matplotlib-users Mailing List for matplotlib

I'm guessing this is currently impossible with the current mplot3d
functionality, but I was wondering if there was any way I could generate a
3d graph with r, phi, z coordinates rather than x, y, z?  

The point is that I want to make a figure that looks like the following:
http://upload.wikimedia.org/wikipedia/commons/7/7b/Mexican_hat_potential_polar.svg

Using the x, y, z system, I end up with something that has long tails like
this:
http://upload.wikimedia.org/wikipedia/commons/4/44/Mecanismo_de_Higgs_PH.png

If I try to artificially cut off the data beyond some radius, I end up with
jagged edges that are not at all visually appealing.

I would appreciate any crazy ideas you can come up with.

Thanks,
Jeff

P.S. Code to produce the ugly jaggedness is included below:

-------------------------------------------------------
from mpl_toolkits.mplot3d import Axes3D
import matplotlib
import numpy as np
from matplotlib import cm
from matplotlib import pyplot as plt

step = 0.04
maxval = 1.0
fig = plt.figure()
ax = Axes3D(fig)
X = np.arange(-maxval, maxval, step)
Y = np.arange(-maxval, maxval, step)
X, Y = np.meshgrid(X, Y)
R = np.sqrt(X**2 + Y**2)
Z = ((R**2 - 1)**2) * (R < 1.25)
ax.plot_surface(X, Y, Z, rstride=1, cstride=1, cmap=cm.jet)
ax.set_zlim3d(0, 1)
#plt.setp(ax.get_xticklabels(), visible=False)
ax.set_xlabel(r'$\phi_\mathrm{real}$')
ax.set_ylabel(r'$\phi_\mathrm{im}$')
ax.set_zlabel(r'$V(\phi)$')
ax.set_xticks([])
plt.show()

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Dear Michael,

I deeply appreciate your help with this!

On 17/03/10 20:34, Michael Droettboom wrote:

>> I have tried
>>
>> import matplotlib
>> matplotlib.use('GtkCairo')
>>
>> as you suggested, but they had no effect whatsoever. Even the error
>> output is the same.
> I'm surprised that isn't having any effect. The Cairo backend should not
> be running any code in backend_ps.py -- where the source of the error
> is. If you put "backend: GtkCairo" in your matplotlibrc, does that work?

No, in fact, after adding that line to matplotlibrc the CJK isn't even 
rendered in the png anymore! *

My error message has changed:

In [1]: run dea.py
/usr/lib/pymodules/python2.6/matplotlib/backends/backend_gtk.py:614: 
DeprecationWarning: Use the new widget gtk.Tooltip
   self.tooltips = gtk.Tooltips()

(this with "backend: GtkCairo" in matplotlibrc and the following two 
lines in my dea.py:

import matplotlib
matplotlib.use('GtkCairo')

Incidentally, if I uncomment those two lines, then the (Western) font of 
my graph actually changes.

> What version of matplotlib are you running?

In [2]: matplotlib.__version__
Out[2]: '0.99.0'

>> Note: in line 327 and 328 of the matplotlibrc I have added
>>
>> ps.fonttype=42
>> pdf.fonttype=42

I haven taken those out again, because I got an error message.

I continue to be at a loss!

David

* I had the same problem yesterday, I solved it by reinstalling a backup 
of matplotlibrc. Weird.


