npctransport/Statistics.h

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/**
 *  \file npctransport/Statistics.h
 *  \brief statistics and order parameters about the simulations
 *         that is associated with a SimulationData object
 *
 *  \author Barak Raveh, Daniel Russell
 *  Copyright 2007-2019 IMP Inventors. All rights reserved.
 */

#ifndef IMPNPCTRANSPORT_STATISTICS_H
#define IMPNPCTRANSPORT_STATISTICS_H


#include "npctransport_config.h"
#include <IMP/Model.h>
#include <IMP/PairContainer.h>
#include <IMP/atom/BrownianDynamics.h>
#include <IMP/atom/Hierarchy.h>
#include <IMP/container/CloseBipartitePairContainer.h>
#include <IMP/container/ListSingletonContainer.h>
#include <IMP/container/PairContainerSet.h>
#include <IMP/container/PredicatePairsRestraint.h>
#include <IMP/core/pair_predicates.h>
#include <IMP/core/BoundingBox3DSingletonScore.h>
#include <IMP/core/Typed.h>
#include <IMP/display/declare_Geometry.h>
#include <IMP/rmf/SaveOptimizerState.h>
#include <IMP/Pointer.h>
#include <IMP/set_map_macros.h>
#include <RMF/HDF5/File.h>
#include "io.h"
#include "BodyStatisticsOptimizerState.h"
#include "GlobalStatisticsOptimizerState.h"
#include "ParticleTransportStatisticsOptimizerState.h"
#include "ChainStatisticsOptimizerState.h"
#include "BipartitePairsStatisticsOptimizerState.h"
#include "Parameter.h"
#include "Scoring.h"
#include "typedefs.h"

#include <boost/timer.hpp>
#include "boost/tuple/tuple.hpp"
#include <boost/utility/value_init.hpp>
#include <boost/unordered_map.hpp>
#include <boost/unordered_set.hpp>
#include <stdint.h>
#include <string>

#ifdef SWIG
namespace boost {
struct timer {};
}
#endif


IMPNPCTRANSPORT_BEGIN_NAMESPACE

class SimulationData; // fwd incomplete declaration

//! Statistics and order parameters about the simulations
class IMPNPCTRANSPORTEXPORT Statistics : public Object {
 private:
  UncheckedWeakPointer<SimulationData> owner_sd_;

  // Whether statistics gathering has been activated (= optimizer states added to optimizer)
  bool is_activated_;

  // interval of simulation frames for gathering stats
  Parameter<int> statistics_interval_frames_;

  // the file to which simulation statistics are dumped:
  std::string output_file_name_;

  IMP::PointerMember<GlobalStatisticsOptimizerState> global_stats_;

  // statistics about all fgs, per particle, per chain, per particle type
  typedef std::vector< BodyStatisticsOptimizerStates >
    FGsBodyStatisticsOSs;
  typedef IMP_KERNEL_LARGE_UNORDERED_MAP<core::ParticleType, FGsBodyStatisticsOSs>
    FGsBodyStatisticsOSsMap;
  FGsBodyStatisticsOSsMap fgs_bodies_stats_map_;

  // statistics about all floaters (kaps etc.), per particle type
  typedef IMP_KERNEL_LARGE_UNORDERED_MAP<core::ParticleType, BodyStatisticsOptimizerStates>
    BodyStatisticsOSsMap;
  BodyStatisticsOSsMap floaters_stats_map_;

  // transport statistics about all floaters (kaps etc.) per particle type
  typedef IMP_KERNEL_LARGE_UNORDERED_MAP< core::ParticleType,
    ParticleTransportStatisticsOptimizerStates>
    ParticleTransportStatisticsOSsMap;
  ParticleTransportStatisticsOSsMap floaters_transport_stats_map_;

