[Insight-developers] [slicer-devel] bug in vtkITKArchetypeImageSeriesReader and possible improvement in slicer and ITK

[Matt McCormick]

Hi Kevin,

Thanks for proposing your patch and mentioning it on the list.  Your
patches are always welcome.  Instructions for submitting a patch can
be found here:

  http://insightsoftwareconsortium.github.io/ITKBarCamp-doc/CommunitySoftwareProcess/SubmitAPatchToGerrit/index.html

As I understand the problem, (which may be incorrect), a change should
not be necessary on itk::ImageSeriesReader.  itk::ImageFileReader and
itk::ImageSeriesReader are template based, and the output pixel type
is determined by the pixel type of the output image template
parameter, so an OutputImagePixelScalarType does not apply to
itk::ImageSeriesReader.

In vtkITKArchetypeImageSeriesReader.cxx, after determining the correct
imageIO in ::ExecuteInformation(), around line 720, would gathering an
array of NativeScalarTypes to expose to the user of
vtkITKArchetypeImageSeriesReader generate the functionality that is
desired?  Pseudocode:

  this->SliceNativeScalarTypes.resize( this->FileNames.size() );
  for( const_iterator fileNamesIt = this->FileNames.begin(), iterator
scalarTypesIt = this->SliceNativeScalarTypes.begin(); fileNamesIt !=
this->FileNames.end(); ++fileNamesIt, ++scalarTypesIt )
  {
  imageIO->SetFileName( *fileNamesIt );
  imageIO->ReadImageInformation();
  *scalarTypesIt = imageIO->GetComponentType();
  }

Thanks,
Matt

On Fri, Sep 13, 2013 at 3:11 PM, Wang, Kevin <kevin.wang at rmp.uhn.on.ca> wrote:
> Hi slicer,
>
>
>
> I am developing a module in Slicer and I found a bug in
> vtkITKArchetypeImageSeriesReader class. Here is the issue.
>
>
>
> Since dicom utilizes the concept of slope and intercept, the scalar range
> for each 2D slice can be much different. However, in Slicer, the scalar type
> is determined by checking the ComponentType returned by GDCMImageIO which
> only tells the last slice ComponentType in
> vtkITKArchetypeImageSeriesReader.cxx.
>
> I propose to change vtkITKArchetypeImageSeriesReader.cxx as well as the
> itkImageSeriesReader class in ITK. The idea is that the scalar range will be
> checked for each 2D slice in itkImageSeriesReader and then a new variable
> OutputImagePixelScalarType will be set accordingly, then in
> vtkITKArchetypeImageSeriesReader.cxx it will check the
> OutputImagePixelScalarType from the itkImageSeriesReader to correctly
> determine the scalar type.
>
>
>
> If you think this makes sense, I will create an ITK ticket and submit a
> patch to ITK. The slicer patch has to wait until slicer start to use the
> newly patched ITK. I have created a ticket for tracking this:
> http://na-mic.org/Mantis/view.php?id=3386
>
>
>
> Thanks,
>
>
>
> Kevin
>
>
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