>>
>> whereas I have uncommented
>>
>> pdf.fonttype : 3
>>
>> Any ideas? I would most welcome any hint and suggestion!
> I don't think these settings will resolve the problem -- either font
> type (42 or 3) still expects glyph names.
>
> Mike
>>
>>
>>
>>
>> On 17/03/10 04:15, Michael Droettboom wrote:
>>> The font you are using (SimHei) does not have any glyph names -- these
>>> are used in the Postscript backend to refer to glyphs outside of the
>>> ASCII range. More specifically, it looks like it has at least one
>>> invalid glyph name (glyph names can only contain ASCII characters) --
>>> loading it in FontForge complains about this. I haven't come across such
>>> a font before, but maybe that's common in CJK fonts. I don't know. I'm
>>> looking through the spec to find a way that glyphs can be referenced
>>> without a name, but I'm not finding one. Note, the PDF backend has the
>>> same issue.
>>>
>>> Do you have the same problem if you remove "SimHei" from the
>>> font.sans-serif list and thus use "Adobe Song Std" instead? (I was able
>>> to find an online download of SimHei to test with, but not Adobe Song
>>> Std).
>>>
>>> As a workaround, the Cairo backend seems to handle this font just fine.
>>> You can add
>>>
>>> import matplotlib
>>> matplotlib.use('GtkCairo')
>>>
>>> to the top of your script.
>>>
>>> Mike
>>>
>>> David wrote:
>>>> Hello everybody,
>>>>
>>>> I have a final problem with my graph. As a last step I produce an
>>>> *.eps file that I use in conjunction with LaTeX.
>>>>
>>>> Here is the last part of my code:
>>>>
>>>> # plt.title('Title')
>>>> xlab = plt.xlabel(u'输入 1')
>>>> #xlab.set_position((0.2, 0.1))
>>>> ylab = plt.ylabel(u'输入 2')
>>>> plt.grid(True)
>>>> plt.subplots_adjust(bottom=0.2)
>>>> plt.show()
>>>> plt.savefig('dea.eps')
>>>>
>>>>
>>>> plt.show() produces the correct output,
>>>>
>>>> but
>>>>
>>>> plt.savefig('dea.eps') produces an error (the error message is
>>>> attached).
>>>>
>>>> The error is clearly linked to the Chinese, as it runs through if I
>>>> take the Chinese out of the code.
>>>> Also, plt.savefig('dea.png') works fine.
>>>>
>>>> Could anyone indicate where I would have to look for the mistake? The
>>>> matplotlibrc should be fine, but I am not sure.
>>>>
>>>> Your help would be greatly appreciated!
>>>>
>>>> Many thanks,
>>>>
>>>> David
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>>
>>>>
>>>> Download Intel® Parallel Studio Eval
>>>> Try the new software tools for yourself. Speed compiling, find bugs
>>>> proactively, and fine-tune applications for parallel performance.
>>>> See why Intel Parallel Studio got high marks during beta.
>>>> http://p.sf.net/sfu/intel-sw-dev
>>>> ------------------------------------------------------------------------
>>>>
>>>>
>>>> _______________________________________________
>>>> Matplotlib-users mailing list
>>>> Mat...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>>
>>
>>
>> ------------------------------------------------------------------------
>>
>

Is it possible to serialize a figure constructed in matplotlib/pyplot,
so that you could quickly load it and then
save it in new formats and/or interactively explore it?

thanks,

ilya

Maybe:

from matplotlib import pyplot as plt

figureOne = plt.figure()
axesOne = figureOne.add_axes([0, 0, 1, 1])
axesOne.plot([-1, 1], [-2, 2])
axesOne.plot([-2, 2], [-1, 1])

axesOne.set_xlim((-3, 3))
axesOne.set_ylim((-3, 3))
figureOne.set_figwidth(2)
figureOne.set_figheight(2)

plt.savefig("Friedrich.png")

Friedrich

Hi everyone, 

Is there a straightforward way for me to ensure that my data is 
centered: allways present on the figure? I'm plotting the results
from complicated geometrical calculations and I need high dpi
so that I can debug the code. I've recorded the session in a log
file and I've modified the ipython logfile into a script. The
result is here:

http://img87.imageshack.us/img87/8306/interfaceprojections.png

and the script is here:

http://pastebin.com/3dkfNDuk

As you see, in the image, a part of the rectangle is missing. It is 
actually sort of a rectangle shaped set of finite volumes. What 
I'm looking for is to have the whole rectangle (or any other shape)
visible on the axes of the figure, with a properly scaled axes ratio
('equal' in the script). And to reduce the output, could it be possible
to plot just the diagram, without the remaining whitespace?

