matplotlib-users Mailing List for matplotlib (Page 15)

Eric Firing wrote:
> Fabrice Silva wrote:
>> Le mardi 09 septembre 2008 à 08:26 -0400, Michael Droettboom a écrit :
>>> You can use
>>>
>>>     def ticklabel_format(self, **kwargs):
>> It did not figure how to use that!
>> I've tried in ipython :
>>         import numpy as np
>>         t = np.linspace(0,1,1024)
>>         f = np.sin(10*t)/1e5
>>         plot(t,f)
>>         ax = gca()
>>         ax.ticklabel_format(style='sci', axis='y')
> 
>            ax.yaxis.major.formatter.set_powerlimits((0,0))
> 
>>         show()
>>
>> but the yticklabels are still in plain notation...
>> I've googled, but I still can not find where I am wrong!
> 
> Yes, this is confusing. The problem is that the "scientific" style uses 
> scientific notation only for sufficiently large or small numbers, with 
> thresholds determined by the powerlimits parameter.  The line I added 
> above will force scientific notation.
> 
> The ticklabel_format method needs another kwarg to enable setting the 
> powerlimits.

Done in svn 6148.  I called the kwarg 'scilimits' to emphasize that it 
works with the 'sci' style; if there are comments to the effect that I 
should have called it 'powerlimits' for consistency with the 
corresponding ScalarFormatter method, I can change it.

With the change in svn, instead of the line I added above, your call to 
ticklabel_format would be:

ax.ticklabel_format(style='sci', scilimits=(0,0), axis='y')

Eric

Fabrice Silva wrote:
> Le mardi 09 septembre 2008 à 08:26 -0400, Michael Droettboom a écrit :
>> You can use
>>
>>     def ticklabel_format(self, **kwargs):
> It did not figure how to use that!
> I've tried in ipython :
>         import numpy as np
>         t = np.linspace(0,1,1024)
>         f = np.sin(10*t)/1e5
>         plot(t,f)
>         ax = gca()
>         ax.ticklabel_format(style='sci', axis='y')

           ax.yaxis.major.formatter.set_powerlimits((0,0))

>         show()
> 
> but the yticklabels are still in plain notation...
> I've googled, but I still can not find where I am wrong!

Yes, this is confusing. The problem is that the "scientific" style uses 
scientific notation only for sufficiently large or small numbers, with 
thresholds determined by the powerlimits parameter.  The line I added 
above will force scientific notation.

The ticklabel_format method needs another kwarg to enable setting the 
powerlimits.

Eric

John Hunter wrote:
> On Tue, Sep 30, 2008 at 5:07 PM, Jae-Joon Lee <lee...@gm...> wrote:
> 
>> The problem is already well explained by Eric. And my solution is to
>> interpret the legend.pad as a fraction of the textsize (pad=0.3 seems
>> to work fine in my eyes). Note that this breaks the backward
>> compatibility. I personally think the original behavior may have
>> produced unsatisfactory results in most of the cases and keeping it as
>> a default may not be a good idea. While I hope others come out with an
>> elegant solution, I prefer to break the API in this case.
> 
> How about using a new kwarg and raising an exception if the old one is
> passed in, with the exception pointing to the new arg?  I am a little
> uncomfortable silently changing the meaning of the old arg.

Done, except that it just raises a warning, and still works with the old 
kwarg.  The new kwarg is "borderpad"; it is used if pad==0, which is the 
new rc default.  I set the default borderpad=0.5.

There is still too much other positioning in legend that is based on 
axes units.  I briefly tried to start changing others, again with 
additional kwargs, and things quickly fell apart.  Legend needs 
considerable reworking to take full advantage of the transforms 
framework (and maybe other mpl improvements since the original legend) 
and to put all positioning kwargs and code in sensible units.  It is 
amazing that the present code works as well as it does.

The way to make a transition may be via a separate version for a while.
There could be a single interface, with a kwarg to choose the version.

Eric

I guess you need to put draw() after plot()

self.canvas.figure.clf()
self.canvas.axes.plot([1.,2.,4.])
self.canvas.draw()

Let us know if it does not help.

-JJ



On Sat, Oct 4, 2008 at 7:17 PM, rocha <ber...@me...> wrote:
> Hi Guys,
>
> I need to clear the Figure after the user has clicked the some button in
> PyQt, but when I try to plot the graphics again nothing appear. In
> ipython it works, but when I try it inside my application it does not
> work. What am I missing?
>
> Inside my MplCanvas class (actually it is a QWidget - see
> embedding_in_qt4.py in matplotlib examples file - user_interface) I have
> this code:
>
> self.fig = Figure(figsize=(self.width, self.height), dpi=dpi)
>
> And then in my main application I'm trying to do:
>
> self.canvas.figure.clf()
> self.canvas.draw()
> self.canvas.axes.plot([1.,2.,4.])
>
> and nothing is plotted. The Figure is totally gray. I tried to do the
> same thing in embedding_in_qt4.py example, modifying some parts, but it
> didn't work too.
>
> Do you have any suggestions?
>
> Thanks!
> Best regards,
> Bernardo M. Rocha
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
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John Hunter wrote:
> On Sat, Sep 27, 2008 at 1:04 PM, Eric Firing <ef...@ha...> wrote:
> 
>> Good answer, but there may be one exception.  The Matlab function
>> description indicates that it can produce eps files with the cmyk color
>> space, which is indeed something that publishers tend to want, and
>> something that we don't do.  Whether Matlab does it well, and whether
>> with some reasonable modification to the mpl ps backend we could do at
>> least as well, I don't know.
> 
> This is certainly something that would be nice to have.  There was
> some recent work on agg to support different colorspaces, I think CMYK
> was among them, but it hasn't yet been contributed into the mainline
> as far as I know.  It would take quite a bit of work for us to support
> a generic colorspace model, but it would be a nice feature....

John,

Is it still true that we will not be able to take advantage of any agg 
improvements because of the agg license change?

Eric

Hi Guys,

I need to clear the Figure after the user has clicked the some button in 
PyQt, but when I try to plot the graphics again nothing appear. In 
ipython it works, but when I try it inside my application it does not 
work. What am I missing?

Inside my MplCanvas class (actually it is a QWidget - see 
embedding_in_qt4.py in matplotlib examples file - user_interface) I have 
this code:

self.fig = Figure(figsize=(self.width, self.height), dpi=dpi)      

And then in my main application I'm trying to do:

self.canvas.figure.clf()
self.canvas.draw()
self.canvas.axes.plot([1.,2.,4.])

and nothing is plotted. The Figure is totally gray. I tried to do the 
same thing in embedding_in_qt4.py example, modifying some parts, but it 
didn't work too.

Do you have any suggestions?

Thanks!
Best regards,
Bernardo M. Rocha

functions like raw_input blok the mianloop of some gui backends (e.g.,
gtk) but work fine with some other backend (although Tk is the only
backend I know of). So my guess is that you used a different backend
with 0.98.1.
I guess you have a few options.

 * try different backend (Tk) with 0.98.3
 * use ginput
 * or try a ginput-like routine that I made sometime ago which works
okay with raw_input.
   http://sourceforge.net/mailarchive/message.php?msg_id=6e8d907b0803101609s7bd8fecaj851a6ecf1ab2a316%40mail.gmail.com

IHTH,

-JJ


On Thu, Oct 2, 2008 at 5:18 PM, Zane Selvans <za...@id...> wrote:
> I have a Python module that I've written with some pylab plotting
> routines in it.  One of them loops over a list of objects, generating
> some plots based on the data associated with each list member in
> turn.  It's meant to be an interactive way to step through the list
> and see what the things look like.
>
> I have the loop set up to wait for user input before going on to the
> next object, using
>
> x = raw_input("press return for next fit: ")
>
> but for some reason, the plot window never updates.  I've tried
> putting both draw() and show() immediately
> before the raw_input() line, and neither works.  The plot only seems
> to update when I ctrl-C out of the loop, and otherwise, I just get the
> spinning beachball when I mouseover the plot.
>
> I'm using Matplotlib 0.98.3 on OS X (10.5.5) with the built-in python
> from Apple I think (2.5.1).  I'm calling the plotting routine from
> ipython 0.8.3 using the -pylab option.
>
> The same script previously worked fine under Matplotlib 0.98.1
>
> Other plotting routines from the same module seem to work fine - it's
> only this plot within a loop that's giving me trouble.
>
> Any ideas?
>
> --
> Zane Selvans
> Amateur Earthling
> za...@id...
> 303/815-6866
> http://zaneselvans.org
> PGP Key: 55E0815F
>
>
>
>
>
>
>
> -------------------------------------------------------------------------
> 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
>

I have a problem with every matplot version since 0.90.1. One of my
installed fonts causes afm.py to bail out. I am sure I reported this
problem before without reaction. After I installed python 1.6 and a
recent numpy 0.90.1 does not work anymore so I tried the latest again,
and get the afm error again:

