[Insight-developers] Wrong behaviour of ImageFileReader when reading an itk::VectorImage<itk::FixedArray<double, 6>, 3> ?
Benoit Scherrer
benoitscherrer at gmail.com
Thu Jan 20 20:07:51 EST 2011
Ok thanks a lot i will try that!!
Benoit
On Wed, Jan 19, 2011 at 1:27 AM, Karthik Krishnan <
karthik.krishnan at kitware.com> wrote:
> I also think adaptors would be slow here. Here is something that might
> work, taking advantage of the fact that the memory representation is
> unchanged. You can replace the buffer pointer directly under the hood after
> reading..
>
>
> In other words read the image as :
>
> VectorImage< double, 3 > ReaderImageType;
>
>
> Then later on, cast it brutally by replacing the pixel container under the
> hood....
>
> typedef DiffusionTensor< double > PixelType;
> typedef VectorImage< PixelType, 3 > VectorOfTensorsImageType;
>
> const unsigned int nTensorsPerVector = readerImage->GetVectorLength() /
> 6; // will be 2 for this example
> const unsigned long nVectorsInImage =
> readerImage->GetLargestPossibleRegion()->GetNumberOfPixels();
> const unsigned long nTensors = nVectorsInImage * nTensorsPerVector;
>
> typedef VectorOfTensorsImageType::PixelContainer
> VectorOfTensorsPixelContainer;
> VectorOfTensorsPixelContainer::Pointer votPixelContainer =
> VectorOfTensorsPixelContainer::New();
> votPixelContainer->SetImportPointer( reinterpret_cast< PixelType *
> >(readImage->GetBufferPointer()), nTensors, false ); // keep readerImage
> alive since we let it manage the memory.
>
> VectorOfTensorsImageType::Pointer votImage =
> VectorOfTensorsImageType::New();
> votImage->SetVectorLength( readerImage->GetVectorLength() / 6 );
> votImage->PixelContainer( votPixelContainer );
>
> // Copy metadata from the readerImage.
> votImage->SetSpacing(readerImage->GetSpacing());
> votImage->SetOrigin(readerImage->GetOrigin());
> votImage->SetDirection(readerImage->GetDirection());
> votImage->SetBufferedRegion(readerImage->GetBufferedRegion() );
> votImage->SetRequestedRegion(readerImage->GetRequestedRegion() );
>
>
> Its untested, but I think it should work :)
>
> --
> karthik
>
>
> On Wed, Jan 19, 2011 at 8:18 AM, Benoit Scherrer <benoitscherrer at gmail.com
> > wrote:
>
>> Hi,
>>
>> Thank you very much for all these answers!
>>
>> I don't know of a way to get the number of components in
>>> TOutputImage::PixelType. It would require us to define a NumberOfComponents
>>> in the traits of all pixels in itkNumericTraits. The IO class has no way of
>>> knowing the specific pixel type you've instantiated. One has to rely on the
>>> IO, for instance if the pixel type is an Array, (in which case, the image
>>> cannot tell you the number of components in the array. The IO tells you by
>>> parsing the file). You have a peculiar situation where you want to get the
>>> number of components from the pixel and not from the IO.
>>
>>
>> Yes i think it is really the point. Now i understand that the IO class has
>> no way to know the size of the pixel type without
>> a NumberOfComponents property in the itkNumericTraits.
>>
>> You could use ImageAdaptors for presenting
>>> a VectorImage as an Image of Tensors.
>>
>>
>> Thanks, i will look at it (i m a little bit concerned about the speed
>> though. but there is no free lunch...)
>>
>> Also, since
>> typedef itk::VectorImage<itk::DiffusionTensor<double>,3>
>> ImageOfVariableNumberOfTensorsType;
>> seems to work as long as you don't write/load the data, i could also
>> convert the output of
>> the IO class to my ImageOfVariableNumberOfTensorsType type, knowing that
>> each tensor is composed
>> of 6 elements.
>>
>> Thanks
>> Benoit
>>
>>
>>>
>>> -----------------------------------------------------------------
>>> On Mon, Jan 17, 2011 at 10:46 AM, Benoit Scherrer
>>> <benoitscherrer at gmail.com> wrote:
>>> > Ok thanks!
>>> > But so there is no way to use:
>>> > typedef itk::VectorImage<itk::DiffusionTensor<double>, 3>
>>> TensorVectorImage;
>>> >
>>> > to read a set of tensors at each voxel ?
