plottingfunction.m

% plotting functions

% plot reference image and mask
im =reshape(mean(VSData,1),pixX,pixY);
im = imrotate(im,90);
% in this experiment MEA stage was flipped upside-down
im = flipud(im);

titlefig{1} = 'reference image, 4x magnification';
titlefig{2} = 'Mask pixels for wave propagation';

h=subplot(121), imshow(im,[min(im(:)) max(im(:))])
set(h,'FontSize',16,'FontWeight','bold')
h1=subplot(122), imshow(bw_mask,[0 1])
title(titlefig{1},'FontSize',16,'FontWeight','bold')
title(h1,titlefig{2},'FontSize',16,'FontWeight','bold')

% change legend
h = get(gcf,'Children')
hLeg = [];
for k = 1:length(h)
    if strcmpi(get(h(k),'Tag'),'legend')
        hLeg = h(k);
        break;
    end
end
set(hLeg,'Location','SouthEast')
%% distinguishable plots for lineplots
colors = distinguishable_colors(length(p));
    for j = 1:length(p)
        set(p(j),'Color',colors(j,:))
    end
    
%%  create string array for legend
vector_string = [50:50:500];
string_array = cell(1,length(vector_string));
for i = 1:length(vector_string)
    string_array{i} = strcat('object distance = ','  ',num2str(vector_string(i)),', mm');
end

%% edit axes in figure
figure_handle = gcf;
allAxesInFigure = findall(figure_handle,'type','axes');
h_axLabels = get(allAxesInFigure,{'XLabel' 'YLabel'}); 
set(allAxesInFigure,'FontSize',12,'FontWeight','bold')
set([h_axLabels{:}],'FontSize',12,'FontWeight','bold')
%% edit axes in double plots
% set(allAxesInFigure(2),'YLim',[-0.02 0.02],'YTick',[0 0.005 0.1])
set(allAxesInFigure(2),'YLim',[-0.012 0.012],'YTick',[0 0.005 0.1],'YTickLabel',[0 0.005 0.1],'YTickMode','manual','YTickLabelMode','manual')
set(allAxesInFigure(3),'YLim',[-800 800],'YTick',[-700 700])
set(allAxesInFigure(2:3),'XLim',[75000 105000])
%% get handles of current object in figure
h = get(allAxesInFigure(2),'Children');
legend(flipud(h(1:4)),'raw fluorescene','F0 median filter window = 1386','F0 median filter window = 2773','F0 median filter window = 4621')
legend('window length = 4621 frames','window length = 1386 frames','window length = 2773 frames','Location','SouthWest')
%%

% save figures
set(gcf,'PaperPositionMode','auto')
cd \\storage.laur.corp.brain.mpg.de\Personal\CoattiAlex\Presentations\VSD_calibration\figures\2015_09_16

print sampleB_rec1_vsd_rawtrace  -djpeg -r300;   % % % print MEA_187_avg_VSD_550nm  -djpeg -r300;