> python -i -c "from matplotlib import pylab"
/usr/local/lib/python2.6/site-packages/matplotlib-0.98.3-py2.6-linux-i686.egg/matplotlib/__init__.py:96: DeprecationWarning: the md5 module is deprecated; use hashlib instead
  import md5, os, re, shutil, sys, warnings
/usr/local/lib/python2.6/site-packages/matplotlib-0.98.3-py2.6-linux-i686.egg/pytz/tzinfo.py:5: DeprecationWarning: the sets module is deprecated
  from sets import Set
Found an unknown keyword in AFM header (was MetricsSets)
Found an unknown keyword in AFM header (was IsBaseFont)
Found an unknown keyword in AFM header (was IsCIDFont)
Found an unknown keyword in AFM header (was StartDirection)
Found an unknown keyword in AFM header (was EndDirection)
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/usr/local/lib/python2.6/site-packages/matplotlib-0.98.3-py2.6-linux-i686.egg/matplotlib/pylab.py", line 206, in <module>
    from matplotlib import mpl  # pulls in most modules
  File "/usr/local/lib/python2.6/site-packages/matplotlib-0.98.3-py2.6-linux-i686.egg/matplotlib/mpl.py", line 2, in <module>
    from matplotlib import axis
  File "/usr/local/lib/python2.6/site-packages/matplotlib-0.98.3-py2.6-linux-i686.egg/matplotlib/axis.py", line 9, in <module>
    import matplotlib.font_manager as font_manager
  File "/usr/local/lib/python2.6/site-packages/matplotlib-0.98.3-py2.6-linux-i686.egg/matplotlib/font_manager.py", line 1129, in <module>
    _rebuild()
  File "/usr/local/lib/python2.6/site-packages/matplotlib-0.98.3-py2.6-linux-i686.egg/matplotlib/font_manager.py", line 1120, in _rebuild
    fontManager = FontManager()
  File "/usr/local/lib/python2.6/site-packages/matplotlib-0.98.3-py2.6-linux-i686.egg/matplotlib/font_manager.py", line 910, in __init__
    self.afmdict = createFontDict(self.afmfiles, fontext='afm')
  File "/usr/local/lib/python2.6/site-packages/matplotlib-0.98.3-py2.6-linux-i686.egg/matplotlib/font_manager.py", line 521, in createFontDict
    prop = afmFontProperty(font)
  File "/usr/local/lib/python2.6/site-packages/matplotlib-0.98.3-py2.6-linux-i686.egg/matplotlib/font_manager.py", line 420, in afmFontProperty
    name = font.get_familyname()
  File "/usr/local/lib/python2.6/site-packages/matplotlib-0.98.3-py2.6-linux-i686.egg/matplotlib/afm.py", line 440, in get_familyname
    return self._header['FamilyName']
KeyError: 'FamilyName'
>>> import pdb
>>> pdb.pm()
> /usr/local/lib/python2.6/site-packages/matplotlib-0.98.3-py2.6-linux-i686.egg/matplotlib/afm.py(440)get_familyname()
-> return self._header['FamilyName']
(Pdb) print self._header
{'Notice': 'Copyright (c) 1999 Ministry of Education, Taipei, Taiwan. All Rights Reserved.', 'Ascender': 880.0, 'FontBBox': [-123, -250, 1000, 880], 'Weight': 'Regular', 'Descender': -250.0, 'CharacterSet': 'Adobe-CNS1-0', 'IsFixedPitch': False, 'FontName': 'MOEKai-Regular', 'StartFontMetrics': 4.0999999999999996, 'CapHeight': 880.0, 'Version': '1.000', 'UnderlinePosition': -100, 'Characters': 13699, 'UnderlineThickness': 50, 'ItalicAngle': 0.0, 'StartCharMetrics': 13699}
(Pdb) 

What is there to do?

Regards
Berthold

-- 
A: Weil es die Lesbarkeit des Textes verschlechtert.
F: Warum ist TOFU so schlimm?
A: TOFU
F: Was ist das größte Ärgernis im Usenet?

On Tue, Sep 30, 2008 at 5:07 PM, Jae-Joon Lee <lee...@gm...> wrote:

> The problem is already well explained by Eric. And my solution is to
> interpret the legend.pad as a fraction of the textsize (pad=0.3 seems
> to work fine in my eyes). Note that this breaks the backward
> compatibility. I personally think the original behavior may have
> produced unsatisfactory results in most of the cases and keeping it as
> a default may not be a good idea. While I hope others come out with an
> elegant solution, I prefer to break the API in this case.

How about using a new kwarg and raising an exception if the old one is
passed in, with the exception pointing to the new arg?  I am a little
uncomfortable silently changing the meaning of the old arg.

JDH

On Sat, Sep 27, 2008 at 1:04 PM, Eric Firing <ef...@ha...> wrote:

> Good answer, but there may be one exception.  The Matlab function
> description indicates that it can produce eps files with the cmyk color
> space, which is indeed something that publishers tend to want, and
> something that we don't do.  Whether Matlab does it well, and whether
> with some reasonable modification to the mpl ps backend we could do at
> least as well, I don't know.

This is certainly something that would be nice to have.  There was
some recent work on agg to support different colorspaces, I think CMYK
was among them, but it hasn't yet been contributed into the mainline
as far as I know.  It would take quite a bit of work for us to support
a generic colorspace model, but it would be a nice feature....

JDH

On vendredi 3 octobre 2008, Alan wrote:

> We are developing an application (CING: cing.googlecodes.com) and we

  You mean http://cing.googlecode.com  (no "s")

[...]
> I don't have much idea at moment how to debug it better, but it seems
> that I cannot generate the PDFs because mtplib functions don't guess a
> finite number of pages.

[...]
> "/sw/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py", line
> 124, in pdfRepr
>     raise ValueError, "Can only output finite numbers in PDF"
> ValueError: Can only output finite numbers in PDF

  Is this not a problem with non-finite *values* in your data ? Do you have 
NaN of Inf numbers oin your data ?

-- 
Vincent Favre-Nicolin                   http://vincefn.net
Université Joseph Fourier       http://www.ujf-grenoble.fr
CEA/ Institut Nanosciences & Cryogénie  http://inac.cea.fr
ObjCryst & Fox             http://objcryst.sourceforge.net

Are you perhaps trying to plot data containing NaN or Inf?  If so, this 
is a known bug in 0.98.3 that has seen been corrected on SVN trunk.

A workaround is to pass masked arrays (where the NaNs and Infs are 
masked out) to matplotlib instead.

But this bug should be gone in the next release of matplotlib.  If 
you're comfortable building from SVN, you could even try that now.

