matplotlib-users Mailing List for matplotlib

On 11/4/10 2:29 PM, John Hunter wrote:
> I added a new section of the docs users/recipes.rst. This is meant to
> be a cookbook style place to place short tutorials, annotated
> examples, idioms and snippets.
>
> http://matplotlib.sourceforge.net/users/recipes.html
Nice!
Once you get past twenty or so of these, it would be nice to have them 
categorized -- is that possible with the current system?
-Chris
-- 
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Oceanographer
Emergency Response Division
NOAA/NOS/OR&R (206) 526-6959 voice
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Chr...@no...

I added a new section of the docs users/recipes.rst. This is meant to
be a cookbook style place to place short tutorials, annotated
examples, idioms and snippets.
 http://matplotlib.sourceforge.net/users/recipes.html
I've added a few things already and would love to see contributions
from users and developers, which you can submit as a svn diff
 http://matplotlib.sourceforge.net/faq/howto_faq.html#contribute-to-matplotlib-documentation
JDH

Thanks !
matplotlib (import pylab) works in the sage notebook (
http://www.sagemath.org/ )on my machine. The sage installation compiles
everything from source!!
We are actually thinking of abandoning SUSE (after 5 years) and switch to
ubuntu !
Thanks again!
Elizabeth
On Thu, Nov 4, 2010 at 10:13 AM, John Hunter <jd...@gm...> wrote:
> On Thu, Nov 4, 2010 at 12:06 PM, Elizabeth Yip Dembart
> <ely...@gm...> wrote:
> > Thanks !!
> >
> > Here is the output from the python section you suggested:
> >
> > /sampledoc> python
> > Python 2.6 (r26:66714, Dec 3 2008, 10:55:18)
> > [GCC 4.3.2 [gcc-4_3-branch revision 141291]] on linux2
> > Type "help", "copyright", "credits" or "license" for more information.
> >>>> import numpy as np
> >>>> print np.__file__
> > /usr/lib64/python2.6/site-packages/numpy/__init__.pyc
> >>>> print np.__version__
> > 1.2.1
> >>>> import matplotlib as mpl
> >>>> print mpl.__file__
> > /usr/lib64/python2.6/site-packages/matplotlib/__init__.pyc
> >>>> print mpl.__version__
> > 1.0.0
> >>>>
>
> Well, they are both coming from the same place so it looks like the
> SUSE build of each. But the numpy version is quite old. Looks like
> it may be an OPENSUSE bug
>
>
> http://forums.opensuse.org/english/development/programming-scripting/416182-python-matplolib.html
>
> You could consider building matplotlib from source.
>
> http://matplotlib.sourceforge.net/users/installing.html
> http://matplotlib.sourceforge.net/faq/installing_faq.html#source-install
>
> http://matplotlib.sourceforge.net/faq/installing_faq.html#install-from-svn
>
> or upgrading your linux distribution (ubuntu 10.10 is nice)
>
> JDH
>

On Wed, Nov 3, 2010 at 1:18 AM, David Frey <dp...@sh...> wrote:
> ...
> My data in the y-axis (address space usage) is fairly uniform (0-2000 MB
> values), but my data in the x-axis (the time at which the the trace statements
> were executed) is highly clustered. For example, I have approximately 150
> data points over a 5 minute run, but some of the data points are only 10ms
> apart.
>
> I would like to annotate each point on the graph with the line number in the
> log file so that the user can look up what was happening at that point. I have
> succeeded, but the graph isn't readable because there is so much overlap in
> the points.
You might want to create multiple subplots, with some of the
subplots/axes zoomed in on the main axes. See this example:
 http://matplotlib.sourceforge.net/examples/pylab_examples/axes_zoom_effect.html
It looks like the image isn't on the website. You can run the example
on your local machine by saving it from the [source code] link at the
top of the page.
That seems to work well if you know in advance how many zoom areas you
want, or are working with it interactively.
If you want to auto-generate the whole figure, you might want to try
something like this:
 - figure out how many zoom regions you need (e.g., by figuring out
how many clusters you have)
 - use figure.add_subplot() or axes_grid1
(http://matplotlib.sourceforge.net/mpl_toolkits/axes_grid/users/overview.html)
to place all of your separate axes
 - plot the main figure and all of the zoom regions
BTW, if the "axes_zoom_effect" image could be added to the gallery,
it's the example I was thinking about in the "Vlines across multiple
subplots" thread:
 http://permalink.gmane.org/gmane.comp.python.matplotlib.general/24999
Hope that helps,
 Justin

