SM_PlotOneOrMultVideos.m

function SM_PlotOneOrMultVideos(roi_ave)

%% Prepare reading in the data

[Videos]=length(roi_ave.raw);
[Frames]=length(roi_ave.raw{1}(1,:));
[ROIS]=length(roi_ave.raw{1}(:,1));

%% VARIABLES make sure to adjust if necessary

VideosSelected = [11:29]; %[7 10 13 15 17 ]; 
framerate = 30; % nr of frames per second
comptime=10; % frames to delete at beginning & compensate in graph
BOSselection = comptime:Frames;
savefilename = ['multiple_plot_' datestr(clock)];

%% Calculate values and preallocate matrix
BOStime = length(BOSselection);

data = zeros(ROIS,Frames,Videos);
total_raw = zeros(ROIS,BOStime,Videos); 
total_dff = zeros(ROIS,BOStime,Videos); 
total_videos = zeros(ROIS,BOStime,Videos);
total_dffvideos = zeros(ROIS,BOStime,Videos);

%% Read in data
for videoIter = VideosSelected
data(:,:,videoIter)=(roi_ave.raw{videoIter});
end

%% loop through data to calculate DFF
figure(); hold on
c = colormap(lines(ROIS*Videos+10));

for videoIter2=VideosSelected
    dataPerVideo = data(:,BOSselection,videoIter2);
          
    for ROIiter=1:ROIS
    
    dataPerROI = dataPerVideo(ROIiter,:);
    baseline=prctile(dataPerROI,0); % 0 is  the min
    dff=(dataPerROI-baseline)./baseline;
    total_raw(ROIiter,:,videoIter2)=dataPerROI;
    total_dff(ROIiter,:,videoIter2)=dff;
    
    end
    
    total_videos=total_videos+total_raw;
    total_dffvideos=total_dffvideos+total_dff;
end

%% Plotting 

for videoIter3 = VideosSelected
    plotPerVideo = total_dffvideos(:,:,videoIter3);
    
    counter = 1;               
     
    for ROIiter2 = 1:ROIS    
        dff = plotPerVideo(ROIiter2,:);
        shiftup = (0.15*counter-1); 
        plot(((comptime+(1:length(dff)))/framerate),dff+shiftup,'Color',c(ROIiter2,:),'LineWidth',1.0);
        xlim([0 ((comptime+BOStime)/framerate)]);
        counter = counter+1;
    end

%% More figure stuff & save data and variables
ylabel('');
xlabel('Time (s)');
set(findall(gcf,'type','text'),'FontSize',13,'fontWeight','bold')
  
save(savefilename);
  
end



%% ----[ Setup Sonogram ]------%

% fs=24.4141e3;
% [b,a]=ellip(5,.2,80,[500]/(fs/2),'high');
% [IMAGE,F,T]=fb_pretty_sonogram(filtfilt(b,a,mic_data./abs(max(mic_data))),fs,'low',1.5,'zeropad',0);

%% ----[ Plotting ]------%
% h(1) = subplot(10,1,1:2);
%       imagesc((T*framerate - startTime*framerate + 1)/framerate,F,log(abs(IMAGE)+1e+2));set(gca,'YDir','normal');
%       colormap(flipud(bone)*.8)
%       freezeColors;
%       ylim([0 9000]);
%       hold on

% here, you can make a subplot on top with a sonogram, for example
% h(2) = subplot(10,1,3:10);
% title('Calcium transients LNY19RB 9/2/15 BOS playback #4 (normalized ROIs)');


%% ---------[ Optional: picking peaks ] --------------%

% This code is for selecting peaks in fluorescense change and constructing
% a raster plot based on those
%      
%   [pks,locs] = findpeaks(dff,'MinPeakWidth',100,'MinPeakProminence',1.0*std(dff));
% 	hold on; plot(locs/framerate,pks+shiftup,'*','Color',c(i,:));% line([locs(:,:)/framerate,locs(:,:)/framerate],[-1 9],'Color',c(i,:))
% 	hold off
%     
%   locs = transpose(locs);
%    
%   hold on
%   line([locs(:,:)/framerate,locs(:,:)/framerate],[500 2000],'Color',c(i,:))
%   hold off