Cheers,
Mike

Alan wrote:
> Dear all,
>
> I don't know much how to express this issue I am having but I will try.
>
> We are developing an application (CING: cing.googlecodes.com) and we
> have some routines to test the sanity of our code.
>
> I am developing in python, on a mac book pro with Mac OSX tiger and FINK.
>
> So when we were using matplotlib 0.90.1 and numpy 1.0.4 the routine
> below was running fine.
>
> Then I updated all from Fink, having now mtplib 0.98.3 and numpy 1.1.1
> and problems started to appear.
>
> I could solve all (e.g. replace verify_intervals()) but one, as shown below.
>
> I don't have much idea at moment how to debug it better, but it seems
> that I cannot generate the PDFs because mtplib functions don't guess a
> finite number of pages.
>
> I hope someone can give any idea.
>
> Many thanks in advance.
>
> Alan
>
> ======================================================================
> ERROR: testMoleculePlot (cing.Libs.test.test_NTMoleculePlot.AllChecks)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/Users/alan/workspace/cingWork/python/cing/Libs/test/test_NTMoleculePlot.py",
> line 178, in testMoleculePlot
>     createPngCopyToo=True  )
>   File "/Users/alan/workspace/cingWork/python/cing/Libs/NTmoleculePlot.py",
> line 176, in renderMoleculePlotSet
>     if ps.hardcopy(fileNameList[r-1]):
>   File "/Users/alan/workspace/cingWork/python/cing/Libs/NTplot.py",
> line 1201, in hardcopy
>     savefig(fileName)
>   File "/sw/lib/python2.5/site-packages/matplotlib/pyplot.py", line
> 342, in savefig
>     return fig.savefig(*args, **kwargs)
>   File "/sw/lib/python2.5/site-packages/matplotlib/figure.py", line
> 964, in savefig
>     self.canvas.print_figure(*args, **kwargs)
>   File "/sw/lib/python2.5/site-packages/matplotlib/backend_bases.py",
> line 1310, in print_figure
>     **kwargs)
>   File "/sw/lib/python2.5/site-packages/matplotlib/backend_bases.py",
> line 1204, in print_pdf
>     return pdf.print_pdf(*args, **kwargs)
>   File "/sw/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py",
> line 1864, in print_pdf
>     self.figure.draw(renderer)
>   File "/sw/lib/python2.5/site-packages/matplotlib/figure.py", line 759, in draw
>     for a in self.axes: a.draw(renderer)
>   File "/sw/lib/python2.5/site-packages/matplotlib/axes.py", line 1523, in draw
>     a.draw(renderer)
>   File "/sw/lib/python2.5/site-packages/matplotlib/lines.py", line 437, in draw
>     markerFunc(renderer, gc, tpath, affine.frozen())
>   File "/sw/lib/python2.5/site-packages/matplotlib/lines.py", line
> 885, in _draw_plus
>     path, path_trans)
>   File "/sw/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py",
> line 1253, in draw_markers
>     marker, Op.use_xobject)
>   File "/sw/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py",
> line 451, in output
>     self.write(fill(map(pdfRepr, data)))
>   File "/sw/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py",
> line 124, in pdfRepr
>     raise ValueError, "Can only output finite numbers in PDF"
> ValueError: Can only output finite numbers in PDF
>
> ----------------------------------------------------------------------
>   

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

Dear all,

I don't know much how to express this issue I am having but I will try.

We are developing an application (CING: cing.googlecodes.com) and we
have some routines to test the sanity of our code.

I am developing in python, on a mac book pro with Mac OSX tiger and FINK.

So when we were using matplotlib 0.90.1 and numpy 1.0.4 the routine
below was running fine.

Then I updated all from Fink, having now mtplib 0.98.3 and numpy 1.1.1
and problems started to appear.

I could solve all (e.g. replace verify_intervals()) but one, as shown below.

I don't have much idea at moment how to debug it better, but it seems
that I cannot generate the PDFs because mtplib functions don't guess a
finite number of pages.

I hope someone can give any idea.

Many thanks in advance.

Alan

======================================================================
ERROR: testMoleculePlot (cing.Libs.test.test_NTMoleculePlot.AllChecks)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/alan/workspace/cingWork/python/cing/Libs/test/test_NTMoleculePlot.py",
line 178, in testMoleculePlot
    createPngCopyToo=True  )
  File "/Users/alan/workspace/cingWork/python/cing/Libs/NTmoleculePlot.py",
line 176, in renderMoleculePlotSet
    if ps.hardcopy(fileNameList[r-1]):
  File "/Users/alan/workspace/cingWork/python/cing/Libs/NTplot.py",
line 1201, in hardcopy
    savefig(fileName)
  File "/sw/lib/python2.5/site-packages/matplotlib/pyplot.py", line
342, in savefig
    return fig.savefig(*args, **kwargs)
  File "/sw/lib/python2.5/site-packages/matplotlib/figure.py", line
964, in savefig
    self.canvas.print_figure(*args, **kwargs)
  File "/sw/lib/python2.5/site-packages/matplotlib/backend_bases.py",
line 1310, in print_figure
    **kwargs)
  File "/sw/lib/python2.5/site-packages/matplotlib/backend_bases.py",
line 1204, in print_pdf
    return pdf.print_pdf(*args, **kwargs)
  File "/sw/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py",
line 1864, in print_pdf
    self.figure.draw(renderer)
  File "/sw/lib/python2.5/site-packages/matplotlib/figure.py", line 759, in draw
    for a in self.axes: a.draw(renderer)
  File "/sw/lib/python2.5/site-packages/matplotlib/axes.py", line 1523, in draw
    a.draw(renderer)
  File "/sw/lib/python2.5/site-packages/matplotlib/lines.py", line 437, in draw
    markerFunc(renderer, gc, tpath, affine.frozen())
  File "/sw/lib/python2.5/site-packages/matplotlib/lines.py", line
885, in _draw_plus
    path, path_trans)
  File "/sw/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py",
line 1253, in draw_markers
    marker, Op.use_xobject)
  File "/sw/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py",
line 451, in output
    self.write(fill(map(pdfRepr, data)))
  File "/sw/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py",
line 124, in pdfRepr
    raise ValueError, "Can only output finite numbers in PDF"
ValueError: Can only output finite numbers in PDF

