<div dir="ltr">That patch should fix the release branch: <div><br></div><div><div>diff --git a/Modules/IO/DCMTK/src/itkDCMTKImageIO.cxx b/Modules/IO/DCMTK/src/itkDCMTKImageIO.cxx</div><div>index ee107a0..0f2abdd 100644</div>
<div>--- a/Modules/IO/DCMTK/src/itkDCMTKImageIO.cxx</div><div>+++ b/Modules/IO/DCMTK/src/itkDCMTKImageIO.cxx</div><div>@@ -267,15 +267,8 @@ void DCMTKImageIO::ReadImageInformation()</div><div> reader.GetDimensions(rows,columns);</div>
<div> this->m_Dimensions[0] = columns;</div><div> this->m_Dimensions[1] = rows;</div><div>- if(numPhases == 1)</div><div>- {</div><div>- this->m_Dimensions[2] = reader.GetFrameCount();</div><div>- }</div>
<div>- else</div><div>- {</div><div>- this->m_Dimensions[2] = reader.GetFrameCount() / numPhases;</div><div>- this->m_Dimensions[3] = numPhases;</div><div>- }</div><div>+ this->m_Dimensions[2] = reader.GetFrameCount();</div>
<div>+</div><div> vnl_vector<double> rowDirection(3),columnDirection(3),sliceDirection(3);</div><div> reader.GetDirCosines(rowDirection,columnDirection,sliceDirection);</div><div> // orthogonalize</div></div>
</div>
<div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Aug 28, 2013 at 6:49 PM, Jean-Christophe Fillion-Robin <span dir="ltr"><<a href="mailto:jchris.fillionr@kitware.com" target="_blank">jchris.fillionr@kitware.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Matt, <div><br></div><div>The commits associated with file Modules/IO/DCMTK/src/itkDCMTKImageIO.cxx</div>
<div><br></div><div>on release branch are:</div><div><br></div><div>
<div>* 376aeec - BUG: Row/Column assignment into ImageDimensions was wrong (7 hours ago) <Kent Williams></div><div>* ca8dedd - BUG: Dicom method for Dir Cosines made non-orthogonal directions (4 months ago) <Kent Williams></div>
<div>* 9c530ae - COMP: Fix all valid cppcheck warnings in "ITK/Module" directory (5 months ago) <Ali Ghayoor></div><div>* e081d83 - ENH: Add DCMTKImageIO to ITK (10 months ago) <Kent Williams></div>
<div>
<br></div><div><br></div><div>on master branch are:</div><div><br></div><div><div>* d30bd1f - BUG: Row/Column assignment into ImageDimensions was wrong (6 days ago) <Kent Williams></div><div>* 4207729 - ENH: Accomodate Philips 4D Multiframe DICOM files (6 weeks ago) <Kent Williams></div>
<div>* df53542 - BUG: Need to set 3rd dir cosine for DICOM images (6 weeks ago) <Kent Williams></div><div>* ca8dedd - BUG: Dicom method for Dir Cosines made non-orthogonal directions (4 months ago) <Kent Williams></div>
<div>* 9c530ae - COMP: Fix all valid cppcheck warnings in "ITK/Module" directory (5 months ago) <Ali Ghayoor></div><div>* e081d83 - ENH: Add DCMTKImageIO to ITK (10 months ago) <Kent Williams></div>
<div>
<br></div><div><br></div><div>Considering the <span style="font-family:arial,sans-serif;font-size:12.800000190734863px">numPhases variable has been introduced by commit </span>4207729, I would suggest to also backport it.</div>
<div><br></div><div>Not sure about "df53542" what would be the implication for Slicer ?</div><div><br></div><div>Steve, Kent: Could you comment ?</div><div><br></div><div>Thanks</div><span class="HOEnZb"><font color="#888888">
