ImaGIN_spike_detect.m
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function [SpikeRate,MinLoc,MaxLoc]=ImaGIN_spike_detect(Data,Time,FreqSpike,ThreshData,ThreshCC,FlagDetrend,Coarse,FlagContinuous)
% -=============================================================================
% This function is part of the ImaGIN software:
% https://f-tract.eu/
%
% This software is distributed under the terms of the GNU General Public License
% as published by the Free Software Foundation. Further details on the GPLv3
% license can be found at http://www.gnu.org/copyleft/gpl.html.
%
% FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE AUTHORS
% DO NOT ASSUME ANY LIABILITY OR RESPONSIBILITY FOR ITS USE IN ANY CONTEXT.
%
% Copyright (c) 2000-2018 Inserm U1216
% =============================================================================-
%
% Authors: Olivier David
try
FlagContinuous;
catch
FlagContinuous=0;
end
%Data is a vector with artefact removed
%Downsample data
Time0=Time;
tmp=20*FreqSpike;
try
Coarse;
catch
Coarse=floor((1/(Time(2)-Time(1)))/tmp);
end
if isempty(Coarse)||Coarse==0
Coarse=floor((1/(Time(2)-Time(1)))/tmp);
end
Data=Data(1:Coarse:end);
Time=Time(1:Coarse:end);
TimeWindowWidth=1/FreqSpike;
TimeWindowWidth2=ceil(0.25*TimeWindowWidth/(Time(2)-Time(1)));
TimeWindowWidth=ceil(0.5*TimeWindowWidth/(Time(2)-Time(1)));
BigWin=20*TimeWindowWidth2;
%find local Maxima & Minima
MinLoc=zeros(size(Data));
MaxLoc=zeros(size(Data));
if ThreshData==0
ThreshData=std(Data);
end
if ~FlagDetrend
for i1=TimeWindowWidth2+1:length(Data)-TimeWindowWidth2-1
% if Data(i1)==Data(i1-1)&Data(i1)==Data(i1+1)
% if Data(i1)-Data(i1-2)<=0&Data(i1)-Data(i1+2)<=0&Data(i1)<-ThreshData&Data(i1)-Data(i1-TimeWindowWidth2)<=0&Data(i1)-Data(i1+TimeWindowWidth2)<=0
% MinLoc(i1)=1;
% end
% if Data(i1)-Data(i1-2)>=0&Data(i1)-Data(i1+2)>=0&Data(i1)>ThreshData&Data(i1)-Data(i1-TimeWindowWidth2)>=0&Data(i1)-Data(i1+TimeWindowWidth2)>=0
% MaxLoc(i1)=1;
% end
% else
% if Data(i1)-Data(i1-1)<=0&Data(i1)-Data(i1+1)<=0&Data(i1)<-ThreshData&Data(i1)-Data(i1-TimeWindowWidth2)<=0&Data(i1)-Data(i1+TimeWindowWidth2)<=0
% MinLoc(i1)=1;
% end
% if Data(i1)-Data(i1-1)>=0&Data(i1)-Data(i1+1)>=0&Data(i1)>ThreshData&Data(i1)-Data(i1-TimeWindowWidth2)>=0&Data(i1)-Data(i1+TimeWindowWidth2)>=0
