ITK/Examples/Registration/LandmarkBasedTransformInitializer: Difference between revisions

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==LandmarkBasedTransformInitializer.cxx==
{{warning|1=The media wiki content on this page is no longer maintainedThe examples presented on the https://itk.org/Wiki/* pages likely require ITK version 4.13 or earlier releasesIn many cases, the examples on this page no longer conform to the best practices for modern ITK versions.}}
<source lang="cpp">
#include "itkImageFileWriter.h"
#include "itkImage.h"
#include "itkVector.h"
#include "itkResampleImageFilter.h"
#include "itkLandmarkBasedTransformInitializer.h"
#include "itkRigid2DTransform.h"
 
const    unsigned int  Dimension = 2;
typedef  unsigned char  PixelType;
typedef  itk::Image< PixelType, Dimension > ImageType;
 
static void CreateFixedImage(ImageType::Pointer image);
static void CreateMovingImage(ImageType::Pointer image);
 
int main(int argc, char * argv[])
{
  typedef  float          VectorComponentType;
 
  typedef  itk::Vector< VectorComponentType, Dimension >    VectorType;
  typedef  itk::Image< VectorType,  Dimension >  DeformationFieldType;
 
  ImageType::Pointer fixedImage = ImageType::New();
  CreateFixedImage(fixedImage);
 
  ImageType::Pointer movingImage = ImageType::New();
  CreateMovingImage(movingImage);
 
  typedef itk::Rigid2DTransform< double > Rigid2DTransformType;
  typedef itk::LandmarkBasedTransformInitializer< Rigid2DTransformType, ImageType, ImageType >
      LandmarkBasedTransformInitializerType;
     
  LandmarkBasedTransformInitializerType::Pointer landmarkBasedTransformInitializer =
    LandmarkBasedTransformInitializerType::New();
  //  Create source and target landmarks.
  typedef LandmarkBasedTransformInitializerType::LandmarkPointContainer    LandmarkContainerType;
  typedef LandmarkBasedTransformInitializerType::LandmarkPointType          LandmarkPointType;
 
  LandmarkContainerType fixedLandmarks;
  LandmarkContainerType movingLandmarks;
 
  LandmarkPointType fixedPoint;
  LandmarkPointType movingPoint;
 
  fixedPoint[0] = 10;
  fixedPoint[1] = 10;
  movingPoint[0] = 50;
  movingPoint[1] = 50;
  fixedLandmarks.push_back( fixedPoint );
  movingLandmarks.push_back( movingPoint );
 
  fixedPoint[0] = 10;
  fixedPoint[1] = 20;
  movingPoint[0] = 50;
  movingPoint[1] = 60;
  fixedLandmarks.push_back( fixedPoint );
  movingLandmarks.push_back( movingPoint );
 
  fixedPoint[0] = 20;
  fixedPoint[1] = 10;
  movingPoint[0] = 60;
  movingPoint[1] = 50;
  fixedLandmarks.push_back( fixedPoint );
  movingLandmarks.push_back( movingPoint );
 
  fixedPoint[0] = 20;
  fixedPoint[1] = 20;
  movingPoint[0] = 60;
  movingPoint[1] = 60;
  fixedLandmarks.push_back( fixedPoint );
  movingLandmarks.push_back( movingPoint );
 
  landmarkBasedTransformInitializer->SetFixedLandmarks( fixedLandmarks );
  landmarkBasedTransformInitializer->SetMovingLandmarks( movingLandmarks );
 
