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itkLandmarkBasedTransformInitializer.h
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itkLandmarkBasedTransformInitializer.h
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/*=========================================================================
*
* Copyright Insight Software Consortium
*
* 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 itkLandmarkBasedTransformInitializer_h
#define itkLandmarkBasedTransformInitializer_h
#include "itkObject.h"
#include "itkObjectFactory.h"
#include "itkVersorRigid3DTransform.h"
#include "itkRigid2DTransform.h"
#include "itkAffineTransform.h"
#include "itkBSplineTransform.h"
#include "itkPoint.h"
#include "itkPointSet.h"
#include "itkBSplineScatteredDataPointSetToImageFilter.h"
#include "itkVectorIndexSelectionCastImageFilter.h"
#include <vector>
namespace itk
{
/** \class LandmarkBasedTransformInitializer
* This class computes the transform that aligns the fixed and moving images
* given a set of pair landmarks. The class is templated over the Transform type
* as well as fixed image and moving image types.
* The transform computed gives the best fit transform that maps the fixed
* and moving images in a least squares sense. The indices are taken to
* correspond, so point 1 in the first set will get mapped close to point
* 1 in the second set, etc.
*
* Currently, the following transforms are supported by the class:
* VersorRigid3DTransform
* Rigid2DTransform
* AffineTransform
* BSplineTransform
*
* An equal number of fixed and moving landmarks need to be specified using
* SetFixedLandmarks() and SetMovingLandmarks(). Any number of landmarks may
* be specified. In the case of the Affine transformation the number
* of landmarks must be greater than the landmark dimensionality. If
* this is not the case an exception is thrown. In the case of the
* VersorRigid3DTransform and Rigid2DTransform the number of landmarks
* must be equal or greater than the landmark dimensionality. If this
* is not the case, only the translational component of the
* transformation is computed and the rotation is the identity.
* In the case of using Affine or BSpline transforms, each landmark pair can
* contribute in the final transform based on its defined weight. Number of
* weights should be equal to the number of landmarks and can be specified using
* SetLandmarkWeight(). By defaults are weights are set to one.
* Call InitializeTransform() to initialize the transform.
*
* The class is based in part on Hybrid/vtkLandmarkTransform originally
* implemented in python by David G. Gobbi.
*
* The solution is based on
* Berthold K. P. Horn (1987), "Closed-form solution of absolute orientation
* using unit quaternions,"
* http://people.csail.mit.edu/bkph/papers/Absolute_Orientation.pdf
*
* The Affine Transform initializer is based on an algorithm by H Spaeth,
* and is described in the Insight Journal Article
* "Affine Transformation for Landmark Based Registration Initializer
* in ITK" by Kim E.Y., Johnson H., Williams N.
* available at http://midasjournal.com/browse/publication/825
*
* \ingroup ITKRegistrationCommon
*
* \wiki
* \wikiexample{Registration/LandmarkBasedTransformInitializer,Rigidly register one image to another using manually specified landmarks}
* \endwiki
*/
template< typename TTransform,
typename TFixedImage = itk::ImageBase<TTransform::InputSpaceDimension > ,
typename TMovingImage = itk::ImageBase<TTransform::OutputSpaceDimension> >
class ITK_TEMPLATE_EXPORT LandmarkBasedTransformInitializer:
public Object
{
public:
ITK_DISALLOW_COPY_AND_ASSIGN(LandmarkBasedTransformInitializer);
/** Standard class type aliases. */
using Self = LandmarkBasedTransformInitializer;
using Superclass = Object;
using Pointer = SmartPointer<Self>;
using ConstPointer = SmartPointer<const Self>;
/** New macro for creation of through a Smart Pointer. */
itkNewMacro(Self);
/** Run-time type information (and related methods). */
itkTypeMacro(LandmarkBasedTransformInitializer, Object);
