function [lowpasssig,maxinfo,mininfo]=peak_picker(sig,options);
% sophisticated peak picker
% the signal is first lowpassfilterd with the frequency given in options
% options comes with:
% frequency with witch the psth is filtered
% options.lowpassfrequency=500;
% search for peaks in the range from to:
% options.search_peak_start_search=0.001; % seach also before the offical latency
% options.search_peak_stop_search=0.025; % seach this time for peaks
% every distinct peak must comply the following conditions:
% a certain activity during the duration of the maximum (a spike count per
% presentation)
if ~isfield(options,'min_count_per_peak')
options.min_count_per_peak=-inf;% default: no certain activity: all peaks are significant
end
% a certain height of the maximum peak
if ~isfield(options,'min_height_of_heighest_peak')
options.min_height_of_heighest_peak=0; % default: no certain height: all peaks are significant
end
% return values are the filtered signal and information about the found
% peaks:
% maxinfo.values % the hights of the found maxima
% maxinfo.times % where are the found maxima
% maxinfo.contrast % the contrast is the relation between the maximum and the surrounding minima
% maxinfo.qvalue % how wide the maximum is at half height.
% maxinfo.activity % sum of activity between the adjacent minima
% every found maxima (except the first and the last) is surrounded by two
% minima. Same is true for the found minimas
% do we want some grafical output (for debugging)
grafix=options.grafix;
% define the return values
maxinfo=[];
mininfo=[];
%do the lowpassfiltering
lowpasssig=lowpass(sig,options.lowpassfrequency);
[atmax,ahmax]=getlocalmaxima(lowpasssig);
[atmin,ahmin]=getlocalminima(lowpasssig);
% restrict to the requiered range
indeces1=find(atmax>options.search_peak_start_search);
indeces2=find(atmax<options.search_peak_stop_search);
indeces=intersect(indeces1,indeces2);
tmax=atmax(indeces);
hmax=ahmax(indeces);
indeces1=find(atmin>options.search_peak_start_search);
indeces2=find(atmin<options.search_peak_stop_search);
indeces=intersect(indeces1,indeces2);
tmin=atmin(indeces);
hmin=ahmin(indeces);
% make an iterated search through all maxima and decide which ones to keep
finished=0;
while ~finished
% throw out exactly one maximum
[tmaxnew,tminnew,hmaxnew,hminnew]=try_reduce_maxima(tmax,tmin,hmax,hmin,options);
if length(tmaxnew)==length(tmax) || length(tmaxnew)==1 || length(tminnew)==1
finished=1;
end
tmax=tmaxnew; tmin=tminnew; hmax=hmaxnew; hmin=hminnew; % new values
% if grafix
% plotall(fignum,lowpasssig,tmax,tmin,hmax,hmin);
% p=0;
% end
end
if grafix
fignum=figure;
set(gcf,'Number','off');
% set(gcf,'name',sprintf('peak picker (An:%s Un:%s Ex:%s) ',data.unitinfo.an_num,data.unitinfo.un_num,data.unitinfo.ex_num));
set(gcf,'name',('peak picker'));
plotall(fignum,lowpasssig,tmax,tmin,hmax,hmin);
end
% if grafix
% plotall(lowpasssig,tmax,tmin,hmax,hmin);
% end
% now only significant values are left!
% put them in the return structure:
nr_max=length(tmax);
maxinfo.values=hmax; % the hights of the found maxima
maxinfo.times=tmax; % where are the found maxima
[highest_peak_height,highest_peak_index]=max(hmax);
for i=1:nr_max
maxinfo.contrast(i)=getcontrast(i,tmax,tmin,hmax,hmin); % the contrast is the relation between the maximum and the surrounding minima
maxinfo.qvalue(i)=getquality(i,tmax,tmin,hmax,hmin); % how wide the maximum is at half height.
maxinfo.activity(i)=getactivity(i,lowpasssig,tmax,tmin,hmax,hmin,options.latency); % sum of activity between the adjacent minima
end
nr_min=length(tmin);
mininfo.values=hmin; % the hights of the found maxima
mininfo.times=tmin; % where are the found maxima
for i=1:nr_min
mininfo.contrast(i)=getmincontrast(i,tmax,tmin,hmax,hmin); % the contrast is the relation between the maximum and the surrounding minima
mininfo.qvalue(i)=getminquality(i,tmax,tmin,hmax,hmin); % how wide the maximum is at half height.
