matplotlib-users Mailing List for matplotlib (Page 2)

This has now been fixed in SVN.  See the 
example/pylab_examples/image_clip_path.py for usage.

Mike

Federico Milano wrote:
> Dear Mike,
>
> thanks a lot for the information.
>
> Best wishes,
>
> Federico
>
>
>
> Michael Droettboom wrote:
>   
>> Unfortunately, clip paths are not implemented for the Agg backend.  
>> Other backends (Ps, Pdf, Svg) may work, but I haven't tried that in a 
>> while.
>>
>> I've spent a few tries trying to come up with the magic Agg 
>> incantation to make this work.  It's not really documented in Agg, but 
>> it should theoretically be possible.  It would take someone probably 
>> to dig through the Agg source code and figure it out.  Any volunteers? ;)
>>
>> Cheers,
>> Mike
>>
>> Federico Milano wrote:
>>     
>>> Dear All,
>>>
>>> I am a new user of python and of matplotlib, so, please excuse me if I
>>> am asking a trivial question.
>>>
>>> I am trying to use the funciton imshow to plot a temperature map of the
>>> voltage levels of an electrical grid.  After creating the grid data
>>> using "meshgrid" and "griddata" functions, "imshow" works nicely and
>>> fills up the whoe axes box.
>>>
>>> Since, I also have the border line of the electrical grid (in the form
>>> of a closed polygon coordinates), my next step is to clip the
>>> temperature map using this polygon as a patch.  Thus, I have created a
>>> Path instance with the polygon coordinates, subsequently, a PathPatch
>>> instance, say "patch".
>>>
>>> Finally, I call the imshow function using the Artist options
>>> "clip_on=True" and "clip_path=patch".  I was expecting that imshow would
>>> have filed up only the region inside the polygon, but imshow is still
>>> mapping the full figure axis box, i.e., the plots with and without the
>>> clip_path option are identical.
>>>
>>> What am I missing or doing wrong?
>>>
>>> Thank you very much in advance for any help,
>>>
>>> Best wishes,
>>>
>>> Federico
>>>
>>>
>>>
>>> ------------------------------------------------------------------------- 
>>>
>>> This SF.Net email is sponsored by the Moblin Your Move Developer's 
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>>> great prizes
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>>> world
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>>> _______________________________________________
>>> Matplotlib-users mailing list
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>>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>>   
>>>       
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
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> Matplotlib-users mailing list
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>   

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

Hi,

I don't think this is possible - but I wanted to check in case I'm
missing something.

Is there a way of changing the appearance of the plot interactively?
I'm thinking of things like dragging the position of a legend, right
clicking to be able to insert a text box or access properties of the
axes etc like with Matlab.

The programmatic interface is great - but, as just happened, I often
find myself trying to drag the legend out of the way by force of
habit!

Thanks,

Robin

You could use the (admittedly inscrutable) "unzip" technique:

ax.plot_date(*zip(*items))

See this blog post for explanation:

http://paddy3118.blogspot.com/2007/02/unzip-un-needed-in-python.html

If you use Numpy arrays, of course, you could use slicing, which, IMHO, 
is clearer:

items = numpy.asarray(items)
ax.plot_date(items[:,0], items[:,1])

Mike

Thomas Guettler wrote:
> Hi,
>
> I use the API of matplotlib and have a basic problem:
>
> Up to now I am used to gather my data into a list of tuples. But
> matplotlib uses serveral lists instead.
>
> Example:
>   me: [(date1, count1), (date2, count2), ...]
>   matplotlib: ax.plot_date(dates, counts)
>
> Finally I use something like this quite often:
>    method([item[0] for item in items], [item[1] for item in items])
> But I think thats to much looping.
>
> That's my personal problem, but I think a more pythonic
> API would be nice...
>
>   Thomas
>
>   

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

Hi Michael,

2008/10/22 Michael Droettboom <md...@st...>:
> You need to "rewind" the StringIO cursor before opening with PIL:
>
> imgdata = StringIO.StringIO()
> fig.savefig(imgdata, format='png')
> imgdata.seek(0)
> im = Image.open(imgdata)

Thanks. It works fine now.

Best regards,
Jesper

Fixed.  These errors were all in new content.

