ITK
6.0.0
Insight Toolkit
Examples/RegistrationITKv4/ImageRegistration16.cxx
/*=========================================================================
*
* Copyright NumFOCUS
*
* 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
*
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
// Software Guide : BeginLatex
//
// This example illustrates how to do registration with a 2D Translation
// Transform, the Normalized Mutual Information metric and the Amoeba
// optimizer.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
#include "
itkImageRegistrationMethod.h
"
#include "
itkTranslationTransform.h
"
#include "
itkMattesMutualInformationImageToImageMetric.h
"
#include "
itkAmoebaOptimizer.h
"
#include "
itkMersenneTwisterRandomVariateGenerator.h
"
#include "
itkImageFileReader.h
"
#include "
itkImageFileWriter.h
"
#include "
itkResampleImageFilter.h
"
#include "
itkCastImageFilter.h
"
// The following section of code implements a Command observer
// used to monitor the evolution of the registration process.
//
#include "
itkCommand.h
"
class
CommandIterationUpdate :
public
itk::Command
{
public
:
using
Self
= CommandIterationUpdate;
using
Superclass
=
itk::Command
;
using
Pointer
=
itk::SmartPointer<Self>
;
itkNewMacro(
Self
);
protected
:
CommandIterationUpdate() { m_IterationNumber = 0; }
public
:
using
OptimizerType =
itk::AmoebaOptimizer
;
using
OptimizerPointer =
const
OptimizerType *;
void
Execute
(
itk::Object
* caller,
const
itk::EventObject
& event)
override
{
Execute
((
const
itk::Object
*)caller, event);
}
void
Execute
(
const
itk::Object
*
object
,
const
itk::EventObject
& event)
override
{
auto
optimizer = static_cast<OptimizerPointer>(
object
);
if
(!itk::IterationEvent().CheckEvent(&event))
{
return
;
}
std::cout << m_IterationNumber++ <<
" "
;
std::cout << optimizer->GetCachedValue() <<
" "
;
std::cout << optimizer->GetCachedCurrentPosition() << std::endl;
}
private
:
unsigned
long
m_IterationNumber;
};
int
main(
int
argc,
char
* argv[])
{
if
(argc < 4)
{
std::cerr <<
"Missing Parameters "
<< std::endl;
std::cerr <<
"Usage: "
<< argv[0];
std::cerr <<
" fixedImageFile movingImageFile "
;
std::cerr <<
" outputImagefile "
;
std::cerr <<
" [initialTx] [initialTy]"
;
std::cerr <<
"[useExplicitPDFderivatives ] "
<< std::endl;
return
EXIT_FAILURE;
}
constexpr
unsigned
int
Dimension
= 2;
using
PixelType =
unsigned
char;
using
FixedImageType =
itk::Image<PixelType, Dimension>
;
using
MovingImageType =
itk::Image<PixelType, Dimension>
;
using
TransformType =
itk::TranslationTransform<double, Dimension>
;
using
OptimizerType =
itk::AmoebaOptimizer
;
using
InterpolatorType =
itk::LinearInterpolateImageFunction<MovingImageType, double>
;
using
RegistrationType =
itk::ImageRegistrationMethod<FixedImageType, MovingImageType>
;
using
MetricType =
itk::MattesMutualInformationImageToImageMetric
<FixedImageType,
MovingImageType>;
auto
transform =
TransformType::New
();
auto
optimizer =
OptimizerType::New
();
auto
interpolator =
InterpolatorType::New
();
auto
registration =
RegistrationType::New
();
registration->SetOptimizer(optimizer);
registration->SetTransform(transform);
registration->SetInterpolator(interpolator);
auto
metric =
MetricType::New
();
registration->SetMetric(metric);
// Software Guide : BeginLatex
//
// The metric requires two parameters to be selected: the number
// of bins used to compute the entropy and the number of spatial samples
// used to compute the density estimates. In typical application, 50
// histogram bins are sufficient and the metric is relatively insensitive
// to changes in the number of bins. The number of spatial samples
// to be used depends on the content of the image. If the images are
// smooth and do not contain much detail, then using approximately
// $1$ percent of the pixels will do. On the other hand, if the images
// are detailed, it may be necessary to use a much higher proportion,
// such as $20$ percent.