On Thu, Nov 4, 2010 at 12:06 PM, Elizabeth Yip Dembart
<ely...@gm...> wrote:
> Thanks !!
>
> Here is the output from the python section you suggested:
>
> /sampledoc> python
> Python 2.6 (r26:66714, Dec 3 2008, 10:55:18)
> [GCC 4.3.2 [gcc-4_3-branch revision 141291]] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>>>> import numpy as np
>>>> print np.__file__
> /usr/lib64/python2.6/site-packages/numpy/__init__.pyc
>>>> print np.__version__
> 1.2.1
>>>> import matplotlib as mpl
>>>> print mpl.__file__
> /usr/lib64/python2.6/site-packages/matplotlib/__init__.pyc
>>>> print mpl.__version__
> 1.0.0
>>>>
Well, they are both coming from the same place so it looks like the
SUSE build of each. But the numpy version is quite old. Looks like
it may be an OPENSUSE bug
http://forums.opensuse.org/english/development/programming-scripting/416182-python-matplolib.html
You could consider building matplotlib from source.
 http://matplotlib.sourceforge.net/users/installing.html
 http://matplotlib.sourceforge.net/faq/installing_faq.html#source-install
 http://matplotlib.sourceforge.net/faq/installing_faq.html#install-from-svn
or upgrading your linux distribution (ubuntu 10.10 is nice)
JDH

Thanks !!
Here is the output from the python section you suggested:
/sampledoc> python
Python 2.6 (r26:66714, Dec 3 2008, 10:55:18)
[GCC 4.3.2 [gcc-4_3-branch revision 141291]] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy as np
>>> print np.__file__
/usr/lib64/python2.6/site-packages/numpy/__init__.pyc
>>> print np.__version__
1.2.1
>>> import matplotlib as mpl
>>> print mpl.__file__
/usr/lib64/python2.6/site-packages/matplotlib/__init__.pyc
>>> print mpl.__version__
1.0.0
>>>
Elizabeth
On Thu, Nov 4, 2010 at 9:53 AM, John Hunter <jd...@gm...> wrote:
> On Thu, Nov 4, 2010 at 11:43 AM, Elizabeth Yip Dembart
> <ely...@gm...> wrote:
> > Thank you for the prompt response.
> > I cannot run matplotlib directly. It crashes as I tried to import
> > matplotlib.pyplot:
> >
> > sphinx/sampledoc> python
> > Python 2.6 (r26:66714, Dec 3 2008, 10:55:18)
> > [GCC 4.3.2 [gcc-4_3-branch revision 141291]] on linux2
> > Type "help", "copyright", "credits" or "license" for more information.
> >>>> import matplotlib.pyplot as plt
> > Segmentation fault (core dumped)
> >
> > What do you mean by the Agg backend?
>
> This is our core rendering engine -- see
> http://matplotlib.sourceforge.net/faq/installing_faq.html#what-is-a-backend
>
> The problem you are experiencing has nothing to do with sphinx or the
> sphinx extensions, but is in your matplotlib installation. It may be
> a SUSE bug, or you may be getting conflicting installs from the stuff
> you are getting from SUSE and the stuff you are easy installing.
> First thing to do is start nailing down what you are getting and where
> you are getting it from. Paste these commands into your python shell
> and report the output
>
> import numpy as np
> print np.__file__
> print np.__version__
>
> import matplotlib as mpl
> print mpl.__file__
> print mpl.__version__
>
> A likely culprit is that you have an mpl compiled against one version
> of numpy and you are dynamically linking against another that is not
> ABI compliant.
>
> JDH
>

Hi all,
I've run into an aspect of matplotlib's setup that seems awkward. I'm seeing this on Ubuntu, but I imagine it would happen on any *nix platform.
If python is running under sudo the first time matplotlib is imported, then matplotlib creates its config dir (~/.matplotlib) with root as the owner. Subsequent attempts to import matplotlib while running python as a non-privileged user result in this:
-----------------------------------------------------------------
RuntimeError: '/home/philip' is not a writable dir; you must set /home/philip/.matplotlib to be a writable dir. You can also set environment variable MPLCONFIGDIR to any writable directory where you want matplotlib data stored 
-----------------------------------------------------------------
A simple way to re-create this -- 
1. Delete or rename ~/.matplotlib
2. sudo python -c "import matplotlib"
3. python -c "import matplotlib"
This not-improbable real-world scenario would create ~/.matplotlib owned by root --
1) Download app FooBar that has matplotlib as a dependency
2) Install matplotlib
3) Run FooBar's setup.py as sudo. It imports matplotlib, perhaps just to ensure that matplotlib is installed and working.
We ran into a similar situation with our app ('sudo python setup.py install' created desktop icons owned by root) and we resolved it by invoking chown after using a getenv() call to sniff out who we really wanted to own the file. 
It looks like the diff below (untested!) applied to lib/matplotlib/__init__.py would prevent this from happening. Does it seems reasonable to add it?
474a475,485
> if not sys.platform.lower().startswith("win"):
> # Ensure that we didn't just create a root-owned directory in the 
> # user's HOME directory. That happens if this is being run under 
> # sudo. If the SUDO_USER env. var (which contains the user that 
> # invoked sudo) then we're running under sudo. If it doesn't 
> # exist, we're not running under sudo.
> current_user = os.getenv("SUDO_USER")
> if current_user:
> subprocess.call(["chown", "-R", current_user, p])
Thanks
Philip

