ITK  5.2.0
Insight Toolkit
Examples/RegistrationITKv4/DeformableRegistration1.cxx
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*
* Copyright NumFOCUS
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* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
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* http://www.apache.org/licenses/LICENSE-2.0.txt
*
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* distributed under the License is distributed on an "AS IS" BASIS,
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* See the License for the specific language governing permissions and
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// Software Guide : BeginLatex
//
// The finite element (FEM) library within the Insight Toolkit can be
// used to solve deformable image registration problems. The first step in
// implementing a FEM-based registration is to include the appropriate
// header files.
//
// \index{Registration!Finite Element-Based}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
#include "itkFEMRegistrationFilter.h"
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Next, we use \code{using} type alias to instantiate all necessary classes.
// We define the image and element types we plan to use to solve a
// two-dimensional registration problem. We define multiple element
// types so that they can be used without recompiling the code.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using DiskImageType = itk::Image<unsigned char, 2>;
using ImageType = itk::Image<float, 2>;
using ElementType = itk::fem::Element2DC0LinearQuadrilateralMembrane;
using ElementType2 = itk::fem::Element2DC0LinearTriangularMembrane;
using FEMObjectType = itk::fem::FEMObject<2>;
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Note that in order to solve a three-dimensional registration
// problem, we would simply define 3D image and element types in lieu
// of those above. The following declarations could be used for a 3D
// problem:
//
// SoftwareGuide : EndLatex
// SoftwareGuide : BeginCodeSnippet
using FileImage3DType = itk::Image<unsigned char, 3>;
using Image3DType = itk::Image<float, 3>;
using Element3DType = itk::fem::Element3DC0LinearHexahedronMembrane;
using Element3DType2 = itk::fem::Element3DC0LinearTetrahedronMembrane;
using FEMObject3DType = itk::fem::FEMObject<3>;
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Once all the necessary components have been instantiated, we can
// instantiate the \doxygen{FEMRegistrationFilter}, which depends on the
// image input and output types.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using RegistrationType =
itk::fem::FEMRegistrationFilter<ImageType, ImageType, FEMObjectType>;
// Software Guide : EndCodeSnippet
int
main(int argc, char * argv[])
{
const char *fixedImageName, *movingImageName;
if (argc < 2)
{
std::cout << "Image file names missing" << std::endl;
std::cout << "Usage: " << argv[0] << " fixedImageFile movingImageFile"
<< std::endl;
return EXIT_FAILURE;
}
else
{
fixedImageName = argv[1];
movingImageName = argv[2];
}
// Software Guide : BeginLatex
//
// In order to begin the registration, we declare an instance of the
// \code{FEMRegistrationFilter} and set its parameters. For simplicity, we
// will call it \code{registrationFilter}.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
RegistrationType::Pointer registrationFilter = RegistrationType::New();
registrationFilter->SetMaxLevel(1);
registrationFilter->SetUseNormalizedGradient(true);
registrationFilter->ChooseMetric(0);
unsigned int maxiters = 20;
float E = 100;
float p = 1;
registrationFilter->SetElasticity(E, 0);
registrationFilter->SetRho(p, 0);
registrationFilter->SetGamma(1., 0);
registrationFilter->SetAlpha(1.);
registrationFilter->SetMaximumIterations(maxiters, 0);
registrationFilter->SetMeshPixelsPerElementAtEachResolution(4, 0);
registrationFilter->SetWidthOfMetricRegion(1, 0);
registrationFilter->SetNumberOfIntegrationPoints(2, 0);
registrationFilter->SetDoLineSearchOnImageEnergy(0);
registrationFilter->SetTimeStep(1.);
registrationFilter->SetEmployRegridding(false);
registrationFilter->SetUseLandmarks(false);
// Software Guide : EndCodeSnippet
// Read the image files
using FileSourceType = itk::ImageFileReader<DiskImageType>;
FileSourceType::Pointer movingfilter = FileSourceType::New();
movingfilter->SetFileName(movingImageName);
FileSourceType::Pointer fixedfilter = FileSourceType::New();
fixedfilter->SetFileName(fixedImageName);
std::cout << " reading moving " << movingImageName << std::endl;
std::cout << " reading fixed " << fixedImageName << std::endl;
try
{
movingfilter->Update();
}
catch (const itk::ExceptionObject & e)
{
std::cerr << "Exception caught during reference file reading "
<< std::endl;
std::cerr << e << std::endl;
return EXIT_FAILURE;
}
try
{
fixedfilter->Update();
}
catch (const itk::ExceptionObject & e)
{
std::cerr << "Exception caught during target file reading " << std::endl;
std::cerr << e << std::endl;
return EXIT_FAILURE;
}
// Rescale the image intensities so that they fall between 0 and 255
using FilterType =
FilterType::Pointer movingrescalefilter = FilterType::New();
