MATLAB: Distance between all points in array and delete the second point if it is less that certian value (Victorized)

distancevectorization

I have this loop to calculate the distance between all of the points in R_all array and delete the second point if the distace less that 0.002, but if I have a huge number of points like 100000 it takes long time, I need to vectorize my code, if you can help me ,, thank you in advance,,
Rx=rand(n,1)*0.2;
Ry=rand(n,1)*0.2;
Rz=rand(n,1)*0.2;
R_all=[Rx Ry Rz];
n= 1000;
Df=0.002;
while j<n
    i=j+1;
    while i<=n
         k  = norm(R_all(j,:)-R_all(i,:)); %function of distance between points
         
         if k < 1.5*Df  % check the distance between all points; should not be < 1.5 Df
             R_all(i,:)=[];
             n=n-1;
         end
         
         
         i=i+1;
    end
     j=j+1; 
end

Best Answer

After a few runs I think this would be equivalent to your loop version. Note that it generates a matrix of size [n n 3] in one of the steps, so memory might become an issue. The pdist function would probably help, but I don't have the statistics and machine learning toolbox.
n= 1000;
Rx=rand(n,1)*0.2;
Ry=rand(n,1)*0.2;
Rz=rand(n,1)*0.2;
R_all=[Rx,Ry,Rz];
Df=0.002;
%calculate distance matrix for every point pair
A=permute(R_all,[1 3 2]);
B=permute(R_all,[3 1 2]);
dist=sqrt( sum( (A-B).^2 , 3) );
%mask the distance to the point itself and to all previous points
dist(1:(1+size(dist,1)):end)=inf;
dist(logical(triu(ones(size(dist)))))=inf;
L=dist<1.5*Df;
L=any(L,1);
R_all(L,:)=[];
Related Question