/** Type of the transform to initialize */
using TransformType = TTransform;
using TransformPointer = typename TransformType::Pointer;
/** Dimension of parameters. */
static constexpr unsigned int InputSpaceDimension = TransformType::InputSpaceDimension;
static constexpr unsigned int OutputSpaceDimension = TransformType::OutputSpaceDimension;
/** Set the transform to be initialized */
itkSetObjectMacro(Transform, TransformType);
/** Image Types to use in the initialization of the transform */
using FixedImageType = TFixedImage;
using MovingImageType = TMovingImage;
/** Set the reference image to define the parametric domain for the BSpline transform */
itkSetConstObjectMacro(ReferenceImage, FixedImageType);
/** Set the number of control points to define the parametric domain for the BSpline transform */
itkSetMacro(BSplineNumberOfControlPoints, unsigned int);
using FixedImagePointer = typename FixedImageType::ConstPointer;
using MovingImagePointer = typename MovingImageType::ConstPointer;
/** Determine the image dimension. */
static constexpr unsigned int ImageDimension = FixedImageType::ImageDimension;
/** Convenience type alias */
using InputPointType = typename TransformType::InputPointType;
using OutputVectorType = typename TransformType::OutputVectorType;
using LandmarkPointType = Point< double, ImageDimension >;
using LandmarkPointContainer = std::vector< LandmarkPointType >;
using PointsContainerConstIterator = typename LandmarkPointContainer::const_iterator;
using ParametersType = typename TransformType::ParametersType;
using ParametersValueType = typename ParametersType::ValueType;
using LandmarkWeightType = std::vector< double >;
using LandmarkWeightConstIterator = LandmarkWeightType::const_iterator;
/** Set the Fixed landmark point containers */
void SetFixedLandmarks(const LandmarkPointContainer & fixedLandmarks)
{
this->m_FixedLandmarks = fixedLandmarks;
}
/** Set the Moving landmark point containers */
void SetMovingLandmarks(const LandmarkPointContainer & movingLandmarks)
{
this->m_MovingLandmarks = movingLandmarks;
}
/** Set the landmark weight point containers
* Weight includes diagonal elements of weight matrix
*/
void SetLandmarkWeight(LandmarkWeightType & landmarkWeight)
{
this->m_LandmarkWeight= landmarkWeight;
}
/** Supported Transform type alias */
using VersorRigid3DTransformType = VersorRigid3DTransform< ParametersValueType >;
using Rigid2DTransformType = Rigid2DTransform< ParametersValueType >;
using AffineTransformType = AffineTransform< ParametersValueType, FixedImageType::ImageDimension >;
constexpr static unsigned int SplineOrder = 3;
using BSplineTransformType = BSplineTransform< ParametersValueType,
FixedImageType::ImageDimension,
SplineOrder>;
/** Initialize the transform from the landmarks */
virtual void InitializeTransform();
protected:
LandmarkBasedTransformInitializer();
~LandmarkBasedTransformInitializer() override = default;
void PrintSelf(std::ostream & os, Indent indent) const override;
private:
/** fallback Initializer just sets transform to identity */
template <typename TTransform2>
void InternalInitializeTransform(TTransform2 *);
/** Initializer for VersorRigid3D */
void InternalInitializeTransform(VersorRigid3DTransformType *);
/** Initializer for Rigid2DTransform */
void InternalInitializeTransform(Rigid2DTransformType *);
/** Initializer for AffineTransform */
void InternalInitializeTransform(AffineTransformType *);
/** Initializer for BSplineTransform */
void InternalInitializeTransform(BSplineTransformType *);
FixedImagePointer m_ReferenceImage;
TransformPointer m_Transform;
LandmarkPointContainer m_FixedLandmarks;
LandmarkPointContainer m_MovingLandmarks;
/** weights for affine landmarks */
LandmarkWeightType m_LandmarkWeight;
unsigned int m_BSplineNumberOfControlPoints{4};
}; //class LandmarkBasedTransformInitializer
} // namespace itk
#ifndef ITK_MANUAL_INSTANTIATION
#include "itkLandmarkBasedTransformInitializer.hxx"
#endif
#endif /* itkLandmarkBasedTransformInitializer_h */