Any comments on the content? ... :)

Xavier Gnata wrote:
> ok.
> It is way better now but still:
> http://validator.w3.org/check?uri=https%3A%2F%2Ffanyv88.com%3A443%2Fhttp%2Fmatplotlib.sourceforge.net%2F&charset=(detect+automatically)&doctype=Inline&group=0 
>
>
> hum I should spend some time on this because:
> http://validator.w3.org/check?uri=https%3A%2F%2Ffanyv88.com%3A443%2Fhttp%2Fmatplotlib.sourceforge.net%2Fgallery.html&charset=(detect+automatically)&doctype=Inline&group=0&user-agent=W3C_Validator%2F1.591 
>
>
> but this gallery is so nice...
>
> Xavier
>
>> This has now been fixed in SVN.
>>
>> index.html is the only page that includes hand-written HTML.  If you 
>> see any errors of this nature on other pages, please file bugs with 
>> Sphinx and/or docutils.
>>
>> Cheers,
>> Mike
>>
>> Xavier Gnata wrote:
>>> Looks great but there are too many errors:
>>> http://validator.w3.org/check?uri=https%3A%2F%2Ffanyv88.com%3A443%2Fhttp%2Fmatplotlib.sourceforge.net%2F&charset=(detect+automatically)&doctype=Inline&group=0 
>>>
>>>
>>> I'm not a geek and I do not care about w3c small warnings but it 
>>> would be so nice to have a xhtml compliant website (as close as 
>>> possible)
>>>
>>>  From an "artistic" point of view, I would put more emphasis on the 
>>> screenshot (pylab purpose is to produce *very* nice images...)
>>>
>>> xavier
>>>
>>>
>>>  
>>>> We've been working behind the scenes on a new documentation system for
>>>> matplotlib, which integrates the web site, API documentation and PDF
>>>> guide into a single source of sphinx/rest documents which are easier
>>>> to maintain and extend, hopefully leading to better and more
>>>> up-to-date docs.
>>>>
>>>> We went live with the new site yesterday:
>>>>
>>>>   http://matplotlib.sf.net
>>>>
>>>> so check it out and let us know if something is broken or missing.  We
>>>> don't have everything that was on the old site (some stuff from the
>>>> FAQ, "what's new" and "user's guide" has not been ported over) but we
>>>> do have should be current, searchable, indexed and cross-linked.
>>>>
>>>> Thanks to Darren Dale who spear-headed the effort to use the sphinx
>>>> documentation, and to the developers who have contributed, especially
>>>> Michael Droettboom, who has developed several nice sphinx extensions
>>>> to do inheritance diagrams, syntax highlighting of ipython sessions,
>>>> and inline plotting.  As an example we can include plots in our API
>>>> documentation, see
>>>>
>>>>   
>>>> http://matplotlib.sourceforge.net/api/axes_api.html#matplotlib.axes.Axes.acorr 
>>>>
>>>>
>>>> We embed these plots with a "plot" directive that generates the
>>>> figures from external code at documentation build time, which
>>>> guarantees that the example code you see in the docs generate the
>>>> figures you see in the docs.  For example, in the acorr docstring, all
>>>> we have to do is::
>>>>
>>>>         **Example:**
>>>>
>>>>         .. plot:: ../mpl_examples/pylab_examples/xcorr_demo.py
>>>>
>>>> and the figure and source code links automagically appear in the docs.
>>>>
>>>> Because some of these extensions are generally useful, Michael,
>>>> Fernando and I have been working on a "sphinx_template" which contains
>>>> the template of a sphinx documentation project with these extensions
>>>> in place, so people who want to get started using sphinx (the official
>>>> documentation system for python, numpy, ipython and matplotlib) can do
>>>> so more easily.  Right now it is available in svn
>>>>
>>>>   > svn co 
>>>> https://matplotlib.svn.sourceforge.net/svnroot/matplotlib/trunk/py4science/examples/sphinx_template2 
>>>>
>>>>
>>>> and see the README in the checkout directory.  Michael also did a talk
>>>> on matplotlib's use of sphinx and the sphinx template at the last
>>>> scipy conference.  We're still waiting for the videos of the talks to
>>>> be posted (can someone poke someone?)  but you can see the talk PDF
>>>> from the proceedings here:
>>>>
>>>>   http://conference.scipy.org/proceedings/SciPy2008/paper_6/
>>>>
>>>> JDH
>>>>
>>>> ------------------------------------------------------------------------- 
>>>>
>>>> This SF.Net email is sponsored by the Moblin Your Move Developer's 
>>>> challenge
>>>> Build the coolest Linux based applications with Moblin SDK & win 
>>>> great prizes
>>>> Grand prize is a trip for two to an Open Source event anywhere in 
>>>> the world
>>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>>>> _______________________________________________
>>>> Matplotlib-users mailing list
>>>> Mat...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>>>       
>>>
>>>
>>> ------------------------------------------------------------------------- 
>>>
>>> This SF.Net email is sponsored by the Moblin Your Move Developer's 
>>> challenge
>>> Build the coolest Linux based applications with Moblin SDK & win 
>>> great prizes
>>> Grand prize is a trip for two to an Open Source event anywhere in 
>>> the world
>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>>> _______________________________________________
>>> Matplotlib-users mailing list
>>> Mat...@li...
>>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>>   
>>
>

