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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 itkMultiphaseDenseFiniteDifferenceImageFilter_h
#define itkMultiphaseDenseFiniteDifferenceImageFilter_h
#include "itkMultiphaseFiniteDifferenceImageFilter.h"
#include "itkBinaryThresholdImageFilter.h"
#include "itkSignedMaurerDistanceMapImageFilter.h"
#include "itkNumericTraits.h"
#include "itkNeighborhoodAlgorithm.h"
#include <list>
namespace itk
{
/**
* \class MultiphaseDenseFiniteDifferenceImageFilter
*
* This filter implements a layer of the finite difference solver hierarchy that
* performs ``dense'' iteration, ie. iteration over all pixels in the input and
* output at each change calculation and update step. Dense iteration is in
* contrast to a ``sparse'' iteration over a subset of the pixels. See
* documentation for FiniteDifferenceImageFilter for an overview of the
* iterative finite difference algorithm:
*
* \par
* \f$u_{\mathbf{i}}^{n+1}=u^n_{\mathbf{i}}+\Delta u^n_{\mathbf{i}}\Delta t\f$
*
* \par
* The generic code for performing iterations and updates at each time
* step is inherited from the parent class. This class defines an update
* buffer for \f$ \Delta \f$ and the methods CalculateChange() and
* ApplyUpdate(). These methods are designed to automatically thread their
* execution. \f$ \Delta \f$ is defined as an image of identical size and type
* as the output image.
*
* \par
* As we descend through each layer in the hierarchy, we know more and more
* about the specific application of our filter. At this level, we
* have committed to iteration over each pixel in an image. We take advantage
* of that knowledge to multithread the iteration and update methods.
*
* \par Inputs and Outputs
* This is an image to image filter. The specific types of the images are not
* fixed at this level in the hierarchy.
*
* \par How to use this class
* This filter is only one layer in a branch the finite difference solver
* hierarchy. It does not define the function used in the CalculateChange() and
* it does not define the stopping criteria (Halt method). To use this class,
* subclass it to a specific instance that supplies a function and Halt()
* method.
*
* Based on the paper:
*
* "An active contour model without edges"
* T. Chan and L. Vese.
* In Scale-Space Theories in Computer Vision, pages 141-151, 1999.
*
* \author Mosaliganti K., Smith B., Gelas A., Gouaillard A., Megason S.
*
* This code was taken from the Insight Journal paper:
*
* "Cell Tracking using Coupled Active Surfaces for Nuclei and Membranes"
* http://www.insight-journal.org/browse/publication/642
* https://hdl.handle.net/10380/3055
*
* That is based on the papers:
*
* "Level Set Segmentation: Active Contours without edge"
* http://www.insight-journal.org/browse/publication/322
* https://hdl.handle.net/1926/1532
*
* and
*
* "Level set segmentation using coupled active surfaces"
* http://www.insight-journal.org/browse/publication/323
* https://hdl.handle.net/1926/1533
*
*
* \ingroup ImageFilters
* \sa FiniteDifferenceImageFilter
* \ingroup ITKReview
*/
template< typename TInputImage, typename TFeatureImage, typename TOutputImage, typename TFunction,
typename TIdCell = unsigned int >
class MultiphaseDenseFiniteDifferenceImageFilter:
public MultiphaseFiniteDifferenceImageFilter< TInputImage, TFeatureImage,
TOutputImage, TFunction, TIdCell >
{
public:
/** Standard class typedefs */
typedef MultiphaseDenseFiniteDifferenceImageFilter Self;
typedef MultiphaseFiniteDifferenceImageFilter< TInputImage,
TFeatureImage, TOutputImage, TFunction, TIdCell > Superclass;
typedef SmartPointer< Self > Pointer;
typedef SmartPointer< const Self > ConstPointer;
/** Run-time type information (and related methods) */
itkTypeMacro(MultiphaseDenseFiniteDifferenceImageFilter, ImageToImageFilter);
/** Dimensionality of input and output data is assumed to be the same.
