matplotlib-users Mailing List for matplotlib (Page 6)

On Thursday 16 November 2006 23:45, Josh Lifton wrote:
> I've been having problems using the subplot command's comma notation 

Seems to work here. On a Gentoo (OK, seriously: on matplotlib 0.87.7)
Josh, what version of matplotlib are you using ?

I've been having problems using the subplot command's comma notation for
describing how many plots to use (e.g. subplot(2,1,1) instead of
subplot(211)).  Using the comma notation, all plots are overlaid in the
first position and remaining positions are blank but sized correctly as if
there should be a plots there.  Here's an example demonstrating
this problem.  This code is a minimally modified version of that given in
the online tutorial.

##################################################

from pylab import *

def f(t):
    s1 = cos(2*pi*t)
    e1 = exp(-t)
    return multiply(s1,e1)

t1 = arange(0.0, 5.0, 0.1)
t2 = arange(0.0, 5.0, 0.02)

figure(1)
subplot(2,1,1)
plot(t1, f(t1), 'bo', t2, f(t2), 'k')

subplot(2,1,2)
plot(t2, cos(2*pi*t2), 'r--')
show()

##################################################

I will probably end up using the axes command, but it would be nice to
know how to resolve this issue with subplot.  I'm using Python 2.4 on
Ubuntu 6.06

Thanks,
Josh

I am getting an error from the 'hist' function.  It occurs when running 
the 'histogram_demo.py' example from http://matplotlib.sourceforge.net/. 
  I'm using matplotlib version 0.87.4 and Numeric 24.2.  Has anyone had 
this problem?  Thanks.

Steve

# histogram_demo.py
 >>> from pylab import *
 >>>
 >>> mu, sigma = 100, 15
 >>> x = mu + sigma*randn(10000)
 >>>
 >>> # the histogram of the data
... n, bins, patches = hist(x, 50, normed=1)
Traceback (most recent call last):
   File "<stdin>", line 2, in ?
   File "/usr/lib/python2.4/site-packages/matplotlib/pylab.py", line 
1851, in hist
     ret =  gca().hist(*args, **kwargs)
   File "/usr/lib/python2.4/site-packages/matplotlib/axes.py", line 
4078, in hist
     patches = self.bar(bins, n, width=width, bottom=bottom, align=align)
   File "/usr/lib/python2.4/site-packages/matplotlib/axes.py", line 
2481, in bar
     yerr = asarray([yerr]*nbars, Float) # Float converts Nones to NANs
   File "/usr/lib/python2.4/site-packages/Numeric/Numeric.py", line 134, 
in asarray
     return multiarray.array(a, typecode, copy=0, savespace=savespace)
TypeError: a float is required

Jose Gomez-Dans wrote:
> Hi!
> I don't know whether it is easy to produce a plot of a shapefile (a
> geographical information systems vector file format, with an attached
> database) using MPL: An example would be to have the a map with the
> mean temperature for every country in the month of august mapped to a
> colour. The shapefile has a "dbf" database with the temperature, and
> the polygons making up the country boundaries can be extracted with
> GDAL/OGR.
>
> Has anyone done anything like this? I guess that for very detailed
> shapes (lots of polygons with loads of vertexes), it might be slow,
> and of course, we need to get the data into Python first, but any
> pointers would be very welcomed!
>
> Cheers!
> Jose
>   

Jose:  You can do this with the basemap toolkit (which can read simple 
shapefiles). See the 'fillstates.py' example in the examples directory.

-Jeff

-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
NOAA/OAR/PSD  R/PSD1        Email  : Jef...@no...
325 Broadway                Office : Skaggs Research Cntr 1D-124
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

Hi!
I don't know whether it is easy to produce a plot of a shapefile (a
geographical information systems vector file format, with an attached
database) using MPL: An example would be to have the a map with the
mean temperature for every country in the month of august mapped to a
colour. The shapefile has a "dbf" database with the temperature, and
the polygons making up the country boundaries can be extracted with
GDAL/OGR.

