clear all
clc
%This code calculates speed of bacteria after results from tracking code
a=csvread('results_tracking_10.csv')
a4=diff(a(:,4))
c=1;
cal=0.095*30;
leng=length(a)
leng_new=leng;
pos(1)=0;
b=zeros(leng,5)
for i=1:length(a)-1
    
if a4(i)==1
pos(c+1)=i; c=c+1;
end
   
    
    
    
end
pos(c+1)=length(a);
summ=0;
for i=1:a(end,4) %1 to no. of bacteria
    for j=pos(i)+1:pos(i+1)% from start to end index of i th bacteria
        s=pos(i)+1;
        e=pos(i+1);
     b(s:e,1:2)=[abs(diff(a(s:e,1:2))); 0 0];
     b(s:e,3:4)=b(s:e,1:2)*cal;
     b(s:e,5)=(b(s:e,3).^2+b(s:e,4).^2).^(0.5);
     avg_sb(i)=mean(b(s:e-1,5));
     
    end
    frames(i)=e-s+1
    if avg_sb(i)>0
    summ=summ+(e-s+1)*avg_sb(i);
    else
    leng_new=leng_new-(e-s+1);    
    end
    
    
end
avg_ab=(summ/leng_new);
avg_sb_col=avg_sb.'
mx=max(avg_sb);
mn=min(avg_sb);
result=[a b];
csvwrite('analysed_data.csv',result)
frames_col=frames.'
frame_data=[avg_sb_col frames_col]