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Copy pathdrgGetTrialLFPData.m
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drgGetTrialLFPData.m
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function [dataforch,trialNo,can_read] = drgGetTrialLFPData(handles, lfpElectrode, evNo, evTypeNo, time_start, time_end)
%This function either extracts the LFP data from drg.data_dg
%or generates simulated data with specific theta/gamma oscillations
%evNo is the event number for the evTypeNo
%If testLFP==0 the function reads the trial
%If testLFP~=0 the function simulates data assuming that the trace is noise
%before t=0, an oscillatory signal from 0 to 2.5 and noise from 2.5 onwards
can_read=1;
testLFP=handles.data_vs_simulate;
% if testLFP>0
% if time_start==handles.startRef+handles.time_pad
% if time_end==handles.endRef-handles.time_pad
% testLFP=4; %This is the reference period in a simulation trial
% end
% end
% end
sessionNo=handles.sessionNo;
LFPtheta=[];
LFPtheta2=[];
LFPbursts=[];
try
% trialNo=find(handles.drg.session(sessionNo).trial_start<handles.drg.session(sessionNo).events(evTypeNo).times(evNo),1,'last');
trialNo=drgFindTrNo(handles,evNo,sessionNo,evTypeNo);
data_allch = drgGetThisTrial(handles,evNo,evTypeNo);
% data_allch=zeros(floor(handles.drg.session(sessionNo).draq_p.ActualRate*handles.drg.session(sessionNo).draq_p.sec_per_trigger),handles.drg.session(sessionNo).draq_p.no_chans);
% for ii=1:handles.drg.session(sessionNo).draq_p.no_chans
% data_allch(1:end-2000,ii)=data_this_trial(floor((ii-1)*handles.drg.session(sessionNo).draq_p.ActualRate*handles.drg.session(sessionNo).draq_p.sec_per_trigger)+1:...
% floor((ii-1)*handles.drg.session(sessionNo).draq_p.ActualRate*handles.drg.session(sessionNo).draq_p.sec_per_trigger)...
% +floor(handles.drg.session(sessionNo).draq_p.ActualRate*handles.drg.session(sessionNo).draq_p.sec_per_trigger)-2000);
% end
data=[];
data=data_allch(:,lfpElectrode);
if handles.notch60==1
notch60HzFilt = designfilt('bandstopiir','FilterOrder',2, ...
'HalfPowerFrequency1',59,'HalfPowerFrequency2',61, ...
'DesignMethod','butter','SampleRate',floor(handles.drg.session(sessionNo).draq_p.ActualRate));
data=filtfilt(notch60HzFilt,data);
end
try
if handles.notch50==1
notch50HzFilt = designfilt('bandstopiir','FilterOrder',2, ...
'HalfPowerFrequency1',49,'HalfPowerFrequency2',51, ...
'DesignMethod','butter','SampleRate',floor(handles.drg.session(sessionNo).draq_p.ActualRate));
data=filtfilt(notch50HzFilt,data);
end
catch
end
%Get the data
ii_from=round(((handles.drg.session(sessionNo).events(evTypeNo).times(evNo)-handles.drg.session(sessionNo).trial_start(trialNo))+time_start)...
*handles.drg.draq_p.ActualRate+1);
ii_to=floor(((handles.drg.session(sessionNo).events(evTypeNo).times(evNo)-handles.drg.session(sessionNo).trial_start(trialNo))...
+time_end)*handles.drg.draq_p.ActualRate);
ii_zero1=floor(((handles.drg.session(sessionNo).events(evTypeNo).times(evNo)-handles.drg.session(sessionNo).trial_start(trialNo)))...
