mitkPAInSilicoTissueVolume.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 MITKPHOTOACOUSTICVOLUME_H
#define MITKPHOTOACOUSTICVOLUME_H

#include <MitkPhotoacousticsLibExports.h>
#include <mitkImage.h>
#include <mitkProperties.h>
#include <mitkPATissueGeneratorParameters.h>
#include <mitkPAVolume.h>

//Includes for smart pointer usage
#include "mitkCommon.h"
#include "itkLightObject.h"

namespace mitk {
  namespace pa {
    class MITKPHOTOACOUSTICSLIB_EXPORT InSilicoTissueVolume : public itk::LightObject
    {
    public:
      mitkClassMacroItkParent(InSilicoTissueVolume, itk::LightObject);
      mitkNewMacro2Param(Self, TissueGeneratorParameters::Pointer, std::mt19937*);

      enum SegmentationType
      {
        AIR = -1,
        BACKGROUND = 0,
        VESSEL = 1,
        FAT = 2,
        SKIN = 3
      };

      mitk::Image::Pointer ConvertToMitkImage();

      void SetVolumeValues(int x, int y, int z, double absorption, double scattering, double anisotropy, SegmentationType segmentType);

      void SetVolumeValues(int x, int y, int z, double absorption, double scattering, double anisotropy);

      bool IsInsideVolume(int x, int y, int z);

      void AddDoubleProperty(std::string label, double value);

      void AddIntProperty(std::string label, int value);

      Volume::Pointer GetAbsorptionVolume();
      Volume::Pointer GetScatteringVolume();
      Volume::Pointer GetAnisotropyVolume();
      Volume::Pointer GetSegmentationVolume();

      void SetAbsorptionVolume(Volume::Pointer volume);
      void SetScatteringVolume(Volume::Pointer volume);
      void SetAnisotropyVolume(Volume::Pointer volume);
      void SetSegmentationVolume(Volume::Pointer volume);

      double GetSpacing();
      void SetSpacing(double spacing);

      void FinalizeVolume();
      itkGetMacro(TissueParameters, TissueGeneratorParameters::Pointer);
      itkGetMacro(TDim, unsigned int);

      static InSilicoTissueVolume::Pointer New(mitk::pa::Volume::Pointer absorptionVolume,
        Volume::Pointer scatteringVolume,
        Volume::Pointer anisotropyVolume,
        Volume::Pointer segmentationVolume,
        TissueGeneratorParameters::Pointer tissueParameters,
        mitk::PropertyList::Pointer propertyList);

    protected:
      InSilicoTissueVolume(TissueGeneratorParameters::Pointer parameters, std::mt19937* rng);
      InSilicoTissueVolume(Volume::Pointer absorptionVolume,
        Volume::Pointer scatteringVolume,
        Volume::Pointer anisotropyVolume,
        Volume::Pointer segmentationVolume,
        TissueGeneratorParameters::Pointer tissueParameters,
        mitk::PropertyList::Pointer propertyList);
      ~InSilicoTissueVolume() override;

      mitk::pa::Volume::Pointer m_AbsorptionVolume;
      mitk::pa::Volume::Pointer m_ScatteringVolume;
      mitk::pa::Volume::Pointer m_AnisotropyVolume;
      mitk::pa::Volume::Pointer m_SegmentationVolume;

      TissueGeneratorParameters::Pointer m_TissueParameters;

      unsigned int m_TDim;

      double m_InitialBackgroundAbsorption;

      std::mt19937* m_Rng;

      void RandomizeTissueCoefficients(long rngSeed, bool useRngSeed, double percentage);

      mitk::PropertyList::Pointer m_PropertyList;

    private:
      void FillZLayer(int x, int y, double startIdx, double endIdx,
        double absorption, double scattering, double anisotropy,
        SegmentationType segmentationType);
      void AddSkinAndAirLayers();
      void UpdatePropertyList();
    };
  }
}
#endif // MITKPHOTOACOUSTICVOLUME_H