matplotlib-users Mailing List for matplotlib (Page 65)

Runs to completion without errors on my installation:

OS X  10.9.4
MacBook Air w/ 8GB of memory
Python 2.7 and matplotlib 1.3.1-1  lib 

-Dale


On Aug 10, 2014, at 13:43 , Hartmut Kaiser <har...@gm...> wrote:

> All,
> 
> I'm running into a crash while trying to construct a
> tri.LinearTriInterpolator. Here is the short version of the code:
> 
>    import netCDF4
>    import matplotlib.tri as tri
> 
>    var = netCDF4.Dataset('filename.cdf').variables
>    x = var['x'][:]
>    y = var['y'][:]
>    data = var['attrname'][:]     
>    elems = var['element'][:,:]-1
> 
>    triang = tri.Triangulation(x, y, triangles=elems)
> 
>    # this crashes the python interpreter
>    interp = tri.LinearTriInterpolator(triang, data)
> 
> The data arrays (x, y, data, elems) are fairly large (>1 mio elements), all
> represented as numpy arrays (as returned by netCDF4). The 'data' array is a
> masked array and contains masked values.
> 
> If somebody cares, I'd be able to post a link to the netCDF data file
> causing this.
> 
> All this happens when using matplotlib 1.3.1, Win32, Python 2.7.
> 
> Any help would be highly appreciated!
> Regards Hartmut
> ---------------
> http://boost-spirit.com
> http://stellar.cct.lsu.edu
> 
> 
> 
> ------------------------------------------------------------------------------
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

Hi Hartmut.

I ran the example on my machine (which is a 64-bit Linux box with 8 GB of
RAM; Python 2.7, matplotlib 1.3.1) and it runs fine. However, it does use
around 2 GB of memory, perhaps slightly more. I think the memory usage
might be a problem for you if you are using 32-bit Windows. I'm not
familiar with the details but I believe the memory available to a single
32-bit process on Win32 may be only 2 GB. I'm also not familiar with the
data you provided, but is it possible to reduce to number of points in
order to test if memory limitations are the underlying problemhere?




On 11 August 2014 14:54, Hartmut Kaiser <har...@gm...> wrote:

> Ian,
>
> > I'm running into a crash while trying to construct a
> > tri.LinearTriInterpolator. Here is the short version of the code:
> >
> >     import netCDF4
> >     import matplotlib.tri as tri
> >
> >     var = netCDF4.Dataset('filename.cdf').variables
> >     x = var['x'][:]
> >     y = var['y'][:]
> >     data = var['zeta_max'][:]
> >     elems = var['element'][:, :]-1
> >
> >     triang = tri.Triangulation(x, y, triangles=elems)
> >
> >     # this crashes the python interpreter
> >     interp = tri.LinearTriInterpolator(triang, data)
> >
> > The data arrays (x, y, data, elems) are fairly large (>1 mio elements),
> > all
> > represented as numpy arrays (as returned by netCDF4). The 'data' array is
> > a
> > masked array and contains masked values.
> >
> > If somebody cares, I'd be able to post a link to the netCDF data file
> > causing this.
> >
> > All this happens when using matplotlib 1.3.1, Win32, Python 2.7.
> >
> > Any help would be highly appreciated!
> > Regards Hartmut
> >
> > Hartmut,
> > That is an excellent issue report; all the relevant information and
> > nothing extraneous.  Hence the quick response.
> > The second argument to TriLinearInterpolator (and other TriInterpolator
> > classes), i.e. your 'data' array, is expected to be an array of the same
> > size as the 'x' and 'y' arrays.  It is not expecting a masked array.  If
> a
> > masked array is used the mask will be ignored, and so the values behind
> > the mask will be used as though they were real values.  If my memory of
> > netCDF is correct, this will be whatever 'FillValue' is defined for the
> > file, but it may depend on what is used to generate the netCDF file.
> > I would normally expect the code to work but produce useless output.  A
> > crash is possible though.  It would be best if you could post a link to
> > the netCDF file and I will take a closer look to check there is not
> > something else going wrong.
>
> Thanks for the quick response!
>
> Here is the data file: http://tinyurl.com/ms7vzxw. I did some more
> experiments. The picture stays unchanged, even if I fill the masked values
> in the array with some real numbers (I'm not saying that this would give me
> any sensible results...):
>
>     import netCDF4
>     import matplotlib.tri as tri
>
>     var = netCDF4.Dataset('maxele.63.nc').variables
>     x = var['x'][:]
>     y = var['y'][:]
>     data = var['zeta_max'][:]
>     elems = var['element'][:, :]-1
>
>     triang = tri.Triangulation(x, y, triangles=elems)
>
>     data = data.filled(0.0)
>
>     # this still crashes the python interpreter
>     interp = tri.LinearTriInterpolator(triang, data)
>
> Thanks again!
> Regards Hartmut
> ---------------
> http://boost-spirit.com
> http://stellar.cct.lsu.edu
>
>
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>



-- 
Dr Andrew Dawson
Atmospheric, Oceanic & Planetary Physics
Clarendon Laboratory
Parks Road
Oxford OX1 3PU, UK
Tel: +44 (0)1865 282438
Email: da...@at...
Web Site: http://www2.physics.ox.ac.uk/contacts/people/dawson

Ian,

> I'm running into a crash while trying to construct a
> tri.LinearTriInterpolator. Here is the short version of the code:
> 
>     import netCDF4
>     import matplotlib.tri as tri
> 
>     var = netCDF4.Dataset('filename.cdf').variables
>     x = var['x'][:]
>     y = var['y'][:]
>     data = var['zeta_max'][:]
>     elems = var['element'][:, :]-1
> 
>     triang = tri.Triangulation(x, y, triangles=elems)
> 
>     # this crashes the python interpreter
>     interp = tri.LinearTriInterpolator(triang, data)
> 
> The data arrays (x, y, data, elems) are fairly large (>1 mio elements),
> all
> represented as numpy arrays (as returned by netCDF4). The 'data' array is
> a
> masked array and contains masked values.
> 
> If somebody cares, I'd be able to post a link to the netCDF data file
> causing this.
> 
> All this happens when using matplotlib 1.3.1, Win32, Python 2.7.
> 
> Any help would be highly appreciated!
> Regards Hartmut
> 
> Hartmut,
> That is an excellent issue report; all the relevant information and
> nothing extraneous.  Hence the quick response.
> The second argument to TriLinearInterpolator (and other TriInterpolator
> classes), i.e. your 'data' array, is expected to be an array of the same
> size as the 'x' and 'y' arrays.  It is not expecting a masked array.  If a
> masked array is used the mask will be ignored, and so the values behind
> the mask will be used as though they were real values.  If my memory of
> netCDF is correct, this will be whatever 'FillValue' is defined for the
> file, but it may depend on what is used to generate the netCDF file.
> I would normally expect the code to work but produce useless output.  A
> crash is possible though.  It would be best if you could post a link to
> the netCDF file and I will take a closer look to check there is not
> something else going wrong.

