[Insight-developers] Patches for v4.4.2 point release

Matt McCormick matt.mccormick at kitware.com
Wed Aug 28 23:52:48 EDT 2013


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
<jchris.fillionr at kitware.com> 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
> <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
>>>>> >>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
>>>>> >
>>>>> >
>>>>> >
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>>>>> Visit other Kitware open-source projects at
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>>>>> Kitware offers ITK Training Courses, for more information visit:
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>>>>> Please keep messages on-topic and check the ITK FAQ at:
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>>>>
>>>>
>>>>
>>>>
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>>>
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>>
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