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FFT_LFP_fraction.m
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%% Before starting, load everything
clear all
close all
files=Data_Listing();
rat=1;
load('1CA1','-mat');
load('1EC1','-mat');
load('1EC2','-mat');
area={CA1,EC1,EC2};
lfp={Days(CA1),Days(EC1),Days(EC2)};
name=['1CA1';'1EC1';'1EC2'];
rat=2;
load('2CA1','-mat');
load('2EC1','-mat');
load('2EC2','-mat');
area={CA1_2,EC1_2,EC2_2};
lfp={Days(CA1_2),Days(EC1_2),Days(EC2_2)};
name=['2CA1';'2EC1';'2EC2'];
rat=3;
load('3CA1','-mat');
load('3EC1','-mat');
load('3EC2','-mat');
area={CA1_3,EC1_3,EC2_3};
lfp={Days(CA1_3),Days(EC1_3),Days(EC2_3)};
name=['3CA1';'3EC1';'3EC2'];
prot='C';
n_fs=400;
Fs = n_fs; % Sampling frequency
T = 1/Fs; % Sampling period
%% fraction of band in hole registration
protocol={'A','B','C','IC'};
[n m]=size(area);
for a=1:3
for prot=1:3
counter=1;
clear matrix
for i=1:length(lfp{a})
session_number=RecordingSession(files,rat,area{a},lfp{a}(i,:),protocol{prot});
if 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(1));
[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));
n = 2^10;
Y=fft(eeg,n);
L=length(Y);
f = Fs*(0:(L-1))/L;
matrix(counter,:)=abs(Y/sqrt(L));
counter=counter+1;
end
end
end
[n1 n2]=size(matrix);
f = Fs*(0:(L/2))/L;
delta=zeros(n1,1);
theta=zeros(n1,1);
gamma=zeros(n1,1);
other=zeros(n1,1);
for i=1:length(f)
if f(i)>1.5 && f(i)<4
delta=delta+matrix(:,i)*(Fs/L);
else
if f(i)>6 && f(i)<12
theta=theta+matrix(:,i)*(Fs/L);
else
if f(i)>40 && f(i)<100
gamma=gamma+matrix(:,i)*(Fs/L);
else
other=other+matrix(:,i)*(Fs/L);
end
end
end
end
fraction(:,1)=delta./(delta+theta+gamma+other+eps);
fraction(:,2)=theta./(delta+theta+gamma+other+eps);
fraction(:,3)=gamma./(delta+theta+gamma+other+eps);
fraction(:,4)=other./(delta+theta+gamma+other+eps);
nombre=strcat('/home/melisa/Escritorio/Melisa/Doctorado/Spectrogram/Figuras2/frac_',int2str(rat),'_',name(a,:),'_',protocol{prot});
save(nombre,'fraction','-ASCII')
clear fraction
end
end
%% Fraction of a band in different dynamic condition. Esto es solo para la rata 3!!!!!
rat=3;
load('3CA1','-mat');
load('3EC1','-mat');
load('3EC2','-mat');
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];
% rat 3
fast_time=6;
slow_time=36;
non_mov_time=6;
for a=1:m
counter=0;
clear matrix1 matrix2 matrix3 matrix4 matrix5 matrix6 matrix7 matrix8 matrix
clear matrix fraction
for i=1:length(lfp{a})
session_number=RecordingSession(files,rat,area{a},lfp{a}(i,:),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));
n_fs=floor(fs/floor(fs/n_fs));
[qual4,qual,qual2]=egf_theta_quality_2016(eeg);
if qual>0.5
eeg=resample(eeg,1,floor(fs/n_fs));
pos=Loading_Pos(register,session_number(se));
tf = isfield(pos.data, 'log');
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);
n= 2^10;
for trial=1:length(sl)-1
counter=counter+1;
Y1=fft(eeg(srr(trial):err(trial)),n);
Y2=fft(eeg(srl(trial):erl(trial)),n);
Y3=fft(eeg(s1(trial):sr(trial)),n);
Y4=fft(eeg(s2(trial):sl(trial)),n);
Y5=fft(eeg(sr(trial):er1(trial)),n);
Y6=fft(eeg(el1(trial):el(trial)),n);
Y7=fft(eeg(er1(trial):er(trial)),n);
Y8=fft(eeg(sl(trial):el1(trial)),n);
L1=length(Y1);
L2=length(Y3);
L3=length(Y5);
L4=length(Y7);
f1 = Fs*(0:(L1-1))/L1;
