how to transfer the pairwise distance value in a distance matrix

Question

I am pretty new to Matlab, now i want to use the matlab to do some clustering job. if I have 3 columns values

id1 id2 distvalue1

id1 id3 distvalue2 ....

id2 id4 distvalue i .....

5000 ids in total, but some ids pairs are missing the distance value in python I can make loops to import these distance value into a matrix form. How I can do it in matlab? and also let the matlab knows id1,...idx are identifies and the third column is the value

Thanks!

Answer 1

Based on the comments, you know how to get the data into the form of an N x 3 matrix, called X, where X(:,1) is the first index, X(:,2) is the second index, and X(:,3) is the corresponding distance.

Let's assume that the indices (id1... idx) are arbitrary numeric labels.

So then we can do the following:

% First, build a list of all the unique indices    
indx = unique([X(:,1); X(:,2)]);
Nindx = length(indx);

% Second, initialize an empty connection matrix, C
C = zeros(Nindx, Nindx);  %or you could use NaN(Nindx, Nindx)

% Third, loop over the rows of X, and map them to points in the matrix C
for n = 1:size(X,1)
     row = find(X(n,1) == indx);
     col = find(X(n,2) == indx);
     C(row,col) = X(n,3);
end

This is not the most efficient method (that would be to remap the indices of X to the range [1... Nindx] in a vectorized manner), but it should be fine for 5000 ids.

If you end up dealing with very large numbers of unique indices, for which only very few of the index-pairs have assigned distance values, then you may want to look at using sparse matrices -- try help sparse -- instead of pre-allocating a large zero matrix.