Slicer4

COMP: Update ITKv4 to fix MINC build error using redhat devtoolset 2 This commit updates ITK and fix an error reported when building Slicer using redhat toolset 2 on CircleCI. Details: 8 Date: Wed May 17 03:52:36 2017 -0400 COMP: libminc: ... [More] Define _GNU_SOURCE to enable C99 extension during introspection This commit addresses failure to detect "round" function on compiler like g++ 4.8.2 provided by redhat devtoolset 2 [1]. More specifically, since the macro __USE_ISOC99 wasn't defined, function "round" declared in "mathcalls.h" (itself included from "math.h") wasn't found during introspection. Defining _GNU_SOURCE allows to enable c99. See features.h for more details. Error fixed by this commit is the following: /path/to/ITKv4/Modules/ThirdParty/MINC/src/libminc/libsrc2/hyper.c:64:1: error: redefinition of ‘round’ round(double x) ^ and it is reproducible using docker-centos-build [2]. CMake macro was adapated from python-cmake-buildsystem [3] [1] https://access.redhat.com/documentation/en-US/Red_Hat_Developer_Toolset/2/html/2.0_Release_Notes/DTS2.0_Release.html [2] https://github.com/thewtex/docker-centos-build [3] https://github.com/python-cmake-buildsystem/python-cmake-buildsystem/blob/d0f47193837db6ad9e08bc99617276d4a24687c3/cmake/ConfigureChecks.cmake#L415 8 [Less]

BUG: Segment editor widget layout issue fixed Most of the layout problems are solved. There are minor spaces between the widgets in certain rare cases, but there are no cramped widgets any more at all.

ENH: Improved segment editor shortcuts Switch between last two effects using space bar (it can be used to quickly inactivate/reactivate scissors; switch between paint/erase; etc). Added shortcut for choosing more than 10+ effects by clicking shift+number (Shift+1, Shift+2, ...).

BUG: Further improvement of segment editor widget layout issue Still not perfect, but at least the layout is not completely cramped after changing modules and back

BUG: Fix warning message in extension wizard Fix warning message in extension wizard displayed when publishing from a Git branch other than master. Previously, the following error occurred when logging this warning message: TypeError: not all arguments converted during string formatting

BUG: Remove explicit path to git executable for GitPython (Windows) On Windows, remove the explicit path to the git executable for GitPython. On modern versions of Git for Windows, the specified path (/bin/git) is not correct. This results in errors ... [More] when running the command line extension wizard, for example when publishing an extension: $ slicerExtensionWizard --publish ~/Slicer-MyExtension/ ... git.exc.GitCommandNotFound: Cmd('C:/Program Files/Git/usr/bin/git') not found due to: WindowsError('[Error 2] The system cannot find the file specified') When the GIT_PYTHON_GIT_EXECUTABLE environment variable is not set, GitPython uses the git executable found in the path. Since the user is expected to run slicerExtensionWizard from Git Bash, it's reasonable to assume that the correct git executable is in the path. [Less]

ENH: Add support for MINC image IO Issue #4085 This enables MINC Image IO via ITK. This currently supports MINC version 2 (HDF5-based). Reviewed-by: Andriy Fedorov

ENH: Update SimpleITK (Support for debug build) Fixes #3816 Tested-by: Andras Lasso

BUG: Attempt to fix Segment Editor layout issue The effect options widget was truncated and vertically pressed in some cases after changing the active effect.

ENH: Update ITK to 4.12.0rc1 $ git shortlog 1619816..9c91cb6 --no-merges Ben Boeckel (1): ENH: Add a script to help update third-party sources Brad King (5): ENH: Update KWIML import script for new upstream URL ENH: Teach ... [More] update-third-party.bash to add a Change-Id ENH: Port KWSys update script to update-third-party.bash ENH: KWSys: Filter out unused attributes during import ENH: KWSys: Apply attribute changes made upstream Bradley Lowekamp (19): COMP: Enable hidden visibility property with NIFTI static libraries COMP: Enable hidden visibility property with GIFTI static libraries BUG: Correct variable name used to check CXX version BUG: Correct variable name used to check CXX version COMP: Enable hidden visibility property with NIFTI static libraries COMP: Enable hidden visibility property with GIFTI static libraries BUG: Initialize ConvergenceValue in constructor BUG: Initialize ConvergenceValue in constructor ENH: Update CircleCi script to download latest binary tar-ball BUG: Use CMAKE_DL_LIBS instead of explict "dl" library COMP: Fix CircleCI ITK data download file name ENH: Update CircleCI yaml file BUG: Apply changes from MetaIO upstream to remove static variables ENH: Update SWIG version to 3.0.12 ENH: Update PCRE version to 8.40 ENH: Add OrientedBoudingBox attributes to ShapeLabelMap COMP: Use std::abs over vnl_math_abs BUG: Initialize image data to 0 ENH: Fix clearing build tree error David T. Chen (1): BUG: Fixed quote style Dženan Zukić (3): STYLE: Simplify code by using TestingMacros BUG: fixing wrong check for argument count ENH: Add Strain as a remote module Floris Berendsen (2): COMP: Added missing png_get_uint_31 name mangling COMP: Added missing png_get_uint_31 name mangling Francois Budin (58): STYLE: Typo corrections in itk*TopHatImageFilter.h ENH: Prefer std::atomic over compiler specific implementation BUG: Addresses 'ordered comparison between pointer and zero' error (clang-4) BUG: Addresses InDoxygenGroup Test with Python 3.6 failures BUG: BSplineScatteredDataPointSetToImageFilter output image is not generated BUG: itk::RGBPixel [Less]