matplotlib-users Mailing List for matplotlib

First, you folks respond faster than lightning -- I can't keep up!
Second, thanks for the tip -- that's definitely more elegant than my callow
approach.
John Hunter-4 wrote:
> 
> On Thu, Sep 1, 2011 at 1:23 PM, CompBio <rog...@cs...> wrote:
> 
>> BTW, the reason I specify a PDF backend is because I thought it would
>> tell
>> matplotlib not to try to use anything else "behind the scenes" such as an
>> X-window display. It's working the way I want now, so I assume that's
>> what
>> it's doing.
> 
> But at others have pointed out, your code is unnecessarily complex. Just
> do
> 
> import matplotlib
> matplotlib.use('agg')
> import pylab
> 
> and when you call savefig, you can pass ps, eps, pdf, png or svg and
> the mpl code will choose the right backend, and never launch a GUI.
> 
> JDH
> 
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On Thu, Sep 1, 2011 at 1:23 PM, CompBio <rog...@cs...> wrote:
> BTW, the reason I specify a PDF backend is because I thought it would tell
> matplotlib not to try to use anything else "behind the scenes" such as an
> X-window display. It's working the way I want now, so I assume that's what
> it's doing.
But at others have pointed out, your code is unnecessarily complex. Just do
import matplotlib
matplotlib.use('agg')
import pylab
and when you call savefig, you can pass ps, eps, pdf, png or svg and
the mpl code will choose the right backend, and never launch a GUI.
JDH

Thanks for your fast response -- faster than I could post a follow-up.
You're right about the stack trace. It occurred to me after I posted that I
should look to see exactly where the exception was triggered. As it turned
out, I'd added a new module a few days ago and wasn't careful about where I
added the import. Here at work it didn't make a difference, but launching
from home...
Once I reordered the new import the error disappeared.
BTW, the reason I specify a PDF backend is because I thought it would tell
matplotlib not to try to use anything else "behind the scenes" such as an
X-window display. It's working the way I want now, so I assume that's what
it's doing.
Benjamin Root-2 wrote:
> 
> On Thursday, September 1, 2011, CompBio <rog...@cs...> wrote:
>>
>> I'm trying to get a script to work in batch mode to produce a large
>> number
> of
>> plots. I've got the following sequence of imports in a matplotlib Python
>> script:
>>
>> import matplotlib, os, sys
>> ...
>> if file_ext == 'png' :
>> sys.stderr.write('Using PNG output format\n')
>> matplotlib.use('agg')
>> elif file_ext == 'pdf' :
>> sys.stderr.write('Using PDF output format\n')
>> matplotlib.use('PDF')
>>
>> from pylab import *
>>
>> ... remainder of plotting code ...
>>
>> At first this appeared to work without any problems. I could kick off a
> job
>> in background, log off the machine and return later when all the graphs
> had
>> been produced.
>>
>> Now I get this RuntimeError exception. Is there anything else I need to
> do
>> to convince matplotlib that it doesn't need my local display?
>>
>> thanks!
>> --
> 
> Without the stack trace, it would be hard to tell. Plus, there is already
> logic in the backends to switch to PDF and such for saving files. It
> should
> only be necessary to set the backend to AGG if you want a headless batch
> script.
> 
> Ben Root
> 
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> 
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On 09/01/2011 05:37 AM, CompBio wrote:
>
> I'm trying to get a script to work in batch mode to produce a large number of
> plots. I've got the following sequence of imports in a matplotlib Python
> script:
Is the script being run standalone, from a shell, and are the following 
the very first imports?
>
> import matplotlib, os, sys
> ...
> if file_ext == 'png' :
> sys.stderr.write('Using PNG output format\n')
> matplotlib.use('agg')
> elif file_ext == 'pdf' :
> sys.stderr.write('Using PDF output format\n')
> matplotlib.use('PDF')
As Ben notes, you don't need the above logic to choose between agg and 
pdf; but you are correct in choosing a non-interactive backend before 
any import of pylab or pyplot. That should be enough to prevent any 
subsequent attempt to open a display.
I'll bet the problem is that when the code above is run, file_ext is 
neither 'png' nor 'pdf', so matplotlib.use is not being executed.
>
> from pylab import *
>
And at this point pylab is simply setting the default (interactive) backend.
> ... remainder of plotting code ...
>
> At first this appeared to work without any problems. I could kick off a job
> in background, log off the machine and return later when all the graphs had
> been produced.
>
> Now I get this RuntimeError exception. Is there anything else I need to do
> to convince matplotlib that it doesn't need my local display?
No--you just have to make sure that a non-interactive backend is getting 
set before the first pylab or pyplot import.
Eric
>
> thanks!

