Re: [Matplotlib-users] zorder seems to cause problems when embed python in latex files

[Michael D. <md...@st...>]

With the file you sent, I can see the messed up footer in xpdf, but not 
in acroread.  There are a number of times that I have seen xpdf not 
completely support the PDF spec, and this may be one of them.

Creating my own files, however, I'm not able to reproduce this here.

When I compile your test.tex, I get an error, even though it seems to 
have loaded the python.sty file.  Not sure why (see attached log).

When I generate the plots "offline", and then hack test.tex to simply 
include the files, everything works fine, and I don't see a problem with 
the footers with either xpdf or acroread.

There was a recent bug discovered in matplotlib where PDF files weren't 
always getting flushed completely.  I don't *think* that's the cause of 
this, but if you could reproduce what I did (generate the plots 
independently of TeX and then load them), and that works for you, that 
might point to something like that. 

There was also a bug a few months back where xpdf didn't like the way 
matplotlib handled reusing the same graphic multiple times (which is 
used for markers).  That may be why you're seeing the footer bug and I'm 
not -- you didn't mention which version of matplotlib you're running, so 
it's hard to say.

Here's my versions of all the various moving pieces:
> pdfTeX (Web2C 7.4.5) 3.14159-1.10b
> kpathsea version 3.4.5
> Copyright (C) 1997-2003 Han The Thanh.
Beamer 3.00
python 2.5.2
matplotlib SVN (today)
Acroread 8.1.1
xpdf 3.00

That python.sty stuff looks really cool, by the way.  I haven't come 
across it before.

Mike

ch...@se... wrote:
> On Tue, Oct 14, 2008 at 08:21:08AM -0400, Michael Droettboom wrote:
>   
>> But I've never tried this combination of python.sty/Beamer/LaTeX
>> personally.  Can you send us the output of your plot on its own (ps or
>> pdf...)?
>>     
>
> Mike
>
> Wow thanks.  I was afraid no one would respond.  I suppose if Matplotlib is so
> mature that we are left worrying about bugs when embedding it in Latex then it
> has come a long way. :)
>
> I created a tiny test.tex that shows the problem.  Just type
>
> pdflatex -shell-escape test.tex ; xpdf test.pdf
>
> in the same directory with the 2 files test.tex and python.sty below and
> attached.  I also attached the final PDF since you asked for it.
>
> \documentclass{beamer}
> \usepackage{beamerthemesplit}
> \usepackage{graphicx}
> \usepackage{python}
> \begin{document}
> \title[Example of zorder trouble]{Example of zorder trouble}
> \author[Matplotlib fan]{Matplotlib fan}
> \date{}
> \setbeamertemplate{navigation symbols}{}
> \frame{\titlepage}
>
> \begin{frame}[fragile]\frametitle{No zorder - notice footer ok}
> \begin{python}
> import pylab
> pylab.plot(range(10), range(10))
> pylab.scatter([5], [5])
> pylab.savefig('plot1.pdf')
> print r'\includegraphics[width=200pt]{plot1.pdf}'
> \end{python}
> \end{frame}
>
> \begin{frame}[fragile]\frametitle{zorder - notice footer messed up}
> \begin{python}
> import pylab
> pylab.plot(range(10), range(10), zorder = 1)
> pylab.scatter([5], [5], zorder = 9)
> pylab.savefig('plot2.pdf')
> print r'\includegraphics[width=200pt]{plot2.pdf}'
> \end{python}
> \end{frame}
>
> \end{document}
>
>
>
>
>
>
> %% This program is free software; you can redistribute it and/or
> %% modify it under the terms of the GNU General Public License
> %% as published by the Free Software Foundation; either version 2
> %% of the License, or (at your option) any later version.
> %%
> %% This program is distributed in the hope that it will be useful,
> %% but WITHOUT ANY WARRANTY; without even the implied warranty of
> %% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
> %% GNU General Public License for more details.
> %%
> %% You should have received a copy of the GNU General Public License
> %% along with this program; if not, write to the Free Software
> %% Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
> %%
> %% Author: Martin R. Ehmsen, eh...@im....
> %% Department of Mathematics and Computer Science,
> %% University of Southern Denmark, DK
> %%
> %% You can find an online copy of the GPL at
> %% http://www.gnu.org/copyleft/gpl.html .
> %%
> %% Note: shell-escape needs to be activated for this to work.
> %% This can either be done by passing -shell-escape as an option to
> %% latex or by adding/changing "shell_escape = t" in your texmf.cnf .
>
> % 0.2 -> 0.21: Moved \newwrite\@module from \@writemodule and out, since
> % no more than 15 \newwrites are allowed (and the previous version created a new
> % every time \@writemodule was called.
>
> \NeedsTeXFormat{LaTeX2e}[1994/12/01]
> \ProvidesPackage{python}[2007/06/07 v0.21 Python in LaTeX]
>
> \newwrite\@out
> \newwrite\@module
>
> \begingroup \catcode `|=0 \catcode `[=1
> \catcode`]=2 \catcode `\{=12 \catcode `\}=12
> \catcode`\\=12 |gdef|@xpython#1\end{python}[|immediate|write|@out[#1]|end[python]]
> |endgroup
>
> \def\python{\kernel@ifnextchar [{\@python}{\@python[]}}
>
> \def\@python[#1]{%
> \gdef\@pythoninclude{#1}
> \immediate\openout\@out=\jobname.py
> \newlinechar='15
> \begingroup \catcode`\^^M=12 %
> \let\do\@makeother\dospecials\obeyspaces%
> \@xpython}
>
> \def\endpython{%
> \endgroup
> \immediate\closeout\@out
> \@writemodule
> \immediate\write18{cat \@pythoninclude\space\jobname.py | python > \jobname.py.out 2> \jobname.py.err}
> \immediate\input\jobname.py.out}
> %\immediate\write{\begin{verbatim}}
> %\immediate\input\jobname.py.err
> %\immediate\write{\end{verbatim}}}
>
> \def\@writemodule{%
> \immediate\openout\@module=latex.py
> \immediate\write\@module{jobname="\jobname"}
> \immediate\closeout\@module}
>
> % BUGS:
> % 1. If anything gets send to stderr then it should be included
> % in \begin{verbatim}...\end{verbatim} to be properly displayed
> %
> % \immediate\write18{cat \@pythoninclude\space\jobname.py | python > \jobname.py.out 2>\jobname.py.err}
> %
> % 2. Watch out for indentation done by aucTeX in Emacs
> %
> % 3. Let the package accept a "final version" option, such
> % that the output of each python run is saved such that it can be
> % inserted into the document by hand
> % (conference, journals are not likely to compile with
> % shell_escape or have python).
> %
> % \gdef\@prepython{}
> % \def\prepython#1{%
> % \gdef\@prepython{#1}
> % }
> % sed -e 's/^  //g' cluster.py
> % \immediate\write18{\@prepython\space\jobname.py > \
>   

-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA