GatedSpatialTransformation.h

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//
/*
 Copyright (C) 2009 - 2013, King's College London
 This file is part of STIR.

 SPDX-License-Identifier: Apache-2.0

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

#include "stir/GatedDiscretisedDensity.h"
#include "stir/DiscretisedDensity.h"
#include "stir/spatial_transformation/SpatialTransformation.h"
#include "stir/numerics/BSplinesRegularGrid.h"
#include "stir/RegisteredParsingObject.h"
#include "stir/Succeeded.h"
#include <fstream>
#include <iostream>

START_NAMESPACE_STIR


class GatedSpatialTransformation : public RegisteredParsingObject<GatedSpatialTransformation, SpatialTransformation>
{
public:
  static const char* const registered_name;

  GatedSpatialTransformation();           
  ~GatedSpatialTransformation() override; 
  GatedSpatialTransformation(const TimeGateDefinitions& time_gate_definitions,
                             const shared_ptr<DiscretisedDensity<3, float>>& density_sptr);

  void read_from_files(const std::string input_string);
  void write_to_files(const std::string output_string);

  GatedDiscretisedDensity get_spatial_transformation_z() const;
  GatedDiscretisedDensity get_spatial_transformation_y() const;
  GatedDiscretisedDensity get_spatial_transformation_x() const;
  const TimeGateDefinitions& get_time_gate_definitions() const;
  void set_spatial_transformations(const GatedDiscretisedDensity& motion_z,
                                   const GatedDiscretisedDensity& motion_y,
                                   const GatedDiscretisedDensity& motion_x);
  void set_gate_defs(const TimeGateDefinitions& gate_defs);

  void warp_image(GatedDiscretisedDensity& new_gated_image, const GatedDiscretisedDensity& gated_image) const;
  void warp_image(DiscretisedDensity<3, float>& new_reference_image, const GatedDiscretisedDensity& gated_image) const;
  void warp_image(GatedDiscretisedDensity& gated_image, const DiscretisedDensity<3, float>& reference_image) const;
  void accumulate_warp_image(DiscretisedDensity<3, float>& new_reference_image, const GatedDiscretisedDensity& gated_image) const;
  void set_defaults() override;
  Succeeded set_up() override;
private:
  typedef RegisteredParsingObject<GatedSpatialTransformation, SpatialTransformation> base_type;
  void initialise_keymap() override;
  bool post_processing() override;
  std::string _transformation_filename_prefix;
  GatedDiscretisedDensity _spatial_transformation_z;
  GatedDiscretisedDensity _spatial_transformation_y;
  GatedDiscretisedDensity _spatial_transformation_x;
  std::string _spline_level_number;
  bool _spatial_transformations_are_stored;
  BSpline::BSplineType _spline_type;
  std::string _time_gate_definition_filename;
  TimeGateDefinitions _gate_defs;
};

END_NAMESPACE_STIR
#endif