PoissonLogLikelihoodWithLinearKineticModelAndDynamicProjectionData.h

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//
//
/*
    Copyright (C) 2006- 2013, Hammersmith Imanet Ltd
    Copyright (C) 2018, University College London

    SPDX-License-Identifier: Apache-2.0

    See STIR/LICENSE.txt for details
*/
#ifndef __stir_recon_buildblock_PoissonLogLikelihoodWithLinearKineticModelAndDynamicProjectionData_H__
#define __stir_recon_buildblock_PoissonLogLikelihoodWithLinearKineticModelAndDynamicProjectionData_H__
#include "stir/RegisteredParsingObject.h"
#include "stir/recon_buildblock/PoissonLogLikelihoodWithLinearModelForMeanAndProjData.h"
#include "stir/recon_buildblock/PoissonLogLikelihoodWithLinearModelForMean.h"
#include "stir/VectorWithOffset.h"
#include "stir/DynamicProjData.h"
#include "stir/DynamicDiscretisedDensity.h"
#include "stir/modelling/ParseAndCreateParametricDiscretisedDensityFrom.h"
#include "stir/modelling/ParametricDiscretisedDensity.h"
#include "stir/modelling/KineticParameters.h"
#include "stir/modelling/PatlakPlot.h"

START_NAMESPACE_STIR

template <typename TargetT>
class PoissonLogLikelihoodWithLinearKineticModelAndDynamicProjectionData
    : public RegisteredParsingObject<PoissonLogLikelihoodWithLinearKineticModelAndDynamicProjectionData<TargetT>,
                                     GeneralisedObjectiveFunction<TargetT>,
                                     PoissonLogLikelihoodWithLinearModelForMean<TargetT>>
{
private:
  typedef RegisteredParsingObject<PoissonLogLikelihoodWithLinearKineticModelAndDynamicProjectionData<TargetT>,
                                  GeneralisedObjectiveFunction<TargetT>,
                                  PoissonLogLikelihoodWithLinearModelForMean<TargetT>>
      base_type;
  typedef PoissonLogLikelihoodWithLinearModelForMeanAndProjData<DiscretisedDensity<3, float>> SingleFrameObjFunc;
  VectorWithOffset<SingleFrameObjFunc> _single_frame_obj_funcs;

public:
  static const char* const registered_name;

  PoissonLogLikelihoodWithLinearKineticModelAndDynamicProjectionData();


  TargetT* construct_target_ptr() const override;

  std::unique_ptr<ExamInfo> get_exam_info_uptr_for_target() const override;

protected:
  double actual_compute_objective_function_without_penalty(const TargetT& current_estimate, const int subset_num) override;

  Succeeded set_up_before_sensitivity(shared_ptr<const TargetT> const& target_sptr) override;


  void add_subset_sensitivity(TargetT& sensitivity, const int subset_num) const override;

  Succeeded actual_add_multiplication_with_approximate_sub_Hessian_without_penalty(TargetT& output,
                                                                                   const TargetT& input,
                                                                                   const int subset_num) const override;

  Succeeded actual_accumulate_sub_Hessian_times_input_without_penalty(TargetT& output,
                                                                      const TargetT& current_image_estimate,
                                                                      const TargetT& input,
                                                                      const int subset_num) const override;

public:
  const DynamicProjData& get_dyn_proj_data() const;
  const shared_ptr<DynamicProjData>& get_dyn_proj_data_sptr() const;
  const int get_max_segment_num_to_process() const;
  const bool get_zero_seg0_end_planes() const;
  const DynamicProjData& get_additive_dyn_proj_data() const;
  const shared_ptr<DynamicProjData>& get_additive_dyn_proj_data_sptr() const;
  const ProjectorByBinPair& get_projector_pair() const;
  const shared_ptr<ProjectorByBinPair>& get_projector_pair_sptr() const;
  const BinNormalisation& get_normalisation() const;
  const shared_ptr<BinNormalisation>& get_normalisation_sptr() const;

  void set_recompute_sensitivity(const bool);
  void set_sensitivity_sptr(const shared_ptr<TargetT>&);
  int set_num_subsets(const int num_subsets) override;

  void set_normalisation_sptr(const shared_ptr<BinNormalisation>&) override;
  void set_additive_proj_data_sptr(const shared_ptr<ExamData>&) override;

  void set_input_data(const shared_ptr<ExamData>&) override;
  const DynamicProjData& get_input_data() const override;
protected:
  std::string _input_filename;

  shared_ptr<DynamicProjData> _dyn_proj_data_sptr;


  int _max_segment_num_to_process;

  /**********************/
  ParseAndCreateFrom<TargetT, DynamicProjData> target_parameter_parser;

  /********************************/
  std::string _additive_dyn_proj_data_filename;

  shared_ptr<DynamicProjData> _additive_dyn_proj_data_sptr;
  shared_ptr<BinNormalisation> _normalisation_sptr;
  shared_ptr<ProjectorByBinPair> _projector_pair_ptr;
  bool _zero_seg0_end_planes;
  // Patlak Plot Parameters
  shared_ptr<PatlakPlot> _patlak_plot_sptr;
  DynamicDiscretisedDensity _dyn_image_template;

  bool actual_subsets_are_approximately_balanced(std::string& warning_message) const override;

  void actual_compute_subset_gradient_without_penalty(TargetT& gradient,
                                                      const TargetT& current_estimate,
                                                      const int subset_num,
                                                      const bool add_sensitivity) override;


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

END_NAMESPACE_STIR

//#include "stir/recon_buildblock/PoissonLogLikelihoodWithLinearKineticModelAndDynamicProjectionData.inl"

#endif