On Thursday, September 1, 2011, CompBio <rog...@cs...> wrote:
>
> I'm trying to get a script to work in batch mode to produce a large number
of
> plots. I've got the following sequence of imports in a matplotlib Python
> script:
>
> import matplotlib, os, sys
> ...
> if file_ext == 'png' :
> sys.stderr.write('Using PNG output format\n')
> matplotlib.use('agg')
> elif file_ext == 'pdf' :
> sys.stderr.write('Using PDF output format\n')
> matplotlib.use('PDF')
>
> from pylab import *
>
> ... remainder of plotting code ...
>
> At first this appeared to work without any problems. I could kick off a
job
> in background, log off the machine and return later when all the graphs
had
> been produced.
>
> Now I get this RuntimeError exception. Is there anything else I need to
do
> to convince matplotlib that it doesn't need my local display?
>
> thanks!
> --
Without the stack trace, it would be hard to tell. Plus, there is already
logic in the backends to switch to PDF and such for saving files. It should
only be necessary to set the backend to AGG if you want a headless batch
script.
Ben Root

I'm trying to get a script to work in batch mode to produce a large number of
plots. I've got the following sequence of imports in a matplotlib Python
script:
import matplotlib, os, sys
...
if file_ext == 'png' :
 sys.stderr.write('Using PNG output format\n')
 matplotlib.use('agg')
elif file_ext == 'pdf' :
 sys.stderr.write('Using PDF output format\n')
 matplotlib.use('PDF')
from pylab import *
... remainder of plotting code ...
At first this appeared to work without any problems. I could kick off a job
in background, log off the machine and return later when all the graphs had
been produced.
Now I get this RuntimeError exception. Is there anything else I need to do
to convince matplotlib that it doesn't need my local display?
thanks!
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Hi:
I am having problems with the \dagger LaTex symbol. The following code
import matplotlib.pyplot as plt
plt.plot([1,2,3])
plt.title(r'$ \dagger $')
plt.show()
produce a long Traceback that ends in
File "/usr/lib/pymodules/python2.6/matplotlib/mathtext.py", line 1997,
in raise_error
 raise ParseFatalException(msg + "\n" + s)
ParseFatalException: Expected end of math '$'
$ \dagger $ (at char 0), (line:1, col:1)
Other LaTex symbols works OK. For instance, if I use plt.title(r'$
\diamond $') instead, it works. I checked in mathtext.py, and \dagger
is in the list of symbols.
I am running Matplotlib '0.99.1.1'.
Any idea about this problem?
Alejandro.

