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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 itkOtsuMultipleThresholdsImageFilter_h
#define itkOtsuMultipleThresholdsImageFilter_h
#include "itkImageToImageFilter.h"
#include "itkFixedArray.h"
#include "itkOtsuMultipleThresholdsCalculator.h"
#include "itkScalarImageToHistogramGenerator.h"
namespace itk
{
/**
* \class OtsuMultipleThresholdsImageFilter
* \brief Threshold an image using multiple Otsu Thresholds.
*
* This filter creates a labeled image that separates the input
* image into various classes. The filter
* computes the thresholds using the OtsuMultipleThresholdsCalculator and
* applies those thresholds to the input image using the
* ThresholdLabelerImageFilter. The NumberOfHistogramBins and
* NumberOfThresholds can be set
* for the Calculator. The LabelOffset can be set
* for the ThresholdLabelerImageFilter.
*
* This filter also includes an option to use the valley emphasis algorithm from
* H.F. Ng, "Automatic thresholding for defect detection", Pattern Recognition Letters, (27): 1644-1649, 2006.
* The valley emphasis algorithm is particularly effective when the object to be thresholded is small.
* See the following tests for examples:
* itkOtsuMultipleThresholdsImageFilterTest3 and itkOtsuMultipleThresholdsImageFilterTest4
* To use this algorithm, simple call the setter: SetValleyEmphasis(true)
* It is turned off by default.
*
* \sa ScalarImageToHistogramGenerator
* \sa OtsuMultipleThresholdsCalculator
* \sa ThresholdLabelerImageFilter
* \ingroup IntensityImageFilters MultiThreaded
* \ingroup ITKThresholding
*
* \sphinx
* \sphinxexample{Filtering/Thresholding/ThresholdAnImageUsingOtsu,Threshold An Image Using Otsu}
* \endsphinx
*/
template <typename TInputImage, typename TOutputImage>
class ITK_TEMPLATE_EXPORT OtsuMultipleThresholdsImageFilter : public ImageToImageFilter<TInputImage, TOutputImage>
{
public:
ITK_DISALLOW_COPY_AND_MOVE(OtsuMultipleThresholdsImageFilter);
/** Standard Self type alias */
using Self = OtsuMultipleThresholdsImageFilter;
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(OtsuMultipleThresholdsImageFilter);
/** Image pixel value type alias. */
using InputPixelType = typename TInputImage::PixelType;
using OutputPixelType = typename TOutputImage::PixelType;
/** Image related type alias. */
using InputImagePointer = typename TInputImage::Pointer;
using OutputImagePointer = typename TOutputImage::Pointer;
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;
/** Threshold vector types. */
using HistogramGeneratorType = itk::Statistics::ScalarImageToHistogramGenerator<TInputImage>;
using HistogramType = typename HistogramGeneratorType::HistogramType;
using OtsuCalculatorType = OtsuMultipleThresholdsCalculator<HistogramType>;
using ThresholdVectorType = typename OtsuCalculatorType::OutputType;
/** Image related type alias. */
static constexpr unsigned int InputImageDimension = TInputImage::ImageDimension;
static constexpr unsigned int OutputImageDimension = TOutputImage::ImageDimension;
/** Set/Get the number of histogram bins. Default is 128. */
itkSetClampMacro(NumberOfHistogramBins, SizeValueType, 1, NumericTraits<SizeValueType>::max());
itkGetConstMacro(NumberOfHistogramBins, SizeValueType);
/** Set/Get the number of thresholds. Default is 1. */
itkSetClampMacro(NumberOfThresholds, SizeValueType, 1, NumericTraits<SizeValueType>::max());
itkGetConstMacro(NumberOfThresholds, SizeValueType);
/** Set/Get the offset which labels have to start from. Default is 0. */
itkSetClampMacro(LabelOffset, OutputPixelType, OutputPixelType{}, NumericTraits<OutputPixelType>::max());
itkGetConstMacro(LabelOffset, OutputPixelType);
/** Set/Get the use of valley emphasis. Default is false. */
itkSetMacro(ValleyEmphasis, bool);
itkGetConstReferenceMacro(ValleyEmphasis, bool);
itkBooleanMacro(ValleyEmphasis);
/** Should the threshold value be mid-point of the bin or the maximum?
* Default is to return bin maximum. */
itkSetMacro(ReturnBinMidpoint, bool);
itkGetConstReferenceMacro(ReturnBinMidpoint, bool);
itkBooleanMacro(ReturnBinMidpoint);
/** Get the computed threshold. */
const ThresholdVectorType &
GetThresholds() const
{
return m_Thresholds;
}
#ifdef ITK_USE_CONCEPT_CHECKING
// Begin concept checking
itkConceptMacro(OutputComparableCheck, (Concept::Comparable<OutputPixelType>));
itkConceptMacro(OutputOStreamWritableCheck, (Concept::OStreamWritable<OutputPixelType>));
// End concept checking
#endif
protected:
OtsuMultipleThresholdsImageFilter();
~OtsuMultipleThresholdsImageFilter() override = default;
void
PrintSelf(std::ostream & os, Indent indent) const override;
void
GenerateInputRequestedRegion() override;
void
GenerateData() override;
private:
SizeValueType m_NumberOfHistogramBins{ 128 };
SizeValueType m_NumberOfThresholds{ 1 };
OutputPixelType m_LabelOffset{};
ThresholdVectorType m_Thresholds{};
bool m_ValleyEmphasis{ false };
#if defined(ITKV4_COMPATIBILITY)
bool m_ReturnBinMidpoint{ true };
#else
bool m_ReturnBinMidpoint{ false };
#endif
};
} // end namespace itk
#ifndef ITK_MANUAL_INSTANTIATION
# include "itkOtsuMultipleThresholdsImageFilter.hxx"
#endif
#endif
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