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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 elxResamplerBase_hxx
#define elxResamplerBase_hxx
#include "elxResamplerBase.h"
#include "elxConversion.h"
#include <itkDeref.h>
#include "itkImageFileCastWriter.h"
#include "itkChangeInformationImageFilter.h"
#include "itkAdvancedRayCastInterpolateImageFunction.h"
#include "itkTimeProbe.h"
#include <cassert>
namespace elastix
{
/**
* ******************* BeforeRegistrationBase *******************
*/
template <class TElastix>
void
ResamplerBase<TElastix>::BeforeRegistrationBase()
{
/** Connect the components. */
this->SetComponents();
/** Set the size of the image to be produced by the resampler. */
/** Get a pointer to the fixedImage.
* \todo make it a cast to the fixed image type
*/
using FixedImageType = typename ElastixType::FixedImageType;
FixedImageType & fixedImage = itk::Deref(this->m_Elastix->GetFixedImage());
ITKBaseType & resampleImageFilter = this->GetSelf();
/** Set the region info to the same values as in the fixedImage. */
resampleImageFilter.SetSize(fixedImage.GetLargestPossibleRegion().GetSize());
resampleImageFilter.SetOutputStartIndex(fixedImage.GetLargestPossibleRegion().GetIndex());
resampleImageFilter.SetOutputOrigin(fixedImage.GetOrigin());
resampleImageFilter.SetOutputSpacing(fixedImage.GetSpacing());
resampleImageFilter.SetOutputDirection(fixedImage.GetDirection());
const Configuration & configuration = itk::Deref(Superclass::GetConfiguration());
/** Set the DefaultPixelValue (for pixels in the resampled image
* that come from outside the original (moving) image.
*/
OutputPixelType defaultPixelValue{};
configuration.ReadParameter(defaultPixelValue, "DefaultPixelValue", 0, false);
/** Set the defaultPixelValue. */
resampleImageFilter.SetDefaultPixelValue(defaultPixelValue);
} // end BeforeRegistrationBase()
/**
* ******************* AfterEachResolutionBase ********************
*/
template <class TElastix>
void
ResamplerBase<TElastix>::AfterEachResolutionBase()
{
/** Set the final transform parameters. */
this->GetElastix()->GetElxTransformBase()->SetFinalParameters();
/** What is the current resolution level? */
const unsigned int level = this->m_Registration->GetAsITKBaseType()->GetCurrentLevel();
const Configuration & configuration = itk::Deref(Superclass::GetConfiguration());
/** Decide whether or not to write the result image this resolution. */
bool writeResultImageThisResolution = false;
configuration.ReadParameter(
writeResultImageThisResolution, "WriteResultImageAfterEachResolution", "", level, 0, false);
const std::string outputDirectoryPath = configuration.GetCommandLineArgument("-out");
/** Writing result image. */
if (writeResultImageThisResolution && !outputDirectoryPath.empty())
{
/** Create a name for the final result. */
const auto resultImageName = configuration.RetrieveParameterStringValue("result", "ResultImageName", 0, false);
std::string resultImageFormat = "mhd";
configuration.ReadParameter(resultImageFormat, "ResultImageFormat", 0, false);
std::ostringstream makeFileName;
makeFileName << outputDirectoryPath << resultImageName << '.' << configuration.GetElastixLevel() << ".R" << level
<< "." << resultImageFormat;
/** Time the resampling. */
itk::TimeProbe timer;
timer.Start();
/** Apply the final transform, and save the result. */
log::info("Applying transform this resolution ...");
try
{
this->ResampleAndWriteResultImage(makeFileName.str(), true);
}
catch (const itk::ExceptionObject & excp)
{
log::error(std::ostringstream{} << "Exception caught: \n" << excp << "Resuming elastix.");
}
/** Print the elapsed time for the resampling. */
timer.Stop();
log::info(std::ostringstream{} << " Applying transform took " << Conversion::SecondsToDHMS(timer.GetMean(), 2));
} // end if
} // end AfterEachResolutionBase()
