Faster Matlab Code for Spike Time Distances Between Labeled (Multineuronal) Spike Trains, Parallel in q and k

Thomas Kreuz:

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Faster Matlab code for Multineuronal Spike Time Metric, Parallel in q and k

function labdist_faster_qk_mat = labdist_faster_qkpara(sa,la,sb,lb,q,k) % LABDIST_FASTER_QKPARA(SA,LA,SB,LB,Q,K), parallel in q and k % Calculates the multi-unit metric distance between two spike trains % Uses a fast version of the algorithm % SA, SB - spike times on the two spike trains % LA, LB - spike labels (positive integers) % Q - vector of timing precision parameters % K - vector of label reassigning parameters % % Thomas Kreuz, 10/19/08; based on code by Dmitriy Aronov, 6/20/01; %Assign labels in the form 1,2,...,L and count spikes of each label lbs = unique([la lb]); L = size(lbs,2); for c = 1:L j = find(la==lbs(c)); la(j) = c; numa(c) = size(j,2); j = find(lb==lbs(c)); lb(j) = c; numb(c) = size(j,2); end %Choose the spike train to separate to subtrains if prod(numb+1)*(sum(numa)+1) > prod(numa+1)*(sum(numb)+1) t = la; la = lb; lb = t; t = sa; sa = sb; sb = t; t = numa; % numa=numb; numb = t; end tb=zeros(L,max(numb)); for c = 1:L tb(c,1:numb(c))=sb(logical(lb==c)); end %Set up an indexing system ind = []; for c = 1:L j = repmat(0:numb(c),prod(numb(c+1:end)+1),1); j = repmat(reshape(j,numel(j),1),prod(numb(1:c-1)+1),1); ind = [ind j]; end ind = sortrows([sum(ind,2) ind]); ind = ind(:,2:end); %Initialize the array m = zeros(size(ind,1),size(sa,2)+1); m(1,:) = 0:size(sa,2); m(:,1) = sum(ind,2); m = repmat(shiftdim(m,-2),[length(k),length(q),1,1]); %Perform the calculation for v = 2:size(m,3) fa2=find(shiftdim(m(1,1,:,1),2)==m(1,1,v,1)-1); fa=fa2(logical(sum(ind(fa2,:)-repmat(ind(v,:),length(fa2),1)==0,2)==L-1)); fth=find(ind(v,:)>0)'; bsv=diag(tb(fth,ind(v,fth))); for w = 2:size(m,4) m(:,:,v,w)=min(cat(3,m(:,:,v,w-1)+1,m(:,:,fa,w)+1,m(:,:,fa,w-1)+ ... repmat(shiftdim(q'*abs(sa(w-1)-bsv'),-1),[length(k),1,1])+ ... permute(repmat(shiftdim(k'*not(la(w-1)==fth)',-1),[length(q),1,1]),[2 1 3])),[],3); end end labdist_faster_qk_mat = m(:,:,end,end);