[Insight-developers] Patches for v4.4.2 point release
Jean-Christophe Fillion-Robin
jchris.fillionr at kitware.com
Wed Aug 28 18:49:51 EDT 2013
Hi Matt,
The commits associated with file Modules/IO/DCMTK/src/itkDCMTKImageIO.cxx
on release branch are:
* 376aeec - BUG: Row/Column assignment into ImageDimensions was wrong (7
hours ago) <Kent Williams>
* ca8dedd - BUG: Dicom method for Dir Cosines made non-orthogonal
directions (4 months ago) <Kent Williams>
* 9c530ae - COMP: Fix all valid cppcheck warnings in "ITK/Module" directory
(5 months ago) <Ali Ghayoor>
* e081d83 - ENH: Add DCMTKImageIO to ITK (10 months ago) <Kent Williams>
on master branch are:
* d30bd1f - BUG: Row/Column assignment into ImageDimensions was wrong (6
days ago) <Kent Williams>
* 4207729 - ENH: Accomodate Philips 4D Multiframe DICOM files (6 weeks ago)
<Kent Williams>
* df53542 - BUG: Need to set 3rd dir cosine for DICOM images (6 weeks ago)
<Kent Williams>
* ca8dedd - BUG: Dicom method for Dir Cosines made non-orthogonal
directions (4 months ago) <Kent Williams>
* 9c530ae - COMP: Fix all valid cppcheck warnings in "ITK/Module" directory
(5 months ago) <Ali Ghayoor>
* e081d83 - ENH: Add DCMTKImageIO to ITK (10 months ago) <Kent Williams>
Considering the numPhases variable has been introduced by commit 4207729, I
would suggest to also backport it.
Not sure about "df53542" what would be the implication for Slicer ?
Steve, Kent: Could you comment ?
Thanks
Jc
On Wed, Aug 28, 2013 at 6:38 PM, Jean-Christophe Fillion-Robin <
jchris.fillionr at kitware.com> wrote:
> Hi Matt,
>
> I tried to locally build against the latest commit (3b54bc800) of the
> release branch and ITKv4 failed to build.
>
> Here is the error:
>
> [ 99%] Building CXX object
> Modules/IO/DCMTK/src/CMakeFiles/ITKIODCMTK.dir/itkDCMTKImageIO.cxx.o
> /home/jchris/Projects/Slicer-AHM-Superbuild-Release/ITKv4/Modules/IO/DCMTK/src/itkDCMTKImageIO.cxx:
> In member function ‘virtual void itk::DCMTKImageIO::ReadImageInformation()’:
> /home/jchris/Projects/Slicer-AHM-Superbuild-Release/ITKv4/Modules/IO/DCMTK/src/itkDCMTKImageIO.cxx:270:
> error: ‘numPhases’ was not declared in this scope
> At global scope:
> cc1plus: warning: unrecognized command line option "-Wno-long-double"
> make[2]: ***
> [Modules/IO/DCMTK/src/CMakeFiles/ITKIODCMTK.dir/itkDCMTKImageIO.cxx.o]
> Error 1
> make[1]: *** [Modules/IO/DCMTK/src/CMakeFiles/ITKIODCMTK.dir/all] Error 2
> make: *** [all] Error 2
>
> Jc
>
>
> On Wed, Aug 28, 2013 at 6:14 PM, Jean-Christophe Fillion-Robin <
> jchris.fillionr at kitware.com> wrote:
>
>> Hi Matt,
>>
>> Thanks for backporting these commit to the release branch. Today, I plan
>> on updating the ITK has used by Slicer from 35b90133a7 to 3b54bc800.
>>
>> If you plan on backporting other commits before the end of the day, let
>> me know.
>>
>> Thanks
>> Jc
>>
>>
>> On Wed, Aug 28, 2013 at 5:54 PM, Matt McCormick <
>> matt.mccormick at kitware.com> wrote:
>>
>>> Thanks for the feedback.
>>>
>>> Current list:
>>>
>>> Arnaud Gelas (2):
>>> BUG: Check that region for thread is not empty
>>> BUG: Fix failure in InteractivePause test
>>>
>>> Dirk Padfield (1):
>>> BUG: ConstPointer assigned to non-const raw pointer
>>>
>>> Jim Miller (2):
>>> BUG: GDCMImageIO ignore image orienations from MetaDataDictionary
>>> BUG: Two tests were writing to same filename.
>>>
>>> Jonathan Guinet (1):
>>> BUG: {Opening,Closing}ByReconstructionImageFilter information
>>> propagation
>>>
>>> Kent Williams (2):
>>> BUG: Guard against Divide by Zero
>>> BUG: Row/Column assignment into ImageDimensions was wrong
>>>
>>> Matthew McCormick (7):
>>> BUG: Add missing ITKOpenJPEG dependency for ITKReview Module.