>>> > ( itk::DiffusionTensor inherits itk::FixedArray)
>>> > It would be useful to do for example:
>>> > TensorVectorImage tensors;
>>> > tensors[i].GetFractionalAnisotropy()
>>> > Thanks
>>> > Benoit
>>> >
>>> > On Thu, Jan 13, 2011 at 11:26 PM, Karthik Krishnan
>>> > <karthik.krishnan at kitware.com> wrote:
>>> >>
>>> >>
>>> >> On Fri, Jan 14, 2011 at 6:26 AM, Benoit Scherrer
>>> >> <benoitscherrer at gmail.com> wrote:
>>> >>>
>>> >>> Hi,
>>> >>> I wanted to use the type:
>>> >>> typedef itk::VectorImage<itk::FixedArray<double, 6>, 3>
>>> >>> TensorVectorImage;
>>> >>> to make a vector image of tensors.
>>> >>> Everything compiles well. But when i use the
>>> >>> itk::ImageFileReader<TensorVectorImage>
>>> >>> it seems that things goes wrong. When trying to iterate on the image
>>> :
>>> >>> itk::ImageRegionConstIterator<TensorVectorImage>
>>> >>> it(image, image->GetLargestPossibleRegion());
>>> >>> while(!it.IsAtEnd())
>>> >>> {
>>> >>> itk::VariableLengthVector<itk::FixedArray<double, 6> > tensors =
>>> >>> it.Get();
>>> >>> (...)
>>> >>> ++it;
>>> >>> }
>>> >>> it compiles but during the execution goes out of the data bounds.
>>> >>> By looking into ImageFileReader<TOutputImage,
>>> >>> ConvertPixelTraits>::GenerateOutputInformation
>>> >>> I found the lines:
>>> >>> if( strcmp( output->GetNameOfClass(), "VectorImage" ) == 0 )
>>> >>> {
>>> >>> typedef typename TOutputImage::AccessorFunctorType
>>> >>> AccessorFunctorType;
>>> >>> AccessorFunctorType::SetVectorLength( output,
>>> >>> m_ImageIO->GetNumberOfComponents() );
>>> >>> }
>>> >>> So here m_ImageIO->GetNumberOfComponents() will returns 6 for a
>>> simple
>>> >>> tensor file (Dimension
>>> >>> of the VectorImage = 1), instead of 1 (after the offsets computed
>>> >>> in ImageRegionConstIterator are wrong).
>>> >>> So should ImageFileReader divides m_ImageIO->GetNumberOfComponents()
>>> by
>>> >>> the number of components
>>> >>> of TOutputImage::PixelType ? (i manually set it to 1 in the debugger,
>>> >>> it's working. However i didn't tried
>>> >>> with an image with 12 components, ie two tensors)
>>> >>> Or is it a bad idea to use itk::VectorImage<itk::FixedArray<double,
>>> 6>,
>>> >>> 3> ?
>>> >>
>>> >> To make a VectorImage of tensors, you declare it simply as
>>> >> itk::VectorImage< double, 3 > and set the VectorLength on the image to
>>> 6.
>>> >>
>>> >> Or you could use itk::Image< FixedArray< double, 6 >, 3 >.
>>> >>
>>> >> The two are equivalent.
>>> >>
>>> >>
>>> >>>
>>> >>> Thanks a lot
>>> >>> Benoit
>>> >>>
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>>> >>
>>> >
>>> >
>>> >
>>> > --
>>> > / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
>>> / /
>>> > / /
>>> > Benoit Scherrer
>>> > Postdoctoral Research Fellow
>>> > Computational Radiology Laboratory,
>>> > Harvard Medical School (Boston)
>>> >
>>> > http://www.crl.med.harvard.edu/
>>> > http://www.BenoitScherrer.com
>>> > / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
>>> / /
>>> > / /
>>> >
>>> > _______________________________________________
>>> > 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.html
>>> >
>>> > 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
>>> >
>>> >
>>>
>>
>>
>>
>> --
>> / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
>> / / /
>>
>> Benoit Scherrer
>> Postdoctoral Research Fellow
>> Computational Radiology Laboratory,
>> Harvard Medical School (Boston)
>>
>> http://www.crl.med.harvard.edu/
>> http://www.BenoitScherrer.com
>> / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
>> / / /
>>
>
>
--
/ / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
/ /
Benoit Scherrer
Postdoctoral Research Fellow
Computational Radiology Laboratory,
Harvard Medical School (Boston)
http://www.crl.med.harvard.edu/
http://www.BenoitScherrer.com
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