<div>Jc</div></font></span></div></div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Aug 28, 2013 at 6:38 PM, Jean-Christophe Fillion-Robin <span dir="ltr"><<a href="mailto:jchris.fillionr@kitware.com" target="_blank">jchris.fillionr@kitware.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Matt, <div><br></div><div>I tried to locally build against the latest commit (<span style="font-family:arial,sans-serif;font-size:12.800000190734863px">3b54bc800</span>) of the release branch and ITKv4 failed to build. </div>
<div><br></div><div>Here is the error: </div><div><br></div><div><div>[ 99%] Building CXX object Modules/IO/DCMTK/src/CMakeFiles/ITKIODCMTK.dir/itkDCMTKImageIO.cxx.o</div><div>/home/jchris/Projects/Slicer-AHM-Superbuild-Release/ITKv4/Modules/IO/DCMTK/src/itkDCMTKImageIO.cxx: In member function ‘virtual void itk::DCMTKImageIO::ReadImageInformation()’:</div>
<div>/home/jchris/Projects/Slicer-AHM-Superbuild-Release/ITKv4/Modules/IO/DCMTK/src/itkDCMTKImageIO.cxx:270: error: ‘numPhases’ was not declared in this scope</div><div>At global scope:</div><div>cc1plus: warning: unrecognized command line option "-Wno-long-double"</div>
<div>make[2]: *** [Modules/IO/DCMTK/src/CMakeFiles/ITKIODCMTK.dir/itkDCMTKImageIO.cxx.o] Error 1</div><div>make[1]: *** [Modules/IO/DCMTK/src/CMakeFiles/ITKIODCMTK.dir/all] Error 2</div><div>make: *** [all] Error 2</div>
<span><font color="#888888"><div>
<br></div><div>Jc</div></font></span></div></div><div><div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Aug 28, 2013 at 6:14 PM, Jean-Christophe Fillion-Robin <span dir="ltr"><<a href="mailto:jchris.fillionr@kitware.com" target="_blank">jchris.fillionr@kitware.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Matt, <div><br></div><div>Thanks for backporting these commit to the release branch. Today, I plan on updating the ITK has used by Slicer from 35b90133a7 to 3b54bc800. </div>
<div><br></div><div>
If you plan on backporting other commits before the end of the day, let me know. </div><div><br></div><div>Thanks</div><div>Jc</div></div><div class="gmail_extra"><div><div><br><br><div class="gmail_quote">On Wed, Aug 28, 2013 at 5:54 PM, Matt McCormick <span dir="ltr"><<a href="mailto:matt.mccormick@kitware.com" target="_blank">matt.mccormick@kitware.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Thanks for the feedback.<br>
<br>
Current list:<br>
<br>
Arnaud Gelas (2):<br>
<div> BUG: Check that region for thread is not empty<br>
BUG: Fix failure in InteractivePause test<br>
<br>
</div>Dirk Padfield (1):<br>
<div> BUG: ConstPointer assigned to non-const raw pointer<br>
<br>
</div><div>Jim Miller (2):<br>
BUG: GDCMImageIO ignore image orienations from MetaDataDictionary<br>
BUG: Two tests were writing to same filename.<br>
<br>
Jonathan Guinet (1):<br>
BUG: {Opening,Closing}ByReconstructionImageFilter information propagation<br>
<br>
Kent Williams (2):<br>
BUG: Guard against Divide by Zero<br>
BUG: Row/Column assignment into ImageDimensions was wrong<br>
<br>
</div>Matthew McCormick (7):<br>
<div> BUG: Add missing ITKOpenJPEG dependency for ITKReview Module.<br>
