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master 14a9c5ca

2016-05-21 07:24:33

lassoan

Details Diff 		BUG: Fixed crash in vtkNRRDReader when attepting to read a 4D spatial file

Problem was that when scalar type was not supported, target memory area pointer for memcpy remained NULL.
Also reduced the number of cases when CanReadFile returns true but the reader cannot actually read the file.

The reader was really messy, so cleaned it up (smart pointers, variable definitions, formatting, etc), without any functional changes.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25105 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/vtkTeem/vtkNRRDReader.cxx Diff File
mod - Libs/vtkTeem/vtkNRRDReader.h Diff File

master 9cf170a4

2016-05-21 06:13:32

jcfr

Details Diff 		PERF: Reduce startup time by lazily loading Welcome module HTML. Fixes 0004198

This commit reduces startup time by 0000020:0000030% (5.5s -> 3.9s).

Results obtained for a release build on Ubuntu 15.10, 64GB/M.2 PCIe
NVMe SSD/Quad Core 3.80GHz.

While loading the Welcome module is still slower (~10ms), the improvement
is significant.


Details Stats:


Notes: MeasureStartupTimes.py has been locally modified to avoid generating
Modules.json. Modules.json has been updated to list only 4 modules.


$ ~/Projects/Slicer/Applications/SlicerApp/Testing/Python/MeasureStartupTimes.py --excluding-one-module -n5 ./Slicer

[1/4]
Slicer --no-splash --exit-after-startup --testing --modules-to-ignore EventBroker
1/5: 3.81s
Slicer --no-splash --exit-after-startup --testing --modules-to-ignore EventBroker
2/5: 3.81s
Slicer --no-splash --exit-after-startup --testing --modules-to-ignore EventBroker
3/5: 3.79s
Slicer --no-splash --exit-after-startup --testing --modules-to-ignore EventBroker
4/5: 3.82s
Slicer --no-splash --exit-after-startup --testing --modules-to-ignore EventBroker
5/5: 3.84s
Average: 3.81s

[2/4]
Slicer --no-splash --exit-after-startup --testing --modules-to-ignore GradientAnisotropicDiffusion
1/5: 3.84s
Slicer --no-splash --exit-after-startup --testing --modules-to-ignore GradientAnisotropicDiffusion
2/5: 3.83s
Slicer --no-splash --exit-after-startup --testing --modules-to-ignore GradientAnisotropicDiffusion
3/5: 3.83s
Slicer --no-splash --exit-after-startup --testing --modules-to-ignore GradientAnisotropicDiffusion
4/5: 3.75s
Slicer --no-splash --exit-after-startup --testing --modules-to-ignore GradientAnisotropicDiffusion
5/5: 3.85s
Average: 3.82s

[3/4]
Slicer --no-splash --exit-after-startup --testing --modules-to-ignore Welcome
1/5: 3.70s
Slicer --no-splash --exit-after-startup --testing --modules-to-ignore Welcome
2/5: 3.75s
Slicer --no-splash --exit-after-startup --testing --modules-to-ignore Welcome
3/5: 3.73s
Slicer --no-splash --exit-after-startup --testing --modules-to-ignore Welcome
4/5: 3.76s
Slicer --no-splash --exit-after-startup --testing --modules-to-ignore Welcome
5/5: 3.68s
Average: 3.72s

[4/4]
Slicer --no-splash --exit-after-startup --testing --modules-to-ignore CompareVolumes
1/5: 3.78s
Slicer --no-splash --exit-after-startup --testing --modules-to-ignore CompareVolumes
2/5: 3.78s
Slicer --no-splash --exit-after-startup --testing --modules-to-ignore CompareVolumes
3/5: 3.80s
Slicer --no-splash --exit-after-startup --testing --modules-to-ignore CompareVolumes
4/5: 3.82s
Slicer --no-splash --exit-after-startup --testing --modules-to-ignore CompareVolumes
5/5: 3.76s
Average: 3.79s

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25104 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/SlicerWelcome/Resources/UI/qSlicerWelcomeModuleWidget.ui Diff File
mod - Modules/Loadable/SlicerWelcome/qSlicerWelcomeModuleWidget.cxx Diff File
mod - Modules/Loadable/SlicerWelcome/qSlicerWelcomeModuleWidget.h Diff File

master e4c49494

2016-05-21 06:13:30

jcfr

Details Diff 		ENH: Improve MeasureStartupTimes script adding "--repeat" argument

timecall decorator learned how to repeat a run and compute the average time
across all runs.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25103 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Applications/SlicerApp/Testing/Python/MeasureStartupTimes.py Diff File
mod - Applications/SlicerApp/Testing/Python/SlicerAppTesting.py Diff File

master a1151ccb

2016-05-21 02:34:40

jcfr

Details Diff 		ENH: Welcome: Add shortcut button to open extensions manager. Fixes 0003839