  Rigid2DTransformType::Pointer transform = Rigid2DTransformType::New();
 
  transform->SetIdentity();
  landmarkBasedTransformInitializer->SetTransform(transform);
  landmarkBasedTransformInitializer->InitializeTransform();
 
  typedef itk::ResampleImageFilter<ImageType, ImageType, double >    ResampleFilterType;
  ResampleFilterType::Pointer resampleFilter = ResampleFilterType::New();
  resampleFilter->SetInput( movingImage );
  resampleFilter->SetTransform( transform );
  resampleFilter->SetSize( fixedImage->GetLargestPossibleRegion().GetSize() );
  resampleFilter->SetOutputOrigin( fixedImage->GetOrigin() );
  resampleFilter->SetOutputSpacing( fixedImage->GetSpacing() );
  resampleFilter->SetOutputDirection( fixedImage->GetDirection() );
  resampleFilter->SetDefaultPixelValue( 200 );
  resampleFilter->GetOutput();
 
  // Write the output
  typedef itk::ImageFileWriter<  ImageType  > WriterType;
  WriterType::Pointer writer = WriterType::New();
  writer->SetInput (  resampleFilter->GetOutput() );
  writer->SetFileName( "output.png" );
  writer->Update();
 
  return EXIT_SUCCESS;
}
 
void CreateFixedImage(ImageType::Pointer image)
{
  // Create a black image with a white square
  ImageType::IndexType start;
  start.Fill(0);
  ImageType::SizeType size;
  size.Fill(100);
  ImageType::RegionType region;
  region.SetSize(size);
  region.SetIndex(start);
  image->SetRegions(region);
  image->Allocate();
  image->FillBuffer(0);
  itk::ImageRegionIterator<ImageType> imageIterator(image,region);
  while(!imageIterator.IsAtEnd())
    {
    if(imageIterator.GetIndex()[0] > 10 && imageIterator.GetIndex()[0] < 20 &&
      imageIterator.GetIndex()[1] > 10 && imageIterator.GetIndex()[1] < 20)
      {
      imageIterator.Set(255);
      }
    ++imageIterator;
    }
 
  // Write the deformation field
  typedef itk::ImageFileWriter<  ImageType  > WriterType;
  WriterType::Pointer writer = WriterType::New();
  writer->SetInput (  image );
  writer->SetFileName( "fixed.png" );
  writer->Update();
}
 
 
void CreateMovingImage(ImageType::Pointer image)
{
  // Create a black image with a white square
  ImageType::IndexType start;
  start.Fill(0);
   
  ImageType::SizeType size;
  size.Fill(100);
  ImageType::RegionType region;
  region.SetSize(size);
  region.SetIndex(start);
   image->SetRegions(region);
  image->Allocate();
  image->FillBuffer(0);
  itk::ImageRegionIterator<ImageType> imageIterator(image,region);
  while(!imageIterator.IsAtEnd())
    {
    if(imageIterator.GetIndex()[0] > 50 && imageIterator.GetIndex()[0] < 60 &&
      imageIterator.GetIndex()[1] > 50 && imageIterator.GetIndex()[1] < 60)
      {
      imageIterator.Set(100);
      }
    ++imageIterator;
    }
 
  // Write the deformation field
  typedef itk::ImageFileWriter<  ImageType  > WriterType;
  WriterType::Pointer writer = WriterType::New();
  writer->SetInput (  image );
  writer->SetFileName( "moving.png" );
  writer->Update();
}
 
</source>
 
==LandmarkBasedTransformInitializer.py==
<source lang="python">
#!/usr/bin/env python
 
import itk
 
Dimension = 2
PixelType = itk.ctype('unsigned char')
ImageType = itk.Image[PixelType, Dimension]
 
def CreateFixedImage(image):
    start = itk.Index[Dimension]()
    start.Fill(0)
 
    size = itk.Size[Dimension]()
    size.Fill(100)
 
    region = itk.ImageRegion[Dimension]()
    region.SetSize(size)
    region.SetIndex(start)
 
    image.SetRegions(region)
    image.Allocate()
    image.FillBuffer(0)
 
    index = itk.Index[Dimension]()
    for ii in range(10, 20):
        for jj in range(10, 20):
            index[0] = ii
            index[1] = jj
            image.SetPixel(index, 255)
 
