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Comudulogramas4_speads.m
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%% Before starting, load everything
clear all
close all
files=Data_Listing();
lowf1=log(-0.01);
lowf2=4;
highf1=log(0.8);
highf2=20;
fstep=0.50;
n_fs=400;
number=20;
freq_data.phasef1=lowf1;
freq_data.phasef2=highf1;
freq_data.ampf1=lowf2;
freq_data.ampf2=highf2;
freq_data.sf=n_fs;
freq_data.ampstep=fstep;
freq_data.phasestep=logspace(-0.01,0.8,number);
%% Just for rat 14566
load('1CA1','-mat');
load('1EC1','-mat');
load('1EC2','-mat');
rat=1;
area={CA1,EC1,EC2};
lfp={Days(CA1),Days(EC1),Days(EC2)};
name=['1CA1';'1EC1';'1EC2'];
totaltime=[20,20,42];
non_mov_time=6;
totaltime=20;
jump_time=5*n_fs;
protocol={'A','B','C'};
[n m]=size(area);
for a=2:2
clear matrix5 matrix6 matrix7 matrix8 matrix9 matrix10 matrix11 matrix12
prot=3;
count=1;
for i=1:length(lfp{a})
session_number=RecordingSession(files,rat,area{a},lfp{a}(i,:),protocol{prot});
if length(session_number)
for se=1:length(session_number)
order=Wished_Register_Order(area{a},lfp{a}(i,:));
register=Rat_Register(files,area{a},rat,order);
[eeg,fs]=ReadEEG(register,session_number(se));
[qual4,qual,qual2]=egf_theta_quality_2016(eeg);
if qual>0.5
n_fs=floor(fs/floor(fs/n_fs));
eeg=resample(eeg,1,floor(fs/n_fs));
pos=Loading_Pos(register,session_number(se));
tf = isfield(pos.data, 'log');
if ~(prot=='C') tf=1; end
if tf==1
[sr sl]=ReadStartTime(pos);
s1=sr-non_mov_time;
s2=sl-non_mov_time;
[srr err srl erl]=RestingTime(pos,totaltime,non_mov_time);
s1=floor(s1*n_fs)+1;
s2=floor(s2*n_fs)+1;
er=floor((sr+totaltime)*n_fs);
el=floor((sl+totaltime)*n_fs);
srr=floor(srr*n_fs)+1;
err=floor(err*n_fs);
srl=floor(srl*n_fs)+1;
erl=floor(erl*n_fs);
sr=floor(sr*n_fs);
sl=floor(sl*n_fs);
%for speed=1:4
% for track=1:length(sr)
% t=floor(sr(i)/400*50);
% v(speed,:,track)=pos.data.vx(t+(speed-1)*5*50:t+speed*5*50);
% end
%end
Y1=[];Y2=[];Y3=[];Y4=[];Y5=[];Y6=[];Y7=[];Y8=[];Y9=[];Y10=[];Y11=[];Y12=[];
for trial=1:length(s1)-1
Y1=[Y1,eeg(srr(trial):err(trial))'];% resting period
Y2=[Y2,eeg(srl(trial):erl(trial))'];
Y3=[Y3,eeg(s1(trial):sr(trial))'];%expecting period
Y4=[Y4,eeg(s2(trial):sl(trial))'];
Y5=[Y5,eeg(sr(trial):sr(trial)+jump_time)'];%running1
Y6=[Y6,eeg(sr(trial)+jump_time:sr(trial)+2*jump_time)'];
Y7=[Y7,eeg(sr(trial)+2*jump_time:sr(trial)+3*jump_time)'];
Y8=[Y8,eeg(sr(trial)+3*jump_time:sr(trial)+4*jump_time)'];
Y9=[Y9,eeg(sl(trial):sl(trial)+jump_time)'];%running1
Y10=[Y10,eeg(sl(trial)+jump_time:sl(trial)+2*jump_time)'];
Y11=[Y11,eeg(sl(trial)+2*jump_time:sl(trial)+3*jump_time)'];
