find_transients.m

function files = find_transients(files,exp_ids,rep_ids,shift,centremass_option)


% obtain frames when LED switches on and off (at frames when the light
% intensity changes abruptly the absolute difference in mean intensity between two
% successive frames exceeds shift times the mean fluctuations observed between successive frames) 
for i = exp_ids
    for ii = rep_ids
        
        meanI_frames = files{i,ii}.RawData.meanI_fullframe;
        d_meanI = abs(diff(meanI_frames));
        d_meanI = d_meanI-mean(d_meanI); 
        times = find(d_meanI > shift);

        % cluster times of abrupt change based on distance between point within 4
        % frames
        MaxDist = 4;
        Map = unique( abs(bsxfun(@minus,times(:),times(:).'))<=MaxDist ,'rows');
        events = NaN(7,size(Map,1));
        Abrupt_changes = cell(size(Map,1),1);
        for iii = 1:size(Map,1)
           seq = floor(mean(times(Map(iii,:))))-2:floor(mean(times(Map(iii,:))))+2;
           temp_seq = d_meanI(seq); %meanI_frames( seq );
           [~, peak_t] = max(temp_seq);
           Abrupt_changes{iii} = [seq(peak_t+1)-3 : seq(peak_t+1)+3];
           events(:,iii) = meanI_frames( [seq(peak_t+1)-3 : seq(peak_t+1)+3] );
        end

        % define types of changes (synch, on and off transients)
        criterion = abs(diff(events));
        diff_events = diff(events);
        sign_inversion = NaN(size(criterion,2),1);
        continuity_flag = NaN(size(criterion,2),1);
        value_d = NaN(size(criterion,2),1);
        for c = 1:size(criterion,2);
            ctemp = criterion(:,c);
            ind = find(ctemp < max(ctemp)/10);
            diff_events(ind,c) = zeros(length(ind),1);
            [a,b] = sort(ctemp,'descend');
            sign_inversion(c) = sign(diff_events(b(1),c)).*sign(diff_events(b(2),c));
            value_d(c) = mean(diff_events(b(1:2),c));
            continuity_flag(c) = abs(diff(b(1:2))) == 1;
        end

        synch_events = find(sign_inversion < 0);
        onset_events = find(sign_inversion >= 0 & value_d > 0);
        offset_events = find(sign_inversion >= 0 & value_d < 0);
        single_frame_precision = find(continuity_flag == 0);

        % find centre of mass of events of abrupt change
        centre_mass = zeros(length(Abrupt_changes),1);
        timestamp = zeros(length(Abrupt_changes),2);
        for iii = 1:length(Abrupt_changes)
            tempseq = Abrupt_changes{iii}';
            intensities = meanI_frames(tempseq);
            centre_mass(iii) = sum(tempseq.*intensities) / sum(intensities);
            if ismember(iii,synch_events) | ismember(iii,onset_events)
                sort_intensities = sort(intensities);
                frame = find(intensities > mean(sort_intensities(1:3))+0.1*mean(sort_intensities(1:3)),1,'first');                
            else ismember(iii,offset_events)
                sort_intensities = sort(intensities,'descend');
                frame = find(intensities < mean(sort_intensities(1:3))-0.1*mean(sort_intensities(1:3)),1,'first');
            end
            timestamp(iii,:) = tempseq([frame-1:frame]);
        end
        
        if centremass_option
            files{i,ii}.synch_timestamps = sort(centre_mass(synch_events));
            files{i,ii}.onset_timestamps = sort(centre_mass(onset_events));
            files{i,ii}.offset_timestamps = sort(centre_mass(offset_events));
        else
            files{i,ii}.synch_timestamps = timestamp(synch_events,:);
            files{i,ii}.onset_timestamps = timestamp(onset_events,:);
            files{i,ii}.offset_timestamps = timestamp(offset_events,:);
        end
        
       figure, plot(meanI_frames), hold on
       y_lim = ylim;
       for iii = 1:length(Abrupt_changes)
            plot([mean(timestamp(iii,:)) mean(timestamp(iii,:))],y_lim,'k')
            plot([centre_mass(iii) centre_mass(iii)],y_lim,'r')
       end
       title(['synch, onset & offsets: files{ ',num2str(i),' , ',num2str(ii),' }',...
           '  in black time defined based on change > 10%; in red time defined based on centre of mass'])
       
    end
end