[Insight-developers] Patches for v4.4.2 point release
Jean-Christophe Fillion-Robin
jchris.fillionr at kitware.com
Wed Aug 28 18:57:17 EDT 2013
That patch should fix the release branch:
diff --git a/Modules/IO/DCMTK/src/itkDCMTKImageIO.cxx
b/Modules/IO/DCMTK/src/itkDCMTKImageIO.cxx
index ee107a0..0f2abdd 100644
--- a/Modules/IO/DCMTK/src/itkDCMTKImageIO.cxx
+++ b/Modules/IO/DCMTK/src/itkDCMTKImageIO.cxx
@@ -267,15 +267,8 @@ void DCMTKImageIO::ReadImageInformation()
reader.GetDimensions(rows,columns);
this->m_Dimensions[0] = columns;
this->m_Dimensions[1] = rows;
- if(numPhases == 1)
- {
- this->m_Dimensions[2] = reader.GetFrameCount();
- }
- else
- {
- this->m_Dimensions[2] = reader.GetFrameCount() / numPhases;
- this->m_Dimensions[3] = numPhases;
- }
+ this->m_Dimensions[2] = reader.GetFrameCount();
+
vnl_vector<double> rowDirection(3),columnDirection(3),sliceDirection(3);
reader.GetDirCosines(rowDirection,columnDirection,sliceDirection);
// orthogonalize
On Wed, Aug 28, 2013 at 6:49 PM, Jean-Christophe Fillion-Robin <
jchris.fillionr at kitware.com> wrote:
> 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
>>>> >>>
>>>> >>> Visit other Kitware open-source projects at
>>>> >>> http://www.kitware.com/opensource/opensource.html
>>>> >>>
>>>> >>> Kitware offers ITK Training Courses, for more information visit:
>>>> >>> http://kitware.com/products/protraining.php
>>>> >>>
>>>> >>> Please keep messages on-topic and check the ITK FAQ at:
>>>> >>> http://www.itk.org/Wiki/ITK_FAQ
>>>> >>>
>>>> >>> Follow this link to subscribe/unsubscribe:
>>>> >>> http://www.itk.org/mailman/listinfo/insight-developers
>>>> >>
>>>> >>_______________________________________________
>>>> >>Powered by www.kitware.com
>>>> >>
>>>> >>Visit other Kitware open-source projects at
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>>>> >>
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>>>> >>
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>>>> >
>>>> >
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