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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 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://hdl.handle.net/1926/367
*
* \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:
/** Standard Self typedef */
typedef KappaSigmaThresholdImageFilter Self;
typedef ImageToImageFilter< TInputImage, TOutputImage > Superclass;
typedef SmartPointer< Self > Pointer;
typedef SmartPointer< const Self > ConstPointer;
/** Method for creation through the object factory. */
itkNewMacro(Self);
/** Runtime information support. */
itkTypeMacro(KappaSigmaThresholdImageFilter, ImageToImageFilter);
/** Standard image type within this class. */
typedef TInputImage InputImageType;
typedef TMaskImage MaskImageType;
/** Image pixel value typedef. */
typedef typename TInputImage::PixelType InputPixelType;
typedef typename TOutputImage::PixelType OutputPixelType;
typedef typename TMaskImage::PixelType MaskPixelType;
/** Image related typedefs. */
typedef typename TInputImage::Pointer InputImagePointer;
typedef typename TOutputImage::Pointer OutputImagePointer;
typedef typename TMaskImage::Pointer MaskImagePointer;
/** Set the "outside" pixel value. The default value
* NumericTraits<OutputPixelType>::ZeroValue(). */
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() ITK_OVERRIDE {}
virtual void PrintSelf(std::ostream & os, Indent indent) const ITK_OVERRIDE;
virtual void GenerateInputRequestedRegion() ITK_OVERRIDE;
virtual void GenerateData() ITK_OVERRIDE;
typedef typename TInputImage::SizeType InputSizeType;
typedef typename TInputImage::IndexType InputIndexType;
typedef typename TInputImage::RegionType InputImageRegionType;
typedef typename TOutputImage::SizeType OutputSizeType;
typedef typename TOutputImage::IndexType OutputIndexType;
typedef typename TOutputImage::RegionType OutputImageRegionType;
typedef KappaSigmaThresholdImageCalculator< TInputImage, TMaskImage > CalculatorType;
/** Image related typedefs. */
itkStaticConstMacro(InputImageDimension, unsigned int,
TInputImage::ImageDimension);
itkStaticConstMacro(OutputImageDimension, unsigned int,
TOutputImage::ImageDimension);
private:
ITK_DISALLOW_COPY_AND_ASSIGN(KappaSigmaThresholdImageFilter);
MaskPixelType m_MaskValue;
double m_SigmaFactor;
unsigned int m_NumberOfIterations;
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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