I'm currently using the Matlab/Octave online IDE at http://www.tutorialspoint.com/execute_matlab_online.php and I'm trying to save a graph that I'm plotting to .pdf format. I've done the following:
- octave
- x = [ 1: 10 ]
- y = x
- plot(x,y)
- print -dpdf graph.pdf
I then refresh the the files and folders to the left, double click on the graph.pdf file and am always greeted with a black filled rectangle. I've then attempted to run the following:
- axis("off")
- print -dpdf graph2.pdf
And the graph appears to save to pdf correctly. However, without the axes. Could you please assist me in finding a solution?
P.S. I have already attempted octave --force-gui and graphics_toolkit('gnu_toolkit')/graphics_toolkit('fltk') with no luck.
At the site hosted, the only graphics toolkit available is gnuplot, which support in octave was mostly dropped several versions ago.
gnuplot has the bug you've described. In the link, people got plotting working by rolling back to previous gnuplot versions.
Guess the only way of getting printing working on the site would be signalling about the issue to its administration.
Also, note that octave crudely depicts the copy of the plot in terminal window. That might suffice for correctness check of the plotting code itself.
Alternatively, you can save octave graphics objects with hgsave command, those then can be loaded in octave on another computer to obtain same plot as one that would be drawn there. (Although, at this point there might be no reason for using online interpreter then.)
Related
I need some to produce some publication-quality figures. I first export the figures from matlab in .svg format, and then I do some post-processing in inkscape. I am no problem with figures generated using plot or scatter, but when I export figures generated using surf (in view(2)), I run into problems. If I use plot or scatter, I am able to ungroup and process various parts like the title, axes, scattered points, lines, etc. in inkscape. For surf, however, matlab just exports one single figures with all various parts grouped into one single unit. I can't separate individual part, and when I zoom very close I can actually see the bitmap resolution for the axes and titles (if I use plot, the titles and axes have 'infinite' resolution when I zoom very close). I am fine with the surface plot having finite resolution, but I need to at least be able to process the axes and titles (which I currently cannot do). What should I do so that I can 'separate' the title and axes from the main plot, just like figures generated from plot and scatter?
I stumbled across this question, since I encountered the same problem.
As mentioned by #vindarmagnus, it is possible to use tikz and get rather nice results. However, tikz experiences problems with large data sets in my experience as present when using surf etc..
Solution, that worked for me:
Change the renderer to painters and the exported .svg file will retain its vectorgraphic properties when opened e.g. in inkscape:
figure('Renderer','Painters');
I used to use Inkscape for my scientific publications as well, but I found that a lot of the time you can get better results with pgfplots in latex, together with the matlab2tikz matlabscript. There’s a ton of resources about this online, but here’s how my workflow would look adopted to your surf situation. I have macOSX with latex, matlab and matlab2tikz installed. Will work with little to no modifications on linux.
In Matlab:
surf(peaks(25))
matlab2tikz('plot.tikz’)
Then I have the following bash-script (just a script in the same folder as the image, which is executed by mere double-click). (Needs to be chmod-ed as an executable for that).
#!/bin/bash
cd ~/Desktop
rm *.eps
cat > plot.tex << EOF
\documentclass{standalone}
\usepackage{pgfplots}
\pgfplotsset{max space between ticks=50}
\pgfplotsset{scaled ticks = false}
\pgfplotsset{compat=1.6}
\pgfplotsset{xticklabel style={/pgf/number format/fixed}}
\pgfplotsset{yticklabel style={/pgf/number format/fixed}}
\begin{document}
\input{plot.tikz}
\end{document}
EOF
pdflatex plot.tex
pdf2ps plot.pdf
ps2eps plot.ps
Note that the row cd ~/Desktop above should be changed as to reflect which folder the script is supposed to be run from (a bit crappy, but needed since Finder doesn’t properly pass along the folder from a program is executed, afaik).
This yields high-quality images in eps or pdf or what you like, with a ton of settings for axes and ticks etc. And it all uses native latex fonts.