* It is inherited from the superclass. */
itkStaticConstMacro(ImageDimension, unsigned int, Superclass::ImageDimension);
/** Convenient typedefs */
typedef typename Superclass::InputImageType InputImageType;
typedef typename Superclass::InputImagePointer InputImagePointer;
typedef typename Superclass::InputRegionType InputRegionType;
typedef typename Superclass::InputSizeType InputSizeType;
typedef typename Superclass::InputSizeValueType InputSizeValueType;
typedef typename Superclass::InputIndexType InputIndexType;
typedef typename Superclass::InputIndexValueType InputIndexValueType;
typedef typename Superclass::InputPixelType InputPixelType;
typedef typename Superclass::InputPointType InputPointType;
typedef typename Superclass::InputSpacingType InputSpacingType;
typedef typename InputImageType::ValueType ValueType;
typedef typename Superclass::FeatureImageType FeatureImageType;
typedef typename Superclass::FeatureSizeType FeatureSizeType;
typedef typename Superclass::FeatureImagePointer FeatureImagePointer;
typedef typename Superclass::FeatureRegionType FeatureRegionType;
typedef typename Superclass::FeatureSpacingType FeatureSpacingType;
typedef typename Superclass::FeaturePointType FeaturePointType;
typedef typename Superclass::FeaturePixelType FeaturePixelType;
typedef typename Superclass::OutputImageType OutputImageType;
typedef typename Superclass::OutputImagePointer OutputImagePointer;
typedef typename Superclass::OutputRegionType OutputRegionType;
typedef typename Superclass::OutputSizeType OutputSizeType;
typedef typename Superclass::OutputSizeValueType SizeValueType;
typedef typename Superclass::OutputIndexType OutputIndexType;
typedef typename Superclass::OutputIndexValueType OutputIndexValueType;
typedef typename OutputImageType::PixelType OutputPixelType;
typedef typename Superclass::IdCellType IdCellType;
typedef BinaryThresholdImageFilter< InputImageType, InputImageType > ThresholdFilterType;
typedef typename ThresholdFilterType::Pointer ThresholdFilterPointer;
typedef SignedMaurerDistanceMapImageFilter< InputImageType, InputImageType > MaurerType;
typedef typename MaurerType::Pointer MaurerPointer;
typedef typename Superclass::FiniteDifferenceFunctionType FiniteDifferenceFunctionType;
typedef typename Superclass::FiniteDifferenceFunctionPointer FiniteDifferenceFunctionPointer;
typedef typename FiniteDifferenceFunctionType::NeighborhoodType NeighborhoodIteratorType;
/** The value type of a time step. Inherited from the superclass. */
typedef typename Superclass::TimeStepType TimeStepType;
typedef NeighborhoodAlgorithm::ImageBoundaryFacesCalculator< InputImageType > FaceCalculatorType;
typedef typename FaceCalculatorType::FaceListType FaceListType;
void SetFunctionCount(const IdCellType & n);
#ifdef ITK_USE_CONCEPT_CHECKING
// Begin concept checking
itkConceptMacro( OutputTimesDoubleCheck,
( Concept::MultiplyOperator< OutputPixelType, double > ) );
itkConceptMacro( OutputAdditiveOperatorsCheck,
( Concept::AdditiveOperators< OutputPixelType > ) );
itkConceptMacro( InputConvertibleToOutputCheck,
( Concept::Convertible< FeaturePixelType, OutputPixelType > ) );
// End concept checking
#endif
itkSetMacro(ReinitializeCounter, unsigned int);
itkGetMacro(ReinitializeCounter, unsigned int);
protected:
MultiphaseDenseFiniteDifferenceImageFilter()
{
this->m_ReinitializeCounter = 1;
// FIXME: this->m_UpdateCounter really used?
// this->m_UpdateCounter = 0; // FIXME: Should this be a bool ?
}
~MultiphaseDenseFiniteDifferenceImageFilter() {}
virtual void PrintSelf(std::ostream &, Indent indent) const ITK_OVERRIDE;
/** A simple method to copy the data from the input to the output. ( Supports
* "read-only" image adaptors in the case where the input image type converts
* to a different output image type. ) */
virtual void CopyInputToOutput() ITK_OVERRIDE;
virtual void PostProcessOutput() ITK_OVERRIDE;
/** This method applies changes from the m_UpdateBuffer to the output using
* the ThreadedApplyUpdate() method and a multithreading mechanism. "dt" is
* the time step to use for the update of each pixel. */
virtual void ApplyUpdate(TimeStepType dt) ITK_OVERRIDE;
unsigned int m_ReinitializeCounter; // FIXME: Should this be a boolean ?
// unsigned int m_UpdateCounter; // FIXME: Should this be a boolean ?
private:
MultiphaseDenseFiniteDifferenceImageFilter(const Self &);
void operator=(const Self &) ITK_DELETE_FUNCTION;
/** This method allocates storage in m_UpdateBuffer. It is called from
* Superclass::GenerateData(). */
virtual void AllocateUpdateBuffer() ITK_OVERRIDE;
/** This method populates an update buffer with changes for each pixel in the
* output using the ThreadedCalculateChange() method and a multithreading
* mechanism. Returns value is a time step to be used for the update. */
virtual TimeStepType CalculateChange() ITK_OVERRIDE;
/** The buffer that holds the updates for an iteration of the algorithm. */
std::vector< InputImagePointer > m_UpdateBuffers;
};
} // end namespace itk
#ifndef ITK_MANUAL_INSTANTIATION
#include "itkMultiphaseDenseFiniteDifferenceImageFilter.hxx"
#endif
#endif
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