It seems that when I use

figureOne.set_figheight(number)
figureOne.set_figwidth(number)

it stands for the figure, but not for the axes. I'm interested just in 
the axes since it's the only subplot. 

Any advice?

I looked in the user guide but I didn't find anything so far... I'll keep
looking.

Thank you in advance,
Tomislav

On Wed, Mar 17, 2010 at 4:10 AM, Matthias Michler
<Mat...@gm...> wrote:

> once more I'd like to ask for comments about my feature request and proposed
> patch.
> Should I post it at the 'feature request' or  'patch' tracker?
>
> Thanks in advance for any comments.

Hey Matthias -- This should be placed on the patch tracker, and you
can respond back to this list with a link to the patch.  I'll review
it when I get a minute.  Thanks for following up and for making
patches against branch and HEAD.

JDH

David wrote:
> Dear Michael,
>
> thanks for your input. So far, though, no luck.
>
> I have deleted "SimHei" in matplotlibrc, and I can then continue 
> generating CJK characters. The png is generated, the eps is not. Thus, 
> no change. The error output is also the same:
>
> RuntimeError: Face has no glyph names
> WARNING: Failure executing file: <dea.py>
>
> I have tried
>
>  import matplotlib
>  matplotlib.use('GtkCairo')
>
> as you suggested, but they had no effect whatsoever. Even the error 
> output is the same.
I'm surprised that isn't having any effect.  The Cairo backend should 
not be running any code in backend_ps.py -- where the source of the 
error is.  If you put "backend: GtkCairo" in your matplotlibrc, does 
that work?

What version of matplotlib are you running?
>
> I attach my code, maybe that gives a hint.
>
> Note: in line 327 and 328 of the matplotlibrc I have added
>
> ps.fonttype=42
> pdf.fonttype=42
>
> whereas I have uncommented
>
> pdf.fonttype    : 3
>
> Any ideas? I would most welcome any hint and suggestion!
I don't think these settings will resolve the problem -- either font 
type (42 or 3) still expects glyph names.

Mike
>
>
>
>
> On 17/03/10 04:15, Michael Droettboom wrote:
>> The font you are using (SimHei) does not have any glyph names -- these
>> are used in the Postscript backend to refer to glyphs outside of the
>> ASCII range. More specifically, it looks like it has at least one
>> invalid glyph name (glyph names can only contain ASCII characters) --
>> loading it in FontForge complains about this. I haven't come across such
>> a font before, but maybe that's common in CJK fonts. I don't know. I'm
>> looking through the spec to find a way that glyphs can be referenced
>> without a name, but I'm not finding one. Note, the PDF backend has the
>> same issue.
>>
>> Do you have the same problem if you remove "SimHei" from the
>> font.sans-serif list and thus use "Adobe Song Std" instead? (I was able
>> to find an online download of SimHei to test with, but not Adobe Song 
>> Std).
>>
>> As a workaround, the Cairo backend seems to handle this font just fine.
>> You can add
>>
>> import matplotlib
>> matplotlib.use('GtkCairo')
>>
>> to the top of your script.
>>
>> Mike
>>
>> David wrote:
>>> Hello everybody,
>>>
>>> I have a final problem with my graph. As a last step I produce an
>>> *.eps file that I use in conjunction with LaTeX.
>>>
>>> Here is the last part of my code:
>>>
>>> # plt.title('Title')
>>> xlab = plt.xlabel(u'输入 1')
>>> #xlab.set_position((0.2, 0.1))
>>> ylab = plt.ylabel(u'输入 2')
>>> plt.grid(True)
>>> plt.subplots_adjust(bottom=0.2)
>>> plt.show()
>>> plt.savefig('dea.eps')
>>>
>>>
>>> plt.show() produces the correct output,
>>>
>>> but
>>>
>>> plt.savefig('dea.eps') produces an error (the error message is 
>>> attached).
>>>
>>> The error is clearly linked to the Chinese, as it runs through if I
>>> take the Chinese out of the code.
>>> Also, plt.savefig('dea.png') works fine.
>>>
>>> Could anyone indicate where I would have to look for the mistake? The
>>> matplotlibrc should be fine, but I am not sure.
>>>
>>> Your help would be greatly appreciated!
>>>
>>> Many thanks,
>>>
>>> David
>>>
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------ 
>>>
>>>
>>> ------------------------------------------------------------------------------ 
>>>
>>>
>>> Download Intel&#174; Parallel Studio Eval
>>> Try the new software tools for yourself. Speed compiling, find bugs
>>> proactively, and fine-tune applications for parallel performance.
>>> See why Intel Parallel Studio got high marks during beta.
>>> http://p.sf.net/sfu/intel-sw-dev
>>> ------------------------------------------------------------------------ 
>>>
>>>
>>> _______________________________________________
>>> 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