Thanks for the quick response!

Here is the data file: http://tinyurl.com/ms7vzxw. I did some more experiments. The picture stays unchanged, even if I fill the masked values in the array with some real numbers (I'm not saying that this would give me any sensible results...):

    import netCDF4
    import matplotlib.tri as tri

    var = netCDF4.Dataset('maxele.63.nc').variables
    x = var['x'][:]
    y = var['y'][:]
    data = var['zeta_max'][:]
    elems = var['element'][:, :]-1

    triang = tri.Triangulation(x, y, triangles=elems)

    data = data.filled(0.0)

    # this still crashes the python interpreter
    interp = tri.LinearTriInterpolator(triang, data)

Thanks again!
Regards Hartmut
---------------
http://boost-spirit.com
http://stellar.cct.lsu.edu

On 10 August 2014 18:43, Hartmut Kaiser <har...@gm...> wrote:

> All,
>
> I'm running into a crash while trying to construct a
> tri.LinearTriInterpolator. Here is the short version of the code:
>
>     import netCDF4
>     import matplotlib.tri as tri
>
>     var = netCDF4.Dataset('filename.cdf').variables
>     x = var['x'][:]
>     y = var['y'][:]
>     data = var['attrname'][:]
>     elems = var['element'][:,:]-1
>
>     triang = tri.Triangulation(x, y, triangles=elems)
>
>     # this crashes the python interpreter
>     interp = tri.LinearTriInterpolator(triang, data)
>
> The data arrays (x, y, data, elems) are fairly large (>1 mio elements), all
> represented as numpy arrays (as returned by netCDF4). The 'data' array is a
> masked array and contains masked values.
>
> If somebody cares, I'd be able to post a link to the netCDF data file
> causing this.
>
> All this happens when using matplotlib 1.3.1, Win32, Python 2.7.
>
> Any help would be highly appreciated!
> Regards Hartmut
>

Hartmut,

That is an excellent issue report; all the relevant information and nothing
extraneous.  Hence the quick response.

The second argument to TriLinearInterpolator (and other TriInterpolator
classes), i.e. your 'data' array, is expected to be an array of the same
size as the 'x' and 'y' arrays.  It is not expecting a masked array.  If a
masked array is used the mask will be ignored, and so the values behind the
mask will be used as though they were real values.  If my memory of netCDF
is correct, this will be whatever 'FillValue' is defined for the file, but
it may depend on what is used to generate the netCDF file.

I would normally expect the code to work but produce useless output.  A
crash is possible though.  It would be best if you could post a link to the
netCDF file and I will take a closer look to check there is not something
else going wrong.

Ian Thomas

Exec. summary - I was having strange behavior with matshow in a loop and 
also with discrepancies between how iPython Notebook and Python via IDE 
displayed plots.

Solutions:
1) Using pause instead of show fixed matshow in a loop

2) Explicitly invoking %matplotblib qt or generally %matplotlib 
{backend} before  importing or using  matplotlib fixed various problems 
with plots in notebooks.  Now when I create a plot in a notebook, it 
appears, I can work with it, close it when appropriate, and 
simultaneously be able to do other work in notebook cells.

Thanks to everyone for the rapid responses.

JBB

On 7/30/14, 10:04 PM, JBB wrote:
> I've followed up on several suggestions and here is what I've done/found.
>
> (I know I don't use mlab or pylab but I pulled the import lines from
> another source and am leaving them in for the heck of it)


[ Woe/intrigue trimmed ]


>>      Is there a pointer to why this worked when my initial approach did not?
>>         I thought from the documentation/videos that preparing a plot with
>>      relevant commands then issuing the show() command was the preferred
>>      approach within Python/Matplotlib.
>>
>>      JBB
>>

All,

I'm running into a crash while trying to construct a
tri.LinearTriInterpolator. Here is the short version of the code:

    import netCDF4
    import matplotlib.tri as tri

    var = netCDF4.Dataset('filename.cdf').variables
    x = var['x'][:]
    y = var['y'][:]
    data = var['attrname'][:]     
    elems = var['element'][:,:]-1

    triang = tri.Triangulation(x, y, triangles=elems)

    # this crashes the python interpreter
    interp = tri.LinearTriInterpolator(triang, data)

The data arrays (x, y, data, elems) are fairly large (>1 mio elements), all
represented as numpy arrays (as returned by netCDF4). The 'data' array is a
masked array and contains masked values.

If somebody cares, I'd be able to post a link to the netCDF data file
causing this.

All this happens when using matplotlib 1.3.1, Win32, Python 2.7.

Any help would be highly appreciated!
Regards Hartmut
---------------
http://boost-spirit.com
http://stellar.cct.lsu.edu

Hi,

On Wed, Aug 6, 2014 at 8:15 PM, discolemonade <sch...@gm...> wrote:
> Thanks Paul. I'm new to all of this and the interplay between GTK, it's
> headers and matplotlib is admittedly still a bit of a mystery to me. I have
> GTK installed. I installed it after installing matplotlib because I tried to
> use TKAgg as a backend and ended up running into some problems.

As a matter of interest - what problem did you have?  How did you
install matplotlib?

>  I'm on
> MacOSX Mavericks. I've been googling around and there don't seem to be any
> direct answers for how to gett these headers installed on Mac OS. What's the
> quickest way to get these headers on my system(via homebrew?)?

Does 'brew install gtk+' work for that?

> And once I
> get them, do I have to reinstall matplotlib so that it can recognize the
> headers?

I'm afraid so.  If I were you, I'd check out the source for that, as in:

git clone git://github.com/matplotlib/matplotlib.git
cd matplotlib
git checkout v1.3.1
python setup.py install

Feel free to post again if that doesn't work.

Cheers,

Matthew

I recommend MacPorts [1] to install open source packages on Mac, including matplotlib.
-Sterling
[1] http://www.macports.org/
On Aug 6, 2014, at 8:15PM, discolemonade wrote:

> Thanks Paul. I'm new to all of this and the interplay between GTK, it's
> headers and matplotlib is admittedly still a bit of a mystery to me. I have
> GTK installed. I installed it after installing matplotlib because I tried to
> use TKAgg as a backend and ended up running into some problems. I'm on
> MacOSX Mavericks. I've been googling around and there don't seem to be any
> direct answers for how to gett these headers installed on Mac OS. What's the
> quickest way to get these headers on my system(via homebrew?)? And once I
> get them, do I have to reinstall matplotlib so that it can recognize the
> headers? 
> 
> 
> 
> --
> View this message in context: http://matplotlib.1069221.n5.nabble.com/ImportError-No-module-named-backend-gdk-tp43753p43761.html
> Sent from the matplotlib - users mailing list archive at Nabble.com.
> 
> ------------------------------------------------------------------------------
> Infragistics Professional
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Is test data not installed my default?  I didn't used to have to do
anything than pip install then run the tests, but perhaps something has
changed?

Could it be a pip thing somehow?  I will try a straight up setup.py
installation.



On Thu, Aug 7, 2014 at 1:07 PM, Benjamin Root <ben...@ou...> wrote:

> Just to note, the first log also has the font-manager issue as well. What
> I see as odd here is that while it was configured to install the tests (and
> presumedly the test data), it doesn't seem to have done that. At the very
> least, the test data wasn't installed.
>
> Ben
>
>
> On Thu, Aug 7, 2014 at 12:15 PM, Russell Warren <ru...@pe...>
> wrote:
>
>> Since my test script was using nose directly, I figured I would try the
>> "proper" `tests.py` script in the repo, but there seems to be a font_manger
>> issue.  An exception is thrown with:
>>
>> "<snip> matplotlib/ft2font.so: undefined symbol: inflateEnd"
>>
>> Full log here:
>> http://bpaste.net/raw/MVuf4UlQ1g9xCecivwlQ/
>>
>>
>>
>> On Thu, Aug 7, 2014 at 12:00 PM, Russell Warren <ru...@pe...>
>> wrote:
>>
>>> I'm trying to run the matplotlib unit tests on linux with the agg
>>> backend, and am getting a tonne of errors.
>>>
>>> Here is my test method and output (method is the script created at the
>>> top):
>>> http://bpaste.net/raw/n0JVrWcXnlPVxaAlArHJ/
>>>
>>> It is not clear to me why the tests don't exist.  I have run this test
>>> successfully several times on this platform over the last couple of years,
>>> although I haven't tried it in (I'm guessing) a year or so.
>>>
>>> Searching around I found this in the mailing list:
>>> http://goo.gl/9nDILp
>>>
>>> The testing output is similar (bottom of the mail), but perusing the
>>> rest of the thread it does not seem to have a resolution, nor does it seem
>>> like the same issue.
>>>
>>> For reference, matplotlib was installed with `pip install matplotlib`,
>>> and the output log is here:
>>> http://bpaste.net/raw/5tfTFJepFRAwGF5tSkyb/
>>>
>>> Does anybody know what is wrong, or have any tips on where/how I can dig
>>> further?
>>>
>>> Thanks,
>>> Russ
>>>
>>>
>>
>>
>> --
>> Russell Warren
>> Perspexis Technologies Inc.
>>
>> This information is confidential and intended solely for the use of the
>> individual or entity to whom it is addressed.
>> If you have received this email in error, please notify the sender
>> immediately.
>>
>>
>> ------------------------------------------------------------------------------
>> Infragistics Professional
>> Build stunning WinForms apps today!
>> Reboot your WinForms applications with our WinForms controls.
>> Build a bridge from your legacy apps to the future.
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>>
>


-- 
Russell Warren
Perspexis Technologies Inc.

This information is confidential and intended solely for the use of the
individual or entity to whom it is addressed.
If you have received this email in error, please notify the sender
immediately.

Just to note, the first log also has the font-manager issue as well. What I
see as odd here is that while it was configured to install the tests (and
presumedly the test data), it doesn't seem to have done that. At the very
least, the test data wasn't installed.

Ben


On Thu, Aug 7, 2014 at 12:15 PM, Russell Warren <ru...@pe...> wrote:

> Since my test script was using nose directly, I figured I would try the
> "proper" `tests.py` script in the repo, but there seems to be a font_manger
> issue.  An exception is thrown with:
>
> "<snip> matplotlib/ft2font.so: undefined symbol: inflateEnd"
>
> Full log here:
> http://bpaste.net/raw/MVuf4UlQ1g9xCecivwlQ/
>
>
>
> On Thu, Aug 7, 2014 at 12:00 PM, Russell Warren <ru...@pe...>
> wrote:
>
>> I'm trying to run the matplotlib unit tests on linux with the agg
>> backend, and am getting a tonne of errors.
>>
>> Here is my test method and output (method is the script created at the
>> top):
>> http://bpaste.net/raw/n0JVrWcXnlPVxaAlArHJ/
>>
>> It is not clear to me why the tests don't exist.  I have run this test
>> successfully several times on this platform over the last couple of years,
>> although I haven't tried it in (I'm guessing) a year or so.
>>
>> Searching around I found this in the mailing list:
>> http://goo.gl/9nDILp
>>
>> The testing output is similar (bottom of the mail), but perusing the rest
>> of the thread it does not seem to have a resolution, nor does it seem like
>> the same issue.
>>
>> For reference, matplotlib was installed with `pip install matplotlib`,
>> and the output log is here:
>> http://bpaste.net/raw/5tfTFJepFRAwGF5tSkyb/
>>
>> Does anybody know what is wrong, or have any tips on where/how I can dig
>> further?
>>
>> Thanks,
>> Russ
>>
>>
>
>
> --
> Russell Warren
> Perspexis Technologies Inc.
>
> This information is confidential and intended solely for the use of the
> individual or entity to whom it is addressed.
> If you have received this email in error, please notify the sender
> immediately.
>
>
> ------------------------------------------------------------------------------
> Infragistics Professional
> Build stunning WinForms apps today!
> Reboot your WinForms applications with our WinForms controls.
> Build a bridge from your legacy apps to the future.
>
> http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>

Since my test script was using nose directly, I figured I would try the
"proper" `tests.py` script in the repo, but there seems to be a font_manger
issue.  An exception is thrown with:

"<snip> matplotlib/ft2font.so: undefined symbol: inflateEnd"

Full log here:
http://bpaste.net/raw/MVuf4UlQ1g9xCecivwlQ/



On Thu, Aug 7, 2014 at 12:00 PM, Russell Warren <ru...@pe...> wrote:

> I'm trying to run the matplotlib unit tests on linux with the agg backend,
> and am getting a tonne of errors.
>
> Here is my test method and output (method is the script created at the
> top):
> http://bpaste.net/raw/n0JVrWcXnlPVxaAlArHJ/
>
> It is not clear to me why the tests don't exist.  I have run this test
> successfully several times on this platform over the last couple of years,
> although I haven't tried it in (I'm guessing) a year or so.
>
> Searching around I found this in the mailing list:
> http://goo.gl/9nDILp
>
> The testing output is similar (bottom of the mail), but perusing the rest
> of the thread it does not seem to have a resolution, nor does it seem like
> the same issue.
>
> For reference, matplotlib was installed with `pip install matplotlib`, and
> the output log is here:
> http://bpaste.net/raw/5tfTFJepFRAwGF5tSkyb/
>
> Does anybody know what is wrong, or have any tips on where/how I can dig
> further?
>
> Thanks,
> Russ
>
>


-- 
Russell Warren
Perspexis Technologies Inc.

