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Copy pathnewest_only_ripple_nl.m
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newest_only_ripple_nl.m
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function [sig1_nl,sig2_nl,ripple_nl,carajo_nl,veamos_nl,CHTM2,timeasleep2,RipFreq3]=newest_only_ripple_nl
%{
LOAD DATA, easy and quick.
timeasleep2=sum(cellfun('length',V9_nl))*(1/1000)/60; % In minutes
RipFreq3=sum(s17_nl)/(timeasleep2*(60));
The V signals are the monopolar recordings of the 4 channels.
The S signals are the bipolar recordings which have been substracted the
reference signal (V6)
%}
%Load Bipolar signals
S17=load('S17.mat');
S17_nl=S17.S17;
S12=load('S12.mat');
S12_nl=S12.S12;
S9=load('S9.mat');
S9_nl=S9.S9;
%Load Monopolar signals
V17=load('V17.mat');
V17_nl=V17.V17;
V12=load('V12.mat');
V12_nl=V12.V12;
V9=load('V9.mat');
V9_nl=V9.V9;
V6=load('V6.mat');
V6_nl=V6.V6;
'Loaded channels'
% if art==1
%
% % Removing artifacts.
% S9n=cell(length(V6),1);
% S12n=cell(length(V6),1);
% S17n=cell(length(V6),1);
%
% B9n=cell(length(V6),1);
% B12n=cell(length(V6),1);
% B17n=cell(length(V6),1);
%
% V6n=cell(length(V6),1);
% V9n=cell(length(V6),1);
% V12n=cell(length(V6),1);
% V17n=cell(length(V6),1);
%
% R6n=cell(length(V6),1);
% R9n=cell(length(V6),1);
% R12n=cell(length(V6),1);
% R17n=cell(length(V6),1);
%
% for i=1:length(V6)
% %Original Bipolar
% pro=S9{i};
% S9n{i,1}=outlier(pro,2.5);
% pro=S12{i};
% S12n{i,1}=outlier(pro,2.5);
% pro=S17{i};
% S17n{i,1}=outlier(pro,1.5);
%
% %Bipolar after ICA
% pro=B9{i};
% B9n{i,1}=outlier(pro,2.5);
% pro=B12{i};
% B12n{i,1}=outlier(pro,2.5);
% pro=B17{i};
% B17n{i,1}=outlier(pro,2.5);
%
% %Original Monopolar
% pro=V6{i};
% V6n{i,1}=outlier(pro,2.5);
% pro=V9{i};
% V9n{i,1}=outlier(pro,2.5);
% pro=V12{i};
% V12n{i,1}=outlier(pro,2.5);
% pro=V17{i};
% V17n{i,1}=outlier(pro,1.5);
%
% %Monopolar after ICA
% pro=R6{i};
% R6n{i,1}=outlier(pro,2.5);
% pro=R9{i};
% R9n{i,1}=outlier(pro,2.5);
% pro=R12{i};
% R12n{i,1}=outlier(pro,2.5);
% pro=R17{i};
% R17n{i,1}=outlier(pro,2.5);
%
% end
%
% S9=S9n;
% S12=S12n;
% S17=S17n;
%
% B9=B9n;
% B12=B12n;
% B17=B17n;
%
% V6=V6n;
% V9=V9n;
% V12=V12n;
% V17=V17n;
%
% R6=R6n;
% R9=R9n;
% R12=R12n;
% R17=R17n;
%
% 'Artifact detection performed'
% end
%Band pass filter design:
fn=1000; % New sampling frequency.
