# Matlab Code for Spike Interval Distances Between Spike Trains, Optimized for Matlab

#### Christina Behrend: ceb48@duke.edu Jim Hokanson: jim.hokanson@duke.edu

main cost-based metrics page
algorithm page for cost-based metrics

## Matlab code for Spike Interval Metric, Optimized for Matlab

function [d,scr]=spkd_int_FAST_post(tli,tlj,cost,tsamp) % % d=spkd(tli,tlj,cost) calculates the "spike time" distance % (Victor & Purpura 1996) for a single cost % % tli: vector of spike times for first spike train % tlj: vector of spike times for second spike train % cost: cost per unit time to move a spike % % Copyright (c) 1999 by Daniel Reich and Jonathan Victor. % Translated to Matlab by Christina Behrend from FORTRAN code by Jonathan Victor. % Matlab code optimized for faster processing by Jim Hokanson % calculates distance between two spike trains in the spike interval metric % by a continuum modification of the sellers algorithm % end conditions: the first and last ISI are expanded as needed to minimize % the total cost % input variables % tli: vector spike times for first spike train % tlj: vector spike times for second spike train % cost: cost per unit time to move a spike % tsamp: the length of the entire interval nspi=length(tli); % number of spike times in train 1 nspj=length(tlj); % number of spike times in train 2 ni = nspi+1; % number of intervals in train 1 nj = nspj+1; % number of intervals in train 2 scr=zeros(ni+1,nj+1); % define calculation for a cost of zero if cost==0 d=abs(ni-nj); return end % INITIALIZE MARGINS WITH COST OF ADDING A SPIKE scr(:,1)=(0:ni)'; scr(1,:)=(0:nj); tli_diff = diff(tli); tlj_diff = diff(tlj); for i = 1:ni if (i > 1) && (i < ni) %di = tli(i)-tli(i-1); di = tli_diff(i-1); elseif (i == 1) && (i == ni) di = tsamp; elseif (i == 1) && (i < ni) di = tli(i); else %(i > 1) && (i == ni) di = tsamp-tli(i-1); end iend = ((i == 1) || (i == ni)); % unrolled loop for j = 1 % ------------------------ if (nj == 1) dj = tsamp; else %(j < nj) dj = tlj(1); end if iend dist = 0; else %jend dist = max(0,dj-di); end scr(i+1,2)=min([scr(i,2)+1 scr(i+1,1)+1 scr(i,1)+cost*dist]); % main code % --------- for j = 2:nj-1 dj = tlj_diff(j-1); if iend dist = max(0,di-dj); else dist = abs(di-dj); end tmp = min(scr(i,j+1)+1,scr(i+1,j)+1); scr(i+1,j+1)=min(tmp,scr(i,j)+cost*dist); end % unrolled loop for j = nj % ------------------------ if (nj == 1) dj = tsamp; else %(j > 1) && (j == nj) dj = tsamp-tlj(nj-1); end if iend dist = 0; else %jend dist = max(0,dj-di); end scr(i+1,nj+1)=min([scr(i,nj+1)+1 scr(i+1,nj)+1 scr(i,nj)+cost*dist]); end d = scr(ni+1,nj+1);