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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 elxMetricBase_h
#define elxMetricBase_h
/** Needed for the macros. */
#include "elxMacro.h"
#include "elxBaseComponentSE.h"
#include "itkAdvancedImageToImageMetric.h"
#include "itkImageGridSampler.h"
#include "itkPointSet.h"
namespace elastix
{
/**
* \class MetricBase
* \brief This class is the elastix base class for all Metrics.
*
* This class contains the common functionality for all Metrics.
*
* The parameters used in this class are:
* \parameter ShowExactMetricValue: Flag that can set to "true" or "false".
* If "true" the metric computes the exact metric value (computed on all
* voxels rather than on the set of spatial samples) and shows it each
* iteration. Must be given for each resolution. \n
* example: <tt>(ShowExactMetricValue "true" "true" "false")</tt> \n
* Default is "false" for all resolutions.
* \parameter ExactMetricSampleGridSpacing: Set an integer downsampling rate for
* computing the "exact" metric. Only meaningful if set in combination with the
* ShowExactMetricValue set to "true". In some cases, it might be an overkill
* to really compute the exact metric with the ShowExactMetricValue.
* The metric computed on a downsampled image might already be accurate
* enough to draw conclusions about the rate of convergence for example.
* The downsampling rate must be given for each resolution, for each dimension.\n
* example: <tt>(ExactMetricSampleGridSpacing 1 1 2 2 )</tt> \n
* This example for a 2D registration of 2 resolutions sets the downsampling rate
* to 1 in the first resolution (so: use really all pixels), and to 2 in the
* second resolution. Default: 1 in each resolution and each dimension.
* \parameter CheckNumberOfSamples: Whether the metric checks if at least
* a certain fraction (default 1/4) of the samples map inside the moving
* image. Can be given for each resolution or for all resolutions at once. \n
* example: <tt>(CheckNumberOfSamples "false" "true" "false")</tt> \n
* The default is true. In general it is wise to set this to true,
* since it detects if the registration is going really bad.
* \parameter RequiredRatioOfValidSamples: Defines the fraction needed in
* CheckNumberOfSamples. \n
* example: <tt>(RequiredRatioOfValidSamples 0.1)</tt> \n
* The default is 0.25.
*
* \ingroup Metrics
* \ingroup ComponentBaseClasses
*/
template <class TElastix>
class ITK_TEMPLATE_EXPORT MetricBase : public BaseComponentSE<TElastix>
{
public:
ITK_DISALLOW_COPY_AND_MOVE(MetricBase);
/** Standard ITK stuff. */
using Self = MetricBase;
using Superclass = BaseComponentSE<TElastix>;
/** Run-time type information (and related methods). */
itkTypeMacro(MetricBase, BaseComponentSE);
/** Typedef's inherited from Elastix. */
using typename Superclass::ElastixType;
using typename Superclass::RegistrationType;
/** Other typedef's. */
using FixedImageType = typename ElastixType::FixedImageType;
using FixedPointType = typename FixedImageType::PointType;
using FixedPointValueType = typename FixedPointType::ValueType;
using MovingImageType = typename ElastixType::MovingImageType;
using MovingPointType = typename MovingImageType::PointType;
using MovingPointValueType = typename MovingPointType::ValueType;
/** ITKBaseType. */
using ITKBaseType = itk::SingleValuedCostFunction;
using AdvancedMetricType = itk::AdvancedImageToImageMetric<FixedImageType, MovingImageType>;
using MovingImageDerivativeScalesType = typename AdvancedMetricType::MovingImageDerivativeScalesType;
/** Get the dimension of the fixed image. */
itkStaticConstMacro(FixedImageDimension, unsigned int, FixedImageType::ImageDimension);
/** Get the dimension of the moving image. */
itkStaticConstMacro(MovingImageDimension, unsigned int, MovingImageType::ImageDimension);
/** Typedefs for point sets. */
using CoordinateRepresentationType = typename ITKBaseType::ParametersValueType;
using FixedPointSetType = itk::PointSet<CoordinateRepresentationType,
FixedImageDimension,
itk::DefaultStaticMeshTraits<CoordinateRepresentationType,
FixedImageDimension,
FixedImageDimension,
CoordinateRepresentationType,
CoordinateRepresentationType,
CoordinateRepresentationType>>;
using MovingPointSetType = itk::PointSet<CoordinateRepresentationType,
MovingImageDimension,
itk::DefaultStaticMeshTraits<CoordinateRepresentationType,
MovingImageDimension,
MovingImageDimension,
CoordinateRepresentationType,
CoordinateRepresentationType,
CoordinateRepresentationType>>;
/** Typedefs for sampler support. */
using ImageSamplerBaseType = typename AdvancedMetricType::ImageSamplerType;
/** Return type of GetValue */
using MeasureType = typename ITKBaseType::MeasureType;
/** Retrieves this object as ITKBaseType. */
ITKBaseType *
GetAsITKBaseType()
{
return &(this->GetSelf());
}
/** Retrieves this object as ITKBaseType, to use in const functions. */
const ITKBaseType *
GetAsITKBaseType() const
{
return &(this->GetSelf());
}
/** Execute stuff before each resolution:
* \li Check if the exact metric value should be computed
* (to monitor the progress of the registration).
