matplotlib

On Dec 28, 2005, at 6:29 PM, Christopher Barker wrote:
> I just compiled Matplotlib 0.85 with the WXAgg back end.
>
> It seems to work fine, but when I run it, I get:
<errors snipped>
> This happens with pylab.show(), or if I use wxmpl.PlotPanel in an  
> App of my own.

This looks like another weird wxPython/wxWidgets/Gnome/CUPS problem,  
similar to the one Ryan Krauss had in October.  Given that you're  
getting very different error messages, I'm not sure that his solution  
is applicable:

On Oct 20, 2005, at 5:12 PM, Ryan Krauss wrote:
> So, it appears this is a problem with CUPS and wxPython.  I had never
> plugged a printer into this fairly new installation of ubuntu.  After
> doing so and making sure that cups is running, the IPP error went
> away.
>
> On 10/20/05, Ken McIvor <mcivor@...> wrote:
>> Based on the strace output, I believe that the warning is getting  
>> generated
>> when trying to start up CUPS (`/etc/cups/client.conf' is opened at  
>> line
>> 10484), from within lincups, which is loaded by libgnomeprintcups,  
>> which is
>> loaded by libgnomeprint, which is loaded by wxWidgets, which is  
>> loaded by
>> wxPython (whee!).  Do you have a working CUPS installation on your  
>> computer?
>> If that's not the solution, then I don't know what is; try  
>> emailing the
>> wxPython-users list.


On Dec 28, 2005, at 6:29 PM, Christopher Barker wrote:
> I haven't noticed this in any other wxPython apps. I have no idea  
> how to debug this, as it's not an error at the Python level.

I had Ryan send me some strace output:
	$ strace python -c short_wxagg_script.py > strace.txt 2>&1

You probably don't want to send it to the lists, but I'll be happy to  
take a look at it.  I also have  the strace output from October, if  
that would help the wxPython gurus better understand what's going on.

Another useful bit of information would be whether or not the  
wxPython demo's printing framework example causes the same errors  
when you run it.  That might help us nail down the source of the  
problem (e.g. is it at the wxPython-level, or something WxAgg is  
doing to wxPython, or the inclusion of the printing framework?).

Ken

Well, it is there and it works.  There is no toolbar, and the
save image button is not implemented.  I really haven't had access to
a mac in a while, so there hasn't been much development.  I basically
figured out the hard part of how to do the agg buffer to NSImage
bridge.  The rest of the perks should be pretty simple.  The code is
in backend_cocoaagg.py and the nib files are in the backends folder.

- Charlie

On 12/27/05, Christopher Barker <Chris.Barker@...> wrote:
> Charlie,
>
> IIRC, you were working on a Cocoa back-end for MPL a while back. How's
> that coming?
>
> If it was someone else, please speak up!
>
> -Chris
>
>
>
>
> --
> Christopher Barker, Ph.D.
> Oceanographer
>
> NOAA/OR&R/HAZMAT         (206) 526-6959   voice
> 7600 Sand Point Way NE   (206) 526-6329   fax
> Seattle, WA  98115       (206) 526-6317   main reception
>
> Chris.Barker@...
>

Charles R. Twardy wrote:
> For some reason, the FIRST time I try to plot something in an ipython
> session, I get:
> 
> SystemError: ../Objects/moduleobject.c:48: bad argument to internal function
> 
>>/usr/lib/python2.3/site-packages/matplotlib/pylab.py(774)figtext()
> 
> -> ret =  gcf().text(*args, **kwargs)
> 
> The last entry in the stacktrace is:
> /usr/lib/python2.3/site-packages/matplotlib/pylab.py in figtext(*args,
> **kwargs)    772 def figtext(*args, **kwargs):
>     773
> --> 774     ret =  gcf().text(*args, **kwargs)
>     775     draw_if_interactive()
>     776     return ret
> 
> After that everything works fine.  This error is robust: every first
> plot in ipython.  Haven't tried command-line yet.

Mmh, this may be the tip of the thread to unravel a long-standing problem 
which has stumped both John and me several times.  I've seen the message

SystemError: ../Objects/moduleobject.c:48: bad argument to internal function

when using the GtkAgg backend, but the funny thing is that the issue wouldn't 
appear for John even when we were both running _as the same user, on the same 
box_.  The only difference was that I was executing from the console and he 
was logged in remotely.  However, in that case it would always silently 
segfault, so we never saw the traceback you are seeing, which made the problem 
very hard to debug without really sinking time into it.  But with your 
behavior, we may get more info.