This information is confidential and intended solely for the use of the
individual or entity to whom it is addressed.
If you have received this email in error, please notify the sender
immediately.

I'm trying to run the matplotlib unit tests on linux with the agg backend,
and am getting a tonne of errors.

Here is my test method and output (method is the script created at the top):
http://bpaste.net/raw/n0JVrWcXnlPVxaAlArHJ/

It is not clear to me why the tests don't exist.  I have run this test
successfully several times on this platform over the last couple of years,
although I haven't tried it in (I'm guessing) a year or so.

Searching around I found this in the mailing list:
http://goo.gl/9nDILp

The testing output is similar (bottom of the mail), but perusing the rest
of the thread it does not seem to have a resolution, nor does it seem like
the same issue.

For reference, matplotlib was installed with `pip install matplotlib`, and
the output log is here:
http://bpaste.net/raw/5tfTFJepFRAwGF5tSkyb/

Does anybody know what is wrong, or have any tips on where/how I can dig
further?

Thanks,
Russ

Thanks Paul. I'm new to all of this and the interplay between GTK, it's
headers and matplotlib is admittedly still a bit of a mystery to me. I have
GTK installed. I installed it after installing matplotlib because I tried to
use TKAgg as a backend and ended up running into some problems. I'm on
MacOSX Mavericks. I've been googling around and there don't seem to be any
direct answers for how to gett these headers installed on Mac OS. What's the
quickest way to get these headers on my system(via homebrew?)? And once I
get them, do I have to reinstall matplotlib so that it can recognize the
headers? 



--
View this message in context: http://matplotlib.1069221.n5.nabble.com/ImportError-No-module-named-backend-gdk-tp43753p43761.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

Hi Nicolas

I do not have any slides of this material yet. I will try at some point to
upload them on github, although I'm already working on tutorial part two,
so it may take a while.

In the meantime, I have a set of slides from 2012 when I presented this talk:
http://www.cspg.org/cspg/documents/Conventions/Archives/Annual/2012/155_GC2012_A_More_Perceptual_Color_Palette_for_Structure_Maps.pdf

Let me know if you're interested and I will upload them on github.


Hi Damon, yes, I did see your talk and Kristen's and I am really excited
there's good momentum on this topic. I will write you later today about
the matplotlib webpage, great idea.

Thanks to both for your feedback.
Matteo

On Wed, August 6, 2014 2:05 pm, Nicolas P. Rougier wrote:
>

> Really great material (ipython notebook and videos), thanks a lot to you
> all.
>
> Are the slides available somewhere by any chance ?
>
>
>
> Nicolas
>
>
>
> On 06 Aug 2014, at 15:25, Damon McDougall <dam...@gm...>
> wrote:
>
>
>> On Mon, Aug 4, 2014 at 5:20 PM, Matteo Niccoli <ma...@my...>
>> wrote:
>>
>>> Hi All
>>>
>>>
>>> I recently wrote a tutorial on how to evaluate and compare colormaps
>>> using perceptual principle. It is geared towards Matplotlib.
>>>
>>> http://nbviewer.ipython.org/github/mycarta/tutorials/blob/master/1408
>>> _Evaluate_and_compare_colormaps/How_to_evaluate_and_compare_colormaps
>>> .ipynb
>>>
>>>
>>> Although I am a newbie and some of my code may be not all that
>>> pythonic yet, I hope you enjoy the read.
>>>
>>> Any feedback would be welcome.
>>>
>>>
>>> THank you
>>> Matteo
>>>
>>
>> Hi Matteo,
>>
>>
>> Thanks for sharing this resource.
>>
>>
>> Also, I wanted to personally thank you for MyCarta.  It's a great
>> resource and Kristen Thyng and I have learned a lot from it.  Kristen
>> cited you in a talk she gave at SciPy 2014 last month.  We both gave
>> talks at SciPy 2014 about colour maps I think you might find
>> interesting.  They were recorded and put on YouTube by Enthought and you
>> can check them out here<https://www.youtube.com/watch?v=Alnc9E1RnD8> and
>>  here<https://www.youtube.com/watch?v=rkDgBvT-giw>.
>>
>>
>> I think it would be a good idea to link to your IPython (read Jupyter)
>> notebook, along with some of the work Kristen as done with matplotlib
>> colour maps, from the matplotlib web page.  Would you be amenable to
>> this?
>>
>> All the best,
>> Damon
>>
>>
>> --
>> Damon McDougall
>> http://www.damon-is-a-geek.com
>> Institute for Computational Engineering Sciences
>> 201 E. 24th St.
>> Stop C0200
>> The University of Texas at Austin
>> Austin, TX 78712-1229
>>
>>
>> -----------------------------------------------------------------------
>> -------
>> Infragistics Professional
>> Build stunning WinForms apps today!
>> Reboot your WinForms applications with our WinForms controls.
>> Build a bridge from your legacy apps to the future.
>> http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.cl
>> ktrk _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>
>

Really great material (ipython notebook and videos), thanks a lot to you all.

Are the slides available somewhere by any chance ?


