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/*=========================================================================
*
* Copyright NumFOCUS
*
* 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
*
* https://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 itkTimeVaryingVelocityFieldIntegrationImageFilter_h
#define itkTimeVaryingVelocityFieldIntegrationImageFilter_h
#include "itkImageToImageFilter.h"
#include "itkVectorInterpolateImageFunction.h"
namespace itk
{
/**
* \class TimeVaryingVelocityFieldIntegrationImageFilter
* \brief Integrate a time-varying velocity field using 4th order Runge-Kutta.
*
* Diffeomorphisms are topology-preserving mappings that are useful for
* describing biologically plausible deformations. Mathematically, a
* diffeomorphism, \f$ \phi \f$, is generated from a time-varying velocity field, v, as
* described by the integral equation:
*
* \f[
* \phi(t_b) = \phi(t_a) + \int_{t_a}^{t_b} v(\phi(t),t) dt
* \f]
*
* In this class, the input is the time-varying velocity field and an initial
* diffeomorphism. The output diffeomorphism is produced using fourth order
* Runge-Kutta.
*
* \warning The output deformation field needs to have dimensionality of 1
* less than the input time-varying velocity field.
*
* \author Nick Tustison
* \author Brian Avants
*
* \ingroup ITKDisplacementField
*/
template <typename TTimeVaryingVelocityField,
typename TDisplacementField =
Image<typename TTimeVaryingVelocityField::PixelType, TTimeVaryingVelocityField::ImageDimension - 1>>
class ITK_TEMPLATE_EXPORT TimeVaryingVelocityFieldIntegrationImageFilter
: public ImageToImageFilter<TTimeVaryingVelocityField, TDisplacementField>
{
public:
ITK_DISALLOW_COPY_AND_MOVE(TimeVaryingVelocityFieldIntegrationImageFilter);
using Self = TimeVaryingVelocityFieldIntegrationImageFilter;
using Superclass = ImageToImageFilter<TTimeVaryingVelocityField, TDisplacementField>;
using Pointer = SmartPointer<Self>;
using ConstPointer = SmartPointer<const Self>;
/** Method for creation through the object factory. */
itkNewMacro(Self);
/** \see LightObject::GetNameOfClass() */
itkOverrideGetNameOfClassMacro(TimeVaryingVelocityFieldIntegrationImageFilter);
/**
* Dimensionality of input data is assumed to be one more than the output
* data the same. */
static constexpr unsigned int InputImageDimension = TTimeVaryingVelocityField::ImageDimension;
static constexpr unsigned int OutputImageDimension = TDisplacementField::ImageDimension;
using TimeVaryingVelocityFieldType = TTimeVaryingVelocityField;
using DisplacementFieldType = TDisplacementField;
using DisplacementFieldPointer = typename DisplacementFieldType::Pointer;
using VectorType = typename DisplacementFieldType::PixelType;
using RealType = typename VectorType::RealValueType;
using ScalarType = typename VectorType::ValueType;
using PointType = typename DisplacementFieldType::PointType;
using OutputRegionType = typename DisplacementFieldType::RegionType;
using VelocityFieldInterpolatorType = VectorInterpolateImageFunction<TimeVaryingVelocityFieldType, ScalarType>;
using VelocityFieldInterpolatorPointer = typename VelocityFieldInterpolatorType::Pointer;
using DisplacementFieldInterpolatorType = VectorInterpolateImageFunction<DisplacementFieldType, ScalarType>;
using DisplacementFieldInterpolatorPointer = typename DisplacementFieldInterpolatorType::Pointer;
/** Get/Set the time-varying velocity field interpolator. Default = linear. */
itkSetObjectMacro(VelocityFieldInterpolator, VelocityFieldInterpolatorType);
itkGetModifiableObjectMacro(VelocityFieldInterpolator, VelocityFieldInterpolatorType);
/**
* Get/Set the deformation field interpolator for the initial diffeomorphism
* (if set). Default = linear.
*/
itkSetObjectMacro(DisplacementFieldInterpolator, DisplacementFieldInterpolatorType);
itkGetModifiableObjectMacro(DisplacementFieldInterpolator, DisplacementFieldInterpolatorType);
/**
* Get/Set the initial diffeomorphism
*/
itkSetObjectMacro(InitialDiffeomorphism, DisplacementFieldType);
itkGetModifiableObjectMacro(InitialDiffeomorphism, DisplacementFieldType);
/**
* Set the lower time bound defining the integration domain of the transform.
* We assume that the total possible time domain is [0,1].
*/
itkSetClampMacro(LowerTimeBound, RealType, 0, 1);
/**
* Get the lower time bound defining the integration domain of the transform.
* We assume that the total possible time domain is [0,1].
*/
itkGetConstMacro(LowerTimeBound, RealType);
/**
* Set the upper time bound defining the integration domain of the transform.
* We assume that the total possible time domain is [0,1].
*/
itkSetClampMacro(UpperTimeBound, RealType, 0, 1);
/**
* Get the upper time bound defining the integration domain of the transform.
* We assume that the total possible time domain is [0,1].
*/
itkGetConstMacro(UpperTimeBound, RealType);
/**
* Set the number of integration steps used in the Runge-Kutta solution of the
* initial value problem. Default = 10.
*/
itkSetMacro(NumberOfIntegrationSteps, unsigned int);
/**
* Get the number of integration steps used in the Runge-Kutta solution of the
* initial value problem. Default = 10.
*/
itkGetConstMacro(NumberOfIntegrationSteps, unsigned int);
/**
* Get/Set a flag to interpret LowerTimeBound and UpperTimeBound as rates
* in the velocity field time span. This is equivalent to consider that the velocity
* field is defined in the normalized time interval [0, 1], ignoring the input origin
* and spacing in the temporal dimension.
*
* The default is true for backwards compatibility.
*/
itkSetMacro(TimeBoundsAsRates, bool);
itkGetConstMacro(TimeBoundsAsRates, bool);
itkBooleanMacro(TimeBoundsAsRates);
protected:
TimeVaryingVelocityFieldIntegrationImageFilter();
~TimeVaryingVelocityFieldIntegrationImageFilter() override = default;
void
PrintSelf(std::ostream & os, Indent indent) const override;
void
GenerateOutputInformation() override;
void
BeforeThreadedGenerateData() override;
void
DynamicThreadedGenerateData(const OutputRegionType &) override;
VectorType
IntegrateVelocityAtPoint(const PointType & initialSpatialPoint, const TimeVaryingVelocityFieldType * inputField);
RealType m_LowerTimeBound{};
RealType m_UpperTimeBound{};
DisplacementFieldPointer m_InitialDiffeomorphism{};
unsigned int m_NumberOfIntegrationSteps{};
unsigned int m_NumberOfTimePoints{};
DisplacementFieldInterpolatorPointer m_DisplacementFieldInterpolator{};
bool m_TimeBoundsAsRates{ true };
private:
VelocityFieldInterpolatorPointer m_VelocityFieldInterpolator{};
};
} // namespace itk
#ifndef ITK_MANUAL_INSTANTIATION
# include "itkTimeVaryingVelocityFieldIntegrationImageFilter.hxx"
#endif
#endif
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