----------------------------------------------------------------------
-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<

I am under the impression that the way to go is now the mlab interface 
to mayavi2. Here is a nice talk by Gael : 
http://gael-varoquaux.info/physics/slides_Scipy2007.pdf
Johann

Eric Firing wrote:
> Lisa Tauxe wrote:
>   
>> Are there any plans for incorporating this (what used to be mplot3d)  
>> into the new matplotlib version?
>>     
>
> Not that I know of.  It was not being maintained even before the move to 
> 0.98.x.
>
> Eric
>
> -------------------------------------------------------------------------
> 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
>   

I am writing a GUI application in wxPython and using MPL that plots figures,
saves them to image files, and then closes them all from within a thread to
keep the GUI responsive. Using the Enthought 2.3 install I would
sporatically have crashes that were hard to reproduce, but now that I've
upgrade to Enthought 2.5 (Python 2.5 and MPL 0.91.2.0001) it started
throwing exceptions when attempting to close a figure that I don't
understand. I've created an example script that excites the exception. I'm
not sure if the syptoms are a combination of problems caused by my use of
threads but this problem does not occur if threading is removed from the
script. I've read of others experiencing memory leaks and such when closing
figures, but no situations quite like this.

I am working from a desktop in Windows XP and I use the WXAgg backend.

Does anyone have any ideas, or any feedback on my use of threads? Thanks,
Josh

-------------------------------------------------------------------------------------------
#!/usr/bin/python

import wx
import time
from threading import Thread

import matplotlib
matplotlib.interactive(False)
matplotlib.use('WXAgg')
import matplotlib.pylab

class TestThread(Thread):
    def __init__(self, notify_window):
        Thread.__init__(self)

    def run(self):
        while True:  # Continuous loop that plots and destroys a figure
            matplotlib.pylab.figure(1)
            matplotlib.pylab.plot(range(0,5), range(0,5))
            matplotlib.pylab.show()
            time.sleep(1)
            matplotlib.pylab.close(1)  ### ERROR OCCURS HERE

class MainPanel(wx.Panel):
    def __init__(self, *args, **kwargs):
        wx.Panel.__init__(self, *args, **kwargs)
        self.test_thread = None

        # GUI objects and bindings
        self.run_test_button = wx.Button(self, -1, "Run")
        self.top_sizer = wx.BoxSizer(wx.VERTICAL)
        self.top_sizer.Add(self.run_test_button,      0, wx.EXPAND|wx.ALL,
border=2)
        self.SetSizer(self.top_sizer)
        self.Bind(wx.EVT_BUTTON,   self.run_test_button_bind,   id =
self.run_test_button.GetId())

    ### Binding Methods
    def run_test_button_bind(self, event):
        self.test_thread = TestThread(self)
        self.test_thread.start()
        #self.test_thread.run()
        
class MainFrame(wx.Frame):
    def __init__(self, *args, **kwargs):
        mFrame = wx.Frame.__init__(self, *args, **kwargs)
        self.mPanel = MainPanel(self, -1)
    
class mainApp(wx.App):
    def OnInit(self):
        self.frame = MainFrame(None, title="Test", size=wx.Size(100, 100))
        self.frame.Show()
        self.SetTopWindow(self.frame)
        return True

if __name__ == "__main__":
    app = mainApp()
    app.MainLoop()

--------------------------------------------------------------------------------------------------

Exception in thread Thread-1:
Traceback (most recent call last):
  File "C:\Python25\lib\threading.py", line 486, in __bootstrap_inner
    self.run()
  File ".\test.py", line 22, in run
    matplotlib.pylab.close(1)  ### ERROR OCCURS HERE
  File
"C:\python25\lib\site-packages\matplotlib-0.91.2.0001-py2.5-win32.egg\matplotlib\pyplot.py",
line 245, in close
    _pylab_helpers.Gcf.destroy(arg)
  File
"C:\python25\lib\site-packages\matplotlib-0.91.2.0001-py2.5-win32.egg\matplotlib\_pylab_helpers.py",
line 28, in destroy
    figManager.destroy()
  File
"C:\python25\lib\site-packages\matplotlib-0.91.2.0001-py2.5-win32.egg\matplotlib\backends\backend_wx.py",
line 1406, in destroy
    self.frame.Destroy()
  File
"C:\python25\lib\site-packages\matplotlib-0.91.2.0001-py2.5-win32.egg\matplotlib\backends\backend_wx.py",
line 1365, in Destroy
    wxapp.Yield()
  File
"C:\python25\lib\site-packages\wxpython-2.8.4.0.0003_s-py2.5-win32.egg\wx\_core.py",
line 7119, in Yield
    return _core_.PyApp_Yield(*args, **kwargs)
PyAssertionError: C++ assertion "wxThread::IsMain()" failed at
..\..\src\msw\evtloop.cpp(244) in wxEventLoop::Dispatch(): only the main
thread can process Windows messages
-- 
View this message in context: http://www.nabble.com/Problems-plotting-closing-figures-within-a-thread-tp19789227p19789227.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

I have a Python module that I've written with some pylab plotting  
routines in it.  One of them loops over a list of objects, generating  
some plots based on the data associated with each list member in  
turn.  It's meant to be an interactive way to step through the list  
and see what the things look like.