Wn1=[100/(fn/2) 300/(fn/2)]; % Cutoff=500 Hz
[b1,a1] = butter(3,Wn1,'bandpass'); %Filter coefficients
% Bandpass filtering:
% % % %Declare empty cell arrays
% % % Mono6_nl=cell(length(S9_nl),1);
% % % Mono9_nl=cell(length(S9_nl),1);
% % % Mono12_nl=cell(length(S9_nl),1);
% % % Mono17_nl=cell(length(S9_nl),1);
% % %
% % % Bip9_nl=cell(length(S9_nl),1);
% % % Bip12_nl=cell(length(S9_nl),1);
% % % Bip17_nl=cell(length(S9_nl),1);
% % %
% % % %Filtering
% % % for i=1:length(S9_nl)
% % %
% % % Bip9_nl{i}=filtfilt(b1,a1,S9_nl{i});
% % % Bip12_nl{i}=filtfilt(b1,a1,S12_nl{i});
% % % Bip17_nl{i}=filtfilt(b1,a1,S17_nl{i});
% % %
% % % Mono6_nl{i}=filtfilt(b1,a1,V6_nl{i});
% % % Mono9_nl{i}=filtfilt(b1,a1,V9_nl{i});
% % % Mono12_nl{i}=filtfilt(b1,a1,V12_nl{i});
% % % Mono17_nl{i}=filtfilt(b1,a1,V17_nl{i});
% % %
% % % end
Mono6_nl=cellfun(@(equis) filtfilt(b1,a1,equis), V6_nl ,'UniformOutput',false);
Mono9_nl=cellfun(@(equis) filtfilt(b1,a1,equis), V9_nl ,'UniformOutput',false);
Mono12_nl=cellfun(@(equis) filtfilt(b1,a1,equis), V12_nl ,'UniformOutput',false);
Mono17_nl=cellfun(@(equis) filtfilt(b1,a1,equis), V17_nl ,'UniformOutput',false);
Bip9_nl=cellfun(@(equis) filtfilt(b1,a1,equis), S9_nl ,'UniformOutput',false);
Bip12_nl=cellfun(@(equis) filtfilt(b1,a1,equis), S12_nl ,'UniformOutput',false);
Bip17_nl=cellfun(@(equis) filtfilt(b1,a1,equis), S17_nl ,'UniformOutput',false);
'Bandpass performed'
s17_nl=nan(length(S9_nl),1);
swr17_nl=cell(length(S9_nl),3);
s217_nl=nan(length(S9_nl),1);
swr217_nl=cell(length(S9_nl),3);
rep=5; %Number of thresholds+1
%thr=140;
% % thr=linspace(max(signal)/(2.^(4)),max(signal),rep);
% % thr=sort(thr,'descend');
%thr=180;
%%
%CHTM2=nan(length(S9_nl),1);
chtm2=median(cellfun(@max,Bip17_nl))*(1/0.195); %Minimum maximum value among epochs.
CHTM2=floor([chtm2 chtm2/2 chtm2/4 chtm2/8 chtm2/16]);
%Scale magnitude,create time vector
signal_nl=cellfun(@(equis) times((1/0.195), equis) ,Bip17_nl,'UniformOutput',false);
signal2_nl=cellfun(@(equis) times((1/0.195), equis) ,Mono17_nl,'UniformOutput',false);
ti_nl=cellfun(@(equis) linspace(0, length(equis)-1,length(equis))*(1/fn) ,signal_nl,'UniformOutput',false);
%Find ripples
%for k=1:rep-1
for k=1:rep-2
[S2x_nl,E2x_nl,M2x_nl] =cellfun(@(equis1,equis2) findRipplesLisa(equis1, equis2.', CHTM2(k+1), (CHTM2(k+1))*(1/2), [] ), signal_nl,ti_nl,'UniformOutput',false);
swr17_nl(:,:,k)=[S2x_nl E2x_nl M2x_nl];
s17_nl(:,k)=cellfun('length',S2x_nl);
k
end
% % % for i=1:length(S9_nl)
% % %
% % % signal_nl=Bip17_nl{i}*(1/0.195);
% % % signal2_nl=Mono17_nl{i}*(1/0.195);
% % %
% % % % signal_array=[Mono17{i} Mono12{i} Mono9{i} Mono6{i}];
% % % % signal_array2=[V17{i} V12{i} V9{i} V6{i}];
% % % % signal_arrayQ=[envelope1(Mono17{i}) envelope1(Mono12{i}) envelope1(Mono9{i}) envelope1(Mono6{i})];
% % % signal_array_nl=[Mono17_nl{i} Mono12_nl{i} Mono9_nl{i}];
% % % signal_array2_nl=[V17_nl{i} V12_nl{i} V9_nl{i} ];
% % % %signal_arrayQ=[envelope1(Mono17{i}) envelope1(Mono12{i}) envelope1(Mono9{i})];
% % %
% % %
% % % ti_nl=(0:length(signal_nl)-1)*(1/fn); %IN SECONDS
% % %
% % % %thr=linspace(max(signal)/(2.^(rep-1)),max(signal),rep);
% % % %thr=sort(thr,'descend');
% % %
% % % %Thresholds for Bipolar recording of Hippocampus.
% % % % % % % % % % % % % % thr_nl=[max(signal_nl) max(signal_nl)/2 max(signal_nl)/4 max(signal_nl)/8 max(signal_nl)/16];
% % % % % % % % % % % % % % thr_nl=round(thr_nl);
% % %
% % % % %Thresholds for Monopolar recording of Hippocampus.