/**
* ******************* AfterEachIterationBase ********************
*/
template <class TElastix>
void
ResamplerBase<TElastix>::AfterEachIterationBase()
{
/** What is the current resolution level? */
const unsigned int level = this->m_Registration->GetAsITKBaseType()->GetCurrentLevel();
/** What is the current iteration number? */
const unsigned int iter = this->m_Elastix->GetIterationCounter();
const Configuration & configuration = itk::Deref(Superclass::GetConfiguration());
/** Decide whether or not to write the result image this iteration. */
bool writeResultImageThisIteration = false;
configuration.ReadParameter(writeResultImageThisIteration, "WriteResultImageAfterEachIteration", "", level, 0, false);
const std::string outputDirectoryPath = configuration.GetCommandLineArgument("-out");
/** Writing result image. */
if (writeResultImageThisIteration && !outputDirectoryPath.empty())
{
/** Set the final transform parameters. */
this->GetElastix()->GetElxTransformBase()->SetFinalParameters();
/** Create a name for the final result. */
const auto resultImageName = configuration.RetrieveParameterStringValue("result", "ResultImageName", 0, false);
std::string resultImageFormat = "mhd";
configuration.ReadParameter(resultImageFormat, "ResultImageFormat", 0, false);
std::ostringstream makeFileName;
makeFileName << outputDirectoryPath << resultImageName << '.' << configuration.GetElastixLevel() << ".R" << level
<< ".It" << std::setfill('0') << std::setw(7) << iter << "." << resultImageFormat;
/** Apply the final transform, and save the result. */
try
{
this->ResampleAndWriteResultImage(makeFileName.str(), false);
}
catch (const itk::ExceptionObject & excp)
{
log::error(std::ostringstream{} << "Exception caught: \n" << excp << "Resuming elastix.");
}
} // end if
} // end AfterEachIterationBase()
/**
* ******************* AfterRegistrationBase ********************
*/
template <class TElastix>
void
ResamplerBase<TElastix>::AfterRegistrationBase()
{
/** Set the final transform parameters. */
this->GetElastix()->GetElxTransformBase()->SetFinalParameters();
const Configuration & configuration = itk::Deref(Superclass::GetConfiguration());
/** Decide whether or not to write the result image. */
std::string writeResultImage = "true";
configuration.ReadParameter(writeResultImage, "WriteResultImage", 0);
const auto isElastixLibrary = BaseComponent::IsElastixLibrary();
/** The library interface may executed multiple times in
* a session in which case the images should not be released
* However, if this is not the library interface:
* Release memory to be able to resample in case a limited
* amount of memory is available.
*/
bool releaseMemoryBeforeResampling{ !isElastixLibrary };
configuration.ReadParameter(releaseMemoryBeforeResampling, "ReleaseMemoryBeforeResampling", 0, false);
if (releaseMemoryBeforeResampling)
{
this->ReleaseMemory();
}
/** Writing result image. */
if (writeResultImage == "true")
{
/**
* Create the result image and put it in ResultImageContainer
* Only necessary when compiling elastix as a library!
*/
if (isElastixLibrary)
{
this->CreateItkResultImage();
}
if (const std::string outputDirectoryPath = configuration.GetCommandLineArgument("-out");
!outputDirectoryPath.empty())
{
/** Create a name for the final result. */
const auto resultImageName = configuration.RetrieveParameterStringValue("result", "ResultImageName", 0, false);
std::string resultImageFormat = "mhd";
configuration.ReadParameter(resultImageFormat, "ResultImageFormat", 0);
std::ostringstream makeFileName;
makeFileName << outputDirectoryPath << resultImageName << '.' << configuration.GetElastixLevel() << "."
<< resultImageFormat;
/** Time the resampling. */
itk::TimeProbe timer;
timer.Start();
/** Apply the final transform, and save the result,
* by calling ResampleAndWriteResultImage.
