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Commits on Jul 20, 2017
  1. ENH: Update DCMTK to 3.6.2

    $ git shortlog d8ed091..DCMTK-3.6.2
    Jan Schlamelcher (43):
          Fixed CMake check for <png.h> resp. <libpng/png.h>.
          Removed dead code from dcmnet.
          Hid some Visual Studio warnings regarding libxml.
          Moved config/arith.cc to config/tests/arith.cc
          Added configuration options for STL and C++11.
          Fixed segmentation fault in DcmDataDictionary.
          Enhanced recently introduced STL configuration tests.
          Fixed some code relying on C++11 features.
          Updated copyright notice in recently modified file.
          Fixed wrong paths to 'config' dir in CMake scripts.
          Added association negotiation profiles to dcmqrscp.
          Added attribute matching functions to DcmElement etc.
          Fixed combined date time range matching.
          Refactored dcmwlm's attribute matching implementation.
          Added a partial workaround for DCMTK bug #758.
          Added a workaround for a bug in x87 FPUs/GCC.
          Removed broken attributes from dcmqrdb.
          Fixed using wrong build type for configuration test.
          Several fixes for the SunPro compiler (Solaris).
          Fixed configuration test errors.
          Workaround for SunPro C vs. C++ inconsistencies.
          Fixed wrong syntax in previous commit.
          Many workarounds for SunPro.
          Fixed compiler errors on Visual Studio with OpenSSL.
          Fixed compiling with Oracle Developer Studio (SunPro).
          Fixed unexpected iconv behavior on FreeBSD.
          Fixed wrong usage of alignas.
          Silenced output of FIND_PACKAGE(ICU).
          Added a workaround for C++11 compiling errors.
          Added DCMTK_ENABLE_LFS for choosing LFS type (CMake).
          Workaround for strange LFS implementation on Windows.
          Small fixes for a previous commit.
          More fixes for SunPro.
          Added a workaround for inconsistent LFS API under QNX.
          Removed no longer required section from COPYRIGHT.
          Removed several macros from config/docs/macros.txt.
          Added support for suppressing C4307 on Visual Studio.
          Made including third-party libraries version agnostic.
          Updated ANNOUNCE and INSTALL for DCMTK release 3.6.2.
          Updated Makefile dependencies.
          Updated version information for DCMTK release 3.6.2.
          Updated man pages for DCMTK release 3.6.2.
          Created CHANGES.362 for DCMTK release 3.6.2.
    
    Joerg Riesmeier (29):
          Removed unused local variable.
          Fixed inconsistent documentation in man page.
          Fixed documentation and other minor issues.
          Fixed issue with Simplified Adult Echo SR.
          Added unsigned suffix to large decimal constants.
          Fixed various stylistic issues.
          Fixed typo and rewrapped new text paragraphs.
          Changed the way XMLLIBS is set (Autoconf).
          Minor changes for supporting QNX 6.5.
          Added explicit type cast to keep QNX 6.5 quiet.
          Fixed issue with configure test on QNX 6.5.
          Updated Makefile dependencies.
          Updated data dictionary for DICOM 2017b.
          Added definition of new Storage SOP Class UIDs.
          Support new SOP Classes by networking tools.
          Added support for new "SR" and "PR" SOP Classes.
          Initial support for "Patient Radiation Dose SR".
          Added definition of new Presentation States.
          Added new Storage SOP Classes to comment sections.
          Updated latest tested CMake version.
          Enhanced documentation of gotoNamedChildNode().
          Added new method gotoNamedNodeInSubTree().
          Removed 2nd parameter from gotoNamedChildNode().
          Link MATHLIBS to all test programs.
          Moved MATHLIBS to LOCALLIBS.
          Removed useless target "tclabutil" from Makefile.
          Minor fixes in Makefile.
          Fixed typo in Coding Scheme Description.
          Updated copyright date.
    
    Marco Eichelberg (4):
          Removed unused variables.
          Converting large attributes to UN in explicit VR.
          Fixed handling of EINTR in networkDataAvailable().
          Removed support for HAVE_GUSI_H (MacOS classic).
    