On Thu, Nov 4, 2010 at 11:43 AM, Elizabeth Yip Dembart
<ely...@gm...> wrote:
> Thank you for the prompt response.
> I cannot run matplotlib directly. It crashes as I tried to import
> matplotlib.pyplot:
>
> sphinx/sampledoc> python
> Python 2.6 (r26:66714, Dec 3 2008, 10:55:18)
> [GCC 4.3.2 [gcc-4_3-branch revision 141291]] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>>>> import matplotlib.pyplot as plt
> Segmentation fault (core dumped)
>
> What do you mean by the Agg backend?
This is our core rendering engine -- see
http://matplotlib.sourceforge.net/faq/installing_faq.html#what-is-a-backend
The problem you are experiencing has nothing to do with sphinx or the
sphinx extensions, but is in your matplotlib installation. It may be
a SUSE bug, or you may be getting conflicting installs from the stuff
you are getting from SUSE and the stuff you are easy installing.
First thing to do is start nailing down what you are getting and where
you are getting it from. Paste these commands into your python shell
and report the output
import numpy as np
print np.__file__
print np.__version__
import matplotlib as mpl
print mpl.__file__
print mpl.__version__
A likely culprit is that you have an mpl compiled against one version
of numpy and you are dynamically linking against another that is not
ABI compliant.
JDH

"Stan West" <sta...@pu...> writes:
>> From: Nikolaus Rath [mailto:Nik...@pu...] 
>> Sent: Tuesday, November 02, 2010 21:38
>> 
>> In [16]: matplotlib.__version__
>> Out[16]: '1.0.0'
>> 
>> I attached the result of fig.savefig(). Let's see if it makes 
>> it through
>> the list.
>
> The bug in question was fixed at revision 8652, after 1.0.0 was released. The
> distinction between the x and y axes in your case is because the y axis is
> inverted.
>
> You can work around the bug by avoiding the Axes.set_xticks() and set_yticks()
>
[...]
> I hope that helps.
It does, thanks!
 -Nikolaus
-- 
 »Time flies like an arrow, fruit flies like a Banana.«
 PGP fingerprint: 5B93 61F8 4EA2 E279 ABF6 02CF A9AD B7F8 AE4E 425C

> From: Nikolaus Rath [mailto:Nik...@ra...] 
> Sent: Tuesday, November 02, 2010 21:38
> 
> In [16]: matplotlib.__version__
> Out[16]: '1.0.0'
> 
> I attached the result of fig.savefig(). Let's see if it makes 
> it through
> the list.
The bug in question was fixed at revision 8652, after 1.0.0 was released. The
distinction between the x and y axes in your case is because the y axis is
inverted.
You can work around the bug by avoiding the Axes.set_xticks() and set_yticks()
methods and instead setting the tick locator and formatter [1] for each axis.
(That's what set_xticks and set_yticks do, in addition to other conveniences
wherein the bug lies.) This would look something like:
 import matplotlib.ticker as mticker
 
 # (Plot here.)
 tick_locs = 2 * np.arange(len(modes)) + 0.5
 tick_labels = ['%d/%d' % (x[1], x[0]) for x in modes]
 for axis in (ax.xaxis, ax.yaxis):
 axis.set_major_locator(mticker.FixedLocator(tick_locs))
 axis.set_major_formatter(mticker.FixedFormatter(tick_labels))
Separately, because you're ticking on the element boundaries instead of
centers, you might consider passing a custom extent to matshow, as in
 N = 5
 res = np.diag(np.arange(2 * N))
 modes = [ (x+1, 0) for x in range(N) ]
 cs = ax.matshow(res, extent=[-0.5, N - 0.5, N - 0.5, -0.5])
Then you can simply tick on the integers, using
 tick_locs = np.arange(N)
I hope that helps.
[1] http://matplotlib.sourceforge.net/api/ticker_api.html

