matplotlib-users

[Matplotlib-users] savefig problems with matplotlib

[James L. <jwl...@gm...>]

I have intermittent problems with the savefig('foo.eps') command when I am
using my native LaTeX interpreter to produce eps files.  The really
frustrating thing is that it is intermittent.  Sometimes I can save a file
that looks fine and sometimes I can't.

My box is running Fedora Core 4 and kernel 2.6.14.

I have the following rpms:
python-2.4.1-2
ipython-0.6.15-1.fc4
python-tools-2.4.1-2
python-matplotlib-0.84-1.fc4
python-numeric-23.7-2

Fedora has an out of date ghostscript 7.07, so I installed
ghostscript-8.51from source into /usr/local, but not the fonts, since
they seemed
unnecessary.

As long as I don't use

rc('text', usetex=3DTrue)

I'm ok, but whenever I turn it on, it doesn't work consistently.

Here's some sample code to demonstrate the problem.  If I comment out the r=
c
line, it works fine.

#!/usr/bin/env python

from matplotlib import rc
from matplotlib.numerix import arange, cos, pi
from pylab import *

forces =3D [1, 2, 3, 4]
pofn =3D [.2, .09, .01, .005]

rc('text', usetex=3DTrue)
figure(1)
semilogy(forces,pofn,'k')
xlabel(r'$f_n =3D F_n/\langle F_n \rangle$')
ylabel(r'$P(f_n)$')
axis([0,5,.001,1])

savefig('mtest1.eps')

However, if I run it as is, then I get the following:

[jwlandry@merrimac hopper]$ ./mat-test.py --verbose-helpful
matplotlib data path /usr/share/matplotlib
$HOME=3D/home/jwlandry
CONFIGDIR=3D/home/jwlandry/.matplotlib
loaded rc file /home/jwlandry/.matplotlib/matplotlibrc
matplotlib version 0.84
verbose.level helpful
interactive is False
platform is linux2
numerix Numeric 23.7
font search path ['/usr/share/matplotlib']
loaded ttfcache file /home/jwlandry/.matplotlib/ttffont.cache
backend GTK version 2.6.2

This is dvips(k) 5.95a Copyright 2005 Radical Eye Software (
www.radicaleye.com)
' TeX output 2005.11.25:1645' -> e0dab64d0b15f2821ec713a6e7903ff4.ps
<tex.pro><psfrag.pro><texps.pro><special.pro><color.pro>. <cmr8.pfb>
<cmsy8.pfb><cmsy10.pfb><cmmi8.pfb><cmmi10.pfb><cmr10.pfb>[1
<e0dab64d0b15f2821ec713a6e7903ff4.eps>]

When it doesn't work, a dialog box opens with this message

Save figure failure:
None: Interrupted system call


Help!

James Landry


--
James W. Landry
jwl...@gm...

Re: [Matplotlib-users] savefig problems with matplotlib

[James L. <jwl...@gm...>]

Thanks for the suggestion Jose.  I installed the new version and the same
problem appeared again.  I'm getting some ideas though.  When I tried it
again by uncommenting the rc line, it worked the first time but not the
second.  Doesn't it cache some of the information?  Could that be the
problem?

James Landry

On 11/25/05, Jos=E9 Matos <jao...@gm...> wrote:
>
> On 25/11/05, James Landry <jwl...@gm...> wrote:
> > I have intermittent problems with the savefig('foo.eps') command when I
> am
> > using my native LaTeX interpreter to produce eps files.  The really
> > frustrating thing is that it is intermittent.  Sometimes I can save a
> file
> > that looks fine and sometimes I can't.
> >
> >  My box is running Fedora Core 4 and kernel 2.6.14.
> >
> >  I have the following rpms:
> >  python-2.4.1-2
> >  ipython-0.6.15-1.fc4
> >  python-tools-2.4.1-2
> >  python-matplotlib-0.84-1.fc4
> >  python-numeric-23.7-2
>
>   Probably it is irrelevant to this problem and it does not help here
> but notice that 0.85 is available from extras.
>



--
James W. Landry
jwl...@gm...

Re: [Matplotlib-users] savefig problems with matplotlib

[John H. <jdh...@ac...>]

>>>>> "James" == James Landry <jwl...@gm...> writes:

    James> When it doesn't work, a dialog box opens with this message

    James> Save figure failure: None: Interrupted system call

What backend are you using?  I have seen something like this on GTK*.
I'm pretty sure it is a threading problem.  Basically, we need a
backend dependent thread-safe way to make system calls.  Not a trivial
task.  I've posted a thread about this to the pygtk mailing list a few
months ago, but have yet to find a reliable recipe.  gtk gurus, please
advise.

In the meantime, you may want to try a different GUI backend, eg,
tkagg.  If this helps, let us know, because it will help determine
that this is indeed your problem.