end
% now we have all peaks, find out which ones are significant for us
maxinfo.distinct_max=[];
count=1;
height_criterium=options.min_height_of_heighest_peak*highest_peak_height;
count_criterium=options.min_count_per_peak;
for i=1:nr_max
% it must have a certain contrast
if maxinfo.contrast(i)>=options.min_contrast_for_distinct_peak
% and it must have a certain height
if maxinfo.values(i)>=height_criterium
if maxinfo.activity(i)>=count_criterium
maxinfo.distinct_max(count).contrast=maxinfo.contrast(i);
maxinfo.distinct_max(count).qvalue=maxinfo.qvalue(i);
maxinfo.distinct_max(count).activity=maxinfo.activity(i);
maxinfo.distinct_max(count).hmax=hmax(i);
maxinfo.distinct_max(count).tmax=tmax(i);
count=count+1;
end
end
end
end
if grafix
nr_all_max=length(atmax);
for i=1:nr_all_max
plot(atmax(i)*1000,ahmax(i),'o','markersize',2,'Markerfacecolor','r','Markeredgecolor','r');
end
nr_all_min=length(atmin);
for i=1:nr_all_min
plot(atmin(i)*1000,ahmin(i),'o','markersize',2,'Markerfacecolor','g','Markeredgecolor','g');
end
% plot a dot for every disticnt maximum found
for i=1:nr_max
testmaxpos=maxinfo.times(i);
testmaxval=maxinfo.values(i);
contrast=maxinfo.contrast(i);
count=maxinfo.activity(i);
plot(testmaxpos*1000,testmaxval,'o','markersize',8,'Markerfacecolor','r','Markeredgecolor','r');
end
% plot a dot for every minimum found
for i=1:length(maxinfo.distinct_max);
testmaxpos=maxinfo.distinct_max(i).tmax;
testmaxval=maxinfo.distinct_max(i).hmax;
contrast=maxinfo.distinct_max(i).contrast;
count=maxinfo.distinct_max(i).activity;
text(testmaxpos*1000+1,testmaxval,sprintf('contr %3.3f',contrast),'fontsize',6,'ver','bottom');
text(testmaxpos*1000+1,testmaxval,sprintf('count %3.3f',count),'fontsize',6,'ver','top');
end
for i=1:nr_min
testminpos=mininfo.times(i);
testminval=mininfo.values(i);
plot(testminpos*1000,testminval,'o','markersize',4,'Markerfacecolor','g','Markeredgecolor','g');
end
end
return
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function plotall(fignum,lowpasssig,tmax,tmin,hmax,hmin);
figure(fignum);
clf
hold on
fill(lowpasssig,'b');
set(gca,'xlim',[0,60]);
for i=1:length(tmax)
plot(tmax(i)*1000,hmax(i),'Marker','o','MarkerSize',6,'MarkerFaceColor','r','MarkerEdgeColor','r')
end
for i=1:length(tmin)
% plot(time2bin(lowpasssig,tmin(i)),hmin(i),'Marker','o','MarkerSize',6,'MarkerFaceColor','g','MarkerEdgeColor','g')
end
xlabel('time (ms)');
ylabel('spikes / sweep / bin');
title(' PSTH plus found maxima');
% movegui(nfig,'northwest');
return
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function [tmaxnew,tminnew,hmaxnew,hminnew]=try_reduce_maxima(tmax,tmin,hmax,hmin,options)
% throw out the peak with the smallest contrast
% if removed, the minimum to the right of it is removed too
nr_max=length(tmax);
% find the maximum with the neighbour that is closest in height and throw
% it out!
for i=1:nr_max
contrastr(i)=getrightcontrast(i,tmax,tmin,hmax,hmin);
end
for i=1:nr_max
contrastl(i)=getleftcontrast(i,tmax,tmin,hmax,hmin);
end
[mincontrastr,minconindexr]=min(abs(contrastr)); % thats the smallest right
[mincontrastl,minconindexl]=min(abs(contrastl)); % thats the smallest left
if mincontrastr<mincontrastl
side='right';
[mincontrast,minconindex]=min(contrastr);
else
side='left';
[mincontrast,minconindex]=min(contrastl);
end
testmaxpos=tmax(minconindex);
% if mincontrast<options.min_contrast_for_distinct_peak
if mincontrast<options.min_contrast_for_peak
switch side
case 'right'
[testminpos,testminval,indexmin]=getminimumrightof(testmaxpos,tmax,tmin,hmax,hmin);
case 'left'
[testminpos,testminval,indexmin]=getminimumleftof(testmaxpos,tmax,tmin,hmax,hmin);
end
% remove the minimum right of the maximum
tmaxnew=mysetdiff(tmax,tmax(minconindex));
hmaxnew=mysetdiff(hmax,hmax(minconindex));
if indexmin>0 && indexmin <length(tmin)
tminnew=mysetdiff(tmin,tmin(indexmin));
hminnew=mysetdiff(hmin,hmin(indexmin));
else
tminnew=tmin;
hminnew=hmin;
end
return % only remove one!