Has anyone done anything like this? I guess that for very detailed
shapes (lots of polygons with loads of vertexes), it might be slow,
and of course, we need to get the data into Python first, but any
pointers would be very welcomed!

Cheers!
Jose

Received from Russell E. Owen on Wed, Nov 15, 2006 at 03:47:52PM EST:
> In article <200...@av...>,
>  Lev Givon <le...@co...> wrote:
> 
> > Received from Adam Mercer on Tue, Nov 14, 2006 at 03:55:15PM EST:
> > > On 14/11/06, Lev Givon <le...@co...> wrote:
> > > 
> > > >I am also using Apple's X11 1.1.2 / Xfree86 4.4.0. Has anyone had any
> > > >success using the above Fink packages?
> > > 
> > > There is a font problem with X11 1.1.2, upgrade to X11 1.1.3 which was
> > > released yesterday and you should be OK.
> > > 
> > > Cheers
> > > 
> > > Adam
> > 
> > I upgraded X11 as indicated and rebuilt/reinstalled matplotlib, but
> > the problem persists. Should I rebuild/install the graphical libraries
> > matplotlib depends on (e.g., freetype, gtk)?
> 
> I had guessed it was the known X11 1.1.2 font problem, too. Oh well...
> 
> Some more info might help, such as:
> - What python are you using (where did it come from and what version is 
> it)?

Python 2.4.3, installed via Fink.

> - What back end are you trying to use?

GTKAgg.

> - Did you create and configure a matplotlibrc file?

Yes.

> Admittedly errors in these errors usually result in a traceback instead 
> of a segfault, but it's a start.
> 
> -- Russell

I managed to fix the problem by wiping my Fink tree and rebuilding the
various library dependencies of matplotlib.

						Thanks,
						L.G.

John Hunter
<jdh...@ac...> writes:

> the place to look.  Squares typically mean that the character you are
> requesting is not in the font file you have loaded.
>
Thanks for the last sentence. I had set TTFPATH properly but
I don't know why matplotlib didn't see the ttf fonts in
$HOME/.fonts. I searched gmane and found your article which do apply
my case:
  If you are sure on both counts, it may help to remove your font cache
  (typically  ~/.ttffont.cache on linux like systems) and let matplotlib
  regenerate it's cache.  

No it works all ok!

Thanks a lot.
regards
SK

Hello at all.
I need to do a real time plot where on the frame i have this like limit
line:
        import math
        dati =3D []
        for freq in range(int(freqiniziale), (int(freqfinale    )+ 1)):
            forza =3D float(massa) * ((2*math.pi*freq)**2)/10
            dati.append(forza)
        ax1 =3D subplot(111)
        plot(dati)
        xlabel('Frequenza HZ')
        ylabel('Deg')
        title('Grafico Calibrazione')
        ax2 =3D twinx()
        plot([0.1,0.2,0.3],'r-')
        ylabel('Forza')
        ax2.yaxis.tick_right()
        #dlg =3D wx.FileDialog(self, "Choose a file", ".", "", "*.*",
wx.SAVE)
        #try:
          #  if dlg.ShowModal() =3D=3D wx.ID_OK:
            #    filename =3D dlg.GetPath()

              #  savefig(filename+'.pdf')
        #finally:
          #  dlg.Destroy()
        show()

with this i have the grap on the screen but i have to update every time 
that i receive others data coming from two instruments (10 seconds),
how i can update the grap? 

Regards

Luca=0A=0A=0A------------------------------------------------------=0ASco=
pri MOTOROLA K1, la nuova icona di design Motorola.Clicca e vinci !=0Ahtt=
p://click.libero.it/motorola16nov=0A

>>>>> "Seweryn" == Seweryn Kokot <sk...@po...> writes:

    Seweryn> Hello, Since I have problems with unicode conversion when
    Seweryn> using wxagg and gtkagg backends I would like to ask which
    Seweryn> files in matplotlib sources are responsible for this?  To
    Seweryn> understand the mechanism, if in the figure I get empty
    Seweryn> squares instead of special characters where is the
    Seweryn> problem: in the phase of processing a text by antigrain
    Seweryn> or earlier?