I have the loop set up to wait for user input before going on to the  
next object, using

x = raw_input("press return for next fit: ")

but for some reason, the plot window never updates.  I've tried  
putting both draw() and show() immediately
before the raw_input() line, and neither works.  The plot only seems  
to update when I ctrl-C out of the loop, and otherwise, I just get the  
spinning beachball when I mouseover the plot.

I'm using Matplotlib 0.98.3 on OS X (10.5.5) with the built-in python  
from Apple I think (2.5.1).  I'm calling the plotting routine from  
ipython 0.8.3 using the -pylab option.

The same script previously worked fine under Matplotlib 0.98.1

Other plotting routines from the same module seem to work fine - it's  
only this plot within a loop that's giving me trouble.

Any ideas?

--
Zane Selvans
Amateur Earthling
za...@id...
303/815-6866
http://zaneselvans.org
PGP Key: 55E0815F

Hello,
I am making some plots using the upperlimit keyword in the errorbar 
command as in the examples.
The arrows are drawn correctly but I notice that the exact limit point 
is in the middle of the arrow and not where the arrow starts.
Is it any way to improve it and have the beginning of the arrow 
represent the actual limit measure?
Also is there any way to increase the thickness of the arrow?

Thanks,
Nino

-- 

Antonino Cucchiara
PhD candidate
Department of Astronomy&Astrophysics
Penn State University
website: www.astro.psu.edu/~cucchiara/

Florian Koelling wrote:
> Hello again!
> 
> I think it's not a namespace problem.
> I tried:
> 
> from pylab import plot as pplot
> import pylab as p
> 
> As result I received busted SD Files. I ' ve this problem nearly for

I am not familiar with pybel and I don't know what an SD file is, so I 
have no idea what you mean above.  It would be nice to know where the 
interference is coming from, even if you can work around it by using the 
  OO api or some other suggestion.

First, for plotting capability, don't use pylab, use pyplot:

import matplotlib.pyplot as plt
plt.plot(...)
or
fig = plt.figure()
ax = fig.add_subplot(111)
ax.plot(...)
plt.show()

Many of the examples have been converted to use this recommended idiom.

Pyplot has the plotting part of pylab without dumping numpy into the 
namespace.  I suspect, however, that in your case the result of 
importing matplotlib.pyplot will be the same

Second, do you need plots on the screen, or is it enough to generate 
plot files?  If the latter, see the agg_oo.py example of how to 
eliminate pylab/pyplot completely (watch out for spurious line breaks in 
the following paste-in):

from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas
from matplotlib.figure import Figure

fig = Figure()
canvas = FigureCanvas(fig)
ax = fig.add_subplot(111)
ax.plot([1,2,3])
ax.set_title('hi mom')
ax.grid(True)
ax.set_xlabel('time')
ax.set_ylabel('volts')
canvas.print_figure('test')

This makes png files. If you want ps or pdf, the method would be the 
same but with the appropriate backend.

Eric

> three months - so I switched to Gnuplot - now recognizing that it is
> doesn't  have
> enough performance to make a large amount of plots.
> 
> (I tried local imports in a function as well -- same result)
> 
> Actually I'm not using any matplotlib code -- just the import statement
> -- and it's enough that all goes to hell.
> 
> With "import matplotlib" I do not have  those  problems - most plotting
> examples are dealing with pylab -- what can I use instead?
> 
> Maybe one of you Harry Plotters  has  an idea!
> 
> Thanks,
> 
> Florian
> 
> 
> Gary Pajer wrote:
>> On Wed, Oct 1, 2008 at 12:34 PM, Florian Koelling
>> <flo...@tu... <mailto:flo...@tu...>> wrote:
>>
>>     Hi Folks!
>>
>>     Is there a way to plot simple x/y Data in matplotlib WITHOUT using the
>>     "import pylab" command? (in all examples I only saw pylab).
>>
>>     I' working with openbabel(pybel) as well and I've got serious problems
>>     whenever I use "from pylab import plot" or similar commands -
>>
>>     (if I do, SDF files aren't read out anymore properly...)
>>
>>
>>     Thanks alot
>>
>>
>> If the problem is "namespace pollution"  (one package overriding names
>> defined earlier) then the following should work:
>>
>> from pylab import plot as pplot  (where "pplot" is an unused name)
>>
>> or
>>
>> import pylab as p
>>
>> then use, p.plot() instead of plot()
>> (this latter method is what I use.)
>>
>> hth,
>> gary

I see that my tcl/tk email made it through this time, but that this 
list has failed to achieve at the modest task given to them.  All of 
you are unwilling, or unable, to rise to the challenge of finding 
tcl/tk.  You leave me no option but to denounce and deprecate you.  I 
demand a full refund!

All tongue in cheek :)

But I would like some guidance.

Dave

Florian Koelling wrote:
> Actually I'm not using any matplotlib code -- just the import statement
> -- and it's enough that all goes to hell.

