itkLabelStatisticsImageFilter.h

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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 itkLabelStatisticsImageFilter_h
#define itkLabelStatisticsImageFilter_h

#include "itkImageToImageFilter.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 ImageToImageFilter< TInputImage, TInputImage >
{
public:
  ITK_DISALLOW_COPY_AND_ASSIGN(LabelStatisticsImageFilter);

  using Self = LabelStatisticsImageFilter;
  using Superclass = ImageToImageFilter< TInputImage, TInputImage >;
  using Pointer = SmartPointer< Self >;
  using ConstPointer = SmartPointer< const Self >;

  itkNewMacro(Self);

  itkTypeMacro(LabelStatisticsImageFilter, ImageToImageFilter);

  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;
  }

  void SetLabelInput(const TLabelImage *input)
  {
    // Process object is not const-correct so the const casting is required.
    this->SetNthInput( 1, const_cast< TLabelImage * >( input ) );
  }

  const LabelImageType * GetLabelInput() const
  {
    return itkDynamicCastInDebugMode< LabelImageType * >( const_cast< DataObject * >( this->ProcessObject::GetInput(1) ) );
  }

  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);

#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 AllocateOutputs() override;

  void AfterThreadedGenerateData() override;

  void DynamicThreadedGenerateData( const RegionType & ) override;

  // Override since the filter produces all of its output
  void EnlargeOutputRequestedRegion(DataObject *data) 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