matplotlib-users Mailing List for matplotlib

On Fri, 02 May 2008 10:21:50 -0300, Zoho Vignochi wrote:

> On Fri, 2008-05-02 at 08:33 -0400, Michael Droettboom wrote:
>> I converted your example to a standalone one (attached), and it does
>> work for me.  It's hard to say what may be going wrong for you without
>> knowing what a_steady and L_range are and what the limits of the axes
>> are getting set to etc.   Can you provide a fully self-contained script
>> that exhibits this behavior?  Also, what version of matplotlib and
>> platform are you using?
>> 
>> Cheers,
>> Mike
> 
> Hello:
> 
> I am running Debian sid on Powerpc and I have the Debian sid
> python-matplotlib version 0.91.2-2. Your stand alone script also works
> for me. Strange.
> 
> I have included the script I am using set to plot 5 lines. The script is
> designed to solve the Daisyworld model proposed by James Lovelock in the
> early 80's. Thank you for your help!
> 
> Zoho

The problem was with the line:

lines.set_array(L_range)

If I just delete it everything goes well. I was following along from the 
line_collection2.py included in the examples. 

Thanks for your help!

Zoho

Is it possible to plot dates on the y axis?

Regards,
Kenneth Miller

I think you've run into this bug:

http://sourceforge.net/tracker/index.php?func=detail&aid=1738494&group_id=80706&atid=560720

matplotlib-0.90.1 is not compatible with Python 2.5 due to a change made 
in cp1252 in Python 2.5.  You can try applying the patch included with 
the bug report, or upgrading to matplotlib 0.91.2.  A bug should 
probably be submitted to the Debian packagers (I suspect they will want 
to apply the patch if they don't want to upgrade the version).  I'll 
look into doing that.

Cheers,
Mike

Lorenzo Isella wrote:
> Dear All,
> I am running Debian testing on my box and I use pylab as installed
> from the standard repositories.
> Unfortunately, it seems that there is something broken either with
> pylab or Python (I have been upgrading the system these days) since I
> am now unable to create .pdf files:
> For instance, consider the following simple script:
>
>  #! /usr/bin/env python
>
> import scipy as s
> import numpy as n
> import pylab as p
>
>
> a=s.linspace(0.,40.,20)
> b=s.linspace(-20.,90.,20)
>
> fig = p.figure()
> axes = fig.gca()
>
>
> axes.plot(a,b, "bo",label="test plot")
> p.xlabel('Time')
> p.ylabel('Number of clusters')
> p.title("Evolution Number of clusters")
> p.grid(True)
> cluster_name="test.pdf"
> axes.legend()
> p.savefig(cluster_name)
>
> p.clf()
>
>
> The output generated by the script is:
>
> Traceback (most recent call last):
>   File "<stdin>", line 25, in <module>
>   File "/usr/lib/python2.5/site-packages/matplotlib/pylab.py", line
> 796, in savefig
>     return fig.savefig(*args, **kwargs)
>   File "/usr/lib/python2.5/site-packages/matplotlib/figure.py", line
> 759, in savefig
>     self.canvas.print_figure(*args, **kwargs)
>   File "/usr/lib/python2.5/site-packages/matplotlib/backends/backend_gtkagg.py",
> line 114, in print_figure
>     orientation, **kwargs)
>   File "/usr/lib/python2.5/site-packages/matplotlib/backends/backend_agg.py",
> line 497, in print_figure
>     printfunc(filename, dpi, facecolor, edgecolor, orientation, **kwargs)
>   File "/usr/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py",
> line 1395, in print_figure
>     file.close()
>   File "/usr/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py",
> line 401, in close
>     self.writeFonts()
>   File "/usr/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py",
> line 456, in writeFonts
>     fontdictObject = self.embedTTF(filename)
>   File "/usr/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py",
> line 508, in embedTTF
>     widths = [ get_char_width(charcode) for charcode in
> range(firstchar, lastchar+1) ]
>   File "/usr/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py",
> line 505, in get_char_width
>     unicode = cp1252.decoding_map[charcode] or 0
> AttributeError: 'module' object has no attribute 'decoding_map'
>
> and no pdf file is produced. However, if I try saving it as a .png
> file (by setting  cluster_name="test.png"), then everything works
> fine.
> This is very annoying and I wonder if anyone else is having the same
> problem and can put forward a suggestion to help.
> Many thanks
>
> Lorenzo
>
> -------------------------------------------------------------------------
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>   