Some things to try which will help:

1. Version info, for everything (OS, python, ipython, mpl, gcc)

2. In ipython, type 'xmode verbose' before testing, and paste the entire 
ipython traceback.  I don't care if it's big, for this problem anything can help.

3. Backend info.  Try cycling through all the backends, and see if the problem 
appears with all or only with some.


With more details, it may be possible to make some progress on this one...

Cheers,

f

OK, here 'goes.  Verbose stacktrace and version info.  Haven't tried
other backends, won't tonight.

I. STACKTRACE: 'xmode verbose'
-------------------------------------------------------

In [5]:a.plot_status_histograms('Personality')
---------------------------------------------------------------------------
exceptions.SystemError                               Traceback (most
recent call last)

/home/ctwardy/Projects/SARBayes/Data/Docs/Natsar Report/<console>

/home/ctwardy/Projects/SARBayes/Data/Docs/Natsar Report/sardata.py in
plot_status_histograms(self=3D<sardata.SarData instance>,
category=3D'Personality')
    788                                     colors =3D status_colors,
    789                                     x_bins =3D status_order,
--> 790                                     pies =3D True)
        global pies =3D undefined
        global True =3D undefined
    791
    792     def plot_histograms(self,

/home/ctwardy/Projects/SARBayes/Data/Docs/Natsar Report/sardata.py in
plot_histograms(self=3D<sardata.SarData instance>, varX=3D'Status',
category=3D'Personality', bigtitle=3D'Status by Personality', colors=3D['b'=
,
'g', 'r', 'k'], contin=3DFalse, grid=3DFalse, missing=3DFalse, numcols=3D2,
N_label=3D'N_S', pies=3DTrue, x_bins=3D['Unhurt', 'Injured', 'Fatality', 'N=
o
Trace'], x_label=3D'Status', x_ticks=3D[0.5, 1.5, 2.5, 3.5],
x_ticklabels=3D['Unhurt', 'Injured', 'Fatality', 'No Trace'],
y_prop=3DTrue)
    902         # Now begin the plotting proper
    903         plotnum  =3D 0
--> 904         figtext(0.5, 0.95, bigtitle, font, fontsize=3D12)
        global figtext =3D <function figtext at 0x30806170>
        bigtitle =3D 'Status by Personality'
        font =3D {'color': 'k', 'fontweight': 'bold', 'fontname':
'Sans', 'verticalalignment': 'top', 'horizontalalignment': 'center'}
        global fontsize =3D undefined
    905         for value in values:
    906             plotnum +=3D 1

/usr/lib/python2.3/site-packages/matplotlib/pylab.py in
figtext(*args=3D(0.5, 0.94999999999999996, 'Status by Personality',
{'color': 'k', 'fontname': 'Sans', 'fontweight': 'bold',
'horizontalalignment': 'center', 'verticalalignment': 'top'}),
**kwargs=3D{'fontsize': 12})
    772 def figtext(*args, **kwargs):
    773
--> 774     ret =3D  gcf().text(*args, **kwargs)
        ret =3D undefined
        global gcf.text =3D undefined
        args =3D (0.5, 0.94999999999999996, 'Status by Personality',
{'color': 'k', 'fontweight': 'bold', 'fontname': 'Sans',
'verticalalignment': 'top', 'horizontalalignment': 'center'})
        kwargs =3D {'fontsize': 12}
    775     draw_if_interactive()
    776     return ret

SystemError: ../Objects/moduleobject.c:48: bad argument to internal functio=
n
> /usr/lib/python2.3/site-packages/matplotlib/pylab.py(774)figtext()
-> ret =3D  gcf().text(*args, **kwargs)



II. Versions
----------------------------------
> uname -a
Linux amelia 2.6.14-2-powerpc #1 Sat Nov 26 18:12:00 UTC 2005 ppc GNU/Linux
> python -V
Python 2.3.5
> ipython -V
0.6.15
>
>>> matplotlib.__version__
'0.85.1.cvs'
> gcc --version
gcc (GCC) 4.0.3 20051201 (prerelease) (Debian 4.0.2-5)