*/
log::info("\nApplying final transform ...");
try
{
this->ResampleAndWriteResultImage(makeFileName.str(), true);
}
catch (const itk::ExceptionObject & excp)
{
log::error(std::ostringstream{} << "Exception caught: \n" << excp << "Resuming elastix.");
}
/** Print the elapsed time for the resampling. */
timer.Stop();
log::info(std::ostringstream{} << " Applying final transform took "
<< Conversion::SecondsToDHMS(timer.GetMean(), 2));
}
}
else
{
/** Do not apply the final transform. */
log::info(std::ostringstream{} << '\n'
<< "Skipping applying final transform, no resulting output image generated.");
} // end if
} // end AfterRegistrationBase()
/**
* *********************** SetComponents ************************
*/
template <class TElastix>
void
ResamplerBase<TElastix>::SetComponents()
{
/** Set the transform, the interpolator and the inputImage
* (which is the moving image).
*/
ITKBaseType & resampleImageFilter = this->GetSelf();
resampleImageFilter.SetTransform(BaseComponent::AsITKBaseType(this->m_Elastix->GetElxTransformBase()));
resampleImageFilter.SetInterpolator(BaseComponent::AsITKBaseType(this->m_Elastix->GetElxResampleInterpolatorBase()));
resampleImageFilter.SetInput(this->m_Elastix->GetMovingImage());
} // end SetComponents()
/**
* ******************* ResampleAndWriteResultImage ********************
*/
template <class TElastix>
void
ResamplerBase<TElastix>::ResampleAndWriteResultImage(const std::string & filename, const bool showProgress)
{
ITKBaseType & resampleImageFilter = this->GetSelf();
/** Make sure the resampler is updated. */
resampleImageFilter.Modified();
const Configuration & configuration = itk::Deref(Superclass::GetConfiguration());
/** Add a progress observer to the resampler. */
const bool showProgressPercentage = configuration.RetrieveParameterValue(false, "ShowProgressPercentage", 0, false);
const auto progressObserver =
(showProgress && showProgressPercentage) ? ProgressCommand::CreateAndConnect(resampleImageFilter) : nullptr;
/** Do the resampling. */
try
{
resampleImageFilter.Update();
}
catch (itk::ExceptionObject & excp)
{
/** Add information to the exception. */
excp.SetLocation("ResamplerBase - WriteResultImage()");
std::string err_str = excp.GetDescription();
err_str += "\nError occurred while resampling the image.\n";
excp.SetDescription(err_str);
/** Pass the exception to an higher level. */
throw;
}
/** Perform the writing. */
this->WriteResultImage(resampleImageFilter.GetOutput(), filename, showProgress);
/** Disconnect from the resampler. */
if (showProgress && (progressObserver != nullptr))
{
progressObserver->DisconnectObserver(this->GetAsITKBaseType());
}
} // end ResampleAndWriteResultImage()
/**
* ******************* WriteResultImage ********************
*/
template <class TElastix>
void
ResamplerBase<TElastix>::WriteResultImage(OutputImageType * image,
const std::string & filename,
const bool showProgress)
{
ITKBaseType & resampleImageFilter = this->GetSelf();
/** Check if ResampleInterpolator is the RayCastResampleInterpolator */
const auto testptr = dynamic_cast<itk::AdvancedRayCastInterpolateImageFunction<InputImageType, CoordRepType> *>(
resampleImageFilter.GetInterpolator());
/** If RayCastResampleInterpolator is used reset the Transform to
* overrule default Resampler settings.
*/
if (testptr != nullptr)
{
resampleImageFilter.SetTransform(testptr->GetTransform());
}
const Configuration & configuration = itk::Deref(Superclass::GetConfiguration());
/** Read output pixeltype from parameter the file. Replace possible " " with "_". */
std::string resultImagePixelType = "short";
configuration.ReadParameter(resultImagePixelType, "ResultImagePixelType", 0, false);
const std::string::size_type pos = resultImagePixelType.find(" ");
if (pos != std::string::npos)
{
resultImagePixelType.replace(pos, 1, "_");
}
/** Read from the parameter file if compression is desired. */
bool doCompression = false;
configuration.ReadParameter(doCompression, "CompressResultImage", 0, false);
/** Possibly change direction cosines to their original value, as specified
* in the tp-file, or by the fixed image. This is only necessary when
* the UseDirectionCosines flag was set to false.