COMP: ITKOpenJPEG EXCLUDE_FROM_ALL.<br>
BUG: Fix Module_Review enable with a single configure.<br>
</div><div> COMP: Do not try to include float.h for MinGW.<br>
</div> BUG: itkSingleLevelSetsv4WhitakerImage2DTest output clobber.<br>
<div> COMP: Avoid MetaIO config conflict with USE_SYSTEM_GDCM.<br>
<br>
</div>Xiaoxiao Liu (4):<br>
<div> ENH: Exclude ITKGDCM module when system GDCM is ON.<br>
BUG: A fix for using sys installed GDCM.<br>
COMP: New baseline image for MultiResImageRegistrationTest.<br>
<br>
</div><div><div>On Wed, Aug 28, 2013 at 2:10 PM, Johnson, Hans J <<a href="mailto:hans-johnson@uiowa.edu" target="_blank">hans-johnson@uiowa.edu</a>> wrote:<br>
> Matt,<br>
><br>
> Kent's changes are definitely a good candidate. It was clearly a bug that<br>
> rarely affects the results (due to most data being square). But for<br>
> non-square data it was a bug.<br>
><br>
> Hans<br>
><br>
><br>
> On 8/28/13 8:38 AM, "Bradley Lowekamp" <<a href="mailto:blowekamp@mail.nih.gov" target="_blank">blowekamp@mail.nih.gov</a>> wrote:<br>
><br>
>>Matt,<br>
>><br>
>>I believe the Slicer developers were talking about Jim's GDCM patches<br>
>>would be good in the release branch.<br>
>><br>
>>Also it looked like these from Gordon and Kent may be import IO fixes as<br>
>>well:<br>
>>> BUG: airOneLinify() infinite loop, synch w/ Teem for its 1.11.1 release<br>
>>> BUG: Row/Column assignment into ImageDimensions was wrong<br>
>><br>
>><br>
>>Brad<br>
>><br>
>>On Aug 28, 2013, at 12:22 AM, Matt McCormick <<a href="mailto:matt.mccormick@kitware.com" target="_blank">matt.mccormick@kitware.com</a>><br>
>>wrote:<br>
>><br>
>>> Hi,<br>
>>><br>
>>> Requesting feedback for patches to include on the release branch for<br>
>>>v4.4.2.<br>
>>><br>
>>><br>
>>> Currently:<br>
>>><br>
>>> Matthew McCormick (3):<br>
>>> BUG: Add missing ITKOpenJPEG dependency for ITKReview Module.<br>
>>> COMP: ITKOpenJPEG EXCLUDE_FROM_ALL.<br>
>>> BUG: Fix Module_Review enable with a single configure.<br>
>>><br>
>>> Sean McBride (1):<br>
>>> COMP: Fixed compiler error in C++11<br>
>>><br>
>>> Xiaoxiao Liu (1):<br>
>>> BUG: Exclude ITKReview when ITK_USE_REVIEW if off.<br>
>>><br>
>>> Although the last one will be reverted to prevent unexpected behavior<br>
>>> on a bugfix release.<br>
>>><br>
>>><br>
>>><br>
>>> Patches since v4.4.1 release:<br>
>>><br>
>>> Ali Ghayoor (3):<br>
>>> ENH: transform reader/writer filters are templated on output<br>
>>> precision type<br>
>>> BUG: Fix memory leak error in itkHDF5TransformIO<br>
>>> DOC: Migration guide is updated for multi precision of ITK<br>
>>><br>
>>> Arnaud Gelas (9):<br>
>>> BUG: Check that region for thread is not empty<br>
>>> COMP: use concept checking instead of runtime checking<br>
>>> BUG: Fix failure in InteractivePause test<br>
>>> ENH: updating level sets sparse layer visualization<br>
>>> ENH: Upgrade doxygen config file<br>
>>> BUG: fix KWStyle errors in itkVTKVisualize* files<br>
>>> BUG: Fix visualization of 3D level-sets<br>
>>> ENH: Add Concept checking for 2D Visualization<br>
>>> ENH: Use partial template specialization for iso value vis<br>