 On 11/04/2010 01:46 AM, Elizabeth Yip Dembart wrote:
> Hi
>
> I was going through the sampledoc tutorial in 
> http://matplotlib.sourceforge.net/sampledoc/.
>
> When I came to "Sphinx extensions for embedded plots ... ", 
> sphinx-build crashes when "matplotlib.sphinx.mathmpl" ... were added 
> to the extensions section of conf.py.
>
> I noticed a similar problem was reported on this mailing list March 
> 23, 2010.
>
> I am running OPENSUSE 11.1 on a x86-64 computer, and my python is 
> version 2.6. I reinstalled the latest matplotlib, 
> "python-matplotlib -1.0.0-5.1.x86_64.rpm" from the opensuse 
> repository: 
> http://download.opensuse.org/repositories/science/openSUSE_11.1/x86_64. 
> I also installed the latest sphinx with "easy-install -U Sphinx".
>
> When I run 'make html', here is what happened:
> sphinx/sampledoc> make html
> sphinx-build -b html -d _build/doctrees . _build/html
> Making output directory...
> Running Sphinx v1.0.4
> make: *** [html] Segmentation fault (core dumped)
>
> I attached my conf.py and I uploaded the coredump (core.bz2) at:
> http://sites.google.com/site/mislwagroup/coredumps-1
Are you able to generate matplotlib plots directly -- in particular 
using the Agg backend?
Unfortunately, this coredump file isn't useful unless we have the exact 
same binaries as you.
Can you instead run this inside of gdb and get a traceback?
To get this, you will do something like (from the doc directory):
 > gdb python
(gdb) run /usr/bin/sphinx-build -b html -d _build/doctrees . _build/html
... it runs for a while and then crashes ...
(gdb) bt
Mike

Hi,
Thanks for your answer! I really appreciate it. Are there any examples of ProjectFigure classes out there from which I could learn how to implement such a functionality?
Best wishes,
Anita
-------- Original-Nachricht --------
> Datum: Wed, 3 Nov 2010 17:04:54 -0700
> Von: Chloe Lewis <ch...@be...>
> An: Anita Graser <ani...@gm...>
> Betreff: Re: [Matplotlib-users] save figure object
> Hi;
> 
> I don't think so, though I'm no expert. A common thing to do, with 
> other good side-effects, is to set up your data in a systematic way 
> and write ProjectFigure classes that easily deal with your data; then 
> pickle the data and make a figure with ProjectFigure when you un- 
> pickle it. That 'live' figure can be tweaked before you save an image, 
> or perhaps you can improve the whole ProjectFigure class. (Other 
> niceties: decide how you want to do print, onscreen, overhead images, 
> and switch fonts and weights and sizes in the custom Figure class; etc.)
> 
> Not the same as Matlab, though.
> 
> &C
> 
> 
> On Nov 3, 2010, at 3 Nov, 7:31 AM, Anita Graser wrote:
> 
> > Hi,
> >
> > I'm looking for a way to save Matplotlib figure objects the way 
> > Matlab can do it. I found the same request from 2008:
> >
> >
> http://sourceforge.net/mailarchive/forum.php?thread_name=48D02DF2.2020401%40lanl.gov&forum_name=matplotlib-users
> >
> > The answer basically was "There is currently no easy way".
> >
> > Has the status changed since 2008?
> >
> > Best wishes,
> > Anita
> > -- 
> > GMX DSL Doppel-Flat ab 19,99 &euro;/mtl.! Jetzt auch mit
> > gratis Notebook-Flat! http://portal.gmx.net/de/go/dsl
> >
> >
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> 
> Chloe Lewis
> Ecosystem Sciences, Policy and Management, UC Berkeley
> 137 Mulford Hall
> Berkeley, CA 94720-3114
> http://nature.berkeley.edu/~chlewis
> 
> 
> 
> 
> 
> 
> 
> 
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Hi
I was going through the sampledoc tutorial in
http://matplotlib.sourceforge.net/sampledoc/.
When I came to "Sphinx extensions for embedded plots ... ", sphinx-build
crashes when "matplotlib.sphinx.mathmpl" ... were added to the extensions
section of conf.py.
I noticed a similar problem was reported on this mailing list March 23,
2010.
I am running OPENSUSE 11.1 on a x86-64 computer, and my python is version
2.6. I reinstalled the latest matplotlib, "python-matplotlib
-1.0.0-5.1.x86_64.rpm" from the opensuse repository:
http://download.opensuse.org/repositories/science/openSUSE_11.1/x86_64. I
also installed the latest sphinx with "easy-install -U Sphinx".
When I run 'make html', here is what happened:
sphinx/sampledoc> make html
sphinx-build -b html -d _build/doctrees . _build/html
Making output directory...
Running Sphinx v1.0.4
make: *** [html] Segmentation fault (core dumped)
I attached my conf.py and I uploaded the coredump (core.bz2) at:
http://sites.google.com/site/mislwagroup/coredumps-1
Thank you for your help!
Elizabeth