[Insight-users] extract filter problem

[Michael Kuhn]

Hi,

A) here the output of "preFilter->GetOutput()->Print(std::cout)" after
modifying the program.


Image (0136A100)
  RTTI typeinfo:   class itk::Image<double,3>
  Reference Count: 2
  Modified Time: 199
  Debug: Off
  Observers:
    none
  Source: (0136A220)
  Source output index: 0
  Release Data: Off
  Data Released: False
  Global Release Data: Off
  PipelineMTime: 126
  UpdateMTime: 200
  LargestPossibleRegion:
    Dimension: 3
    Index: [0, 0, 0]
    Size: [65, 65, 127]
  BufferedRegion:
    Dimension: 3
    Index: [0, 0, 0]
    Size: [65, 65, 127]
  RequestedRegion:
    Dimension: 3
    Index: [0, 0, 0]
    Size: [65, 65, 127]
  Spacing: [0.127664, 0.127664, 0.127664]
  Origin: [0, 0, 0]
  PixelContainer:
    ImportImageContainer (0136A090)
      RTTI typeinfo:   class itk::ImportImageContainer<unsigned long,double>
      Reference Count: 1
      Modified Time: 134
      Debug: Off
      Observers:
        none
      Pointer: 0136A0C0
      Container manages memory: true
      Size: 536575
      Capacity: 536575


B) The behaviour using the RegionOfInterestImageFilter is identical.

When going through the program with a debugger, it crashes in
DiscreteGaussianImageFilter after line 201.

Thanks,

Michael

P.S.: When should I use the RegionOfInterestImageFilter and when the
ExtractImageFilter (only if I want to change the dimensionality?)?





