minianalysis.m

function  [neg_failure, pos_failure PD1 PD2 IR1_r IR1_b IR2_b]=minianalysis(list, idx, pathName, fc, show, user, filterephys,adata_dir);
%SW181229
%Function that extracts minis by using the std threshold criterion

%list=      information of folders for each cell SW000XX
%idx=       vector with idx of which recording is mini recording
%pathName=  folder name of cell
%fc=        factor of how many stds the signal should be included
%show=      show plots or not (1 or 0)

base_start          =   1;
base_end            =   99;
pulse_start         =   100;
pulse_end           =   110;
pulse2_start        =   351;
pulse2_end          =   360;

%Calibration curves for blue/red at the 2 setups (in mW/mm2) irradiance
%compare to Klapoetke 2014
%SW
% yirr_red=(12.19*PD1-0.4319)/100;
% yirr_blue=(7.232*PD2-0.9951)/100;
% %MF
% yirr_red=(104.1 *PD1-3.467)/100;
% yirr_blue=(679.2*PD2-26.82)/100;

%% TR2019: filtering
% filterephys = 1;        % filtering yes/no?
cutoff      = 500;      % Hz (use 500 Hz for mini event / amplitude detection and 1000Hz for max currents. Chen & Regehr 2000)
order       = 4;        % filter order ('pole'). (use 4 pole for minis and max current. Chen & Regehr 2000)
type        = 'Bessel'; % filter type ('Bessel' or 'Butter' (for Butterworth -> ). Default: Bessel. Use Bessel at > 4 order to prevent ripples)

%% TR2019: plot specs
plotlength = .3; %seconds
savefig = 1; %save main figure

if filterephys
    disp('- - - - - - - -')
    disp(['Filtering: ' num2str(order) ' pole ' type '-Filter w/ ' num2str(cutoff) ' Hz cutoff']);
    disp('- - - - - - - -')
end


for i=1:length(idx);
    load([char(pathName) filesep list(idx(i)).name],'-mat');
    sr = header.ephys.ephys.sampleRate;%check sample rate
    srF = 1/(1000/sr);
    samples_per_sweep = header.ephys.ephys.traceLength*sr;
    timebase=1/sr:1/sr:samples_per_sweep/sr; %TR2019: timebase

    ephystraces=data.ephys.trace_1;

    if filterephys % TR2019: filtering
        ephystraces = lowpassfilt(ephystraces, order, cutoff, sr, type);
    end

    if user==0%SW %TR2019 should now work w/o user exceptions... kept it in, though
        traces=reshape(ephystraces, samples_per_sweep, length(ephystraces)/samples_per_sweep);
        photodiode=data.acquirer.trace_1;
        photodiode=reshape(photodiode, samples_per_sweep, length(ephystraces)/samples_per_sweep);
    else %MF
        traces=reshape(ephystraces, samples_per_sweep, length(ephystraces)/samples_per_sweep);
        photodiode=data.acquirer.trace_1;
        photodiode=reshape(photodiode, samples_per_sweep, length(ephystraces)/samples_per_sweep);
    end

    bs=traces(base_start*srF:base_end*srF,:);
    bs_std=std(bs);
    bs_traces=bsxfun(@minus, traces, mean(bs));
    bs_photodiode=bsxfun(@minus, photodiode, mean(photodiode(base_start*srF:base_end*srF,:)));
    neg_peak=min(bs_traces(pulse_start*srF:pulse_end*srF+40*srF,:));
    pos_peak=max(bs_traces(pulse_start*srF:pulse_end*srF+40*srF,:));
    neg_fail=neg_peak<fc*bs_std*(-1);
    pos_fail=pos_peak>fc*bs_std;
    neg_idx=find(neg_fail==1);
    pos_idx=find(pos_fail==1);
    neg_m=zeros(1,size(traces,2));
    neg_m(neg_idx)=neg_peak(neg_idx);
    pos_m=zeros(1,size(traces,2));
    pos_m(pos_idx)=pos_peak(pos_idx);

    try
        neg_fail(neg_idx)=neg_peak(neg_idx);
        pos_fail(pos_idx)=pos_peak(pos_idx);
    catch
        neg_fail=zeros(length(pos_peak));
        pos_fail=zeros(length(pos_peak));
    end

    neg_failure(:,i)=neg_m;
    pos_failure(:,i)=pos_m;
    PD1(:,i)=mean(photodiode(pulse_start *srF:pulse_end*srF,:));
    PD2(:,i)=mean(photodiode(pulse2_start *srF:pulse2_end*srF,:));

    if user==0%SW
        IR1_r(:,i)=(12.19*PD1(:,i)-0.4319)/100;
        IR1_b(:,i)=(7.232*PD1(:,i)-0.9951)/100;
        IR2_b(:,i)=(7.232*PD2(:,i)-0.9951)/100;
    else
        IR1_r(:,i)=(104.1*PD1(:,i)-3.467)/100;
        IR1_b(:,i)=(679.2*PD1(:,i)-26.82)/100;
        IR2_b(:,i)=(679.2*PD2(:,i)-26.82)/100;
    end

    %PLOT
    if show==1
        try; close(fig2); end
        fig2=figure;
        for k=1:size(traces,2)
            subplot(size(bs_traces,2)/10,10,k);
            if user==0%SW
                plot(timebase(1:plotlength*sr),bs_traces(1:plotlength*sr,k));
            else%MF
                plot(timebase(1:plotlength*sr),bs_traces(1:plotlength*sr,k));
            end
            xlabel('time [s]'); ylabel('I [pA]')
            ylim([min(neg_peak) - 10 max(pos_peak) + 10]); % TR2019: fixed axis scaling
        end
        figure;
        plot(neg_peak,'*');
        hold on
        plot(pos_peak,'*');
        hold on;
        plot(repmat(fc*(mean(bs_std))*(-1),length(pos_peak)));
        hold on;
        plot(repmat(fc*(mean(bs_std)),length(pos_peak)));
    end
end
if savefig
    cd(adata_dir);
    saveas(fig2, [char(pathName) '.png'])
end
end