Hi Jc, Thank you very much for testing and the investigation!
I did not turn the ITKIODCMTK Module when building and testing, and I missed those errors. It looks like Kent made some more patches before the 4.4.1 release that were not merged until after the release. It is a good thing he writes good tests :-). I added the following: BUG: Need to set 3rd dir cosine for DICOM images DOC: Rename DCMTKException DCMTKExceptionOrErrorReturn ENH: Accomodate Philips 4D Multiframe DICOM files Build/test was verified. The other possible patch to be added depending on tomorrow's dashboard: http://itk.org/gitweb?p=ITK.git;a=commit;h=6c095c513e22730d6b5d185d14338353136a5eb5 This only effects WrapITK. Thanks, Matt On Wed, Aug 28, 2013 at 10:57 PM, Jean-Christophe Fillion-Robin <[email protected]> wrote: > 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 > <[email protected]> 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 >> <[email protected]> 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 >>> <[email protected]> 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 >>>> <[email protected]> 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 >>>>> <[email protected]> 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" <[email protected]> >>>>> > 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 >>>>> >> <[email protected]> >>>>> >>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: >>>>> >>> 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