> With "import matplotlib" I do not have  those  problems

It sounds like you have a problem with whatever back-end is the default. 
Try changing that in your .matplotlibrc file, or try:

import matplotlib
matplotlib.use('Agg') # or 'wxagg', or 'whatever'

import pylab

that should do it.

What back end - are you/do you want to - use?

despite all the pylab examples, the OO inteface has a lot of advantages...

-Chris


-- 
Christopher Barker, Ph.D.
Oceanographer

Emergency Response Division
NOAA/NOS/OR&R            (206) 526-6959   voice
7600 Sand Point Way NE   (206) 526-6329   fax
Seattle, WA  98115       (206) 526-6317   main reception

Chr...@no...

Florian Koelling wrote:
> Hello again!
>
> I think it's not a namespace problem.
> I tried:
>
> from pylab import plot as pplot
> import pylab as p
>
> As result I received busted SD Files. I ' ve this problem nearly for
> three months - so I switched to Gnuplot - now recognizing that it is
> doesn't  have
> enough performance to make a large amount of plots.
>
> (I tried local imports in a function as well -- same result)
>
> Actually I'm not using any matplotlib code -- just the import statement
> -- and it's enough that all goes to hell.
>
> With "import matplotlib" I do not have  those  problems - most plotting
> examples are dealing with pylab -- what can I use instead?
>
> Maybe one of you Harry Plotters  has  an idea!
>   
As I said before, look in the examples/api directory (available here 
http://matplotlib.sourceforge.net/matplotlib_examples_0.98.3.zip) for 
examples of using the non-pyplot API.

Cheers,
Mike

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

Andrew Charles wrote:
> The latest beta of CDAT (Climate Data Analysis Tools, widely used in
> the atmospheric/oceanographic sciences) is distributed with the
> matplotlib source included.
>
> On OSX, while it seems to compile without a hitch, plotting
> interactively (or calling show() ) with the TkAgg backend results in a
> seg fault. The non-interactive backends have so far worked just fine.
>
> The output from a simple interactive hello world line plot with
> --verbose-helpful set is:
>
> =================
> Executing /opt/cdat/bin/python
> $HOME=/Users/acharles
> CONFIGDIR=/Users/acharles/.matplotlib
> matplotlib data path /opt/cdat/lib/python2.5/site-packages/matplotlib/mpl-data
> loaded rc file /opt/cdat/lib/python2.5/site-packages/matplotlib/mpl-data/matplotlibrc
> matplotlib version 0.98.3
> verbose.level helpful
> interactive is False
> units is False
> platform is darwin
> Using fontManager instance from /Users/acharles/.matplotlib/fontManager.cache
> backend TkAgg version 8.5
> Testing matplotlib
> Segmentation fault
> =================
>
> CDAT builds almost everything from source. I've always found building
> matplotlib for OSX to be tricky, so tend to just install binary eggs
> these days. Nevertheless I have tried a couple of solutions:
>
> 1. setting export PKG_CONFIG_PATH=/usr/X11/lib/pkgconfig
> 2. editing setupext.py to put the system X11 libraries ahead of any
> fink/macports versions
> 3. setting CFLAGS="-Os -arch i386 -arch ppc" LDFLAGS="-Os -arch i386 -arch ppc"
>
> but to no avail. Is there a simple solution that can be applied to the
> script that builds matplotlib?
>
>   

Andrew:   I think I ran into this before.  Correct me if I'm wrong ..

1) CDAT builds a unix version (not a framework build) of python for you, 
and installs itself in the unix python.
2) CDAT links against X11 versions of all the GUI toolkits (including Tk).

I think the segfault happens because you're picking up either the 
headers or libs for the framework version of Tk included with MacOS X.  
You need to use an X11 build.  To fix this, you need to edit the 
matplotlib setupext.py file to make sure that it's not finding the 
framework version of Tk (i.e, make sure the variable tk_framework ends 
up being zero or False).

HTH,

-Jeff

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

Dean N. Williams wrote:
> Hi Jeff,
>
>     You are correct on both assumptions below. On the Mac, we know how 
> to build CDAT using framework and have done so for various projects. 
> Is there a huge advantage for building CDAT on the Mac using 
> framework?  Perhaps in the future we will do this as the default.
>
> Thanks for the help on this.
>
> Best regards,
>     Dean

Dean:  If you use a framework build, you can use the builtin mac-native 
Tk and Wx.  If you use unix python, you must use X11 versions of the 
toolkits.  Personally, I don't mind that, but a lot of people don't want 
to mess with X11.  I like it because you can run stuff on your mac 
remotely and display windows over an ssh tunnel.

