itkLabelStatisticsImageFilter.h

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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 itkLabelStatisticsImageFilter_h
#define itkLabelStatisticsImageFilter_h
 
#include "itkImageSink.h"
#include "itkNumericTraits.h"
#include "itkSimpleDataObjectDecorator.h"
#include "itkHistogram.h"
#include <mutex>
#include <unordered_map>
#include <vector>
 
namespace itk
{
template <typename TInputImage, typename TLabelImage>
class ITK_TEMPLATE_EXPORT LabelStatisticsImageFilter : public ImageSink<TInputImage>
{
public:
  ITK_DISALLOW_COPY_AND_MOVE(LabelStatisticsImageFilter);
 
  using Self = LabelStatisticsImageFilter;
  using Superclass = ImageSink<TInputImage>;
  using Pointer = SmartPointer<Self>;
  using ConstPointer = SmartPointer<const Self>;
 
  itkNewMacro(Self);
 
  itkTypeMacro(LabelStatisticsImageFilter, ImageSink);
 
  using InputImagePointer = typename TInputImage::Pointer;
  using RegionType = typename TInputImage::RegionType;
  using SizeType = typename TInputImage::SizeType;
  using IndexType = typename TInputImage::IndexType;
  using PixelType = typename TInputImage::PixelType;
 
  using LabelImageType = TLabelImage;
  using LabelImagePointer = typename TLabelImage::Pointer;
  using LabelRegionType = typename TLabelImage::RegionType;
  using LabelSizeType = typename TLabelImage::SizeType;
  using LabelIndexType = typename TLabelImage::IndexType;
  using LabelPixelType = typename TLabelImage::PixelType;
 
  static constexpr unsigned int ImageDimension = TInputImage::ImageDimension;
 
  using RealType = typename NumericTraits<PixelType>::RealType;
 
  using DataObjectPointer = typename DataObject::Pointer;
 
  using RealObjectType = SimpleDataObjectDecorator<RealType>;
 
  using BoundingBoxType = std::vector<IndexValueType>;
 
  using HistogramType = itk::Statistics::Histogram<RealType>;
  using HistogramPointer = typename HistogramType::Pointer;
 
  class LabelStatistics
  {
  public:
    // default constructor
    LabelStatistics()
    {
      // initialized to the default values
      m_Count = NumericTraits<IdentifierType>::ZeroValue();
      m_Sum = NumericTraits<RealType>::ZeroValue();
      m_SumOfSquares = NumericTraits<RealType>::ZeroValue();
 
      // Set such that the first pixel encountered can be compared
      m_Minimum = NumericTraits<RealType>::max();
      m_Maximum = NumericTraits<RealType>::NonpositiveMin();
 
      // Default these to zero
      m_Mean = NumericTraits<RealType>::ZeroValue();
      m_Sigma = NumericTraits<RealType>::ZeroValue();
      m_Variance = NumericTraits<RealType>::ZeroValue();
 
      const unsigned int imageDimension = Self::ImageDimension;
      m_BoundingBox.resize(imageDimension * 2);
      for (unsigned int i = 0; i < imageDimension * 2; i += 2)
      {
        m_BoundingBox[i] = NumericTraits<IndexValueType>::max();
        m_BoundingBox[i + 1] = NumericTraits<IndexValueType>::NonpositiveMin();
      }
      m_Histogram = nullptr;
    }
 
    // constructor with histogram enabled
    LabelStatistics(int size, RealType lowerBound, RealType upperBound)
    {
      // initialized to the default values
      m_Count = NumericTraits<IdentifierType>::ZeroValue();
      m_Sum = NumericTraits<RealType>::ZeroValue();
      m_SumOfSquares = NumericTraits<RealType>::ZeroValue();
 
      // Set such that the first pixel encountered can be compared
      m_Minimum = NumericTraits<RealType>::max();
      m_Maximum = NumericTraits<RealType>::NonpositiveMin();
 
      // Default these to zero
      m_Mean = NumericTraits<RealType>::ZeroValue();
      m_Sigma = NumericTraits<RealType>::ZeroValue();
      m_Variance = NumericTraits<RealType>::ZeroValue();
 
      const unsigned int imageDimension = Self::ImageDimension;
      m_BoundingBox.resize(imageDimension * 2);
      for (unsigned int i = 0; i < imageDimension * 2; i += 2)
      {
        m_BoundingBox[i] = NumericTraits<IndexValueType>::max();
        m_BoundingBox[i + 1] = NumericTraits<IndexValueType>::NonpositiveMin();
      }
 
      // Histogram
      m_Histogram = HistogramType::New();
      typename HistogramType::SizeType              hsize;
      typename HistogramType::MeasurementVectorType lb;
      typename HistogramType::MeasurementVectorType ub;
      hsize.SetSize(1);
      lb.SetSize(1);
      ub.SetSize(1);
      m_Histogram->SetMeasurementVectorSize(1);
      hsize[0] = size;
      lb[0] = lowerBound;
      ub[0] = upperBound;
      m_Histogram->Initialize(hsize, lb, ub);
    }
 