Gökhan SEVER-2 wrote:
> 
> Oh these busy chemical compound plots :) Are those results of gas
> chromatography analysis?
> 
> Something like below produces a nice fully plotted output here. Could you
> give it a try?
> 
> import matplotlib.pyplot as plt
> plt.plot(range(100))
> locs, labels = plt.xticks(range(100), range(100))
> plt.setp(labels, rotation=90, fontsize=7)
> plt.show()
> 
> 
> -- 
> Gökhan
> 


Gokhan,

Your suggestion works great. I guess the MaxNLocator approach I have been
using will place __up__to__ N ticks but not necessarily N ticks?

And yes, these chemical profiles are from GCMS and other devices/techniques.
I added upper X axis tick labels so you know a given chemical species' name
and number; I chose to only have one legend to keep the clutter down as much
as possible; I position the upper X axis labels in or outside the plot
depending on whether the plot title exists. Luckily, I don't imagine having
to deal with more species than 105 any time soon. Thanks again! Here is the
improved plot (sorry for the pink background, I am not sure why it is
showing up that way):


http://old.nabble.com/file/p27927991/PMF2BasecaseProfiles.jpeg 


-----
Josh Hemann
Statistical Advisor 
http://www.vni.com/ Visual Numerics 
jhemann at vni dizzot com 

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Eric,
   Thank you, thank you, thank you.  This not only fixes the problem I
reported with with
FixedLocator(..) but also another one where I was using MultipleLocator(..)
and getting
the same problem issue with dropping first and last contours.  The later
isn't as easy
to work-around but your change fixed it.

David Smith

On Sat, Mar 13, 2010 at 12:30 PM, Eric Firing <ef...@ha...> wrote:

> David Smith wrote:
>
>> This is a bug report.
>>
>> I am using matplotlib 0.99.1 on Windows.  When using contour with the
>> keyword
>> argument locator=ticker.FixedLocator(levels), the plot is always dropping
>> the first
>> and last contour level.  If there are less than 3 levels, contour.py
>> throws an
>> exception.
>>
>> My workaround is to duplicate the first and last levels when using the
>> fixed locator: e.g. my argument becomes
>>
>>     locator=FixedLocator( [levels[0]] + levels + [levels[-1]] )
>>
>> I have traced the problem to the last line in contour.py, method
>> _autolev() which
>> strips the first and last levels if the contours are not filled:
>>
>>      return lev[1:-1]
>>
>> This line occurs at line 682 in my version of contour.py which came with
>> the 0.991 installation.
>>
>> I realize that I could specify the levels in the argument V and this does
>> work.  However
>> this code is embedded in GUI-ness which allows the user to choose how the
>> contours
>> are selected.  Passing the locator seems to be the best option code-wise.
>>
>
> I committed a small change to svn trunk (r8190) that I think will handle
> your use case without fouling anything else up.
>
> Eric
>
>
>> Thank you,
>>
>> Dave Smith
>>
>>