Transparent background for figures to make a movie

Hey,
I have some cloud data (ice optical depths) to plot and make a movie that shows the evolution of clouds over time. I managed to make a movie with the cloud data, but now I want to include the topography map as the transparent background. In the movie it should look like that clouds are moving over the topography map. I tried several methods and failed. The topography map is attached. Cloud data are in an array with dimensions (120,120,365). The dimensions represent, (latitide, longitude, time). So each cloud map (120X120) should plot on the attached picture with a 0.01 time interval. I just need to know how to include the map as the transparent background. Does anyone think this is possible? I have included the movie I made and some of the cloud data (120X120X40). Any help will be appreciated.
Also, the clouds should be in grey color scale and the topography map can be modified in order to fit the cloud data.
Below is the code I used to make the movie.
figure(1);
vidfile = VideoWriter('Olympus10.mp4','MPEG-4');
% vidfile.FrameRate = 60;
open(vidfile);
for ind = 1:365%(change 365 to 40 to run with the data I uploaded)
imagesc(H(:,:,ind));
colormap(gray);
c=[0.01 1];
h=imagesc(squeeze(H(:,:,ind)),c);
h1 = colorbar;
stng='F';
title(h1,stng);
h1 = colorbar;
fclose all
grid on
ax=gca;
ax.GridColor = 'w';
ax.GridLineStyle='--';
ax.GridAlpha = 0.5;
ax.Layer='top';
set(gca,'ytick',[0:24:120],'fontsize',18);
yticklabels(27:-3:12);
set(gca,'xtick',[0:24:120],'fontsize',18);
xticklabels(-141:3:-126);
xlabel('East Longitude (\circ)')
ylabel('Latitude (\circ)')
s = num2str(ind);
t = strcat(s);
title(t);
drawnow;
pause(0.01);
F(ind) = getframe(gcf);
writeVideo(vidfile,F(ind));
end
close(vidfile);

Answer 1

[Simon Chan]

Try using function pcolor so that you can adjust the FaceAlpha value.

I = imread('image.png');
[Ny,Nx,Nz]=size(H);
[X,Y]=meshgrid(1:Nx,1:Ny);
figure(1)
ax = gca;
imagesc(ax,imresize(I,[Ny Nx]));
hold(ax,'on');
for ind = 1:Nz%(change 365 to 40 to run with the data I uploaded) 
    p = pcolor(ax,X,Y,H(:,:,ind));
    p.FaceAlpha=0.6;                            % You may adjust this value
    p.EdgeColor = 'none';
    colormap(ax,'gray');
    c=[0.01 1];    
    h1 = colorbar;
    h1.Limits = [0 1];
    stng='F';
    title(h1,stng);
    %fclose all
    grid on
    ax.GridColor = 'w';
    ax.GridLineStyle='--';
    ax.GridAlpha = 0.5;
    ax.Layer='top';
    set(gca,'ytick',[0:24:120],'fontsize',18);
    yticklabels(27:-3:12);
    set(gca,'xtick',[0:24:120],'fontsize',18);
    xticklabels(-141:3:-126);
    xlabel('East Longitude (\circ)')
    ylabel('Latitude (\circ)')
    s = num2str(ind);
    t = strcat(s);
    title(t);
    drawnow;
    pause(0.1);
    F(ind) = getframe(gcf); 
    delete(p)
    writeVideo(vidfile,F(ind));
end

[Anton Fernando]

This is amazing. Thank you. You saved me a lot of time.

[Anton Fernando]

There is one problem though. The scale of the color bar changes in each frame. Is there a way to keep the colorbar constant in all the figures?

Thank you.

[Simon Chan]

Did you added the following line to fix the colorbar limits?

Sorry forgot to mention on my previous reply.

h1 = colorbar;
h1.Limits = [0 1];

[Anton Fernando]

Yes. I did. But to no avail.

[Simon Chan]

Strange, I also encountered the same issue but can be fixed by setting the limit.

Attached is the movie from my testing.

I may need more time to think about it since I am not available at the moment.

[Anton Fernando]

I fixed it. Change the following commented lines.

% h1 = colorbar;
% h1.Limits = [0 1];
% stng='F';
% title(h1,stng);


colorbar; 
caxis([0.1 1]);
stng='F';
title(stng);

[Simon Chan]

Great! Also learn the solution from you.

[Anton Fernando]

Master learned from the student!! :)