track_box.h

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//Copyright 2008,2009 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_BOX
#define TRACK_BOX
#include <vector>
#include "tuple.h"
namespace utilities{

class Wrapper_out;


}

namespace tracking{
// forward declaration
class particle_track;
class Track_shelf;


class Track_box{
public:
  const particle_track * at(int n) const;

  particle_track * get_first() const{
    return t_first_;
  }

  particle_track * get_last() const{
    return t_last_;
  }




  void extract_raw_pos(std::vector<float> & output,std::vector<unsigned int> & dims) const;
  void extract_corrected_pos(std::vector<float> & output,std::vector<unsigned int> & dims) const;
    
  void extract_raw_disp(std::vector<float> & output,std::vector<unsigned int> & dims) const;
  void extract_corrected_disp(std::vector<float> & output,std::vector<unsigned int> & dims) const;
  
  Track_box(particle_track * first);
  // empty constructor
  Track_box();
    
  virtual void print();
  void push_back(particle_track* next);

  unsigned int get_id() const
  {
    return id_;
  }

  virtual ~Track_box();
  
  int get_length()const
  {
    return length_;
  };
  void output_to_wrapper(utilities::Wrapper_out & wrapper) const;
  
  void split_to_parts(Track_shelf & shelf);

  void average_cord(utilities::Tuple<float,3> & pos,float & I) const ;

  void set_track_id(unsigned int in)
  {
    id_ = in;
  }
   
  
protected:
  particle_track * t_first_;
  //pointer to last particle in track
  particle_track * t_last_;
  int length_;
  static int running_count_;
  unsigned int id_;

  
  particle_track * at(int n) ;


    
  
  Track_box * split_track(int indx);
  
  void trim_track(int ind_start, int length);

  

};
}


#endif