FilterType::Pointer fixedrescalefilter = FilterType::New();
movingrescalefilter->SetInput(movingfilter->GetOutput());
fixedrescalefilter->SetInput(fixedfilter->GetOutput());
constexpr double desiredMinimum = 0.0;
constexpr double desiredMaximum = 255.0;
movingrescalefilter->SetOutputMinimum(desiredMinimum);
movingrescalefilter->SetOutputMaximum(desiredMaximum);
movingrescalefilter->UpdateLargestPossibleRegion();
fixedrescalefilter->SetOutputMinimum(desiredMinimum);
fixedrescalefilter->SetOutputMaximum(desiredMaximum);
fixedrescalefilter->UpdateLargestPossibleRegion();
// Histogram match the images
using HEFilterType =
HEFilterType::Pointer IntensityEqualizeFilter = HEFilterType::New();
IntensityEqualizeFilter->SetReferenceImage(fixedrescalefilter->GetOutput());
IntensityEqualizeFilter->SetInput(movingrescalefilter->GetOutput());
IntensityEqualizeFilter->SetNumberOfHistogramLevels(100);
IntensityEqualizeFilter->SetNumberOfMatchPoints(15);
IntensityEqualizeFilter->ThresholdAtMeanIntensityOn();
IntensityEqualizeFilter->Update();
// Set the images for registration filter
registrationFilter->SetFixedImage(fixedrescalefilter->GetOutput());
registrationFilter->SetMovingImage(IntensityEqualizeFilter->GetOutput());
std::string ofn = "fixed.mha";
writer->SetFileName(ofn.c_str());
writer->SetInput(registrationFilter->GetFixedImage());
try
{
writer->Write();
}
catch (const itk::ExceptionObject & excp)
{
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
ofn = "moving.mha";
writer2->SetFileName(ofn.c_str());
writer2->SetInput(registrationFilter->GetMovingImage());
try
{
writer2->Write();
}
catch (const itk::ExceptionObject & excp)
{
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
// Software Guide : BeginLatex
//
// In order to initialize the mesh of elements, we must first create
// ``dummy'' material and element objects and assign them to the
// registration filter. These objects are subsequently used to
// either read a predefined mesh from a file or generate a mesh using
// the software. The values assigned to the fields within the
// material object are arbitrary since they will be replaced with
// those specified earlier. Similarly, the element
// object will be replaced with those from the desired mesh.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
// Create the material properties
itk::fem::MaterialLinearElasticity::Pointer m;
m = itk::fem::MaterialLinearElasticity::New();
m->SetGlobalNumber(0);
// Young's modulus of the membrane
m->SetYoungsModulus(registrationFilter->GetElasticity());
m->SetCrossSectionalArea(1.0); // Cross-sectional area
m->SetThickness(1.0); // Thickness
m->SetMomentOfInertia(1.0); // Moment of inertia
m->SetPoissonsRatio(0.); // Poisson's ratio -- DONT CHOOSE 1.0!!
m->SetDensityHeatProduct(1.0); // Density-Heat capacity product
// Create the element type
ElementType::Pointer e1 = ElementType::New();
e1->SetMaterial(m);
registrationFilter->SetElement(e1);
registrationFilter->SetMaterial(m);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Now we are ready to run the registration:
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
registrationFilter->RunRegistration();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// To output the image resulting from the registration, we can call
// \code{GetWarpedImage()}. The image is written in floating point
// format.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
warpedImageWriter = itk::ImageFileWriter<ImageType>::New();
warpedImageWriter->SetInput(registrationFilter->GetWarpedImage());
warpedImageWriter->SetFileName("warpedMovingImage.mha");
try
{
warpedImageWriter->Update();
}
catch (const itk::ExceptionObject & excp)
{
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// We can also output the displacement field resulting from the
// registration; we can call \code{GetDisplacementField()} to get the
// multi-component image.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
DispWriterType::Pointer dispWriter = DispWriterType::New();
dispWriter->SetInput(registrationFilter->GetDisplacementField());
dispWriter->SetFileName("displacement.mha");
try
{
dispWriter->Update();
}
catch (const itk::ExceptionObject & excp)
{
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
// Software Guide : EndCodeSnippet
return EXIT_SUCCESS;
}
itk::HistogramMatchingImageFilter
Normalize the grayscale values for a source image by matching the shape of the source image histogram...
Definition: itkHistogramMatchingImageFilter.h:75
itkHistogramMatchingImageFilter.h
itkImageFileReader.h
itk::SmartPointer< Self >
itk::ImageFileReader
Data source that reads image data from a single file.
Definition: itkImageFileReader.h:75
itk::ImageFileWriter
Writes image data to a single file.
Definition: itkImageFileWriter.h:87
itkRescaleIntensityImageFilter.h
itkImageFileWriter.h
itk::ImageFileWriter::New
static Pointer New()
itk::RescaleIntensityImageFilter
Applies a linear transformation to the intensity levels of the input Image.
Definition: itkRescaleIntensityImageFilter.h:154
itk::Math::e
static constexpr double e
Definition: itkMath.h:54
itk::Image
Templated n-dimensional image class.
Definition: itkImage.h:86