1. 31 Mar, 2016 2 commits
    • naucoin's avatar
      BUG: fix hide from editor flag on volume rendering nodes · 6b2539c1
      naucoin authored
      The volume rendering nodes are appearing in the Data tree
      after the change to set the default of the hide from editors
      flag to false on the MRML node superclass.
      This change sets them hidden by default and sets up the
      display node combo box to show them in the Volume
      Rendering Inputs panel.
      
      Issue #2906
      
      git-svn-id: http://svn.slicer.org/Slicer4/trunk@24995 3bd1e089-480b-0410-8dfb-8563597acbee
      6b2539c1
    • naucoin's avatar
      ENH: Allow setting color node when loading volumes · 94c1b41f
      naucoin authored
      Add support to pick a non default color node when loading in a volume
      via python or the Add Data widget.
      
      In the volumes reader, check for a new property, colorNodeID, and use it to
      set the color node information on the volume's display node after reading.
      
      This can be used from python:
      
      properties = {}
      properties['colorNodeID'] = 'vtkMRMLColorTableNodeWarm1'
      slicer.util.loadVolume(fileName, properties)
      
      Added a color table node selector to the Volumes module IO widget. Set the
      default color nodes via the color logic pointer, for label maps and
      greyscales. Pass the colorNodeID property to the Volumes IO reader.
      Added testing the color node setting to the widget test.
      
      git-svn-id: http://svn.slicer.org/Slicer4/trunk@24994 3bd1e089-480b-0410-8dfb-8563597acbee
      94c1b41f
  2. 30 Mar, 2016 2 commits
  3. 22 Mar, 2016 3 commits
  4. 21 Mar, 2016 15 commits
    • jcfr's avatar
      BUG: Slicer_EXTENSION_DESCRIPTION_DIR is a PATH, not a STRING · effb4246
      jcfr authored
      Slicer_EXTENSION_DESCRIPTION_DIR was declared as a STRING. cmake-gui
      does not offer the possibility to open a file browser and select a
      directory from the user interface if a variable is not defined as a
      PATH or FILEPATH.
      
      From: Francois Budin <francois.budin@kitware.com>
      
      git-svn-id: http://svn.slicer.org/Slicer4/trunk@24988 3bd1e089-480b-0410-8dfb-8563597acbee
      effb4246
    • jcfr's avatar
      ENH: Update extension driver dashboard script to display variables. · fde71c6f
      jcfr authored
      This will facilitate understanding of the build context.
      
      Here is an example of output:
      
      $ ctest -S slicer_extensions_testing_experimental.cmake -VV
      * Extra verbosity turned on
      Reading Script: /home/jcfr/Projects/sandbox/slicer_extensions_testing_experimental.cmake
      -- Setting 'MIDAS_PACKAGE_URL' variable with default value 'http://slicer.kitware.com/midas3'
      -- Setting 'MIDAS_PACKAGE_EMAIL' variable with environment variable value 'OBFUSCATED'
      -- Setting 'MIDAS_PACKAGE_API_KEY' variable with environment variable value 'OBFUSCATED'
      -- Setting 'run_ctest_submit' variable with default value 'TRUE'
      -- Setting 'run_ctest_with_update' variable with default value 'TRUE'
      -- Setting 'run_ctest_with_configure' variable with default value 'TRUE'
      -- Setting 'run_ctest_with_build' variable with default value 'TRUE'
      -- Setting 'run_ctest_with_notes' variable with default value 'TRUE'
      -- Setting 'Slicer_UPLOAD_EXTENSIONS' variable with default value 'TRUE'
      -- CTEST_SITE ........................: cerrotorre.kitware
      -- CTEST_BUILD_NAME ..................: Linux-g++5.2.1-64bits-QT4.8.7-PythonQt-With-Tcl-CLI-origin-master-Release
      -- SCRIPT_MODE .......................: experimental
      -- CTEST_BUILD_CONFIGURATION .........: Release
      -- ADDITIONAL_CMAKECACHE_OPTION ......:
      
