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Add comments and cleaning the code
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@tomcombriat
tomcombriat committed Aug 4, 2016
1 parent 612c43f commit 126207e
Showing 1 changed file with 44 additions and 57 deletions.
101 changes: 44 additions & 57 deletions sources/link_particules.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -19,12 +19,12 @@



#include<iostream>
#include<cmath>
#include<fstream>
#include<iomanip>
#include<stdlib.h>
#include<vector>
#include <iostream>
#include <cmath>
#include <fstream>
#include <iomanip>
#include <stdlib.h>
#include <vector>
#include "point.hpp"
#include <opencv2/core/core.hpp>
#include <opencv2/highgui/highgui.hpp>
Expand All @@ -48,6 +48,17 @@ using namespace cv;
// **********************************************/


/**************************************************
Cost functions compute the cost to link to different particles.
This function can be computed from different factors: the distance,
the size, the form factor etc…
Currently, the first version computes the cost from the distance only,
the second includes the size…
Finally these functions will be merged in order to have the same prototypes,
thus it will be easier to make this function evolve…
****************************************************/

double cost_function(double * current, double * expected)
{
return (sqrt((current[0]-expected[0])*(current[0]-expected[0])+(current[1]-expected[1])*(current[1]-expected[1])));
Expand All @@ -73,26 +84,6 @@ bool in_area(double * current, double * expected, double radius)
else return false;
}

/*
double cost_function(int * current, double * expected)
{
return sqrt((current[0]-expected[0])*(current[0]-expected[0])+(current[1]-expected[1])*(current[1]-expected[1]));
}
*/

// /***********************************************
// ************IN AREA****************************
// **********************************************/
/*
bool in_area(int * current, double * expected, double radius)
{
if (sqrt((current[0]-expected[0])*(current[0]-expected[0])+(current[1]-expected[1])*(current[1]-expected[1]))<radius) return true;
else return false;
}
*/





Expand All @@ -104,53 +95,50 @@ void link_particules(vector<Points> * & points,vector<Track> & tracks,double sea
/*///////////////////////////////STRATEGY//////////////////////////////
if 0 : neirest neighbor
if 1 : linear prediction
if 2 : quadratic predicition
if 2 : quadratic predicition (not implementated… (Yet?))
*/
//test(0);


double expected_position[2];
unsigned int frame=0;
//initialisation
//initialisation: will assign every point in frame 0 to a new track
for (unsigned int i=0;i<points[0].size();i++)
{
if (points[0].at(i).area()>=size_min && points[0].at(i).area()<=size_max)
{
tracks.push_back(Track(points[0].at(i).center_position()[0],points[0].at(i).center_position()[1],0,points[0].at(i).area()));
//cout<<points[0].at(i).area()<<endl;
points[0].at(i).track_index=i;
}
}


//calcul
for (unsigned int i=0;i<NB_frames-1;i++) // expected_position[0]=points[i][j].center[0];

for (unsigned int i=0;i<NB_frames-1;i++) // loop on all frames of the movie
{

if (mode_low_ram) ia >> points[i+1];
if (mode_low_ram) ia >> points[i+1]; //Backup the archive

if (i%100==0)
{
cout<<"\r"<<i<<"/"<<NB_frames;
fflush(stdout);
}
for (unsigned int j=0;j<tracks.size();j++) //loop on particule of frame N
for (unsigned int j=0;j<tracks.size();j++) //loop on ALL tracks (not so efficient…)
{
// test(j);
if (tracks[j].Frame.back()<=i && tracks[j].Frame.back()>=i-gap)
if (tracks[j].Frame.back()<=i && tracks[j].Frame.back()>=i-gap) //test if track is still open.
{
//Linking of particules already linked in the precedent frame
//TO change in further developments
if (strategy==1)
{
if (tracks[j].X.size()>1)
if (tracks[j].X.size()>1) //linear interpolation
{
int size=tracks[j].X.size();
expected_position[0]=(tracks[j].X.at(size-1)-tracks[j].X.at(size-2))/((tracks[j].Frame.at(size-1)-tracks[j].Frame.at(size-2)))+tracks[j].X.at(size-1)+flow_x;
expected_position[1]=(tracks[j].Y.at(size-1)-tracks[j].Y.at(size-2))/((tracks[j].Frame.at(size-1)-tracks[j].Frame.at(size-2)))+tracks[j].Y.at(size-1)+flow_y;