% MaxLoc(i1)=1;
% end
% end
% if Data(i1)==Data(i1-1)&Data(i1)==Data(i1+1)
% if Data(i1)-Data(i1-2)<=0&Data(i1)-Data(i1+2)<=0&Data(i1)-Data(i1-TimeWindowWidth2)<=0&Data(i1)-Data(i1+TimeWindowWidth2)<=0
% MinLoc(i1)=1;
% end
% if Data(i1)-Data(i1-2)>=0&Data(i1)-Data(i1+2)>=0&Data(i1)-Data(i1-TimeWindowWidth2)>=0&Data(i1)-Data(i1+TimeWindowWidth2)>=0
% MaxLoc(i1)=1;
% end
% else
% if Data(i1)-Data(i1-1)<=0&Data(i1)-Data(i1+1)<=0&Data(i1)-Data(i1-TimeWindowWidth2)<=0&Data(i1)-Data(i1+TimeWindowWidth2)<=0
% MinLoc(i1)=1;
% end
% if Data(i1)-Data(i1-1)>=0&Data(i1)-Data(i1+1)>=0&Data(i1)-Data(i1-TimeWindowWidth2)>=0&Data(i1)-Data(i1+TimeWindowWidth2)>=0
% MaxLoc(i1)=1;
% end
% end
if Data(i1)==Data(i1-1)&Data(i1)==Data(i1+1)
if Data(i1)-Data(i1-2)<=0&Data(i1)-Data(i1+2)<=0
MinLoc(i1)=1;
end
if Data(i1)-Data(i1-2)>=0&Data(i1)-Data(i1+2)>=0
MaxLoc(i1)=1;
end
else
if Data(i1)-Data(i1-1)<=0&Data(i1)-Data(i1+1)<=0
MinLoc(i1)=1;
end
if Data(i1)-Data(i1-1)>=0&Data(i1)-Data(i1+1)>=0
MaxLoc(i1)=1;
end
end
end
else
% for i1=BigWin+1:length(Data)-BigWin-1
% win=i1-BigWin:i1+BigWin;
% tmp=detrend(Data(win),2);
% if tmp(BigWin+1)==tmp(BigWin+1-1)&tmp(BigWin+1)==tmp(BigWin+1+1)
% if tmp(BigWin+1)-tmp(BigWin+1-2)<=0&tmp(BigWin+1)-tmp(BigWin+1+2)<=0&tmp(BigWin+1)<-ThreshData&tmp(BigWin+1)-tmp(BigWin+1-TimeWindowWidth2)<=0&tmp(BigWin+1)-tmp(BigWin+1+TimeWindowWidth2)<=0
% MinLoc(i1)=1;
% end
% if tmp(BigWin+1)-tmp(BigWin+1-2)>=0&tmp(BigWin+1)-tmp(BigWin+1+2)>=0&tmp(BigWin+1)>ThreshData&tmp(BigWin+1)-tmp(BigWin+1-TimeWindowWidth2)>=0&tmp(BigWin+1)-tmp(BigWin+1+TimeWindowWidth2)>=0
% MaxLoc(i1)=1;
% end
% else
% if tmp(BigWin+1)-tmp(BigWin+1-1)<=0&tmp(BigWin+1)-tmp(BigWin+1+1)<=0&tmp(BigWin+1)<-ThreshData&tmp(BigWin+1)-tmp(BigWin+1-TimeWindowWidth2)<=0&tmp(BigWin+1)-tmp(BigWin+1+TimeWindowWidth2)<=0
% MinLoc(i1)=1;
% end
% if tmp(BigWin+1)-tmp(BigWin+1-1)>=0&tmp(BigWin+1)-tmp(BigWin+1+1)>=0&tmp(BigWin+1)>ThreshData&tmp(BigWin+1)-tmp(BigWin+1-TimeWindowWidth2)>=0&tmp(BigWin+1)-tmp(BigWin+1+TimeWindowWidth2)>=0
% MaxLoc(i1)=1;
% end
% end
% end
for i1=BigWin+1:length(Data)-BigWin-1
win=i1-BigWin:i1+BigWin;
tmp=detrend(Data(win),2);
if tmp(BigWin+1)==tmp(BigWin+1-1)&tmp(BigWin+1)==tmp(BigWin+1+1)
