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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 elxFixedImagePyramidBase_hxx
#define elxFixedImagePyramidBase_hxx
#include "elxFixedImagePyramidBase.h"
#include <itkDeref.h>
#ifndef ELX_NO_FILESYSTEM_ACCESS
# include "itkImageFileCastWriter.h"
#endif
namespace elastix
{
/**
* ******************* BeforeRegistrationBase *******************
*/
template <typename TElastix>
void
FixedImagePyramidBase<TElastix>::BeforeRegistrationBase()
{
/** Call SetFixedSchedule.*/
this->SetFixedSchedule();
} // end BeforeRegistrationBase()
/**
* ******************* BeforeEachResolutionBase *******************
*/
template <typename TElastix>
void
FixedImagePyramidBase<TElastix>::BeforeEachResolutionBase()
{
/** 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 pyramid images this resolution. */
bool writePyramidImage = false;
configuration.ReadParameter(writePyramidImage, "WritePyramidImagesAfterEachResolution", "", level, 0, false);
/** Get the desired extension / file format. */
std::string resultImageFormat = "mhd";
configuration.ReadParameter(resultImageFormat, "ResultImageFormat", 0, false);
const std::string outputDirectoryPath = configuration.GetCommandLineArgument("-out");
/** Writing result image. */
if (writePyramidImage && !outputDirectoryPath.empty())
{
/** Create a name for the final result. */
std::ostringstream makeFileName;
makeFileName << outputDirectoryPath;
makeFileName << this->GetComponentLabel() << "." << configuration.GetElastixLevel() << ".R" << level << "."
<< resultImageFormat;
/** Save the fixed pyramid image. */
log::info(std::ostringstream{} << "Writing fixed pyramid image " << this->GetComponentLabel() << " from resolution "
<< level << "...");
try
{
this->WritePyramidImage(makeFileName.str(), level);
}
catch (const itk::ExceptionObject & excp)
{
log::error(std::ostringstream{} << "Exception caught: \n" << excp << "Resuming elastix.");
}
} // end if
} // end BeforeEachResolutionBase()
/**
* ********************** SetFixedSchedule **********************
*/
template <typename TElastix>
void
FixedImagePyramidBase<TElastix>::SetFixedSchedule()
{
/** Get the ImageDimension. */
const unsigned int ImageDimension = InputImageType::ImageDimension;
const Configuration & configuration = itk::Deref(Superclass::GetConfiguration());
/** Read numberOfResolutions. */
unsigned int numberOfResolutions = 3;
configuration.ReadParameter(numberOfResolutions, "NumberOfResolutions", 0, true);
if (numberOfResolutions == 0)
{
itkExceptionMacro("The NumberOfResolutions parameter must have a non-zero value!");
}
/** Create a default schedule. Set the numberOfLevels first. */
this->GetAsITKBaseType()->SetNumberOfLevels(numberOfResolutions);
ScheduleType schedule = this->GetAsITKBaseType()->GetSchedule();
/** Set the fixedPyramidSchedule to the FixedImagePyramidSchedule given
* in the parameter-file. The following parameter file fields can be used:
* ImagePyramidSchedule
* FixedImagePyramidSchedule
* FixedImagePyramid<i>Schedule, for the i-th fixed image pyramid used.
*/
bool found = true;
for (unsigned int i = 0; i < numberOfResolutions; ++i)
{
for (unsigned int j = 0; j < ImageDimension; ++j)
{
bool ijfound = false;
const unsigned int entrynr = i * ImageDimension + j;
ijfound |= configuration.ReadParameter(schedule[i][j], "ImagePyramidSchedule", entrynr, false);
ijfound |= configuration.ReadParameter(schedule[i][j], "FixedImagePyramidSchedule", entrynr, false);
ijfound |= configuration.ReadParameter(schedule[i][j], "Schedule", this->GetComponentLabel(), entrynr, -1, false);
/** Remember if for at least one schedule element no value could be found. */
found &= ijfound;
} // end for ImageDimension
} // end for numberOfResolutions
if (!found && configuration.GetPrintErrorMessages())
{
log::warn(std::ostringstream{} << "WARNING: the fixed pyramid schedule is not fully specified!\n"
<< " A default pyramid schedule is used.");
}
else
{
/** Set the schedule into this class. */
this->GetAsITKBaseType()->SetSchedule(schedule);
}
} // end SetFixedSchedule()
/**
* ******************* WritePyramidImage ********************
*/
template <typename TElastix>
void
FixedImagePyramidBase<TElastix>::WritePyramidImage(const std::string & filename,
const unsigned int level) // const
{
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);
/** Do the writing. */
log::to_stdout(" Writing fixed pyramid image ...");
#ifndef ELX_NO_FILESYSTEM_ACCESS
try
{
itk::WriteCastedImage(*(this->GetAsITKBaseType()->GetOutput(level)), filename, resultImagePixelType, doCompression);
}
catch (itk::ExceptionObject & excp)
{
#else
// Always throw -- do not include support code or access filesystem with wasm
itk::ExceptionObject excp;
#endif
/** Add information to the exception. */
excp.SetLocation("FixedImagePyramidBase - BeforeEachResolutionBase()");
std::string err_str = excp.GetDescription();
err_str += "\nError occurred while writing pyramid image.\n";
excp.SetDescription(err_str);
/** Pass the exception to an higher level. */
#ifndef ELX_NO_FILESYSTEM_ACCESS
throw;
}
#else
throw excp;
#endif
} // end WritePyramidImage()
} // end namespace elastix
#endif // end #ifndef elxFixedImagePyramidBase_hxx
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