    // need copy constructor because of smart pointer to histogram
    LabelStatistics(const LabelStatistics & l)
    {
      m_Count = l.m_Count;
      m_Minimum = l.m_Minimum;
      m_Maximum = l.m_Maximum;
      m_Mean = l.m_Mean;
      m_Sum = l.m_Sum;
      m_SumOfSquares = l.m_SumOfSquares;
      m_Sigma = l.m_Sigma;
      m_Variance = l.m_Variance;
      m_BoundingBox = l.m_BoundingBox;
      m_Histogram = l.m_Histogram;
    }
 
    LabelStatistics(LabelStatistics &&) = default;
 
    // added for completeness
    LabelStatistics &
    operator=(const LabelStatistics & l)
    {
      if (this != &l)
      {
        m_Count = l.m_Count;
        m_Minimum = l.m_Minimum;
        m_Maximum = l.m_Maximum;
        m_Mean = l.m_Mean;
        m_Sum = l.m_Sum;
        m_SumOfSquares = l.m_SumOfSquares;
        m_Sigma = l.m_Sigma;
        m_Variance = l.m_Variance;
        m_BoundingBox = l.m_BoundingBox;
        m_Histogram = l.m_Histogram;
      }
      return *this;
    }
 
    IdentifierType                  m_Count;
    RealType                        m_Minimum;
    RealType                        m_Maximum;
    RealType                        m_Mean;
    RealType                        m_Sum;
    RealType                        m_SumOfSquares;
    RealType                        m_Sigma;
    RealType                        m_Variance;
    BoundingBoxType                 m_BoundingBox;
    typename HistogramType::Pointer m_Histogram;
  };
 
  using MapType = std::unordered_map<LabelPixelType, LabelStatistics>;
  using MapIterator = typename MapType::iterator;
  using MapConstIterator = typename MapType::const_iterator;
  using MapSizeType = IdentifierType;
 
  using ValidLabelValuesContainerType = std::vector<LabelPixelType>;
 
  // macros for Histogram enables
  itkSetMacro(UseHistograms, bool);
  itkGetConstMacro(UseHistograms, bool);
  itkBooleanMacro(UseHistograms);
 
 
  virtual const ValidLabelValuesContainerType &
  GetValidLabelValues() const
  {
    return m_ValidLabelValues;
  }
 
  itkSetInputMacro(LabelInput, TLabelImage);
  itkGetInputMacro(LabelInput, TLabelImage);
  bool
  HasLabel(LabelPixelType label) const
  {
    return m_LabelStatistics.find(label) != m_LabelStatistics.end();
  }
 
  MapSizeType
  GetNumberOfObjects() const
  {
    return static_cast<MapSizeType>(m_LabelStatistics.size());
  }
 
  MapSizeType
  GetNumberOfLabels() const
  {
    return static_cast<MapSizeType>(this->GetNumberOfObjects());
  }
 
  RealType
  GetMinimum(LabelPixelType label) const;
 
  RealType
  GetMaximum(LabelPixelType label) const;
 
  RealType
  GetMean(LabelPixelType label) const;
 
  RealType
  GetMedian(LabelPixelType label) const;
 
  RealType
  GetSigma(LabelPixelType label) const;
 
  RealType
  GetVariance(LabelPixelType label) const;
 
  BoundingBoxType
  GetBoundingBox(LabelPixelType label) const;
 
  RegionType
  GetRegion(LabelPixelType label) const;
 
  RealType
  GetSum(LabelPixelType label) const;
 
  MapSizeType
  GetCount(LabelPixelType label) const;
 
  HistogramPointer
  GetHistogram(LabelPixelType label) const;
 
  void
  SetHistogramParameters(const int numBins, RealType lowerBound, RealType upperBound);
 
  // Change the access from protected to public to expose streaming option, a using statement can not be used due to
  // limitations of wrapping.
  void
  SetNumberOfStreamDivisions(const unsigned int n) override
  {
    Superclass::SetNumberOfStreamDivisions(n);
  }
  unsigned int
  GetNumberOfStreamDivisions() const override
  {
    return Superclass::GetNumberOfStreamDivisions();
  }
 
 
#ifdef ITK_USE_CONCEPT_CHECKING
  // Begin concept checking
  itkConceptMacro(InputHasNumericTraitsCheck, (Concept::HasNumericTraits<PixelType>));
  // End concept checking
#endif
 
protected:
  LabelStatisticsImageFilter();
  ~LabelStatisticsImageFilter() override = default;
  void
  PrintSelf(std::ostream & os, Indent indent) const override;
 
  void
  BeforeStreamedGenerateData() override
  {
    this->AllocateOutputs();
    m_LabelStatistics.clear();
  }
 
  void
  AfterStreamedGenerateData() override;
 
  void
  ThreadedStreamedGenerateData(const RegionType &) override;
 
private:
  void
  MergeMap(MapType &, MapType &) const;
 
  MapType                       m_LabelStatistics{};
  ValidLabelValuesContainerType m_ValidLabelValues{};
 
  bool m_UseHistograms{};
 
  typename HistogramType::SizeType m_NumBins{};
 
  RealType m_LowerBound{};
  RealType m_UpperBound{};
 
  std::mutex m_Mutex{};
 
}; // end of class
} // end namespace itk
 
#ifndef ITK_MANUAL_INSTANTIATION
#  include "itkLabelStatisticsImageFilter.hxx"
#endif
 
#endif