      -- CTEST_NOTES_FILES .................: /home/jcfr/Projects/sandbox/slicer_extensions_testing_experimental.cmake
      -- CTEST_DASHBOARD_ROOT ..............: /home/jcfr/Projects/
      -- CTEST_CMAKE_GENERATOR .............: Unix Makefiles
      -- CTEST_TEST_TIMEOUT ................: 500
      -- CTEST_BUILD_FLAGS .................: -j8
      -- CTEST_PROJECT_NAME ................: Slicer4
      -- EXTENSIONS_TRACK_QUALIFIER ........: master
      -- EXTENSIONS_BUILDSYSTEM_SOURCE_DIRECTORY: /home/jcfr/Projects//Slicer/Extensions/CMake
      -- EXTENSIONS_BUILDSYSTEM_TESTING ....: TRUE
      -- EXTENSIONS_INDEX_GIT_REPOSITORY ...: git://github.com/Slicer/ExtensionsIndex.git
      -- EXTENSIONS_INDEX_GIT_TAG ..........: origin/master
      -- CTEST_BINARY_DIRECTORY ............: /home/jcfr/Projects//SlicerExtensions-build-64bits-QT4.8.7-PythonQt-With-Tcl-CLI-Release-experimental-Testing-master
      -- CTEST_SVN_COMMAND .................: /usr/bin/svn
      -- CTEST_GIT_COMMAND .................: /usr/bin/git
      -- Slicer_DIR ........................: /home/jcfr/Projects//Slicer-Release/Slicer-build
      -- CTEST_CONFIGURATION_TYPE ..........: Release
      -- CTEST_LOG_FILE ....................: NOT DEFINED
      -- CTEST_NOTES_FILES .................: /home/jcfr/Projects/sandbox/slicer_extensions_testing_experimental.cmake
      -- CTEST_PARALLEL_LEVEL ..............: 8
      -- MIDAS_PACKAGE_URL .................: http://slicer.kitware.com/midas3
      -- run_ctest_submit ..................: TRUE
      -- run_ctest_with_update .............: TRUE
      -- run_ctest_with_configure ..........: TRUE
      -- run_ctest_with_build ..............: TRUE
      -- run_ctest_with_notes ..............: TRUE
      -- Slicer_UPLOAD_EXTENSIONS ..........: TRUE
      -- CTEST_SOURCE_DIRECTORY ............: /home/jcfr/Projects//Slicer/Extensions/CMake
      -- Slicer_EXTENSION_DESCRIPTION_DIR ..: NOT DEFINED
      -- empty_binary_directory ............: FALSE
      -- force_build .......................: TRUE
      -- model .............................: Experimental
      -- track .............................: Extensions-Experimental
      -- CTEST_USE_LAUNCHERS ...............: 1
      [...]
      
      From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
      
      git-svn-id: http://svn.slicer.org/Slicer4/trunk@24987 3bd1e089-480b-0410-8dfb-8563597acbee
      fde71c6f
    • jcfr's avatar
      STYLE: ExtensionsDashboardScripts: Remove reference to unused variables · 4e887339
      jcfr authored
      From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
      
      git-svn-id: http://svn.slicer.org/Slicer4/trunk@24986 3bd1e089-480b-0410-8dfb-8563597acbee
      4e887339
    • jcfr's avatar
      ENH: Update Slicer driver dashboard script to display variables. · 82e3b359
      jcfr authored
      This will facilitate understanding of the build context.
      
      Here is an example of output:
      
      $ ctest -S slicer_experimental.cmake -VV
      * Extra verbosity turned on
      Reading Script: /home/jcfr/Projects/sandbox/slicer_experimental.cmake
      -- Setting 'MIDAS_PACKAGE_URL' variable with default value 'http://slicer.kitware.com/midas3'
      -- Setting 'MIDAS_PACKAGE_EMAIL' variable with environment variable value 'OBFUSCATED'
      -- Setting 'MIDAS_PACKAGE_API_KEY' variable with environment variable value 'OBFUSCATED'
      -- Setting 'run_ctest_with_disable_clean' variable with default value 'FALSE'
      -- Setting 'run_ctest_with_configure' variable with default value 'TRUE'
      -- Setting 'run_ctest_with_coverage' variable with default value 'TRUE'
      -- Setting 'run_ctest_with_memcheck' variable with default value 'TRUE'
      -- Setting 'run_ctest_with_packages' variable with default value 'TRUE'
      -- Setting 'run_ctest_with_upload' variable with default value 'TRUE'
      -- Setting 'run_ctest_with_notes' variable with default value 'TRUE'
      -- CTEST_SITE ........................: cerrotorre.kitware
      -- CTEST_BUILD_NAME ..................: Linux-g++5.2.1-64bits-QT4.8.7-PythonQt-With-Tcl-NoCLI-Release
      -- SCRIPT_MODE .......................: experimental
      -- CTEST_BUILD_CONFIGURATION .........: Release
      -- WITH_MEMCHECK .....................: FALSE
      -- WITH_COVERAGE .....................: FALSE
      -- WITH_DOCUMENTATION ................: FALSE
      -- ADDITIONAL_CMAKECACHE_OPTION ......:
      