On 12/22/05, Fernando Perez <Fernando.Perez@...> wrote:
> Mmh, this may be the tip of the thread to unravel a long-standing problem
> which has stumped both John and me several times.  I've seen the message
>
> SystemError: ../Objects/moduleobject.c:48: bad argument to internal funct=
ion
>
> when using the GtkAgg backend, but the funny thing is that the issue woul=
dn't
> appear for John even when we were both running _as the same user, on the =
same
> box_.  The only difference was that I was executing from the console and =
he
> was logged in remotely.  However, in that case it would always silently
> segfault, so we never saw the traceback you are seeing, which made the pr=
oblem
> very hard to debug without really sinking time into it.  But with your
> behavior, we may get more info.
>
> Some things to try which will help:
>
> 1. Version info, for everything (OS, python, ipython, mpl, gcc)
>
> 2. In ipython, type 'xmode verbose' before testing, and paste the entire
> ipython traceback.  I don't care if it's big, for this problem anything c=
an help.
>
> 3. Backend info.  Try cycling through all the backends, and see if the pr=
oblem
> appears with all or only with some.
>
>
> With more details, it may be possible to make some progress on this one..=
.
>
> Cheers,
>
> f
>


--
Charles R. Twardy

Charles R. Twardy wrote:
> OK, here 'goes.  Verbose stacktrace and version info.  Haven't tried
> other backends, won't tonight.

Thanks for the info.  Nothing jumps at me, but I was mostly providing you with 
pointers on what kind of info may help John, who is the one who actually knows 
that code.  I've only bumped into the problem (which he has never found on a 
machine he works on) and failed to produce any kind of solution.  Let's hope 
some of this flips a switch for him.

Cheers,

f

>>>>> "Clovis" == Clovis Goldemberg <clovis@...> writes:

    Clovis> When I use the zoom feature of the NavigationToolbar, the
    Clovis> xaxis is shared between all 3 graphs.  But the yaxis
    Clovis> limits are free. Obviously, they could also be shared but
    Clovis> this is not want I want.  I would like to "force" or
    Clovis> "freeze" the Y axis to a given value. Consequently, the
    Clovis> zoom feature would act only along the X axis.

When using the right mouse zoom in pan/zoom mode, if you hold 'x' down
the zoom will only be in the x direction.  ditto for 'y'.  It would be
nice to support this for zoom to rect as well.  On the todo list!

JDH

Dear John,

Thanks for your support.
Pressing the X/Y key works fine in the pan menu! I tested it!
But my first suggestion would be an additional keyword in the subplot 
command, something like:

ax2 = subplot(312, sharex=ax1, freezey=True)

In fact, there would be necessary 2 additional keywords (freezex, 
freezey) that would disable
limit changes after the subplot creation. Obviouly, if freezey=False or 
None, the axis limits would
be free to be changed by the zooming tool.

Clovis

John Hunter wrote:

>>>>>>"Clovis" == Clovis Goldemberg <clovis@...> writes:
>>>>>>            
>>>>>>
>
>    Clovis> When I use the zoom feature of the NavigationToolbar, the
>    Clovis> xaxis is shared between all 3 graphs.  But the yaxis
>    Clovis> limits are free. Obviously, they could also be shared but
>    Clovis> this is not want I want.  I would like to "force" or
>    Clovis> "freeze" the Y axis to a given value. Consequently, the
>    Clovis> zoom feature would act only along the X axis.
>
>When using the right mouse zoom in pan/zoom mode, if you hold 'x' down
>the zoom will only be in the x direction.  ditto for 'y'.  It would be
>nice to support this for zoom to rect as well.  On the todo list!
>
>JDH
>
>
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>
>  
>

Apologies for the double-post.

An update:  installing scipy, then rebuilding and reinstalling 
matplotlib get things working using Numeric; numarray still fails.  That 
fragility makes me worry something is still wrong, but I just got a 
basic test plot (1,2,3) to display using ipython, and that's good enough 
for me for now.  Advice would still be welcome, but is no longer as 
desperate.  =)

Also, I should have mentioned that the machine in question is Ubuntu 
5.10 PPC.  Tomorrow I'll see if I can get matplotlib successfully 
installed on the MacOS X side...