Nicolas


On 06 Aug 2014, at 15:25, Damon McDougall <dam...@gm...> wrote:

> On Mon, Aug 4, 2014 at 5:20 PM, Matteo Niccoli <ma...@my...> wrote:
>> Hi All
>> 
>> I recently wrote a tutorial on how to evaluate and compare colormaps using
>> perceptual principle. It is geared towards Matplotlib.
>> 
>> http://nbviewer.ipython.org/github/mycarta/tutorials/blob/master/1408_Evaluate_and_compare_colormaps/How_to_evaluate_and_compare_colormaps.ipynb
>> 
>> Although I am a newbie and some of my code may be not all that pythonic
>> yet, I hope you enjoy the read.
>> 
>> Any feedback would be welcome.
>> 
>> THank you
>> Matteo
> 
> Hi Matteo,
> 
> Thanks for sharing this resource.
> 
> Also, I wanted to personally thank you for MyCarta.  It's a great
> resource and Kristen Thyng and I have learned a lot from it.  Kristen
> cited you in a talk she gave at SciPy 2014 last month.  We both gave
> talks at SciPy 2014 about colour maps I think you might find
> interesting.  They were recorded and put on YouTube by Enthought and
> you can check them out
> here<https://www.youtube.com/watch?v=Alnc9E1RnD8> and
> here<https://www.youtube.com/watch?v=rkDgBvT-giw>.
> 
> I think it would be a good idea to link to your IPython (read Jupyter)
> notebook, along with some of the work Kristen as done with matplotlib
> colour maps, from the matplotlib web page.  Would you be amenable to
> this?
> 
> All the best,
> Damon
> 
> -- 
> Damon McDougall
> http://www.damon-is-a-geek.com
> Institute for Computational Engineering Sciences
> 201 E. 24th St.
> Stop C0200
> The University of Texas at Austin
> Austin, TX 78712-1229
> 
> ------------------------------------------------------------------------------
> Infragistics Professional
> Build stunning WinForms apps today!
> Reboot your WinForms applications with our WinForms controls. 
> Build a bridge from your legacy apps to the future.
> http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

On Mon, Aug 4, 2014 at 5:20 PM, Matteo Niccoli <ma...@my...> wrote:
> Hi All
>
> I recently wrote a tutorial on how to evaluate and compare colormaps using
> perceptual principle. It is geared towards Matplotlib.
>
> http://nbviewer.ipython.org/github/mycarta/tutorials/blob/master/1408_Evaluate_and_compare_colormaps/How_to_evaluate_and_compare_colormaps.ipynb
>
> Although I am a newbie and some of my code may be not all that pythonic
> yet, I hope you enjoy the read.
>
> Any feedback would be welcome.
>
> THank you
> Matteo

Hi Matteo,

Thanks for sharing this resource.

Also, I wanted to personally thank you for MyCarta.  It's a great
resource and Kristen Thyng and I have learned a lot from it.  Kristen
cited you in a talk she gave at SciPy 2014 last month.  We both gave
talks at SciPy 2014 about colour maps I think you might find
interesting.  They were recorded and put on YouTube by Enthought and
you can check them out
here<https://www.youtube.com/watch?v=Alnc9E1RnD8> and
here<https://www.youtube.com/watch?v=rkDgBvT-giw>.

I think it would be a good idea to link to your IPython (read Jupyter)
notebook, along with some of the work Kristen as done with matplotlib
colour maps, from the matplotlib web page.  Would you be amenable to
this?

All the best,
Damon

-- 
Damon McDougall
http://www.damon-is-a-geek.com
Institute for Computational Engineering Sciences
201 E. 24th St.
Stop C0200
The University of Texas at Austin
Austin, TX 78712-1229

discolemonade, on 2014-08-05 21:29,  wrote:
> Hi,
> 
> I'm using the GTKAgg backend and when I run "import matplotlib.pyplot as
> plt" in the Python shell, I get the   _backend_gdk error. I checked all the
> files in my backend and there is no _backend_gdk.py. In fact, there are no
> python modules that start with an underscore.

As a rule of thumb, modules that start with an underscore come
from a compiled C or C++ extension. In this case, the source
file in question lives in src/_backend_gdk.c of the matplotlib
directory.

> It seems that some files were not installed. Is there some kind
> of a gtk dependancy I need to install before installing
> matplotlib? If so, where can I get it? My matplot version is
> 1.3.1. 

Yes, you'll need GTK and its headers installed, something like 

  sudo apt-get install libgtk2.0-dev python-gtk2-dev 

should work on a Debian system, though you should probably just 

  sudo apt-get build-dep python-matplotlib

best,
-- 
                   _
                  / \
                A*   \^   -
             ,./   _.`\\ / \
            / ,--.S    \/   \
           /  `"~,_     \    \
     __o           ?
   _ \<,_         /:\
--(_)/-(_)----.../ | \
--------------.......J
Paul Ivanov
ipython and matplotlib core developer
http://pirsquared.org

Hi,

I'm using the GTKAgg backend and when I run "import matplotlib.pyplot as
plt" in the Python shell, I get the   _backend_gdk error. I checked all the
files in my backend and there is no _backend_gdk.py. In fact, there are no
python modules that start with an underscore. It seems that some files were
not installed. Is there some kind of a gtk dependancy I need to install
before installing matplotlib? If so, where can I get it? My matplot version
is 1.3.1. 

thanks




--
View this message in context: http://matplotlib.1069221.n5.nabble.com/ImportError-No-module-named-backend-gdk-tp43753.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

Hi all! I'm a bit confused now, since I've never had any problems with bluemarble. The problems have always been in me and how I handle the data, and it probably is like that also this time... But the problem is that bluemarble won't show up, the data seems to plot just fine and so do for example drawcoastlines and drawcountries. Where should I dig into?

import matplotlib.pyplot as plt
from mpl_toolkits.basemap import Basemap
from scipy.io.netcdf import netcdf_file as Dataset
import numpy as np
import pylab
import os

months = [3,45]

for month in months:

        SIT = Dataset('SIT.nc','r')
        
        lons = SIT.variables['lon'][:,:]
        lats = SIT.variables['lat'][:,:]

        masked_SIT = np.ma.masked_where(np.isnan(SIT.variables['sea_ice_thickness'][month,:,:] ), SIT.variables['sea_ice_thickness'][month,:,:] )
        
        m = Basemap(width=5400000*2,height=5400000*2,resolution='l',projection='laea',lat_0=90,lon_0=0)


        fig = plt.figure()
        m.pcolormesh(lons, lats, masked_SIT, latlon = True, vmin=0, vmax=5)
        m.bluemarble(scale=0.5)
        m.drawcoastlines()
        m.drawcountries()
        #m.fillcontinents(color='white')
        cbar = plt.colorbar()
        cbar.cmap.set_over('#ff0066')
        cbar.set_label('SIT [m]', fontsize='x-large')
        plt.title('Sea Ice Thickness %s' % (title), fontsize='x-large')

plt.show()


Cheers, Bill
 		 	   		  

Hi All

I recently wrote a tutorial on how to evaluate and compare colormaps using
perceptual principle. It is geared towards Matplotlib.

http://nbviewer.ipython.org/github/mycarta/tutorials/blob/master/1408_Evaluate_and_compare_colormaps/How_to_evaluate_and_compare_colormaps.ipynb

Although I am a newbie and some of my code may be not all that pythonic
yet, I hope you enjoy the read.