>>> COMP: ITKOpenJPEG EXCLUDE_FROM_ALL.
>>> BUG: Fix Module_Review enable with a single configure.
>>> COMP: Do not try to include float.h for MinGW.
>>> BUG: itkSingleLevelSetsv4WhitakerImage2DTest output clobber.
>>> COMP: Avoid MetaIO config conflict with USE_SYSTEM_GDCM.
>>>
>>> Xiaoxiao Liu (4):
>>> ENH: Exclude ITKGDCM module when system GDCM is ON.
>>> BUG: A fix for using sys installed GDCM.
>>> COMP: New baseline image for MultiResImageRegistrationTest.
>>>
>>> On Wed, Aug 28, 2013 at 2:10 PM, Johnson, Hans J <hans-johnson at uiowa.edu>
>>> wrote:
>>> > Matt,
>>> >
>>> > Kent's changes are definitely a good candidate. It was clearly a bug
>>> that
>>> > rarely affects the results (due to most data being square). But for
>>> > non-square data it was a bug.
>>> >
>>> > Hans
>>> >
>>> >
>>> > On 8/28/13 8:38 AM, "Bradley Lowekamp" <blowekamp at mail.nih.gov> wrote:
>>> >
>>> >>Matt,
>>> >>
>>> >>I believe the Slicer developers were talking about Jim's GDCM patches
>>> >>would be good in the release branch.
>>> >>
>>> >>Also it looked like these from Gordon and Kent may be import IO fixes
>>> as
>>> >>well:
>>> >>> BUG: airOneLinify() infinite loop, synch w/ Teem for its 1.11.1
>>> release
>>> >>> BUG: Row/Column assignment into ImageDimensions was wrong
>>> >>
>>> >>
>>> >>Brad
>>> >>
>>> >>On Aug 28, 2013, at 12:22 AM, Matt McCormick <
>>> matt.mccormick at kitware.com>
>>> >>wrote:
>>> >>
>>> >>> Hi,
>>> >>>
>>> >>> Requesting feedback for patches to include on the release branch for
>>> >>>v4.4.2.
>>> >>>
>>> >>>
>>> >>> Currently:
>>> >>>
>>> >>> Matthew McCormick (3):
>>> >>> BUG: Add missing ITKOpenJPEG dependency for ITKReview Module.
>>> >>> COMP: ITKOpenJPEG EXCLUDE_FROM_ALL.
>>> >>> BUG: Fix Module_Review enable with a single configure.
>>> >>>
>>> >>> Sean McBride (1):
>>> >>> COMP: Fixed compiler error in C++11
>>> >>>
>>> >>> Xiaoxiao Liu (1):
>>> >>> BUG: Exclude ITKReview when ITK_USE_REVIEW if off.
>>> >>>
>>> >>> Although the last one will be reverted to prevent unexpected behavior
>>> >>> on a bugfix release.
>>> >>>
>>> >>>
>>> >>>
>>> >>> Patches since v4.4.1 release:
>>> >>>
>>> >>> Ali Ghayoor (3):
>>> >>> ENH: transform reader/writer filters are templated on output
>>> >>> precision type
>>> >>> BUG: Fix memory leak error in itkHDF5TransformIO
>>> >>> DOC: Migration guide is updated for multi precision of ITK
>>> >>>
>>> >>> Arnaud Gelas (9):
>>> >>> BUG: Check that region for thread is not empty
>>> >>> COMP: use concept checking instead of runtime checking
>>> >>> BUG: Fix failure in InteractivePause test
>>> >>> ENH: updating level sets sparse layer visualization
>>> >>> ENH: Upgrade doxygen config file
>>> >>> BUG: fix KWStyle errors in itkVTKVisualize* files
>>> >>> BUG: Fix visualization of 3D level-sets
>>> >>> ENH: Add Concept checking for 2D Visualization
>>> >>> ENH: Use partial template specialization for iso value vis
>>> >>>
>>> >>> Bill Lorensen (1):
>>> >>> ENH: Reduce test times for Debug builds
>>> >>>
>>> >>> Brad King (1):
>>> >>> MetaIO: Removed the deprecated _CM24 CMake variables
>>> >>>
>>> >>> Bradley Lowekamp (14):
>>> >>> ENH: Enabling shared IO modules on windows
>>> >>> DOC: adding Examples directory to ITK Doxygen
>>> >>> DOC: remove explicit doxygen example commands now automatically
>>> >>>added
>>> >>> BUG: add installation of Export headers
>>> >>> BUG: Remove ENABLED_SHARED option for IOSpatialObjects module
>>> >>> BUG: Fix linking of factory register method on static windows
>>> >>> STYLE: Fix some style errors reported in continuous test
>>> >>> BUG: Remove Spurious testing file
>>> >>> COMP: Use relative path for generate output header parameter
>>> >>> BUG: Enable slice-by-slice streaming for ShrinkImageFilter
>>> >>> STYLE: Fix ShrinkImageStreamingTest style
>>> >>> PERF: Flip filter use increment in scanline direction
>>> >>> PERF: Additional FlipImageFilter performance by using input
>>> >>>iterator
>>> >>> PERF: Move test to IntegratedTest directory
>>> >>>
>>> >>> Brian Helba (10):
>>> >>> STYLE: Unify style of "operator delete[]"
>>> >>> STYLE: Remove superfluous return statements at the end of void
>>> >>>functions
>>> >>> STYLE: Fix miscellaneous KWStyle errors
>>> >>> ENH: Remove superfluous IMMEDIATE option from CMake
>>> CONFIGURE_FILE
>>> >>> STYLE: Replace Unicode in ITK source with ASCII homoglyphs
>>> >>> ENH: Use MINC API to free memory allocated by MINC
>>> >>> PERF: Allow delete of NULL pointers
>>> >>> PERF: Refactor some deletion code
>>> >>> ENH: Refactor KWStyle testing
>>> >>> COMP: Make find_package usage compatible with < CMake-2.8.8
>>> >>>
>>> >>> C Cagatay Bilgin (1):
>>> >>> DOC: Modify ShapeLabelObject comments.