f2 = Fs*(0:(L2-1))/L2;
f3 = Fs*(0:(L3-1))/L3;
f4 = Fs*(0:(L4-1))/L4;
matrix1(counter,1:length(Y1))=abs(Y1/sqrt(L1));
matrix2(counter,1:length(Y2))=abs(Y2/sqrt(L1));
matrix3(counter,1:length(Y3))=abs(Y3/sqrt(L2));
matrix4(counter,1:length(Y4))=abs(Y4/sqrt(L2));
matrix5(counter,1:length(Y5))=abs(Y5/sqrt(L3));
matrix6(counter,1:length(Y6))=abs(Y6/sqrt(L3));
matrix7(counter,1:length(Y7))=abs(Y7/sqrt(L4));
matrix8(counter,1:length(Y8))=abs(Y8/sqrt(L4));
end
end
end
end
end
end
matrix{1}=[matrix1;matrix2]; %quiet
matrix{2}=[matrix3;matrix4]; %expecting
matrix{3}=[matrix7;matrix8]; %slow
matrix{4}=[matrix5;matrix6]; %fast
L=[L1,L2,L4,L3];
for state=1:4
f= Fs*(0:(L(state)/2))/L(state);
[n m]=size(matrix{state});
delta=zeros(n,1);
theta=zeros(n,1);
gamma=zeros(n,1);
other=zeros(n,1);
for i=1:length(f)
if f(i)>1.5 && f(i)<4
delta=delta+matrix{state}(:,i)*(Fs/L(state));
else
if f(i)>6 && f(i)<12
theta=theta+matrix{state}(:,i)*(Fs/L(state));
else
if f(i)>60 && f(i)<80
gamma=gamma+matrix{state}(:,i)*(Fs/L(state));
else
other=other+matrix{state}(:,i)*(Fs/L(state));
end
end
end
end
fraction(:,state,1)=delta./(delta+theta+gamma+other+eps);
fraction(:,state,2)=theta./(delta+theta+gamma+other+eps);
fraction(:,state,3)=gamma./(delta+theta+gamma+other+eps);
fraction(:,state,4)=other./(delta+theta+gamma+other+eps);
end
figure(a)
[n m l]=size(fraction);
fraction_mean=mean(fraction);
fraction_var=var(fraction);
fraction_mean_error=sqrt(fraction_var)/n;
c = colormap(jet(3));
for i=1:3
errorbar([1:4],fraction_mean(1,:,i),fraction_var(1,:,i),'Color',c(:,i))
hold on
%errorbar([1:4],fraction_mean(1,:,i),fraction_mean_error(1,:,i),'Color',c(:,i))
end
legend('Delta','Theta','Gamma')
for i=1:3
%errorbar([1:4],fraction_mean(1,:,i),fraction_var(1,:,i),'Color',c(:,i))
hold on
errorbar([1:4],fraction_mean(1,:,i),fraction_mean_error(1,:,i),'Color',c(:,i))
end
axis([1 5.5 0 0.3])
xlabel('Different Behavioural Conditions','Fontsize',15)
ylabel('Fraction of LFP','Fontsize',15)
nombre=strcat('C:\Users\meli__000\Desktop\Melisa\Doctorado\Spectrogram\Figuras2\','fraction_',int2str(rat),'_',name(a,:),'_',prot);
saveas(a,nombre,'png')
close(a)
end
%% Fraction of a band in different dynamic condition. Esto es solo para la rata 1!!!!!
rat=1;
load('1CA1','-mat');
load('1EC1','-mat');
load('1EC2','-mat');
area={CA1,EC1,EC2};
lfp={Days(CA1),Days(EC1),Days(EC2)};
name=['1CA1';'1EC1';'1EC2'];
[n m]=size(area);
totaltime=[20,20,42];
non_mov_time=6;
jump_time=4;
for a=1:m
counter=1;
clear matrix1 matrix2 matrix3 matrix4 matrix5 matrix6 matrix7 matrix8 matrix9 matrix10 matrix11 matrix12 matrix13 matrix14
clear matrix fraction
for i=1:length(lfp{a})
session_number=RecordingSession(files,rat,area{a},lfp{a}(i,:),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));
n_fs=floor(fs/floor(fs/n_fs));
[qual4,qual,qual2]=egf_theta_quality_2016(eeg);
if qual>0.5
eeg=resample(eeg,1,floor(fs/n_fs));
pos=Loading_Pos(register,session_number(se));
tf = isfield(pos.data, 'log');
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+jump_time)*n_fs);
el1=floor((sl+jump_time)*n_fs);
er2=floor(er1+jump_time*n_fs);
el2=floor(el1+jump_time*n_fs);
er3=floor(er2+jump_time*n_fs);
el3=floor(el2+jump_time*n_fs);
er4=floor(er3+jump_time*n_fs);
el4=floor(el3+jump_time*n_fs);