//
// \index{itk::Mattes\-Mutual\-Information\-Image\-To\-Image\-Metric!SetNumberOfHistogramBins()}
// \index{itk::Mattes\-Mutual\-Information\-Image\-To\-Image\-Metric!SetNumberOfSpatialSamples()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
metric->SetNumberOfHistogramBins(20);
metric->SetNumberOfSpatialSamples(10000);
// Software Guide : EndCodeSnippet
// For consistent results when regression testing.
metric->ReinitializeSeed(121212);
if
(argc > 6)
{
// Define whether to calculate the metric derivative by explicitly
// computing the derivatives of the joint PDF with respect to the
// Transform parameters, or doing it by progressively accumulating
// contributions from each bin in the joint PDF.
metric->SetUseExplicitPDFDerivatives(std::stoi(argv[6]));
}
const
unsigned
int
numberOfParameters = transform->GetNumberOfParameters();
using
FixedImageReaderType =
itk::ImageFileReader<FixedImageType>
;
using
MovingImageReaderType =
itk::ImageFileReader<MovingImageType>
;
auto
fixedImageReader =
FixedImageReaderType::New
();
auto
movingImageReader =
MovingImageReaderType::New
();
fixedImageReader->SetFileName(argv[1]);
movingImageReader->SetFileName(argv[2]);
registration->SetFixedImage(fixedImageReader->GetOutput());
registration->SetMovingImage(movingImageReader->GetOutput());
fixedImageReader->Update();
movingImageReader->Update();
const
FixedImageType::ConstPointer
fixedImage =
fixedImageReader->GetOutput();
registration->SetFixedImageRegion(fixedImage->GetBufferedRegion());
transform->SetIdentity();
using
ParametersType = RegistrationType::ParametersType;
ParametersType initialParameters = transform->GetParameters();
initialParameters[0] = 0.0;
initialParameters[1] = 0.0;
if
(argc > 5)
{
initialParameters[0] = std::stod(argv[4]);
initialParameters[1] = std::stod(argv[5]);
}
registration->SetInitialTransformParameters(initialParameters);
std::cout <<
"Initial transform parameters = "
;
std::cout << initialParameters << std::endl;
// Software Guide : BeginLatex
//
// The AmoebaOptimizer moves a simplex around the cost surface. Here we
// set the initial size of the simplex (5 units in each of the parameters)
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
OptimizerType::ParametersType simplexDelta(numberOfParameters);
simplexDelta.Fill(5.0);
optimizer->AutomaticInitialSimplexOff();
optimizer->SetInitialSimplexDelta(simplexDelta);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// We also adjust the tolerances on the optimizer to define convergence.
// Here, we used a tolerance on the parameters of 0.1 (which will be one
// tenth of image unit, in this case pixels). We also set the tolerance on
// the cost function value to define convergence. The metric we are using
// returns the value of Mutual Information. So we set the function
// convergence to be 0.001 bits (bits are the appropriate units for
// measuring Information).
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
optimizer->SetParametersConvergenceTolerance(0.1);
// 1/10th pixel
optimizer->SetFunctionConvergenceTolerance(0.001);
// 0.001 bits
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// In the case where the optimizer never succeeds in reaching the desired
// precision tolerance, it is prudent to establish a limit on the number of
// iterations to be performed. This maximum number is defined with the
// method \code{SetMaximumNumberOfIterations()}.
//
// \index{itk::Amoeba\-Optimizer!SetMaximumNumberOfIterations()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
optimizer->SetMaximumNumberOfIterations(200);
// Software Guide : EndCodeSnippet
// Create the Command observer and register it with the optimizer.
//
auto
observer =
CommandIterationUpdate::New
();
optimizer->AddObserver(itk::IterationEvent(), observer);
try
{
registration->Update();
std::cout <<
"Optimizer stop condition: "
<< registration->GetOptimizer()->GetStopConditionDescription()
<< std::endl;
}
catch
(
const
itk::ExceptionObject
& err)
{
std::cout <<
"ExceptionObject caught !"