end
% if still here, then nothing happend
tmaxnew=tmax; tminnew=tmin; hmaxnew=hmax; hminnew=hmin;
return
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function ret=mysetdiff(values,singleval)
% the same as setdiff, but without the sorting
ret=[];
for i=1:length(values)
if singleval~=values(i)
ret=[ret values(i)];
end
end
return
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function contrast=getcontrast(peaknumber,tmax,tmin,hmax,hmin)
% return the contrast of the peak with the number
testmaxpos=tmax(peaknumber);
testmaxval=hmax(peaknumber);
[leftminpos,leftminval]=getminimumleftof(testmaxpos,tmax,tmin,hmax,hmin);
[rightminpos,rightminval]=getminimumrightof(testmaxpos,tmax,tmin,hmax,hmin);
if isempty(leftminpos) && isempty(rightminpos) % if both are empty, its difficult
contrast=0;
elseif isempty(leftminpos) % if only the left is empty, take the right instead
contrast=(testmaxval-rightminval)/(testmaxval+rightminval);
elseif isempty(rightminpos) % if only the right is empty, take the left instead
contrast=(testmaxval-leftminval)/(testmaxval+leftminval);
else
mean_min_val=mean([leftminval rightminval]);
contrast=(testmaxval-mean_min_val)/(testmaxval+mean_min_val);
end
return
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function contrast=getrightcontrast(peaknumber,tmax,tmin,hmax,hmin)
% return the contrast with the right minimum of the peak with the number
testmaxpos=tmax(peaknumber);
testmaxval=hmax(peaknumber);
% [leftminpos,leftminval]=getminimumleftof(testmaxpos,tmax,tmin,hmax,hmin);
[rightminpos,rightminval]=getminimumrightof(testmaxpos,tmax,tmin,hmax,hmin);
% if isempty(leftminpos) && isempty(rightminpos) % if both are empty, its difficult
% contrast=0;
% elseif isempty(leftminpos) % if only the left is empty, take the right instead
% contrast=(testmaxval-rightminval)/(testmaxval+rightminval);
if isempty(rightminpos) % if only the right is empty, take the left instead
contrast=inf;
else
% mean_min_val=mean([leftminval rightminval]);
contrast=(testmaxval-rightminval)/(testmaxval+rightminval);
end
return
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function contrast=getleftcontrast(peaknumber,tmax,tmin,hmax,hmin)
% return the contrast with the right minimum of the peak with the number
testmaxpos=tmax(peaknumber);
testmaxval=hmax(peaknumber);
[leftminpos,leftminval]=getminimumleftof(testmaxpos,tmax,tmin,hmax,hmin);
% [rightminpos,rightminval]=getminimumrightof(testmaxpos,tmax,tmin,hmax,hmin);
% if isempty(leftminpos) && isempty(rightminpos) % if both are empty, its difficult
% contrast=0;
% elseif isempty(leftminpos) % if only the left is empty, take the right instead
% contrast=(testmaxval-rightminval)/(testmaxval+rightminval);
if isempty(leftminpos) % if only the right is empty, take the left instead
contrast=inf;
else
% mean_min_val=mean([leftminval rightminval]);
contrast=(testmaxval-leftminval)/(testmaxval+leftminval);
end
return
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function contrast=getmincontrast(troughnumber,tmax,tmin,hmax,hmin)
% return the contrast of the peak with the number
testminpos=tmin(troughnumber);
testminval=hmin(troughnumber);
[leftmaxpos,leftmaxval]=getmaximumleftof(testminpos,tmax,tmin,hmax,hmin);
[rightmaxpos,rightmaxval]=getmaximumrightof(testminpos,tmax,tmin,hmax,hmin);
if isempty(leftmaxpos) && isempty(rightmaxpos) % if both are empty, its difficult
contrast=0;
elseif isempty(leftmaxpos) % if only the left is empty, take the right instead
contrast=(testminval-rightmaxval)/(testminval+rightmaxval);
elseif isempty(rightmaxpos) % if only the right is empty, take the left instead
contrast=(testminval-leftmaxval)/(testminval+leftmaxval);
else
mean_max_val=mean([leftmaxval rightmaxval]);
contrast=(testminval-mean_max_val)/(testminval+mean_max_val);
end
return
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function peakheight=getpeakheight(peaknumber,tmax,tmin,hmax,hmin)