*handles.drg.draq_p.ActualRate+1);
dataforch=[];
if ii_to<=length(data)
if (ii_from<1)
%The data was not long enough
can_read=0;
dataforch=[zeros(-ii_from+1,1); data(1:ii_to)];
else
dataforch=data(ii_from:ii_to);
end
else
%data is too short
can_read=0;
dataforch=[data(ii_from:end);zeros(ii_to-length(data)+1,1)];
end
if (testLFP==0)
dataforch=dataforch';
else
dataforch_original=dataforch;
dataforch=[];
%Setup a signal with high and low frequency oscillations
Fs=handles.drg.draq_p.ActualRate;
%Generate an oscillatory signal for the entire length (this is
%trimmed below)
t = 0:1/Fs:time_end-time_start;
t_tort=1:1:length(t);
%Theta
Ftheta=handles.phaseHz;
LFPtheta = cos(2*pi*Ftheta*t);
%This is a Gaussian high gamma burst
FWHMdt=(1/Ftheta)/2; %0.0440 msec FWHM burst, 25 Hz
FWHM=ceil(Fs*FWHMdt);
X=[1:3*FWHM]; %Burst is calculated for 3*FWHM samples with peak in the middle
k=normpdf(X,3*FWHM/2,FWHM/2.35482); %normpdf(x,mu,sigma), FWHM=2*sqrt(2*ln(2))=2.3548*sigma
k=k/max(k); %Normalized to 1 at peak
% handles.amplitudeHz=40;
Fgamma=handles.amplitudeHz; %75
g_burst=k.*cos(2*pi*Fgamma*t(1:length(k)));
LFPbursts=zeros(1,length(LFPtheta));
%Important: It is key to have noise, otherwise the fourier is broad
noiseFact=0.1; %0.2
dataforch=zeros(1,length(LFPtheta));
time=time_start:(time_end-time_start)/length(dataforch):time_end;
time=time(1:end-1);
odorLFP=~((time<0)|(time>2.5));
no_odorLFP=((time<0)|(time>2.5));
%Genetrate pink noise
% https://www.dsprelated.com/freebooks/sasp/Example_Synthesis_1_F_Noise.html
% Pink noise``1/f noise''
Nx = length(LFPtheta); % number of samples to synthesize
B = [0.049922035 -0.095993537 0.050612699 -0.004408786];
A = [1 -2.494956002 2.017265875 -0.522189400];
nT60 = round(log(1000)/(1-max(abs(roots(A))))); % T60 est.
v = randn(1,Nx+nT60); % Gaussian white noise: N(0,1)
pink_noise = filter(B,A,v); % Apply 1/F roll-off to PSD
pink_noise = pink_noise(nT60+1:end); % Skip transient response
pink_n_fact=2000;
%Generate licks at the peaks of the theta LFP
[peaks,loc]=findpeaks(LFPtheta,1,'MinPeakHeight',0.5,'MinPeakDistance',0);
licks=zeros(1,length(LFPtheta));
for peakNo=1:length(loc)
licks(loc(peakNo):loc(peakNo)+200)=500;
end
switch testLFP
case 1
%LFP gamma burst at trough of theta, zero degrees, high MI
gammaFact=15;
shift_burst=-ceil(length(k)/2);
shift_trough=0.5*(1/Ftheta)*Fs; %trough
for ii=1:floor((time_end-time_start)*Ftheta)
LFPbursts(floor(ii*(Fs/Ftheta)+shift_burst+shift_trough)+1:floor(ii*(Fs/Ftheta)+shift_trough+shift_burst)+length(k))=gammaFact*g_burst;
end
if lfpElectrode==19
dataforch=licks;
else
dataforch=500*(LFPtheta+0.03*LFPbursts(1:length(LFPtheta))).*(0.02*no_odorLFP+odorLFP)+pink_n_fact*pink_noise;
% dataforch=500*(LFPtheta+0.015*LFPbursts(1:length(LFPtheta))).*(0.02*no_odorLFP+odorLFP)+pink_n_fact*pink_noise;
end
pffft=1;
% figure(10)
% plot(dataforch)
case 2