Apologies -- I should have read the subject line! :)
On 1 September 2011 14:00, Carlos Grohmann <car...@gm...>wrote:
> Hello Robert,
>
> Thank you for your kind response, but I'm looking into py2app, for Mac OSX,
> and it is a bit different than py2exe. I do have a py2exe script working
> (lots of examples around), but I'm still a bit lost on the Mac-related
> stuff.
>
> cheers
>
> Carlos
>
>
> On Thu, Sep 1, 2011 at 05:34, Robert Sudwarts <rob...@gm...>wrote:
>
>> Hi Carlos,
>>
>> It's a bit tricky giving you a complete example as the specifics will vary
>> considerably depending on which versions of python, matplotlib & wx you're
>> using:
>>
>> I'd point you toward the wxPyWiki page at:
>> http://wiki.wxpython.org/py2exe-python26 which gives a pretty sound
>> example based on an output produced by GUI2Exe (written by Andrea Gavana)
>>
>> As for matplotlib specifically, see:
>> http://www.py2exe.org/index.cgi/MatPlotLib (again depending very much on
>> the versions you're using), I've found that the first example given works
>> perfectly.
>>
>> Hope that helps!
>>
>>
>>
>>
>>
>> On 1 September 2011 04:42, Carlos Grohmann <car...@gm...>wrote:
>>
>>> Hello all.
>>>
>>> I've been looking for a good example of setup.py to build a bundle app
>>> with wxpython+matplotlib.
>>> Can someone share or point me in a direction?
>>>
>>> thanks
>>>
>>> --
>>> Prof. Carlos Henrique Grohmann - Geologist D.Sc.
>>> Institute of Geosciences - Univ. of São Paulo, Brazil
>>> http://www.igc.usp.br/pessoais/guano
>>> http://lattes.cnpq.br/5846052449613692
>>> Linux User #89721
>>> ________________
>>> Can’t stop the signal.
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Special Offer -- Download ArcSight Logger for FREE!
>>> Finally, a world-class log management solution at an even better
>>> price-free! And you'll get a free "Love Thy Logs" t-shirt when you
>>> download Logger. Secure your free ArcSight Logger TODAY!
>>> http://p.sf.net/sfu/arcsisghtdev2dev
>>> _______________________________________________
>>> Matplotlib-users mailing list
>>> Mat...@li...
>>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>>
>>>
>>
>
>
> --
> Prof. Carlos Henrique Grohmann - Geologist D.Sc.
> Institute of Geosciences - Univ. of São Paulo, Brazil
> http://www.igc.usp.br/pessoais/guano
> http://lattes.cnpq.br/5846052449613692
> Linux User #89721
> ________________
> Can’t stop the signal.
>

Hello Robert,
Thank you for your kind response, but I'm looking into py2app, for Mac OSX,
and it is a bit different than py2exe. I do have a py2exe script working
(lots of examples around), but I'm still a bit lost on the Mac-related
stuff.
cheers
Carlos
On Thu, Sep 1, 2011 at 05:34, Robert Sudwarts <rob...@gm...>wrote:
> Hi Carlos,
>
> It's a bit tricky giving you a complete example as the specifics will vary
> considerably depending on which versions of python, matplotlib & wx you're
> using:
>
> I'd point you toward the wxPyWiki page at:
> http://wiki.wxpython.org/py2exe-python26 which gives a pretty sound
> example based on an output produced by GUI2Exe (written by Andrea Gavana)
>
> As for matplotlib specifically, see:
> http://www.py2exe.org/index.cgi/MatPlotLib (again depending very much on
> the versions you're using), I've found that the first example given works
> perfectly.
>
> Hope that helps!
>
>
>
>
>
> On 1 September 2011 04:42, Carlos Grohmann <car...@gm...>wrote:
>
>> Hello all.
>>
>> I've been looking for a good example of setup.py to build a bundle app
>> with wxpython+matplotlib.
>> Can someone share or point me in a direction?
>>
>> thanks
>>
>> --
>> Prof. Carlos Henrique Grohmann - Geologist D.Sc.
>> Institute of Geosciences - Univ. of São Paulo, Brazil
>> http://www.igc.usp.br/pessoais/guano
>> http://lattes.cnpq.br/5846052449613692
>> Linux User #89721
>> ________________
>> Can’t stop the signal.
>>
>>
>> ------------------------------------------------------------------------------
>> Special Offer -- Download ArcSight Logger for FREE!
>> Finally, a world-class log management solution at an even better
>> price-free! And you'll get a free "Love Thy Logs" t-shirt when you
>> download Logger. Secure your free ArcSight Logger TODAY!
>> http://p.sf.net/sfu/arcsisghtdev2dev
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>>
>
-- 
Prof. Carlos Henrique Grohmann - Geologist D.Sc.
Institute of Geosciences - Univ. of São Paulo, Brazil
http://www.igc.usp.br/pessoais/guano
http://lattes.cnpq.br/5846052449613692
Linux User #89721
________________
Can’t stop the signal.