<< std::endl;
std::cout << err << std::endl;
return
EXIT_FAILURE;
}
ParametersType finalParameters = registration->GetLastTransformParameters();
const
double
finalTranslationX = finalParameters[0];
const
double
finalTranslationY = finalParameters[1];
const
double
bestValue = optimizer->GetValue();
// Print out results
//
std::cout <<
"Result = "
<< std::endl;
std::cout <<
" Translation X = "
<< finalTranslationX << std::endl;
std::cout <<
" Translation Y = "
<< finalTranslationY << std::endl;
std::cout <<
" Metric value = "
<< bestValue << std::endl;
using
ResampleFilterType =
itk::ResampleImageFilter<MovingImageType, FixedImageType>
;
auto
finalTransform =
TransformType::New
();
finalTransform->SetParameters(finalParameters);
finalTransform->SetFixedParameters(transform->GetFixedParameters());
auto
resample =
ResampleFilterType::New
();
resample->SetTransform(finalTransform);
resample->SetInput(movingImageReader->GetOutput());
resample->SetSize(fixedImage->GetLargestPossibleRegion().GetSize());
resample->SetOutputOrigin(fixedImage->GetOrigin());
resample->SetOutputSpacing(fixedImage->GetSpacing());
resample->SetOutputDirection(fixedImage->GetDirection());
resample->SetDefaultPixelValue(100);
using
OutputImageType =
itk::Image<PixelType, Dimension>
;
using
WriterType =
itk::ImageFileWriter<OutputImageType>
;
auto
writer =
WriterType::New
();
writer->SetFileName(argv[3]);
writer->SetInput(resample->GetOutput());
writer->Update();
// Software Guide : EndCodeSnippet
return
EXIT_SUCCESS;
}
Pointer
SmartPointer< Self > Pointer
Definition:
itkAddImageFilter.h:93
ConstPointer
SmartPointer< const Self > ConstPointer
Definition:
itkAddImageFilter.h:94
itkImageFileReader.h
itk::ImageRegistrationMethod
Base class for Image Registration Methods.
Definition:
itkImageRegistrationMethod.h:70
itk::SmartPointer< Self >
itkCastImageFilter.h
itkAmoebaOptimizer.h
itkTranslationTransform.h
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:51
itk::Command
Superclass for callback/observer methods.
Definition:
itkCommand.h:45
itk::ImageFileWriter
Writes image data to a single file.
Definition:
itkImageFileWriter.h:90
itk::Command
class ITK_FORWARD_EXPORT Command
Definition:
itkObject.h:42
itk::TranslationTransform
Translation transformation of a vector space (e.g. space coordinates)
Definition:
itkTranslationTransform.h:43
itkImageRegistrationMethod.h
itk::Command::Execute
virtual void Execute(Object *caller, const EventObject &event)=0
itkMersenneTwisterRandomVariateGenerator.h
itkImageFileWriter.h
itk::ExceptionObject
Standard exception handling object.
Definition:
itkExceptionObject.h:50
itk::AmoebaOptimizer
Wrap of the vnl_amoeba algorithm.
Definition:
itkAmoebaOptimizer.h:67
itk::ResampleImageFilter
Resample an image via a coordinate transform.
Definition:
itkResampleImageFilter.h:90
itk::Object
Base class for most ITK classes.
Definition:
itkObject.h:61
itk::Image
Templated n-dimensional image class.
Definition:
itkImage.h:88
itk::EventObject
Abstraction of the Events used to communicating among filters and with GUIs.
Definition:
itkEventObject.h:58
New
static Pointer New()
AddImageFilter
Definition:
itkAddImageFilter.h:81
itkResampleImageFilter.h
itk::GTest::TypedefsAndConstructors::Dimension2::Dimension
constexpr unsigned int Dimension
Definition:
itkGTestTypedefsAndConstructors.h:44
itkCommand.h
Superclass
BinaryGeneratorImageFilter< TInputImage1, TInputImage2, TOutputImage > Superclass
Definition:
itkAddImageFilter.h:90
itkMattesMutualInformationImageToImageMetric.h
itk::MattesMutualInformationImageToImageMetric
Computes the mutual information between two images to be registered using the method of Mattes et al.
Definition:
itkMattesMutualInformationImageToImageMetric.h:117
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