      -- CTEST_NOTES_FILES .................: /home/jcfr/Projects/sandbox/slicer_experimental.cmake
      -- CTEST_DASHBOARD_ROOT ..............: /home/jcfr/Projects/
      -- CTEST_CMAKE_GENERATOR .............: Unix Makefiles
      -- CTEST_TEST_TIMEOUT ................: 500
      -- CTEST_BUILD_FLAGS .................: -j8
      -- TEST_TO_EXCLUDE_REGEX .............:
      -- CTEST_PROJECT_NAME ................: Slicer4
      -- CTEST_SOURCE_DIRECTORY ............: /home/jcfr/Projects//Slicer
      -- CTEST_BINARY_DIRECTORY ............: /home/jcfr/Projects//Slicer-Release
      -- CTEST_COVERAGE_COMMAND ............: /usr/bin/gcov
      -- CTEST_MEMORYCHECK_COMMAND .........: /usr/bin/valgrind
      -- CTEST_SVN_COMMAND .................: /usr/bin/svn
      -- CTEST_GIT_COMMAND .................: /usr/bin/git
      -- QT_QMAKE_EXECUTABLE ...............: /home/jcfr/Support/qt-everywhere-opensource-build-4.8.7/bin/qmake
      -- CTEST_CONFIGURATION_TYPE ..........: Release
      -- CTEST_LOG_FILE ....................: NOT DEFINED
      -- CTEST_NOTES_FILES .................: /home/jcfr/Projects/sandbox/slicer_experimental.cmake
      -- CTEST_PARALLEL_LEVEL ..............: 8
      -- MIDAS_PACKAGE_URL .................: http://slicer.kitware.com/midas3
      -- run_ctest_submit ..................: 1
      -- run_ctest_with_disable_clean ......: FALSE
      -- run_ctest_with_update .............: 0
      -- run_ctest_with_configure ..........: TRUE
      -- run_ctest_with_build ..............: 0
      -- run_ctest_with_test ...............: 0
      -- run_ctest_with_coverage ...........: TRUE
      -- run_ctest_with_memcheck ...........: TRUE
      -- run_ctest_with_packages ...........: TRUE
      -- run_ctest_with_upload .............: TRUE
      -- run_ctest_with_notes ..............: TRUE
      -- SVN_REPOSITORY ....................: http://svn.slicer.org/Slicer4
      -- SVN_BRANCH ........................: trunk
      -- SVN_REVISION ......................:
      -- SVN_URL ...........................: http://svn.slicer.org/Slicer4/trunk
      -- empty_binary_directory ............: FALSE
      -- force_build .......................: TRUE
      -- model .............................: Experimental
      -- track .............................: Experimental-Packages
      -- CTEST_USE_LAUNCHERS ...............: 1
      [...]
      
      From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
      
      git-svn-id: http://svn.slicer.org/Slicer4/trunk@24985 3bd1e089-480b-0410-8dfb-8563597acbee
      82e3b359
    • jcfr's avatar
      BUG: Update Slicer build system to report packaging errors on CDash. · ca38f539
      jcfr authored
      See #3032
      
      This commit adds a new target named "packageupload" that will
      (1) build the standard 'package' target,
      (2) extract the list of generated packages from its standard output and
      (3) append the list of generated package filepaths to a file named PACKAGES.txt,
      (4) upload the packages on midas.
      
      Using this target a Slicer package can be uploaded to midas without
      relying on CTest.
      
      Within the ctest script, the target "packageupload" is built and then
      the URL to download packages from midas are uploaded to CDash based on the
      content of the file PACKAGES.txt
      
      From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
      
      git-svn-id: http://svn.slicer.org/Slicer4/trunk@24984 3bd1e089-480b-0410-8dfb-8563597acbee
      ca38f539
    • jcfr's avatar
      ENH: Remove support for building an ExtensionsIndex directly from Slicer · ffc788d9
      jcfr authored
      This commit simplifies Slicer build system removing the (untested) support
      for building extensions given a directory containing *.s4ext files.
      