if tmp(BigWin+1)-tmp(BigWin+1-2)<=0&tmp(BigWin+1)-tmp(BigWin+1+2)<=0&tmp(BigWin+1)-tmp(BigWin+1-TimeWindowWidth2)<=0&tmp(BigWin+1)-tmp(BigWin+1+TimeWindowWidth2)<=0
MinLoc(i1)=1;
end
if tmp(BigWin+1)-tmp(BigWin+1-2)>=0&tmp(BigWin+1)-tmp(BigWin+1+2)>=0&tmp(BigWin+1)-tmp(BigWin+1-TimeWindowWidth2)>=0&tmp(BigWin+1)-tmp(BigWin+1+TimeWindowWidth2)>=0
MaxLoc(i1)=1;
end
else
if tmp(BigWin+1)-tmp(BigWin+1-1)<=0&tmp(BigWin+1)-tmp(BigWin+1+1)<=0&tmp(BigWin+1)-tmp(BigWin+1-TimeWindowWidth2)<=0&tmp(BigWin+1)-tmp(BigWin+1+TimeWindowWidth2)<=0
MinLoc(i1)=1;
end
if tmp(BigWin+1)-tmp(BigWin+1-1)>=0&tmp(BigWin+1)-tmp(BigWin+1+1)>=0&tmp(BigWin+1)-tmp(BigWin+1-TimeWindowWidth2)>=0&tmp(BigWin+1)-tmp(BigWin+1+TimeWindowWidth2)>=0
MaxLoc(i1)=1;
end
end
end
end
MinLoc=find(MinLoc);
MaxLoc=find(MaxLoc);
%Keep only large peaks
MinLoc2=zeros(size(MinLoc));
n=0;
for i1=1:length(MinLoc)
% tmp=MaxLoc(find(max(find(MaxLoc<MinLoc(i1)))));
% if Data(tmp)-Data(MinLoc(i1))>ThreshData
% n=n+1;
% MinLoc2(n)=MinLoc(i1);
% else
% tmp=MaxLoc(find(min(find(MaxLoc>MinLoc(i1)))));
% if Data(tmp)-Data(MinLoc(i1))>ThreshData
% n=n+1;
% MinLoc2(n)=MinLoc(i1);
% end
% end
tmp1=MaxLoc(max(find(MaxLoc<MinLoc(i1))));
tmp2=MaxLoc(min(find(MaxLoc>MinLoc(i1))));
if ~isempty(tmp1)&&~isempty(tmp2)
if Data(tmp1)-Data(MinLoc(i1))>ThreshData && Data(tmp2)-Data(MinLoc(i1))>ThreshData
n=n+1;
MinLoc2(n)=MinLoc(i1);
end
end
end
MinLoc2=MinLoc2(1:n);
MaxLoc2=zeros(size(MaxLoc));
n=0;
for i1=1:length(MaxLoc)
% tmp=MinLoc(find(max(find(MinLoc<MaxLoc(i1)))));
% if -Data(tmp)+Data(MaxLoc(i1))>ThreshData
% n=n+1;
% MaxLoc2(n)=MaxLoc(i1);
% else
% tmp=MinLoc(find(min(find(MinLoc>MaxLoc(i1)))));
% if -Data(tmp)+Data(MaxLoc(i1))>ThreshData
% n=n+1;
% MaxLoc2(n)=MaxLoc(i1);
% end
% end
tmp1=MinLoc(max(find(MinLoc<MaxLoc(i1))));
tmp2=MinLoc(min(find(MinLoc>MaxLoc(i1))));
if ~isempty(tmp1)&&~isempty(tmp2)
if -Data(tmp1)+Data(MaxLoc(i1))>ThreshData && -Data(tmp2)+Data(MaxLoc(i1))>ThreshData
n=n+1;
MaxLoc2(n)=MaxLoc(i1);
end
end
end
MaxLoc2=MaxLoc2(1:n);
MaxLoc=MaxLoc2;
MinLoc=MinLoc2;
%try to remove non spikes first by assuming a standard shape
MinLoc2=zeros(size(MinLoc));
n=0;
for i1=1:length(MinLoc)
tmp=setdiff(find(abs(MinLoc-MinLoc(i1))<=TimeWindowWidth),i1);
if isempty(tmp)|Data(MinLoc(i1))<=min(Data(MinLoc(tmp)))
if i1>1
if Data(MinLoc(i1))~=Data(MinLoc(i1-1))
n=n+1;
MinLoc2(n)=MinLoc(i1);
