MLEstimateComponentBasedNormalisation refactor

src/include/stir/recon_buildblock/ML_estimate_component_based_normalisation.h

@@ -1,5 +1,6 @@
 /*
  Copyright (C) 2022, University College London
+ Copyright (C) 2024
  This file is part of STIR.
 
  SPDX-License-Identifier: Apache-2.0
@@ -14,15 +15,25 @@
  */
 #include "stir/common.h"
 #include <string>
+#include "stir/ProjData.h"
+#include "stir/ML_norm.h"
 
 START_NAMESPACE_STIR
 
-class ProjData;
-
 /*!
- \brief Find normalisation factors using a maximum likelihood approach
-
+ \brief Find normalisation factors using a maximum likelihood approach
  \ingroup recon_buildblock
+ \param out_filename_prefix The prefix for the output files
+ \param measured_data The measured projection data
+ \param model_data The model projection data
+ \param num_eff_iterations The number of (sub-)efficiency iterations to perform per iteration of the algorithm
+ \param num_iterations The number of algorithm iterations to perform
+ \param do_geo Whether to perform geo normalization calculations
+ \param do_block Whether to perform block normalization calculations
+ \param do_symmetry_per_block Whether to perform block normalization calculations with symmetry
+ \param do_KL Whether to perform Kullback-Leibler divergence calculations and display the KL value. This can be slow.
+ \param do_display Whether to display the progress of the algorithm.
+ \param do_save_to_file Whether to save the each iteration of the efficiencies, geo data and block data to file.
 */
 void ML_estimate_component_based_normalisation(const std::string& out_filename_prefix,
  const ProjData& measured_data,
@@ -33,6 +44,136 @@ void ML_estimate_component_based_normalisation(const std::string& out_filename_p
  bool do_block,
  bool do_symmetry_per_block,
  bool do_KL,
- bool do_display);
+ bool do_display,
+ bool do_save_to_file = true);
+
+/*!
+ \brief Find normalisation factors using a maximum likelihood approach
+ \ingroup recon_buildblock
+*/
+class MLEstimateComponentBasedNormalisation
+{
+public:
+ /*!
+ \brief Constructor
+ \param out_filename_prefix The prefix for the output files
+ \param measured_data The measured projection data
+ \param model_data The model projection data
+ \param num_eff_iterations The number of (sub-)efficiency iterations to perform per iteration of the algorithm
+ \param num_iterations The number of algorithm iterations to perform
+ \param do_geo Whether to perform geo normalization calculations
+ \param do_block Whether to perform block normalization calculations
+ \param do_symmetry_per_block Whether to perform block normalization calculations with symmetry
+ \param do_KL Whether to perform Kullback-Leibler divergence calculations and display the KL value. This can be slow.
+ \param do_display Whether to display the progress of the algorithm.
+ \param do_save_to_file Whether to save the each iteration of the efficiencies, geo data and block data to file.
+ */
+ MLEstimateComponentBasedNormalisation(std::string out_filename_prefix,
+ const ProjData& measured_data,
+ const ProjData& model_data,
+ int num_eff_iterations,
+ int num_iterations,
+ bool do_geo,
+ bool do_block,
+ bool do_symmetry_per_block,
+ bool do_KL,
+ bool do_display,
+ bool do_save_to_file);
+
+ /*!
+ \brief Run the normalisation estimation algorithm using the parameters provided in the constructor.
+ */
+ void process();
+
+private:
+ /*!
+ \brief Performs an efficiency iteration to update the efficiancies from the data_fan_sums and model.
+ Additionally, handles the saving of the efficiencies iteration to file, KL calculation and display.
+ \param[in] iter_num The iteration number
+ \param[in] eff_iter_num The efficiency iteration number
+ */
+ void efficiency_iteration(int iter_num, int eff_iter_num);
+
+ /*!
+ \brief Performs a geo normalization iteration to update the geo data from the measured_geo_data and model_data.
+ Additionally, handles the saving of the geo data iteration to file, KL calculation and display.
+ \param[in] iter_num The iteration number
+ */
+ void geo_normalization_iteration(int iter_num);
+
+ /*!
+ \brief Performs a block normalization iteration to update the block data from the measured_block_data and model_data.
+ Additionally, handles the saving of the block data iteration to file, KL calculation and display.
+ * @param iter_num The iteration number
+ */
+ void block_normalization_iteration(int iter_num);
+
+ /*!
+ \brief Write the efficiencies to a file (regardless of the value of do_save_to_file)
+ \param[in] iter_num The iteration number
+ \param[in] eff_iter_num The efficiency iteration number
+ */
+ void write_efficiencies_to_file(int iter_num, int eff_iter_num) const;
+
+ /*!
+ \brief Write the efficiencies to a file (regardless of the value of do_save_to_file)
+ \param[in] iter_num The iteration number
+ */
+ void write_geo_data_to_file(int iter_num) const;
+
+ /*!
+ \brief Write the efficiencies to a file (regardless of the value of do_save_to_file)
+ \param[in] iter_num The iteration number
+ */
+ void write_block_data_to_file(int iter_num) const;
+
+ /*!
+ \brief Computes the threshold for the Kullback-Leibler divergence calculation. This is a purely heuristic value.
+ \return The threshold value
+ */
+ float compute_threshold_for_KL();
+
+ // Constructor parameters
+ //! The prefix for the output files
+ std::string out_filename_prefix;
+ //! The measured projection data
+ const ProjData& measured_data;
+ //! The model projection data
+ const ProjData& model_data;
+ //! The number of (sub-)efficiency iterations to perform per iteration of the algorithm
+ int num_eff_iterations;
+ //! The number of algorithm iterations to perform
+ int num_iterations;
+ //! Whether to perform geo normalization calculations
+ bool do_geo;
+ //! Whether to perform block normalization calculations
+ bool do_block;
+ //! Whether to perform block normalization calculations with symmetry
+ bool do_symmetry_per_block;
+ //! Whether to perform Kullback-Leibler divergence calculations and display the KL value. This can be slow.
+ bool do_KL;
+ //! Whether to display the progress of the algorithm.
+ bool do_display;
+ //! Whether to save the each iteration of the efficiencies, geo data and block data to file.
+ bool do_save_to_file;
+
+ // Calculated variables
+ //! The threshold for the Kullback-Leibler divergence calculation
+ float threshold_for_KL;
+ FanProjData model_fan_data;
+ FanProjData fan_data;
+ DetectorEfficiencies data_fan_sums;
+ DetectorEfficiencies efficiencies;
+ BlockData3D norm_block_data;
+ BlockData3D measured_block_data;
+ GeoData3D norm_geo_data;
+ GeoData3D measured_geo_data;
+
+ // do_KL specific varaibles
+ FanProjData measured_fan_data;
+ DetectorEfficiencies fan_sums;
+ GeoData3D geo_data;
+ BlockData3D block_data;
+};
 
 END_NAMESPACE_STIR