[Insight-developers] The 3D vs 2D ImageSeriesWriter mess (Was Re: ImageSeriesWriter + GDCMImageIO)

[Mathieu Malaterre]

Ok, I made another attempt:

$ cvs ci -m"BUG: Attempt to fix segfault. Indeed ITK_Direction comes
in lexical order before ITK_NumberOfDimensions. So changed the name to
ITK_ZDirection. Modify the tricky part of itkImageIOBase.cxx where a
3D images was filled from a 2D image, we cannot copy more value in
SetDirection than what is stored in 'direction'."
? Code/IO/.itkGDCMImageIO.cxx.swp
Committer: Mathieu Malaterre <mathieu.malaterre at gmail.com>
Running style check
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Processing itkGDCMImageIO.cxx



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Processing itkIOCommon.cxx



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Processing itkIOCommon.h



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Processing itkImageIOBase.cxx



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Processing itkImageSeriesWriter.txx



/cvsroot/Insight/Insight/Code/IO/itkGDCMImageIO.cxx,v  <--
Code/IO/itkGDCMImageIO.cxx
new revision: 1.169; previous revision: 1.168
/cvsroot/Insight/Insight/Code/IO/itkIOCommon.cxx,v  <--  Code/IO/itkIOCommon.cxx
new revision: 1.31; previous revision: 1.30
/cvsroot/Insight/Insight/Code/IO/itkIOCommon.h,v  <--  Code/IO/itkIOCommon.h
new revision: 1.29; previous revision: 1.28
/cvsroot/Insight/Insight/Code/IO/itkImageIOBase.cxx,v  <--
Code/IO/itkImageIOBase.cxx
new revision: 1.87; previous revision: 1.86
/cvsroot/Insight/Insight/Code/IO/itkImageSeriesWriter.txx,v  <--
Code/IO/itkImageSeriesWriter.txx
new revision: 1.35; previous revision: 1.34


If this creates more problem, I'll revert both patches.

Thanks

On Thu, Dec 3, 2009 at 2:07 PM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
> Mathieu,
>
> But now 3 tests are failing:
> http://www.cdash.org/CDash/viewTest.php?onlyfailed&buildid=485280
>
> Bill
>
> On Thu, Dec 3, 2009 at 6:37 AM, Mathieu Malaterre
> <mathieu.malaterre at gmail.com> wrote:
>> On Wed, Sep 30, 2009 at 3:44 PM, Daniele E. Domenichelli
>> <daniele.domenichelli at gmail.com> wrote:
>>> Mathieu Malaterre wrote:
>>>>> 2) When I read a DICOM set as a volume that has direction cosines
>>>>> written as:
>>>>>
>>>>>  Ax\Ay\Az\Bx\By\Bz
>>>>>
>>>>> these values are stored in a 3x3 matrix as:
>>>>>
>>>>>  Ax  Bx  Cx
>>>>>  Ay  By  Cy   (where C=AxB)
>>>>>  Az  Bz  Cz
>>>>>
>>>>> When I write back this volume as 2D DICOM, direction cosines are:
>>>>>
>>>>>  Ax\Bx\Cx\Ay\By\Cy
>>>>>
>>>>>
>>>>> The second attached file (GDCMDirectionCosines.diff) should correct this
>>>>> behaviour. (I tested this only for GDCM 2)
>>>>
>>>> This is exactly the opposite of bug 0007748 which was recently applied
>>>> to CVS HEAD
>>>> http://public.kitware.com/cgi-bin/viewcvs.cgi/Code/IO/itkGDCMImageIO.cxx?root=Insight&r1=1.161&r2=1.162
>>>
>>>
>>> Ok now I understand what happened:
>>>
>>> With the first patch (ITK_Direction.diff) I wrote m_Direction in this way:
>>>
>>>
>>> ---
>>>
>>>       ExposeMetaData< DoubleMatrixType >( dict, key, directionMatrix );
>>>        for(int i = 0; i<3; i++)
>>>            for(int j = 0; j<3; j++)
>>>                m_Direction[i][j]=directionMatrix[i][j];
>>>
>>> ---
>>>
>>> but reading in the discussion of bug #7748 I understand that
>>>
>>>> The short hand explanation should be that the member m_Direction of
>>>> itk::GDCMImageIO (inherited from itk::ImageIOBase) is a vector that
>>>> points to vectors, where the first vector contains the direction
>>>> cosines of the image rows, the second the direction cosines of the
>>>> image columns and the third contains the direction cosines of the
>>>> image slices. So, m_Direction[0][0], m_Direction[0][1],
>>>> m_Direction[0][2] are the direction cosines of the image rows.
>>>> itk::GDCMImageIO::m_Direction stores the direction cosines as rows.
>>>
>>> Then m_Direction is transposed and should be written in this way:
>>>
>>> ---
>>>
>>>       ExposeMetaData< DoubleMatrixType >( dict, key, directionMatrix );
>>>        for(int i = 0; i<3; i++)
>>>            for(int j = 0; j<3; j++)
>>>                m_Direction[j][i]=directionMatrix[i][j];
>>>
>>> ---
>>>
>>> I attached a new file to bug #9622
>>
>> I applied your proposed patch : ITK_Direction.diff (and not
>> ITK_Direction2.diff). Thanks !
>>
>> $ cvs ci -m"BUG: 0009622 Thanks to Daniele E. Domenichelli for
>> providing the patch"
>>
>>                                 ~/Kitware/Insight
>> Committer: Mathieu Malaterre <mathieu.malaterre at gmail.com>
>> Running style check
>> Running style check
>> Processing itkGDCMImageIO.cxx
>>
>>
>>
>> Running style check
>> Processing itkIOCommon.cxx
>>
>>
>>
>> Running style check
>> Processing itkIOCommon.h
>>
>>
>>
>> Running style check
>> Processing itkImageSeriesWriter.txx
>>
>>
>>
>> /cvsroot/Insight/Insight/Code/IO/itkGDCMImageIO.cxx,v  <--
>> Code/IO/itkGDCMImageIO.cxx
>> new revision: 1.168; previous revision: 1.167
>> /cvsroot/Insight/Insight/Code/IO/itkIOCommon.cxx,v  <--  Code/IO/itkIOCommon.cxx
>> new revision: 1.30; previous revision: 1.29
>> /cvsroot/Insight/Insight/Code/IO/itkIOCommon.h,v  <--  Code/IO/itkIOCommon.h
>> new revision: 1.28; previous revision: 1.27
>> /cvsroot/Insight/Insight/Code/IO/itkImageSeriesWriter.txx,v  <--
>> Code/IO/itkImageSeriesWriter.txx
>> new revision: 1.34; previous revision: 1.33
>>
>>
>> --
>> Mathieu
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>



-- 
Mathieu