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

master 5975a3a2

2014-08-14 15:11:47

jcfr

Details Diff
BUG: Ensure application can be killed using CTRL-C. Fixes 0003804

This commits fixes a regression introduced by the addition of the
SlicerExtensionWizard module. See inlined comment for more details.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23567 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTCore/qSlicerAbstractModuleFactoryManager.cxx Diff File

master 6dd8a342

2014-08-14 14:10:10

jcfr

Details Diff
ENH: Add enhanced scalarbar actor class based on VTK6. Fixes 0002919

The VTK6 vtkScalarBarActor class allows displaying annotations in
conjunction with labels. However, in Slicer we want to sample the
annotations for display just like color values since some color
tables have more than 10000 values and annotations.

The vtkSlicerScalarBarActor is based on vtkScalarBarActor class and
only overrides its LayoutTicks method to slightly modify the method
to enable sampling the annotations and display it as labels.

Additional remarks:

* Change colors module logic using the new class.

* Keep backward compatibility to VTK5.

* Added a python selftest based on scripted module superclass.

* Added a check box to toggle using the color names as labels, and set
default label formats when it's toggled to support strings or numbers.

* Added simple label format testing to avoid crashes that were seen when
using a string format with a number value.

* Regular expression associated with LabelFormat could be improved. This
is tracked by issue 3802

Co-authored-by: Nicole Aucoin <nicole@bwh.harvard.edu>

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23566 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Colors/CMakeLists.txt Diff File
mod - Modules/Loadable/Colors/Resources/UI/qSlicerColorsModuleWidget.ui Diff File
mod - Modules/Loadable/Colors/Testing/CMakeLists.txt Diff File
add - Modules/Loadable/Colors/Testing/Python/CMakeLists.txt Diff File
add - Modules/Loadable/Colors/Testing/Python/ColorsScalarBarSelfTest.py Diff File
add - Modules/Loadable/Colors/VTKWidgets/CMakeLists.txt Diff File
add - Modules/Loadable/Colors/VTKWidgets/vtkSlicerScalarBarActor.cxx Diff File
add - Modules/Loadable/Colors/VTKWidgets/vtkSlicerScalarBarActor.h Diff File
mod - Modules/Loadable/Colors/qSlicerColorsModuleWidget.cxx Diff File
mod - Modules/Loadable/Colors/qSlicerColorsModuleWidget.h Diff File

master ad32fd41

2014-08-12 22:32:22

jcfr

Details Diff
ENH: Update OpenIGTLink from 1.10.4 to 1.10.10 to include bug fixes.

$ git shortlog 3ac5311..849b434 --no-merges
Andras Lasso (1):
Add the MSG_NOSIGNAL flag to socket send calls to prevent application crash on disconnect on linux systems

Gergely Zombori (1):
Bug 0001912 - Merged the changes and enhancements from upstream into 'master'

Isaiah Norton (1):
BUG: use shutdown() instead of close() for sockets

Junichi Tokuda (7):
BUG: Address issue 0000029: copy igtl_win32hearder.h to the install directory.
ENH: Update patch number.
STYLE: Update patch number.
COMP: Fix compilation error due to lack of MSG_NOSIGNAL option in send() in Mac OS X. For Mac OS X, call setsockopt() with SO_NOSIGPIPE instead.
STYLE: Update revision number.
BUG: Set timestamp zero, when no timestamp object is registered to image meta message.
STYLE: Update patch number

Laurent Chauvin (1):
BUG: Initialize ImageMessage matrix to identity (issue 0000039)

Matt Clarkson (3):
0000044: Put nanosleep in loop to ensure sleep is for the correct time.
0000049: Avoid crash on division by zero, which should never happen
0000050: Convenience methods to set/get igtl_image matrix from 4x4 array of floats

z0022myy (1):
BUG: Intializing pointer should not be in a loop

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23565 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_OpenIGTLink.cmake Diff File

master 8e5ad137

2014-08-12 16:53:10

pinter

Details Diff
ENH: Log to file

Enabled file logging in CTK error log model, bumping up hash. The number of files to keep and the log file paths are stored in the revision settings. The log files are saved in the temp folder with file name Slicer_[revision]_[date]_[time].log. If number of log files is larger than number of files to keep, then the old log file is deleted.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23564 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTGUI/qSlicerApplication.cxx Diff File
mod - Base/QTGUI/qSlicerApplication.h Diff File
mod - SuperBuild/External_CTK.cmake Diff File

master a653d8e0

2014-08-12 14:31:31

pinter

Details Diff
BUG: Fixed clone when cloned volume does not have display node. Fixes 0003795