Reviewed-by: Lauren O'Donnell <odonnell@bwh.harvard.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25102 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/SlicerWelcome/Resources/UI/qSlicerWelcomeModuleWidget.ui Diff File
mod - Modules/Loadable/SlicerWelcome/qSlicerWelcomeModuleWidget.cxx Diff File

master f14ba786

2016-05-21 02:06:01

jcfr

Details Diff 		ENH: Improve MeasureStartupTimes script

collect_startup_times_overall:

* Move existing code into "collect_startup_times_overall" function and
save stats to a json file "StartupTimes.json" to facilitate analysis.

collect_startup_times_excluding_one_module:

* Added "collect_startup_times_excluding_one_module" starting Slicer N
times excluding each one of the N modules one by one. Stats are
then saved to "StartupTimesExcludingOneModule.json".

* List of module names (and their type) is also saved to "Modules.json"

* This allows to check if there are modules impacting the startup
time more than the average.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25101 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Applications/SlicerApp/Testing/Python/MeasureStartupTimes.py Diff File
mod - Applications/SlicerApp/Testing/Python/SlicerAppTesting.py Diff File

master acd8220e

2016-05-21 01:44:14

jcfr

Details Diff 		BUG: Fix regression: python code "exit(status)" will now exit with "status"

This commit fixes py_nomainwindow_SlicerPythonCodeTest2 fixing a regression
introduced in r25083 (STYLE: Automatically enable "ignore-slicerrc" if
"testing" option is given).

Associating the test with "--testing" option was causing the application
to always exit with EXIT_SUCCESS when "exit(EXIT_FAILURE)" was called.

This commit ensures the all to slicer.app.exit() in "slicer.util.exit()"
is considered.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25100 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Applications/SlicerApp/Testing/Python/CMakeLists.txt Diff File
mod - Base/Python/slicer/util.py Diff File

master 2b2a3ac4

2016-05-20 20:10:14

jcfr

Details Diff 		STYLE: Simplifies SlicerApp tests

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25099 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Applications/SlicerApp/Testing/Cpp/CMakeLists.txt Diff File
mod - Applications/SlicerApp/Testing/Python/CMakeLists.txt Diff File

master c6052458

2016-05-20 19:46:56

jcfr

Details Diff 		ENH: Update ITK

$ git shortlog 8ac0d60..7db7b60 --no-merges
Bradley Lowekamp (1):
ENH: Use ITK_USE_64BITS_IDS for windows 64 by default

Davis Vigneault (1):
BUG: Improve error checking and testing for ConnectedRegionsMesh

Hyun Jae Kang (2):
BUG: Address the issue of "Missing Delete" within SwapZeroCornerToIRP.
COMP: Fixed Mac OSX wrapping configuration warning

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

Matthew McCormick (7):
BUG: Fix Python wrapping on Windows when ITK_USE_64BIT_IDS is ON.
BUG: The ImageFileReader internal pipeline methods should be protected.
BUG: Use new VNL include directory variables.
COMP: Add missing NeighborhoodAccessor methods to PhasedArray3D image.
BUG: Adjust itk.org ExternalData URL.
COMP: Do not use target_include_directories with CMake 2.8.11.2.
BUG: Address missing shared_ptr for VS9

Michka Popoff (1):
ENH: Use https URL for OS X castxml binary (for consistency)

Ziv Yaniv (1):
BUG: Interpretation of the Euler angles ZYX or ZXY was not exported.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25098 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_ITKv4.cmake Diff File

master 174d0145

2016-05-20 18:40:06

jcfr

Details Diff 		STYLE: Refactor code to use vtkAddonMathUtilities::Matrix4x4AreEqual

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

From: Davide <punzodavide@hotmail.it>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25097 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/Testing/vtkMRMLTransformNodeTest1.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLSliceNode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLSliceNode.h Diff File
mod - Libs/MRML/Logic/vtkMRMLSliceLayerLogic.cxx Diff File

master 86790c47

2016-05-20 18:40:04

jcfr

Details Diff 		STYLE: Add vtkAddonMathUtilities::Matrix4x4AreEqual method

This is done anticipating the refactoring of Slicer core
to use one implementation of this method.

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

From: Davide <punzodavide@hotmail.it>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25096 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/vtkAddon/CMakeLists.txt Diff File
mod - Libs/vtkAddon/Testing/CMakeLists.txt Diff File
add - Libs/vtkAddon/Testing/vtkAddonMathUtilitiesTest1.cxx Diff File
add - Libs/vtkAddon/vtkAddonMathUtilities.cxx Diff File
add - Libs/vtkAddon/vtkAddonMathUtilities.h Diff File

master 4101ff50

2016-05-20 18:40:02

jcfr

Details Diff 		STYLE: Add vtkAddonTestingUtilities and vtkAddonTestingMacros

This is done anticipating the addition of "vtkAddonMathUtilities" and
associated test to vtkAddon.