Y12=[Y12,eeg(sl(trial)+3*jump_time:sl(trial)+4*jump_time)'];
end
figure(i)
%subplot(2,6,1)
%como1=comodulogram(Y1,lowf2:fstep:highf2,lowf1:fstep/2:highf1,n_fs);
%COMODOplot(lowf2:fstep:highf2,lowf1:fstep/2:highf1,como1);
%subplot(2,6,7)
%como2=comodulogram(Y2,lowf2:fstep:highf2,lowf1:fstep/2:highf1,n_fs);
%COMODOplot(lowf2:fstep:highf2,lowf1:fstep/2:highf1,como2);
%subplot(2,5,1)
%como3=comodulogram(Y3,lowf2:fstep:highf2,lowf1:fstep/2:highf1,n_fs);
%COMODOplot(lowf2:fstep:highf2,lowf1:fstep/2:highf1,como3);
%subplot(2,5,6)
%como4=comodulogram(Y4,lowf2:fstep:highf2,lowf1:fstep/2:highf1,n_fs);
%COMODOplot(lowf2:fstep:highf2,lowf1:fstep/2:highf1,como4);
subplot(2,2,1)
como5=comodulogram([Y5,Y12],lowf2:fstep:highf2,logspace(-0.01,0.8,number),n_fs,'FilterMethod','wavelet','FilterWidth',[5 3]);
COMODOplot(lowf2:fstep:highf2,logspace(-0.01,0.8,number),como5);
colormap(jet)
subplot(2,2,2)
como6=comodulogram([Y6,Y11],lowf2:fstep:highf2,logspace(-0.01,0.8,number),n_fs,'FilterMethod','wavelet','FilterWidth',[5 3]);
COMODOplot(lowf2:fstep:highf2,logspace(-0.01,0.8,number),como6);
colormap(jet)
subplot(2,2,3)
como7=comodulogram([Y7,Y10],lowf2:fstep:highf2,logspace(-0.01,0.8,number),n_fs,'FilterMethod','wavelet','FilterWidth',[5 3]);
COMODOplot(lowf2:fstep:highf2,logspace(-0.01,0.8,number),como7);
colormap(jet)
subplot(2,2,4)
como8=comodulogram([Y8,Y9],lowf2:fstep:highf2,logspace(-0.01,0.8,number),n_fs,'FilterMethod','wavelet','FilterWidth',[5 3]);
COMODOplot(lowf2:fstep:highf2,logspace(-0.01,0.8,number),como8);
colormap(jet)
%subplot(2,4,5)
%como9=comodulogram(Y12,lowf2:fstep:highf2,lowf1:fstep/2:highf1,n_fs,'FilterMethod','wavelet');
%COMODOplot(lowf2:fstep:highf2,lowf1:fstep/2:highf1,como9);
%colormap(jet)
%subplot(2,4,6)
%como10=comodulogram(Y11,lowf2:fstep:highf2,lowf1:fstep/2:highf1,n_fs,'FilterMethod','wavelet');
%COMODOplot(lowf2:fstep:highf2,lowf1:fstep/2:highf1,como10);
%colormap(jet)
%subplot(2,4,7)
%como11=comodulogram(Y10,lowf2:fstep:highf2,lowf1:fstep/2:highf1,n_fs,'FilterMethod','wavelet');
%COMODOplot(lowf2:fstep:highf2,lowf1:fstep/2:highf1,como11);
%colormap(jet)
%subplot(2,4,8)
%como12=comodulogram(Y9,lowf2:fstep:highf2,lowf1:fstep/2:highf1,n_fs,'FilterMethod','wavelet');
%COMODOplot(lowf2:fstep:highf2,lowf1:fstep/2:highf1,como12);
%colormap(jet)
%como=[como5,como6,como7,como8,como9,como10,como11,como12];
como=[como5,como6,como7,como8];
color=[max(max(como))];
for j=1:4
subplot(2,2,j)
caxis([0 color])
end
saveas(i,strcat('/home/melisa/Escritorio/Melisa/Doctorado/BandsCoupling/10-05/Speeds2/',name(a,:),'_',lfp{a}(i,:)),'png')