Hoping this message helps someone else down the line (and that the list 
will forgive me asking and then answering my own question...),

Andrew Stout

Andrew Stout wrote:
> Hi--
> 
> I'm trying to get matplotlib installed on my laptop before my holiday 
> travels begin.  I've acquired all the dependencies through synaptic and 
> built matplotlib from source, but when I attempt to import pylab I get 
> the following error:
> 
> andrew@...$ python
> Python 2.4.2 (#2, Sep 30 2005, 22:23:39)
> [GCC 4.0.2 20050808 (prerelease) (Ubuntu 4.0.1-4ubuntu8)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>  >>> import pylab
> /usr/lib/python2.4/site-packages/matplotlib/__init__.py:843: 
> UserWarning: Bad key "lines.data_clipping" on line 55 in 
> /home/andrew/.matplotlib/matplotlibrc
>   warnings.warn('Bad key "%s" on line %d in %s' % (key, cnt, fname))
> /usr/lib/python2.4/site-packages/matplotlib/__init__.py:843: 
> UserWarning: Bad key "tick.major.size" on line 145 in 
> /home/andrew/.matplotlib/matplotlibrc
>   warnings.warn('Bad key "%s" on line %d in %s' % (key, cnt, fname))
> /usr/lib/python2.4/site-packages/matplotlib/__init__.py:843: 
> UserWarning: Bad key "tick.minor.size" on line 146 in 
> /home/andrew/.matplotlib/matplotlibrc
>   warnings.warn('Bad key "%s" on line %d in %s' % (key, cnt, fname))
> /usr/lib/python2.4/site-packages/matplotlib/__init__.py:843: 
> UserWarning: Bad key "tick.major.pad" on line 147 in 
> /home/andrew/.matplotlib/matplotlibrc
>   warnings.warn('Bad key "%s" on line %d in %s' % (key, cnt, fname))
> /usr/lib/python2.4/site-packages/matplotlib/__init__.py:843: 
> UserWarning: Bad key "tick.minor.pad" on line 148 in 
> /home/andrew/.matplotlib/matplotlibrc
>   warnings.warn('Bad key "%s" on line %d in %s' % (key, cnt, fname))
> /usr/lib/python2.4/site-packages/matplotlib/__init__.py:843: 
> UserWarning: Bad key "tick.color" on line 149 in 
> /home/andrew/.matplotlib/matplotlibrc
>   warnings.warn('Bad key "%s" on line %d in %s' % (key, cnt, fname))
> /usr/lib/python2.4/site-packages/matplotlib/__init__.py:843: 
> UserWarning: Bad key "tick.labelsize" on line 150 in 
> /home/andrew/.matplotlib/matplotlibrc
>   warnings.warn('Bad key "%s" on line %d in %s' % (key, cnt, fname))
> Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
>   File "/usr/lib/python2.4/site-packages/pylab.py", line 1, in ?
>     from matplotlib.pylab import *
>   File "/usr/lib/python2.4/site-packages/matplotlib/pylab.py", line 194, 
> in ?
>     import cm
>   File "/usr/lib/python2.4/site-packages/matplotlib/cm.py", line 5, in ?
>     import colors
>   File "/usr/lib/python2.4/site-packages/matplotlib/colors.py", line 33, 
> in ?
>     from numerix import array, arange, take, put, Float, Int, where, \
>   File 
> "/usr/lib/python2.4/site-packages/matplotlib/numerix/__init__.py", line 
> 62, in ?
>     from Matrix import Matrix
> ImportError: No module named Matrix
>  >>>
> 
> This happens with Numeric specified in my matplotlibrc.  If I specify 
> numarray, I get a different import error:
> 
> andrew@...$ python
> Python 2.4.2 (#2, Sep 30 2005, 22:23:39)
> [GCC 4.0.2 20050808 (prerelease) (Ubuntu 4.0.1-4ubuntu8)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>  >>> import pylab
> /usr/lib/python2.4/site-packages/matplotlib/__init__.py:843: 
> UserWarning: Bad key "lines.data_clipping" on line 55 in 
> /home/andrew/.matplotlib/matplotlibrc
>   warnings.warn('Bad key "%s" on line %d in %s' % (key, cnt, fname))
> /usr/lib/python2.4/site-packages/matplotlib/__init__.py:843: 
> UserWarning: Bad key "tick.major.size" on line 145 in 
> /home/andrew/.matplotlib/matplotlibrc
>   warnings.warn('Bad key "%s" on line %d in %s' % (key, cnt, fname))
> /usr/lib/python2.4/site-packages/matplotlib/__init__.py:843: 
> UserWarning: Bad key "tick.minor.size" on line 146 in 
> /home/andrew/.matplotlib/matplotlibrc
>   warnings.warn('Bad key "%s" on line %d in %s' % (key, cnt, fname))
> /usr/lib/python2.4/site-packages/matplotlib/__init__.py:843: 
> UserWarning: Bad key "tick.major.pad" on line 147 in 
> /home/andrew/.matplotlib/matplotlibrc
>   warnings.warn('Bad key "%s" on line %d in %s' % (key, cnt, fname))
> /usr/lib/python2.4/site-packages/matplotlib/__init__.py:843: 
> UserWarning: Bad key "tick.minor.pad" on line 148 in 
> /home/andrew/.matplotlib/matplotlibrc
>   warnings.warn('Bad key "%s" on line %d in %s' % (key, cnt, fname))
> /usr/lib/python2.4/site-packages/matplotlib/__init__.py:843: 
> UserWarning: Bad key "tick.color" on line 149 in 
> /home/andrew/.matplotlib/matplotlibrc
>   warnings.warn('Bad key "%s" on line %d in %s' % (key, cnt, fname))
> /usr/lib/python2.4/site-packages/matplotlib/__init__.py:843: 
> UserWarning: Bad key "tick.labelsize" on line 150 in 
> /home/andrew/.matplotlib/matplotlibrc
>   warnings.warn('Bad key "%s" on line %d in %s' % (key, cnt, fname))
> Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
>   File "/usr/lib/python2.4/site-packages/pylab.py", line 1, in ?
>     from matplotlib.pylab import *
>   File "/usr/lib/python2.4/site-packages/matplotlib/pylab.py", line 194, 
> in ?
>     import cm
>   File "/usr/lib/python2.4/site-packages/matplotlib/cm.py", line 5, in ?
>     import colors
>   File "/usr/lib/python2.4/site-packages/matplotlib/colors.py", line 33, 
> in ?
>     from numerix import array, arange, take, put, Float, Int, where, \
>   File 
> "/usr/lib/python2.4/site-packages/matplotlib/numerix/__init__.py", line 
> 53, in ?
>     from numarray.convolve import cross_correlate, convolve
> ImportError: No module named convolve
>  >>>
> 
> 
> So, I suspect something is wrong in Numerix, but I have no idea what, or 
> more importantly how to fix it.  Could anyone help?  It would be much 
> appreciated.
> 
> Please cc me; I am not subscrived to the list.
> 
> Thanks in advance,
> Andrew Stout
>