Edit:
Recently I’ve begun to use patch() in matlab and then export it to tikz in the same manner as above, with great results. That’s another suggestion!
You can use also:
set(gcf,'Renderer','Painters')
I'm using the still undocumented HG2-Update to create my MATLAB plots, because they just look that much nicer.
(Source: Yair Altman)
Actually, using the current version Release 2013b it works quite nicely and there are not much issues. Except one wants to export the figures as vector graphics (renderer: '-painters'), especially as pdf.
I use the commands:
saveas(gcf,'test.pdf','pdf')
or
print(gcf,'test.pdf','-dpdf')
There are rendering issues, the print does not contain the whole figure and some parts are cropped or non-default fonts are not recognized.
But I'd really like to stay with HG2 and I'd still like to use vector graphics. Is there any solution or workaround?
Exporting vector graphics using the yet not official HG2-Update is quite an issue. The .pdf-export is still totally screwed up.
What is working fine is the .svg-export, apart from that the boundary box is not set properly.
The long workaround would be:
Save the plot with '-dsvg' (print-command) or 'svg' (saveas-command) as vector graphic, open the file in the open source application Inkscape and save again as .pdf with the Export area is drawing checkmark set.
Quite complicated, so I found a way to do it via command-line directly from Matlab (Inkscape still required!):
filename = 'test';
inkscapepath = '"C:\Program Files (x86)\Inkscape\inkscape.exe"';
%// save as .svg
saveas(gcf,filename,'svg')
%// open and save with "export-area-drawing" set via command line
system( [inkscapepath ' ' filename ...
'.svg --export-area-drawing --export-pdf=' filename '.pdf'])
It takes some time, but works without any known issues for now.
Additionally delete the svg-File afterwards:
delete([filename '.svg'])
I had the same problem and used the workaround from thewaywewalk. Now I discovered the MATLAB function "hgexport" works under HG2 (in R2014a).
An issue still was the paper size. I want to use the same size for all graphs with as little white frame as possible. Here you have to set two sizes:
The papersize is set with set(gcf,'PaperSize',[width height]) and the size of your chart is set through export styles. These are set in "Export Setup" or command line:
exp_style=hgexport('readstyle','default');
exp_style.Width = 'width';
exp_style.Height = 'height';
exp_style.Renderer = 'painters';
Now you can export your pdf:
hgexport(gcf,'pdfname',exp_style,'Format','pdf');
PS: In HG2 you may also use Latex for tick labels:
set(gca,'TickLabelInterpreter','latex');
I am looking to export my MATLAB plot as a high quality figure. Specifically, I would like to save it as a vector based file format such as EPS or SVG.
I have tried print and saveas commands:
saveas(h,'myFileName','epsc2');
print('-r150','-depsc2', 'myFilename');
On all occasions this produces poor quality parts of the graph, although the axis-labels are indeed vector. Why does MatLab do some horrible rendering before putting it into an EPS?
Example of poor quality plot here:
http://users.ox.ac.uk/~pemb2372/myFileName.eps
Edit:
It is also worth noting that if you use a Mac viewing an EPS file from Matlab, 'Preview' app may render inner graph content rasterized and poor quality, while leaving the axis and labels vectorized and high quality. This is very misleading but when you open said EPS file in, for example, Inkscape, the quality is actually vector and quite high.
Edit 2:
My university hosting account has expired, so you can no longer view the figure. Suffice it to say that it showed a poor quality raster-style plot within high quality beautiful axis lines, ticks and labels.
I thought I would share the issue I had, and how I overcame it...
I was getting terrible results because I had the wrong renderer set to default. In my startup.m, I had the zbuffer renderer enabled. This is an example eps output.
I made that eps output with: print(gcf,'-depsc2','filename.eps'). This eps is so OBVIOUSLY rasterised. It makes me angry at matlab. Then, I had a brainwave - perhaps my default renderer zbuffer is interfering with the image save process. So, adding the line:
set(gcf,'renderer','painters')
and running the print command as before, here is the output:
Note that I just took screenshots of the eps output files at 100%. And I can confirm the second image is actually vector. Here is a good question/explanation on choosing Renderers in MATLAB.