*/
void
BeforeEachResolutionBase() override;
/** Execute stuff after each iteration:
* \li Optionally compute the exact metric value and plot it to screen.
*/
void
AfterEachIterationBase() override;
/** Force the metric to base its computation on a new subset of image samples.
* Not every metric may have implemented this.
*/
virtual void
SelectNewSamples();
/** Returns whether the metric uses a sampler. When the metric is not of
* AdvancedMetricType, the function returns false immediately.
*/
virtual bool
GetAdvancedMetricUseImageSampler() const;
/** Method to set the image sampler. The image sampler is only used when
* the metric is of type AdvancedMetricType, and has UseImageSampler set
* to true. In other cases, the function does nothing.
*/
virtual void
SetAdvancedMetricImageSampler(ImageSamplerBaseType * sampler);
/** Methods to get the image sampler. The image sampler is only used when
* the metric is of type AdvancedMetricType, and has UseImageSampler set
* to true. In other cases, the function returns 0.
*/
virtual ImageSamplerBaseType *
GetAdvancedMetricImageSampler() const;
/** Get if the exact metric value is computed */
virtual bool
GetShowExactMetricValue() const
{
return this->m_ShowExactMetricValue;
}
/** Get the last computed exact metric value */
virtual MeasureType
GetCurrentExactMetricValue() const
{
return this->m_CurrentExactMetricValue;
}
protected:
/** The parameters type. */
using ParametersType = typename ITKBaseType::ParametersType;
/** The full sampler used by the GetExactValue method. */
using ExactMetricImageSamplerType = itk::ImageGridSampler<FixedImageType>;
using ExactMetricImageSamplerPointer = typename ExactMetricImageSamplerType::Pointer;
using ExactMetricSampleGridSpacingType = typename ExactMetricImageSamplerType::SampleGridSpacingType;
/** The constructor. */
MetricBase() = default;
/** The destructor. */
~MetricBase() override = default;
/** Get the exact value. Mutual information computed over all points.
* It is meant in situations when you optimize using just a subset of pixels,
* but are interested in the exact value of the metric.
*
* This method only works when the itkYourMetric inherits from
* the AdvancedMetricType.
* In other cases it returns 0. You may re-implement this method in
* the elxYourMetric, if you like.
*/
virtual MeasureType
GetExactValue(const ParametersType & parameters);
/** \todo the method GetExactDerivative could as well be added here. */
bool m_ShowExactMetricValue{ false };
ExactMetricImageSamplerPointer m_ExactMetricSampler{ nullptr };
MeasureType m_CurrentExactMetricValue{ 0.0 };
ExactMetricSampleGridSpacingType m_ExactMetricSampleGridSpacing{ itk::MakeFilled<ExactMetricSampleGridSpacingType>(
1) };
unsigned int m_ExactMetricEachXNumberOfIterations{ 1 };
private:
elxDeclarePureVirtualGetSelfMacro(ITKBaseType);
};
} // end namespace elastix
#ifndef ITK_MANUAL_INSTANTIATION
# include "elxMetricBase.hxx"
#endif
#endif // end #ifndef elxMetricBase_h
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