ModelMatrix.h

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//
//
/*
    Copyright (C) 2006 - 2011, Hammersmith Imanet Ltd
    This file is part of STIR.

    SPDX-License-Identifier: Apache-2.0

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

#include "stir/Array.h"
#include "stir/BasicCoordinate.h"
#include "stir/VectorWithOffset.h"
#include "stir/DynamicDiscretisedDensity.h"
#include "stir/modelling/ParametricDiscretisedDensity.h"
#include "stir/Succeeded.h"
#include <fstream>
#include <iostream>

START_NAMESPACE_STIR

template <int num_param>
class ModelMatrix
{
public:
  inline ModelMatrix(); 

  inline ~ModelMatrix(); 

  inline void read_from_file(const std::string input_string);

  inline Succeeded write_to_file(const std::string output_string);

  inline Array<2, float> get_model_array() const;
  inline const VectorWithOffset<float> get_model_array_sum() const;
  inline VectorWithOffset<float> get_time_vector() const;
  inline void set_model_array(const Array<2, float>& model_array);
  inline void set_time_vector(const VectorWithOffset<float>& time_vector);
  inline void set_is_uncalibrated(const bool is_uncalibrated);
  inline void set_is_in_correct_scale(const bool in_correct_scale);

  inline void threshold_model_array(const float threshold_value);

  inline void uncalibrate(const float cal_factor);

  inline void scale_model_matrix(const float scale_factor);

  inline void convert_to_total_frame_counts(const TimeFrameDefinitions& time_frame_definitions);

  inline void multiply_dynamic_image_with_model_and_add_to_input(ParametricVoxelsOnCartesianGrid& parametric_image,
                                                                 const DynamicDiscretisedDensity& dynamic_image) const;

  inline void multiply_dynamic_image_with_model(ParametricVoxelsOnCartesianGrid& parametric_image,
                                                const DynamicDiscretisedDensity& dynamic_image) const;
  inline void
  multiply_parametric_image_with_model_and_add_to_input(DynamicDiscretisedDensity& dynamic_image,
                                                        const ParametricVoxelsOnCartesianGrid& parametric_image) const;

  inline void multiply_parametric_image_with_model(DynamicDiscretisedDensity& dynamic_image,
                                                   const ParametricVoxelsOnCartesianGrid& parametric_image) const;

  inline void normalise_parametric_image_with_model_sum(ParametricVoxelsOnCartesianGrid& parametric_image_out,
                                                        const ParametricVoxelsOnCartesianGrid& parametric_image) const;
private:
  Array<2, float> _model_array;
  VectorWithOffset<float> _time_vector;
  bool _is_uncalibrated;
  bool _in_correct_scale;
  bool _is_converted_to_total_counts;
};

END_NAMESPACE_STIR

#include "stir/modelling/ModelMatrix.inl"

#endif //__stir_modelling_ModelMatrix_H__