}
else
else //track to short to compute the interpolation (2 points needed)
{
expected_position[0]=tracks[j].X.back()+flow_x;
expected_position[1]=tracks[j].Y.back()+flow_y;
Expand All @@ -165,17 +153,16 @@ void link_particules(vector<Points> * & points,vector<Track> & tracks,double sea



Points * candidate=NULL;
Points * candidate=NULL; //Windows compatibility…
double candidate_cost=search_radius*2;
for (unsigned int k=0;k<points[i+1].size();k++) //loop in particules in next frame
{

if (points[i+1].at(k).track_index==-1 && points[i+1].at(k).area()>=size_min && points[i+1].at(k).area()<=size_max)
{
if (points[i+1].at(k).track_index==-1 && points[i+1].at(k).area()>=size_min && points[i+1].at(k).area()<=size_max) //test if particle is not attributed (track_index=-1) and its size
{
double x_current=points[i+1].at(k).center_position()[0];
double y_current=points[i+1].at(k).center_position()[1];

if (in_area(points[i+1].at(k).center_position(),expected_position,search_radius)) //put the cost function here ?
if (in_area(points[i+1].at(k).center_position(),expected_position,search_radius)) //check if the particle is close enought to the expected position
{
//if (cost_function(points[i+1].at(k).center_position(),expected_position)<=candidate_cost)
if (cost_function(expected_position,points[i+1].at(k),tracks[j].size_P.back())<=candidate_cost)
Expand All @@ -188,18 +175,19 @@ void link_particules(vector<Points> * & points,vector<Track> & tracks,double sea
}// end if in area
}//end if not already allocated
}//end loop particules in next frame
if (candidate_cost<search_radius+1){
tracks[j].X.push_back(candidate->center_position()[0]);
tracks[j].Y.push_back(candidate->center_position()[1]);
tracks[j].Frame.push_back(i+1);
tracks[j].size_P.push_back(candidate->area());
candidate->track_index=j;
// cout<<"Track "<<j<<" found a match at position "<<candidate->center[0]<<" "<<candidate->center[1]<<endl;
} //end of if there is a match

if (candidate_cost<search_radius+1) //a match is found:
{
//put the particle at the end of the track
tracks[j].X.push_back(candidate->center_position()[0]);
tracks[j].Y.push_back(candidate->center_position()[1]);
tracks[j].Frame.push_back(i+1);
tracks[j].size_P.push_back(candidate->area());
//give the number of the track to the particle (then it will not be attributed a second time…)
candidate->track_index=j;
} //end of if there is a match
} //end of if on particles who are between N and N-gap
} //end loop on tracks of frame N



for (unsigned int j=0;j<points[i].size();j++) //loop on particules not being attributed on a tracks previously
Expand Down Expand Up @@ -236,7 +224,7 @@ void link_particules(vector<Points> * & points,vector<Track> & tracks,double sea
}// end if in area
}//end if not already allocated
}//end loop particules in next frame
if (candidate_cost<search_radius+1)
if (candidate_cost<search_radius+1) //put the two particle in a new track
{
tracks.push_back(Track(points[i].at(j).center_position()[0],points[i].at(j).center_position()[1],i,points[i].at(j).area()));
tracks.back().add_point(candidate->center_position()[0],candidate->center_position()[1],i+1,candidate->area());
Expand All @@ -245,10 +233,9 @@ void link_particules(vector<Points> * & points,vector<Track> & tracks,double sea
}
} //not already attributed
} //not previously attributed
vector<Points> tamp_vec;
points[i].swap(tamp_vec);
vector<Points> tamp_vec;
points[i].swap(tamp_vec); //free memory
} //loop on frames

} //end of function


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