#ifndef SWIG
  // distributions
  typedef IMP_KERNEL_LARGE_UNORDERED_MAP< core::ParticleType,
    std::vector< std::vector<int> > >
    ParticleTypeZRDistributionMap;
  ParticleTypeZRDistributionMap particle_type_zr_distribution_map_;
  typedef IMP_KERNEL_LARGE_UNORDERED_MAP< uint_fast8_t,
    IMP_KERNEL_LARGE_UNORDERED_MAP< uint_fast8_t,
    IMP_KERNEL_LARGE_UNORDERED_MAP< uint_fast8_t,
    boost::value_initialized<unsigned int> > > >
    t_sparse_3d_matrix;
  typedef IMP_KERNEL_LARGE_UNORDERED_MAP< core::ParticleType,
    t_sparse_3d_matrix >
    //    std::vector< std::vector< std::vector<int> > > >
    ParticleTypeXYZDistributionMap;
  ParticleTypeXYZDistributionMap particle_type_xyz_distribution_map_;
  struct t_size_3d_matrix{
    uint_fast8_t d0;
    uint_fast8_t d1;
    uint_fast8_t d2;
  };
  t_size_3d_matrix xyz_distribution_sizes_;
#endif

  // statistics about entire FG chains, for each FG type
  typedef IMP_KERNEL_LARGE_UNORDERED_MAP<core::ParticleType, ChainStatisticsOptimizerStates>
    ChainStatisticsOSsMap;
  ChainStatisticsOSsMap chains_stats_map_;

  // statistics of pairs of interactions for each interaction type
  typedef IMP_KERNEL_LARGE_UNORDERED_MAP< npctransport::InteractionType,
    PointerMember<BipartitePairsStatisticsOptimizerState> >
    BipartitePairsStatisticsOSMap;
  BipartitePairsStatisticsOSMap interaction_stats_map_;

  // true if statistics were recently reset, so that update()
  // should restart averaging from 0 frames
  mutable bool is_stats_reset_;


 public:

  //! Remove all statistics related to particle type pt
  /**
   Removes statistics of particle type pt from all internal maps
   and from the optimizer states of get_sd()->get_bd()

   @param pt the particle type to be removed
  */
  void remove_particle_type(core::ParticleType pt);

  /**
     @param sd the sd that owns and uses this statistics object
     @param statistics_interval_frames the interval of simulation frames for gathering
                                       statistics
     @param output_file_name name of output file to which to dump statistics (or update
                             if it already exists) when calling update()
   */
  Statistics(SimulationData* sd,
             unsigned int statistics_interval_frames,
             std::string output_file_name);

  //! add statistics about an FG chain
  /** add statistics about an FG chains

      @param fg_chain the chain
  */
  void add_fg_chain_stats(FGChain* fg_chain);

  //! add statistics about a floater particle
  /** add statistics about a floater particle

      @param p the particle
  */
  void add_floater_stats(IMP::Particle* p);

  //! add statistics about interactions between particles of type 0 and 1
  /** add statistics about interactions between particles of type 0 and 1
      (order does not matter)

      @param type0 type of first interacting particles
      @param type1 type of other interacting particles
  */
  void add_interaction_stats
    ( core::ParticleType type0, core::ParticleType type1);

  //! add all statistics-related optimizer states to o
  /**
      @param o optimizer to which optimizer states are added,
               use get_sd()->get_bd() if nullptr
      @return the list of optimizer states that were added

      @note If called for more than one optimizer, only the last
            optimizer will be guaranteed to work well.
  */
  OptimizerStates add_optimizer_states(Optimizer* o = nullptr);

  /**
     updates the map of z-r distributions of particle coordinates
     with p's binned position counts (if z-symmetry flag is on,
     z is absolute vertical location; r is distance from pore axis)

     Comment: assume a pore geometry, no checks made that it is so
   */
  void update_particle_type_zr_distribution_map(Particle* p);

    /**
     updates the map of x-y-z distributions of particle coordinates
     with p's binned position counts (if z-symmetry flag is on,
     z is absolute vertical location)

     Comment: assume a pore geometry, no checks made that it is so
   */
  void update_particle_type_xyz_distribution_map(Particle* p);


  /**
      opens / creates statistics protobuf file, and update it
      with appropriate statistics, using statistics file
      originally specified in the constructor, and based on statistics
      gathered from the optimizer that was specified by
      add_optimizer_states().

