Faster Matlab Code for Spike Time Distances Between Labeled (Multineuronal) Spike
Trains, Parallel in q and k
main cost-based metrics page
algorithm page for cost-based metrics
Faster Matlab code for Multineuronal Spike Time Metric, Parallel in q and k
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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);
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