%LFP gamma burst at 180 degrees, peak of theta high MI
gammaFact=15;
shift_burst=-ceil(length(k)/2);
shift_trough=0; %peak
for ii=1:floor((time_end-time_start)*Ftheta)
LFPbursts(floor(ii*(Fs/Ftheta)+shift_burst+shift_trough)+1:floor(ii*(Fs/Ftheta)+shift_trough+shift_burst)+length(k))=gammaFact*g_burst;
end
if lfpElectrode==19
dataforch=licks;
else
dataforch=500*(LFPtheta+0.03*LFPbursts(1:length(LFPtheta))).*(0.02*no_odorLFP+odorLFP)+pink_n_fact*pink_noise;
end
case 3
%LFP gamma burst at zero degrees, low MI
gammaFact=10;
shift_burst=-ceil(length(k)/2);
shift_trough=0.5*(1/Ftheta)*Fs; %trough
for ii=1:floor((time_end-time_start)*Ftheta)
LFPbursts(floor(ii*(Fs/Ftheta)+shift_burst+shift_trough)+1:floor(ii*(Fs/Ftheta)+shift_trough+shift_burst)+length(k))=gammaFact*g_burst;
end
if lfpElectrode==19
dataforch=licks;
else
% dataforch=500*(LFPtheta+0.015*LFPbursts(1:length(LFPtheta))).*(0.02*no_odorLFP+odorLFP)+pink_n_fact*pink_noise;
dataforch=500*(LFPtheta+0.015*LFPbursts(1:length(LFPtheta))).*(0.02*no_odorLFP+odorLFP)+pink_n_fact*pink_noise;
end
case 4
%LFP gamma burst at 180 degrees, low MI
gammaFact=10;
shift_burst=-ceil(length(k)/2);
shift_trough=0; %peak
for ii=1:floor((time_end-time_start)*Ftheta)
LFPbursts(floor(ii*(Fs/Ftheta)+shift_burst+shift_trough)+1:floor(ii*(Fs/Ftheta)+shift_trough+shift_burst)+length(k))=gammaFact*g_burst;
end
if lfpElectrode==19
dataforch=licks;
else
dataforch=500*(LFPtheta+0.0125*LFPbursts(1:length(LFPtheta))).*(0.02*no_odorLFP+odorLFP)+pink_n_fact*pink_noise;
end
case 5
%10 Hz and 80Hz 10 dB
if lfpElectrode>=18
dataforch=licks';
else
dataforch=0.002*(6*sin(2*pi*t_tort*Ftheta/Fs)+6*sin(2*pi*t_tort*Fgamma/Fs));
dataforch= dataforch+noiseFact*randn(1,length(dataforch));
dataforch=dataforch.*(0.02*no_odorLFP+odorLFP)+noiseFact*randn(1,length(dataforch));
end
case 6
%10 Hz and 80Hz 20 dB
if lfpElectrode>=18
dataforch=licks';
else
dataforch=0.005*(6*sin(2*pi*t_tort*Ftheta/Fs)+6*sin(2*pi*t_tort*Fgamma/Fs));
dataforch= dataforch+noiseFact*randn(1,length(dataforch));
dataforch=dataforch.*(0.02*no_odorLFP+odorLFP)+noiseFact*randn(1,length(dataforch));
end
case 7
%10 and 80Hz centered on the lick
if lfpElectrode==19
%Licks
dataforch=licks;
else
%0.4sec 80 Hz sine wave burst centered at the lick
LFPburst=(~((time<1.3)|(time>1.7)));
noLFPburst=~LFPburst;
dataforch=0.005*(6*sin(2*pi*t_tort*Ftheta/Fs)+6*sin(2*pi*t_tort*Fgamma/Fs));
dataforch=dataforch.*(0.05*noLFPburst+LFPburst)+noiseFact*randn(1,length(dataforch));
end
case 8
if (lfpElectrode>=18)
dataforch=licks';
else
%LFP gamma burst at zero degrees, low MI, low power
gammaFact=1;
shift_burst=-ceil(length(k)/2);
shift_trough=0.5*(1/Ftheta)*Fs; %trough
for ii=1:floor((time_end-time_start)*Ftheta)
LFPbursts(floor(ii*(Fs/Ftheta)+shift_burst+shift_trough)+1:floor(ii*(Fs/Ftheta)+shift_trough+shift_burst)+length(k))=gammaFact*g_burst;
end
if lfpElectrode==19
dataforch=licks;
else
