ITK  5.2.0
Insight Toolkit
Examples/RegistrationITKv4/DeformableRegistration17.cxx
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/*******************************************************************************
Abstract: - Multiresolution symmetric forces demons registration - 4
multiresolution levels Created: July 8 2008 Last Revision 7/9/2008 by Vidya
Rajagopalan on 7/9/2008
Copyright (c) 2008, Bioimaging Systems Lab, Virginia Tech
All rights reserved.
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// Software Guide : BeginLatex
//
// This example illustrates the use of the
// \doxygen{MultiResolutionPDEDeformableRegistration} class for performing
// deformable registration of two $2D$ images using multiple resolution
// levels.
//
// The MultiResolution filter drives a SymmetricForcesDemonsRegistrationFilter
// at every level of resolution in the pyramid.
//
// \index{itk::MultiResolutionPDEDeformableRegistration}
// \index{itk::SymmetricForcesDemonsRegistrationFilter}
//
// Software Guide : EndLatex
//
// CREDITS:
//
// This example was contributed to ITK by
//
// Vidya Rajagopalan, Bioimaging Systems Lab, Virginia Tech
//
// The example was improved during the NAMIC programming week on July 2008
// http://wiki.na-mic.org/Wiki/index.php/2008_Summer_Project_Week
//
// National Alliance for Medical Image Computing (NAMIC),
// funded by the National Institutes of Health
// through the NIH Roadmap for Medical Research,
// Grant U54 EB005149.
//
// Data for these examples have been contributed by
//
// Paul Laurienti, Wake Forest University School of Medicine,
// Data acquired under NIH grant number NS042568
//
//
#include <iostream>
#include <cstdlib>
// ITK IO includes
// ITK Registration includes
unsigned int RmsCounter = 0;
double MaxRmsE[4] = { 0.8, 0.75, 0.4, 0.2 };
// The following section of code implements a Command observer
// that will monitor the evolution of the registration process.
// This observer has a layer of intelligence, for deciding what
// MaximumRMS convergence criteria to use at every resolution level.
//
class CommandIterationUpdate : public itk::Command
{
public:
using Self = CommandIterationUpdate;
using Superclass = itk::Command;
using Pointer = itk::SmartPointer<Self>;
itkNewMacro(Self);
protected:
CommandIterationUpdate() = default;
// define ITK short-hand types
using PixelType = short;
using InternalPixelType = float;
using ImageType = itk::Image<PixelType, 2>;
using InternalImageType = itk::Image<InternalPixelType, 2>;
using VectorPixelType = itk::Vector<float, 2>;
using DisplacementFieldType = itk::Image<VectorPixelType, 2>;
using RegistrationFilterType =
InternalImageType,
DisplacementFieldType>;
public:
void
Execute(const itk::Object *, const itk::EventObject &) override
{
std::cout << "Warning: The const Execute method shouldn't be called"
<< std::endl;
}
void
Execute(itk::Object * caller, const itk::EventObject & event) override
{
auto * filter = static_cast<RegistrationFilterType *>(caller);
if (!(itk::IterationEvent().CheckEvent(&event)))
{
return;
}
if (filter)
{
filter->SetMaximumRMSError(MaxRmsE[RmsCounter]);
std::cout << filter->GetMetric()
<< " RMS Change: " << filter->GetRMSChange() << std::endl;
std::cout << "Level Tolerance= " << filter->GetMaximumRMSError()
<< std::endl;
}
}
};
//
// The following command observer reports the progress of the registration
// inside a given resolution level.
//
class CommandResolutionLevelUpdate : public itk::Command
{
public:
using Self = CommandResolutionLevelUpdate;
using Superclass = itk::Command;
using Pointer = itk::SmartPointer<Self>;
itkNewMacro(Self);
protected:
CommandResolutionLevelUpdate() = default;
public:
void
Execute(itk::Object * caller, const itk::EventObject & event) override
{
Execute((const itk::Object *)caller, event);
}
void
Execute(const itk::Object *, const itk::EventObject &) override
{
std::cout << "----------------------------------" << std::endl;
RmsCounter = RmsCounter + 1;
std::cout << "----------------------------------" << std::endl;
}
};
int
main(int argc, char * argv[])
{
// Verify the number of parameters in the command line
if (argc != 5)
{
std::cerr << "usage: " << std::endl;
std::cerr << argv[0]
<< " fixedImage movingImage registeredImage deformationField"
<< std::endl;
return EXIT_FAILURE;
}
// define ITK short-hand types
constexpr unsigned int Dimension = 2;
using PixelType = short;
using InternalPixelType = float;
using InternalImageType = itk::Image<InternalPixelType, Dimension>;
// setup input file readers
using ReaderType = itk::ImageFileReader<ImageType>;
ReaderType::Pointer targetReader = ReaderType::New();
targetReader->SetFileName(argv[1]);
targetReader->Update();
ReaderType::Pointer sourceReader = ReaderType::New();
sourceReader->SetFileName(argv[2]);
sourceReader->Update();
// cast target and source to float
ImageCasterType::Pointer targetImageCaster = ImageCasterType::New();
ImageCasterType::Pointer sourceImageCaster = ImageCasterType::New();
targetImageCaster->SetInput(targetReader->GetOutput());
sourceImageCaster->SetInput(sourceReader->GetOutput());
// match the histograms between source and target
using MatchingFilterType =
MatchingFilterType::Pointer matcher = MatchingFilterType::New();
matcher->SetInput(sourceImageCaster->GetOutput());
matcher->SetReferenceImage(targetImageCaster->GetOutput());
matcher->SetNumberOfHistogramLevels(1024);
matcher->SetNumberOfMatchPoints(7);
matcher->ThresholdAtMeanIntensityOn();
// setup the deformation field and filter
using VectorPixelType = itk::Vector<float, Dimension>;
using DisplacementFieldType = itk::Image<VectorPixelType, Dimension>;
using RegistrationFilterType =
InternalImageType,
DisplacementFieldType>;
RegistrationFilterType::Pointer filter = RegistrationFilterType::New();
filter->SetStandardDeviations(1.0);
//
// Create the Command observer and register it with the registration filter.