    writer = itk.ImageFileWriter.New(Input=image)
    writer.SetFileName("fixed.png")
    writer.Update()
 
def CreateMovingImage(image):
    start = itk.Index[Dimension]()
    start.Fill(0)
 
    size = itk.Size[Dimension]()
    size.Fill(100)
 
    region = itk.ImageRegion[Dimension]()
    region.SetSize(size)
    region.SetIndex(start)
 
    image.SetRegions(region)
    image.Allocate()
    image.FillBuffer(0)
 
    index = itk.Index[Dimension]()
    for ii in range(50, 60):
        for jj in range(50, 60):
            index[0] = ii
            index[1] = jj
            image.SetPixel(index, 100)
 
    writer = itk.ImageFileWriter.New(Input=image)
    writer.SetFileName("moving.png")
    writer.Update()
 
fixed_image = ImageType.New()
CreateFixedImage(fixed_image)
 
moving_image = ImageType.New()
CreateMovingImage(moving_image)
 
VectorComponentType = itk.ctype('float')
VectorType = itk.Vector[VectorComponentType, Dimension]
DisplacementFieldType = itk.Image[VectorType, Dimension]
 
Rigid2DTransformType = itk.Rigid2DTransform[itk.D]
landmark_based_transform_initializer = \
        itk.LandmarkBasedTransformInitializer[itk.Transform[itk.D, Dimension,
            Dimension]].New()
 
LandmarkPointType = itk.Point[itk.D, Dimension]
LandmarkContainerType = itk.vector[LandmarkPointType]
 
fixed_landmarks = LandmarkContainerType()
moving_landmarks = LandmarkContainerType()
 
fixed_point = LandmarkPointType()
moving_point = LandmarkPointType()
 
fixed_point[0] = 10
fixed_point[1] = 10
moving_point[0] = 50
moving_point[1] = 50
fixed_landmarks.push_back(fixed_point)
moving_landmarks.push_back(moving_point)
 
fixed_point[0] = 10
fixed_point[1] = 20
moving_point[0] = 50
moving_point[1] = 60
fixed_landmarks.push_back(fixed_point)
moving_landmarks.push_back(moving_point)
 
fixed_point[0] = 20
fixed_point[1] = 10
moving_point[0] = 60
moving_point[1] = 50
fixed_landmarks.push_back(fixed_point)
moving_landmarks.push_back(moving_point)
 
fixed_point[0] = 20
fixed_point[1] = 20
moving_point[0] = 60
moving_point[1] = 60
fixed_landmarks.push_back(fixed_point)
moving_landmarks.push_back(moving_point)
 
landmark_based_transform_initializer.SetFixedLandmarks(fixed_landmarks)
landmark_based_transform_initializer.SetMovingLandmarks(moving_landmarks)
 
transform = Rigid2DTransformType.New()
transform.SetIdentity()
landmark_based_transform_initializer.SetTransform(transform)
landmark_based_transform_initializer.InitializeTransform()
 
resampler = itk.ResampleImageFilter.New(Input=moving_image)
resampler.SetTransform(transform)
# resampler.SetReferenceImage(fixed_image)
resampler.SetSize(fixed_image.GetLargestPossibleRegion().GetSize())
resampler.SetOutputOrigin(fixed_image.GetOrigin())
resampler.SetOutputSpacing(fixed_image.GetSpacing())
resampler.SetOutputDirection(fixed_image.GetDirection())
resampler.SetDefaultPixelValue(200)
resampler.UpdateLargestPossibleRegion()
 
writer = itk.ImageFileWriter.New(Input=resampler.GetOutput())
writer.SetFileName("output.png")
writer.UpdateLargestPossibleRegion()
</source>

Latest revision as of 14:32, 7 June 2019

Warning: The media wiki content on this page is no longer maintained. The examples presented on the https://itk.org/Wiki/* pages likely require ITK version 4.13 or earlier releases. In many cases, the examples on this page no longer conform to the best practices for modern ITK versions.