[Insight-users] question ? [ITK]

[Luis Ibanez]

Hi Agata,

Please find attached the working code.

Here is the hierarchy that you may want to keep in mind:


   - One TPS transform has two PointSets
   - One PointSet has a PointContainer
   - One PointContainer have PointIterators (const and non-const)


You can get points from a PointSet by using GetPointid)

    PointType  point = pointSet->GetPoint( pointId );

or you can get them from the PointContainer by using GetElement(id)

    PointType  point = pointContainer->GetElement( pointId );

or you can get them via Iterators from the PointContainer

    PointConstIterator pointItr = pointContainer->Begin();
    PointType  point = pointItr.Value();
    ++pointItr;
   ...etc...

Note that you shouldn't use "int" or "short" or "long" for the
PointId type. One must use PointIdType (which is typedefed
from the ElementIdentifier type), this is very important if you
are working on 64 bits.


The attached code shows you both ways of doing this
at the end of the file.

The key lines of code are:


  TPSTransformType::InputPointType  trackerPointSourcePosition;
  TPSTransformType::OutputPointType trackerPointNewPosition;

  // Test transforming the input landmark themselves
  for( PointIdType i = 0; i < sourceLandMarks->GetNumberOfPoints(); i++ )
    {
    trackerPointSourcePosition = sourceLandMarks->GetPoint(i);
    trackerPointNewPosition =
tps->TransformPoint(trackerPointSourcePosition);
    transformed_points_container->InsertElement(i,trackerPointNewPosition);
    std::cout << "Input " << trackerPointSourcePosition << " : ";
    std::cout << "Output " << trackerPointNewPosition << std::endl;
    }


  // Do the same using Iterators
  std::cout << std::endl << "Now using Iterators " << std::endl;

  PointConstIterator inputPointItr = sourceLandMarkContainer->Begin();
  PointConstIterator inputPointEnd = sourceLandMarkContainer->End();

  PointIdType pointId = itk::NumericTraits< PointIdType >::Zero;

  while( inputPointItr != inputPointEnd )
    {
    trackerPointNewPosition = tps->TransformPoint(inputPointItr.Value());

transformed_points_container->InsertElement(pointId,trackerPointNewPosition);
    std::cout << "Input " << inputPointItr.Value() << " : ";
    std::cout << "Output " << trackerPointNewPosition << std::endl;
    ++inputPointItr;
    }





 Hope this helps,

      Luis


------------------------------------------------------------
On Sat, Aug 18, 2012 at 12:17 PM, Agata Krasoń <agatakrason at gmail.com>wrote:

> Dear Luis,
>
> I am trying to use tps transformation in ITK.
> ...
> I created sources and target points.
> I made Tps transformation.
> I need to receive points after registration
>


