mitkImageStatisticsCalculator.h

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/*============================================================================

The Medical Imaging Interaction Toolkit (MITK)

Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.

Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.

============================================================================*/

#ifndef MITKIMAGESTATISTICSCALCULATOR
#define MITKIMAGESTATISTICSCALCULATOR

#include <MitkImageStatisticsExports.h>
#include <mitkImage.h>
#include <mitkMaskGenerator.h>
#include <mitkImageStatisticsContainer.h>

namespace mitk
{
    class MITKIMAGESTATISTICS_EXPORT ImageStatisticsCalculator: public itk::Object
    {
    public:
        typedef ImageStatisticsCalculator        Self;
        typedef itk::Object                         Superclass;
        typedef itk::SmartPointer< Self >           Pointer;
        typedef itk::SmartPointer< const Self >     ConstPointer;

        itkNewMacro(Self); 
        itkTypeMacro(ImageStatisticsCalculator_v2, itk::Object);

        typedef double statisticsValueType;
        typedef std::map<std::string, statisticsValueType> statisticsMapType;
        typedef itk::Statistics::Histogram<double> HistogramType;
        typedef unsigned short MaskPixelType;
        using LabelIndex = ImageStatisticsContainer::LabelIndex;

        void SetInputImage(const mitk::Image* image);

        void SetMask(mitk::MaskGenerator* mask);

        void SetSecondaryMask(mitk::MaskGenerator* mask);

        void SetNBinsForHistogramStatistics(unsigned int nBins);

        unsigned int GetNBinsForHistogramStatistics() const;

        void SetBinSizeForHistogramStatistics(double binSize);

        double GetBinSizeForHistogramStatistics() const;

        ImageStatisticsContainer* GetStatistics(LabelIndex label=1);

    protected:
        ImageStatisticsCalculator(){
            m_nBinsForHistogramStatistics = 100;
            m_binSizeForHistogramStatistics = 10;
            m_UseBinSizeOverNBins = false;
        };


    private:
        //Calculates statistics for each timestep for image
        template < typename TPixel, unsigned int VImageDimension > void InternalCalculateStatisticsUnmasked(
                typename itk::Image< TPixel, VImageDimension >* image, const TimeGeometry* timeGeometry, TimeStepType timeStep);

        template < typename TPixel, unsigned int VImageDimension > void InternalCalculateStatisticsMasked(
                typename itk::Image< TPixel, VImageDimension >* image, const TimeGeometry* timeGeometry,
                unsigned int timeStep);

        template < typename TPixel, unsigned int VImageDimension >
        double GetVoxelVolume(typename itk::Image<TPixel, VImageDimension>* image) const;

        bool IsUpdateRequired(LabelIndex label) const;

        mitk::Image::ConstPointer m_Image;
        mitk::Image::Pointer m_ImageTimeSlice;
        mitk::Image::ConstPointer m_InternalImageForStatistics;

        mitk::MaskGenerator::Pointer m_MaskGenerator;
        mitk::Image::Pointer m_InternalMask;

        mitk::MaskGenerator::Pointer m_SecondaryMaskGenerator;
        mitk::Image::Pointer m_SecondaryMask;

        unsigned int m_nBinsForHistogramStatistics;
        double m_binSizeForHistogramStatistics;
        bool m_UseBinSizeOverNBins;

        std::map<LabelIndex,ImageStatisticsContainer::Pointer> m_StatisticContainers;
    };

}
#endif // MITKIMAGESTATISTICSCALCULATOR