      Note that building extensions by configuring and building the project
      in "Extensions/CMake" can still be done. Extensions dashboards use and
      test this approach. The template extension dashboard script can be used
      as a model.
      
      From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
      
      git-svn-id: http://svn.slicer.org/Slicer4/trunk@24983 3bd1e089-480b-0410-8dfb-8563597acbee
      ffc788d9
    • jcfr's avatar
      BUG: UseSlicer: Do not display value of Email and ApiKey. · f6ba259b
      jcfr authored
      From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
      
      git-svn-id: http://svn.slicer.org/Slicer4/trunk@24982 3bd1e089-480b-0410-8dfb-8563597acbee
      f6ba259b
    • jcfr's avatar
      ENH: Update slicer_setting_variable_message to understand OBFUSCATE option. · f0037c53
      jcfr authored
      From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
      
      git-svn-id: http://svn.slicer.org/Slicer4/trunk@24981 3bd1e089-480b-0410-8dfb-8563597acbee
      f0037c53
    • jcfr's avatar
      STYLE: SlicerExtensionPackageAndUploadTarget: Display location of log · 3d8c0a80
      jcfr authored
      From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
      
      git-svn-id: http://svn.slicer.org/Slicer4/trunk@24980 3bd1e089-480b-0410-8dfb-8563597acbee
      3d8c0a80
    • jcfr's avatar
      STYLE: SlicerExtensionPackageAndUploadTarget: Improve documentation · 57cf4d70
      jcfr authored
      From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
      
      git-svn-id: http://svn.slicer.org/Slicer4/trunk@24979 3bd1e089-480b-0410-8dfb-8563597acbee
      57cf4d70
    • jcfr's avatar
      STYLE: Remove unneeded check for "ctest_upload" command · 2dc8e7da
      jcfr authored
      This code is now required anymore since the CMake minimum required
      version (2.8.9) provided the command.
      
      From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
      
      git-svn-id: http://svn.slicer.org/Slicer4/trunk@24978 3bd1e089-480b-0410-8dfb-8563597acbee
      2dc8e7da
    • jcfr's avatar
      COMP: Fix -Wnarrowing and -Wunused-variable warnings · e95cfd6e
      jcfr authored
      /path/to/Slicer/Modules/Loadable/Tables/qSlicerTablesModuleWidget.cxx: In member function ‘void qSlicerTablesModuleWidget::onMRMLTableNodeModified(vtkObject*)’:
      /path/to/Slicer/Modules/Loadable/Tables/qSlicerTablesModuleWidget.cxx:167:21: warning: unused variable ‘tableNode’ [-Wunused-variable]
         vtkMRMLTableNode* tableNode = vtkMRMLTableNode::SafeDownCast(caller);
                           ^
      
      /path/to/Slicer/Libs/MRML/DisplayableManager/vtkMRMLOrientationMarkerDisplayableManager.cxx: In member function ‘void vtkMRMLOrientationMarkerDisplayableManager::vtkInternal::UpdateMarkerSize()’:
      /path/to/Slicer/Libs/MRML/DisplayableManager/vtkMRMLOrientationMarkerDisplayableManager.cxx:511:38: warning: narrowing conversion of ‘(maxX - minX)’ from ‘double’ to ‘int’ inside { } is ill-formed in C++11 [-Wnarrowing]
         int rendererSizeInPixels[2] = {maxX-minX, maxY-minY};
                                            ^
      /path/to/Slicer/Libs/MRML/DisplayableManager/vtkMRMLOrientationMarkerDisplayableManager.cxx:511:49: warning: narrowing conversion of ‘(maxY - minY)’ from ‘double’ to ‘int’ inside { } is ill-formed in C++11 [-Wnarrowing]
         int rendererSizeInPixels[2] = {maxX-minX, maxY-minY};
                                                       ^
      /path/to/Slicer/Libs/MRML/DisplayableManager/vtkMRMLRulerDisplayableManager.cxx: In member function ‘void vtkMRMLRulerDisplayableManager::vtkInternal::UpdateRuler()’:
      /path/to/Slicer/Libs/MRML/DisplayableManager/vtkMRMLRulerDisplayableManager.cxx:289:42: warning: narrowing conversion of ‘(maxX - minX)’ from ‘double’ to ‘int’ inside { } is ill-formed in C++11 [-Wnarrowing]
             int rendererSizeInPixels[2] = {maxX-minX, maxY-minY};
                                                ^
      /path/to/Slicer/Libs/MRML/DisplayableManager/vtkMRMLRulerDisplayableManager.cxx:289:53: warning: narrowing conversion of ‘(maxY - minY)’ from ‘double’ to ‘int’ inside { } is ill-formed in C++11 [-Wnarrowing]
             int rendererSizeInPixels[2] = {maxX-minX, maxY-minY};
                                                           ^
      