> Hi Michael
> 
> 
> 
> Please do the following:
> 
> 
> 
> A) Check on image size
> 
> 1) In the try/catch block
> 
>  > 	try {
>  > 		extractFilter->Update();
>  > 	} catch (itk::ExceptionObject &e) {
> 
> replace "extractFilter" with the gradientFilter
> "preFilter". Then just after Update() add
> 
>    preFilter->GetOutput()->Print( std::cout );
> 
> 2) Rerun your program
> 
> 3) Let us know the region sized that are printed.
> 
> 
> 
> 
> B) Check for a bug in the ExtractImageFilter
> 
>    1) Replace the ExtractImageFilter with the
>       "RegionOfInterestImageFilter"
> 
>    This filter is described in the SoftwareGuide
> 
>         http://www.itk.org/ItkSoftwareGuide.pdf
> 
>    Section 7.4, pdf-page 225.
> 
> 
> If your program works with this filter, then there
> is probably a buggy condition in the ExtractImageFilter.
> 
> 
> 
>    Please let us know what you find.
> 
> 
>           Thanks
> 
> 
>              Luis
> 
> 
> 
> ---------------------------
> michakuhn at gmx.ch wrote:
> 
> > Hi,
> > 
> > I've written the following program, which is supposed to create the
> gradient
> > image for a particular region of the input image.
> > 
> > ----
> > 
> > #include <iostream>
> > 
> > #include "itkImage.h"
> > #include "itkImageFileReader.h"
> > #include "itkImageFileWriter.h"
> > #include "itkGradientImageFilter.h"
> > #include "itkGradientRecursiveGaussianImageFilter.h"
> > #include "itkNumericTraits.h"
> > #include "itkImageRegionConstIterator.h"
> > #include "itkDiscreteGaussianImageFilter.h"
> > #include "itkCastImageFilter.h"
> > #include "itkExtractImageFilter.h"
> > 
> > int main(int argc, char** argv)
> > {
> > 	const unsigned int Dimension = 3;
> > 	typedef short PixelType;
> > 	typedef itk::Image<PixelType, Dimension> ImageType;
> > 
> > 	typedef double RealType;
> > 
> > 	typedef itk::Image<RealType, Dimension> IntermediateImageType;
> > 
> > 	typedef itk::CovariantVector<RealType, Dimension> GradientPixelType;
> > 	typedef itk::Image<GradientPixelType, Dimension> GradientImageType;
> > 	
> > 	
> > 	typedef itk::ImageFileReader<ImageType> ReaderType;
> > 
> > 	ReaderType::Pointer reader = ReaderType::New();
> > 
> > 	if (argc < 2) {
> > 		std::cout << "image in required" << std::endl;
> > 		return -1;
> > 	}
> > 	reader->SetFileName(argv[1]);
> > 
> > 	try {
> > 		reader->Update();
> > 	} catch (itk::ExceptionObject &e) {
> > 		std::cout << e << std::endl;
> > 		return -1;
> > 	}
> > 
> > 	typedef itk::CastImageFilter<ImageType, IntermediateImageType>
> > 		CastFilterType;
> > 
> > 	CastFilterType::Pointer castFilter = CastFilterType::New();
> > 
> > 	castFilter->SetInput(reader->GetOutput());
> > 
> > 
> > 	typedef itk::DiscreteGaussianImageFilter<IntermediateImageType,
> > 		IntermediateImageType>	PreFilterType;
> > 
> > 	PreFilterType::Pointer preFilter = PreFilterType::New();
> > 	preFilter->SetInput(castFilter->GetOutput());
> > 	preFilter->SetUseImageSpacing(false);
> > 	preFilter->SetMaximumKernelWidth(8);
> > 	std::cout << "default variance: " << preFilter->GetVariance() <<
> std::endl;
> > 	preFilter->SetVariance(1);
> > 
> > 	typedef itk::GradientImageFilter<IntermediateImageType, RealType, 
> > 		RealType> Filter1Type;
> > 
> > 	Filter1Type::Pointer filter1 = Filter1Type::New();
> > 	filter1->SetInput(preFilter->GetOutput());
> > 
> > 	typedef itk::ExtractImageFilter<GradientImageType, GradientImageType>
> > 		ExtractFilterType;
> > 	ExtractFilterType::Pointer extractFilter = ExtractFilterType::New();
> > 
> > 	extractFilter->SetInput(filter1->GetOutput());
> > 
> > 	typedef GradientImageType::RegionType RegionType;
> > 	RegionType region;
> > 	RegionType::SizeType size;
> > 	RegionType::IndexType index;
> > 
> > 	size[0] = 1;
> > 	size[1] = 32;
> > 	size[2] = 32;
> > 
> > 	index[0] = 64;
> > 	index[1] = 0;
> > 	index[2] = 0;
> > 
> > 	region.SetSize(size);
> > 	region.SetIndex(index);
> > 
> > 	extractFilter->SetExtractionRegion(region);
> > 
> > 	try {
> > 		extractFilter->Update();
> > 	} catch (itk::ExceptionObject &e) {
> > 		std::cout << e << std::endl;
> > 		return -1;
> > 	}
> > 
> > 	GradientImageType::Pointer image1 = extractFilter->GetOutput();
> > 
> > 	std::cout << "image1: " << image1 << std::endl;
> > 
> > 	return 0;
> > }
> > 
> > ----
> > 
> > This program crashes, if my input image has a size of 65x65x127 pixels.
> It
> > works fine, however, as soon as I change (in the source code) "index[0]
> =
> > 64" to "index[0] = 63". It still works when increasing size[0] to 2
> after
> > changing the index. Can somebody explain me, why I am not allowed to
> extract
> > this particular region I've set in the code? Or is there something else
> > wrong?
> > 
> > Thanks,
> > 
> > Michael
> > 
> > P.S.: Below the input image file (in.mhd):
> > 
> > ----
> > 
> > ObjectType = Image
> > NDims = 3
> > BinaryData = True
> > BinaryDataByteOrderMSB = False
> > ElementSpacing = 0.127664 0.127664 0.127664
> > DimSize = 65 65 127
> > ElementType = MET_SHORT
> > ElementDataFile = in.raw
> > 
> > ----
> > 
> 
> 
> 
> 
> _______________________________________________
> Insight-users mailing list
> Insight-users at itk.org
> http://www.itk.org/mailman/listinfo/insight-users
> 

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