PoissonLogLikelihoodWithLinearModelForMeanAndGatedProjDataWithMotion.h

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//
//
/*
    Copyright (C) 2005- 2011, Hammersmith Imanet Ltd
    This file is part of STIR.

    SPDX-License-Identifier: Apache-2.0

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

#include "stir/RegisteredParsingObject.h"
#include "stir/recon_buildblock/PoissonLogLikelihoodWithLinearModelForMeanAndProjData.h"
#include "stir/GatedProjData.h"
#include "stir/recon_buildblock/ProjectorByBinPair.h"
#include "stir/DataProcessor.h"
#include "stir/recon_buildblock/BinNormalisation.h"
#include "stir/recon_buildblock/SumOfGeneralisedObjectiveFunctions.h"
#include "stir/TimeFrameDefinitions.h"

START_NAMESPACE_STIR
class GatedProjData;

template <typename TargetT>
class PoissonLogLikelihoodWithLinearModelForMeanAndGatedProjDataWithMotion
    : public RegisteredParsingObject<
          PoissonLogLikelihoodWithLinearModelForMeanAndGatedProjDataWithMotion<TargetT>,
          GeneralisedObjectiveFunction<TargetT>,
          SumOfGeneralisedObjectiveFunctions<PoissonLogLikelihoodWithLinearModelForMeanAndProjData<TargetT>,
                                             TargetT,
                                             PoissonLogLikelihoodWithLinearModelForMean<TargetT>>>
{
private:
  typedef RegisteredParsingObject<
      PoissonLogLikelihoodWithLinearModelForMeanAndGatedProjDataWithMotion<TargetT>,
      GeneralisedObjectiveFunction<TargetT>,
      SumOfGeneralisedObjectiveFunctions<PoissonLogLikelihoodWithLinearModelForMeanAndProjData<TargetT>,
                                         TargetT,
                                         PoissonLogLikelihoodWithLinearModelForMean<TargetT>>>
      base_type;

public:
  static const char* const registered_name;

  PoissonLogLikelihoodWithLinearModelForMeanAndGatedProjDataWithMotion();

  void set_proj_data_sptr(const shared_ptr<GatedProjData>&);
  void set_max_segment_num_to_process(const int);
  void set_zero_seg0_end_planes(const bool);
  void set_additive_proj_data_sptr(const shared_ptr<GatedProjData>&);
  void set_projector_pair_sptr(const shared_ptr<ProjectorByBinPair>&);
  void set_frame_num(const int);
  void set_frame_definitions(const TimeFrameDefinitions&);

  virtual TargetT* construct_target_ptr() const;

  virtual void
  compute_sub_gradient_without_penalty_plus_sensitivity(TargetT& gradient, const TargetT& target, const int subset_num);

protected:
  virtual Succeeded set_up_before_sensitivity(shared_ptr<TargetT> const& target_sptr);

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

  std::string _input_filename;


  int max_segment_num_to_process;

  /**********************/
  // image stuff
  // TODO to be replaced with single class or so (TargetT obviously)

  int output_image_size_xy; // KT 10122001 appended _xy


  int output_image_size_z; // KT 10122001 new

  double zoom;

  double Xoffset;

  double Yoffset;

  // KT 20/06/2001 new
  double Zoffset;
  /********************************/

  shared_ptr<ProjectorByBinPair> projector_pair_ptr;

  bool zero_seg0_end_planes;

  std::string _additive_projection_data_filename;

  // TODO doc
  int frame_num;
  std::string frame_definition_filename;
  TimeFrameDefinitions frame_defs;
  VectorWithOffset<shared_ptr<BinNormalisation>> _normalisation_sptrs;

private:
  virtual void set_defaults();
  virtual void initialise_keymap();
  virtual bool post_processing();

  shared_ptr<GatedProjData> _gated_proj_data_sptr;
  shared_ptr<GatedProjData> _gated_additive_proj_data_sptr;

  shared_ptr<DataSymmetriesForViewSegmentNumbers> symmetries_sptr;

  VectorWithOffset<shared_ptr<DataProcessor<TargetT>>> _forward_transformations;
};

END_NAMESPACE_STIR

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

#endif