testmaxpos=tmax(peaknumber);
testmaxval=hmax(peaknumber);
[leftminpos,leftminval]=getminimumleftof(testmaxpos,tmax,tmin,hmax,hmin);
[rightminpos,rightminval]=getminimumrightof(testmaxpos,tmax,tmin,hmax,hmin);
if isempty(leftminpos) && isempty(rightminpos) % if both are empty, its difficult
peakheight=testmaxval;
elseif isempty(leftminpos) % if only the left is empty, take the right instead
peakheight=testmaxval-rightminval;
elseif isempty(rightminpos) % if only the right is empty, take the left instead
peakheight=testmaxval-leftminval;
else
mean_min_val=mean([leftminval rightminval]);
peakheight=testmaxval-mean_min_val;
end
return
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function troughheight=gettroughheight(troughnumber,tmax,tmin,hmax,hmin)
testminpos=tmin(troughnumber);
testminval=hmin(troughnumber);
[leftmaxpos,leftmaxval]=getminimumleftof(testminpos,tmax,tmin,hmax,hmin);
[rightmaxpos,rightmaxval]=getminimumrightof(testminpos,tmax,tmin,hmax,hmin);
if isempty(leftmaxpos) && isempty(rightmaxpos) % if both are empty, its difficult
troughheight=abs(testminval);
elseif isempty(leftmaxpos) % if only the left is empty, take the right instead
troughheight=abs(testminval-rightmaxval);
elseif isempty(rightmaxpos) % if only the right is empty, take the left instead
troughheight=abs(testminval-leftmaxval);
else
mean_min_val=mean([leftmaxval rightmaxval]);
troughheight=abs(testminval-mean_min_val);
end
return
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function quality=getquality(peaknumber,tmax,tmin,hmax,hmin); % how wide the maximum is at the height of its surrounding minima
testmaxpos=tmax(peaknumber);
testmaxval=hmax(peaknumber);
[leftminpos,leftminval]=getminimumleftof(testmaxpos,tmax,tmin,hmax,hmin);
[rightminpos,rightminval]=getminimumrightof(testmaxpos,tmax,tmin,hmax,hmin);
if isempty(leftminpos) && isempty(rightminpos) % if both are empty, its difficult
quality=0;
elseif isempty(leftminpos) % if only the left is empty, take the right instead
quality=0;
elseif isempty(rightminpos) % if only the right is empty, take the left instead
quality=0;
else
diff_min_val=abs(leftminpos-rightminpos);
quality=testmaxval/diff_min_val;
end
return
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function quality=getminquality(troughknumber,tmax,tmin,hmax,hmin); % how wide the maximum is at the height of its surrounding maxima
testminpos=tmin(troughknumber);
testminval=hmin(troughknumber);
[leftmaxpos,leftmaxval]=getmaximumleftof(testminpos,tmax,tmin,hmax,hmin);
[rightmaxpos,rightmaxval]=getmaximumrightof(testminpos,tmax,tmin,hmax,hmin);
if isempty(leftmaxpos) && isempty(rightmaxpos) % if both are empty, its difficult
quality=0;
elseif isempty(leftmaxpos) % if only the left is empty, take the right instead
quality=0;
elseif isempty(rightmaxpos) % if only the right is empty, take the left instead
quality=0;
else
diff_min_val=abs(leftmaxval-rightmaxval);
quality=testminval/diff_min_val;
end
return
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function activity=getactivity(peaknumber,sig,tmax,tmin,hmax,hmin,latency); % sum of activity between the adjacent minima
testmaxpos=tmax(peaknumber);
testmaxval=hmax(peaknumber);
[leftminpos,leftminval]=getminimumleftof(testmaxpos,tmax,tmin,hmax,hmin);
[rightminpos,rightminval]=getminimumrightof(testmaxpos,tmax,tmin,hmax,hmin);
if isempty(leftminpos) && isempty(rightminpos) % if both are empty, its difficult
activity=0;
elseif isempty(leftminpos) % if only the left is empty, take the right instead
activity=0; % take the activity from the start of the signal instead
sr=1000/getsr(sig);
activity=sum(sig,latency,rightminpos)/sr;
elseif isempty(rightminpos) % if only the right is empty, take the left instead
activity=0;
else
sr=1000/getsr(sig);
activity=sum(sig,leftminpos,rightminpos)/sr;
end
return
