[Insight-users] Cannot run the Resampling filter

[Luis Ibanez]

Hi Motes,


1) The Scope of the "try" block doesn't destroy any of the
     components of the registration framework.


2) I don't see how you are passing any arguments to the
    function:

                     computeRegisteredImage();

     are you declaring them as global ?


3)  No offense,
      but your custom Transform is the main suspect.

     Here is the important question:


                    Have you written a Unit Test
                    for your new Transform ?


     I can anticipate that the answer is "no",    :-)

     and therefore

     I will strongly,
     very, very, very strongly suggest

     that you write such unit test and fully debug
     your transform before you attempt to use it
     as part of a larger program.

     For examples on how to test Transforms,
     Please look at the files

      Insight/Testing/Code/Common/

itkAffineTransformTest.cxx
itkAzimuthElevationToCartesianTransformTest.cxx
itkBSplineDeformableTransformTest2.cxx
itkBSplineDeformableTransformTest.cxx
itkCenteredAffineTransformTest.cxx
itkCenteredEuler3DTransformTest.cxx
itkCenteredRigid2DTransformTest.cxx
itkCenteredTransformInitializerTest.cxx
itkCenteredVersorTransformInitializerTest.cxx
itkEuler2DTransformTest.cxx
itkEuler3DTransformTest.cxx
itkFixedCenterOfRotationAffineTransformTest.cxx
itkIdentityTransformTest.cxx
itkImageTransformTest.cxx
itkLandmarkBasedTransformInitializerTest.cxx
itkQuaternionRigidTransformTest.cxx
itkRigid2DTransformTest.cxx
itkRigid3DPerspectiveTransformTest.cxx
itkRigid3DTransformTest.cxx
itkRigid3DTransformTest.cxx.orig
itkScaleLogarithmicTransformTest.cxx
itkScaleSkewVersor3DTransformTest.cxx
itkScaleTransformTest.cxx
itkSimilarity2DTransformTest.cxx
itkSimilarity3DTransformTest.cxx
itkSplineKernelTransformTest.cxx
itkTransformsSetParametersTest.cxx
itkTransformTest.cxx
itkTranslationTransformTest.cxx
itkVersorRigid3DTransformTest.cxx
itkVersorTransformTest.cxx



   Regards,


        Luis


------------------------------------------------------------------------------------------
On Wed, Nov 25, 2009 at 8:44 PM, motes motes <mort.motes at gmail.com> wrote:
> Which objects survive in the transform component when the image
> registration method is finished?
>
> By finished I mean reaches the scope after this try/catch block:
>
>    try {
>      registration->Update();
>    }
>    catch( itk::ExceptionObject & err ) {
>      std::cerr << "ExceptionObject caught !" << std::endl;
>      std::cerr << err << std::endl;
>      return EXIT_FAILURE;
>    }
>
> // What lives in the image registration method when arriving here?
>
>
>
>
>
> The reason I ask is because I am trying to compute the registered
> image AFTER the registration method is done. Something like this:
>
>    try {
>
>      registration->Update();
>    }
>    catch( itk::ExceptionObject & err ) {
>      std::cerr << "ExceptionObject caught !" << std::endl;
>      std::cerr << err << std::endl;
>      return EXIT_FAILURE;
>    }
>
>    computeRegisteredImage();
>    return EXIT_SUCCESS;
>
>
> where:
>
>  void computeRegisteredImage(){
>    ResampleFilterType::Pointer resampler = ResampleFilterType::New();
>    resampler->SetInput(imageM);
>    resampler->SetTransform(registration->GetTransform());
>    resampler->SetInterpolator(registration->GetInterpolator());
>    resampler->SetOutputOrigin(imageF->GetOrigin());
>    resampler->SetOutputSpacing(imageF->GetSpacing());
>    resampler->SetSize(imageF->GetLargestPossibleRegion().GetSize());
>    resampler->SetDefaultPixelValue(default_pixel_value);
>    try {
>      resampler->Update();
>    }
>    catch( itk::ExceptionObject & err ) {
>      std::cerr << "ExceptionObject caught !" << std::endl;
>      std::cerr << err << std::endl;
>    }
>
>
>    imageR = resampler->GetOutput();
>
>
>  }
>
>
>
> But:
>
> resampler->Update();
>
> never returns. It thows a segmentation fault. I have located the error
> to be in the TransformPoint method. I have made my own transform which
> uses a kdTree in the TransformPoint function. This kdTree is stored
> locally in my transform like:
>
>
> #include "kd_tree.h" // My own itk:kdTree wrapper.
> namespace itk
> {
> template <
>    class TScalarType = double,          // Data type for scalars
>    unsigned int NDimensions = 3,        // Number of dimensions
>    unsigned int VSplineOrder = 3 >      // Spline order
> class ITK_EXPORT MyDeformableTransform :
>          public Transform< TScalarType, NDimensions, NDimensions >
> {
> public:
>  /** Standard class typedefs. */
>  typedef MyDeformableTransform                                          Self;
> ...
> ...
> ...
>
>  typedef KdTree<VectorType, ControlPointContainerType, NDimensions>
>               KdTreeType;
>
>
> ....
> .....
> ...
> protected:
>  mutable KdTreeType m_kdTree;
>
>
>
>
>
> Can this have something to do with the segmentation error? Does it
> need to be stored as a smart pointer instead?
>
>
>
>
>
>
>
> In the TransformPoint function I do:
>
> // Transform a point
> template<class TScalarType, unsigned int NDimensions, unsigned int VSplineOrder>
> void
> MyDeformableTransform<TScalarType, NDimensions, VSplineOrder>
> ::TransformPoint(
>  const InputPointType & point,
>  OutputPointType & outputPoint,
>  WeightsType & weights,
>  ParameterIndexArrayType & indices,
>  bool & inside ) const
> {
>  unsigned int j;
>  IndexType supportIndex;
>  inside = true;
>  InputPointType transformedPoint;
>
>  if ( m_BulkTransform ) {
>    transformedPoint = m_BulkTransform->TransformPoint( point );
>  } else {
>    transformedPoint = point;
>  }
>
>  outputPoint.Fill( NumericTraits<ScalarType>::Zero );
>  if ( GetNumberOfParameters()>0) {
>    outputPoint.Fill( NumericTraits<ScalarType>::Zero );
>
>
>
>     NeighborContainerType neighbors;
>
>      // This results in a segmentation error
>      this->FindNeighbors(point, m_kernel_radius, neighbors);
>
>
>
> its the call:
>
>      this->FindNeighbors(point, m_kernel_radius, neighbors);
>
> that gives the error which basically just calls the itk::kdTree class.
>
> Any suggestions are most welcome!
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