end
else
n=n+1;
MinLoc2(n)=MinLoc(i1);
end
end
end
MinLoc2=MinLoc2(1:n);
MaxLoc2=zeros(size(MaxLoc));
n=0;
for i1=1:length(MaxLoc)
tmp=setdiff(find(abs(MaxLoc-MaxLoc(i1))<=TimeWindowWidth),i1);
if isempty(tmp)|Data(MaxLoc(i1))>=max(Data(MaxLoc(tmp)))
if i1>1
if Data(MaxLoc(i1))~=Data(MaxLoc(i1-1))
n=n+1;
MaxLoc2(n)=MaxLoc(i1);
end
else
n=n+1;
MaxLoc2(n)=MaxLoc(i1);
end
end
end
MaxLoc2=MaxLoc2(1:n);
figure
plot(Time,Data)
hold on
line([Time(MinLoc);Time(MinLoc)],[min(Data(:));max(Data(:))]*ones(1,length(MinLoc)),'color','k')
line([Time(MinLoc2);Time(MinLoc2)],[min(Data(:));max(Data(:))]*ones(1,length(MinLoc2)),'color','r')
hold off
MaxLoc=MaxLoc2;
MinLoc=MinLoc2;
MaxLoc=MaxLoc(find(MaxLoc>TimeWindowWidth&MaxLoc<length(Data)-TimeWindowWidth));
MinLoc=MinLoc(find(MinLoc>TimeWindowWidth&MinLoc<length(Data)-TimeWindowWidth));
if FlagContinuous
%try to fill gaps and make local corrections assuming continuous
%stimulation
ISI=mean(diff(MaxLoc));
ISIerror=0.05*ISI;
for i0=1:2 %Two passes
MaxLocNew=[];
for i1=2:length(MaxLoc)-1;
if MaxLoc(i1+1)-MaxLoc(i1)>2*(ISI-ISIerror)
MaxLocNew=[MaxLocNew MaxLoc(i1)+round(ISI)];
end
if MaxLoc(i1)-MaxLoc(i1-1)<ISI-ISIerror&MaxLoc(i1+1)-MaxLoc(i1)>ISI+ISIerror;
MaxLoc(i1)=round((MaxLoc(i1-1)+MaxLoc(i1+1))/2);
elseif MaxLoc(i1)-MaxLoc(i1-1)>ISI+ISIerror&MaxLoc(i1+1)-MaxLoc(i1)<ISI-ISIerror;
MaxLoc(i1)=round((MaxLoc(i1-1)+MaxLoc(i1+1))/2);
end
end
MaxLoc=sort([MaxLoc MaxLocNew]);
end
ISI=mean(diff(MinLoc));
ISIerror=0.05*ISI;
for i0=1:2 %Two passes
MinLocNew=[];
for i1=2:length(MinLoc)-1;
if MinLoc(i1+1)-MinLoc(i1)>2*(ISI-ISIerror)
MinLocNew=[MinLocNew MinLoc(i1)+round(ISI)];
end
if MinLoc(i1)-MinLoc(i1-1)<ISI-ISIerror&MinLoc(i1+1)-MinLoc(i1)>ISI+ISIerror;
MinLoc(i1)=round((MinLoc(i1-1)+MinLoc(i1+1))/2);
elseif MinLoc(i1)-MinLoc(i1-1)>ISI+ISIerror&MinLoc(i1+1)-MinLoc(i1)<ISI-ISIerror;
MinLoc(i1)=round((MinLoc(i1-1)+MinLoc(i1+1))/2);
end
end
MinLoc=sort([MinLoc MinLocNew]);
end
end
%try to remove non spikes first by constructing a template
if ~isempty(ThreshCC)
TemplateMax=zeros(1,2*TimeWindowWidth+1);
for i1=1:length(MaxLoc)
TemplateMax=TemplateMax+Data(MaxLoc(i1)+[-TimeWindowWidth:TimeWindowWidth]);
end
TemplateMax=TemplateMax/length(MaxLoc);
TemplateMin=zeros(1,2*TimeWindowWidth+1);
for i1=1:length(MinLoc)
