ProjMatrixByBinSPECTUB.h

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/*
    Copyright (C) 2013, Institute for Bioengineering of Catalonia
    Copyright (C) 2013, University College London
    This file is part of STIR.

    SPDX-License-Identifier: Apache-2.0

    See STIR/LICENSE.txt for details
*/
#ifndef __stir_recon_buildblock_ProjMatrixByBinSPECTUB__
#define __stir_recon_buildblock_ProjMatrixByBinSPECTUB__

#include "stir/RegisteredParsingObject.h"
#include "stir/recon_buildblock/ProjMatrixByBin.h"
#include "stir/ProjDataInfo.h"
#include "stir/CartesianCoordinate3D.h"
#include "stir/IndexRange.h"
#include "stir/shared_ptr.h"
#include <iostream>

#include "stir/recon_buildblock/SPECTUB_Tools.h"

START_NAMESPACE_STIR

template <int num_dimensions, typename elemT>
class DiscretisedDensity;
class Bin;
// using namespace SPECTUB;
class ProjMatrixByBinSPECTUB : public RegisteredParsingObject<ProjMatrixByBinSPECTUB, ProjMatrixByBin, ProjMatrixByBin>
{
public:
  static const char* const registered_name;

  ProjMatrixByBinSPECTUB();

  // disable copy-constructor as currently unsafe to copy due to bare pointers
  ProjMatrixByBinSPECTUB(const ProjMatrixByBinSPECTUB&) = delete;

  ~ProjMatrixByBinSPECTUB() override;

  void set_up(const shared_ptr<const ProjDataInfo>& proj_data_info_ptr,
              const shared_ptr<const DiscretisedDensity<3, float>>& density_info_ptr // TODO should be Info only
              ) override;

  bool get_keep_all_views_in_cache() const;

  void set_keep_all_views_in_cache(bool value = true);
  std::string get_attenuation_type() const;

  void set_attenuation_type(const std::string& value);
  shared_ptr<const DiscretisedDensity<3, float>> get_attenuation_image_sptr() const;

  void set_attenuation_image_sptr(const shared_ptr<const DiscretisedDensity<3, float>> value);
  void set_attenuation_image_sptr(const std::string& value);

  void set_resolution_model(const float collimator_sigma_0_in_mm, const float collimator_slope_in_mm, const bool full_3D = true);

  // Alex
  // Fix to compile, missing function definition in header
  ProjMatrixByBinSPECTUB* clone() const override;

private:
  // parameters that will be parsed

  float minimum_weight;
  float maximum_number_of_sigmas;
  float spatial_resolution_PSF;
  std::string psf_type;
  float collimator_sigma_0;
  float collimator_slope;
  std::string attenuation_type;
  std::string attenuation_map;
  std::string mask_type;
  std::string mask_file;
  bool keep_all_views_in_cache; 

  // explicitly list necessary members for image details (should use an Info object instead)
  CartesianCoordinate3D<float> voxel_size;
  CartesianCoordinate3D<float> origin;
  IndexRange<3> densel_range;

  shared_ptr<const ProjDataInfo> proj_data_info_ptr;

  bool already_setup;

  mutable SPECTUB::wm_da_type wm;
  mutable SPECTUB::wmh_type wmh; // this could be an arry of wmh_type for each index
  float* Rrad;

  void calculate_proj_matrix_elems_for_one_bin(ProjMatrixElemsForOneBin&) const override;

  void set_defaults() override;
  void initialise_keymap() override;
  bool post_processing() override;

  shared_ptr<const DiscretisedDensity<3, float>> attenuation_image_sptr;

  // wm_SPECT starts here ---------------------------------------------------------------------------------------------
  bool* msk_3d; 
  bool* msk_2d; 

  //... variables for estimated sizes of arrays to allocate ................................
  int** NITEMS; 

  //... user defined structures (types defined in SPECTUB_Tools.h) .....................................

  SPECTUB::volume_type vol; 
  SPECTUB::proj_type prj;   

  SPECTUB::voxel_type vox; 
  SPECTUB::bin_type bin;   

  SPECTUB::angle_type* ang; 
  float* attmap;            

  SPECTUB::discrf_type gaussdens; 

  int maxszb;

  void compute_one_subset(const int kOS, const float* Rrad) const;
  void delete_UB_SPECT_arrays();
  mutable std::vector<bool> subset_already_processed;
};

END_NAMESPACE_STIR

#endif