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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 elxMultiBSplineTransformWithNormal_h
#define elxMultiBSplineTransformWithNormal_h
#include "elxIncludes.h" // include first to avoid MSVS warning
#include "itkAdvancedCombinationTransform.h"
#include "itkAdvancedBSplineDeformableTransform.h"
#include "itkMultiBSplineDeformableTransformWithNormal.h"
#include "itkGridScheduleComputer.h"
#include "itkUpsampleBSplineParametersFilter.h"
namespace elastix
{
/**
* \class MultiBSplineTransformWithNormal
* \brief A transform based on the itkMultiBSplineDeformableTransformWithNormal.
*
* This transform is a composition of B-spline transformations, allowing sliding motion between different labels.
*
* The parameters used in this class are:
* \parameter Transform: Select this transform as follows:\n
* <tt>(%Transform "MultiBSplineTransformWithNormal")</tt>
* \parameter BSplineTransformSplineOrder: choose a B-spline order 1,2, or 3. \n
* example: <tt>(BSplineTransformSplineOrder 3)</tt>\n
* Default value: 3 (cubic B-splines).
* \parameter FinalGridSpacingInVoxels: the grid spacing of the B-spline transform for each dimension. \n
* example: <tt>(FinalGridSpacingInVoxels 8.0 8.0 8.0)</tt> \n
* If only one argument is given, that factor is used for each dimension. The spacing
* is not in millimeters, but in "voxel size units".
* The default is 16.0 in every dimension.
* \parameter FinalGridSpacingInPhysicalUnits: the grid spacing of the B-spline transform for each dimension. \n
* example: <tt>(FinalGridSpacingInPhysicalUnits 8.0 8.0 8.0)</tt> \n
* If only one argument is given, that factor is used for each dimension. The spacing
* is specified in millimeters.
* If not specified, the FinalGridSpacingInVoxels is used, or the FinalGridSpacing,
* to compute a FinalGridSpacingInPhysicalUnits. If those are not specified, the default
* value for FinalGridSpacingInVoxels is used to compute a FinalGridSpacingInPhysicalUnits.
* If an affine transformation is provided as initial transformation, the control grid
* will be scaled to cover the fixed image domain in the space defined by the initial transformation.
* \parameter GridSpacingSchedule: the grid spacing downsampling factors for the B-spline transform
* for each dimension and each resolution. \n
* example: <tt>(GridSpacingSchedule 4.0 4.0 2.0 2.0 1.0 1.0)</tt> \n
* Which is an example for a 2D image, using 3 resolutions. \n
* For convenience, you may also specify only one value for each resolution:\n
* example: <tt>(GridSpacingSchedule 4.0 2.0 1.0 )</tt> \n
* which is equivalent to the example above.
*
*
* The transform parameters necessary for transformix, additionally defined by this class, are:
* \transformparameter GridSize: stores the size of the B-spline grid. \n
* example: <tt>(GridSize 16 16 16)</tt>
* \transformparameter GridIndex: stores the index of the B-spline grid. \n
* example: <tt>(GridIndex 0 0 0)</tt>
* \transformparameter GridSpacing: stores the spacing of the B-spline grid. \n
* example: <tt>(GridSpacing 16.0 16.0 16.0)</tt>
* \transformparameter GridOrigin: stores the origin of the B-spline grid. \n
* example: <tt>(GridOrigin 0.0 0.0 0.0)</tt>
* \transformparameter GridDirection: stores the direction cosines of the B-spline grid. \n
* example: <tt>(GridDirection 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.1)</tt>
* \transformparameter BSplineTransformSplineOrder: stores the B-spline order 1,2, or 3. \n
* example: <tt>(BSplineTransformSplineOrder 3)</tt>
* Default value: 3 (cubic B-splines).
*
* \todo It is unsure what happens when one of the image dimensions has length 1.
*
* \author Vivien Delmon
*
* \ingroup Transforms
*/
template <class TElastix>
class ITK_TEMPLATE_EXPORT MultiBSplineTransformWithNormal
: public itk::AdvancedCombinationTransform<typename elx::TransformBase<TElastix>::CoordRepType,
elx::TransformBase<TElastix>::FixedImageDimension>
, public TransformBase<TElastix>
{
public:
ITK_DISALLOW_COPY_AND_MOVE(MultiBSplineTransformWithNormal);
/** Standard ITK-stuff. */
using Self = MultiBSplineTransformWithNormal;
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>;
/** Method for creation through the object factory. */
itkNewMacro(Self);
/** Run-time type information (and related methods). */
itkTypeMacro(MultiBSplineTransformWithNormal, AdvancedCombinationTransform);
/** Name of this class.
* Use this name in the parameter file to select this specific transform. \n
* example: <tt>(Transform "BSplineTransform")</tt>\n
*/
elxClassNameMacro("MultiBSplineTransformWithNormal");
/** Dimension of the fixed image. */
itkStaticConstMacro(SpaceDimension, unsigned int, Superclass2::FixedImageDimension);
/** The ITK-class that provides most of the functionality, and
* that is set as the "CurrentTransform" in the CombinationTransform.