Any feedback would be welcome.

THank you
Matteo

Whoops, I hadn't realized I stumbled onto a clone of sourceforge (a
mirror?). Here is the real link:
http://sourceforge.net/p/matplotlib/mailman/message/188760/


On Sun, Aug 3, 2014 at 9:37 PM, Benjamin Root <ben...@ou...> wrote:

> For those interested, I have found the release announcement that
> introduced the jet colormap:
> http://ehc.ac/p/matplotlib/mailman/message/188760/ . We have someone
> named "Perry" to blame... :-P
>
> Ben Root
>
>
> On Fri, Aug 1, 2014 at 9:01 PM, Benjamin Root <ben...@ou...> wrote:
>
>> Just to keep my notes in one place... from Matplotlib's "Introduction"
>> page is prose that I assume was written by John:
>>
>> For years, I used to use MATLAB exclusively for data analysis and
>> visualization. MATLAB excels at making nice looking plots easy. When I
>> began working with EEG data, I found that I needed to write applications to
>> interact with my data, and developed and EEG analysis application in
>> MATLAB. As the application grew in complexity, interacting with databases,
>> http servers, manipulating complex data structures, I began to strain
>> against the limitations of MATLAB as a programming language, and decided to
>> start over in Python. Python more than makes up for all of MATLAB’s
>> deficiencies as a programming language, but I was having difficulty finding
>> a 2D plotting package (for 3D VTK <http://www.vtk.org/> more than
>> exceeds all of my needs).
>>
>> When I went searching for a Python plotting package, I had several
>> requirements:
>>
>>    - Plots should look great - publication quality. One important
>>    requirement for me is that the text looks good (antialiased, etc.)
>>    - Postscript output for inclusion with TeX documents
>>    - Embeddable in a graphical user interface for application development
>>    - Code should be easy enough that I can understand it and extend it
>>    - Making plots should be easy
>>
>> Finding no package that suited me just right, I did what any
>> self-respecting Python programmer would do: rolled up my sleeves and dived
>> in. Not having any real experience with computer graphics, I decided to
>> emulate MATLAB’s plotting capabilities because that is something MATLAB
>> does very well. This had the added advantage that many people have a lot of
>> MATLAB experience, and thus they can quickly get up to steam plotting in
>> python. From a developer’s perspective, having a fixed user interface (the
>> pylab interface) has been very useful, because the guts of the code base
>> can be redesigned without affecting user code.
>>
>>
>>
>>
>>
>> On Wed, Jul 30, 2014 at 11:51 PM, Benjamin Root <ben...@ou...> wrote:
>>
>>> Fernando,
>>>
>>> This information is going to be the preface of my book on using
>>> matplotlib for making an interactive application (sorry, no IPython, the
>>> editor wanted to keep the scope tight). So, what I am looking for are some
>>> of the major interactive features (who supplied them, and their
>>> reasons/purpose). Also, how has interactive matplotlib supported uses "in
>>> the wild" such as the Mars Phoenix Lander and recently, the ISEE3 reboot
>>> project (that abandoned satellite that was recently revived by citizen
>>> scientists).
>>>
>>> Of, course, any insights to John's original needs/use cases in the early
>>> years would be very valuable as well. I could have sworn he has written
>>> such missives on the mailing lists, but I can't seem to find them.
>>>
>>> Cheers!
>>> Ben Root
>>> On Jul 30, 2014 11:21 PM, "Fernando Perez" <fpe...@gm...> wrote:
>>>
>>>> Hi Ben,
>>>>
>>>> if by interactive plotting you refer to using it interactively via
>>>> ipython and other such systems, there's a good part of that history that is
>>>> spread somewhere between the early mpl and ipython archives AND John's and
>>>> my personal inboxes.
>>>>
>>>> A good chunk of that (not all, mind you, since many others contributed)
>>>> happened with John and I working on it, and sadly he's not with us and I
>>>> had a loss of my early email (anything older than 2005) when I left the
>>>> University of Colorado.
>>>>
>>>> I'd be happy to answer some questions if you have them, to the best of
>>>> my memory. Probably quicker over skype/phone, ping me directly (at my
>>>> Berkeley address) if you want.
>>>>
>>>> Cheers
>>>>
>>>> f
>>>>
>>>>
>>>>
>>>> On Wed, Jul 30, 2014 at 7:20 PM, Benjamin Root <ben...@ou...> wrote:
>>>>
>>>>> Hello all,
>>>>>
>>>>> I am trying to put together notes for a writeup on a short history of
>>>>> matplotlib (in particular, its uses for interactive plotting). I have John
>>>>> Hunter's SciPy 2012 Keynote, which helps, but I was hoping for some other
>>>>> sources.
>>>>>
>>>>> Unfortunately, searching for "matplotlib" and "history" gets me lots
>>>>> of results on our trials and tribulations with version control...
>>>>>
>>>>> Anybody have anything bookmarked?
>>>>>
>>>>> Cheers!
>>>>> Ben Root
>>>>>
>>>>> P.S. - Yes... this is for a book. Stay tuned!
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Infragistics Professional
>>>>> Build stunning WinForms apps today!
>>>>> Reboot your WinForms applications with our WinForms controls.
>>>>> Build a bridge from your legacy apps to the future.
>>>>>
>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk
>>>>> _______________________________________________
>>>>> Matplotlib-users mailing list
>>>>> Mat...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Fernando Perez (@fperez_org; http://fperez.org)
>>>> fperez.net-at-gmail: mailing lists only (I ignore this when swamped!)
>>>> fernando.perez-at-berkeley: contact me here for any direct mail
>>>>
>>>
>>
>

For those interested, I have found the release announcement that introduced
the jet colormap: http://ehc.ac/p/matplotlib/mailman/message/188760/ . We
have someone named "Perry" to blame... :-P

Ben Root


On Fri, Aug 1, 2014 at 9:01 PM, Benjamin Root <ben...@ou...> wrote:

