[Insight-developers] Patch for some filters that don't propagate direction cosines

[Kent Williams]

Thanks Peter.  Will you eventually be checking this change into Insight 
when the repository opens up, or should I?

Peter Cech wrote:

>On Tue, Sep 12, 2006 at 09:41:03 -0500, Kent Williams wrote:
>  
>
>>Hans ran into an issue with itk::JoinSeriesImageFilter and 
>>itk::ExtractImageFilter -- they did not propagate the direction cosines 
>>from the input to the output.
>>
>>I have a feeling that this is also the case for a number of the other 
>>filters -- we only notice that they don't set the output Directions when 
>>we try to use them and they're always identity.
>>
>>I can write a simple template function that does the Direction Cosine 
>>assignment between the input and output images, taking into account the 
>>dimensionality of both -- that's what I do in-line with this patch.  
>>Then it can be called from any filter.
>>
>>My question is where I would put this function:
>>
>>1. As a member function of itkImageBase?
>>2. As a free-standing template function in itkImageBase?
>>3. As a member function of itkImageToImageFilter.h
>>4. As a free-standing ""
>>    
>>
>
>I would say 4 as it is unlikely to be used outside image filters and
>does not depend on any member of itkImageToImageFilter. 
>
>  
>
>>5. Something else?
>>    
>>
>
>Namespace itk::ImageToImageFilterDetail
>http://www.itk.org/Doxygen/html/namespaceitk_1_1ImageToImageFilterDetail.html
>
>
>The following patch does not work:
>
>  
>
>>Index: itkExtractImageFilter.txx
>>===================================================================
>>RCS file: /cvsroot/Insight/Insight/Code/BasicFilters/itkExtractImageFilter.txx,v
>>retrieving revision 1.21
>>diff -c -r1.21 itkExtractImageFilter.txx
>>*** itkExtractImageFilter.txx	27 Jan 2006 17:07:07 -0000	1.21
>>--- itkExtractImageFilter.txx	12 Sep 2006 14:40:32 -0000
>>***************
>>*** 200,205 ****
>>--- 200,228 ----
>>          }
>>        }
>>  
>>+     //
>>+     // Copy the direction cosines from the input to the output.
>>+     // On extract the output is always smaller or equal dimension
>>+     // as the input
>>+     typedef typename InputImageType::DirectionType InputDirectionType;
>>+     typedef typename OutputImageType::DirectionType OutputDirectionType;
>>+     InputDirectionType inputDir = inputPtr->GetDirection();
>>+     OutputDirectionType outputDir = outputPtr->GetDirection();
>>+     unsigned inputdim = InputImageType::GetImageDimension();
>>+     unsigned outputdim = OutputImageType::GetImageDimension();
>>+ 
>>+     for(unsigned i = 0; i < inputdim; i++)
>>+       {
>>+       for(unsigned j = 0; j < inputdim; j++)
>>+         {
>>+         if(j < outputdim && i < outputdim)
>>+           {
>>+           outputDir[i][j] = inputDir[i][j];
>>+           }
>>+         }
>>+       }
>>+     outputPtr->SetDirection(outputDir);
>>    
>>
>
>Call to outputPtr->SetDirection(...)
>
>  
>
>>+ 
>>      // set the spacing and origin
>>      outputPtr->SetSpacing( outputSpacing );
>>      outputPtr->SetDirection( outputDirection );
>>    
>>
>
>Another call to outputPtr->SetDirection(...). It overwrites direction
>with stuff prepared in an if-else block just preceding the first lines
>of the patch.
>
>Anyway, this patch is computing output direction incorrectly - it
>ignores collapsed dimensions (or assumes the are always the last ones).
>The current code in CVS is buggy, but I think the attached patch fixes
>it.
>
>Regards,
>Peter Cech
>  
>
>------------------------------------------------------------------------
>
>Index: itkExtractImageFilter.txx
>===================================================================
>RCS file: /cvsroot/Insight/Insight/Code/BasicFilters/itkExtractImageFilter.txx,v
>retrieving revision 1.21
>diff -u -3 -d -r1.21 itkExtractImageFilter.txx
>--- itkExtractImageFilter.txx	27 Jan 2006 17:07:07 -0000	1.21
>+++ itkExtractImageFilter.txx	12 Sep 2006 17:00:03 -0000
>@@ -190,10 +190,15 @@
>           {
>           outputSpacing[nonZeroCount] = inputSpacing[i];
>           outputOrigin[nonZeroCount] = inputOrigin[i];
>+          int nonZeroCount2 = 0;
>           for (unsigned int dim = 0; dim < OutputImageDimension; ++dim)
>             {
>-            outputDirection[nonZeroCount][dim] =
>-              inputDirection[nonZeroCount][dim];
>+            if (m_ExtractionRegion.GetSize()[dim])
>+              {
>+              outputDirection[nonZeroCount][nonZeroCount2] =
>+                inputDirection[nonZeroCount][dim];
>+              ++nonZeroCount2;
>+              }
>             }
>           nonZeroCount++;
>           }
>  
>