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/*=========================================================================
*
* Copyright UMC Utrecht and contributors
*
* 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
*
* http://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.
*
*=========================================================================*/
#ifndef elxDeformationFieldTransform_hxx
#define elxDeformationFieldTransform_hxx
#include "elxDeformationFieldTransform.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkVectorNearestNeighborInterpolateImageFunction.h"
#include "itkVectorLinearInterpolateImageFunction.h"
#include "itkChangeInformationImageFilter.h"
namespace elastix
{
/**
* ********************* Constructor ****************************
*/
template <class TElastix>
DeformationFieldTransform<TElastix>::DeformationFieldTransform()
{
/** Initialize. */
this->SetCurrentTransform(this->m_DeformationFieldInterpolatingTransform);
/** Make sure that the TransformBase::WriteToFile() does
* not read the transformParameters in the file. */
this->SetReadWriteTransformParameters(false);
/** Initialize to identity. */
this->m_OriginalDeformationFieldDirection.SetIdentity();
} // end Constructor
/**
* ************************* ReadFromFile ************************
*/
template <class TElastix>
void
DeformationFieldTransform<TElastix>::ReadFromFile()
{
// \todo Test this ReadFromFile function.
/** Call the ReadFromFile from the TransformBase. */
this->Superclass2::ReadFromFile();
/** Read deformationFieldImage-name from parameter-file. */
std::string fileName = "";
this->m_Configuration->ReadParameter(fileName, "DeformationFieldFileName", 0);
if (fileName.empty())
{
log::error("ERROR: the entry (DeformationFieldFileName \"...\") is missing in the transform parameter file!");
itkExceptionMacro("Error while reading transform parameter file!");
}
/** Possibly overrule the direction cosines. */
const auto infoChanger = itk::ChangeInformationImageFilter<DeformationFieldType>::New();
infoChanger->SetChangeDirection(!this->GetElastix()->GetUseDirectionCosines());
try
{
const auto image = itk::ReadImage<DeformationFieldType>(fileName);
infoChanger->SetInput(image);
infoChanger->Update();
/** Store the original direction for later use */
this->m_OriginalDeformationFieldDirection = image->GetDirection();
}
catch (itk::ExceptionObject & excp)
{
/** Add information to the exception. */
excp.SetLocation("DeformationFieldTransform - ReadFromFile()");
std::string err_str = excp.GetDescription();
err_str += "\nError occurred while reading the deformationField image.\n";
excp.SetDescription(err_str);
/** Pass the exception to an higher level. */
throw;
}
/** Set the deformationFieldImage in the
* itkDeformationFieldInterpolatingTransform.
*/
this->m_DeformationFieldInterpolatingTransform->SetDeformationField(infoChanger->GetOutput());
using InterpolatorType = typename DeformationFieldInterpolatingTransformType::DeformationFieldInterpolatorType;
using NNInterpolatorType = itk::VectorNearestNeighborInterpolateImageFunction<DeformationFieldType, CoordRepType>;
using LinInterpolatorType = itk::VectorLinearInterpolateImageFunction<DeformationFieldType, CoordRepType>;
typename InterpolatorType::Pointer interpolator; // default-constructed (null)
unsigned int interpolationOrder = 0;
this->m_Configuration->ReadParameter(interpolationOrder, "DeformationFieldInterpolationOrder", 0);
if (interpolationOrder == 0)
{
interpolator = NNInterpolatorType::New();
}
else if (interpolationOrder == 1)
{
interpolator = LinInterpolatorType::New();
}
else
{
log::error(
std::ostringstream{} << "Error while reading DeformationFieldInterpolationOrder from the parameter file\n"
<< "DeformationFieldInterpolationOrder can only be 0 or 1!");
itkExceptionMacro("Invalid deformation field interpolation order selected!");
}
this->m_DeformationFieldInterpolatingTransform->SetDeformationFieldInterpolator(interpolator);
} // end ReadFromFile()
/**
* ************************* WriteDerivedTransformDataToFile ************************
*
* Saves the TransformParameters as a vector and if wanted
* also as a deformation field.
*/
template <class TElastix>
void
DeformationFieldTransform<TElastix>::WriteDerivedTransformDataToFile() const
{
// \todo Finish and Test this function.
/** Write the interpolation order to file */
std::string interpolatorName =
this->m_DeformationFieldInterpolatingTransform->GetDeformationFieldInterpolator()->GetNameOfClass();
/** Possibly change the direction cosines to there original value */
const auto infoChanger = itk::ChangeInformationImageFilter<DeformationFieldType>::New();
infoChanger->SetOutputDirection(this->m_OriginalDeformationFieldDirection);
infoChanger->SetChangeDirection(!this->GetElastix()->GetUseDirectionCosines());
infoChanger->SetInput(this->m_DeformationFieldInterpolatingTransform->GetDeformationField());
/** Write the deformation field image. */
try
{
itk::WriteImage(infoChanger->GetOutput(), TransformIO::MakeDeformationFieldFileName(*this));
}
catch (itk::ExceptionObject & excp)
{
/** Add information to the exception. */
excp.SetLocation("DeformationFieldTransform - WriteToFile()");
std::string err_str = excp.GetDescription();
err_str += "\nError while writing the deformationFieldImage.\n";
excp.SetDescription(err_str);
/** Print the exception. */
log::error(std::ostringstream{} << excp);
}
} // end WriteDerivedTransformDataToFile()
/**
* ************************* CustomizeTransformParameterMap ************************
*/
template <class TElastix>
auto
DeformationFieldTransform<TElastix>::CreateDerivedTransformParameterMap() const -> ParameterMapType
{
const std::string interpolatorName =
m_DeformationFieldInterpolatingTransform->GetDeformationFieldInterpolator()->GetNameOfClass();
const auto interpolationOrder = (interpolatorName == "LinearInterpolateImageFunction") ? 1U : 0U;
return { { "DeformationFieldFileName", { TransformIO::MakeDeformationFieldFileName(*this) } },
{ "DeformationFieldInterpolationOrder", { Conversion::ToString(interpolationOrder) } } };
} // end CustomizeTransformParameterMap()
} // end namespace elastix
#endif // end #ifndef elxDeformationFieldTransform_hxx
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