      /path/to/Slicer/Libs/MRML/DisplayableManager/vtkMRMLRulerDisplayableManager.cxx: In member function ‘void vtkMRMLRulerDisplayableManager::vtkInternal::SetupRuler()’:
      /path/to/Slicer/Libs/MRML/DisplayableManager/vtkMRMLRulerDisplayableManager.cxx:213:13: warning: unused variable ‘numberOfTickLines’ [-Wunused-variable]
         const int numberOfTickLines = 11;
                   ^
      
      /path/to/Slicer/Libs/MRML/DisplayableManager/vtkMRMLRulerDisplayableManager.cxx:281:15: warning: unused variable ‘viewport’ [-Wunused-variable]
             double* viewport = this->MarkerRenderer->GetViewport();
                     ^
      
      /path/to/Slicer/Libs/MRML/DisplayableManager/vtkMRMLRulerDisplayableManager.cxx:338:79: warning: narrowing conversion of ‘rulerLineMarginPixel’ from ‘int’ to ‘double’ inside { } is ill-formed in C++11 [-Wnarrowing]
         double pointOrigin[3] = {double(viewWidthPixel)/2.0, rulerLineMarginPixel, 0};
      
      From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
      
      git-svn-id: http://svn.slicer.org/Slicer4/trunk@24977 3bd1e089-480b-0410-8dfb-8563597acbee
      e95cfd6e
    • jcfr's avatar
      COMP: Fix -Wunused-parameter warning in vtkMRMLScene test · 901b1bbb
      jcfr authored
      From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
      
      git-svn-id: http://svn.slicer.org/Slicer4/trunk@24976 3bd1e089-480b-0410-8dfb-8563597acbee
      901b1bbb
    • jcfr's avatar
      COMP: vtkITK: Fix -Wsign-compare and -Wmaybe-uninitialized warnings · d250196c
      jcfr authored
      From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
      
      git-svn-id: http://svn.slicer.org/Slicer4/trunk@24975 3bd1e089-480b-0410-8dfb-8563597acbee
      d250196c
    • jcfr's avatar
      ENH: Modernizing vcl_ to std:: · 8694c131
      jcfr authored
      In all supported compilers, the need for vcl_ specialized
      functions has been removed.  there is no longer a need
      to have these overrides, and code is easier to read
      and easier to maintain without these specializations.
      
      The vcl_* definitions can now be greatly simplified.
      After removing specializations for early non-conformant
      c++ compilers the end result was that only the
      std:: version of the functions could ever be
      used by the compiler.
      
      ITK_SCRIPT=ITK/Utilities/Maintenance/VCL_ModernizeNaming.py
      SRC_BASE_DIR=$(pwd)
      for ext in ".h" ".cxx" ".cpp" ".hxx" ".hpp" ".txx"; do
        find ${SRC_BASE_DIR} -type f -name "*${ext}" \         -exec python ${ITK_SCRIPT} {} \;
      done
      
      From: Hans Johnson <hans-johnson@uiowa.edu>
      
      git-svn-id: http://svn.slicer.org/Slicer4/trunk@24974 3bd1e089-480b-0410-8dfb-8563597acbee
      8694c131
  5. 18 Mar, 2016 1 commit
  6. 17 Mar, 2016 1 commit
  7. 15 Mar, 2016 1 commit
  8. 14 Mar, 2016 2 commits
    • pinter's avatar
      ENH: Add special column type in qMRMLTableView to display checkboxes for boolean values · c0bca601
      pinter authored
      If a vtkBitArray is added as a column to vtkMRMLTableNode, then qMRMLTableView shows a checkbox instead of 0/1 text to make it easier to edit.
      In the future color, position, and other data will possibly be added as further types. The mentioned two will be the same value type (double array), so will need to specify not just type but display option too.
      qMRMLTableItemDelegate that will deliver this functionality is removed form the repository (it was temporarily added in the previous commit so that it can be accessed and uesd later).
      Commented out lines were removed from other classes. Having commented code in the repository makes no sense: the repository itself can be used as a history, no need for three year old comments to make the code harder to read.
      