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

Hi,

I use the API of matplotlib and have a basic problem:

Up to now I am used to gather my data into a list of tuples. But
matplotlib uses serveral lists instead.

Example:
  me: [(date1, count1), (date2, count2), ...]
  matplotlib: ax.plot_date(dates, counts)

Finally I use something like this quite often:
   method([item[0] for item in items], [item[1] for item in items])
But I think thats to much looping.

That's my personal problem, but I think a more pythonic
API would be nice...

  Thomas

-- 
Thomas Guettler, http://www.thomas-guettler.de/
E-Mail: guettli (*) thomas-guettler + de

I'm not aware of that problem.  It should convert any PNG implicitly to 
our native RGBA format.  Can you provide a PNG file that illustrates the 
breakage?

Mike

David Warde-Farley wrote:
> Howdy,
>
> I noticed that MPL's imread() command, when applied to binary (1-bit  
> grayscale) PNGs does some serious mangling.
>
> Anyone know what's going on, or is it just that only RGBA PNG's are  
> supported?
>
> Thanks,
>
> David
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>   

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

Hi mpl users,

I get some strange results when I make a quiver plot of a masked
array. This script:

from numpy.ma import zeros, masked_values
from pylab import quiver, savefig
a = masked_values(zeros((5,5)), 0)
quiver(a,a)
savefig('test.png')

gives me a plot which has 25 horizontal arrows (although they look
strange). It should give me a plot without any arrows. Is this a bug
in matplotlib (I am using 0.98.3)?

Best regards,
Jesper

John [H2O] wrote:
> Hello, 
>
> I'm creating a web application that will take user input from a javascript
> map to give me bounding coordinates (i.e. urcrnrlat, urcrnrlon, llcrnrlat,
> llcrnrlon) and possibly a switch for polar projection. Other than that I
> have no further information. Which projection is the most suitable to handle
> anything from a 'global' plot to a zoom say over a state? I don't see the
> zoom being too tight, but global projections are likely. I personally prefer
> Equal Area, hence right now I'm working with 'aeqd', but I seem to have
> problems if the plot is global with that projection.
>
> Just looking for advice, opinions, and ideally examples if anyone has
> created a similar function / module to use in a web environment.
>
> Thanks!
> -john
>   
John:  Sounds like you need one of the global cylindrical projections, 
such as cylindrical equidistant ('cyl'), miller ('mill') or mercator 
('merc').  In the svn version, you also have Gall Stereographic 
('gall').   See 
http://matplotlib.sourceforge.net/basemap/doc/html/users/mapsetup.html 
for examples.  Unfortunately, none of them are equal-area.  Mollweide 
('moll') is a global equal-area projection, but it's only global (you 
can't specify a domain that isn't global).  For the polar option, I 
suggest polar lambert azimuthal equal-area 
(http://matplotlib.sourceforge.net/basemap/doc/html/users/plaea.html).  
The user can specify whether he/she wants the south or north polar 
aspect, and the latitude of the outer edge.