close(i)
matrix5(count,:,:)=como5;matrix6(count,:,:)=como6;
matrix7(count,:,:)=como7;matrix8(count,:,:)=como8;
%matrix9(count,:,:)=como9;matrix10(count,:,:)=como10;
%matrix11(count,:,:)=como11;matrix12(count,:,:)=como12;
count=count+1;
end
end
end
end
end
[n m l]=size(matrix5);
figure(a)
subplot(2,2,1)
COMODOplot(lowf2:fstep:highf2,logspace(-0.01,0.8,number),reshape(mean(matrix5),[m l]));
colormap(jet)
subplot(2,2,2)
COMODOplot(lowf2:fstep:highf2,logspace(-0.01,0.8,number),reshape(mean(matrix6),[m l]));
colormap(jet)
subplot(2,2,3)
COMODOplot(lowf2:fstep:highf2,logspace(-0.01,0.8,number),reshape(mean(matrix7),[m l]));
colormap(jet)
subplot(2,2,4)
COMODOplot(lowf2:fstep:highf2,logspace(-0.01,0.8,number),reshape(mean(matrix8),[m l]));
colormap(jet)
%subplot(2,4,5)
%COMODOplot(lowf2:fstep:highf2,lowf1:fstep/2:highf1,reshape(mean(matrix9),[m l]));
%subplot(2,4,6)
%COMODOplot(lowf2:fstep:highf2,lowf1:fstep/2:highf1,reshape(mean(matrix10),[m l]));
%subplot(2,4,7)
%COMODOplot(lowf2:fstep:highf2,lowf1:fstep/2:highf1,reshape(mean(matrix11),[m l]));
%subplot(2,4,8)
%COMODOplot(lowf2:fstep:highf2,lowf1:fstep/2:highf1,reshape(mean(matrix12),[m l]));
como=[mean(matrix5),mean(matrix6),mean(matrix7),mean(matrix8)];
color=[max(max(como))];
for j=1:4
subplot(2,2,j)
caxis([0 color])
end
nombre=strcat('/home/melisa/Escritorio/Melisa/Doctorado/BandsCoupling/10-05/Speeds2/',int2str(prot),'_',name(a,:),'_COMODO_mean_speeds');
saveas(a,nombre,'png')
%save(nombre,'matrix5','matrix6','matrix7','matrix8','matrix9','matrix10','matrix11','matrix12','-mat')
save(nombre,'matrix5','matrix6','matrix7','matrix8','freq_data','-mat')
end
%% 14570
load('3CA1','-mat');
load('3EC1','-mat');
load('3EC2','-mat');
rat=3;
area={CA1_3,EC1_3,EC2_3};
lfp={Days(CA1_3),Days(EC1_3),Days(EC2_3)};
name=['3CA1';'3EC1';'3EC2'];
[n m]=size(area);
totaltime=[20,20,42];
non_mov_time=6;
protocol={'A','B','C'};
[n m]=size(area);
[n m]=size(area);
prot='C';
non_mov_time=6;
fast_time=6;
slow_time=36;
lowf1=1;
lowf2=6;
highf1=6;
highf2=20;
fstep=0.5;
filter_width=[0.5 0.25];
n_fs=400;
a=2;
clear matrix1 matrix2 matrix3 matrix4
prot=3;
count=1;
for i=21:length(lfp{a})
session_number=RecordingSession(files,rat,area{a},lfp{a}(i,:),protocol{prot});
if length(session_number)
for se=1:length(session_number)
order=Wished_Register_Order(area{a},lfp{a}(i,:));
register=Rat_Register(files,area{a},rat,order);
[eeg,fs]=ReadEEG(register,session_number(se));
[qual4,qual,qual2]=egf_theta_quality_2016(eeg);
if qual>0.5
n_fs=floor(fs/floor(fs/n_fs));
eeg=resample(eeg,1,floor(fs/n_fs));
