Saveas: missing half the figure!?

I have three axes on a single figure. For each one, I manually set the position instead of using subplot. When I save the file using:

saveas(gcf,fileName,'pdf');

the figure saves, the orientation (portrait/landscape) is maintained, and the figure dimensions are preserved, BUT the content of the image is messed up (see attached figure). This only happens sometimes, other times it works just fine doing very similar plotting.

QUESTION: Why is this happening and how do I avoid it without making my life too much more difficult.

Here are some bits and pieces of my code:

% Setup size and orientation to be that of a landscape letter paper
figure(ifig)
set(gcf,'DefaultAxesFontSize',fontsize,'DefaultTextFontSize',fontsize)
set(gcf, 'Units', 'inches', 'PaperPosition', [0,0,11,8.5]);
set(gcf, 'Position', [2 1.5 11 8.5 ]);
set(gcf, 'PaperOrientation','landscape');

% setup axes position
position = [xshift yshift width height1];
axes('units','inches','position',position);

% then I plot using contourf

% now save
fileName = '/path/to/file.pdf';
saveas(gcf,fileName,'pdf');

Answer 1

[Shashank Prasanna]

Try using export_fig, this is a very popular file central submission that makes exporting figures easy and trouble free:

http://www.mathworks.com/matlabcentral/fileexchange/23629-exportfig

[Shashank Prasanna]

Check what renderer it is:

get(gcf,'renderer')

Try either of the three: painters, opengl or zbuffers

If they don't work you, there is no harm in using export_fig, its tried and tested and popular. Just keep it in your path.

[Kellen]

Thanks, It was using painters. I just tried using export_fig, and it reproduces the problem just as using saveas with painters does.

export_fig file.pdf

I get an image exactly like the one above. Any ideas?

[Shashank Prasanna]

What happens if you don't set all the properties you set but use the default figure properties? If that doesn't work, we may need to see the fig file or some reproduction steps to try and test it out.

[Kellen]

Good idea, just tried it: using default figure properties has the same problems as not setting them... Do you think it has anything to do with setting my axes in inches?

axes('units','inches','position',position);

[Shashank Prasanna]

Possible. Can you share the fig file or something we can work with?

[Kellen]

Unfortunately, no. The data needs to stay with me, I'll try to fake up a dataset tomorrow. Thanks for all of your help so far!

[Kellen]

Just for fun, I tried:

print -dpdf /path/to/file.pdf

and that causes the same problems.

[Kellen]

Okay. I've linked to a zip file including "fig_test_code.m" which will make the plot with the fake data I've provided. "pageLandscape.m" and "puttext.m" are support files that my code uses, "test.pdf" is the problem figure output, and "data1.mat and data2.mat" are the fake datasets I've created. I tested this all to make sure that it still has the same problem, and it does, so this should be a good starting point. Thank you for your help and let me know if anything else will be helpful to you.

http://1kellnet.com/plots_suck.zip

[Shashank Prasanna]

Unfortunately, we won't be able to help much without something to work with.

[Kellen]

Shashank, Thanks again for all of your help. It was a simple fix that a friend caught. I create a new axes for a colorbar, and needed to set 'Visible' to 'Off'. Problem Solved. Thanks again!