    Michael Onken (28):
          Fixed write transfer syntax and support Deflated.
          Suppress error message for missing segm. types.
          Fixed check for transcoding, added documentation.
          First check number of components before value.
          Added OB/OW-related comparison operators.
          Log write errors to error logger.
          Fixed compiler warning on integer casting.
          Fixed wrong copy of SOP class in role selection.
          Made parameter const.
          Fixed possible role selection config. problem.
          Removed dcmStrictRoleSelection config. switch.
          Enhanced role selection documentation.
          Better parameter name and documentation.
          Allow search for role in SCU presentation contexts.
          Added role selection tests.
          Removed leftovers from dcmStrictRoleSelection.
          Fixed doubled space in log output.
          Fixed error message.
          Fixed ASCII art in comment.
          Opt. accept Default role if SCP role expected.
          Test recently introduced role selection option.
          Fixed ASCII art in test.
          Added missing space.
          Fixed typos.
          Removed unused variable.
          Require CMake > 2.8.3. Extended DCMTKConfig.cmake.
          Moved TRY_COMPILE to where it is first needed.
          Export new LFS CMake flag to DCMTKConfig.cmake.
    
    Nikolas Goldhammer (3):
          Replaced 'errno' with OFStandard::getLast*ErrorCode().
          Partially refactored 'errno' usage within dcmnet.
          Fixed OFerror_code's unit test not working on OpenBSD.
    
    Sebastian Grallert (12):
          Enhanced dcm2json application documentation.
          Added an argument conflict check for dcm2json.
          Enhanced value length information in DcmVR.
          Added some Attributes to DcmItem::checkAndUpdateVR().
          Added config test for the feenableexcept function.
          Several fixes for Solaris support.
          Fixed compiling on Solaris.
          Several fixes for NetBSD support.
          Fixed compiling error on Android.
          Added missing compiler flags for NetBSD (Autoconf).
          Modified compiler Flags for Solaris (CMake).
          Fixed configuration test errors on Visual Studio.
    
    Thorben Hasenpusch (2):
          Added feature test files for STL and C++11 support.
          Renamed several HAVE_ macros for better consistency.
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26159 3bd1e089-480b-0410-8dfb-8563597acbee
    jcfr committed Jul 20, 2017
  2. ENH: Updated to latest CTK

    Contains:
    
    ENH: Added Copy metadata button to DICOM metadata widget
    
    Added "Copy metadata" button (next to "Copy path" button) in the DICOM metadata browser (ctkDICOMObjectListWidget) to copy all metadata to the clipboard.
    It is useful for collecting information from users when they reporting DICOM loading errors.
    Also added tooltip for the existing, very useful, but hard-to-discover feature: if user clicks on a tag then its definition is displayed at http://dicomlookup.com.
    
    STYLE: Fix CircleCI link
    
    The CDash project for CTK seems retired. Clicking the test results link should
    navigate to CircleCI. Additionally, update the build status icon to 'shield'
    style, which includes the word 'circleci'.
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26158 3bd1e089-480b-0410-8dfb-8563597acbee
    lassoan committed Jul 20, 2017
Commits on Jul 19, 2017
  1. ENH: AbstractModuleWidget: Expose enter()/exit() to python scripting

    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26157 3bd1e089-480b-0410-8dfb-8563597acbee
    jcfr committed Jul 19, 2017
Commits on Jul 18, 2017
  1. BUG: Ensure function defined in .slicerrc.py are available in console

    Reported-by: Mohamed Moselhy <mmoslehy@uwo.ca>
    Tested-by: Mohamed Moselhy <mmoslehy@uwo.ca>
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26156 3bd1e089-480b-0410-8dfb-8563597acbee
    jcfr committed Jul 18, 2017
  2. ENH: Update CTK: Improve Python console completion, improve CTK build…

    … system
    
    $ git shortlog commontk/CTK@9e6df18..commontk/CTK@3d30e4d --no-merges
    Jean-Christophe Fillion-Robin (4):
          ENH: ctkConsole: Extend API adding cursorPosition, cursorColumn and cursorLine
          ENH: ctkConsole: Restore positions after building the completion model
          ENH: ctkConsole: Improve updateCommandBuffer to limit content of text
          ENH: PythonManagerTest: Add testPythonAttributeValues
    
    Marco Nolden (2):
          Use CMAKE_CXX_STANDARD setting for inner CTK build and sub-projects
          COMP: fix build errors if DCMTK is configured to use STL
    