//
CommandIterationUpdate::Pointer observer = CommandIterationUpdate::New();
filter->AddObserver(itk::IterationEvent(), observer);
// use multiresolution scheme
using MultiResRegistrationFilterType =
InternalImageType,
DisplacementFieldType>;
MultiResRegistrationFilterType::Pointer multires =
MultiResRegistrationFilterType::New();
multires->SetRegistrationFilter(filter);
multires->SetNumberOfLevels(4);
multires->SetFixedImage(targetImageCaster->GetOutput());
multires->SetMovingImage(matcher->GetOutput());
unsigned int nIterations[4] = { 40, 40, 32, 32 };
multires->SetNumberOfIterations(nIterations);
//
// Create the Command observer and register it with the registration filter.
//
CommandResolutionLevelUpdate::Pointer levelobserver =
CommandResolutionLevelUpdate::New();
multires->AddObserver(itk::IterationEvent(), levelobserver);
// apply the registration filter
try
{
multires->Update();
}
catch (const itk::ExceptionObject & excp)
{
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
using DisplacementFieldTransformType =
auto displacementTransform = DisplacementFieldTransformType::New();
displacementTransform->SetDisplacementField(multires->GetOutput());
// compute the output (warped) image
using InterpolatorPrecisionType = double;
using WarperType = itk::ResampleImageFilter<ImageType,
ImageType,
InterpolatorPrecisionType,
InternalPixelType>;
using InterpolatorType =
WarperType::Pointer warper = WarperType::New();
InterpolatorType::Pointer interpolator = InterpolatorType::New();
ImageType::Pointer targetImage = targetReader->GetOutput();
warper->SetInput(sourceReader->GetOutput());
warper->SetInterpolator(interpolator);
warper->SetOutputSpacing(targetImage->GetSpacing());
warper->SetOutputOrigin(targetImage->GetOrigin());
warper->SetOutputDirection(targetImage->GetDirection());
warper->SetTransform(displacementTransform);
using WriterType = itk::ImageFileWriter<ImageType>;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName(argv[3]);
writer->SetInput(warper->GetOutput());
try
{
writer->Update();
}
catch (const itk::ExceptionObject & excp)
{
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
// write the deformation field
using DeformationWriterType = itk::ImageFileWriter<DisplacementFieldType>;
DeformationWriterType::Pointer defwriter = DeformationWriterType::New();
defwriter->SetFileName(argv[4]);
defwriter->SetInput(multires->GetOutput());
try
{
defwriter->Update();
}
catch (const itk::ExceptionObject & excp)
{
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
itk::CastImageFilter
Casts input pixels to output pixel type.
Definition: itkCastImageFilter.h:104
itkDisplacementFieldTransform.h
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
itkMultiResolutionImageRegistrationMethod.h
itkMultiResolutionPDEDeformableRegistration.h
itk::Vector
A templated class holding a n-Dimensional vector.
Definition: itkVector.h:62
itkImageFileReader.h
itk::SmartPointer< Self >
itkCastImageFilter.h
itk::DisplacementFieldTransform
Provides local/dense/high-dimensionality transformation via a a displacement field.
Definition: itkDisplacementFieldTransform.h:86
itk::ImageFileReader
Data source that reads image data from a single file.
Definition: itkImageFileReader.h:75
itk::LinearInterpolateImageFunction
Linearly interpolate an image at specified positions.
Definition: itkLinearInterpolateImageFunction.h:50
itk::Command
Superclass for callback/observer methods.
Definition: itkCommand.h:45
itk::ImageFileWriter
Writes image data to a single file.
Definition: itkImageFileWriter.h:88
itk::Command
class ITK_FORWARD_EXPORT Command
Definition: itkObject.h:43
itk::SymmetricForcesDemonsRegistrationFilter
Deformably register two images using the demons algorithm.
Definition: itkSymmetricForcesDemonsRegistrationFilter.h:70
itk::Command::Execute
virtual void Execute(Object *caller, const EventObject &event)=0
itkImageFileWriter.h
itk::MultiResolutionPDEDeformableRegistration
Framework for performing multi-resolution PDE deformable registration.
Definition: itkMultiResolutionPDEDeformableRegistration.h:88
itkSymmetricForcesDemonsRegistrationFilter.h
itk::ResampleImageFilter
Resample an image via a coordinate transform.
Definition: itkResampleImageFilter.h:90
itk::Object
Base class for most ITK classes.
Definition: itkObject.h:62
itk::Image
Templated n-dimensional image class.
Definition: itkImage.h:86
itk::EventObject
Abstraction of the Events used to communicating among filters and with GUIs.
Definition: itkEventObject.h:57
itkResampleImageFilter.h
itk::GTest::TypedefsAndConstructors::Dimension2::Dimension
constexpr unsigned int Dimension
Definition: itkGTestTypedefsAndConstructors.h:44