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 "itksys/hash_map.hxx"
#include "itkHistogram.h"
#include "itkFastMutexLock.h"
#include <vector>

namespace itk
{
template< typename TInputImage, typename TLabelImage >
class LabelStatisticsImageFilter:
  public ImageToImageFilter< TInputImage, TInputImage >
{
public:
  typedef LabelStatisticsImageFilter                     Self;
  typedef ImageToImageFilter< TInputImage, TInputImage > Superclass;
  typedef SmartPointer< Self >                           Pointer;
  typedef SmartPointer< const Self >                     ConstPointer;

  itkNewMacro(Self);

  itkTypeMacro(LabelStatisticsImageFilter, ImageToImageFilter);

  typedef typename TInputImage::Pointer    InputImagePointer;
  typedef typename TInputImage::RegionType RegionType;
  typedef typename TInputImage::SizeType   SizeType;
  typedef typename TInputImage::IndexType  IndexType;
  typedef typename TInputImage::PixelType  PixelType;

  typedef TLabelImage                      LabelImageType;
  typedef typename TLabelImage::Pointer    LabelImagePointer;
  typedef typename TLabelImage::RegionType LabelRegionType;
  typedef typename TLabelImage::SizeType   LabelSizeType;
  typedef typename TLabelImage::IndexType  LabelIndexType;
  typedef typename TLabelImage::PixelType  LabelPixelType;

  itkStaticConstMacro(ImageDimension, unsigned int,
                      TInputImage::ImageDimension);

  typedef typename NumericTraits< PixelType >::RealType RealType;

  typedef typename DataObject::Pointer DataObjectPointer;

  typedef SimpleDataObjectDecorator< RealType > RealObjectType;

  typedef std::vector< IndexValueType > BoundingBoxType;

  typedef itk::Statistics::Histogram< RealType > HistogramType;
  typedef typename HistogramType::Pointer        HistogramPointer;

  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();

      unsigned int imageDimension = itkGetStaticConstMacro(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 = ITK_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();

      unsigned int imageDimension = itkGetStaticConstMacro(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;
    }

    // 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;
  };

  typedef itksys::hash_map< LabelPixelType, LabelStatistics >                          MapType;
  typedef typename itksys::hash_map< LabelPixelType, LabelStatistics >::iterator       MapIterator;
  typedef typename itksys::hash_map< LabelPixelType, LabelStatistics >::const_iterator MapConstIterator;
  typedef IdentifierType                                                               MapSizeType;

  typedef std::vector<LabelPixelType> ValidLabelValuesContainerType;

  // 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 m_LabelStatistics.size();
  }

  MapSizeType GetNumberOfLabels() const
  {
    return 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(){}
  void PrintSelf(std::ostream & os, Indent indent) const ITK_OVERRIDE;

  void AllocateOutputs() ITK_OVERRIDE;

  void BeforeThreadedGenerateData() ITK_OVERRIDE;

  void AfterThreadedGenerateData() ITK_OVERRIDE;

  void  ThreadedGenerateData(const RegionType &
                             outputRegionForThread,
                             ThreadIdType threadId) ITK_OVERRIDE;

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

private:
  LabelStatisticsImageFilter(const Self &); //purposely not implemented
  void operator=(const Self &);             //purposely not implemented

  std::vector< MapType >        m_LabelStatisticsPerThread;
  MapType                       m_LabelStatistics;
  ValidLabelValuesContainerType m_ValidLabelValues;

  bool m_UseHistograms;

  typename HistogramType::SizeType m_NumBins;

  RealType            m_LowerBound;
  RealType            m_UpperBound;
  SimpleFastMutexLock m_Mutex;
}; // end of class
} // end namespace itk

#ifndef ITK_MANUAL_INSTANTIATION
#include "itkLabelStatisticsImageFilter.hxx"
#endif

#endif