*/
const auto infoChanger = itk::ChangeInformationImageFilter<OutputImageType>::New();
DirectionType originalDirection;
bool retdc = this->GetElastix()->GetOriginalFixedImageDirection(originalDirection);
infoChanger->SetOutputDirection(originalDirection);
infoChanger->SetChangeDirection(retdc && !this->GetElastix()->GetUseDirectionCosines());
infoChanger->SetInput(image);
/** Do the writing. */
if (showProgress)
{
log::to_stdout(" Writing image ...");
}
try
{
itk::WriteCastedImage(*(infoChanger->GetOutput()), filename, resultImagePixelType, doCompression);
}
catch (itk::ExceptionObject & excp)
{
/** Add information to the exception. */
excp.SetLocation("ResamplerBase - AfterRegistrationBase()");
std::string err_str = excp.GetDescription();
err_str += "\nError occurred while writing resampled image.\n";
excp.SetDescription(err_str);
/** Pass the exception to an higher level. */
throw;
}
} // end WriteResultImage()
/*
* ******************* CreateItkResultImage ********************
* \todo: avoid code duplication with WriteResultImage function
*/
template <class TElastix>
void
ResamplerBase<TElastix>::CreateItkResultImage()
{
itk::DataObject::Pointer resultImage;
ITKBaseType & resampleImageFilter = this->GetSelf();
/** Make sure the resampler is updated. */
resampleImageFilter.Modified();
const Configuration & configuration = itk::Deref(Superclass::GetConfiguration());
const bool showProgressPercentage = configuration.RetrieveParameterValue(false, "ShowProgressPercentage", 0, false);
const auto progressObserver =
showProgressPercentage ? ProgressCommand::CreateAndConnect(*(this->GetAsITKBaseType())) : nullptr;
/** Do the resampling. */
try
{
resampleImageFilter.Update();
}
catch (itk::ExceptionObject & excp)
{
/** Add information to the exception. */
excp.SetLocation("ResamplerBase - WriteResultImage()");
std::string err_str = excp.GetDescription();
err_str += "\nError occurred while resampling the image.\n";
excp.SetDescription(err_str);
/** Pass the exception to an higher level. */
throw;
}
/** Check if ResampleInterpolator is the RayCastResampleInterpolator */
const auto testptr = dynamic_cast<itk::AdvancedRayCastInterpolateImageFunction<InputImageType, CoordRepType> *>(
resampleImageFilter.GetInterpolator());
/** If RayCastResampleInterpolator is used reset the Transform to
* overrule default Resampler settings */
if (testptr != nullptr)
{
resampleImageFilter.SetTransform(testptr->GetTransform());
}
/** Read output pixeltype from parameter the file. */
std::string resultImagePixelType = "short";
configuration.ReadParameter(resultImagePixelType, "ResultImagePixelType", 0, false);
/** Possibly change direction cosines to their original value, as specified
* in the tp-file, or by the fixed image. This is only necessary when
* the UseDirectionCosines flag was set to false.