% dataforch=500*(LFPtheta+0.015*LFPbursts(1:length(LFPtheta))).*(0.02*no_odorLFP+odorLFP)+pink_n_fact*pink_noise;
dataforch=100*(LFPtheta+0.015*LFPbursts(1:length(LFPtheta))).*(0.02*no_odorLFP+odorLFP)+pink_n_fact*pink_noise;
end
end
% The cases below are used by batch processing
case 9
%LFP low gamma burst at 180 degrees, high MI S+, low MI S-
%if it is S-handles.drgbchoices.evTypeNos=[3 5 7 9 11 13 16:21];
%First find out if this is S+ or S-
if (lfpElectrode>=18)
dataforch=licks';
else
if sum(handles.drg.session(1).events(5).times==handles.drg.session(1).events(evTypeNo).times(evNo))>0
%This is S+
%LFP gamma burst at 180 degrees, high MI
gammaFact=30; %15 is good for high gamma, 30 great for low gamma
shift_burst=-ceil(length(k)/2);
shift_trough=0; %peak
for ii=1:floor((time_end-time_start)*Ftheta)
LFPbursts(floor(ii*(Fs/Ftheta)+shift_burst+shift_trough)+1:floor(ii*(Fs/Ftheta)+shift_trough+shift_burst)+length(k))=gammaFact*g_burst;
end
if lfpElectrode==19
dataforch=licks;
else
dataforch=500*(LFPtheta+0.0125*LFPbursts(1:length(LFPtheta))).*(0.02*no_odorLFP+odorLFP)+pink_n_fact*pink_noise;
end
else
%This is S-
%LFP gamma burst at 180 degrees, low MI
gammaFact=10;
shift_burst=-ceil(length(k)/2);
shift_trough=0; %peak
for ii=1:floor((time_end-time_start)*Ftheta)
LFPbursts(floor(ii*(Fs/Ftheta)+shift_burst+shift_trough)+1:floor(ii*(Fs/Ftheta)+shift_trough+shift_burst)+length(k))=gammaFact*g_burst;
end
if lfpElectrode==19
dataforch=licks;
else
dataforch=500*(LFPtheta+0.0125*LFPbursts(1:length(LFPtheta))).*(0.02*no_odorLFP+odorLFP)+pink_n_fact*pink_noise;
end
end
end
case 10
if (lfpElectrode>=18)
dataforch=licks';
else
%if it is S-handles.drgbchoices.evTypeNos=[3 5 7 9 11 13 16:21];
%First find out if this is S+ or S-
if sum(handles.drg.session(1).events(5).times==handles.drg.session(1).events(evTypeNo).times(evNo))>0
%This is S+
%LFP gamma burst at 180 degrees, high MI
gammaFact=15;
shift_burst=-ceil(length(k)/2);
shift_trough=0; %peak
for ii=1:floor((time_end-time_start)*Ftheta)
LFPbursts(floor(ii*(Fs/Ftheta)+shift_burst+shift_trough)+1:floor(ii*(Fs/Ftheta)+shift_trough+shift_burst)+length(k))=gammaFact*g_burst;
end
if lfpElectrode==19
dataforch=licks;
else
dataforch=500*(LFPtheta+0.0125*LFPbursts(1:length(LFPtheta))).*(0.02*no_odorLFP+odorLFP)+pink_n_fact*pink_noise;
end
else
%This is S-
%LFP gamma burst at zero degrees, high MI
gammaFact=15;
shift_burst=-ceil(length(k)/2);
shift_trough=0.5*(1/Ftheta)*Fs; %trough
for ii=1:floor((time_end-time_start)*Ftheta)
LFPbursts(floor(ii*(Fs/Ftheta)+shift_burst+shift_trough)+1:floor(ii*(Fs/Ftheta)+shift_trough+shift_burst)+length(k))=gammaFact*g_burst;
end
if lfpElectrode==19
dataforch=licks;
else
dataforch=500*(LFPtheta+0.015*LFPbursts(1:length(LFPtheta))).*(0.02*no_odorLFP+odorLFP)+pink_n_fact*pink_noise;
end
end
end
end
end
catch
can_read=0;
dataforch=[];
trialNo=-1;
end
pffft=1;