JDH

Re: [Matplotlib-users] savefig problems with matplotlib

[James L. <jwl...@gm...>]

I tried using tkagg by setting

backend  : TkAgg

in my matplotlibrc, which includes only the following lines:

backend         : TkAgg

# latex options for matplotlib

font.latex.package    : type1cm
text.usetex        : False
text.tex.engine        : latex

I get the following message, when I try to use it, which I don't understand=
,
because I have tkinter installed:

[jwlandry@merrimac flow]$ ~/grain/plots/hopper/pof-w-insert.py data_hopper-
40k-r1.5.funnel-pof.combo data_hopper-40k-r2.funnel-pof.combo data_hopper-
40k-r4.funnel-pof.combo data_hopper-40k-r6.funnel-pof.combo
Traceback (most recent call last):
  File "/home/jwlandry/grain/plots/hopper/pof-w-insert.py", line 12, in ?
    from pylab import *
  File "/usr/lib/python2.4/site-packages/pylab.py", line 1, in ?
    from matplotlib.pylab import *
  File "/usr/lib/python2.4/site-packages/matplotlib/pylab.py", line 217, in
?
    new_figure_manager, draw_if_interactive, show =3D pylab_setup()
  File "/usr/lib/python2.4/site-packages/matplotlib/backends/__init__.py",
line 24, in pylab_setup
    globals(),locals(),[backend_name])
  File
"/usr/lib/python2.4/site-packages/matplotlib/backends/backend_tkagg.py",
line 8, in ?
    import tkagg                 # Paint image to Tk photo blitter extensio=
n
  File "/usr/lib/python2.4/site-packages/matplotlib/backends/tkagg.py", lin=
e
1, in ?
    import _tkagg
ImportError: No module named _tkagg

James

On 11/25/05, John Hunter <jdh...@ac...> wrote:
>
> >>>>> "James" =3D=3D James Landry <jwl...@gm...> writes:
>
>     James> When it doesn't work, a dialog box opens with this message
>
>     James> Save figure failure: None: Interrupted system call
>
> What backend are you using?  I have seen something like this on GTK*.
> I'm pretty sure it is a threading problem.  Basically, we need a
> backend dependent thread-safe way to make system calls.  Not a trivial
> task.  I've posted a thread about this to the pygtk mailing list a few
> months ago, but have yet to find a reliable recipe.  gtk gurus, please
> advise.
>
> In the meantime, you may want to try a different GUI backend, eg,
> tkagg.  If this helps, let us know, because it will help determine
> that this is indeed your problem.
>
>
> JDH
>



--
James W. Landry
jwl...@gm...

Re: [Matplotlib-users] savefig problems with matplotlib

[John H. <jdh...@ac...>]

>>>>> "James" == James Landry <jwl...@gm...> writes:

    James> I get the following message, when I try to use it, which I
    James> don't understand, because I have tkinter installed:

It means that matpltolib was not able to find the tk src code needed
to compile the tkagg extension.  Usually this is because you haven't
installed the tk-dev and tcl-dev packages.

JDH

Re: [Matplotlib-users] savefig problems with matplotlib

[James L. <jwl...@gm...>]

Maybe this is a dumb question, but I've installed tk-devel and tcl-devel.
Still doesn't work.  Do I need to reinstall matplotlib or do it from source=
?

James

On 11/25/05, John Hunter <jdh...@ac...> wrote:
>
> >>>>> "James" =3D=3D James Landry <jwl...@gm...> writes:
>
>     James> I get the following message, when I try to use it, which I
>     James> don't understand, because I have tkinter installed:
>
> It means that matpltolib was not able to find the tk src code needed
> to compile the tkagg extension.  Usually this is because you haven't
> installed the tk-dev and tcl-dev packages.
>
> JDH
>



--
James W. Landry
jwl...@gm...

Re: [Matplotlib-users] savefig problems with matplotlib

[John H. <jdh...@ac...>]

>>>>> "James" == James Landry <jwl...@gm...> writes:

    James> Maybe this is a dumb question, but I've installed tk-devel
    James> and tcl-devel.  Still doesn't work.  Do I need to reinstall
    James> matplotlib or do it from source?

Yes, after installing the dev headers you will need to rebuild
matplotlib from src.  I suggest you capture the output of the build
process is case you need to post it

> sudo rm -rf build
> sudo python setup.py install >& build.out

JDH

    James> James

    James> On 11/25/05, John Hunter <jdh...@ac...>
    James> wrote:
    >>  >>>>> "James" == James Landry <jwl...@gm...> writes:
    >> 
    James> I get the following message, when I try to use it, which I
    James> don't understand, because I have tkinter installed:
    >>  It means that matpltolib was not able to find the tk src code
    >> needed to compile the tkagg extension.  Usually this is because
    >> you haven't installed the tk-dev and tcl-dev packages.
    >> 
    >> JDH
    >> 



    James> -- James W. Landry jwl...@gm...

Re: [Matplotlib-users] savefig problems with matplotlib

[James L. <jwl...@gm...>]

It works fine in TkAgg.  That implies that you are right and it is a
threading problem in pygtk.  Thanks a lot for tracking this down.

James Landry

On 11/25/05, John Hunter <jdh...@ac...> wrote:
>
> >>>>> "James" =3D=3D James Landry <jwl...@gm...> writes:
>
>     James> Maybe this is a dumb question, but I've installed tk-devel
>     James> and tcl-devel.  Still doesn't work.  Do I need to reinstall
>     James> matplotlib or do it from source?
>
> Yes, after installing the dev headers you will need to rebuild
> matplotlib from src.  I suggest you capture the output of the build
> process is case you need to post it
>
> > sudo rm -rf build
> > sudo python setup.py install >& build.out
>
> JDH
>
>     James> James
>
>     James> On 11/25/05, John Hunter <jdh...@ac...>
>     James> wrote:
>     >>  >>>>> "James" =3D=3D James Landry <jwl...@gm...> writes:
>     >>
>     James> I get the following message, when I try to use it, which I
>     James> don't understand, because I have tkinter installed:
>     >>  It means that matpltolib was not able to find the tk src code
>     >> needed to compile the tkagg extension.  Usually this is because
>     >> you haven't installed the tk-dev and tcl-dev packages.
>     >>
>     >> JDH
>     >>
>
>
>
>     James> -- James W. Landry jwl...@gm...
>



--
James W. Landry
jwl...@gm...