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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 elxMissingStructurePenalty_h
#define elxMissingStructurePenalty_h
#include "elxIncludes.h"
#include "itkMissingStructurePenalty.h"
namespace elastix
{
/**
* \class MissingStructurePenalty
* \brief .
*
* \brief Computes the (pseudo) volume of the transformed surface mesh of a structure.\n
* A metric based on the itk::MissingStructurePenalty.\n
* \author F.F. Berendsen, Image Sciences Institute, UMC Utrecht, The Netherlands
* \note If you use the MissingStructurePenalty anywhere we would appreciate if you cite the following article:\n
* F.F. Berendsen, A.N.T.J. Kotte, A.A.C. de Leeuw, I.M. Juergenliemk-Schulz,\n
* M.A. Viergever and J.P.W. Pluim "Registration of structurally dissimilar \n
* images in MRI-based brachytherapy ", Phys. Med. Biol. 59 (2014) 4033-4045.\n
* http://stacks.iop.org/0031-9155/59/4033
* The parameters used in this class are:
* \parameter Metric: Select this metric as follows:\n
* <tt>(Metric "MissingStructurePenalty")</tt>
* \parameter
* <tt>(WriteResultMeshAfterEachIteration "True")</tt>
* \parameter
* <tt>(WriteResultMeshAfterEachResolution "True")</tt>
* The command-line options for input meshes is: -fmesh<[A-Z]><MetricNumber>.
* \ingroup RegistrationMetrics
*/
template <typename TElastix>
class ITK_TEMPLATE_EXPORT MissingStructurePenalty
: public itk::MissingVolumeMeshPenalty<typename MetricBase<TElastix>::FixedPointSetType,
typename MetricBase<TElastix>::MovingPointSetType>
, public MetricBase<TElastix>
{
public:
ITK_DISALLOW_COPY_AND_MOVE(MissingStructurePenalty);
/** Standard ITK-stuff. */
using Self = MissingStructurePenalty;
using Superclass1 = itk::MissingVolumeMeshPenalty<typename MetricBase<TElastix>::FixedPointSetType,
typename MetricBase<TElastix>::MovingPointSetType>;
using Superclass2 = MetricBase<TElastix>;
using Pointer = itk::SmartPointer<Self>;
using ConstPointer = itk::SmartPointer<const Self>;
/** Method for creation through the object factory. */
itkNewMacro(Self);
/** Run-time type information (and related methods). */
itkOverrideGetNameOfClassMacro(MissingStructurePenalty);
/** Name of this class.
* Use this name in the parameter file to select this specific metric. \n
* example: <tt>(Metric "MissingStructurePenalty")</tt>\n
*/
elxClassNameMacro("MissingStructurePenalty");
/** Typedefs from the superclass. */
using typename Superclass1::FixedMeshType;
using typename Superclass1::FixedMeshPointer;
using typename Superclass1::FixedMeshConstPointer;
using typename Superclass1::CoordinateRepresentationType;
using typename Superclass1::FixedPointSetType;
using typename Superclass1::FixedPointSetConstPointer;
using typename Superclass1::FixedMeshContainerType;
using typename Superclass1::FixedMeshContainerPointer;
using typename Superclass1::MappedMeshContainerType;
using typename Superclass1::MappedMeshContainerPointer;
using typename Superclass1::MovingPointSetType;
using typename Superclass1::MovingPointSetConstPointer;
using typename Superclass1::CellInterfaceType;
// using typename Superclass1::FixedImageRegionType;
using typename Superclass1::TransformType;
using typename Superclass1::TransformPointer;
using typename Superclass1::InputPointType;
using typename Superclass1::OutputPointType;
using typename Superclass1::TransformJacobianType;
// using typename Superclass1::RealType;
using typename Superclass1::FixedImageMaskType;
using typename Superclass1::FixedImageMaskPointer;
using typename Superclass1::MovingImageMaskType;
using typename Superclass1::MovingImageMaskPointer;
using typename Superclass1::MeasureType;
using typename Superclass1::DerivativeType;
using typename Superclass1::ParametersType;
using CoordinateType = typename OutputPointType::CoordinateType;
using typename Superclass1::MeshIdType;
using CombinationTransformType = itk::AdvancedCombinationTransform<CoordinateType, Self::FixedImageDimension>;
using InitialTransformType = typename CombinationTransformType::InitialTransformType;
/** Typedefs inherited from elastix. */
using typename Superclass2::ElastixType;
using typename Superclass2::RegistrationType;
using ITKBaseType = typename Superclass2::ITKBaseType;
using typename Superclass2::FixedImageType;
using typename Superclass2::MovingImageType;
/** The fixed image dimension. */
itkStaticConstMacro(FixedImageDimension, unsigned int, FixedImageType::ImageDimension);
itkStaticConstMacro(MovingImageDimension, unsigned int, MovingImageType::ImageDimension);
/** Assuming fixed and moving pointsets are of equal type, which implicitly
* assumes that the fixed and moving image are of the same type.
*/
using PointSetType = FixedPointSetType;
using MeshType = FixedMeshType;
using ImageType = FixedImageType;
/** Sets up a timer to measure the initialization time and calls the
* Superclass' implementation.
*/
void
Initialize() override;
/**
* Do some things before registration:
* \li Load and set the pointsets.
*/
int
BeforeAllBase() override;
void
BeforeRegistration() override;
void
AfterEachIteration() override;
void
AfterEachResolution() override;
/** Function to read the corresponding points. */
unsigned int
ReadMesh(const std::string & meshFileName, typename FixedMeshType::Pointer & mesh);
void
WriteResultMesh(const std::string & filename, MeshIdType meshId);
unsigned int
ReadTransformixPoints(const std::string & filename, typename MeshType::Pointer & mesh);
/** Overwrite to silence warning. */
void
SelectNewSamples() override
{}
protected:
/** The constructor. */
MissingStructurePenalty();
/** The destructor. */
~MissingStructurePenalty() override = default;
private:
elxOverrideGetSelfMacro;
unsigned int m_NumberOfMeshes;
};
} // end namespace elastix
#ifndef ITK_MANUAL_INSTANTIATION
# include "elxMissingStructurePenalty.hxx"
#endif
#endif // end #ifndef elxMissingStructurePenalty_h
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