      @throw UsageException If add_optimizer_states() was not called yet
         (= get_is_activated() is false)

      @param timer the timer that was used to measure the time
                   that has elapsed for statistics
      @param nf_new the number of frames by which the statistics file
                    should be advanced. This is used to weight the
                    contribution of average statistics over time.

      @note this method is not const cause it may invoke e.g., energy evaluation
            though it does not substantially change anything in the state of the object
   */
  void update(const boost::timer &timer,
                         unsigned int nf_new = 1);

  /** resets all the counters of any statistics counters,
      and the simulation time to zero */
  void reset_statistics_optimizer_states();

  //! Loads the stats file and set the interrupted flag to true
  void set_interrupted(bool tf);

  /************************************************************/
  /************* various simple getters and setters *******************/
  /************************************************************/

  /** returns the model associated with the owned SimulationData */
  Model* get_model();

#ifndef SWIG
  /** returns the model associated with the owned SimulationData */
  Model* get_model() const;
#endif

  /** return the SimulationData object that owns this ScoringFunction */
  SimulationData* get_sd() {
    return owner_sd_;
  }

  //! if true, statistics have been activated, so add_optimizer_states()
  //! was called such that statistics are being tracked
  bool get_is_activated(){
    return is_activated_;
  }

#ifndef SWIG
  /** return the SimulationData object that owns this ScoringFunction */
  SimulationData const* get_sd() const{
    return owner_sd_;
  }
#endif

  std::string get_output_file_name() const{
    return output_file_name_;
  }

 private:

  //! update the xyz distribution of type p_type to a dataset in
  //! hdf5_group, with name p_type.get_string()
  bool update_xyz_distribution_to_hdf5
    (RMF::HDF5::Group hdf5_group,
     core::ParticleType p_type);


  //! updates pStats with all statistics related to fgs, averaged over
  //! nf_new additional frames
  void update_fg_stats( ::npctransport_proto::Statistics* pStats,
                        unsigned int nf_new,
                        unsigned int zr_hist[4][3],
                        RMF::HDF5::File hdf5_file);




  // TODO: move to util.h, possibly internal
  // @param floaters a list of floater particles
  // @param fg_roots a list of hierarchy particles that are the root of an
  //                 fg chain (= all their children are fg typed particles)
  // @return a 4-tuple (1,2,3,4) with:
  // 1 - total # of individual site-site interactions between the specified
  //     floaters and chains
  // 2 - total # of floaters that site-interact with any specified chain
  // 3 - total # of fg bead-floater pairs that site-interact
  // 4 - sum of # of chain-floater that site-intercat
  boost::tuple<double, double, double, double> get_interactions_and_interacting
    ( const ParticlesTemp &floaters, const atom::Hierarchies &chain_roots) const;

  //! @return the top of a z-axis bin for various stats
  double get_z_distribution_top() const;

  //! @return the radius of a outermost radial (x,y) bin for various stats
  double get_r_distribution_max() const;

  /**
     for particles ps, returns the distribution along the z axis, in regions
     z0 = [top...) ;   z1 = [0..top) ;   z2 = [-top..top) ;   z3 = (...top)
     with top being the return value of get_z_distribution_top()

     @param ps the particles

     @return a tuple <z0,z1,z2,z3> with counts of particles from ps
             in z0, z1, z2 and z3 regions
   */
  boost::tuple<int, int, int, int>
    get_z_distribution(const ParticlesTemp& ps) const;

  /** add the z-axis / (x,y)-radial distribution of particles ps
      to zr_hist, a grid with z-axis bins on the first dimension and
      radial bins on the second dimension.

      @param zr_hist a grid on z / (x,y)-radial axis
      @param ps the particles

  */
  void fill_in_zr_hist(unsigned int zr_hist[4][3],
                       ParticlesTemp ps) const;


 public:
  IMP_OBJECT_METHODS(Statistics);


};

inline IMPNPCTRANSPORTEXPORT boost::timer create_boost_timer() {
  return boost::timer();
}

IMPNPCTRANSPORT_END_NAMESPACE

#endif /* IMPNPCTRANSPORT_STATISTICS_H */