ProjMatrixByBinPinholeSPECTUB.h

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/*
    Copyright (C) 2022, Matthew Strugari
    Copyright (C) 2021, 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_ProjMatrixByBinPinholeSPECTUB__
#define __stir_recon_buildblock_ProjMatrixByBinPinholeSPECTUB__

// system libraries
#include <iostream>

// user defined libraries
#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 "stir/recon_buildblock/PinholeSPECTUB_Tools.h"

START_NAMESPACE_STIR

template <int num_dimensions, typename elemT>
class DiscretisedDensity;
class Bin;
class ProjMatrixByBinPinholeSPECTUB
    : public RegisteredParsingObject<ProjMatrixByBinPinholeSPECTUB, ProjMatrixByBin, ProjMatrixByBin>
{
public:
  static const char* const registered_name;

  ProjMatrixByBinPinholeSPECTUB();

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

  ~ProjMatrixByBinPinholeSPECTUB() 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;

  //******************** get/set functions *************

  // no longer set minimum weight, always use 0.
  // float get_minimum_weight() const;
  // void set_minimum_weight( const float value );

  float get_maximum_number_of_sigmas() const;
  void set_maximum_number_of_sigmas(const float value);

  float get_spatial_resolution_PSF() const;
  void set_spatial_resolution_PSF(const float value);

  int get_subsampling_factor_PSF() const;
  void set_subsampling_factor_PSF(const int value);

  // std::string get_detector_file() const;
  void set_detector_file(const std::string& value);

  // std::string get_collimator_file() const;
  void set_collimator_file(const std::string& value);

  std::string get_psf_correction() const;
  void set_psf_correction(const std::string& value);

  std::string get_doi_correction() const;
  void set_doi_correction(const std::string& value);

  float get_object_radius() const;
  void set_object_radius(const float value);

  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);

  // no longer use mask type
  // std::string get_mask_type() const;
  // void set_mask_type(const std::string& value);

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

  bool get_mask_from_attenuation_map() const;
  void set_mask_from_attenuation_map(bool value = false);

  bool get_keep_all_views_in_cache() const;
  void set_keep_all_views_in_cache(bool value = false);

  ProjMatrixByBinPinholeSPECTUB* clone() const override;

private:
  // parameters that will be parsed

  float minimum_weight;
  float maximum_number_of_sigmas;
  float spatial_resolution_PSF;
  int subsampling_factor_PSF;
  std::string detector_file;
  std::string collimator_file;
  std::string psf_correction;
  std::string doi_correction;
  std::string attenuation_type;
  std::string attenuation_map;
  // std::string mask_type;
  float object_radius;
  std::string mask_file;
  bool mask_from_attenuation_map;
  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_mph::wmh_mph_type wmh; // weight matrix header.
  mutable SPECTUB_mph::wm_da_type wm;    // double array weight matrix structure.
  mutable SPECTUB_mph::pcf_type pcf;     // pre-calculated functions

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

  // wm_SPECT starts here ---------------------------------------------------------------------------------------------
  bool* msk_3d;  // voxels to be included in matrix (no weight calculated outside the mask)
  float* attmap; // attenuation map

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

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

  SPECTUB_mph::volume_type vol;  
  SPECTUB_mph::prj_mph_type prj; 
  SPECTUB_mph::bin_type bin;     

  // mutable to allow compute_one_subset() const function to change the fields
  mutable SPECTUB_mph::psf2d_type psf_bin;  // structure for total psf distribution in bins (bidimensional)
  mutable SPECTUB_mph::psf2d_type psf_subs; // structure for total psf distribution: mid resolution (bidimensional)
  mutable SPECTUB_mph::psf2d_type
      psf_aux; // structure for total psf distribution: mid resolution auxiliar for convolution (bidimensional)
  mutable SPECTUB_mph::psf2d_type kern; // structure for intrinsic psf distribution: mid resolution (bidimensional)

  void compute_one_subset(const int kOS) const;
  void delete_PinholeSPECTUB_arrays();
};

END_NAMESPACE_STIR

#endif