In pylab: just choose the number of bins.
Hope this helps.
Alan Isaac

>>> import pylab as P
>>> help(P.hist)
Help on function hist in module matplotlib.pylab:

hist(*args, **kwargs)
    HIST(x, bins=3D10, normed=3D0, bottom=3D0, orientiation=3D'vertical', *=
*kwargs)
    Compute the histogram of x.  bins is either an integer number of
    bins or a sequence giving the bins.  x are the data to be binned.
    The return values is (n, bins, patches)
    If normed is true, the first element of the return tuple will be the
    counts normalized to form a probability distribtion, ie,
    n/(len(x)*dbin)
    orientation =3D 'horizontal' | 'vertical'.  If horizontal, barh
    will be used and the "bottom" kwarg will be the left.
    kwargs are used to update the properties of the
    hist bars

    Addition kwargs: hold =3D [True|False] overrides default hold state

>>>

>>>>> "Alan" == Alan G Isaac <aisaac@...> writes:

    Alan> In pylab: just choose the number of bins.  Hope this helps.
    Alan> Alan Isaac

    >>>> import pylab as P help(P.hist)
    Alan> Help on function hist in module matplotlib.pylab:

If you know your data are integers, you might get nicer results by
specifying the bins rather than autogenerating them by passing in
number of bins.  Eg for a 12 sided dice

  import matplotlib.numerix as nx
  bins = nx.arange(1,13)
  n,bins,patches = P.hist(throws, bins)


JDH