>>><br>
>>> Bill Lorensen (1):<br>
>>> ENH: Reduce test times for Debug builds<br>
>>><br>
>>> Brad King (1):<br>
>>> MetaIO: Removed the deprecated _CM24 CMake variables<br>
>>><br>
>>> Bradley Lowekamp (14):<br>
>>> ENH: Enabling shared IO modules on windows<br>
>>> DOC: adding Examples directory to ITK Doxygen<br>
>>> DOC: remove explicit doxygen example commands now automatically<br>
>>>added<br>
>>> BUG: add installation of Export headers<br>
>>> BUG: Remove ENABLED_SHARED option for IOSpatialObjects module<br>
>>> BUG: Fix linking of factory register method on static windows<br>
>>> STYLE: Fix some style errors reported in continuous test<br>
>>> BUG: Remove Spurious testing file<br>
>>> COMP: Use relative path for generate output header parameter<br>
>>> BUG: Enable slice-by-slice streaming for ShrinkImageFilter<br>
>>> STYLE: Fix ShrinkImageStreamingTest style<br>
>>> PERF: Flip filter use increment in scanline direction<br>
>>> PERF: Additional FlipImageFilter performance by using input<br>
>>>iterator<br>
>>> PERF: Move test to IntegratedTest directory<br>
>>><br>
>>> Brian Helba (10):<br>
>>> STYLE: Unify style of "operator delete[]"<br>
>>> STYLE: Remove superfluous return statements at the end of void<br>
>>>functions<br>
>>> STYLE: Fix miscellaneous KWStyle errors<br>
>>> ENH: Remove superfluous IMMEDIATE option from CMake CONFIGURE_FILE<br>
>>> STYLE: Replace Unicode in ITK source with ASCII homoglyphs<br>
>>> ENH: Use MINC API to free memory allocated by MINC<br>
>>> PERF: Allow delete of NULL pointers<br>
>>> PERF: Refactor some deletion code<br>
>>> ENH: Refactor KWStyle testing<br>
>>> COMP: Make find_package usage compatible with < CMake-2.8.8<br>
>>><br>
>>> C Cagatay Bilgin (1):<br>
>>> DOC: Modify ShapeLabelObject comments.<br>
>>><br>
>>> Cyrille Faucheux (1):<br>
>>> BUG: Fix support for RLE-compressed & upper-left BMP.<br>
>>><br>
>>> Dirk Padfield (2):<br>
>>> BUG: ConstPointer assigned to non-const raw pointer<br>
>>> ENH: Otsu code replaced with OtsuMultiple call<br>
>>><br>
>>> Gordon Kindlmann (1):<br>
>>> BUG: airOneLinify() infinite loop, synch w/ Teem for its 1.11.1<br>
>>>release<br>
>>><br>
>>> Irina Vidal-Migallon (3):<br>
>>> ENH: Remote module: GPU and CPU Smoothing recursive YVV Gaussian<br>
>>>Filter<br>
>>> ENH: Remote module: GPU and CPU Smoothing recursive YVV Gaussian<br>
>>>Filter<br>
>>> ENH: YVV remote module - Add EXCLUDE_FROM_ALL option to itk_module.<br>
>>><br>
>>> Jim Miller (2):<br>
>>> BUG: GDCMImageIO ignore image orienations from MetaDataDictionary<br>
>>> BUG: Two tests were writing to same filename.<br>
>>><br>
>>> Jonathan Guinet (1):<br>
>>> BUG: {Opening,Closing}ByReconstructionImageFilter information<br>
>>>propagation<br>
>>><br>
>>> Kent Williams (2):<br>
>>> BUG: Guard against Divide by Zero<br>
>>> BUG: Row/Column assignment into ImageDimensions was wrong<br>
>>><br>
>>> Kishore Mosaliganti (6):<br>
>>> ENH: Allow visualization of initial level-set<br>
>>> ENH: Add Set/GetNumberOfThreads for evolution<br>
>>> ENH: New binary mask term with test<br>
>>> ENH: Set/Get number of threads for Whitaker evolution class<br>
