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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 _ELXAFFINELOGTRANSFORM_H_
#define _ELXAFFINELOGTRANSFORM_H_
#include "itkAdvancedCombinationTransform.h"
#include "itkAffineLogTransform.h"
#include "itkCenteredTransformInitializer.h"
#include "elxIncludes.h"
namespace elastix
{
/**
* \class AffineLogTransformElastix
* \brief
*
* This transform is an affine transformation, with a different parametrisation
* than the usual one.
*
* \warning: the behaviour of this transform might still change in the future. It is still experimental.
*
* \ingroup Transforms
* \sa AffineLogTransform
*/
template <class TElastix>
class ITK_TEMPLATE_EXPORT AffineLogTransformElastix
: public itk::AdvancedCombinationTransform<typename elx::TransformBase<TElastix>::CoordRepType,
elx::TransformBase<TElastix>::FixedImageDimension>
, public elx::TransformBase<TElastix>
{
public:
ITK_DISALLOW_COPY_AND_MOVE(AffineLogTransformElastix);
/** Standard ITK-stuff.*/
using Self = AffineLogTransformElastix;
using Superclass1 = itk::AdvancedCombinationTransform<typename elx::TransformBase<TElastix>::CoordRepType,
elx::TransformBase<TElastix>::FixedImageDimension>;
using Superclass2 = elx::TransformBase<TElastix>;
using Pointer = itk::SmartPointer<Self>;
using ConstPointer = itk::SmartPointer<const Self>;
/** The ITK-class that provides most of the functionality, and
* that is set as the "CurrentTransform" in the CombinationTransform */
using AffineLogTransformType = itk::AffineLogTransform<typename elx::TransformBase<TElastix>::CoordRepType,
elx::TransformBase<TElastix>::FixedImageDimension>;
/** Method for creation through the object factory. */
itkNewMacro(Self);
/** Run-time type information (and related methods). */
itkTypeMacro(AffineLogTransformElastix, AdvancedCombinationTransform);
/** Name of this class.
* Use this name in the parameter file to select this specific transform. \n
* example: <tt>(Transform "AffineLogTransform")</tt>\n
*/
elxClassNameMacro("AffineLogTransform");
/** Dimension of the fixed image. */
itkStaticConstMacro(SpaceDimension, unsigned int, Superclass2::FixedImageDimension);
/** Typedefs inherited from the superclass. */
using typename Superclass1::ScalarType;
using typename Superclass1::ParametersType;
using typename Superclass1::NumberOfParametersType;
using typename Superclass1::JacobianType;
using typename Superclass1::InputPointType;
using typename Superclass1::OutputPointType;
using typename Superclass1::InputVectorType;
using typename Superclass1::OutputVectorType;
using typename Superclass1::InputCovariantVectorType;
using typename Superclass1::OutputCovariantVectorType;
using typename Superclass1::InputVnlVectorType;
using typename Superclass1::OutputVnlVectorType;
using AffineLogTransformPointer = typename AffineLogTransformType::Pointer;
using OffsetType = typename AffineLogTransformType::OffsetType;
/** Typedef's inherited from TransformBase. */
using typename Superclass2::ElastixType;
using typename Superclass2::ParameterMapType;
using typename Superclass2::RegistrationType;
using typename Superclass2::CoordRepType;
using typename Superclass2::FixedImageType;
using typename Superclass2::MovingImageType;
using ITKBaseType = typename Superclass2::ITKBaseType;
using CombinationTransformType = typename Superclass2::CombinationTransformType;
/** Other typedef's. */
using IndexType = typename FixedImageType::IndexType;
using IndexValueType = typename IndexType::IndexValueType;
using SizeType = typename FixedImageType::SizeType;
using PointType = typename FixedImageType::PointType;
using SpacingType = typename FixedImageType::SpacingType;
using RegionType = typename FixedImageType::RegionType;
using DirectionType = typename FixedImageType::DirectionType;
using TransformInitializerType =
itk::CenteredTransformInitializer<AffineLogTransformType, FixedImageType, MovingImageType>;
using TransformInitializerPointer = typename TransformInitializerType::Pointer;
/** For scales setting in the optimizer */
using typename Superclass2::ScalesType;
/** Execute stuff before the actual registration:
* \li Call InitializeTransform
* \li Set the scales.
*/
void
BeforeRegistration() override;
/** Set the scales
* \li If AutomaticScalesEstimation is "true" estimate scales
* \li If scales are provided by the user use those,
* \li Otherwise use some default value
* This function is called by BeforeRegistration, after
* the InitializeTransform function is called
*/
virtual void
SetScales();
/** Function to read transform-parameters from a file.
*
* It reads the center of rotation and calls the superclass' implementation.
*/
void
ReadFromFile() override;
protected:
/** The constructor. */
AffineLogTransformElastix();
/** The destructor. */
~AffineLogTransformElastix() override = default;
/** Try to read the CenterOfRotationPoint from the transform parameter file
* The CenterOfRotationPoint is already in world coordinates. */
virtual bool
ReadCenterOfRotationPoint(InputPointType & rotationPoint) const;
private:
elxOverrideGetSelfMacro;
/** Initialize Transform.
* \li Set all parameters to zero.
* \li Set center of rotation:
* automatically initialized to the geometric center of the image, or
* assigned a user entered voxel index, given by the parameter
* (CenterOfRotation <index-x> <index-y> ...);
* If an initial transform is present and HowToCombineTransforms is
* set to "Compose", the initial transform is taken into account
* while setting the center of rotation.
* \li Set initial translation:
* the initial translation between fixed and moving image is guessed,
* if the user has set (AutomaticTransformInitialization "true").
*
* It is not yet possible to enter an initial rotation angle.
*/
void
InitializeTransform();
/** Creates a map of the parameters specific for this (derived) transform type. */
ParameterMapType
CreateDerivedTransformParameterMap() const override;
const AffineLogTransformPointer m_AffineLogTransform{ AffineLogTransformType::New() };
};
} // end namespace elastix
#endif // ELXAFFINELOGTRANSFORM_H
#ifndef ITK_MANUAL_INSTANTIATION
#include "elxAffineLogTransform.hxx"
#endif
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