sr=floor(sr*n_fs)+1;
sl=floor(sl*n_fs);
n= 2^10;
for trial=1:length(sl)-1
Y1=fft(eeg(srr(trial):err(trial)),n);
Y2=fft(eeg(srl(trial):erl(trial)),n);
Y3=fft(eeg(s1(trial):sr(trial)),n);
Y4=fft(eeg(s2(trial):sl(trial)),n);
Y5=fft(eeg(sr(trial):er1(trial)),n);
Y6=fft(eeg(er1(trial):er2(trial)),n);
Y7=fft(eeg(er2(trial):er3(trial)),n);
Y8=fft(eeg(er3(trial):er4(trial)),n);
Y9=fft(eeg(er4(trial):er(trial)),n);
Y14=fft(eeg(sl(trial):el1(trial)),n);
Y13=fft(eeg(el1(trial):el2(trial)),n);
Y11=fft(eeg(el2(trial):el3(trial)),n);
Y12=fft(eeg(el3(trial):el4(trial)),n);
Y10=fft(eeg(el4(trial):el(trial)),n);
L1=length(Y1);
L2=length(Y3);
L3=length(Y5);
L4=length(Y6);
L5=length(Y7);
L6=length(Y8);
L7=length(Y9);
matrix1(counter,1:length(Y1))=abs(Y1/sqrt(L1));
matrix2(counter,1:length(Y2))=abs(Y2/sqrt(L1));
matrix3(counter,1:length(Y3))=abs(Y3/sqrt(L2));
matrix4(counter,1:length(Y4))=abs(Y4/sqrt(L2));
matrix5(counter,1:length(Y5))=abs(Y5/sqrt(L3));
matrix6(counter,1:length(Y6))=abs(Y6/sqrt(L4));
matrix7(counter,1:length(Y7))=abs(Y7/sqrt(L5));
matrix8(counter,1:length(Y8))=abs(Y8/sqrt(L6));
matrix9(counter,1:length(Y9))=abs(Y9/sqrt(L7));
matrix10(counter,1:length(Y10))=abs(Y10/sqrt(L3));
matrix11(counter,1:length(Y11))=abs(Y11/sqrt(L4));
matrix12(counter,1:length(Y12))=abs(Y12/sqrt(L5));
matrix13(counter,1:length(Y13))=abs(Y13/sqrt(L6));
matrix14(counter,1:length(Y14))=abs(Y14/sqrt(L7));
counter=counter+1;
end
end
end
end
end
end
matrix{1}=[matrix1;matrix2]; %quiet
matrix{2}=[matrix3;matrix4]; %waiting
matrix{3}=[matrix5;matrix10]; %v1
matrix{4}=[matrix6;matrix11]; %v2
matrix{5}=[matrix7;matrix12]; %v3
matrix{6}=[matrix8;matrix13]; %v4
matrix{7}=[matrix9;matrix14]; %v5
L=[L1,L2,L3,L4,L5,L6,L7];
c = colormap(jet(7));
for state=1:7
f= Fs*(0:(L(state)/2))/L(state);
[n m]=size(matrix{state});
delta=zeros(n,1);
theta=zeros(n,1);
gamma=zeros(n,1);
other=zeros(n,1);
for i=1:length(f)
if f(i)>1.5 && f(i)<4
delta=delta+matrix{state}(:,i)*(Fs/L(state));
else
if f(i)>6 && f(i)<12
theta=theta+matrix{state}(:,i)*(Fs/L(state));
else
if f(i)>60 && f(i)<80
gamma=gamma+matrix{state}(:,i)*(Fs/L(state));
else
other=other+matrix{state}(:,i)*(Fs/L(state));
end
end
end
end
fraction(:,state,1)=delta./(delta+theta+gamma+other+eps);
fraction(:,state,2)=theta./(delta+theta+gamma+other+eps);
fraction(:,state,3)=gamma./(delta+theta+gamma+other+eps);
fraction(:,state,4)=other./(delta+theta+gamma+other+eps);
end
figure(a)
[n m l]=size(fraction);
fraction_mean=mean(fraction);
fraction_var=var(fraction);
fraction_mean_error=sqrt(fraction_var)/n;
c = colormap(jet(3));
for i=1:3
errorbar([1:7],fraction_mean(1,:,i),fraction_var(1,:,i),'Color',c(:,i))
hold on
%errorbar([1:4],fraction_mean(1,:,i),fraction_mean_error(1,:,i),'Color',c(:,i))
end
legend('Delta','Theta','Gamma')
for i=1:3
%errorbar([1:4],fraction_mean(1,:,i),fraction_var(1,:,i),'Color',c(:,i))
hold on
errorbar([1:7],fraction_mean(1,:,i),fraction_mean_error(1,:,i),'Color',c(:,i))
end
axis([1 8 0 0.3])
xlabel('Different Behavioural Conditions','Fontsize',15)
ylabel('Fraction of LFP','Fontsize',15)
nombre=strcat('C:\Users\meli__000\Desktop\Melisa\Doctorado\Spectrogram\Figuras2\','fraction_',int2str(rat),'_',name(a,:),'_',prot);
saveas(a,nombre,'png')
close(a)
end