DiscretisedDensity.h

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//
//
/*
    Copyright (C) 2000 PARAPET partners
    Copyright (C) 2000- 2009-07-08, Hammersmith Imanet Ltd
    Copyright (C) 2011-07-01 - 2011, Kris Thielemans
    Copyright (C) 2018, University College London
    Copyright (C) 2018, Commonwealth Scientific and Industrial Research Organisation
                        Australian eHealth Research Centre
    This file is part of STIR.

    SPDX-License-Identifier: Apache-2.0 AND License-ref-PARAPET-license

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

#include "stir/CartesianCoordinate3D.h"
#include "stir/Array.h"
#include "stir/ExamData.h"
#include "stir/shared_ptr.h"
#include <string>

START_NAMESPACE_STIR

#ifdef SWIG
// SWIG doesn't seem to understand how we define ArrayType (with `using`).
// Do a HORRIBLE work-around for now. It will fail whenever we change ArrayType of course.
// TODO
#  define ArrayType Array
#endif

template <int num_dimensions, typename elemT>
class DiscretisedDensity : public ExamData, public ArrayType<num_dimensions, elemT>
{
#ifdef STIR_COMPILING_SWIG_WRAPPER
  // work-around swig problem. It gets confused when using a private (or protected)
  // typedef in a definition of a public typedef/member
public:
#endif
  typedef ArrayType<num_dimensions, elemT> base_type;
  typedef DiscretisedDensity<num_dimensions, elemT> self_type;

public:

  typedef DiscretisedDensity<num_dimensions, elemT> hierarchy_base_type;

  static DiscretisedDensity* read_from_file(const std::string& filename);

  inline DiscretisedDensity();

  inline DiscretisedDensity(const IndexRange<num_dimensions>& range, const CartesianCoordinate3D<float>& origin);

  inline DiscretisedDensity(const shared_ptr<const ExamInfo>& exam_info_sptr,
                            const IndexRange<num_dimensions>& range,
                            const CartesianCoordinate3D<float>& origin);

  inline const CartesianCoordinate3D<float>& get_origin() const;

  inline void set_origin(const CartesianCoordinate3D<float>& origin);




  inline CartesianCoordinate3D<float>
  get_physical_coordinates_for_indices(const BasicCoordinate<num_dimensions, int>& indices) const;


  inline CartesianCoordinate3D<float>
  get_physical_coordinates_for_indices(const BasicCoordinate<num_dimensions, float>& indices) const;


  inline CartesianCoordinate3D<float>
  get_relative_coordinates_for_indices(const BasicCoordinate<num_dimensions, int>& indices) const;


  inline CartesianCoordinate3D<float>
  get_relative_coordinates_for_indices(const BasicCoordinate<num_dimensions, float>& indices) const;


  inline BasicCoordinate<num_dimensions, int>
  get_indices_closest_to_physical_coordinates(const CartesianCoordinate3D<float>& coords) const;


  inline BasicCoordinate<num_dimensions, int>
  get_indices_closest_to_relative_coordinates(const CartesianCoordinate3D<float>& coords) const;


  inline BasicCoordinate<num_dimensions, float>
  get_index_coordinates_for_physical_coordinates(const CartesianCoordinate3D<float>& coords) const;


  inline BasicCoordinate<num_dimensions, float>
  get_index_coordinates_for_relative_coordinates(const CartesianCoordinate3D<float>& coords) const;

  inline BasicCoordinate<num_dimensions, float>
  get_index_coordinates_for_LPS_coordinates(const CartesianCoordinate3D<float>& coords) const;

  inline CartesianCoordinate3D<float>
  get_LPS_coordinates_for_physical_coordinates(const CartesianCoordinate3D<float>& indices) const;

  inline CartesianCoordinate3D<float> get_LPS_coordinates_for_indices(const BasicCoordinate<num_dimensions, int>& indices) const;

  inline CartesianCoordinate3D<float>
  get_LPS_coordinates_for_indices(const BasicCoordinate<num_dimensions, float>& indices) const;

  inline CartesianCoordinate3D<float>
  get_physical_coordinates_for_LPS_coordinates(const CartesianCoordinate3D<float>& coords) const;

  inline BasicCoordinate<num_dimensions, int>
  get_indices_closest_to_LPS_coordinates(const CartesianCoordinate3D<float>& coords) const;


  virtual DiscretisedDensity<num_dimensions, elemT>* get_empty_copy() const = 0;

  virtual DiscretisedDensity<num_dimensions, elemT>* clone() const = 0;

  //*! \deprecated Use get_empty_copy() instead
  DiscretisedDensity<num_dimensions, elemT>* get_empty_discretised_density() const
  {
    return get_empty_copy();
  }



  inline bool has_same_characteristics(self_type const&, std::string& explanation) const;


  inline bool has_same_characteristics(self_type const&) const;


  inline bool operator==(const self_type&) const;

  inline bool operator!=(const self_type&) const;

protected:

  virtual bool actual_has_same_characteristics(DiscretisedDensity<num_dimensions, elemT> const&, std::string& explanation) const;


  virtual CartesianCoordinate3D<float>
  actual_get_relative_coordinates_for_indices(const BasicCoordinate<num_dimensions, float>& indices) const = 0;

  virtual BasicCoordinate<num_dimensions, float>
  actual_get_index_coordinates_for_relative_coordinates(const CartesianCoordinate3D<float>& coords) const = 0;

private:
  CartesianCoordinate3D<float> origin;

  static inline CartesianCoordinate3D<float> swap_axes_based_on_orientation(const CartesianCoordinate3D<float>& coordinates,
                                                                            const PatientPosition patient_position);
};

#ifdef SWIG
// Undo HORRIBLE work-around.
// TODO
#  undef ArrayType
#endif

END_NAMESPACE_STIR

#include "stir/DiscretisedDensity.inl"
#endif