All of the font rendering happens in src/ft2font.cpp, where the
freetype file is loaded, the glyphs set, and rendered to a pixel buffer.
agg just copies the bitmap into its own pixel buffer.  So ft2font is
the place to look.  Squares typically mean that the character you are
requesting is not in the font file you have loaded.

JDH

>>>>> "Eric" == Eric Firing <ef...@ha...> writes:

    Eric> In June I asked if anyone was still using pcolor_classic
    Eric> (http://www.nabble.com/is-pcolor_classic-needed--tf1743761.html#a4739248).
    Eric> I got no replies, so I have now removed it from svn.

    Eric> Next: it looks like scatter_classic dates from the same era.
    Eric> Does anyone have any objections to its removal?

The only suggestion I have is rather than simply removing them, we
might go through a release cycle with something like

    def pcolor_classic(self, *args, **kwargs):
        raise NotImplementedError('pcolor_class is deprecated, please use pcolor instead')

so people will not have to post questions saying 'what happened to
pcolor?'

JDH

Nils,

Fixed in svn.

Thanks.

Eric

Nils Wagner wrote:

> Hi Eric,
> 
> Thank you very much. Here is another new problem
> 
>     scatter(mu*ones(n),w.real,s=1)
>   File "/usr/lib64/python2.4/site-packages/matplotlib/pylab.py", line
> 3111, in scatter
>     ret =  gca().scatter(*args, **kwargs)
>   File "/usr/lib64/python2.4/site-packages/matplotlib/axes.py", line
> 3329, in scatter
>     self.autoscale_view()
>   File "/usr/lib64/python2.4/site-packages/matplotlib/axes.py", line
> 991, in autoscale_view
>     XL = self.xaxis.get_major_locator().autoscale()
>   File "/usr/lib64/python2.4/site-packages/matplotlib/ticker.py", line
> 836, in autoscale
>     return take(self.bin_boundaries(dmin, dmax), [0,-1])
>   File
> "/usr/lib64/python2.4/site-packages/numpy/oldnumeric/functions.py", line
> 16, in take
>     return N.take(a, indicies, axis)
>   File "/usr/lib64/python2.4/site-packages/numpy/core/fromnumeric.py",
> line 51, in take
>     return take(indices, axis, out, mode)
> IndexError: index out of range for array
>>>> mu
> 0.0
>>>> ones(n)
> array([ 1.,  1.,  1.])
>>>> w
> array([ 2.+0.j, -3.+0.j,  1.+0.j])
> 
> Cheers
>                Nils
> 

On Thu, 16 Nov 2006, Marek Szczypi=C5~Dski wrote:

> Error Type: RuntimeError
> Error Value: '/' is not a writable dir; you must set environment
> variable HOME to be a writable dir

Just before you import matplotlib or pylab, try this:

import os
os.environ['HOME'] =3D '/tmp/'

Does that help?

Also, BTW, the user running Zope should have a home directory that he can=
=20
write to.  Fix that in /etc/passwd and you should be okay (and not need=20
the above hack).

-- Asheesh.

--=20
QOTD:
 =09"I thought I saw a unicorn on the way over, but it was just a
 =09horse with one of the horns broken off."