*/
const auto infoChanger = itk::ChangeInformationImageFilter<OutputImageType>::New();
DirectionType originalDirection;
bool retdc = this->GetElastix()->GetOriginalFixedImageDirection(originalDirection);
infoChanger->SetOutputDirection(originalDirection);
infoChanger->SetChangeDirection(retdc && !this->GetElastix()->GetUseDirectionCosines());
infoChanger->SetInput(resampleImageFilter.GetOutput());
/** cast the image to the correct output image Type */
if (resultImagePixelType == "char")
{
resultImage = CastImage<char>(infoChanger->GetOutput());
}
if (resultImagePixelType == "unsigned char")
{
resultImage = CastImage<unsigned char>(infoChanger->GetOutput());
}
else if (resultImagePixelType == "short")
{
resultImage = CastImage<short>(infoChanger->GetOutput());
}
else if (resultImagePixelType == "ushort" ||
resultImagePixelType == "unsigned short") // <-- ushort for backwards compatibility
{
resultImage = CastImage<unsigned short>(infoChanger->GetOutput());
}
else if (resultImagePixelType == "int")
{
resultImage = CastImage<int>(infoChanger->GetOutput());
}
else if (resultImagePixelType == "unsigned int")
{
resultImage = CastImage<unsigned int>(infoChanger->GetOutput());
}
else if (resultImagePixelType == "long")
{
resultImage = CastImage<long>(infoChanger->GetOutput());
}
else if (resultImagePixelType == "unsigned long")
{
resultImage = CastImage<unsigned long>(infoChanger->GetOutput());
}
else if (resultImagePixelType == "float")
{
resultImage = CastImage<float>(infoChanger->GetOutput());
}
else if (resultImagePixelType == "double")
{
resultImage = CastImage<double>(infoChanger->GetOutput());
}
if (resultImage.IsNull())
{
itkExceptionMacro("Unable to cast result image: ResultImagePixelType must be one of \"char\", \"unsigned "
"char\", \"short\", \"ushort\", \"unsigned short\", \"int\", \"unsigned int\", \"long\", "
"\"unsigned long\", \"float\" or \"double\" but was \""
<< resultImagePixelType << "\".");
}
// put image in container
this->m_Elastix->SetResultImage(resultImage);
if (progressObserver != nullptr)
{
/** Disconnect from the resampler. */
progressObserver->DisconnectObserver(this->GetAsITKBaseType());
}
} // end CreateItkResultImage()
/*
* ************************* ReadFromFile ***********************
*/
template <class TElastix>
void
ResamplerBase<TElastix>::ReadFromFile()
{
/** Connect the components. */
this->SetComponents();
const Configuration & configuration = itk::Deref(Superclass::GetConfiguration());
/** Get spacing, origin and size of the image to be produced by the resampler. */
SpacingType spacing;
IndexType index;
OriginPointType origin;
SizeType size = { { 0 } };
auto direction = DirectionType::GetIdentity();
for (unsigned int i = 0; i < ImageDimension; ++i)
{
/** No default size. Read size from the parameter file. */
configuration.ReadParameter(size[i], "Size", i);
/** Default index. Read index from the parameter file. */
index[i] = 0;
configuration.ReadParameter(index[i], "Index", i);
/** Default spacing. Read spacing from the parameter file. */
spacing[i] = 1.0;
configuration.ReadParameter(spacing[i], "Spacing", i);
/** Default origin. Read origin from the parameter file. */
origin[i] = 0.0;
configuration.ReadParameter(origin[i], "Origin", i);
/** Read direction cosines. Default identity */
for (unsigned int j = 0; j < ImageDimension; ++j)
{
configuration.ReadParameter(direction(j, i), "Direction", i * ImageDimension + j);
}
}
/** Check for image size. */
unsigned int sum = 0;
for (unsigned int i = 0; i < ImageDimension; ++i)
{
if (size[i] == 0)
{
++sum;
}
}
if (sum > 0)
{
log::error("ERROR: One or more image sizes are 0 or unspecified!");
/** \todo quit program nicely. */
}
ITKBaseType & resampleImageFilter = this->GetSelf();
/** Set the region info to the same values as in the fixedImage. */
resampleImageFilter.SetSize(size);
resampleImageFilter.SetOutputStartIndex(index);
resampleImageFilter.SetOutputOrigin(origin);
resampleImageFilter.SetOutputSpacing(spacing);
/** Set the direction cosines. If no direction cosines
* should be used, set identity cosines, to simulate the
* old ITK behavior.
*/
if (!this->GetElastix()->GetUseDirectionCosines())
{
direction.SetIdentity();
}
resampleImageFilter.SetOutputDirection(direction);
/** Set the DefaultPixelValue (for pixels in the resampled image
* that come from outside the original (moving) image.