Fixing second function doing that (rev23561 fixed only vtkSlicerVolumesLogic::CloneVolume, this commit fixes vtkSlicerVolumesLogic::CloneVolumeWithoutImageData)

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23563 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Volumes/Logic/vtkSlicerVolumesLogic.cxx Diff File

master d9d7d672

2014-08-08 12:18:21

pinter

Details Diff
BUG: Handled scene context request in SceneViews subject hierarchy plugin

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23562 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/SceneViews/SubjectHierarchyPlugins/qSlicerSubjectHierarchySceneViewsPlugin.cxx Diff File

master fc2d024e

2014-08-07 14:45:02

jcfr

Details Diff
BUG: Fixed crash when cloned volume does not have display node. Fixes 0003795

From: Csaba Pinter <csaba.pinter@queensu.ca>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23561 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Volumes/Logic/vtkSlicerVolumesLogic.cxx Diff File

master 23f4820f

2014-08-06 18:03:51

pieper

Details Diff
ENH: new LandmarkRegistration feature

Helps when registering two non-overlapping volumes.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23560 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File

master 1ee5b0e8

2014-08-06 10:58:50

jcfr

Details Diff
COMP: Ensure designer plugin provided by Qt are also fixed up

In r23042, install rules have been modified to install designer plugin
provided by Qt but the corresponding pattern to select plugins candidate
for fixup has not been adapted. This commit takes care of it.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23559 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMake/SlicerCPackBundleFixup.cmake.in Diff File

master e403de98

2014-08-06 03:11:38

jcfr

Details Diff
ENH: Update CTK to remove extra debug statements related to ctkDICOMDatabase

Before this commit:

// -------
$ ./Slicer
Number of registered modules: 142
Register compression libraries
TagCacheDatabase not open

TagCacheDatabase verified!

Number of instantiated modules: 142
Number of loaded modules: 142
// -------

After:

// -------
$ ./Slicer
Number of registered modules: 142
Number of instantiated modules: 142
Number of loaded modules: 142
// -------


Summary of changes:

$ git shortlog 9e1c0258..62675d0 --no-merges
Jean-Christophe Fillion-Robin (2):
Remove qDebug statement from registerCompressionLibraries()
Do not display debug info when tagCacheExists method works as expected.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23558 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_CTK.cmake Diff File

master c7cd497f

2014-08-06 03:11:36

jcfr

Details Diff
ENH: Do not log when module UI is successfully displayed

Displaying that everything went well is not useful and add extra "noise"
to the regular Slicer output.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23557 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTGUI/qSlicerModulePanel.cxx Diff File

master 83123977

2014-08-06 02:44:31

jcfr

Details Diff
ENH: Exclude crt extension from git hook line lengths check

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23556 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Utilities/SetupForDevelopment.sh Diff File

master ce22cf97

2014-08-06 02:40:25

jcfr

Details Diff
ENH: For sake of consistency, systematically load Slicer SSL certificates

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23555 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTCore/qSlicerCoreApplication.cxx Diff File

master 4c662301

2014-08-06 02:40:21

jcfr

Details Diff
ENH: Update Slicer.crt based on Base/QtCore/Resources/Certs/README

Update summary:

$ ./make-ca.sh &&
> ./remove-expired-certs.sh certs &&
> REVISION=$(grep CVS_ID certdata.txt | cut -f4 -d'$') &&
> VERSION=$(echo $REVISION | cut -f2 -d" ") &&
> mv "BLFS-ca-bundle-${VERSION}.crt" "Slicer.crt" &&
> unset REVISION VERSION
rm: cannot remove ‘certs/*’: No such file or directory
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git-svn-id: http://svn.slicer.org/Slicer4/trunk@23554 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTCore/Resources/Certs/Slicer.crt Diff File

master c6836fb6

2014-08-06 00:33:12

jcfr

Details Diff
COMP: External_OpenSSL - Fix typo introduced in previous commit r23552

Use "OpenSSL_(URL|MD5)" instead of "OPENSSL_(URL|MD5)" variables.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23553 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_OpenSSL.cmake Diff File

master ff47977d

2014-08-05 22:43:36

jcfr

Details Diff
COMP: Add support for building on windows using Qt 4.8.6 and OpenSSL 1.0.1h

For more details see inlined comment. Also copied below for convenience:

8<----8<----8<----8<----8<----8<----8<----8<----8<----
# Starting with Qt 4.8.6, we compiled [1] OpenSSL binaries specifically for each
# version of Microsoft Visual Studio. To understand the motivation, read below.
#
# As explained in [2][3], if a library meets these two conditions:
# (a) exposes a pure C interface
# (b) is linked against static version of the CRT
# the version of the compiler and runtime used to build the library
# shouldn't matter.
#
# That said, since OpenSSL is built as a shared library using the '/MD' [4]
# flag, it is not possible to use the same library with different runtime
# libraries.
#
# We found out that '/MD' was used by inspecting the the file 'ms/ntdll.mak'
# generated atfer configuring OpenSSL.
#
# If you find mistake in this explanation, do not hesitate to submit a patch
# to fix this text. Thanks.
#
# [1] Script used to compile OpenSSL: https://gist.github.com/jcfr/6030240
# [2] http://siomsystems.com/mixing-visual-studio-versions/
# [3] http://bytes.com/topic/net/answers/505515-compile-different-versions-visual-studio
# [4] http://msdn.microsoft.com/en-us/library/2kzt1wy3.aspx
8<----8<----8<----8<----8<----8<----8<----8<----8<----

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23552 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_OpenSSL.cmake Diff File

master 7dc79124

2014-08-05 22:21:59

pinter

Details Diff
ENH: Added SceneViews and Segment plugins to subject hierarchy

SceneViews is a role plugin for scene view nodes. Provides an icon and allows restoring scene views (request of Sonia)
Segment is a function plugin that adds a context sub-menu ("Segment this using...") to volumes. There is only one action under the sub-menu so far that takes the user to the Editor module, sets the volume as master and creates a labelmap as merge volume.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23551 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/SceneViews/CMakeLists.txt Diff File
add - Modules/Loadable/SceneViews/SubjectHierarchyPlugins/CMakeLists.txt Diff File
add - Modules/Loadable/SceneViews/SubjectHierarchyPlugins/Resources/Icons/SceneView.png Diff File
add - Modules/Loadable/SceneViews/SubjectHierarchyPlugins/Resources/qSlicerSceneViewsSubjectHierarchyPlugins.qrc Diff File
add - Modules/Loadable/SceneViews/SubjectHierarchyPlugins/qSlicerSubjectHierarchySceneViewsPlugin.cxx Diff File
add - Modules/Loadable/SceneViews/SubjectHierarchyPlugins/qSlicerSubjectHierarchySceneViewsPlugin.h Diff File
mod - Modules/Loadable/SceneViews/qSlicerSceneViewsModule.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/CMakeLists.txt Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qMRMLSceneSubjectHierarchyModel.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyChartsPlugin.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyCloneNodePlugin.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyDICOMPlugin.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyDefaultPlugin.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyParseLocalDataPlugin.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyPluginHandler.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyRegisterPlugin.cxx Diff File
add - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchySegmentPlugin.cxx Diff File
add - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchySegmentPlugin.h Diff File
mod - Modules/Loadable/SubjectHierarchy/qSlicerSubjectHierarchyModule.cxx Diff File

master 8379afbb

2014-08-05 13:58:19

jcfr

Details Diff
BUG: Fixed issue of DICOM browser not closed after loading a volume

Browser was not closed after loading a volume even if "Persistent" checkbox was unchecked.

Also added a settings (DICOM/BrowserPersistent) to remember the checkbox setting.

From: Andras Lasso <lasso@queensu.ca>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23550 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/DICOM/DICOM.py Diff File
mod - Modules/Scripted/DICOM/DICOMLib/DICOMWidgets.py Diff File

master 808cbfd7

2014-08-04 14:31:05

naucoin

Details Diff
BUG: fix force color to children checkbox in Models

When converting the model displayable manager to use
more scalar options, missed using the hierarchy display node
for cases when it over rides the model display node. Cast
the hierarchy display node to a model node and use it if defined.

Issue 0003784


git-svn-id: http://svn.slicer.org/Slicer4/trunk@23549 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/DisplayableManager/vtkMRMLModelDisplayableManager.cxx Diff File

master 7a10781f

2014-08-04 13:01:13

jcfr

Details Diff
ENH: Update VTK6 to include backported bug fixes and tweaks

$ git shortlog 169b37b..6c6e5d3
Andrew Bauer (1):
Fixing overflow issue that appeared with GCC compilers.

Ben Boeckel (4):
python: fix leaks when setting constants in wrappers
STLWriter: Raise an error for non-triangles
STLReader: Close the file when an error occurs
STLReader: Fix error signaling when reading files

Bill Lorensen (1):
BUG0013829: vtkAssembly::GetBounds adds bounds which are uninitialized

Brad King (1):
Examples: Set required CMake version and policies before project()

Cory Quammen (1):
Added "sticky" axes mode to vtkCubeAxesActor

David C. Lonie (1):
Handle empty array initialization in numpy_support.

