MapDensity.m

% Script MapDensity.m plots a map of the spatial density of stains, in stains per square centimeter
% INPUT is the '*.mat' file with quantitative stain measurements.
% OUTPUT is a '*.png' picture density_map mapping number spatial density of stains.

%%Copyright (c) 2023, Daniel Attinger
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% developer settings
numBinsX = 12; % number of bins in plot
% developer settings

% hide figures to speed up processing
if verbose==0
  set (0, 'DefaultFigureVisible', 'off');
else
  set (0, 'DefaultFigureVisible', 'on');
end

%set(0, 'DefaultFigureVisible', 'on');
Line_Width=1;
Size_Font=16;

x = zeros(size(stains));
y = zeros(size(stains));
alpha = zeros(size(stains));

for i = 1:size(stains,1)
  x(i) = stains(i).Centroid(1) / scale; % in cm
  y(i) = (photoHeight-stains(i).Centroid(2)) / scale; % this ensures that y-axis runs from bottom to top
  alpha(i) = asin(stains(i).MinorAxisLength / stains(i).MajorAxisLength) * 180 / pi;
end

numBinsY = round(numBinsX*photoHeight/photoWidth);



% Extract the image size (in cm)
photoWidth_cm = photoWidth/scale;
photoHeight_cm = photoHeight/scale;

xmin = 0;
xmax = photoWidth_cm;
ymin = 0;
ymax = photoHeight_cm;



% Compute the bin edges based on the desired range
xEdges = linspace(xmin, xmax, numBinsX + 1);
yEdges = linspace(ymin, ymax, numBinsY + 1);

% Compute the 2D histogram
[counts, centers] = hist3([x, y], 'Edges', {xEdges, yEdges});

bin_area=(xmax-xmin)*(ymax-ymin)/numBinsX/numBinsY; %area of bin in cm2

% Create a heatmap-like visualization of the histogram using imagesc
figure;
imagesc (centers{1}, centers{2}, counts'/bin_area);
colormap('hot');

title('density of stains (count per cm^2)');
xlabel('X, cm');
ylabel('Y, cm');




% Adjust the font size of the axes labels and tick labels
set(gca, 'FontSize', 14);  % Adjust the font size as desired

% Manually set the axis limits to match the desired range
xlim([xmin, xmax]);
ylim([ymin, ymax]);

pos = get(gca, 'Position');
%[ 0.1300   0.1100   0.7750   0.8150]);
% [left, bottom, width, height]

scale_plot=0.8;
pos(2) = pos(2)+0.1;
pos(4) = (1-pos(2))*scale_plot;
pos(1) = pos(1)+0.1;
pos(3) = (1-pos(1))*scale_plot;
set(gca, 'Position', pos)

colorbarHandle = colorbar;
set(colorbarHandle, 'FontSize', 14);  % Adjust the font size as desired
colorbar;

% Use normal y-axis direction
set(gca, 'YDir', 'normal');

%%figure(2); plot(x,y,'o');
%%xlim([xmin, xmax]);
%%ylim([ymin, ymax]);

print(density_map);