> Just to keep my notes in one place... from Matplotlib's "Introduction"
> page is prose that I assume was written by John:
>
> For years, I used to use MATLAB exclusively for data analysis and
> visualization. MATLAB excels at making nice looking plots easy. When I
> began working with EEG data, I found that I needed to write applications to
> interact with my data, and developed and EEG analysis application in
> MATLAB. As the application grew in complexity, interacting with databases,
> http servers, manipulating complex data structures, I began to strain
> against the limitations of MATLAB as a programming language, and decided to
> start over in Python. Python more than makes up for all of MATLAB’s
> deficiencies as a programming language, but I was having difficulty finding
> a 2D plotting package (for 3D VTK <http://www.vtk.org/> more than exceeds
> all of my needs).
>
> When I went searching for a Python plotting package, I had several
> requirements:
>
>    - Plots should look great - publication quality. One important
>    requirement for me is that the text looks good (antialiased, etc.)
>    - Postscript output for inclusion with TeX documents
>    - Embeddable in a graphical user interface for application development
>    - Code should be easy enough that I can understand it and extend it
>    - Making plots should be easy
>
> Finding no package that suited me just right, I did what any
> self-respecting Python programmer would do: rolled up my sleeves and dived
> in. Not having any real experience with computer graphics, I decided to
> emulate MATLAB’s plotting capabilities because that is something MATLAB
> does very well. This had the added advantage that many people have a lot of
> MATLAB experience, and thus they can quickly get up to steam plotting in
> python. From a developer’s perspective, having a fixed user interface (the
> pylab interface) has been very useful, because the guts of the code base
> can be redesigned without affecting user code.
>
>
>
>
>
> On Wed, Jul 30, 2014 at 11:51 PM, Benjamin Root <ben...@ou...> wrote:
>
>> Fernando,
>>
>> This information is going to be the preface of my book on using
>> matplotlib for making an interactive application (sorry, no IPython, the
>> editor wanted to keep the scope tight). So, what I am looking for are some
>> of the major interactive features (who supplied them, and their
>> reasons/purpose). Also, how has interactive matplotlib supported uses "in
>> the wild" such as the Mars Phoenix Lander and recently, the ISEE3 reboot
>> project (that abandoned satellite that was recently revived by citizen
>> scientists).
>>
>> Of, course, any insights to John's original needs/use cases in the early
>> years would be very valuable as well. I could have sworn he has written
>> such missives on the mailing lists, but I can't seem to find them.
>>
>> Cheers!
>> Ben Root
>> On Jul 30, 2014 11:21 PM, "Fernando Perez" <fpe...@gm...> wrote:
>>
>>> Hi Ben,
>>>
>>> if by interactive plotting you refer to using it interactively via
>>> ipython and other such systems, there's a good part of that history that is
>>> spread somewhere between the early mpl and ipython archives AND John's and
>>> my personal inboxes.
>>>
>>> A good chunk of that (not all, mind you, since many others contributed)
>>> happened with John and I working on it, and sadly he's not with us and I
>>> had a loss of my early email (anything older than 2005) when I left the
>>> University of Colorado.
>>>
>>> I'd be happy to answer some questions if you have them, to the best of
>>> my memory. Probably quicker over skype/phone, ping me directly (at my
>>> Berkeley address) if you want.
>>>
>>> Cheers
>>>
>>> f
>>>
>>>
>>>
>>> On Wed, Jul 30, 2014 at 7:20 PM, Benjamin Root <ben...@ou...> wrote:
>>>
>>>> Hello all,
>>>>
>>>> I am trying to put together notes for a writeup on a short history of
>>>> matplotlib (in particular, its uses for interactive plotting). I have John
>>>> Hunter's SciPy 2012 Keynote, which helps, but I was hoping for some other
>>>> sources.
>>>>
>>>> Unfortunately, searching for "matplotlib" and "history" gets me lots of
>>>> results on our trials and tribulations with version control...
>>>>
>>>> Anybody have anything bookmarked?
>>>>
>>>> Cheers!
>>>> Ben Root
>>>>
>>>> P.S. - Yes... this is for a book. Stay tuned!
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Infragistics Professional
>>>> Build stunning WinForms apps today!
>>>> Reboot your WinForms applications with our WinForms controls.
>>>> Build a bridge from your legacy apps to the future.
>>>>
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk
>>>> _______________________________________________
>>>> Matplotlib-users mailing list
>>>> Mat...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>>>
>>>>
>>>
>>>
>>> --
>>> Fernando Perez (@fperez_org; http://fperez.org)
>>> fperez.net-at-gmail: mailing lists only (I ignore this when swamped!)
>>> fernando.perez-at-berkeley: contact me here for any direct mail
>>>
>>
>

Hi,

I am using the standard matplotlib on Ubuntu 14.04.

I was creating a custom colormap using the standard dict with
rgb values method (something I have done before as well). However,
one of the values in the 'r' array was 55 instead of .55 and contourf
would die saying 'invalid rgb value' which was somewhere near 51.

Ideally, matplotlib should catch this, and I did some digging to see what
is happening. I finally saw this bit of code in 473 in colors.py (in the
function
makMappingArray)

np.clip(lut, 0.0, 1.0)

it appears that np.clip does not modify its arguments and this should
instead
be

lut = np.clip(lut, 0.0, 1.0)

which fixed the problem. Of course, if this error(?) was not there, I would
have
never found the problem in my custom colormap, so not all bad afer all ;)

Thanks,
Joy


-- 
The best ruler, when he finishes his
tasks and completes his affairs,
the people say
“It all happened naturally”

                                         - Te Tao Ch'ing

Just to keep my notes in one place... from Matplotlib's "Introduction" page
is prose that I assume was written by John:

For years, I used to use MATLAB exclusively for data analysis and
visualization. MATLAB excels at making nice looking plots easy. When I
began working with EEG data, I found that I needed to write applications to
interact with my data, and developed and EEG analysis application in
MATLAB. As the application grew in complexity, interacting with databases,
http servers, manipulating complex data structures, I began to strain
against the limitations of MATLAB as a programming language, and decided to
start over in Python. Python more than makes up for all of MATLAB’s
deficiencies as a programming language, but I was having difficulty finding
a 2D plotting package (for 3D VTK <http://www.vtk.org/> more than exceeds
all of my needs).

When I went searching for a Python plotting package, I had several
requirements:

   - Plots should look great - publication quality. One important
   requirement for me is that the text looks good (antialiased, etc.)
   - Postscript output for inclusion with TeX documents
   - Embeddable in a graphical user interface for application development
   - Code should be easy enough that I can understand it and extend it
   - Making plots should be easy

Finding no package that suited me just right, I did what any
self-respecting Python programmer would do: rolled up my sleeves and dived
in. Not having any real experience with computer graphics, I decided to
emulate MATLAB’s plotting capabilities because that is something MATLAB
does very well. This had the added advantage that many people have a lot of
MATLAB experience, and thus they can quickly get up to steam plotting in
python. From a developer’s perspective, having a fixed user interface (the
pylab interface) has been very useful, because the guts of the code base
can be redesigned without affecting user code.





