Troble loading and reading LinearTransform.h5

Engineering
,
1

Hello, everyone.

I am implementing a pipeline to load a LinearTransform.h5 and convert that into a displacement field. However, I am having a problem loading the transform into a real transform object-pointer to proceed. Please take a look into (part of) code:

#include "itkVersorRigid3DTransform.h"

#include <iostream>
#include <fstream>

#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"

#include "itkTransformFileReader.h"
#include "itkImageRegionIterator.h"

    > // Writing Transform
    >   using TransformReaderType = itk::TransformFileReaderTemplate<double>;
    >   TransformReaderType::Pointer transformReader = TransformReaderType::New();
    >   transformReader->SetFileName(argv[3]);
    >   transformReader->Update();
    > 
    >   TransformReaderType::TransformListType * transforms = transformReader->GetTransformList();
    >   auto it = transforms->begin();
    >   std::cout<< "Size:" << (*it). << std::endl;
    > 
    >   // Creating and writing the displacement vector image
    >   // Based on example: https://itk.org/Doxygen/html/Examples_2RegistrationITKv3_2DeformableRegistration8_8cxx-example.html
    > 
    >   using VectorType = itk::Vector<float, Dimension>;
    >   using DisplacementFieldType = itk::Image<VectorType, Dimension>;
    >   DisplacementFieldType::Pointer field = DisplacementFieldType::New();
    >   field->SetRegions(fixedImageReader->GetOutput()->GetBufferedRegion());
    >   field->SetSpacing(fixedImageReader->GetOutput()->GetSpacing());
    >   field->SetOrigin(fixedImageReader->GetOutput()->GetOrigin());
    >   field->SetDirection(fixedImageReader->GetOutput()->GetDirection());
    >   field->Allocate();
    > 
    >   using FieldIteratorType = itk::ImageRegionIterator<DisplacementFieldType>;
    >   FieldIteratorType fi( field, movingImageReader->GetOutput()->GetBufferedRegion());
    >   fi.GoToBegin();
    > 
    >   using TransformType = itk::VersorRigid3DTransform<double>;
    >   TransformType::InputPointType movingPoint;
    >   TransformType::OutputPointType transformedPoint;
    >   DisplacementFieldType::IndexType index;
    >   TransformType::Pointer transform = TransformType::New();
    > 
    > 
    >   VectorType displacement;
    > 
    >   while( !fi.IsAtEnd()){
    >       index = fi.GetIndex();
    >       field->TransformIndexToPhysicalPoint( index, movingPoint );
    >       transforms->begin();
    >       transformedPoint = transforms-> ->TransformPoint( movingPoint );
    >       displacement = transformedPoint - movingPoint;
    >       fi.Set(displacement);
    >       ++fi;
    >   }
    > 
    >   using FieldWriterType = itk::ImageFileWriter<DisplacementFieldType>;
    >   FieldWriterType::Pointer fieldWriter = FieldWriterType::New();
    >   fieldWriter->SetInput(field);
    >   fieldWriter->SetFileName(imagePath + "dispField-q=" + id + ".nrrd");
    >   fieldWriter->Update();
    >

Thanks in advance!

2

And what is the problem with this code?

3 
using TransformType = itk::VersorRigid3DTransform<double>;
TransformType::InputPointType movingPoint; 
TransformType::OutputPointType transformedPoint; 
DisplacementFieldType::IndexType index; 
TransformType::Pointer transform = TransformType::New();

The problem is : I do not know how to connect correctly the transform-input-file that I read with the transform pointer object that i created in this last line (above).

4

Have you seen this example?

5

Yes, I did read.
Although I got confused with the Idea of reading a List o transforms. I am loading just one. Do we always have to go through a loop to read a single object?

6

I guess I got it. I read, and then I do a cast to the type I am working (Versor3D).
Although, when I ask the object to print its name class and type it prints as the reader did (Affine), not the type I casted (Versor3D).

Any suggestion?
Thanks.

7

If affine is what is written in the file, and you want versor, you could read an affine transform and then convert it into versor representation.

8

All right I did exactly as the example mentioned, Sounds to work at the beginning, But it yelds an error:

tk::ERROR: ImageFileWriter(0x559f0f047c70): Largest possible region does not fully contain requested paste IO regionPaste IO region: ImageIORegion (0x7fff26c0cf20)
      Dimension: 3
      Index: 0 0 0 
      Size: 0 0 0 
    Largest possible region: ImageRegion (0x7fff26c0cfc0)
      Dimension: 3
      Index: [0, 0, 0]
      Size: [0, 0, 0]

Do not know why.

9

That error is coming from an Image, not a Transform, suggesting the mistake is elsewhere.

10

So, what’s the reason and how to deal with it?