PatlakPlot.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_PatlakPlot_H__
#define __stir_modelling_PatlakPlot_H__

#include "stir/modelling/KineticModel.h"
#include "stir/modelling/ModelMatrix.h"
#include "stir/modelling/PlasmaData.h"
#include "stir/Succeeded.h"
#include "stir/RegisteredParsingObject.h"

START_NAMESPACE_STIR


class PatlakPlot : public RegisteredParsingObject<PatlakPlot, KineticModel>
{
public:
  static const char* const registered_name;

  PatlakPlot();           
  ~PatlakPlot() override; 

  ModelMatrix<2> get_model_matrix() const;
  ModelMatrix<2> get_model_matrix(const PlasmaData& plasma_data,
                                  const TimeFrameDefinitions& time_frame_definitions,
                                  const unsigned int starting_frame);
  unsigned int get_starting_frame() const;
  unsigned int get_ending_frame() const;
  TimeFrameDefinitions get_time_frame_definitions() const;

  void set_model_matrix(ModelMatrix<2> model_matrix); 



  virtual void multiply_dynamic_image_with_model_gradient(ParametricVoxelsOnCartesianGrid& parametric_image,
                                                          const DynamicDiscretisedDensity& dyn_image) const;

  virtual void multiply_dynamic_image_with_model_gradient_and_add_to_input(ParametricVoxelsOnCartesianGrid& parametric_image,
                                                                           const DynamicDiscretisedDensity& dyn_image) const;


  virtual void get_dynamic_image_from_parametric_image(DynamicDiscretisedDensity& dyn_image,
                                                       const ParametricVoxelsOnCartesianGrid& par_image) const;


  void apply_linear_regression(ParametricVoxelsOnCartesianGrid& par_image, const DynamicDiscretisedDensity& dyn_image) const;

  void set_defaults() override;

  Succeeded set_up() override;

  bool _if_cardiac;             
  unsigned int _starting_frame; 
  float _cal_factor;            
  float _time_shift;            
  bool _in_correct_scale; 
  bool _in_total_cnt;     
  std::string _blood_data_filename;            
  PlasmaData _plasma_frame_data;               
  std::string _time_frame_definition_filename; 
  TimeFrameDefinitions _frame_defs;            

private:
  void create_model_matrix(); 
  void initialise_keymap() override;
  bool post_processing() override;
  mutable ModelMatrix<2> _model_matrix;
  bool _matrix_is_stored;
  typedef RegisteredParsingObject<PatlakPlot, KineticModel> base_type;
};

END_NAMESPACE_STIR

#endif //__stir_modelling_PatlakPlot_H__