David Gobbi (7):
Fix a crash when deleting vtk-python objects.
Fix warning about trailing comma in enum list.
In wrappers, guard against #including dirs.
Fix cell picker for images with negative spacing.
Fix uninitialized array warnings.
Bad null pointer check in vtkBSplineTransform.
Fix bad SetColor/GetColor interaction in vtkProperty.

Jean-Christophe Fillion-Robin (2):
vtkPythonCommand - Add support for additional call data types
vtkPythonCommand - Fix indent and variable names

John Stark (1):
Fix pipeline update issues in vtkImageExport

Julien Finet (2):
Prevent error message when deep copying vtkGridTransform
Change GetInputConnection error message into a debug warning message

Sankhesh Jhaveri (1):
BUG: Border visibility from underlying vtkScalarBar actor

Sean McBride (30):
Fix clang analyzer warning about passing null to strcmp
Fixed clang analyzer warning about passing null to memcpy
Fixed clang analyzer warning about reading uninitialized memory
Fixed clang analyzer waring about a dead store.
Fixed clang analyzer warning about dead store
Fixed clang analyzer warning about dead store.
Fixed clang analyzer warning about dead store.
Fixed clang analyzer warning about dead store.
Fixed clang analyzer warning about dead store.
Fixed clang analyzer warning about 2 dead stores.
Fixed clang analyzer warning about dead store.
Fixed clang analyzer warning about reading past an array.
Fixed several clang analyzer warnings.
Fixed clang analyzer warning about reading uninitialized memory.
Fixed clang analyzer warning about dead store to 'pd'.
Fixed clang analyzer warning about passing null to memcpy.
Fixed clang analyzer warning about dead store to 'index'.
Fixed clang analyzer warning about dead store to 'bestTime'.
Workaround clang analyzer warning by creating temp variable.
Fixed clang analyzer warnings about dead stores.
Misc cleanup of code nearby clang analyzer warnings.
Fixed clang analyzer warnings about dead stores.
Fixed clang analyzer warning about dead store at very end of method.
Fixed clang analyzer warning about dead store to 'itr'.
Fixed clang analyzer warning about dead store to 'cptr'.
Fixed null deref found by clang analyzer
Fixed clang analyzer warnings about dereferences
Suppress clang analyzer warning
Fixed clang analyzer warning about null deref
Fixed clang analyzer warning about reading uninitialized data.

Thomas Vaughan (1):
Set origin and spacing in vtkSurfaceReconstructionFilter. Ref: Mantis 0002826.

Tristan Coulange (1):
BUG: Add a missing include for VS 2013

Utkarsh Ayachit (3):
BUG #14599: Handle double values properly.
Add support for empty strinngs in SetInputArrayToProcess.
BUG #14244: Fix stereo image captures.

Will Schroeder (1):
Fixed bug causing plane to disappear on boundary.

Xabi Riobe (1):
BUG: The method vtkClipPlanesPainter::UpdateBounds must not be implemented.

xabi riobe (2):
Fix numerical precision problem in vtkCellLocator::IntersectWithLine
Add default value for argument

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23548 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_VTKv6.cmake Diff File

master 40aac2b5

2014-08-03 21:48:15

jcfr

Details Diff
BUG: Create new indexer for each file

Suggested by Steve Pieper as a way to work around potential issues in CTK

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23547 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/DICOM/DICOMLib/DICOMWidgets.py Diff File

master 1a042591

2014-08-03 21:48:12

jcfr

Details Diff
ENH: Adding the capability to process derived items

DerivedItems is a list of file names attributes on the
loadable with the DICOM instances produced by the plugin,
which will be added to the database after loading
the loadable.

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23546 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/DICOM/DICOMLib/DICOMWidgets.py Diff File

master dae50603

2014-08-03 16:08:26

pinter

Details Diff
ENH: Minor subject hierarchy enhancements

If a subject hierarchy node is deleted that has children, the user is given the option to delete branch.
Subject hierarchy added to favorite module list (still not appearing, because QSettings is pre-loaded from somewhere)

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23545 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTGUI/qSlicerSettingsModulesPanel.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/qSlicerSubjectHierarchyModule.cxx Diff File

master ceef4771

2014-08-03 01:14:38

jcfr

Details Diff
BUG: Update MultiVolumeExplorer to fix issue due to missing cast to int

See fedorov/MultiVolumeExplorer@f9222a25a
and fedorov/MultiVolumeExplorer@9135996ae

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23544 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File

master 57187d75

2014-08-03 01:14:36

jcfr

Details Diff
BUG: Update MultiVolumeImporter to fix DICOM.instanceUIDs initialization

See fedorov/MultiVolumeImporter@fb38cbbd00

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23543 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File
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