pos=Loading_Pos(register,session_number(se));
tf = isfield(pos.data, 'log');
if ~(prot=='C') tf=1; end
if tf==1
[sr sl]=ReadStartTime(pos);
s1=sr-non_mov_time;
s2=sl-non_mov_time;
[srr err srl erl]=RestingTime(pos,totaltime(rat),non_mov_time);
s1=floor(s1*n_fs)+1;
s2=floor(s2*n_fs)+1;
er=floor((sr+totaltime(rat))*n_fs);
el=floor((sl+totaltime(rat))*n_fs);
srr=floor(srr*n_fs)+1;
err=floor(err*n_fs);
srl=floor(srl*n_fs)+1;
erl=floor(erl*n_fs);
er1=floor((sr+fast_time)*n_fs);
el1=floor((sl+slow_time)*n_fs);
sr=floor(sr*n_fs);
sl=floor(sl*n_fs);
Y1=[];Y2=[];Y3=[];Y4=[];Y5=[];Y6=[];Y7=[];Y8=[];
for trial=1:length(s1)-1
Y5=[Y5,eeg(er1(trial):er(trial))'];%running period slow
Y6=[Y6,eeg(sl(trial):el1(trial))'];
Y7=[Y7,eeg(sr(trial):er1(trial))'];%running period fast
Y8=[Y8,eeg(el1(trial):el(trial))'];
end
figure(i)
subplot(2,2,1)
como1=comodulogram(Y5,lowf2:fstep:highf2,lowf1:fstep/2:highf1,n_fs);
COMODOplot(lowf2:fstep:highf2,lowf1:fstep/2:highf1,como1);
subplot(2,2,3)
como2=comodulogram(Y6,lowf2:fstep:highf2,lowf1:fstep/2:highf1,n_fs);
COMODOplot(lowf2:fstep:highf2,lowf1:fstep/2:highf1,como2);
subplot(2,2,2)
como3=comodulogram(Y7,lowf2:fstep:highf2,lowf1:fstep/2:highf1,n_fs);
COMODOplot(lowf2:fstep:highf2,lowf1:fstep/2:highf1,como3);
subplot(2,2,4)
como4=comodulogram(Y8,lowf2:fstep:highf2,lowf1:fstep/2:highf1,n_fs);
COMODOplot(lowf2:fstep:highf2,lowf1:fstep/2:highf1,como4);
como=[como1,como2,como3,como4];
for j=1:4
subplot(2,2,j)
caxis([0 max(max(como))])
end
saveas(i,strcat('C:\Users\meli__000\Desktop\Melisa\Doctorado\BandsCoupling\PAC_DELTA\Prueba\',name(a,:),'_',lfp{a}(i,:)),'png')
close(i)
matrix1(count,:,:)=como1;
matrix2(count,:,:)=como2;
matrix3(count,:,:)=como3;
matrix4(count,:,:)=como4;
count=count+1;
end
end
end
end
end
[n m l]=size(matrix1);
figure(a)
subplot(2,2,1)
COMODOplot(lowf2:fstep:highf2,lowf1:fstep/2:highf1,reshape(mean(matrix1),[m l]));
subplot(2,2,2)
COMODOplot(lowf2:fstep:highf2,lowf1:fstep/2:highf1,reshape(mean(matrix2),[m l]));
subplot(2,2,3)
COMODOplot(lowf2:fstep:highf2,lowf1:fstep/2:highf1,reshape(mean(matrix3),[m l]));
subplot(2,2,4)
COMODOplot(lowf2:fstep:highf2,lowf1:fstep/2:highf1,reshape(mean(matrix4),[m l]));
color=[max(max(mean(matrix1))),max(max(mean(matrix2))),max(max(mean(matrix3))),max(max(mean(matrix4)))];
for j=1:4
subplot(2,2,j)
caxis([0 max(color)])
end
nombre=strcat('C:\Users\meli__000\Desktop\Melisa\Doctorado\BandsCoupling\PAC_DELTA\Prueba\',int2str(prot),'_',name(a,:),'_COMODO_mean_speeds');
saveas(a,nombre,'png')
save(nombre,'matrix1','matrix2','matrix3','matrix4','freq_data','-mat')