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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 itkKappaSigmaThresholdImageFilter_h
#define itkKappaSigmaThresholdImageFilter_h
#include "itkImageToImageFilter.h"
#include "itkKappaSigmaThresholdImageCalculator.h"
namespace itk
{
/**
* \class KappaSigmaThresholdImageFilter
* \brief Threshold an image using Kappa-Sigma-Clipping.
*
* This filter creates a binary thresholded image which separates background and
* foreground modes by iteratively rejecting pixels that do not belong to
* the dominant mode. The filter computes the threshold using the KappaSigmaThre-
* sholdImageCalculator and applies that threshold to the input image using the
* BinaryThresholdImageFilter.
*
* \author Gaetan Lehmann
*
* \note This class was taken from the Insight Journal paper:
* https://www.insight-journal.org/browse/publication/132
*
* \sa KappaSigmaThresholdImageCalculator
* \ingroup IntensityImageFilters
* \ingroup ITKThresholding
*/
template <typename TInputImage,
typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>,
class TOutputImage = TInputImage>
class ITK_TEMPLATE_EXPORT KappaSigmaThresholdImageFilter : public ImageToImageFilter<TInputImage, TOutputImage>
{
public:
ITK_DISALLOW_COPY_AND_MOVE(KappaSigmaThresholdImageFilter);
/** Standard Self type alias */
using Self = KappaSigmaThresholdImageFilter;
using Superclass = ImageToImageFilter<TInputImage, TOutputImage>;
using Pointer = SmartPointer<Self>;
using ConstPointer = SmartPointer<const Self>;
/** Method for creation through the object factory. */
itkNewMacro(Self);
/** \see LightObject::GetNameOfClass() */
itkOverrideGetNameOfClassMacro(KappaSigmaThresholdImageFilter);
/** Standard image type within this class. */
using InputImageType = TInputImage;
using MaskImageType = TMaskImage;
/** Image pixel value type alias. */
using InputPixelType = typename TInputImage::PixelType;
using OutputPixelType = typename TOutputImage::PixelType;
using MaskPixelType = typename TMaskImage::PixelType;
/** Image related type alias. */
using InputImagePointer = typename TInputImage::Pointer;
using OutputImagePointer = typename TOutputImage::Pointer;
using MaskImagePointer = typename TMaskImage::Pointer;
/** Set the "outside" pixel value. The default value
* OutputPixelType{}. */
itkSetMacro(OutsideValue, OutputPixelType);
/** Get the "outside" pixel value. */
itkGetConstMacro(OutsideValue, OutputPixelType);
/** Set the "inside" pixel value. The default value
* NumericTraits<OutputPixelType>::max() */
itkSetMacro(InsideValue, OutputPixelType);
/** Get the "inside" pixel value. */
itkGetConstMacro(InsideValue, OutputPixelType);
/** Get the computed threshold. */
itkGetConstMacro(Threshold, InputPixelType);
/** Set the mask value used to select which pixels will be considered in the
* threshold computation (optional, only in case a MaskImage is set). */
itkSetMacro(MaskValue, MaskPixelType);
itkGetConstMacro(MaskValue, MaskPixelType);
/** Set the Sigma multiplier (Kappa) to adjust the pixel rejection rate. */
itkSetMacro(SigmaFactor, double);
itkGetConstMacro(SigmaFactor, double);
/** Set the number of rejection passes. */
itkSetMacro(NumberOfIterations, unsigned int);
itkGetConstMacro(NumberOfIterations, unsigned int);
#ifdef ITK_USE_CONCEPT_CHECKING
// Begin concept checking
itkConceptMacro(OutputComparableCheck, (Concept::Comparable<OutputPixelType>));
itkConceptMacro(OutputOStreamWritableCheck, (Concept::OStreamWritable<OutputPixelType>));
// End concept checking
#endif
/** Set the mask image */
void
SetMaskImage(const MaskImageType * input)
{
// Process object is not const-correct so the const casting is required.
this->SetNthInput(1, const_cast<MaskImageType *>(input));
}
/** Get the mask image */
const MaskImageType *
GetMaskImage() const
{
return static_cast<MaskImageType *>(const_cast<DataObject *>(this->ProcessObject::GetInput(1)));
}
/** Set the input image */
void
SetInput1(const TInputImage * input)
{
this->SetInput(input);
}
/** Set the marker image */
void
SetInput2(const MaskImageType * input)
{
this->SetMaskImage(input);
}
protected:
KappaSigmaThresholdImageFilter();
~KappaSigmaThresholdImageFilter() override = default;
void
PrintSelf(std::ostream & os, Indent indent) const override;
void
GenerateInputRequestedRegion() override;
void
GenerateData() override;
using InputSizeType = typename TInputImage::SizeType;
using InputIndexType = typename TInputImage::IndexType;
using InputImageRegionType = typename TInputImage::RegionType;
using OutputSizeType = typename TOutputImage::SizeType;
using OutputIndexType = typename TOutputImage::IndexType;
using OutputImageRegionType = typename TOutputImage::RegionType;
using CalculatorType = KappaSigmaThresholdImageCalculator<TInputImage, TMaskImage>;
/** Image related type alias. */
static constexpr unsigned int InputImageDimension = TInputImage::ImageDimension;
static constexpr unsigned int OutputImageDimension = TOutputImage::ImageDimension;
private:
MaskPixelType m_MaskValue{};
double m_SigmaFactor{ 2 };
unsigned int m_NumberOfIterations{ 2 };
InputPixelType m_Threshold{};
OutputPixelType m_InsideValue{};
OutputPixelType m_OutsideValue{};
};
} // end namespace itk
#ifndef ITK_MANUAL_INSTANTIATION
# include "itkKappaSigmaThresholdImageFilter.hxx"
#endif
#endif
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