      git-svn-id: http://svn.slicer.org/Slicer4/trunk@24970 3bd1e089-480b-0410-8dfb-8563597acbee
      c0bca601
    • pinter's avatar
      ENH: Added delegate temporarily for qMRMLTableView · b6360317
      pinter authored
      Will be removed in  next commit. Created to enable special editing of vtkMRMLTableNode cells in qMRMLTableView. This will be useful later for color editing, or if a better solution will be found for checkboxes. This delegate shows a checkbox in the center of the table cell (by default it is on the left), but only allows editing after double click. Thus this will be replaced by simple Qt mechanism with the checkbox on the left.
      
      git-svn-id: http://svn.slicer.org/Slicer4/trunk@24969 3bd1e089-480b-0410-8dfb-8563597acbee
      b6360317
  9. 10 Mar, 2016 5 commits
  10. 09 Mar, 2016 1 commit
    • jcfr's avatar
      BUG: Update BRAINSTools to include BRAINSFit fix for centerOfROI initializer · a6f34123
      jcfr authored
      
      Tested-by: Hans Johnson's avatarHans Johnson <hans-johnson@uiowa.edu>
      
      $ git shortlog e257e62...29d203c --no-merges
      Alexander Leinoff (5):
            COMP: BCD should only request VTK when building GUI
            COMP: CompareImageFilter should only use VTK when building GUI
            BUG: Replaces all baselines for BCDTests
            BUG: Fixes typo in previous commit
            BUG: Fixes version check in top level CMAKELists.txt
      
      Ali Ghayoor (13):
            ENH: Upgrade vnl_powell to itkPowellOptimizerv4 in BCD
            ENH: Write the debug image based on requested debug level
            ENH: BCD can process input images with different dynamic range
            ENH: Change tolerance and step size for Powell optimizer
            BUG: Fixed a bug in BABC when a low debugLevel requested
            ENH: New parameters for multimodal segmentation in BABC
            ENH: Updated purePlugsThreshold value for AutoWorkup
            BUG: fixed a bug in BABC denoise filtering
            ENH: Initialize a matrix variable
            ENH: remove an intermediate variable to avoid extra memory usage
            BUG: defined an orderedmap class for BABC
            STYLE: Cleanup unnecessary if statement
            ENH: Prevent holes in created brain mask by ROIAutoFilter
      
      Andrey Fedorov (2):
            BUG: fix centerOfROI initializer
            ENH: adjust restriction on the required registration phases
      
      Hans J. Johnson (40):
            ENH: Update ITK, ANTS, and teem
            STYLE: Remove MinSizeRel option
            COMP: Resolve clang static analysis warnings
            BUG:  Compilation error fixed due to typo.
            ENH: Update external tools support.
            COMP: Improve coverage by using removeIntensityOutliers flag.
            COMP: Force C++11 compliance testing
            COMP: Added compatibility testing with apple and CXX11
            BUG: Nipype now reqires invert_initial_moving_transform to be set
            ENH: Selection of denoising filter improved.
            ENH: Changed options to reflect current processing
            ENH: Updated ANTs for improved DenoiseImage
            BUG: The Rician noise model fails for DenoiseImage
            ENH: Added key files for new denoised gaussian images.
            ENH: Use denoised images for atlas reference
            ENH: Add atlas images to reference atlas.
            ENH: Fine-tune denoising options in BAW.
            BUG: Need to work around nipype bug
            ENH: Use denoised t1 from atlas for registration
            ENH: Return to using Rician de-noising from ANTs
            BUG: Error in respecting the NSLOTS variable
            PERF:  Constrain memory usage for KNN phase
            PERF: Update ABC workflow to reflect memory with KNN
            BUG: Serialize printing from threaded sections
            STYLE: Print table consistently
            BUG: Need to pass all denoised images into BRAINSABC
            STYLE: Make usage of variable names consistent
            STYLE: Cleanup unsuded ComputeLabels references
            BUG: Internal ordering for dictionary missed first element
            BUG: This is an unsatisfactory solution
            BUG: Fix to allow all allocated slots to be used
            ENH: Consolidate and syncronize different ANTs run parameters
            BUG: Fix running of ANTs consistently
            ENH: Add N4 bias correction after denoising
            BUG: Missing ',' in python list.
            ENH: Improve error reporting for improper input
            STYLE: Uniformly describe registration parameters.
            PERF: New AntsJointFusion is well multithreaded
            ENH: Add automatic image unwrapping
            BUG: Fix mismatched function parameter calls.
      