TemplateMin=TemplateMin+Data(MinLoc(i1)+[-TimeWindowWidth:TimeWindowWidth]);
end
TemplateMin=TemplateMin/length(MinLoc);
ok=1;
n0=0;
while ok
n0=n0+1;
C=zeros(1,length(MaxLoc));
for i1=1:length(MaxLoc)
cc=corrcoef(Data(MaxLoc(i1)+[-TimeWindowWidth:TimeWindowWidth]),TemplateMax);
C(i1)=cc(2);
end
ThreshCCInit=ThreshCC;
if ThreshCCInit==0 && n0==1
y=ImaGIN_kMeansCluster(C',2);
c=zeros(1,2);
c(1)=mean(y(find(y(:,end)==1)));
c(2)=mean(y(find(y(:,end)==2)));
% ThreshCC=(c(1)+c(2))/2;
ThreshCC=min(c);
end
N=find(C>=ThreshCC);
if length(N)~=length(C)
MaxLoc=MaxLoc(N);
TemplateMax=zeros(1,2*TimeWindowWidth+1);
for i1=1:length(MaxLoc)
TemplateMax=TemplateMax+Data(MaxLoc(i1)+[-TimeWindowWidth:TimeWindowWidth]);
end
TemplateMax=TemplateMax/length(MaxLoc);
% plot(TemplateMax);drawnow;length(MaxLoc)
else
ok=0;
end
end
ok=1;
n0=0;
while ok
n0=n0+1;
C=zeros(1,length(MinLoc));
for i1=1:length(MinLoc)
cc=corrcoef(Data(MinLoc(i1)+[-TimeWindowWidth:TimeWindowWidth]),TemplateMin);
C(i1)=cc(2);
end
ThreshCCInit=ThreshCC;
if ThreshCCInit==0 && n0==1
y=ImaGIN_kMeansCluster(C',2);
c=zeros(1,2);
c(1)=mean(y(find(y(:,end)==1)));
c(2)=mean(y(find(y(:,end)==2)));
% ThreshCC=(c(1)+c(2))/2;
ThreshCC=min(c);
end
N=find(C>=ThreshCC);
if length(N)~=length(C)
MinLoc=MinLoc(N);
TemplateMin=zeros(1,2*TimeWindowWidth+1);
for i1=1:length(MinLoc)
TemplateMin=TemplateMin+Data(MinLoc(i1)+[-TimeWindowWidth:TimeWindowWidth]);
end
TemplateMin=TemplateMin/length(MinLoc);
% plot(TemplateMin);drawnow;length(MinLoc)
else
ok=0;
end
end
% figure
% plot(Time,Data)
% hold on
% line([Time(MinLoc2);Time(MinLoc2)],[min(Data(:));max(Data(:))]*ones(1,length(MinLoc2)),'color','r')
% line([Time(MinLoc);Time(MinLoc)],[min(Data(:));max(Data(:))]*ones(1,length(MinLoc)),'color','k')
% hold off
end
%Compute instantaneous spike rate
SpikeRateMax=zeros(size(Data));
for i1=1:length(MaxLoc)-1
SpikeRateMax(MaxLoc(i1):MaxLoc(i1+1))=1/((Time(2)-Time(1))*(MaxLoc(i1+1)-MaxLoc(i1)));
end
SpikeRateMin=zeros(size(Data));
for i1=1:length(MinLoc)-1
SpikeRateMin(MinLoc(i1):MinLoc(i1+1))=1/((Time(2)-Time(1))*(MinLoc(i1+1)-MinLoc(i1)));
end
% SpikeRate=mean([SpikeRateMax;SpikeRateMin]);
SpikeRate=max([SpikeRateMax;SpikeRateMin],[],1);
if Coarse>1
SpikeRate=interp1(Time,SpikeRate,Time0);
MinLoc=MinLoc*Coarse;
MaxLoc=MaxLoc*Coarse;
end