[Insight-users] ExtractImageFilter for vector field

[Sadegh]

Hello Brad!

Sorry, I faced another problem this time which is the compile error.
Actually the previous code had an conceptual error, which must be changed to
the following:

//////////////////////
const    unsigned int InputImageDimension =3;
const    unsigned int FrameDimension =2;

typedef float        InputPixelType3D;

typedef itk::Image< InputPixelType3D,  InputImageDimension >   
InputImageType3D;
typedef itk::Image< InputPixelType3D, FrameDimension >  FixedImageType;
FixedImageType::Pointer fixedimage = FixedImageType::New();

typedef itk::Vector< InputPixelType3D, InputImageDimension >
VectorPixelType;
typedef itk::Image< VectorPixelType, InputImageDimension >            
InputDeformationFieldType;
typedef itk::ImageFileReader< InputDeformationFieldType >
DeformationFieldReaderType;

typedef itk::Vector< float, FrameDimension > VectorPixelType2D;
typedef itk::Image< VectorPixelType2D, FrameDimension >            
FrameDeformationFieldType;
FrameDeformationFieldType::Pointer vectorimage =
FrameDeformationFieldType::New();

typedef itk::ExtractImageFilter< InputDeformationFieldType,
FrameDeformationFieldType> InputFilterType2D;

////////////////
FrameDeformationFieldType::Pointer
extract2DImageSlice(InputDeformationFieldType::Pointer reader, int plane,
int slice) {
    
	reader->UpdateOutputInformation();
	InputFilterType2D::Pointer filter = InputFilterType2D::New();
filter->InPlaceOn(); 
   filter->SetDirectionCollapseToSubmatrix(); 
//filter->SetDirectionCollapseToIdentity();

    InputDeformationFieldType::RegionType inputRegion =
reader->GetRequestedRegion();
    InputDeformationFieldType::SizeType size = inputRegion.GetSize();
    size[plane] = 1;

    InputDeformationFieldType::IndexType start = inputRegion.GetIndex();
    const unsigned int sliceNumber = slice;
    start[plane] = sliceNumber;

    InputDeformationFieldType::RegionType desiredRegion;
    desiredRegion.SetSize(  size  );
    desiredRegion.SetIndex( start );

    filter->SetExtractionRegion( desiredRegion );
    filter->SetInput( reader );
    FrameDeformationFieldType::Pointer img = filter->GetOutput();
    img->Update();
    return img;
}
/////////////////////////////////////////

So the main change is that ExtractImageFilter< InputDeformationFieldType,
FrameDeformationFieldType> receives a 3D vector field as input
(InputDeformationFieldType) and gives back 2D vector field
(FrameDeformationFieldType) as output. so the function  extract2DImageSlice
will do the same.

now I receive the following error :
*error C2440: 'static_cast' : cannot convert from
'itk::Vector<T,NVectorDimension>' to 'itk::Vector<T,NVectorDimension>'
d:\phd-project\open-source\insighttoolkit-4.1.0\modules\core\common\include\itkConceptChecking.h
185*

It might be from the other parts of the code which calculates the jacobian
determinant which I post it below:

/////////////////BEGIN///////////////
typedef
itk::DisplacementFieldJacobianDeterminantFilter<FrameDeformationFieldType,
float> JacobianFilterType;

  DeformationFieldReaderType::Pointer fieldReader =
DeformationFieldReaderType::New();
  typedef itk::Image<float,2> ImageType;
  fieldReader->SetFileName( argv[1] );
    std::cout << "1";
    // Update the reader
    try
      {
      fieldReader->Update();
      }
    catch( itk::ExceptionObject& err )
      {
      std::cout << "Could not read the input field." << std::endl;
      std::cout << err << std::endl;
      exit( EXIT_FAILURE );
      }
    
    //inputVelField = fieldReader->GetOutput();
    InputDeformationFieldType::Pointer deffield;    
    deffield=fieldReader->GetOutput();
   