>>> >>>
>>> >>> Cyrille Faucheux (1):
>>> >>> BUG: Fix support for RLE-compressed & upper-left BMP.
>>> >>>
>>> >>> Dirk Padfield (2):
>>> >>> BUG: ConstPointer assigned to non-const raw pointer
>>> >>> ENH: Otsu code replaced with OtsuMultiple call
>>> >>>
>>> >>> Gordon Kindlmann (1):
>>> >>> BUG: airOneLinify() infinite loop, synch w/ Teem for its 1.11.1
>>> >>>release
>>> >>>
>>> >>> Irina Vidal-Migallon (3):
>>> >>> ENH: Remote module: GPU and CPU Smoothing recursive YVV Gaussian
>>> >>>Filter
>>> >>> ENH: Remote module: GPU and CPU Smoothing recursive YVV Gaussian
>>> >>>Filter
>>> >>> ENH: YVV remote module - Add EXCLUDE_FROM_ALL option to
>>> itk_module.
>>> >>>
>>> >>> Jim Miller (2):
>>> >>> BUG: GDCMImageIO ignore image orienations from
>>> MetaDataDictionary
>>> >>> BUG: Two tests were writing to same filename.
>>> >>>
>>> >>> Jonathan Guinet (1):
>>> >>> BUG: {Opening,Closing}ByReconstructionImageFilter information
>>> >>>propagation
>>> >>>
>>> >>> Kent Williams (2):
>>> >>> BUG: Guard against Divide by Zero
>>> >>> BUG: Row/Column assignment into ImageDimensions was wrong
>>> >>>
>>> >>> Kishore Mosaliganti (6):
>>> >>> ENH: Allow visualization of initial level-set
>>> >>> ENH: Add Set/GetNumberOfThreads for evolution
>>> >>> ENH: New binary mask term with test
>>> >>> ENH: Set/Get number of threads for Whitaker evolution class
>>> >>> BUG: Non-square images mesh not specified correctly
>>> >>> ENH: Set the scaling factor of the level-set function
>>> >>>
>>> >>> Luis Ibanez (4):
>>> >>> STYLE: Fixed miscelaneous style errors.
>>> >>> DOC: Removed Doxygen \example tags for Tests.
>>> >>> COMP: Fix warnings in matrix division by scalar.
>>> >>> COMP: Attempt to fix warning about \param.
>>> >>>
>>> >>> Mark Hiner (1):
>>> >>> STYLE: update SCIFIO module name
>>> >>>
>>> >>> Matthew McCormick (23):
>>> >>> BUG: Add missing ITKOpenJPEG dependency for ITKReview Module.
>>> >>> COMP: ITKOpenJPEG EXCLUDE_FROM_ALL.
>>> >>> COMP: Fix invalid Doxygen LaTeX formula.
>>> >>> BUG: Fix Module_Review enable with a single configure.
>>> >>> COMP: Wrap cost functions for templated precision.
>>> >>> BUG: Fix Module_Review enable with a single configure.
>>> >>> DOC: Fix GradientDescentOptimizer doc grammar.
>>> >>> BUG: Using consistent naming for Transform template name change.
>>> >>> BUG: Remove unused QUASI_NEWTON_STEP_ERROR.
>>> >>> COMP: Do not try to include float.h for MinGW.
>>> >>> STYLE: TScalarType -> TScalar
>>> >>> COMP: Fix NIFTI CMake variable separation warning.