-Jeff

-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
325 Broadway                Boulder, CO, USA 80305-3328

ok.
It is way better now but still:
http://validator.w3.org/check?uri=https%3A%2F%2Ffanyv88.com%3A443%2Fhttp%2Fmatplotlib.sourceforge.net%2F&charset=(detect+automatically)&doctype=Inline&group=0

hum I should spend some time on this because:
http://validator.w3.org/check?uri=https%3A%2F%2Ffanyv88.com%3A443%2Fhttp%2Fmatplotlib.sourceforge.net%2Fgallery.html&charset=(detect+automatically)&doctype=Inline&group=0&user-agent=W3C_Validator%2F1.591

but this gallery is so nice...

Xavier

> This has now been fixed in SVN.
>
> index.html is the only page that includes hand-written HTML.  If you 
> see any errors of this nature on other pages, please file bugs with 
> Sphinx and/or docutils.
>
> Cheers,
> Mike
>
> Xavier Gnata wrote:
>> Looks great but there are too many errors:
>> http://validator.w3.org/check?uri=https%3A%2F%2Ffanyv88.com%3A443%2Fhttp%2Fmatplotlib.sourceforge.net%2F&charset=(detect+automatically)&doctype=Inline&group=0 
>>
>>
>> I'm not a geek and I do not care about w3c small warnings but it 
>> would be so nice to have a xhtml compliant website (as close as 
>> possible)
>>
>>  From an "artistic" point of view, I would put more emphasis on the 
>> screenshot (pylab purpose is to produce *very* nice images...)
>>
>> xavier
>>
>>
>>  
>>> We've been working behind the scenes on a new documentation system for
>>> matplotlib, which integrates the web site, API documentation and PDF
>>> guide into a single source of sphinx/rest documents which are easier
>>> to maintain and extend, hopefully leading to better and more
>>> up-to-date docs.
>>>
>>> We went live with the new site yesterday:
>>>
>>>   http://matplotlib.sf.net
>>>
>>> so check it out and let us know if something is broken or missing.  We
>>> don't have everything that was on the old site (some stuff from the
>>> FAQ, "what's new" and "user's guide" has not been ported over) but we
>>> do have should be current, searchable, indexed and cross-linked.
>>>
>>> Thanks to Darren Dale who spear-headed the effort to use the sphinx
>>> documentation, and to the developers who have contributed, especially
>>> Michael Droettboom, who has developed several nice sphinx extensions
>>> to do inheritance diagrams, syntax highlighting of ipython sessions,
>>> and inline plotting.  As an example we can include plots in our API
>>> documentation, see
>>>
>>>   
>>> http://matplotlib.sourceforge.net/api/axes_api.html#matplotlib.axes.Axes.acorr 
>>>
>>>
>>> We embed these plots with a "plot" directive that generates the
>>> figures from external code at documentation build time, which
>>> guarantees that the example code you see in the docs generate the
>>> figures you see in the docs.  For example, in the acorr docstring, all
>>> we have to do is::
>>>
>>>         **Example:**
>>>
>>>         .. plot:: ../mpl_examples/pylab_examples/xcorr_demo.py
>>>
>>> and the figure and source code links automagically appear in the docs.
>>>
>>> Because some of these extensions are generally useful, Michael,
>>> Fernando and I have been working on a "sphinx_template" which contains
>>> the template of a sphinx documentation project with these extensions
>>> in place, so people who want to get started using sphinx (the official
>>> documentation system for python, numpy, ipython and matplotlib) can do
>>> so more easily.  Right now it is available in svn
>>>
>>>   > svn co 
>>> https://matplotlib.svn.sourceforge.net/svnroot/matplotlib/trunk/py4science/examples/sphinx_template2 
>>>
>>>
>>> and see the README in the checkout directory.  Michael also did a talk
>>> on matplotlib's use of sphinx and the sphinx template at the last
>>> scipy conference.  We're still waiting for the videos of the talks to
>>> be posted (can someone poke someone?)  but you can see the talk PDF
>>> from the proceedings here:
>>>
>>>   http://conference.scipy.org/proceedings/SciPy2008/paper_6/
>>>
>>> JDH
>>>
>>> ------------------------------------------------------------------------- 
>>>
>>> This SF.Net email is sponsored by the Moblin Your Move Developer's 
>>> challenge
>>> Build the coolest Linux based applications with Moblin SDK & win 
>>> great prizes
>>> Grand prize is a trip for two to an Open Source event anywhere in 
>>> the world
>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>>> _______________________________________________
>>> Matplotlib-users mailing list
>>> Mat...@li...
>>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>>       
>>
>>
>> ------------------------------------------------------------------------- 
>>
>> This SF.Net email is sponsored by the Moblin Your Move Developer's 
>> challenge
>> Build the coolest Linux based applications with Moblin SDK & win 
>> great prizes
>> Grand prize is a trip for two to an Open Source event anywhere in the 
>> world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>   
>

Howdy,

I noticed that MPL's imread() command, when applied to binary (1-bit  
grayscale) PNGs does some serious mangling.