//sprintf(filename,"realvalues/deffield%d.mha",this->GetElapsedIterations());
     
	unsigned int Component  = 2;
	unsigned int numberOfFrames = 476;
  if( argc > 2 )
	numberOfFrames= atoi(argv[2]) ;
	std::cout << "1";
  std::ofstream parametersFile;
    std::ostringstream ostr;
    ostr.str("");
	ostr<<argv[3];
	parametersFile.open( ostr.str());
	typedef itk::ImageRegionIterator&lt; ImageType > IteratorType;
  for (int j=1; j <= numberOfFrames; j++)
	 {
		try
  {
    vectorimage = extract2DImageSlice(deffield, Component, j);	 
	}
  catch( itk::ExceptionObject & err )
  {
    std::cerr << "ExceptionObject caught !" << std::endl;
    std::cerr << err << std::endl;
    return EXIT_SUCCESS; 
  }
 
 	
	
	  JacobianFilterType::Pointer jacobianFilter = JacobianFilterType::New();
     jacobianFilter->SetInput( vectorimage );
     jacobianFilter->SetUseImageSpacing( true );
	
	
	
  IteratorType it( jacobianFilter->GetOutput(),
jacobianFilter->GetOutput()->GetRequestedRegion() );  
  int shrink, nochange, increase ;
  shrink = nochange =increase =0;
  int i =0;
   it.Begin();
    while( !it.IsAtEnd() )
      {
      if (it.Get() < 1)
		  shrink++;
	  else if (it.Get() == 1)
		  nochange++;
	  else increase++;
      ++it;i++;
	}
	float shrinkpercent = (float)((shrink*100)/i);
	float nopercent = (float)((nochange*100)/i);
	float incpercent = (float)((increase*100)/i);
	
	typedef itk::MinimumMaximumImageCalculator<ImageType> MinMaxFilterType;
    MinMaxFilterType::Pointer minmaxfilter = MinMaxFilterType::New();
     minmaxfilter->SetImage( jacobianFilter->GetOutput() );
     minmaxfilter->Compute();
    
    std::cout << "Writing "<<j&lt;&lt;&quot;th frame Jacobian result
parameter ...&quot;;
    
	parametersFile &lt;&lt; &quot;Frame No: &quot; &lt;&lt;j&lt;&lt;std::endl;
	parametersFile &lt;&lt; &quot;Max number of Pixels: &quot;
&lt;&lt;i&lt;&lt;std::endl;
	parametersFile &lt;&lt; &quot;Number of pixels Jac &lt; 1: &quot;
&lt;&lt;shrink&lt;&lt;&quot;,
--Percentage:&quot;&lt;&lt;shrinkpercent&lt;&lt;&quot;%&quot;&lt;&lt;std::endl;
	parametersFile &lt;&lt; &quot;Number of pixels Jac > 1:
"<<increase&lt;&lt;&quot;,
--Percentage:&quot;&lt;&lt;incpercent&lt;&lt;&quot;%&quot;&lt;&lt;std::endl;
	parametersFile &lt;&lt; &quot;Number of pixels Jac = 1:
&quot;&lt;&lt;nochange&lt;&lt;&quot;,
--Percentage:&quot;&lt;&lt;nopercent&lt;&lt;&quot;%&quot;&lt;&lt;std::endl;
	parametersFile&lt;&lt;&quot;Minimum of the determinant of the Jacobian of
the warp: &quot;
              &lt;&lt;minmaxfilter->GetMinimum()<<std::endl;
    parametersFile&lt;&lt;&quot;Maximum of the determinant of the Jacobian
of the warp: &quot;
              &lt;&lt;minmaxfilter->GetMaximum()<<std::endl;

parametersFile<<"-------------------------------------------------------------"<<std::endl;
    
    
  }

	parametersFile.close();
   

  return EXIT_SUCCESS;

}
/////////////////END///////////////

Now the concept of what I want to DO should be okay logically. But I do not
understand the meaning of the error and why it comes..

Thanks and sorry again.



-----
Sadegh Riyahi
Politecnico di Milano
--
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