>>> BUG: Non-square images mesh not specified correctly<br>
>>> ENH: Set the scaling factor of the level-set function<br>
>>><br>
>>> Luis Ibanez (4):<br>
>>> STYLE: Fixed miscelaneous style errors.<br>
>>> DOC: Removed Doxygen \example tags for Tests.<br>
>>> COMP: Fix warnings in matrix division by scalar.<br>
>>> COMP: Attempt to fix warning about \param.<br>
>>><br>
>>> Mark Hiner (1):<br>
>>> STYLE: update SCIFIO module name<br>
>>><br>
>>> Matthew McCormick (23):<br>
>>> BUG: Add missing ITKOpenJPEG dependency for ITKReview Module.<br>
>>> COMP: ITKOpenJPEG EXCLUDE_FROM_ALL.<br>
>>> COMP: Fix invalid Doxygen LaTeX formula.<br>
>>> BUG: Fix Module_Review enable with a single configure.<br>
>>> COMP: Wrap cost functions for templated precision.<br>
>>> BUG: Fix Module_Review enable with a single configure.<br>
>>> DOC: Fix GradientDescentOptimizer doc grammar.<br>
>>> BUG: Using consistent naming for Transform template name change.<br>
>>> BUG: Remove unused QUASI_NEWTON_STEP_ERROR.<br>
>>> COMP: Do not try to include float.h for MinGW.<br>
>>> STYLE: TScalarType -> TScalar<br>
>>> COMP: Fix NIFTI CMake variable separation warning.<br>
>>> ENH: Use Transform::Clone() in ImageToImageMetric.<br>
>>> COMP: Remove redundant Typename structs. #3195.<br>
>>> STYLE: Fix include guard in level set visualization.<br>
>>> ENH: Use file(COPY .. instead of exec_process.<br>
>>> COMP: Fix transform wrapping errors with ITK_WRAP_double OFF.<br>
>>> DOC: Fix spelling errors in FourierDescriptors1.cxx.<br>
>>> BUG: Fix ITK_USE_REVIEW compatibility set syntax.<br>
>>> COMP: Avoid MetaIO config conflict with USE_SYSTEM_GDCM.<br>
>>> BUG: itkSingleLevelSetsv4WhitakerImage2DTest output clobber.<br>
>>> ENH: Test conversion writing float transform with templateless<br>
>>>writer.<br>
>>> BUG: BMPImageIO buffer size computation.<br>
>>><br>
>>> Nick Tustison (1):<br>
>>> ENH: Added B-spline registration test.<br>
>>><br>
>>> Sean McBride (1):<br>
>>> COMP: Fixed compiler error in C++11<br>
>>><br>
>>> Sureerat Reaungamornrat (1):<br>
>>> ENH: Make SetFixedImageRegion a virtual function<br>
>>><br>
>>> Taylor Braun-Jones (1):<br>
>>> COMP: Remove unused TransformFileWriter::m_Precision ivar<br>
>>><br>
>>> Xiaoxiao Liu (11):<br>
>>> COMP: Relax tolerance for a regression test.<br>
>>> ENH: Exclude ITKGDCM module when system GDCM is ON.<br>
>>> BUG: Exclude ITKReview when ITK_USE_REVIEW if off.<br>
>>> BUG: A fix for using sys installed GDCM.<br>
>>> BUG: ITK_USE_Review did not turn Review module ON.<br>
>>> ENH: Simplify the steps to build remote modules.<br>
>>> ENH: Turn remote module LSTK off by default.<br>
>>> ENH: Deprecate ITK_USE_REVIEW.<br>
>>> DOC: Migration guide for ITK_USE_REVIEW deprecation.<br>
>>> ENH: Remote module names need to be consistent.<br>
>>> COMP: New baseline image for MultiResImageRegistrationTest.<br>
>>><br>
>>><br>
>>><br>
>>> Planned to include for the bugfix release if they apply cleanly on the<br>
>>> release branch:<br>
>>><br>
>>><br>
>>> Arnaud Gelas:<br>
>>> BUG: Check that region for thread is not empty<br>
