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// This program does SyN registration with hard-coded parameters.
// The whole registration process is included in "simpleSynReg" function.
// The Usage:
// This program does not have any flag. You should just put the arguments after the program name.
/*
~/simpleSynRegistration
fixed image
moving image
initial transform
output prefix file name
*/
#include "antsUtilities.h"
#include "itkantsRegistrationHelper.h"
namespace ants
{
using RegistrationHelperType = ants::RegistrationHelper<double, 3>;
using ImageType = RegistrationHelperType::ImageType;
using CompositeTransformType = RegistrationHelperType::CompositeTransformType;
CompositeTransformType::TransformTypePointer
simpleSynReg(ImageType::Pointer & fixedImage,
ImageType::Pointer & movingImage,
const CompositeTransformType::Pointer compositeInitialTransform)
{
RegistrationHelperType::Pointer regHelper = RegistrationHelperType::New();
const std::string whichMetric = "mattes";
RegistrationHelperType::MetricEnumeration curMetric = regHelper->StringToMetricType(whichMetric);
const float lowerQuantile(0.0F);
const float upperQuantile(1.0F);
const bool doWinsorize(false);
regHelper->SetWinsorizeImageIntensities(doWinsorize, lowerQuantile, upperQuantile);
const bool doHistogramMatch(true);
regHelper->SetUseHistogramMatching(doHistogramMatch);
const bool doEstimateLearningRateAtEachIteration = true;
regHelper->SetDoEstimateLearningRateAtEachIteration(doEstimateLearningRateAtEachIteration);
std::vector<std::vector<unsigned int>> iterationList;
std::vector<double> convergenceThresholdList;
std::vector<unsigned int> convergenceWindowSizeList;
std::vector<std::vector<unsigned int>> shrinkFactorsList;
std::vector<std::vector<float>> smoothingSigmasList;
std::vector<unsigned int> iterations(3);
iterations[0] = 100;
iterations[1] = 70;
iterations[2] = 20;
std::cout << " number of levels = 3 " << std::endl;
iterationList.push_back(iterations);
const double convergenceThreshold = 1e-6;
convergenceThresholdList.push_back(convergenceThreshold);
constexpr unsigned int convergenceWindowSize = 10;
convergenceWindowSizeList.push_back(convergenceWindowSize);
std::vector<unsigned int> factors(3);
factors[0] = 3;
factors[1] = 2;
factors[2] = 1;
shrinkFactorsList.push_back(factors);
std::vector<float> sigmas(3);
sigmas[0] = 2;
sigmas[1] = 1;
sigmas[2] = 0;
smoothingSigmasList.push_back(sigmas);
std::vector<bool> smoothingSigmasAreInPhysicalUnitsList;
smoothingSigmasAreInPhysicalUnitsList.push_back(true); // Historical behavior before 2012-10-07
constexpr float samplingPercentage = 1.0;
RegistrationHelperType::SamplingStrategy samplingStrategy = RegistrationHelperType::none;
constexpr unsigned int binOption = 200;
bool useGradientFilter = false;
regHelper->AddMetric(curMetric, fixedImage, movingImage, 0, 1.0, samplingStrategy, binOption, 1, useGradientFilter, samplingPercentage);
const float learningRate(0.25F);
const float varianceForUpdateField(3.0F);
const float varianceForTotalField(0.0F);
regHelper->AddSyNTransform(learningRate, varianceForUpdateField, varianceForTotalField);
regHelper->SetMovingInitialTransform(compositeInitialTransform);
regHelper->SetIterations(iterationList);
regHelper->SetConvergenceWindowSizes(convergenceWindowSizeList);
regHelper->SetConvergenceThresholds(convergenceThresholdList);
regHelper->SetSmoothingSigmas(smoothingSigmasList);
regHelper->SetShrinkFactors(shrinkFactorsList);
regHelper->SetSmoothingSigmasAreInPhysicalUnits(smoothingSigmasAreInPhysicalUnitsList);
if (regHelper->DoRegistration() == EXIT_SUCCESS)
{
// Get the output transform
CompositeTransformType::Pointer outputCompositeTransform = regHelper->GetModifiableCompositeTransform();
// write out transform actually computed, so skip the initial transform
CompositeTransformType::TransformTypePointer resultTransform = outputCompositeTransform->GetNthTransform(1);
return resultTransform;
}
std::cerr << "FATAL ERROR: REGISTRATION PROCESS WAS UNSUCCESSFUL" << std::endl;
CompositeTransformType::TransformTypePointer invalidTransform = nullptr;
return invalidTransform; // Return an empty registration type.
