICOMPatcher/DICOMPatcher.py Diff File

master d1858286

2017-01-18 08:37:31

lassoan

Details Diff 		BUG: Fixed potential DICOM extension recommendation in DICOMWidgets.py

extensionsToOffer.add method does not exist, need to use append instead


git-svn-id: http://svn.slicer.org/Slicer4/trunk@25640 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/DICOMLib/DICOMWidgets.py Diff File

master 137b41dd

2017-01-12 15:24:29

lassoan

Details Diff 		ENH: Improved slice viewer WW/WL and blending

* Blending now supports blending segmentation (not just labelmaps). If no labelmap is selected to be
shown in the slice viewer then it blends visible segmentation.
* Blending and window level adjustment handles saturation of the values. For example,
if mouse is moved so much that opacity or window level is saturated and then you move back to the other direction,
the saturated value starts to get decrease immediately.
* Simplified and removed several unnecessary code from vtkSliceViewInteractorStyle class.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25639 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/DisplayableManager/vtkSliceViewInteractorStyle.cxx Diff File
mod - Libs/MRML/DisplayableManager/vtkSliceViewInteractorStyle.h Diff File

master 981a79d4

2017-01-12 15:24:24

lassoan

Details Diff 		BUG: Fixed display of labelmaps exported from segmentation

Labelmaps exported from segmentation had an opaque black background.
Color table was fixed to have fully transparent background.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25638 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Segmentations/Logic/vtkSlicerSegmentationsModuleLogic.cxx Diff File

master 7e80585c

2017-01-12 15:24:21

lassoan

Details Diff 		ENH: Updated SegmentEditorAutoCompleteEffect documentation

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25637 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Segmentations/EditorEffects/Python/SegmentEditorAutoCompleteEffect.py Diff File

master 7558e87f

2017-01-12 15:24:17

lassoan

Details Diff 		STYLE: Updated vtkMRMLSegmentationNode documentation

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25636 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/vtkMRMLSegmentationNode.h Diff File

master 0248ee48

2017-01-12 13:53:53

pinter

Details Diff 		BUG: Fixed performance issue when show/hide segment

Terminology tooltip was unnecessarily updated, which slowed down show/hide.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25635 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Segmentations/Widgets/qMRMLSegmentsTableView.cxx Diff File

master a79c5ba5

2017-01-12 12:28:09

pinter

Details Diff 		ENH: Added a function to easily load lists of series by UID
without having to manually create a dicomWidget object. Also changing the loadPatientByUID object to use the new function.

Integrated https://github.com/Slicer/Slicer/pull/643
From: Kevin Mader <https://github.com/kmader>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25634 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/DICOMLib/DICOMUtils.py Diff File

master 2a6e43ec

2017-01-06 12:28:59

fedorov

Details Diff 		ENH: simplify the code handling DICOM db directory

Also use os.makedirs() in place of os.mkdir()

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25633 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/DICOMLib/DICOMWidgets.py Diff File

master ea0268a7

2017-01-06 12:28:55

fedorov

Details Diff 		BUG: fix runtime error related to creation of DICOM database directory

In some situations, user settings may point to a temporary directory with multiple
nesting levels, which cannot be created by os.mkdir().

To solve the issue, when exception occurs, fall back to creating the DICOM DB
directory in the default location.

Also fix a typo for the name of the DICOM DB location in developer mode.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25632 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/DICOMLib/DICOMWidgets.py Diff File

master 0089aeb4

2017-01-05 21:02:33

jcfr

Details Diff 		BUG: Update ITK to fix linux packaging of itkhdf5_cpp library

This patch addresses the issue reported in [1], [2] and [3] by
updating ITK to include InsightSoftwareConsortium/ITK@2a07831 and
by installing the ITK component "cpplibraries" to ensure hdf5_cpp
get packaged in Slicer.

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

[1] http://www.na-mic.org/Bug/view.php?id=4301
[2] http://www.na-mic.org/Bug/view.php?id=4302
[3] https://issues.itk.org/jira/browse/ITK-3504

From: Francois Budin <francois.budin@gmail.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25631 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMake/SlicerBlockInstallCMakeProjects.cmake Diff File
mod - SuperBuild/External_ITKv4.cmake Diff File

master df2b9f2c

2017-01-05 10:32:28

lassoan

Details Diff 		ENH: Disable full connectivity in segment editor island effect

It is usually more intuitive if islands are considered to be disconnected when only corners are touching.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25630 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Segmentations/EditorEffects/Python/SegmentEditorIslandsEffect.py Diff File

master 0fa5202a

2016-12-30 21:48:55

lassoan

Details Diff 		ENH: Consolidated island editor effects

Islands effect can now keep largest, remove small islands, split them to segments; or add/remove/keep selected segment (at click position).

