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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 elxMultiResolutionRegistration_hxx
#define elxMultiResolutionRegistration_hxx
#include "elxMultiResolutionRegistration.h"
#include <vnl/vnl_math.h>
#include "itkTimeProbe.h"
namespace elastix
{
/**
* ******************* BeforeRegistration ***********************
*/
template <class TElastix>
void
MultiResolutionRegistration<TElastix>::BeforeRegistration()
{
/** Check for a common mistake that people make in their parameter
* file: using MultiResolutionRegistration in combination with
* more than 1 metric.
*/
const unsigned int nrOfMetrics = this->GetElastix()->GetNumberOfMetrics();
if (nrOfMetrics > 1)
{
itkExceptionMacro("\nERROR: the parameter file specifies \n"
<< " (Registration \"MultiResolutionRegistration\")\n"
<< " in combination with " << nrOfMetrics << " metrics.\n"
<< " This registration only allows for 1 metric.\n"
<< " You probably mean to use:\n"
<< " (Registration \"MultiMetricMultiResolutionRegistration\")");
}
/** Get the components from this->m_Elastix and set them. */
this->SetComponents();
/** Set the number of resolutions. */
unsigned int numberOfResolutions = 3;
this->m_Configuration->ReadParameter(numberOfResolutions, "NumberOfResolutions", 0);
if (numberOfResolutions == 0)
{
itkExceptionMacro("The NumberOfResolutions parameter must have a non-zero value!");
}
this->SetNumberOfLevels(numberOfResolutions);
/** Set the FixedImageRegion. */
/** Make sure the fixed image is up to date. */
try
{
this->GetElastix()->GetFixedImage()->Update();
}
catch (itk::ExceptionObject & excp)
{
/** Add information to the exception. */
excp.SetLocation("MultiResolutionRegistration - BeforeRegistration()");
std::string err_str = excp.GetDescription();
err_str += "\nError occurred while updating region info of the fixed image.\n";
excp.SetDescription(err_str);
/** Pass the exception to an higher level. */
throw;
}
/** Set the fixedImageRegion. */
this->SetFixedImageRegion(this->GetElastix()->GetFixedImage()->GetBufferedRegion());
} // end BeforeRegistration()
/**
* ******************* BeforeEachResolution ***********************
*/
template <class TElastix>
void
MultiResolutionRegistration<TElastix>::BeforeEachResolution()
{
/** Get the current resolution level. */
unsigned int level = this->GetCurrentLevel();
/** Do erosion, or just reset the original masks in the metric, or
* do nothing when no masks are used.
*/
this->UpdateMasks(level);
} // end BeforeEachResolution()
/**
* *********************** SetComponents ************************
*/
template <class TElastix>
void
MultiResolutionRegistration<TElastix>::SetComponents()
{
/** Get the component from this-GetElastix() (as elx::...BaseType *),
* cast it to the appropriate type and set it in 'this'. */
this->SetFixedImage(this->GetElastix()->GetFixedImage());
this->SetMovingImage(this->GetElastix()->GetMovingImage());
this->SetFixedImagePyramid(this->GetElastix()->GetElxFixedImagePyramidBase()->GetAsITKBaseType());
this->SetMovingImagePyramid(this->GetElastix()->GetElxMovingImagePyramidBase()->GetAsITKBaseType());
this->SetInterpolator(this->GetElastix()->GetElxInterpolatorBase()->GetAsITKBaseType());
MetricType * testPtr = dynamic_cast<MetricType *>(this->GetElastix()->GetElxMetricBase()->GetAsITKBaseType());
if (testPtr)
{
this->SetMetric(testPtr);
}
else
{
itkExceptionMacro(
"ERROR: MultiResolutionRegistration expects the metric to be of type AdvancedImageToImageMetric!");
}
this->SetOptimizer(dynamic_cast<OptimizerType *>(this->GetElastix()->GetElxOptimizerBase()->GetAsITKBaseType()));
this->SetTransform(this->GetElastix()->GetElxTransformBase()->GetAsITKBaseType());
/** Samplers are not always needed: */
if (this->GetElastix()->GetElxMetricBase()->GetAdvancedMetricUseImageSampler())
{
if (this->GetElastix()->GetElxImageSamplerBase())
{
this->GetElastix()->GetElxMetricBase()->SetAdvancedMetricImageSampler(
this->GetElastix()->GetElxImageSamplerBase()->GetAsITKBaseType());
}
else
{
log::error("No ImageSampler has been specified.");
itkExceptionMacro("The metric requires an ImageSampler, but it is not available!");
}
}
} // end SetComponents()
/**
* ************************* UpdateMasks ************************
**/
template <class TElastix>
void
MultiResolutionRegistration<TElastix>::UpdateMasks(unsigned int level)
{
/** some shortcuts */
const unsigned int nrOfFixedMasks = this->GetElastix()->GetNumberOfFixedMasks();
const unsigned int nrOfMovingMasks = this->GetElastix()->GetNumberOfMovingMasks();
const unsigned int oneOrNoFixedMasks = std::min(static_cast<unsigned int>(1), nrOfFixedMasks);
const unsigned int oneOrNoMovingMasks = std::min(static_cast<unsigned int>(1), nrOfMovingMasks);
/** Array of bools, that remembers for each mask if erosion is wanted.
* dummy, we will not use it.
*/
UseMaskErosionArrayType useMaskErosionArray;
/** Bool that remembers if mask erosion is wanted in any of the masks
* remains false when no masks are used.
*/
bool useFixedMaskErosion;
bool useMovingMaskErosion;
/** Read whether mask erosion is wanted, if any masks were supplied
* Only one mask is taken into account.
*/
useFixedMaskErosion = this->ReadMaskParameters(useMaskErosionArray, oneOrNoFixedMasks, "Fixed", level);
useMovingMaskErosion = this->ReadMaskParameters(useMaskErosionArray, oneOrNoMovingMasks, "Moving", level);
/** Create and start timer, to time the whole fixed mask configuration procedure. */
itk::TimeProbe timer;
timer.Start();
FixedMaskSpatialObjectPointer fixedMask = this->GenerateFixedMaskSpatialObject(
this->GetElastix()->GetFixedMask(), useFixedMaskErosion, this->GetFixedImagePyramid(), level);
this->GetModifiableMetric()->SetFixedImageMask(fixedMask);
/** Stop timer and print the elapsed time. */
timer.Stop();
log::info(std::ostringstream{} << "Setting the fixed masks took: " << static_cast<long>(timer.GetMean() * 1000)
<< " ms.");
/** Start timer, to time the whole moving mask configuration procedure. */
timer.Reset();
timer.Start();
MovingMaskSpatialObjectPointer movingMask = this->GenerateMovingMaskSpatialObject(
this->GetElastix()->GetMovingMask(), useMovingMaskErosion, this->GetMovingImagePyramid(), level);
if (movingMask != nullptr)
{
movingMask->Update();
}
this->GetModifiableMetric()->SetMovingImageMask(movingMask);
/** Stop timer and print the elapsed time. */
timer.Stop();
log::info(std::ostringstream{} << "Setting the moving masks took: " << static_cast<long>(timer.GetMean() * 1000)
<< " ms.");
} // end UpdateMasks()
} // end namespace elastix
#endif // end #ifndef elxMultiResolutionRegistration_hxx
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