Hi Carlos,
It's a bit tricky giving you a complete example as the specifics will vary
considerably depending on which versions of python, matplotlib & wx you're
using:
I'd point you toward the wxPyWiki page at:
http://wiki.wxpython.org/py2exe-python26 which gives a pretty sound example
based on an output produced by GUI2Exe (written by Andrea Gavana)
As for matplotlib specifically, see:
http://www.py2exe.org/index.cgi/MatPlotLib (again depending very much on the
versions you're using), I've found that the first example given works
perfectly.
Hope that helps!
On 1 September 2011 04:42, Carlos Grohmann <car...@gm...>wrote:
> Hello all.
>
> I've been looking for a good example of setup.py to build a bundle app with
> wxpython+matplotlib.
> Can someone share or point me in a direction?
>
> thanks
>
> --
> Prof. Carlos Henrique Grohmann - Geologist D.Sc.
> Institute of Geosciences - Univ. of São Paulo, Brazil
> http://www.igc.usp.br/pessoais/guano
> http://lattes.cnpq.br/5846052449613692
> Linux User #89721
> ________________
> Can’t stop the signal.
>
>
> ------------------------------------------------------------------------------
> Special Offer -- Download ArcSight Logger for FREE!
> Finally, a world-class log management solution at an even better
> price-free! And you'll get a free "Love Thy Logs" t-shirt when you
> download Logger. Secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsisghtdev2dev
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>

Hello all.
I've been looking for a good example of setup.py to build a bundle app with
wxpython+matplotlib.
Can someone share or point me in a direction?
thanks
-- 
Prof. Carlos Henrique Grohmann - Geologist D.Sc.
Institute of Geosciences - Univ. of São Paulo, Brazil
http://www.igc.usp.br/pessoais/guano
http://lattes.cnpq.br/5846052449613692
Linux User #89721
________________
Can’t stop the signal.

On 08/31/2011 01:59 PM, Benjamin Root wrote:
> On Wed, Aug 31, 2011 at 6:35 PM, Craig Finch <cf...@ie...
> <mailto:cf...@ie...>> wrote:
>
> I figured it out! I accidentally did something weird. When I built
> NumPy and SciPy, I used the --user option to tell distutils to build
> them in my home directory. I had not realized that --user installs
> the packages in ~/.local/lib/python2.7/site-packages/. I was
> assuming they would be installed in ~/lib/python2.7/site-packages,
> but I didn't notice they were "missing" until just now. When I
> reinstalled NumPy and Scipy using the option --prefix=/home/cfinch
> and then rebuilt matplotlib, everything started working. I didn't
> have to rebuild pycairo or pygtk; I just had to get everything in
> the same location. This is the first I've heard of installing
> anything in a .local directory...why is that even an option???
>
> Thanks for your help!
>
>
> It is a standard directory in linux now. Started by the freedesktop.org
> <http://freedesktop.org>, I think. Personally, I prefer it over having
> ~/lib, ~/bin and such cluttering my home directory.
>
> http://standards.freedesktop.org/basedir-spec/basedir-spec-latest.html
Aha! So that's where .config came from, also. IPython is using it; I 
suppose we should, too.
Eric
>
> Ben Root
>
>
>
> ------------------------------------------------------------------------------
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> price-free! And you'll get a free "Love Thy Logs" t-shirt when you
> download Logger. Secure your free ArcSight Logger TODAY!
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>
>
>
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On 08/31/2011 01:15 PM, José Alexandre Nalon wrote:
> Hello,
>
> some weeks ago, I recompiled matplotlib to get locale support for
> commas, and started to get strange dimension errors while trying
> to save the figure. Now here is another error that I think that
> is somewhat related to it. When I try to run the script below,
> savefig() gives me an IndexError:
>
> --
> from pylab import *
>
> a1 = figure(1).add_subplot(111, polar=True)
> a1.scatter([ 3.*pi/7. ], [ 0.65 ], color='black', marker='o')
> a1.annotate('Target', (3.*pi/7., 0.65), xytext=(3.*pi/7., 0.7))
> savefig("Radar.eps")
>
> <...long stack...>
> IndexError: Unexpected SeqBase<T> length.
This is coming from CXX.
I am not going to be able to figure out what the problem is, but those 
who are (the C++ wizards) will probably want to see the full stack 
trace, as well as the matplotlib version and the compilation parameters: 
platform, compiler, python version, etc. The first part of the output 
from setup.py build has all that.
Eric
> ---
>
> This is in the savefig() function again, and this is related to
> text, since the error disappear if I remove the annotation. But
> I think I can affirm, with a great degree of certainty, that this
> happens because I recompiled matplotlib: this is an old script
> that wouldn't give me any error before.
>
> So, I'm probably missing some dependency, but the setup.py script
> won't tell me what is missing, and the only warning I get during
> compilation is the -Wstrict_prototypes one.
>
> Actually, I am happy to find out this, since it was probably
> a configuration problem that generated the errors (and matplotlib
> source is ok). But if anyone can give me any clue on how to solve
> this, that would be greatly appreciated.
>
> ---
> José Alexandre Nalon
> na...@te...