% % % % thr2=[max(signal2) max(signal2)/2 max(signal2)/4 max(signal2)/8 max(signal2)/16];
% % % % thr2=round(thr2);
% % %
% % % %[thr]=opt_thr(signal,thr);
% % % % thr=max(signal)/2
% % % % [S1, E1, M1] = findRipplesLisa(signal, ti.', thr() , (thr(1))*(1/2), []);
% % % % [S2, E2, M2] = findRipplesLisa(signal, ti.', thr , (thr)*(1/2), []);
% % % % [S3, E3, M3] = findRipplesLisa(signal, ti.', thr , (thr)*(1/2), []);
% % % % [S4, E4, M4] = findRipplesLisa(signal, ti.', thr , (thr)*(1/2), []);
% % % % [S5, E5, M5] = findRipplesLisa(signal, ti.', thr , (thr)*(1/2), []);
% % % for k=1:rep-1
% % % % error('stop here')
% % %
% % % %[S_nl{k}, E_nl{k}, M_nl{k}] = findRipplesLisa(signal_nl, ti_nl.', thr_nl(k+1) , (thr_nl(k+1))*(1/2), []);
% % % [S_nl{k}, E_nl{k}, M_nl{k}] = findRipplesLisa(signal_nl, ti_nl.', CHTM2(k+1) , (CHTM2(k+1))*(1/2), []);
% % %
% % % % [no_rip]=no_ripples(ti,S{k},E{k})
% % % % [no_rip(:,k)]=no_ripples(ti,S{k},E{k})
% % %
% % % %K=4 has shown to give too many ripples and not large enough no ripple
% % % %windows.
% % %
% % %
% % %
% % % % [pks]=no_ripples(ti,S{k},E{k},ro);
% % %
% % % % ch=sig1(1:2:7);
% % % % cch=ch{1};
% % %
% % % s17_nl(i,k)=length(M_nl{k});
% % % swr17_nl{i,1,k}=S_nl{k};
% % % swr17_nl{i,2,k}=E_nl{k};
% % % swr17_nl{i,3,k}=M_nl{k};
% % %
% % % %
% % % % [S2{k}, E2{k}, M2{k}] = findRipplesLisa(signal2, ti.', thr2(k+1) , (thr2(k+1))*(1/2), []);
% % % % s217(i,k)=length(M2{k});
% % % % swr217{i,1,k}=S2{k};
% % % % swr217{i,2,k}=E2{k};
% % % % swr217{i,3,k}=M2{k};
% % %
% % %
% % % end
% % %
% % % % s17(i)=length(M);
% % % % swr17{i,1}=S;
% % % % swr17{i,2}=E;
% % % % swr17{i,3}=M;
% % %
% % % % ti=(0:length(signal2)-1)*(1/fn); %IN SECONDS
% % % % % [thr]=opt_thr(signal,thr);
% % % % [S2, E2, M2] = findRipplesLisa(signal2, ti.', thr , (thr)*(1/3), []);
% % % % s217(i)=length(M2);
% % % % swr217{i,1}=S2;
% % % % swr217{i,2}=E2;
% % % % swr217{i,3}=M2;
% % %
% % %
% % % % i/length(S9)
% % % disp(strcat('Progress:',num2str(round(i*100/length(S9_nl))),'%'))
% % % pause(.01)
% % % end
timeasleep2=sum(cellfun('length',V9_nl))*(1/1000)/60; % In minutes
RipFreq3=sum(s17_nl)/(timeasleep2*(60));
ripple3=sum(s17_nl); %When using same threshold per epoch.
%%
%error('Stop here please')
% Windowing
for ind=1:size(s17_nl,2)
veamos_nl{:,ind}=find(s17_nl(:,ind)~=0); %Epochs with ripples detected
carajo_nl{:,:,ind}=swr17_nl(veamos_nl{:,ind},:,ind);
% veamos2{:,ind}=find(s217(:,ind)~=0); %Epochs with ripples detected
% carajo2{:,:,ind}=swr217(veamos2{:,ind},:,ind);
end
sig1_nl=cell(7,1);
sig1_nl{1}=Mono17_nl;
sig1_nl{2}=Bip17_nl;
sig1_nl{3}=Mono12_nl;
sig1_nl{4}=Bip12_nl;
sig1_nl{5}=Mono9_nl;
sig1_nl{6}=Bip9_nl;
sig1_nl{7}=Mono6_nl;
sig2_nl=cell(7,1);
sig2_nl{1}=V17_nl;
sig2_nl{2}=S17_nl;
sig2_nl{3}=V12_nl;
% sig2{4}=R12;
sig2_nl{4}=S12_nl;
%sig2{6}=SSS12;
sig2_nl{5}=V9_nl;
% sig2{7}=R9;
sig2_nl{6}=S9_nl;
%sig2{10}=SSS9;
sig2_nl{7}=V6_nl;
% ripple=length(M);
%Number of ripples per threshold.
ripple_nl=sum(s17_nl);
end