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25095 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/Testing/vtkMRMLCoreTestingUtilitiesTest.cxx Diff File
mod - Libs/MRML/Core/Testing/vtkMRMLNodeTest1.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/Logic/Testing/Cxx/vtkMRMLColorLogicTest2.cxx Diff File
mod - Libs/vtkAddon/CMakeLists.txt Diff File
mod - Libs/vtkAddon/Testing/CMakeLists.txt Diff File
add - Libs/vtkAddon/Testing/vtkAddonTestingUtilitiesTest1.cxx Diff File
add - Libs/vtkAddon/vtkAddonTestingMacros.h Diff File
add - Libs/vtkAddon/vtkAddonTestingUtilities.cxx Diff File
add - Libs/vtkAddon/vtkAddonTestingUtilities.h Diff File
add - Libs/vtkAddon/vtkAddonTestingUtilities.txx Diff File
mod - Modules/Loadable/Colors/Logic/Testing/Cxx/vtkSlicerColorLogicTest1.cxx Diff File

master fe45f62d

2016-05-20 12:44:02

pieper

Details Diff 		PERF: 0004191 don't update widgets in batch mode

This really improves the performance of LandmarkRegistration,
particularly when there are large numbers of fiducials
being manipulated. I haven't seen any side effects.

ENH: request future update when ignoring batch mrml event

Per suggestion from Andras, include a request for future
update to be sure that the widgets are updated
before the render happens.

BUG: 0004191 update landmark registration

Addresses slowdown with large numbers of fiducials
by entering batch mode for bulk operations on the scene.

From: Steve Pieper <pieper@isomics.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25094 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Markups/MRMLDM/vtkMRMLMarkupsFiducialDisplayableManager2D.cxx Diff File
mod - Modules/Loadable/Markups/MRMLDM/vtkMRMLMarkupsFiducialDisplayableManager3D.cxx Diff File
mod - SuperBuild.cmake Diff File

master 1e498425

2016-05-20 12:10:39

pieper

Details Diff 		COMP: 0004197 fix missing test implementation

function was not defined with OpenGL2 backend

From: Steve Pieper <pieper@isomics.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25093 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/VolumeRendering/Testing/Cxx/qMRMLVolumePropertyNodeWidgetTest1.cxx Diff File

master e9619e37

2016-05-19 18:30:44

jcfr

Details Diff 		STYLE: vtkLoggingMacrosTest1: Fix comment

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25092 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/vtkAddon/Testing/vtkLoggingMacrosTest1.cxx Diff File

master e3637ad5

2016-05-19 10:41:35

naucoin

Details Diff 		BUG: fix failing ModelToLabelMapTest

When putting in a fix for using the passed in label value, the baseline file
OAS10001.1.mha was removed as it didn't seem to be in use any more. A closer
examination of the ctest output showed that that file was being
picked up as the baseline image when the test was passing as of May 11/16:
http://slicer.cdash.org/testDetails.php?test=7318110&build=825978
BaselineImageName OAS10001.1.mha

With the last change[1], the test is failing:
http://slicer.cdash.org/testDetails.php?test=7329855&build=828864
BaselineImageName OAS10001.mha

Local testing shows that the test would pass if the file OAS10001.1.mha was
reinstated, but to avoid confusion going forward as to how ctest globs
the baseline image files, I decided to go with testing the CLI with the
same input model (transformed to overlap the input image volume when both
are loaded in Slicer) for both the 255 and 128 output label cases, and to generate a
new output baseline image. I removed the untransformed model file and the now unused
baseline image and, locally, ctest is comparing the outputs of both tests against
teh correct baselines.

[1] https://github.com/Slicer/Slicer/commit/8707bb9ed2503f67ac0af29782c16db97adeab40

Reported-by: Andras Lasso <lasso@queensu.ca>

Issue 0003233

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25091 3bd1e089-480b-0410-8dfb-8563597acbee
add - Modules/CLI/ModelToLabelMap/Data/Baseline/OAS10001-255.mha Diff File
rm - Modules/CLI/ModelToLabelMap/Data/Baseline/OAS10001.mha Diff File
rm - Modules/CLI/ModelToLabelMap/Data/Input/OAS10001.vtp Diff File
mod - Modules/CLI/ModelToLabelMap/Testing/CMakeLists.txt Diff File

master 0faa67a9

2016-05-19 04:58:11

jcfr

Details Diff 		ENH: Regenerate Extensions/Testings templates

This commit integrates the updated sources after building
SlicerGenerateExtensionTemplates target.