    Max Smolens (1):
          BUG: Fix build when CMAKE_CXX_STANDARD is not set
    
    Mayeul Chassagnard (15):
          ENH: Add test for ctkAbstractPythonManager::pythonAttributes()
          ENH: ctkAbstractPythonManager: pythonAttributes can instantiate class and return instance members
          ENH: ctkConsole: Display output message under command line during autocompletion
          ENH: ctkConsole: Restrict cursor to command_line's end rather than document's end
          BUG: ctkConsole: Ensure autocompleter is updated or hidden when moving left
          ENH: ctkConsole: Prevent autocomplete from interfering with the message area
          BUG: ctkConsole: Allow to replace if cursor at the beginning of the interactive area
          BUG: ctkConsole: Backspace working in every case in the PythonConsole
          BUG: ctkConsole: Fix autocomplete during insertion
          STYLE: ctkConsole: Fix indent
          ENH: ctkAbstractPythonManager: Update autocompletion to support callable with arguments
          BUG: ctkConsole: Fix delete/BackSpace when cursor = commandEnd/InteractivePosition
          ENH: ctkConsole: Support completion within multi-line statement
          BUG: ctkConsole: Do not modify selected text color if outside interactive area
          ENH: ctkConsole: Support 2 different method to InsertCompletion
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26155 3bd1e089-480b-0410-8dfb-8563597acbee
    jcfr committed Jul 18, 2017
Commits on Jul 17, 2017
  1. ENH: Added file IO to load terminologies from json files

    The unique file extension for terminologies is .term.json, but .json only works as well
    
    Fixes QIICR/QuantitativeReporting#167
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26154 3bd1e089-480b-0410-8dfb-8563597acbee
    pinter committed Jul 17, 2017
Commits on Jul 15, 2017
  1. ENH: Updated OpenIGTLink to latest master

    Fixes socket close issue:
    openigtlink/OpenIGTLink#133
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26153 3bd1e089-480b-0410-8dfb-8563597acbee
    lassoan committed Jul 15, 2017
Commits on Jul 12, 2017
  1. ENH: Added vtkSegmentationDisplayNode::UnsetSegmentOverrideColor

    vtkSegmentationDisplayNode::UnsetSegmentOverrideColor is a convenience function
    for removing previously set segment override color.
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26152 3bd1e089-480b-0410-8dfb-8563597acbee
    lassoan committed Jul 12, 2017
  2. BUG: Fixed zip message logging

    When archives were created, info messages (such as "Zip: adding") were logged as errors.
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26151 3bd1e089-480b-0410-8dfb-8563597acbee
    lassoan committed Jul 12, 2017
Commits on Jul 10, 2017
  1. BUG: Use DICOM tags changed programmatically in SH items when exporting

    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26150 3bd1e089-480b-0410-8dfb-8563597acbee
    pinter committed Jul 10, 2017
  2. ENH: Made updateVolumeFromArray work for new volume nodes

    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26149 3bd1e089-480b-0410-8dfb-8563597acbee
    lassoan committed Jul 10, 2017
  3. ENH: Added test for slicer.util.arrayFromModelPoints

    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26148 3bd1e089-480b-0410-8dfb-8563597acbee
    lassoan committed Jul 10, 2017
  4. ENH: Added more numpy array conversions to slicer.util

    Added arrayFromVolume() and arrayFromModelPoints(). These are more explicit MRML node -> numpy array
    conversion functions than array(): they use a MRML node object as input and it is more clear
    what part of the MRML node is retrieved as numpy array.
    
    Added updateVolumeFromArray. It copies content of an existing numpy array into image data of a volume node.
    
    Also added automatic tests to UtilTest.py.
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26147 3bd1e089-480b-0410-8dfb-8563597acbee
    lassoan committed Jul 10, 2017
Commits on Jul 7, 2017
  1. BUG: Fixed loading of DICOM series using quasi-matching filename

    When slicer.util.loadVolume was used for loading a filename sometimes a different DICOM series was loaded
    (https://discourse.slicer.org/t/windows-slicer-util-loadvolume-loads-wrong-volume/641).
    
    The problem was that at some point the filename passed to slicer.util.loadVolume was compared to
    file names in the directory without normalization. Due to differences in path separators
    and capitalization of drive letter or file names, the comparison sometimes failed on Windows.
    
    Fixed by normalizing filenames before comparison.
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26146 3bd1e089-480b-0410-8dfb-8563597acbee
    lassoan committed Jul 7, 2017
Commits on Jul 6, 2017
  1. ENH: Make CLI output update more robust

    After a CLI module is executed, nodes that have references to other nodes are updated:
    their parent transform are set to the referenced transform node; and/or their subject hierarchy
    parent item is set to be the same as the parent of the referenced node.
    
    This scene updated relied on a Qt timer that performed the updates "right after" CLI execution
    was completed. This mechanism was not reliable because the timer required the user to
    force background event processing for a while after the CLI execution was reported to be completed,
    but this workaround was not reliable (see for example this report:
    https://discourse.slicer.org/t/issues-modifying-the-transform-tree/569/13).
    