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25629 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Segmentations/EditorEffects/CMakeLists.txt Diff File
rm - Modules/Loadable/Segmentations/EditorEffects/Python/AbstractScriptedSegmentEditorIslandEffect.py Diff File
mod - Modules/Loadable/Segmentations/EditorEffects/Python/CMakeLists.txt Diff File
rm - Modules/Loadable/Segmentations/EditorEffects/Python/Resources/Icons/FloodFilling.png Diff File
rm - Modules/Loadable/Segmentations/EditorEffects/Python/Resources/Icons/SaveIsland.png Diff File
mod - Modules/Loadable/Segmentations/EditorEffects/Python/SegmentEditorEffects.__init__.py.in Diff File
rm - Modules/Loadable/Segmentations/EditorEffects/Python/SegmentEditorFloodFillingEffect.py Diff File
rm - Modules/Loadable/Segmentations/EditorEffects/Python/SegmentEditorIdentifyIslandsEffect.py Diff File
add - Modules/Loadable/Segmentations/EditorEffects/Python/SegmentEditorIslandsEffect.py Diff File
mod - Modules/Loadable/Segmentations/EditorEffects/qSlicerSegmentEditorAbstractEffect.cxx Diff File
mod - Modules/Loadable/Segmentations/EditorEffects/qSlicerSegmentEditorAbstractEffect.h Diff File
rm - Modules/Loadable/Segmentations/EditorEffects/qSlicerSegmentEditorAbstractIslandEffect.cxx Diff File
rm - Modules/Loadable/Segmentations/EditorEffects/qSlicerSegmentEditorAbstractIslandEffect.h Diff File
rm - Modules/Loadable/Segmentations/EditorEffects/qSlicerSegmentEditorScriptedIslandEffect.cxx Diff File
rm - Modules/Loadable/Segmentations/EditorEffects/qSlicerSegmentEditorScriptedIslandEffect.h Diff File
mod - Modules/Loadable/Segmentations/Logic/vtkSlicerSegmentationsModuleLogic.cxx Diff File
mod - Modules/Loadable/Segmentations/Widgets/qMRMLSegmentEditorWidget.cxx Diff File

master b2bfa60a

2016-12-29 13:11:48

lassoan

Details Diff 		ENH: Improved performance of paint and erase effect

Painting is faster now (especially when there are several segments and the master volume is relatively large).

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25628 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Segmentations/EditorEffects/qSlicerSegmentEditorPaintEffect.cxx Diff File

master f1b6edcd

2016-12-29 13:11:40

lassoan

Details Diff 		ENH: Flood filling performs recoloring instead

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25627 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Segmentations/EditorEffects/Python/CMakeLists.txt Diff File
add - Modules/Loadable/Segmentations/EditorEffects/Python/Resources/Icons/FloodFilling.png Diff File
mod - Modules/Loadable/Segmentations/EditorEffects/Python/SegmentEditorEffects.__init__.py.in Diff File
add - Modules/Loadable/Segmentations/EditorEffects/Python/SegmentEditorFloodFillingEffect.py Diff File
mod - Modules/Loadable/Segmentations/Widgets/qMRMLSegmentEditorWidget.cxx Diff File

master e1fc0a4c

2016-12-29 08:51:52

lassoan

Details Diff 		COMP: Force extension_description_with_depends.s4ext to use LF EOL in SVN

Extension tests fail because line EOL style difference in extension_description_with_depends.s4ext on different computers with different revision control clients (SVN, git) and operating systems.

To simplify matching of EOL characters, set CMake earlier to generate extension description file with LF style EOL. Now forcing SVN to check out extension_description_with_depends.s4ext using LF style EOL, too.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25626 3bd1e089-480b-0410-8dfb-8563597acbee

master df647983

2016-12-28 17:46:32

lassoan

Details Diff 		BUG: Fixed vtkMRMLSegmentationNode::DeepCopy

Display and storage nodes are now cloned, too (these nodes should not be shared).

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25625 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/vtkMRMLSegmentationNode.cxx Diff File

master 487b19f4

2016-12-26 13:38:04

lassoan

Details Diff 		ENH: Simplified vtkMRMLColorLogicTest2

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25624 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Logic/Testing/Cxx/vtkMRMLColorLogicTest2.cxx Diff File

master d7f501e9

2016-12-23 10:54:14

lassoan

Details Diff 		COMP: Force extension_description_without_depends.s4ext to use LF EOL in SVN

Extension tests fail because line EOL style difference in extension_description_without_depends.s4ext on different computers with different revision control clients (SVN, git) and operating systems.

To simplify matching of EOL characters, set CMake earlier to generate extension description file with LF style EOL. Now forcing SVN to check out extension_description_without_depends.s4ext using LF style EOL, too.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25623 3bd1e089-480b-0410-8dfb-8563597acbee
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