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25090 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplate/CLIModuleTemplate.cxx Diff File

master 9971677b

2016-05-19 04:58:10

jcfr

Details Diff 		BUG: CLITemplate: Template argument name was modified in template declaration

Template argument name was modified in template declaration but not
when using it in the templated function.

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25089 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Utilities/Templates/Modules/CLI/TemplateKey.cxx Diff File

master 1d1f07de

2016-05-19 04:10:45

jcfr

Details Diff 		BUG: Update qSlicerSslTest. See 0004194

Now that "http://slicer.org" redirects to "https://slicer.org", this commit
update the test by:

* checking query on http://slicer.org gives the status code 302 corresponding
to URL redirection.

* adding a test checking that query to https://slicer.org works as expected.
It turns out that the SSL certificate associated with slicer.org has some
issue. The test currently list the HostNameMismatch error as expected.
See 0004194.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25088 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTCore/Testing/Cxx/qSlicerSslTest.cxx Diff File

master 79bca4b6

2016-05-19 03:10:54

jcfr

Details Diff 		BUG: Ensure modules set with --modules-to-ignore are not saved in settings

This commit updates the modules panel adding "modulesToAlwaysIgnoreChanged"
signal emitted only with a list of modules excluding the one passed
as argument to "--modules-to-ignore" command line arguments.

Also adds "SlicerOptionModulesToIgnoreTest" and teaches "SlicerAppTesting.run()"
to understand the "shell" parameter

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25087 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Applications/SlicerApp/Testing/Python/CMakeLists.txt Diff File
mod - Applications/SlicerApp/Testing/Python/SlicerAppTesting.py Diff File
add - Applications/SlicerApp/Testing/Python/SlicerOptionModulesToIgnoreTest.py Diff File
mod - Base/QTApp/qSlicerApplicationHelper.cxx Diff File
mod - Base/QTGUI/qSlicerSettingsModulesPanel.cxx Diff File
mod - Base/QTGUI/qSlicerSettingsModulesPanel.h Diff File

master 1bd84621

2016-05-19 03:10:52

jcfr

Details Diff 		STYLE: AbstractModuleFactoryManager: Improve doxygen

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25086 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTCore/qSlicerAbstractModuleFactoryManager.h Diff File

master 3fb97187

2016-05-19 03:10:51

jcfr

Details Diff 		ENH: Add command line option "--modules-to-ignore"

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25085 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Applications/SlicerApp/Main.cxx Diff File
mod - Base/QTCore/qSlicerCoreCommandOptions.cxx Diff File
mod - Base/QTCore/qSlicerCoreCommandOptions.h Diff File

master 7b74f976

2016-05-19 03:10:49

jcfr

Details Diff 		STYLE: Use imperative tense in command line option descriptions

Options are now all using the same tense.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25084 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTCore/qSlicerCoreCommandOptions.cxx Diff File
mod - Base/QTGUI/qSlicerCommandOptions.cxx Diff File

master eacf2811

2016-05-19 03:10:48

jcfr

Details Diff 		STYLE: Automatically enable "ignore-slicerrc" if "testing" option is given

This simplifies writing of tests.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25083 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Applications/SlicerApp/Testing/Python/CMakeLists.txt Diff File
add - Applications/SlicerApp/Testing/Python/SlicerOptionIgnoreSlicerRCTest.py Diff File
mod - Base/QTCore/qSlicerCoreCommandOptions.cxx Diff File
mod - CMake/SlicerMacroPythonTesting.cmake Diff File
mod - Modules/Loadable/SceneViews/Testing/Python/CMakeLists.txt Diff File

master 8e1be199

2016-05-19 03:10:46

jcfr

Details Diff 		ENH: Add "--keep-temporary-settings" option

When specified with "disable-settings", it prevents the temporary settings
from being cleared. This is useful when writing test checking effect
of settings values.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25082 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Applications/SlicerApp/Testing/Python/CMakeLists.txt Diff File
mod - Applications/SlicerApp/Testing/Python/SlicerAppTesting.py Diff File
mod - Applications/SlicerApp/Testing/Python/SlicerOptionDisableSettingsTest.py Diff File
mod - Base/QTCore/qSlicerCoreApplication.cxx Diff File
mod - Base/QTCore/qSlicerCoreCommandOptions.cxx Diff File
mod - Base/QTCore/qSlicerCoreCommandOptions.h Diff File

master 50a5f1d7

2016-05-19 03:10:44

jcfr

Details Diff 		STYLE: qSlicerCoreCommandOptions: Simplify disabling of settings

Also improve and fix doxygen documentation.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25081 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTCore/qSlicerCoreApplication.cxx Diff File
mod - Base/QTCore/qSlicerCoreCommandOptions.cxx Diff File
mod - Base/QTCore/qSlicerCoreCommandOptions.h Diff File
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