Matlab can export to pdf with better quality than EPS, but with its own caveats of setting decent margins and font sizes.
edit:
Examples are similar to the EPS case as explained in the help of e.g. print:
saveas(gcf,'filename.pdf')
or
print('-dpdf','filename.pdf')
You might also want to take a look at the PaperSize, PaperPosition and PaperUnits properties of your figure (by means of the set and get functions).
edit: Another option is to use one of the functions available on FileExchange such as the ones mentioned by #user664303 below. My personal favorite for use with LaTeX is matlab2tikz for which the latest version can be gotten from GitHub. Together with the external library of TikZ, I think this delivers some of the most nicest graphs around.
Probably it's also best to mention that I have been actively involved in the matlab2tikz project since 2012.
The export_fig function on the MATLAB file exchange is a reasonably reliable way of accurately exporting figures to eps and pdf (as well as bitmap formats) in MATLAB.
The plot2svg function, also from the file exchange, allows you to export in svg format. It provides some additional benefits, such as being able to export translucent patch objects in vector format.
A comparison of exporting methods is given in this blog post.
I always acquire the final plots (those which are supposed to be inserted into papers and publications) by matplotlib library of python.
You can bet on the amazing quality of the generated plots, both .pdf and .eps formats.
I'm exporting an image in Matlab using the eps format, but it smooths the image. Matlab does not blur the image using other formats such as png. I would like to know how to export a non-blurry image with eps format. Here is the resulting image using png:
And here is the resulting image using eps:
UPDATE:
The problem is reproducible on a Mac, and the issue is with the eps renderer rather than MATLAB. For e.g., saving imagesc(rand(20)) and viewing with Preview and GSview results in the following:
Preview screenshot
GSview screenshot
Clearly, the information is not lost. It is just not interpreted/read correctly by some EPS viewers. The solution is simple: use GSview to view your eps images. You can download it from here
On Macs especially, if your end application is latex/pdflatex, you will have to explicitly set it to use GS/GSview, because otherwise, it will default to the Quartz engine, which is baked into the OS.
PREVIOUS ANSWER:
I am unable to reproduce the behavior your described. Here is the code I used, tested using R2010b on WinXP 32-bit:
M = fspecial('gaussian',[20 20],5);
imagesc(M)
print('-dpng','a.png')
print('-depsc2','b.eps')
a.png
b.eps
Perhaps this is an issue with your EPS viewer...
not sure why it works but you can try doing the following:
eps2eps oldfile newfile
does the trick for me (on a mac os)
At first I thought you were doing something incorrectly, but then I remembered that this was an issue that was bothering the hell out of me a year or so ago. I couldn't come up with a way to "fix" this behaviour and from what I've researched, this is most likely a bug and several others have had this problem too and there is no known solution. Of course, I could be wrong about the last part and there might be solutions out there that have come out since I looked for them.
Any way, my workaround this problem was to use pcolor with shading flat instead of imagesc. When you export this to an eps format it preserves the image correctly. Example:
pcolor(rand(20));
shading flat
print('-depsc','figure.eps')
NOTE: You might see the appearance of thin, faint white lines along the anti-diagonals of each little square (depends on the OS & viewer). These are the edges of the graphics primitives that are used to render the image. However, this is not a flaw in MATLAB's export, but rather a fault in rendering in your EPS/PDF viewer. For e.g., with the default settings in Preview on my mac, these lines show up, whereas with the default in Adobe Reader 9.4, they don't appear.
If anyone is still interested in a workaround: Open the .eps-file with text editor and search for "interpolate". You'll probably find "/Interpolate true def" two or three times. Replace "true" with "false" and be happy :)
A note regarding Yoda's answer: in Preview in Mac OS X, you can make the thin white diagonal lines across each of the squares disappear by unchecking "Anti-alias text and screen art". Of course, the downside is that then any text (e.g. figure axes, etc) is not anti-aliased. Unfortunately, unchecking that has no effect on blurriness if you're using imagesc.
