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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 elxSimilarityTransform_h
#define elxSimilarityTransform_h
#include "elxIncludes.h" // include first to avoid MSVS warning
#include "itkSimilarityTransform.h"
#include "itkCenteredTransformInitializer.h"
namespace elastix
{
/**
* \class SimilarityTransformElastix
* \brief A transform based on the itk SimilarityTransforms.
*
* This transform is a rigid body transformation, with an isotropic scaling.
* In 2D, the order of parameters is:\n
* [scale, rotation angle, translationx, translationy]\n
* In 3D, the order of parameters is: \n
* [versor1 versor2 versor3 translationx translationy translationz scale]\n
* Make sure, when specifying the Scales manually that you keep in mind this order!
*
* The parameters used in this class are:
* \parameter Transform: Select this transform as follows:\n
* <tt>(%Transform "SimilarityTransform")</tt>
* \parameter Scales: the scale factor between the rotations, translations,
* and the isotropic scaling, used in the optimizer. \n
* example: <tt>(Scales 100000.0 60000.0 ... 80000.0)</tt> \n
* With this transform, the number of arguments should be
* equal to the number of parameters: for each parameter its scale factor.
* If this parameter option is not used, by default the rotations are scaled
* by a factor of 100000.0 and the scale by a factor 10000.0.
* These are rather arbitrary values. See also the AutomaticScalesEstimation parameter.
* See also the comment in the documentation of SimilarityTransformElastix about
* the order of the parameters in 2D and 3D.
* \parameter AutomaticScalesEstimation: if this parameter is set to "true" the Scales
* parameter is ignored and the scales are determined automatically. \n
* example: <tt>( AutomaticScalesEstimation "true" ) </tt> \n
* Default: "false" (for backwards compatibility). Recommended: "true".
* \parameter CenterOfRotation: an index around which the image is rotated. \n
* example: <tt>(CenterOfRotation 128 128 90)</tt> \n
* By default the CenterOfRotation is set to the geometric center of the image.
* \parameter AutomaticTransformInitialization: whether or not the initial translation
* between images should be estimated as the distance between their centers.\n
* example: <tt>(AutomaticTransformInitialization "true")</tt> \n
* By default "false" is assumed. So, no initial translation.
* \parameter AutomaticTransformInitializationMethod: how to initialize this
* transform. Should be one of {GeometricalCenter, CenterOfGravity}.\n
* example: <tt>(AutomaticTransformInitializationMethod "CenterOfGravity")</tt> \n
* By default "GeometricalCenter" is assumed.\n
*
* The transform parameters necessary for transformix, additionally defined by this class, are:
* \transformparameter CenterOfRotation: stores the center of rotation as an index. \n
* example: <tt>(CenterOfRotation 128 128 90)</tt>\n
* <b>depecrated!</b> From elastix version 3.402 this is changed to CenterOfRotationPoint!
* \transformparameter CenterOfRotationPoint: stores the center of rotation, expressed in world coordinates. \n
* example: <tt>(CenterOfRotationPoint 10.555 6.666 12.345)</tt>
*
* \ingroup Transforms
*/
template <class TElastix>
class ITK_TEMPLATE_EXPORT SimilarityTransformElastix
: public itk::AdvancedCombinationTransform<typename elx::TransformBase<TElastix>::CoordRepType,
elx::TransformBase<TElastix>::FixedImageDimension>
, public elx::TransformBase<TElastix>
{
public:
ITK_DISALLOW_COPY_AND_MOVE(SimilarityTransformElastix);
/** Standard ITK-stuff. */
using Self = SimilarityTransformElastix;
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 SimilarityTransformType = itk::SimilarityTransform<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(SimilarityTransformElastix, itk::AdvancedCombinationTransform);
/** Name of this class.
* Use this name in the parameter file to select this specific transform. \n
* example: <tt>(Transform "SimilarityTransform")</tt>\n
*/
elxClassNameMacro("SimilarityTransform");
/** Dimension of the fixed image. */
itkStaticConstMacro(SpaceDimension, unsigned int, Superclass2::FixedImageDimension);
/** Typedefs inherited from the superclass. */
/** These are both in Similarity2D and Similarity3D. */
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;
/** NOTE: use this one only in 3D (otherwise it's just an int). */
using SimilarityTransformPointer = typename SimilarityTransformType::Pointer;
using OffsetType = typename SimilarityTransformType::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<SimilarityTransformType, 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. */
SimilarityTransformElastix();
/** The destructor. */
~SimilarityTransformElastix() override = default;
/** Try to read the CenterOfRotation from the transform parameter file
* This is an index value, and, thus, converted to world coordinates.
* Transform parameter files generated by elastix version < 3.402
* saved the center of rotation in this way.
*/
virtual bool
ReadCenterOfRotationIndex(InputPointType & rotationPoint) const;
/** Try to read the CenterOfRotationPoint from the transform parameter file
* The CenterOfRotationPoint is already in world coordinates.
* Transform parameter files generated by elastix version > 3.402
* save the center of rotation in this way.
*/
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 SimilarityTransformPointer m_SimilarityTransform{ SimilarityTransformType::New() };
};
} // end namespace elastix
#ifndef ITK_MANUAL_INSTANTIATION
# include "elxSimilarityTransform.hxx"
#endif
#endif // end #ifndef elxSimilarityTransform_h
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