-Jeff
>
> On Oct 2, 2008, at 4:39 AM, Jeff Whitaker wrote:
>
>> Andrew Charles wrote:
>>> The latest beta of CDAT (Climate Data Analysis Tools, widely used in
>>> the atmospheric/oceanographic sciences) is distributed with the
>>> matplotlib source included.
>>>
>>> On OSX, while it seems to compile without a hitch, plotting
>>> interactively (or calling show() ) with the TkAgg backend results in a
>>> seg fault. The non-interactive backends have so far worked just fine.
>>>
>>> The output from a simple interactive hello world line plot with
>>> --verbose-helpful set is:
>>>
>>> =================
>>> Executing /opt/cdat/bin/python
>>> $HOME=/Users/acharles
>>> CONFIGDIR=/Users/acharles/.matplotlib
>>> matplotlib data path 
>>> /opt/cdat/lib/python2.5/site-packages/matplotlib/mpl-data
>>> loaded rc file 
>>> /opt/cdat/lib/python2.5/site-packages/matplotlib/mpl-data/matplotlibrc
>>> matplotlib version 0.98.3
>>> verbose.level helpful
>>> interactive is False
>>> units is False
>>> platform is darwin
>>> Using fontManager instance from 
>>> /Users/acharles/.matplotlib/fontManager.cache
>>> backend TkAgg version 8.5
>>> Testing matplotlib
>>> Segmentation fault
>>> =================
>>>
>>> CDAT builds almost everything from source. I've always found building
>>> matplotlib for OSX to be tricky, so tend to just install binary eggs
>>> these days. Nevertheless I have tried a couple of solutions:
>>>
>>> 1. setting export PKG_CONFIG_PATH=/usr/X11/lib/pkgconfig
>>> 2. editing setupext.py to put the system X11 libraries ahead of any
>>> fink/macports versions
>>> 3. setting CFLAGS="-Os -arch i386 -arch ppc" LDFLAGS="-Os -arch i386 
>>> -arch ppc"
>>>
>>> but to no avail. Is there a simple solution that can be applied to the
>>> script that builds matplotlib?
>>>
>>>
>>
>> Andrew:   I think I ran into this before.  Correct me if I'm wrong ..
>>
>> 1) CDAT builds a unix version (not a framework build) of python for 
>> you, and installs itself in the unix python.
>> 2) CDAT links against X11 versions of all the GUI toolkits (including 
>> Tk).
>>
>> I think the segfault happens because you're picking up either the 
>> headers or libs for the framework version of Tk included with MacOS 
>> X.  You need to use an X11 build.  To fix this, you need to edit the 
>> matplotlib setupext.py file to make sure that it's not finding the 
>> framework version of Tk (i.e, make sure the variable tk_framework 
>> ends up being zero or False).
>>
>> HTH,
>>
>> -Jeff
>>
>> -- 
>> Jeffrey S. Whitaker         Phone : (303)497-6313
>> NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
>> 325 Broadway                Boulder, CO, USA 80305-3328
>>
>


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

Hello again!

I think it's not a namespace problem.
I tried:

from pylab import plot as pplot
import pylab as p

As result I received busted SD Files. I ' ve this problem nearly for
three months - so I switched to Gnuplot - now recognizing that it is
doesn't  have
enough performance to make a large amount of plots.

(I tried local imports in a function as well -- same result)

Actually I'm not using any matplotlib code -- just the import statement
-- and it's enough that all goes to hell.

With "import matplotlib" I do not have  those  problems - most plotting
examples are dealing with pylab -- what can I use instead?

Maybe one of you Harry Plotters  has  an idea!

Thanks,

Florian


Gary Pajer wrote:
> On Wed, Oct 1, 2008 at 12:34 PM, Florian Koelling
> <flo...@tu... <mailto:flo...@tu...>> wrote:
>
>     Hi Folks!
>
>     Is there a way to plot simple x/y Data in matplotlib WITHOUT using the
>     "import pylab" command? (in all examples I only saw pylab).
>
>     I' working with openbabel(pybel) as well and I've got serious problems
>     whenever I use "from pylab import plot" or similar commands -
>
>     (if I do, SDF files aren't read out anymore properly...)
>
>
>     Thanks alot
>
>
> If the problem is "namespace pollution"  (one package overriding names
> defined earlier) then the following should work:
>
> from pylab import plot as pplot  (where "pplot" is an unused name)
>
> or
>
> import pylab as p
>
> then use, p.plot() instead of plot()
> (this latter method is what I use.)
>
> hth,
> gary
>  
>
>
>
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>   

The latest beta of CDAT (Climate Data Analysis Tools, widely used in
the atmospheric/oceanographic sciences) is distributed with the
matplotlib source included.

On OSX, while it seems to compile without a hitch, plotting
interactively (or calling show() ) with the TkAgg backend results in a
seg fault. The non-interactive backends have so far worked just fine.

The output from a simple interactive hello world line plot with
--verbose-helpful set is:

=================
Executing /opt/cdat/bin/python
$HOME=/Users/acharles
CONFIGDIR=/Users/acharles/.matplotlib
matplotlib data path /opt/cdat/lib/python2.5/site-packages/matplotlib/mpl-data
loaded rc file /opt/cdat/lib/python2.5/site-packages/matplotlib/mpl-data/matplotlibrc
matplotlib version 0.98.3
verbose.level helpful
interactive is False
units is False
platform is darwin
Using fontManager instance from /Users/acharles/.matplotlib/fontManager.cache
backend TkAgg version 8.5
Testing matplotlib
Segmentation fault
=================

CDAT builds almost everything from source. I've always found building
matplotlib for OSX to be tricky, so tend to just install binary eggs
these days. Nevertheless I have tried a couple of solutions:

1. setting export PKG_CONFIG_PATH=/usr/X11/lib/pkgconfig
2. editing setupext.py to put the system X11 libraries ahead of any
fink/macports versions
3. setting CFLAGS="-Os -arch i386 -arch ppc" LDFLAGS="-Os -arch i386 -arch ppc"

but to no avail. Is there a simple solution that can be applied to the
script that builds matplotlib?

-------------------------
Andrew Charles