On Wed, Jul 30, 2014 at 11:51 PM, Benjamin Root <ben...@ou...> wrote:

> Fernando,
>
> This information is going to be the preface of my book on using matplotlib
> for making an interactive application (sorry, no IPython, the editor wanted
> to keep the scope tight). So, what I am looking for are some of the major
> interactive features (who supplied them, and their reasons/purpose). Also,
> how has interactive matplotlib supported uses "in the wild" such as the
> Mars Phoenix Lander and recently, the ISEE3 reboot project (that abandoned
> satellite that was recently revived by citizen scientists).
>
> Of, course, any insights to John's original needs/use cases in the early
> years would be very valuable as well. I could have sworn he has written
> such missives on the mailing lists, but I can't seem to find them.
>
> Cheers!
> Ben Root
> On Jul 30, 2014 11:21 PM, "Fernando Perez" <fpe...@gm...> wrote:
>
>> Hi Ben,
>>
>> if by interactive plotting you refer to using it interactively via
>> ipython and other such systems, there's a good part of that history that is
>> spread somewhere between the early mpl and ipython archives AND John's and
>> my personal inboxes.
>>
>> A good chunk of that (not all, mind you, since many others contributed)
>> happened with John and I working on it, and sadly he's not with us and I
>> had a loss of my early email (anything older than 2005) when I left the
>> University of Colorado.
>>
>> I'd be happy to answer some questions if you have them, to the best of my
>> memory. Probably quicker over skype/phone, ping me directly (at my Berkeley
>> address) if you want.
>>
>> Cheers
>>
>> f
>>
>>
>>
>> On Wed, Jul 30, 2014 at 7:20 PM, Benjamin Root <ben...@ou...> wrote:
>>
>>> Hello all,
>>>
>>> I am trying to put together notes for a writeup on a short history of
>>> matplotlib (in particular, its uses for interactive plotting). I have John
>>> Hunter's SciPy 2012 Keynote, which helps, but I was hoping for some other
>>> sources.
>>>
>>> Unfortunately, searching for "matplotlib" and "history" gets me lots of
>>> results on our trials and tribulations with version control...
>>>
>>> Anybody have anything bookmarked?
>>>
>>> Cheers!
>>> Ben Root
>>>
>>> P.S. - Yes... this is for a book. Stay tuned!
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Infragistics Professional
>>> Build stunning WinForms apps today!
>>> Reboot your WinForms applications with our WinForms controls.
>>> Build a bridge from your legacy apps to the future.
>>>
>>> http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk
>>> _______________________________________________
>>> Matplotlib-users mailing list
>>> Mat...@li...
>>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>>
>>>
>>
>>
>> --
>> Fernando Perez (@fperez_org; http://fperez.org)
>> fperez.net-at-gmail: mailing lists only (I ignore this when swamped!)
>> fernando.perez-at-berkeley: contact me here for any direct mail
>>
>

OS: OSX 10.8.5 (Mountain Lion)
Matplotlib Version: 1.3.1
ipython: 2.1.0
gcc info:
Configured with: --prefix=/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 5.1 (clang-503.0.38) (based on LLVM 3.4svn)
Target: x86_64-apple-darwin12.5.0
Thread model: posix

Matplotlib Obtained: Installed via pip, auto chosen options below

BUILDING MATPLOTLIB
                matplotlib: yes [1.3.1]
                    python: yes [2.7.6 (default, Jan 28 2014, 11:09:35)  [GCC
                            4.2.1 Compatible Apple LLVM 5.0 (clang-500.2.79)]]
                  platform: yes [darwin]

    REQUIRED DEPENDENCIES AND EXTENSIONS
                     numpy: yes [version 1.8.1]
                  dateutil: yes [using dateutil version 2.2]
                   tornado: yes [using tornado version 4.0]
                 pyparsing: yes [using pyparsing version 2.0.2]
                     pycxx: yes [Couldn't import.  Using local copy.]
                    libagg: yes [pkg-config information for 'libagg' could not
                            be found. Using local copy.]
                  freetype: yes [version 17.2.11]
                       png: yes [version 1.6.12]

    OPTIONAL SUBPACKAGES
               sample_data: yes [installing]
                  toolkits: yes [installing]
                     tests: yes [using nose version 1.3.3]

    OPTIONAL BACKEND EXTENSIONS
                    macosx: yes [installing, darwin]
                    qt4agg: no  [PyQt4 not found]
                   gtk3agg: no  [Requires pygobject to be installed.]
                 gtk3cairo: no  [Requires cairo to be installed.]
                    gtkagg: no  [Requires pygtk]
                     tkagg: yes [installing, version 81008]
                     wxagg: no  [requires wxPython]
                       gtk: no  [Requires pygtk]
                       agg: yes [installing]
                     cairo: no  [cairo not found]
                 windowing: no  [Microsoft Windows only]

    OPTIONAL LATEX DEPENDENCIES
                    dvipng: yes [version 1.14]
               ghostscript: yes [version 9.07]
                     latex: yes [version 3.1415926]
                   pdftops: no

Problem:

Using the default mathtext renderer, axis labels overlap the spine.
Pictures of the problem are available at
http://stackoverflow.com/questions/24997386/latex-tick-label-overlapping-axis-in-graph-generated-by-matplotlib/24999963#24999963.
Turning on tex rendering via rc('text', usetex=True), makes the
problem go away which indicates this is a possible bug in mathtext (or
perhaps the libraries used by it on OSX) and I thought I should report
it.

Minimal Code Producing Error:

from pylab import *

xticks([-np.pi, -np.pi/2, 0, np.pi/2, np.pi],
       [r'$-\pi$', r'$-\frac{\pi}{2}$',r'$0$', r'$\frac{\pi}{2}$',r'$+\pi$'])

show(block=False)

Extra Potential Relevant Information:

When calling verbose-debug, there are a bunch of lines like this one:

Using fontManager instance from /Users/wd239/.matplotlib/fontList.cache
backend MacOSX version unknown

findfont: Matching
:family=sans-serif:style=normal:variant=normal:weight=normal:stretch=normal:size=medium
to Bitstream Vera Sans
(/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/Vera.ttf)
with score of 0.000000
findfont: Matching
:family=STIXGeneral:style=normal:variant=normal:weight=normal:stretch=normal:size=12
to STIXGeneral (/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXGeneral.ttf)
with score of 0.000000
......