track_shelf.h

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//Copyright 2008-2010 Thomas A Caswell
//tcaswell@uchicago.edu
//http://jfi.uchicago.edu/~tcaswell
//
//This program is free software; you can redistribute it and/or modify
//it under the terms of the GNU General Public License as published by
//the Free Software Foundation; either version 3 of the License, or (at
//your option) any later version.
//
//This program is distributed in the hope that it will be useful, but
//WITHOUT ANY WARRANTY; without even the implied warranty of
//MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
//General Public License for more details.
//
//You should have received a copy of the GNU General Public License
//along with this program; if not, see <http://www.gnu.org/licenses>.
//
//Additional permission under GNU GPL version 3 section 7
//
//If you modify this Program, or any covered work, by linking or
//combining it with MATLAB (or a modified version of that library),
//containing parts covered by the terms of MATLAB User License, the
//licensors of this Program grant you additional permission to convey
//the resulting work.
#ifndef TRACK_SHELF
#define TRACK_SHELF

#include <list>
#include <vector>
#include "tuple.h"
//forward declare histogram
namespace utilities{
class Histogram;
class Cell;
class Counted_vector;
class Generic_wrapper;
class Wrapper_out;
class Md_store;


}

namespace tracking{
//forward declare classes
class Track_box;
class particle_track;
class Master_box;
class Trk_accumulator;
class hash_case;

class Track_shelf{

public:
  void add_new_track(particle_track* first_part);
  
  void add_track(Track_box * track);

  void remove_short_tracks(int min_length);

  void print();

  void set_shelf();

  void track_length_histogram(utilities::Histogram & in);


  void msd(std::vector<double> & msd_vec,std::vector<int> & entry_count)const;

  
  void msd_corrected(utilities::Counted_vector & msd)const;
  
  void msd_corrected(utilities::Counted_vector & md,
                     utilities::Counted_vector & msd,
                     utilities::Counted_vector & msd_sq)const;
  

  /*
     Computes the average fourier transform of the tracks
   */
  //void track_fft();
  
  void disp_sq_hist(int time_step,
                    utilities::Histogram & disp_sq_hist
                    )const;

  void set_raw_disp_to_cell(utilities::Cell & output) const;

  void set_corrected_disp_to_cell(utilities::Cell & output) const;

  unsigned int get_track_count() const{
    return track_count_;
    
  }

  void pass_fun_to_track(void(Track_box::*fun)()const)const;

  void output_to_wrapper(utilities::Wrapper_out & wrapper) const;


  
  void output_to_wrapper(utilities::Generic_wrapper & wrapper,
                         const utilities::Md_store * md_store) const;

  
  void output_link_to_wrapper(utilities::Wrapper_out & wrapper, 
                              const utilities::Tuple<float,3> & scale_t,
                              const utilities::Tuple<float,3> & dim) const;

  
  void split_to_parts(Track_shelf & out_put_shelf);
  

  void renumber();
  
  void init(Master_box & mb);



  void init(hash_case & hc);

  void compute_corrected_TA(Trk_accumulator & ta)const;
  
  void compute_corrected_TA_ncuts(Trk_accumulator & ta,int min_neighbors,int max_neighbors)const;
  
  Track_box * get_track(unsigned int track_id) const ;
  
  
  Track_shelf():track_count_(0){};

  ~Track_shelf();
protected:
  std::list<Track_box*> tracks_;
  
  void remove_track_internal_(  std::list<Track_box*>::iterator it);

  unsigned int track_count_;
  
  
};
}


#endif