Eric Firing wrote:
> Nils,
>
> That is fixed now.  I was sure I had removed it last night--I don't
> know how I fouled it up, but I certainly did.  Thanks for the report.
>
> Eric
>
> Nils Wagner wrote:
>> Hi all,
>>
>> I guess this bug is due to recent changes in svn
>>
>>     from pylab import plot, show, xlabel, ylabel, figure, semilogy,
>> savefig, scatter
>>   File "/usr/lib64/python2.4/site-packages/pylab.py", line 1, in ?
>>     from matplotlib.pylab import *
>>   File "/usr/lib64/python2.4/site-packages/matplotlib/pylab.py", line
>> 1995, in ?
>>     if Axes.pcolor_classic.__doc__ is not None:
>> AttributeError: class Axes has no attribute 'pcolor_classic'
>>
>> Nils
Hi Eric,

Thank you very much. Here is another new problem

    scatter(mu*ones(n),w.real,s=1)
  File "/usr/lib64/python2.4/site-packages/matplotlib/pylab.py", line
3111, in scatter
    ret =  gca().scatter(*args, **kwargs)
  File "/usr/lib64/python2.4/site-packages/matplotlib/axes.py", line
3329, in scatter
    self.autoscale_view()
  File "/usr/lib64/python2.4/site-packages/matplotlib/axes.py", line
991, in autoscale_view
    XL = self.xaxis.get_major_locator().autoscale()
  File "/usr/lib64/python2.4/site-packages/matplotlib/ticker.py", line
836, in autoscale
    return take(self.bin_boundaries(dmin, dmax), [0,-1])
  File
"/usr/lib64/python2.4/site-packages/numpy/oldnumeric/functions.py", line
16, in take
    return N.take(a, indicies, axis)
  File "/usr/lib64/python2.4/site-packages/numpy/core/fromnumeric.py",
line 51, in take
    return take(indices, axis, out, mode)
IndexError: index out of range for array
>>>
>>> mu
0.0
>>> ones(n)
array([ 1.,  1.,  1.])
>>> w
array([ 2.+0.j, -3.+0.j,  1.+0.j])

Cheers
               Nils

Nils,

That is fixed now.  I was sure I had removed it last night--I don't know 
how I fouled it up, but I certainly did.  Thanks for the report.

Eric

Nils Wagner wrote:
> Hi all,
> 
> I guess this bug is due to recent changes in svn
> 
>     from pylab import plot, show, xlabel, ylabel, figure, semilogy,
> savefig, scatter
>   File "/usr/lib64/python2.4/site-packages/pylab.py", line 1, in ?
>     from matplotlib.pylab import *
>   File "/usr/lib64/python2.4/site-packages/matplotlib/pylab.py", line
> 1995, in ?
>     if Axes.pcolor_classic.__doc__ is not None:
> AttributeError: class Axes has no attribute 'pcolor_classic'
> 
> Nils

Hello All,

   I'am sorry, for resenting this email, but I had some problems with my
e-mail client, and (probably) lost the response (if there was any)
before I could read it. The archive of matplotlib-users list are messed
up, because the last post there is from 2006-10-02, and it prevent's me
from check if there was any answer to my post.
Please resent to me the answer (if any was given). The original message
is given below, and the traceback from zope below the mail. Thanks in
advance.

Greetings,
Marek Szczypinski

-------- Original Message --------
Subject: matplotlib and zope problem
Date: Sun, 12 Nov 2006 08:20:45 +0100
From: Marek Szczypi=C5=84ski <ma...@as...>
To: mat...@li...

Hello All,

  I've been using matplotlib for some time now, and I want to connect it
with zope. I'am using the example code from page:
http://www.scipy.org/Cookbook/Matplotlib/Matplotlib_and_Zope ,
but whenever I try to import matplotlib, and/or pylab packages i get
this error from zope:

Error Type: RuntimeError
Error Value: '/' is not a writable dir; you must set environment
variable HOME to be a writable dir

Have You got any ideas, on what might go wrong? I'am using matplotlib
0.87.4, and zope 2.9.5 with python 2.4.3 on gentoo linux box.

Thanks in advance for any help.