}
int
simpleSynRegistration(std::vector<std::string> args, std::ostream * /*out_stream = nullptr */)
{
// the arguments coming in as 'args' is a replacement for the standard (argc,argv) format
// Just notice that the argv[i] equals to args[i-1]
// and the argc equals:
int argc = args.size() + 1;
if (argc != 5)
{
std::cerr
<< "Usage: simpleSynRegistration\n"
<< "<Fixed Image> , <Moving Image> , <Initial Transform> , <Output prefix file name without any extension>"
<< std::endl;
return EXIT_FAILURE;
}
// antscout->set_stream( out_stream );
ImageType::Pointer fixedImage;
ImageType::Pointer movingImage;
// ========read the fixed image
using ImageReaderType = itk::ImageFileReader<ImageType>;
ImageReaderType::Pointer fixedImageReader = ImageReaderType::New();
fixedImageReader->SetFileName(args[0]);
fixedImageReader->Update();
fixedImage = fixedImageReader->GetOutput();
try
{
fixedImage->Update();
}
catch (const itk::ExceptionObject & excp)
{
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
// ==========read the moving image
ImageReaderType::Pointer movingImageReader = ImageReaderType::New();
movingImageReader->SetFileName(args[1]);
movingImageReader->Update();
movingImage = movingImageReader->GetOutput();
try
{
movingImage->Update();
}
catch (const itk::ExceptionObject & excp)
{
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
std::cout << " fixed image: " << args[0] << std::endl;
std::cout << " moving image: " << args[1] << std::endl;
// ===========Read the initial transform and write that in a composite transform
using TransformType = RegistrationHelperType::TransformType;
TransformType::Pointer initialTransform = itk::ants::ReadTransform<double, 3>(args[2]);
if (initialTransform.IsNull())
{
std::cerr << "Can't read initial transform " << std::endl;
return EXIT_FAILURE;
}
CompositeTransformType::Pointer compositeInitialTransform = CompositeTransformType::New();
compositeInitialTransform->AddTransform(initialTransform);
// =========write the output transform
// compute the output transform by calling the "simpleSynReg" function
CompositeTransformType::TransformTypePointer outputTransform =
simpleSynReg(fixedImage, movingImage, compositeInitialTransform);
if (outputTransform.IsNull())
{
std::cerr << "ERROR: Registration FAILED TO PRODUCE VALID TRANSFORM ...\n" << std::endl;
return EXIT_FAILURE;
}
std::cout << "***** Ready to write the results ...\n" << std::endl;
std::stringstream outputFileName;
outputFileName << args[3] << "Warp.nii.gz";
itk::ants::WriteTransform<double, 3>(outputTransform, outputFileName.str());
// compute and write the inverse of the output transform
const bool writeInverse(true);
if (writeInverse)
{
using DisplacementFieldTransformType = RegistrationHelperType::DisplacementFieldTransformType;
DisplacementFieldTransformType::Pointer dispTransform =
dynamic_cast<DisplacementFieldTransformType *>(outputTransform.GetPointer());
using DisplacementFieldType = DisplacementFieldTransformType::DisplacementFieldType;
std::stringstream outputInverseFileName;
outputInverseFileName << args[3] << "InverseWarp.nii.gz";
using InverseWriterType = itk::ImageFileWriter<DisplacementFieldType>;
InverseWriterType::Pointer inverseWriter = InverseWriterType::New();
inverseWriter->SetInput(dispTransform->GetInverseDisplacementField());
inverseWriter->SetFileName(outputInverseFileName.str().c_str());
inverseWriter->Update();
}
return EXIT_SUCCESS;
}
} // namespace ants
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