Another note is that if you use preview to make a pdf from your eps, the resulting pdf still displays correctly (non-blurry) when you open it in Acrobat.
I've been long struggling with this problem as well. So far, GSView is the only viewer I've found that displays the eps figures produced by Matlab (R2015b) correctly. eps2eps did not work for me (psutils 1.23).
The following eventually worked for me:
Export the figure to pdf, following the instructions here
pdf2ps file.pdf file.eps
I just wrote this simple drop-in replacement for imagesc. It doesn't support all but the most basic features, but I still hope it helps.
function h = imagesc4pdf(C)
[ny nx] = size(C);
px = bsxfun(#plus, [-0.5; 0.5; 0.5; -0.5], reshape(1:nx, [1 1 nx]));
py = bsxfun(#plus, [-0.5; -0.5; 0.5; 0.5], 1:ny);
n = numel(C);
px = reshape(repmat(px, [1 ny 1]), 4, n);
py = reshape(repmat(py, [1 1 nx]), 4, n);
h = patch(px, py, reshape(C,1,n), 'linestyle', 'none');
xlim([.5 nx+.5]);
ylim([.5 ny+.5]);
set(gca, 'ydir', 'reverse');
Apply opengl renderer to the figure
figure(gcf);
set(gcf,'renderer','opengl');
The blurring actually depends on the rendering software your viewer application or printer uses. To get good results all the time, make each pixel in your image an 8x8 block of pixels of the same color, i.e. resize the image like this:
im2 = imresize(im1, 8, 'nearest');
The blurring then only affects the pixels at the edge of each block. 8x8 blocks are best as they compress without nasty artifacts using DCT compression (sometimes used in eps files).
This page helped me a lot: http://tech.mof-mof.co.jp/blog/machine-learning-octave.html (written in Japanese, please use google translate for it)
And this is also helpful: Octave-Gnuplot-AquaTerm error: set terminal aqua enhanced title "Figure 1"...unknown terminal type"
I also answered at https://www.coursera.org/learn/machine-learning/discussions/weeks/2/threads/Dh-aRfqSEeaHSQ6l4xnh6g.
I reinstalled gnuplot like this:
$ brew cask install xquartz
$ brew cask install aquaterm
$ brew uninstall gnuplot
$ brew install gnuplot --with-aquaterm --with-x11 --with-qt # you can show other options by `$ brew options gnuplot`
You may edit ~/.octaverc like this:
setenv("GNUTERM", "qt")
and in octave window, after typing "system gnuplot", then
set pm3d interpolate 2, 2
After saving the file, open octave-cli.app, and type
imagesc(magic(3)), colorbar
I got this.
I know that Matlab allows for you to format the graph after its created through the interface. However there isn't the same features in Octave. Is there a tool that goes between Octave and GnuPlot? If there isn't such a tool, is there a tool that will generate the formatting options?
I've heard of EasyPlot, but it isn't free.
I've discovered there are some formatting options on the GNU Plot graph after it has been generated through octave. If you press 'm' it's then possible to right click and get a menu with choices to format the plot (line styles/colour/background/print). However, for me it crashes a lot and changing the values doesn't seem to have much effect.
There is some other functionality by using these key presses..
m - allow menu on right-click
a - zoom to full window
p - previous zoom level
r - overlay ruler
g - overlay grid
b - toggle border
1 - toggle output reading format
5 - display radius measure tool (when ruler is displayed)
7 - format aspect ratio (useful to get square plots to not distort scale)
These are just the ones I've found by randomly testing the keyboard (!), so this is hardly exhaustive. But hope that helps.
I've used GNU plot in the past for some visualizations. I didn't find any front end interface to set things like colors or labels but it was easy enough to set some basic things on the command line. This site helped me out: http://t16web.lanl.gov/Kawano/gnuplot/intro/plotcalc-e.html
Octave uses Gnuplot as the default plotting backend, though it supports other options. It also supports most of the graph functions that Matlab does, including ones that change the plot after it was created.