How to combine Matlab's build-in functions dtw and pdist?

Hi, I'm trying to perform hierarchical clustering on my data. I've tried several distance metrics, but now I would like to use the build-in function for dynamic time warping (Signal Processing Toolbox), by passing the function handle @dtw to the function pdist. Following problem occuried:

Error using pdist (line 391)
Error evaluating distance function 'dtw'.

Caused by:
    Error using dtw (line 87)
    The number of rows between X and Y must be equal when X and Y are matrices

Here is the code I'm using:

D = pdist(data,@dtw); %data is a 1184x38 double matrix, where 1184 is the number of time-series
Z = linkage(D,'ward');
res = cluster(Z, 'maxclust', numClusters); %e.g. numClusters = 5

Many thanks in advance!

[Dankur Mcgoo]

Did you end up solving your problem? I am facing the same issue.

Answer 1

[Greg Dionne]

You'll want to take the output of DTW and put it into a form that PDIST can recognize.

This should get you started:

function d = dtwdist(Xi, Xj, varargin)

[m,n] = size(Xj);

% preallocate
d = zeros(m,1);

for j=1:m
    d(j) = dtw(Xi, Xj(j,:), varargin{:});
end

Use it like:

X = randn(118,38);
maxsamp = 10;
d = pdist(X,@(Xi,Xj) dtwdist(Xi,Xj,maxsamp,'squared'))
imagesc(squareform(d));
colorbar;
title('Distance Matrix')

[m qasim]

Hi ,help me to use a different distance metric in DTW algorithm like mahlanobis