*/
using BSplineTransformBaseType =
itk::AdvancedBSplineDeformableTransformBase<typename elx::TransformBase<TElastix>::CoordRepType,
Self::SpaceDimension>;
using BSplineTransformBasePointer = typename BSplineTransformBaseType::Pointer;
/** Typedef for supported BSplineTransform types. */
using MultiBSplineTransformWithNormalLinearType =
itk::MultiBSplineDeformableTransformWithNormal<typename elx::TransformBase<TElastix>::CoordRepType,
Self::SpaceDimension,
1>;
using MultiBSplineTransformWithNormalQuadraticType =
itk::MultiBSplineDeformableTransformWithNormal<typename elx::TransformBase<TElastix>::CoordRepType,
Self::SpaceDimension,
2>;
using MultiBSplineTransformWithNormalCubicType =
itk::MultiBSplineDeformableTransformWithNormal<typename elx::TransformBase<TElastix>::CoordRepType,
Self::SpaceDimension,
3>;
/** Typedefs inherited from the superclass. */
using typename Superclass1::ScalarType;
using typename Superclass1::ParametersType;
using typename Superclass1::NumberOfParametersType;
using typename Superclass1::JacobianType;
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 typename Superclass1::InputPointType;
using typename Superclass1::OutputPointType;
/** Typedef's specific for the BSplineTransform. */
using PixelType = typename BSplineTransformBaseType::PixelType;
using ImageType = typename BSplineTransformBaseType::ImageType;
using ImagePointer = typename BSplineTransformBaseType::ImagePointer;
using RegionType = typename BSplineTransformBaseType::RegionType;
using IndexType = typename BSplineTransformBaseType::IndexType;
using SizeType = typename BSplineTransformBaseType::SizeType;
using SpacingType = typename BSplineTransformBaseType::SpacingType;
using OriginType = typename BSplineTransformBaseType::OriginType;
using DirectionType = typename BSplineTransformBaseType::DirectionType;
using ContinuousIndexType = typename BSplineTransformBaseType::ContinuousIndexType;
using ParameterIndexArrayType = typename BSplineTransformBaseType::ParameterIndexArrayType;
/** Typedef's 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;
/** Typedef's for the GridScheduleComputer and the UpsampleBSplineParametersFilter. */
using GridScheduleComputerType = itk::GridScheduleComputer<CoordRepType, SpaceDimension>;
using GridScheduleComputerPointer = typename GridScheduleComputerType::Pointer;
using GridScheduleType = typename GridScheduleComputerType ::VectorGridSpacingFactorType;
using GridUpsamplerType = itk::UpsampleBSplineParametersFilter<ParametersType, ImageType>;
using GridUpsamplerPointer = typename GridUpsamplerType::Pointer;
/** Typdef's for the Image of Labels */
using ImageLabelType = itk::Image<unsigned char, Self::SpaceDimension>;
using ImageLabelPointer = typename ImageLabelType::Pointer;
/** Execute stuff before anything else is done:
* \li Initialize the right BSplineTransform.
* \li Initialize the right grid schedule computer.
*/
int
BeforeAll() override;
/** Execute stuff before the actual registration:
* \li Create an initial B-spline grid.
* \li Create initial registration parameters.
* \li PrecomputeGridInformation
* Initially, the transform is set to use a 1x1x1 grid, with deformation (0,0,0).
* In the method BeforeEachResolution() this will be replaced by the right grid size.
* This seems not logical, but it is required, since the registration
* class checks if the number of parameters in the transform is equal to
* the number of parameters in the registration class. This check is done
* before calling the BeforeEachResolution() methods.
*/
void
BeforeRegistration() override;
/** Execute stuff before each new pyramid resolution:
* \li In the first resolution call InitializeTransform().
* \li In next resolutions upsample the B-spline grid if necessary (so, call IncreaseScale())
*/
void
BeforeEachResolution() override;
/** Method to increase the density of the BSpline grid.
* \li Determine the new B-spline coefficients that describe the current deformation field.
* \li Set these coefficients as InitialParametersOfNextLevel in the registration object.
* Called by BeforeEachResolution().
*/
virtual void
IncreaseScale();
/** Function to read transform-parameters from a file. */
void
ReadFromFile() override;
/** Set the scales of the edge B-spline coefficients to zero. */
virtual void
SetOptimizerScales(const unsigned int edgeWidth);
protected:
/** The constructor. */
MultiBSplineTransformWithNormal() = default;
/** The destructor. */
~MultiBSplineTransformWithNormal() override = default;
/** Read user-specified gridspacing and call the itkGridScheduleComputer. */
virtual void
PreComputeGridInformation();
private:
elxOverrideGetSelfMacro;
/** Method to set the initial BSpline grid and initialize the parameters (to 0).
* \li Define the initial grid region, origin and spacing, using the precomputed grid information.
* \li Set the initial parameters to zero and set then as InitialParametersOfNextLevel in the registration object.
* Called by BeforeEachResolution().
*/
void
InitializeTransform();
/** Creates a map of the parameters specific for this (derived) transform type. */
ParameterMapType
CreateDerivedTransformParameterMap() const override;
/** Private variables. */
typename MultiBSplineTransformWithNormalCubicType::Pointer m_MultiBSplineTransformWithNormal;
GridScheduleComputerPointer m_GridScheduleComputer;
GridUpsamplerPointer m_GridUpsampler;
ImageLabelPointer m_Labels;
std::string m_LabelsPath;
/** Variable to remember order of MultiBSplineTransformWithNormal. */
unsigned int m_SplineOrder;
/** Initialize the right BSplineTransfrom based on the spline order and periodicity. */
unsigned int
InitializeBSplineTransform();
};
} // end namespace elastix
#ifndef ITK_MANUAL_INSTANTIATION
# include "elxMultiBSplineTransformWithNormal.hxx"
#endif
#endif // end #ifndef elxMultiBSplineTransformWithNormal_h
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