*/
double defaultPixelValue = 0.0;
bool found = configuration.ReadParameter(defaultPixelValue, "DefaultPixelValue", 0, false);
if (found)
{
resampleImageFilter.SetDefaultPixelValue(static_cast<OutputPixelType>(defaultPixelValue));
}
} // end ReadFromFile()
/**
* ******************* WriteToFile ******************************
*/
template <class TElastix>
void
ResamplerBase<TElastix>::WriteToFile(std::ostream & transformationParameterInfo) const
{
ParameterMapType parameterMap;
Self::CreateTransformParameterMap(parameterMap);
/** Write resampler specific things. */
transformationParameterInfo << ("\n// Resampler specific\n" + Conversion::ParameterMapToString(parameterMap));
} // end WriteToFile()
/**
* ******************* CreateTransformParameterMap ******************************
*/
template <class TElastix>
void
ResamplerBase<TElastix>::CreateTransformParameterMap(ParameterMapType & parameterMap) const
{
/** Store the name of this transform. */
parameterMap["Resampler"] = { this->elxGetClassName() };
/** Store the DefaultPixelValue. */
parameterMap["DefaultPixelValue"] = { Conversion::ToString(this->GetSelf().GetDefaultPixelValue()) };
const Configuration & configuration = itk::Deref(Superclass::GetConfiguration());
/** Store the output image format. */
std::string resultImageFormat = "mhd";
configuration.ReadParameter(resultImageFormat, "ResultImageFormat", 0, false);
parameterMap["ResultImageFormat"] = { resultImageFormat };
/** Store output pixel type. */
std::string resultImagePixelType = "short";
configuration.ReadParameter(resultImagePixelType, "ResultImagePixelType", 0, false);
parameterMap["ResultImagePixelType"] = { resultImagePixelType };
/** Store compression flag. */
std::string doCompression = "false";
configuration.ReadParameter(doCompression, "CompressResultImage", 0, false);
parameterMap["CompressResultImage"] = { doCompression };
// Derived classes may add some extra parameters
for (auto & keyAndValue : this->CreateDerivedTransformParameterMap())
{
const auto & key = keyAndValue.first;
assert(parameterMap.count(key) == 0);
parameterMap[key] = std::move(keyAndValue.second);
}
} // end CreateTransformParameterMap()
/**
* ******************* ReleaseMemory ********************
*/
template <class TElastix>
void
ResamplerBase<TElastix>::ReleaseMemory()
{
const Configuration & configuration = itk::Deref(Superclass::GetConfiguration());
/** Release some memory. Sometimes it is not possible to
* resample and write an image, because too much memory is consumed by
* elastix. Releasing some memory at this point helps a lot.
*/
/** Release more memory, but only if this is the final elastix level. */
if (configuration.GetElastixLevel() + 1 == configuration.GetTotalNumberOfElastixLevels())
{
/** Release fixed image memory. */
const unsigned int nofi = this->GetElastix()->GetNumberOfFixedImages();
for (unsigned int i = 0; i < nofi; ++i)
{
this->GetElastix()->GetFixedImage(i)->ReleaseData();
}
/** Release fixed mask image memory. */
const unsigned int nofm = this->GetElastix()->GetNumberOfFixedMasks();
for (unsigned int i = 0; i < nofm; ++i)
{
if (this->GetElastix()->GetFixedMask(i) != nullptr)
{
this->GetElastix()->GetFixedMask(i)->ReleaseData();
}
}
/** Release moving mask image memory. */
const unsigned int nomm = this->GetElastix()->GetNumberOfMovingMasks();
for (unsigned int i = 0; i < nomm; ++i)
{
if (this->GetElastix()->GetMovingMask(i) != nullptr)
{
this->GetElastix()->GetMovingMask(i)->ReleaseData();
}
}
} // end if final elastix level
/** The B-spline interpolator stores a coefficient image of doubles the
* size of the moving image. We clear it by setting the input image to
* zero. The interpolator is not needed anymore, since we have the
* resampler interpolator.
*/
this->GetElastix()->GetElxInterpolatorBase()->GetAsITKBaseType()->SetInputImage(nullptr);
// Clear ImageSampler, metric, optimizer, interpolator, registration, internal images?
} // end ReleaseMemory()
} // end namespace elastix
#endif // end #ifndef elxResamplerBase_hxx
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