[Insight-developers] Wrong behaviour of ImageFileReader when reading an itk::VectorImage<itk::FixedArray<double, 6>, 3> ?

[Bradley Lowekamp]

Hello,


On Jan 17, 2011, at 12:18 PM, Karthik Krishnan wrote:

> Benoit:
> 
> Do you have a variable number of tensors at each pixel ? If not, You should simply declare your image as 
> 
> Image< Vector< DiffusionTensor< double >, N >, 3 >


I think you intended to say that if  you only have one Tensor per pixel then you should declare the image types as follows:

Image< itk::DiffusionTensor3D<double>, 3> ImageOfTensorType;


As opposed to:

typedef itk::VectorImage<itk::DiffusionTensor<double>,3> ImageOfVariableNumberOfTensorsType;

or

typedef Image<Vector<DiffusionTensor<double, 3>, N >, 3> ImageOfNTensorsType;

More information on VectorImage can be found here:
http://www.itk.org/Doxygen/html/classitk_1_1VectorImage.html#_details


> 
> The whole intent of the VectorImage was to avoid memory fragmentation by internally storing images of the type 
>   Image< Array< double >, 3 > 
> as a contiguous set of N doubles for the array, instead of a pointer to the data at each pixel and the length of the data at each pixel (itk::Array< double > has a pointer to the data and an integer to represent the length of the pixel.). The resulting image will behave just as itk::Image< Array< double >, 3 > would behave. It will provide faster memory access, consume less memory and provide a less fragmented memory representation.
> 
> By contrast, the compile time classes, ie Vector and DiffusionTensor are equivalent to a C array, and 0 overhead.
> 
> -
> karthik
> 
> 
> On Mon, Jan 17, 2011 at 9:16 PM, 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
> / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
> 
> <ATT00001..txt>

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