> ...
>


> I have a problem with iterators.
> I would appreciate for any help please.
>
> int main(int argc, char* argv[])
> {
>
> double tab[30] =
> {
>  // Tracker
> -81.29,-31.07, -770.58,
>     -83.11, -21.26, -822.64,
>     -93.45, -32.44, -858.72,
>     -68.08, -126.89,-813.07,
>     -61.04, 75.74, -808.36,
>
>  // Image
>     140.6, 230.7, -30.5,
>     140.2, 231.7, -71.1,
>     144.8, 235.9, -116.1,
>     45.8, 220.2, -66.7,
>     231.6, 211.3, -66.1
>  };
>
>   const     unsigned int   Dimension = 3;
>   typedef   unsigned char  PixelType;
>   typedef   double CoordinateRepType;
>   typedef   itk::ThinPlateSplineKernelTransform<
> CoordinateRepType,Dimension>     TPSTransformType;
>   typedef   itk::Point< CoordinateRepType,Dimension >  PointType;
>   typedef   std::vector< PointType >                   PointArrayType;
>   typedef   TPSTransformType::PointSetType      PointSetType;
>   typedef   PointSetType::Pointer            PointSetPointer;
>   typedef   PointSetType::PointIdentifier  PointIdType;
>
>
>   // Landmarks correspondances may be associated with the
> SplineKernelTransforms
>   // via Point Set containers. Let us define containers for the landmarks.
>   PointSetType::Pointer sourceLandMarks = PointSetType::New();
>   PointSetType::Pointer targetLandMarks = PointSetType::New();
>   PointType trackerPoint;     PointType imagePoint;
>   PointSetType::PointsContainer::Pointer sourceLandMarkContainer =
>                                    sourceLandMarks->GetPoints();
>   PointSetType::PointsContainer::Pointer targetLandMarkContainer =
>                                    targetLandMarks->GetPoints();
>
>
>   // 1 Landmark
>   trackerPoint[0] = tab[0];
>   trackerPoint[1] = tab[1];
>   trackerPoint[2] = tab[2];
>   imagePoint[0] = tab[15];
>   imagePoint[1] = tab[16];
>   imagePoint[2] = tab[17];
>   sourceLandMarkContainer->InsertElement( 0,trackerPoint);
>   targetLandMarkContainer->InsertElement(0,imagePoint);
>
>
>   // 2 Landmark
>   trackerPoint[0] = tab[3];
>   trackerPoint[1] = tab[4];
>   trackerPoint[2] = tab[5];
>   imagePoint[0] = tab[18];
>   imagePoint[1] = tab[19];
>   imagePoint[2] = tab[20];
>   sourceLandMarkContainer->InsertElement(1,trackerPoint);
>   targetLandMarkContainer->InsertElement(1,imagePoint);
>
>   // 3 Landmark
>   trackerPoint[0] = tab[6];
>   trackerPoint[1] = tab[7];
>   trackerPoint[2] = tab[8];
>   imagePoint[0] = tab[21];
>   imagePoint[1] = tab[22];
>   imagePoint[2] = tab[23];
>   sourceLandMarkContainer->InsertElement( 2,trackerPoint);
>   targetLandMarkContainer->InsertElement(2,imagePoint);
>
>   // 4 Landmark
>   trackerPoint[0] = tab[9];
>   trackerPoint[1] = tab[10];
>   trackerPoint[2] = tab[11];
>   imagePoint[0] = tab[24];
>   imagePoint[1] = tab[25];
>   imagePoint[2] = tab[26];
>   sourceLandMarkContainer->InsertElement( 3,trackerPoint);
>   targetLandMarkContainer->InsertElement(3,imagePoint);
>
>   // 5 Landmark
>   trackerPoint[0] = tab[12];
>   trackerPoint[1] = tab[13];
>   trackerPoint[2] = tab[14];
>   imagePoint[0] = tab[27];
>   imagePoint[1] = tab[28];
>   imagePoint[2] = tab[29];
>
>   sourceLandMarkContainer->InsertElement(4,trackerPoint);
>   targetLandMarkContainer->InsertElement(4,imagePoint);
>
>   TPSTransformType::Pointer tps = TPSTransformType::New();
>   tps->SetSourceLandmarks(sourceLandMarks);
>   tps->SetTargetLandmarks(targetLandMarks);
>   tps->ComputeWMatrix();
>
>
>     PointSetType::Pointer transformed_points = PointSetType::New();
>   PointSetType::PointsContainer::Pointer transformed_points_container =
> transformed_points->GetPoints();
>   TPSTransformType::OutputPointType trackerPointNewPosition;
>
>   for( int i = 0; i < sourceLandMarks->GetNumberOfPoints(); i++){
>   PointSetType      src_pnt = sourceLandMarks->GetPoints();  // Here It
> doesn't compile  ?
>     trackerPointNewPosition = tps->TransformPoint(trackerPoint);
>
> transformed_points_container->InsertElement(i,trackerPointNewPosition);
> std::cout<<" "<<trackerPointNewPosition <<std::endl;
>   }
>
>
>   return EXIT_SUCCESS;
>
>
> }
>
>
>
>
> I would appreciate for any help please.
>
> Best,
> Agata
>
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# This is the root ITK CMakeLists file.
cmake_minimum_required(VERSION 2.4)
if(COMMAND CMAKE_POLICY)
  cmake_policy(SET CMP0003 NEW)
endif(COMMAND CMAKE_POLICY)


# This project is designed to be built outside the Insight source tree.
project(tps)

# Find ITK.
find_package(ITK REQUIRED)
include(${ITK_USE_FILE})

add_executable(tps main.cpp )

target_link_libraries(tps ${ITK_LIBRARIES})
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