On 8/31/2011 8:08 PM, Jae-Joon Lee wrote:
> Can you file an github issue for this?
https://github.com/matplotlib/matplotlib/issues/448
Thanks!

On Thu, Sep 1, 2011 at 7:21 AM, Alan G Isaac <ala...@gm...> wrote:
> On 8/31/2011 5:48 PM, Alan G Isaac wrote:
>> How can I change font properties of a legend title?
>
>
> Related question: would it be a reasonable suggestion for
> Legend.set_title to take a ``prop`` argument?
>
> Alan Isaac
Can you file an github issue for this?
Regards,
-JJ
>
>
> ------------------------------------------------------------------------------
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> download Logger. Secure your free ArcSight Logger TODAY!
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>

l = legend()
l.get_title().set_fontproperties(...)
-JJ
On Thu, Sep 1, 2011 at 6:48 AM, Alan G Isaac <ala...@gm...> wrote:
> How can I change font properties of a legend title?
>
> Thanks,
> Alan Isaac
>
> ------------------------------------------------------------------------------
> Special Offer -- Download ArcSight Logger for FREE!
> Finally, a world-class log management solution at an even better
> price-free! And you'll get a free "Love Thy Logs" t-shirt when you
> download Logger. Secure your free ArcSight Logger TODAY!
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>

On Wed, Aug 31, 2011 at 6:35 PM, Craig Finch <cf...@ie...> wrote:
> I figured it out! I accidentally did something weird. When I built NumPy
> and SciPy, I used the --user option to tell distutils to build them in my
> home directory. I had not realized that --user installs the packages in
> ~/.local/lib/python2.7/site-packages/. I was assuming they would be
> installed in ~/lib/python2.7/site-packages, but I didn't notice they were
> "missing" until just now. When I reinstalled NumPy and Scipy using the
> option --prefix=/home/cfinch and then rebuilt matplotlib, everything started
> working. I didn't have to rebuild pycairo or pygtk; I just had to get
> everything in the same location. This is the first I've heard of installing
> anything in a .local directory...why is that even an option???
>
> Thanks for your help!
>
>
It is a standard directory in linux now. Started by the freedesktop.org, I
think. Personally, I prefer it over having ~/lib, ~/bin and such cluttering
my home directory.
http://standards.freedesktop.org/basedir-spec/basedir-spec-latest.html
Ben Root