>>> >>> ENH: Use Transform::Clone() in ImageToImageMetric.
>>> >>> COMP: Remove redundant Typename structs. #3195.
>>> >>> STYLE: Fix include guard in level set visualization.
>>> >>> ENH: Use file(COPY .. instead of exec_process.
>>> >>> COMP: Fix transform wrapping errors with ITK_WRAP_double OFF.
>>> >>> DOC: Fix spelling errors in FourierDescriptors1.cxx.
>>> >>> BUG: Fix ITK_USE_REVIEW compatibility set syntax.
>>> >>> COMP: Avoid MetaIO config conflict with USE_SYSTEM_GDCM.
>>> >>> BUG: itkSingleLevelSetsv4WhitakerImage2DTest output clobber.
>>> >>> ENH: Test conversion writing float transform with templateless
>>> >>>writer.
>>> >>> BUG: BMPImageIO buffer size computation.
>>> >>>
>>> >>> Nick Tustison (1):
>>> >>> ENH: Added B-spline registration test.
>>> >>>
>>> >>> Sean McBride (1):
>>> >>> COMP: Fixed compiler error in C++11
>>> >>>
>>> >>> Sureerat Reaungamornrat (1):
>>> >>> ENH: Make SetFixedImageRegion a virtual function
>>> >>>
>>> >>> Taylor Braun-Jones (1):
>>> >>> COMP: Remove unused TransformFileWriter::m_Precision ivar
>>> >>>
>>> >>> Xiaoxiao Liu (11):
>>> >>> COMP: Relax tolerance for a regression test.
>>> >>> ENH: Exclude ITKGDCM module when system GDCM is ON.
>>> >>> BUG: Exclude ITKReview when ITK_USE_REVIEW if off.
>>> >>> BUG: A fix for using sys installed GDCM.
>>> >>> BUG: ITK_USE_Review did not turn Review module ON.
>>> >>> ENH: Simplify the steps to build remote modules.
>>> >>> ENH: Turn remote module LSTK off by default.
>>> >>> ENH: Deprecate ITK_USE_REVIEW.
>>> >>> DOC: Migration guide for ITK_USE_REVIEW deprecation.
>>> >>> ENH: Remote module names need to be consistent.
>>> >>> COMP: New baseline image for MultiResImageRegistrationTest.
>>> >>>
>>> >>>
>>> >>>
>>> >>> Planned to include for the bugfix release if they apply cleanly on
>>> the
>>> >>> release branch:
>>> >>>
>>> >>>
>>> >>> Arnaud Gelas:
>>> >>> BUG: Check that region for thread is not empty
>>> >>> BUG: Fix failure in InteractivePause test
>>> >>>
>>> >>> Dirk Padfield:
>>> >>> BUG: ConstPointer assigned to non-const raw pointer
>>> >>>
>>> >>> Jim Miller:
>>> >>> BUG: GDCMImageIO ignore image orienations from
>>> MetaDataDictionary
>>> >>> BUG: Two tests were writing to same filename.
>>> >>>
>>> >>> Jonathan Guinet:
>>> >>> BUG: {Opening,Closing}ByReconstructionImageFilter information
>>> >>>propagation
>>> >>>
>>> >>> Kent Williams:
>>> >>> BUG: Guard against Divide by Zero
>>> >>> BUG: Row/Column assignment into ImageDimensions was wrong
>>> >>>
>>> >>> Matthew McCormick:
>>> >>> COMP: Do not try to include float.h for MinGW.
>>> >>> COMP: Remove redundant Typename structs. #3195.
>>> >>> BUG: itkSingleLevelSetsv4WhitakerImage2DTest output clobber.
>>> >>>
>>> >>> Sean McBride:
>>> >>> COMP: Fixed compiler error in C++11
>>> >>>
>>> >>> Xiaoxiao Liu:
>>> >>> COMP: Relax tolerance for a regression test.
>>> >>> ENH: Exclude ITKGDCM module when system GDCM is ON.
>>> >>> BUG: A fix for using sys installed GDCM.
>>> >>> COMP: New baseline image for MultiResImageRegistrationTest.
>>> >>>
>>> >>>
>>> >>>
>>> >>> Please reply in this thread if the proposed additional patches are
>>> not
>>> >>> simple bug fixes that address critical issues or if some patches were
>>> >>> left out.
>>> >>>
>>> >>> Thanks,
>>> >>> Matt
>>> >>> _______________________________________________
>>> >>> Powered by www.kitware.com
>>> >>>
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>>> >>> http://www.kitware.com/opensource/opensource.html
>>> >>>
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>>> >>> http://kitware.com/products/protraining.php
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>>> >>> http://www.itk.org/Wiki/ITK_FAQ
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