Anyone know what's going on, or is it just that only RGBA PNG's are  
supported?

Thanks,

David

On Thu, Oct 23, 2008 at 7:04 AM, Jouni K. Seppänen <jk...@ik...> wrote:

> "David Krapohl" <dav...@gm...>
> writes:
>
> > I am getting an error with savefig and pdf when I try to used matplotlib
> > with latex font rendering (attached below). In etc/matplotlibrc, I set
> > text.latex.preamble : \usepackage{MinionPro},
> > \renewcommand{\sfdefault}{Myriad-LF}
> > It seems that the dviread backend does not find a specific *.vf,
> > MinionPro-It--lcdfj.vf to be specific,
> >  file that is not needed in my opinion. Any ideas how to solve that?
>
> Is that a commercial font? What exact files are installed when you
> install that font in your texmf tree? Can dvipdfm/dvipdfmx/dvipdft
> create a pdf file from a dvi file that uses this font?
>

It is an adobe font that is bundled with the Acrobat Reader. It is an otf
font that was converted with "cfftot1" to *.pfb postscript font. Font
metrics and scripts can be downloaded at
http://developer.berlios.de/projects/minionpro/
I use it very often and so far I didn't have problems.


>
> >From your backtrace, it looks like dviread fails to parse a tfm file:
>
> >   File "/usr/lib/python2.5/site-packages/matplotlib/dviread.py", line
> 398,
> > in __init__
> >     for char in range(0, max(tfm.width)) ]
> > ValueError: max() arg is an empty sequence
>

Yes, with --verbose-debug-annoying I can see that it stops at:
find_tex_file: MinionPro-It--lcdfj.vf ->
Followed by the same error message as in the first post. Unfortunately the
vf-file is not there but the tfm file. As far as I know does this file
describe the dotless-j for whatever reasons. So I think this particular file
is not very important for math output.


> --
> Jouni K. Seppänen
> http://www.iki.fi/jks
>
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

David Krapohl

"David Krapohl" <dav...@gm...>
writes:

> I am getting an error with savefig and pdf when I try to used matplotlib
> with latex font rendering (attached below). In etc/matplotlibrc, I set
> text.latex.preamble : \usepackage{MinionPro},
> \renewcommand{\sfdefault}{Myriad-LF}
> It seems that the dviread backend does not find a specific *.vf,
> MinionPro-It--lcdfj.vf to be specific,
>  file that is not needed in my opinion. Any ideas how to solve that?

Is that a commercial font? What exact files are installed when you
install that font in your texmf tree? Can dvipdfm/dvipdfmx/dvipdft
create a pdf file from a dvi file that uses this font?

>From your backtrace, it looks like dviread fails to parse a tfm file:

>   File "/usr/lib/python2.5/site-packages/matplotlib/dviread.py", line 398,
> in __init__
>     for char in range(0, max(tfm.width)) ]
> ValueError: max() arg is an empty sequence

-- 
Jouni K. Seppänen
http://www.iki.fi/jks

My program runs through a loop and is supposed to re-plot the graph after
each step (which includes a pause of 1 second). I can't get the plot to
refresh. I wrote the following simple program which has the same problem. I
tried both  draw() nor f.canvas.draw() works. I'm running it from ipython
-pylab

A similar problem was encountered here:
http://www.nabble.com/Plotting-loop-refuses-to-update-display-on-OS-X-td19818020.html
but I still don't know what to do.

### teststuff.py

import pylab
import time

def testRef():
    f = pylab.figure()
    ax = pylab.gca()
    pylab.show()
    for x in range(10):
        ax.axhline(x)
        time.sleep(1)
#        pylab.draw()
        f.canvas.draw()
        
testRef()
-- 
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