Marek Szczypinski


> Traceback (innermost last):
>   Module ZPublisher.Publish, line 115, in publish
>   Module ZPublisher.mapply, line 88, in mapply
>   Module ZPublisher.Publish, line 41, in call_object
>   Module Products.ExternalMethod.ExternalMethod, line 59, in manage_add=
ExternalMethod
>   Module Products.ExternalMethod.ExternalMethod, line 111, in __init__
>   Module Products.ExternalMethod.ExternalMethod, line 134, in manage_ed=
it
>   Module Products.ExternalMethod.ExternalMethod, line 141, in getFuncti=
on
>   Module App.Extensions, line 148, in getObject
>    - __traceback_info__: ('/var/lib/zope/zope-markacy/Extensions/mpl.py=
', 'mpl')
>   Module /var/lib/zope/zope-markacy/Extensions/mpl.py, line 1, in ?
>   Module None, line 1011, in ?
>   Module None, line 968, in rc_params
>   Module None, line 914, in matplotlib_fname
>   Module None, line 273, in wrapper
>   Module None, line 324, in _get_configdir
> RuntimeError: '/' is not a writable dir; you must set environment varia=
ble HOME to be a writable dir=20

hey,

i am newbie to both python n matplotlib.
Would like to know if there is a way to save
the co-ordinates of the points ploted in a graph.
So that i could use them for some mouse
over function using javascripts.

the graphs are generated on windows based
browsers so can not use wxpython.

any idea how this could be done.

using python 2.4 and matplotlib 0.86

pranal

Hi all,

I guess this bug is due to recent changes in svn

    from pylab import plot, show, xlabel, ylabel, figure, semilogy,
savefig, scatter
  File "/usr/lib64/python2.4/site-packages/pylab.py", line 1, in ?
    from matplotlib.pylab import *
  File "/usr/lib64/python2.4/site-packages/matplotlib/pylab.py", line
1995, in ?
    if Axes.pcolor_classic.__doc__ is not None:
AttributeError: class Axes has no attribute 'pcolor_classic'

Nils

Whenever I try to use matplotlib from a python session inside emacs, python
freezes. What I do is start GNU Emacs version 21.1.3 for Windows, do ESC-x
shell and enter the commands shown below. Note that I set the backend to PS
and interactive to false, but my python interpreter still freezes. I suspect
that this is because matplotlib is generating some GUI events which upset
emacs. The example works fine if I run python through the shell without
emacs, but I would very much like to run python through an emacs session.
Similar problems happen with other backends. Any suggestions on how to solve
this problem would be much appreciated.

Thanks,
-Emin

-------- Transcript of session follows
--------------------------------------------------

Microsoft Windows XP [Version 5.1.2600]
(C) Copyright 1985-2001 Microsoft Corp.

C:\>c:\python25\python.exe -i
c:\python25\python.exe -i
Python 2.5 (r25:51908, Sep 19 2006, 09:52:17) [MSC v.1310 32 bit (Intel)] on
win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>> print numpy.__version__
1.0
>>> import matplotlib, pylab
>>> matplotlib.interactive(False)
>>> matplotlib.use('PS')
>>> def example(size):
...     pylab.hist(range(size))
...     print 'made hist of size %i' % size
...     return size
...
>>> print [example(i) for i in range(10,20)]
made hist of size 10
made hist of size 11
made hist of size 12
made hist of size 13
made hist of size 14
made hist of size 15
made hist of size 16
made hist of size 17
made hist of size 18
made hist of size 19
[10, 11, 12, 13, 14, 15, 16, 17, 18, 19]
>>>

python is now frozen

Hello,

Since I have problems with unicode conversion when using wxagg and gtkagg
backends I would like to ask which files in matplotlib sources are
responsible for this?
To understand the mechanism, if in the figure I get empty squares
instead of special characters where is the problem: in the phase of
processing a text by antigrain or earlier?

Thanks in advance for any hints,
regards,
SK

In June I asked if anyone was still using pcolor_classic 
(http://www.nabble.com/is-pcolor_classic-needed--tf1743761.html#a4739248). 
  I got no replies, so I have now removed it from svn.

Next: it looks like scatter_classic dates from the same era.  Does 
anyone have any objections to its removal?

Two more deprecated functions are the original quiver and the original 
colorbar.  These have been replaced more recently by new and much more 
capable versions (May-June of this year), but I am hoping that it is not 
too early to remove the originals.  Does anyone still need old-style 
quiver and colorbar?