      Jean-Christophe Fillion-Robin (1):
            COMP: Force CMAKE_CONFIGURATION_TYPES only when using multi-config generator
      
      Regina Kim (7):
            BUG: Fix Landmark Workflow
            ENH: Update antsDenoise IO specification
            ENH: Rewording to JointFusion from MALF
            ENH: Linear Regression Rescaling
            ENH: JointFusion Update for T2
            ENH: Add JointFusion masking option
            ENH: 1.5 Tesla T2-w excluded from JointFusion
      
      From: Andrey Fedorov <fedorov@bwh.harvard.edu>
      
      git-svn-id: http://svn.slicer.org/Slicer4/trunk@24963 3bd1e089-480b-0410-8dfb-8563597acbee
      a6f34123
  11. 08 Mar, 2016 3 commits
    • jcfr's avatar
      STYLE: Rename Build Dir in PreventInSourceBuilds · 83809a20
      jcfr authored
      Make the name used as the build directory consistent with line 22.
      
      From: Alexis Girault <agirault@users.noreply.github.com>
      
      git-svn-id: http://svn.slicer.org/Slicer4/trunk@24962 3bd1e089-480b-0410-8dfb-8563597acbee
      83809a20
    • lassoan's avatar
      ENH: Made view axis labels configurable · 786d2ea1
      lassoan authored
      For some applications standard left/right, posterior/anterior, inferior/superior axis labels are not optimal. For example for eye image analysis temporal/nasal labels are more appropriate than left/right.
      Labels may have to be view-specific, e.g., show standard labels on a large overview image and show custom labels in a view that shows a small segmented structure.
      
      Implemented solution:
      * vtkMRMLAbstractViewNode stores axis labels (SetAxisLabel/GetAxisLabel methods can be used to set/get the labels)
      * vtkMRMLViewDisplayableManager and vtkMRMLOrientationMarkerDisplayableManager read labels from vtkMRMLAbstractViewNode instead of using hard-coded strings to show in Cube and Axes orientation markers and 3D cube labels
      * DataProbe read labels from vtkMRMLAbstractViewNode instead of using hard-coded string
      
      No user interface is implemented, as this is an advanced feature for module developers. Example use:
      
      sliceNode = slicer.mrmlScene.GetNodeByID('vtkMRMLSliceNodeRed')
      sliceNode.SetOrientationMarkerType(slicer.vtkMRMLAbstractViewNode.OrientationMarkerTypeAxes)
      sliceNode.SetOrientationMarkerSize(slicer.vtkMRMLAbstractViewNode.OrientationMarkerSizeLarge)
      sliceNode.SetAxisLabel(0,'Proximal')
      sliceNode.SetAxisLabel(1,'Distal')
      
      viewNode = slicer.mrmlScene.GetNodeByID('vtkMRMLViewNode1')
      viewNode.SetOrientationMarkerType(slicer.vtkMRMLAbstractViewNode.OrientationMarkerTypeAxes)
      viewNode.SetOrientationMarkerSize(slicer.vtkMRMLAbstractViewNode.OrientationMarkerSizeLarge)
      viewNode.SetAxisLabel(0,'Proximal')
      viewNode.SetAxisLabel(1,'Distal')
      
      
      git-svn-id: http://svn.slicer.org/Slicer4/trunk@24961 3bd1e089-480b-0410-8dfb-8563597acbee
      786d2ea1
    • lassoan's avatar
      ENH: Added method for adding custom volume rendering preset · e8fb6dc8
      lassoan authored
      
      git-svn-id: http://svn.slicer.org/Slicer4/trunk@24960 3bd1e089-480b-0410-8dfb-8563597acbee
      e8fb6dc8
  12. 07 Mar, 2016 1 commit
  13. 04 Mar, 2016 1 commit
  14. 03 Mar, 2016 2 commits