I have an iPython notebook that contains an inline plot (i.e. it contains the command plot(x,y)). When I issue the command ipython nbconvert --to latex --post PDF --SphinxTransformer.author='Myself' MyNotebook.ipynb the resulting .PDF file contains the figure, but it has been exported to .PNG, so it doesn't look very good (pixelated). How can I tell nbconvert to export all plots/figures to .EPS instead?
Thank you
First of all the notebook is not responsible for creating plots, but matplotlib and this allows to render your plots as eps, pdf, svg, etc. in great quality to be included in publications.
I agree that the default inline plot format, i.e. png is not optimal to be used for publications due to several reasons. As given in the github issue you posted in your answer, the inline backend can be configured to use svg instead of png by calling
%config InlineBackend.figure_format = 'svg'
in a code cell.
With this, the newly created plots will be vectorial, (as Matt said, already rendered pngs will not be converted!). These svgs are embedded in the notebook (svgs can be rendered by modern browsers) and are subsequently converted to pdfs by nbconvert. These pdfs fulfil the requirements of publication ready plots. However, be aware that the svgs can be really huge (compared with pngs) and may slow down the notebook handling significantly.
Your initial question was about eps graphics. As said above, matplotlib can render eps, hence, you can always do something like savefig('plot1.eps') to create the desired figures. That's actually the way I create my publication figures (png in notebook, eps in paper).
Let's assume we would get IPython to generate eps files (embedded but not renderable in the browser). The tex file generated by nbconvert is designed to work with pdflatex. If fed with eps files pdflatex would convert these to pdf to be included in the final document. So basically it does the same as nbconvert currently does with the svgs. Thus, there is no benefit.
Finally, I want to point out that, even though the tex files generated by nbconvert look great (especially the ones created using the master branch), IMHO there is no way to use these files without touching (e.g. adding captions, scaling images, ...). Therefore, you could always include the eps files at this step into your papers.
NBconvert does not run your code. So if you haven't plotted with SVG matplotlib backend it is not possible.
If you did so, then you need to write a nbconvert preprocessor that does svg-> eps and extend the relevant template to know how to embed EPS.
Evidently this is a missing feature in nbconvert. There is not currently a way to get publication quality plots in your final PDF: https://github.com/ipython/ipython/issues/3603
https://github.com/ipython/ipython/issues/3693
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 am trying to export a figure which includes highlighting of regions - something like this: Highlight parts of matlab plot. Unfortunately, when I export the figures to .eps files the size is of the order of ~10 MB... Thus, when I include them in a tex file, the quality is severely degraded. As expected this problem seems to occur due to the use of the area function for the highlighting. Is there any workaround on this?
You have transparency in your plot which requires the renderer to be OpenGL which causes any EPS to not really be vector graphics but rather bitmaps coerced in some strange way. This is why the file size is much larger than what you would expect for vector graphics. If you open the resulting EPS file with an external editor (Illustrator, Inkscape, etc.) you will see what I am talking about. As a side-note, transparency isn't technically supported in EPS files.
Your options are really to
Save your figures as something else such as TIFF or PNG
You could try saving the figure as an EPS using export_fig from the file exchange but you will likely still have the same issue.
Turn off transparency, save to an EPS, and use Illustrator or an external program to change the transparency and try to save as an EPS file and see if you get better results.
So recently I decided to not use the standard markers that Matlab provides and use my own via: a set of fonts including Webdings or WingDings. I make a standard scatter plot, and plot the text (in wingdings), using the text command, over the locations of the markers.
When I save these plots as png files, they print perfectly. They also appear perfectly on my screen after plotting.
However when I save these plots as eps files, the webdings are turning into their original letters 'l' or 'w'. It also looks like it's plotting them in a Courier font, but my default is Helvetica.
I've read through this previous post, but my question differs in that he is looking to use Latex as the interpreter and to include fonts, whereas I don't want to use Latex as the interpreter. However, it seems like my default interpreter (not sure what that is), isn't doing the job when converting to EPS.
Example:
imageR='w'
text(xf2,yf2,imageR,'fontName',font,'FontSize',fontR,'HorizontalAl','left','color','w')
I figured it out....took me way too long.
Ghostscript / Postscript only export with a few fonts when you are exporting eps files.
This link was incredibly helpful.
I just switched from wingdings/webdings to ZapfDinbats...Practically the same thing...
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.