Thanks.

Eric

Hey everyone,

I was wondering if someone could point me to where you can fine-tune
display options - specifically where you can configure the amount of
whitespace around the plot.  I am using basemap and when I run
savefig(), I want the resulting plot to take up the whole image
instead of leaving 100 or so pixels of white around it, presumably
where the x and y axis labels and tickmarks would go.  Perhaps these
are simply rc kwargs but I can't find a comprehensive list of those
and the various subplot and figure options don't seem to work.

Thanks!
-- 
Warren

Hi gang,

    I apologize to come up always with noob questions, but it's been a
while I used matplotlib seriously...
Related to the "deleting a line from a plot" subject, I was thinking
about *hiding* the line instead of completely erasing it from the
graph. This is because the user can check or unchech a checkbox that
toggles the line visibility, and it would be much easier to call
set_visible() instead of continuously deleting/replotting the line.
Now, how does this impact on legend? I mean, is there a way with which
I can simply hide a line => update the legend by removing the missing
line label, or show a line => restore the legend label?

Thank you for every pointer.

-- 
Andrea.

"Imagination Is The Only Weapon In The War Against Reality."
http://xoomer.virgilio.it/infinity77/

I've built 0.87.7 from source and the problem disappeared. Thanks.

On 11/13/06, Steve Schmerler <el...@gm...> wrote:
>
> W Netzberg wrote:
> > I aggree it doesn't make much sense, but that's what I got and attached
> > a plot to prove it!
> > Seems that some sort of rounding takes place, but only when I use
> > numpy.random.normal(). It is strange.
>
> Can you post a short working and not-working (i.e. chopping off) example?
>
> >
> > I had problems building latest version from source last night. Do you
> > know where I can find the latest rpm for fc5?
> >
>
> No, sry. I'm still building from source myself.
>
> --
> cheers,
> steve
>
> Random number generation is the art of producing pure gibberish as
> quickly as possible.
>
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job
> easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

In article <200...@av...>,
 Lev Givon <le...@co...> wrote:

> Received from Adam Mercer on Tue, Nov 14, 2006 at 03:55:15PM EST:
> > On 14/11/06, Lev Givon <le...@co...> wrote:
> > 
> > >I am also using Apple's X11 1.1.2 / Xfree86 4.4.0. Has anyone had any
> > >success using the above Fink packages?
> > 
> > There is a font problem with X11 1.1.2, upgrade to X11 1.1.3 which was
> > released yesterday and you should be OK.
> > 
> > Cheers
> > 
> > Adam
> 
> I upgraded X11 as indicated and rebuilt/reinstalled matplotlib, but
> the problem persists. Should I rebuild/install the graphical libraries
> matplotlib depends on (e.g., freetype, gtk)?

I had guessed it was the known X11 1.1.2 font problem, too. Oh well...

Some more info might help, such as:
- What python are you using (where did it come from and what version is 
it)?
- What back end are you trying to use?
- Did you create and configure a matplotlibrc file?
Admittedly errors in these errors usually result in a traceback instead 
of a segfault, but it's a start.

-- Russell

Hi,

if I use comments and the last character in the file is not space or \n then 
the last value is not returned by mlab.py's load method, due to a bug in the 
comment stripping (index returns -1 if no comment is found).

If the for loop is changed to the following, it works again:

for i,line in enumerate(fh):
        if i<skiprows: continue
        commentIdx = line.find(comments) #
        if commentIdx!=-1: #
            line = line[:commentIdx].strip() #
        if not len(line): continue
        if usecols is not None:
            vals = line.split(delimiter)
            row = [converters.get(i,float)(vals[i]) for i in usecols]
        else:
            row = [converters.get(j,float)(val) for j,val in 
enumerate(line.split(delimiter))]
        thisLen = len(row)
        X.append(row)

Lines ending with # are changed/added

Have fun,
wr