    Changed the mechanism to use the same event queue that is used for processing reading of results
    back into the scene. This way it can be assured that by the time the CLI execution is reported
    to be complete, all the scene updates are completed as well.
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26145 3bd1e089-480b-0410-8dfb-8563597acbee
    lassoan committed Jul 6, 2017
  2. ENH: Made vtkMRMLTransformableNode::SetAndObserveTransformNodeID more…

    … robust
    
    Check for circular reference when setting a parent transform has improved.
    Circular reference is still possible if parent transform node IDs are set before
    transform nodes are added to the scene.
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26144 3bd1e089-480b-0410-8dfb-8563597acbee
    lassoan committed Jul 6, 2017
Commits on Jul 5, 2017
  1. BUG: Fixed DICOM tag reading from SH series item to DICOM export dialog

    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26143 3bd1e089-480b-0410-8dfb-8563597acbee
    pinter committed Jul 5, 2017
Commits on Jul 1, 2017
  1. ENH: Added lock window/level button to volume module

    Window/level values of scalar volumes can be adjusted by click&drag on the slice view.
    While this allows quick&easy tuning of the volume's appearance, in some cases it is too easy
    to accidentally modify the volume.
    
    Added a lock button to the window/level settings of Volumes module to enable/disable
    modification on the GUI.
    
    Note that window/level adjustment can also be disabled in the slice view interactor.
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26142 3bd1e089-480b-0410-8dfb-8563597acbee
    lassoan committed Jul 1, 2017
  2. COMP: Fixed build warning

    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26141 3bd1e089-480b-0410-8dfb-8563597acbee
    lassoan committed Jul 1, 2017
Commits on Jun 30, 2017
  1. COMP: qSlicerSlicer2SceneReader: Remove deprecated data types

    VTK___INT64 and VTK_UNSIGNED___INT64 have been deprecated
    on 2015-12-08 (Kitware/VTK@36bb09a) and are compiled away
    since 2017-04-13 (Kitware/VTK@bc2e2c5) when VTK_LEGACY_REMOVE
    is ON.
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26140 3bd1e089-480b-0410-8dfb-8563597acbee
    jcfr committed Jun 30, 2017
  2. ENH: ColorFiles: Add diverging colormap

    Slicer lacked a perceptually uniform diverging colormap.
    
    These are useful when the information being plotted has
    a critical middle value, or when the data deviates around zero.
    
    According to matplotlib:
    > Diverging: change in lightness and possibly saturation of two different
    > colors that meet in the middle at an unsaturated color; should be used
    > when the information being plotted has a critical middle value, such as
    > topography or when the data deviates around zero.
    
    More info about why perceptually uniform colormaps should be used over
    older colormaps like Rainbow or Jet:
    
    - matplotlib colormaps [2]
    - Diverging colormaps [3]
    - MATLAB's posts about new perceptually uniform colormaps [4]
    
    [1] https://matplotlib.org/
    [2] https://matplotlib.org/users/colormaps.html
    [3] http://www.kennethmoreland.com/color-maps/
    [4] http://blogs.mathworks.com/steve/2014/10/13/a-new-colormap-for-matlab-part-1-introduction/
    
    From: Fernando <fepegar@gmail.com>
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26139 3bd1e089-480b-0410-8dfb-8563597acbee
    jcfr committed Jun 30, 2017
Commits on Jun 29, 2017
  1. COMP: Add missing semicolons

    Add semicolons after VTK macros. Without these semicolons, the wrapping
    tool that generates hierarchy files fail to parse the declarations. When
    the version of VTK is updated to VTK8, generating the hierarchy files
    will be necessary for wrapping.
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26138 3bd1e089-480b-0410-8dfb-8563597acbee
    msmolens committed Jun 29, 2017
Commits on Jun 26, 2017
  1. ENH: Updating SEM to integrate more explicitly named functions

    - New Slicer Execution model version in Slicer (see Slicer/SlicerExecutionModel#91):
    
      $ git shortlog Slicer/SlicerExecutionModel@61bb14d..Slicer/SlicerExecutionModel@1d3e9a2 --no-merges
      Jean-Baptiste Vimort (2):
          STYLE: Renaming of the 'defaultValue' parameter's attribute to 'Value'
          ENH: Depreciation of the old functions
    
    - Replace the use of deprecated functions with the new ones
    
    - Deprecate the GetParameterDefault method: the GetParameterValue method
      should be used instead
    
    Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
    
    Reviewed-by: Johan Andruejol <johan.andruejol@kitware.com>
    Reviewed-by: Steve Pieper <pieper@bwh.harvard.edu>
    
    From: Jean-Baptiste VIMORT <jb.vimort@kitware.com>
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26137 3bd1e089-480b-0410-8dfb-8563597acbee
    jcfr committed Jun 26, 2017
  2. BUG: ExtensionWizard: Reject improper module name when adding module

    This commit ensures valid class names (e.g without spaces) are used when
    generating module files.
    
    Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
    
    From: AndrewBeers <andrew_beers@alumni.brown.edu>
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26136 3bd1e089-480b-0410-8dfb-8563597acbee
    jcfr committed Jun 26, 2017
Commits on Jun 25, 2017
  1. ENH: ScreenCapture module improvements

    Capturing can be cancelled.
    In "Capture all views" mode all 3D view controller bars are hidden now (not just the first).
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26135 3bd1e089-480b-0410-8dfb-8563597acbee
    lassoan committed Jun 25, 2017
Commits on Jun 24, 2017
  1. ENH: update MultiVolumeImporter hash

    Use scalar volume plugin to load indivudal frames of the MV node
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26134 3bd1e089-480b-0410-8dfb-8563597acbee
    fedorov committed Jun 24, 2017
  2. BUG: remove error messages when testing if nrrd is tensor file

    This change improves exception handling for the tensor reader so that
    'expected' exceptions for incorrect number of components do
    not trigger vtkErrorMacro output.  The extra error output
    apparently led to false negative test failures on the dashboard.
    
    Uses a more fine grained exception type for normal file variations
    and generic exception for unexpected failure conditions.
    
    Thanks @lassoan for reporting the issue!
    
    From Andras:
    
    I’ve noticed new vtkITKArchetypeDiffusionTensorImageReaderFile warnings when I load MRHead data set and there are also 11 new failed tests – related to image reading:
    
    http://trunk.cdash.org/testDetails.php?test=8067501&build=1048542
    
    http://trunk.cdash.org/viewTest.php?onlydelta&buildid=1048542
    
    From: Steve Pieper <pieper@isomics.com>
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26133 3bd1e089-480b-0410-8dfb-8563597acbee
    pieper committed Jun 24, 2017
Commits on Jun 23, 2017
  1. BUG: Reset transform sliders when switching between transforms

    Fixes #4086 (https://issues.slicer.org/view.php?id=4086)
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26132 3bd1e089-480b-0410-8dfb-8563597acbee
    lassoan committed Jun 23, 2017
  2. STYLE: add extra warning in documentation of dicom reader approaches

    Let people know not to re-order the items or people's
    settings could be changed.
    
    From: Steve Pieper <pieper@isomics.com>
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26131 3bd1e089-480b-0410-8dfb-8563597acbee
    pieper committed Jun 23, 2017
  3. STYLE: improved comment

    From: Steve Pieper <pieper@isomics.com>
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26130 3bd1e089-480b-0410-8dfb-8563597acbee
    pieper committed Jun 23, 2017
  4. ENH: move comparison utility from test to plugin

    This will make the utility available for use in the
    plugin and also from other code that needs
    the same functionality.
    
    TODO: this could be moved to the vtkSlicerVolumesLogic
    class for even greater applicability.
    
    From: Steve Pieper <pieper@isomics.com>
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26129 3bd1e089-480b-0410-8dfb-8563597acbee
    pieper committed Jun 23, 2017
  5. ENH: add scalar type detection to DICOM reader compare

    DCMTK imageIO is returning unsigned char data.
    This detects the error that still needs to be fixed.
    
    From: Steve Pieper <pieper@isomics.com>
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26128 3bd1e089-480b-0410-8dfb-8563597acbee
    pieper committed Jun 23, 2017
  6. BUG: move to ITK with fixed DCMTK orientation reading

    In Slicer/ITK for now, moving towards ITK proper
    
    http://review.source.kitware.com/#/c/22458/
    
    From: Steve Pieper <pieper@isomics.com>
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26127 3bd1e089-480b-0410-8dfb-8563597acbee
    pieper committed Jun 23, 2017
  7. ENH: add logic to detect test failures

    If any of the techniques unexpectedly loads a volume
    incorrectly the test will throw and exception and
    print the mismatches.
    
    From: Steve Pieper <pieper@isomics.com>
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26126 3bd1e089-480b-0410-8dfb-8563597acbee
    pieper committed Jun 23, 2017
  8. STYLE: fix typo in comment string

    From: Steve Pieper <pieper@isomics.com>
    
    git-svn-id: http://svn.slicer.org/Slicer4/trunk@26125 3bd1e089-480b-0410-8dfb-8563597acbee
    pieper committed Jun 23, 2017