>>> BUG: Fix failure in InteractivePause test<br>
>>><br>
>>> Dirk Padfield:<br>
>>> BUG: ConstPointer assigned to non-const raw pointer<br>
>>><br>
>>> Jim Miller:<br>
>>> BUG: GDCMImageIO ignore image orienations from MetaDataDictionary<br>
>>> BUG: Two tests were writing to same filename.<br>
>>><br>
>>> Jonathan Guinet:<br>
>>> BUG: {Opening,Closing}ByReconstructionImageFilter information<br>
>>>propagation<br>
>>><br>
>>> Kent Williams:<br>
>>> BUG: Guard against Divide by Zero<br>
>>> BUG: Row/Column assignment into ImageDimensions was wrong<br>
>>><br>
>>> Matthew McCormick:<br>
>>> COMP: Do not try to include float.h for MinGW.<br>
>>> COMP: Remove redundant Typename structs. #3195.<br>
>>> BUG: itkSingleLevelSetsv4WhitakerImage2DTest output clobber.<br>
>>><br>
>>> Sean McBride:<br>
>>> COMP: Fixed compiler error in C++11<br>
>>><br>
>>> Xiaoxiao Liu:<br>
>>> COMP: Relax tolerance for a regression test.<br>
>>> ENH: Exclude ITKGDCM module when system GDCM is ON.<br>
>>> BUG: A fix for using sys installed GDCM.<br>
>>> COMP: New baseline image for MultiResImageRegistrationTest.<br>
>>><br>
>>><br>
>>><br>
>>> Please reply in this thread if the proposed additional patches are not<br>
>>> simple bug fixes that address critical issues or if some patches were<br>
>>> left out.<br>
>>><br>
>>> Thanks,<br>
>>> Matt<br>
>>> _______________________________________________<br>
>>> Powered by <a href="http://www.kitware.com" target="_blank">www.kitware.com</a><br>
>>><br>
>>> Visit other Kitware open-source projects at<br>
>>> <a href="http://www.kitware.com/opensource/opensource.html" target="_blank">http://www.kitware.com/opensource/opensource.html</a><br>
>>><br>
>>> Kitware offers ITK Training Courses, for more information visit:<br>
>>> <a href="http://kitware.com/products/protraining.php" target="_blank">http://kitware.com/products/protraining.php</a><br>
>>><br>
>>> Please keep messages on-topic and check the ITK FAQ at:<br>
>>> <a href="http://www.itk.org/Wiki/ITK_FAQ" target="_blank">http://www.itk.org/Wiki/ITK_FAQ</a><br>
>>><br>
>>> Follow this link to subscribe/unsubscribe:<br>
>>> <a href="http://www.itk.org/mailman/listinfo/insight-developers" target="_blank">http://www.itk.org/mailman/listinfo/insight-developers</a><br>
>><br>
>>_______________________________________________<br>
>>Powered by <a href="http://www.kitware.com" target="_blank">www.kitware.com</a><br>
>><br>
>>Visit other Kitware open-source projects at<br>
>><a href="http://www.kitware.com/opensource/opensource.html" target="_blank">http://www.kitware.com/opensource/opensource.html</a><br>
>><br>
>>Kitware offers ITK Training Courses, for more information visit:<br>
>><a href="http://kitware.com/products/protraining.php" target="_blank">http://kitware.com/products/protraining.php</a><br>
>><br>
>>Please keep messages on-topic and check the ITK FAQ at:<br>
>><a href="http://www.itk.org/Wiki/ITK_FAQ" target="_blank">http://www.itk.org/Wiki/ITK_FAQ</a><br>
>><br>
>>Follow this link to subscribe/unsubscribe:<br>
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><br>
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