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

Dear All,
I am running Debian testing on my box and I use pylab as installed
from the standard repositories.
Unfortunately, it seems that there is something broken either with
pylab or Python (I have been upgrading the system these days) since I
am now unable to create .pdf files:
For instance, consider the following simple script:

 #! /usr/bin/env python

import scipy as s
import numpy as n
import pylab as p


a=s.linspace(0.,40.,20)
b=s.linspace(-20.,90.,20)

fig = p.figure()
axes = fig.gca()


axes.plot(a,b, "bo",label="test plot")
p.xlabel('Time')
p.ylabel('Number of clusters')
p.title("Evolution Number of clusters")
p.grid(True)
cluster_name="test.pdf"
axes.legend()
p.savefig(cluster_name)

p.clf()


The output generated by the script is:

Traceback (most recent call last):
  File "<stdin>", line 25, in <module>
  File "/usr/lib/python2.5/site-packages/matplotlib/pylab.py", line
796, in savefig
    return fig.savefig(*args, **kwargs)
  File "/usr/lib/python2.5/site-packages/matplotlib/figure.py", line
759, in savefig
    self.canvas.print_figure(*args, **kwargs)
  File "/usr/lib/python2.5/site-packages/matplotlib/backends/backend_gtkagg.py",
line 114, in print_figure
    orientation, **kwargs)
  File "/usr/lib/python2.5/site-packages/matplotlib/backends/backend_agg.py",
line 497, in print_figure
    printfunc(filename, dpi, facecolor, edgecolor, orientation, **kwargs)
  File "/usr/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py",
line 1395, in print_figure
    file.close()
  File "/usr/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py",
line 401, in close
    self.writeFonts()
  File "/usr/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py",
line 456, in writeFonts
    fontdictObject = self.embedTTF(filename)
  File "/usr/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py",
line 508, in embedTTF
    widths = [ get_char_width(charcode) for charcode in
range(firstchar, lastchar+1) ]
  File "/usr/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py",
line 505, in get_char_width
    unicode = cp1252.decoding_map[charcode] or 0
AttributeError: 'module' object has no attribute 'decoding_map'

and no pdf file is produced. However, if I try saving it as a .png
file (by setting  cluster_name="test.png"), then everything works
fine.
This is very annoying and I wonder if anyone else is having the same
problem and can put forward a suggestion to help.
Many thanks

Lorenzo

On Fri, 2008-05-02 at 08:33 -0400, Michael Droettboom wrote:
> I converted your example to a standalone one (attached), and it does 
> work for me.  It's hard to say what may be going wrong for you without 
> knowing what a_steady and L_range are and what the limits of the axes 
> are getting set to etc.   Can you provide a fully self-contained script 
> that exhibits this behavior?  Also, what version of matplotlib and 
> platform are you using?
> 
> Cheers,
> Mike

Hello:

I am running Debian sid on Powerpc and I have the Debian sid
python-matplotlib version 0.91.2-2. Your stand alone script also works
for me. Strange.

I have included the script I am using set to plot 5 lines. The script is
designed to solve the Daisyworld model proposed by James Lovelock in the
early 80's. Thank you for your help!

Zoho

I converted your example to a standalone one (attached), and it does 
work for me.  It's hard to say what may be going wrong for you without 
knowing what a_steady and L_range are and what the limits of the axes 
are getting set to etc.   Can you provide a fully self-contained script 
that exhibits this behavior?  Also, what version of matplotlib and 
platform are you using?

Cheers,
Mike

Zoho Vignochi wrote:
> On Thu, 01 May 2008 22:00:33 +0000, Zoho Vignochi wrote:
>
>   
>> Hello:
>>
>> I have a script in which I have been using plot to plot numerous lines
>> on the same graph. I recently wanted to see how Line Collections work so
>> I tried porting it over. Everything successful except I can't seem to
>> get each line to be a different color. Here is the relevant section:
>>
>> # Make a list of colors cycling through the rgbcmyk series.
>> 	colors = [colorConverter.to_rgba(c) for c in
>> ('r','g','b','c','y','m','k')]
>> 	
>> 	fig = plt.figure()
>> 	ax = fig.add_subplot(1,1,1)
>> 	lines = collections.LineCollection([zip(L_range, item) for item
>> in a_steady])
>> 	lines.set_array(L_range)
>> 	lines.set_color(colors)
>> 	ax.add_collection(lines, autolim=True)
>> 	
>> However every line is blue. Any ideas?
>>
>>     
>  I should mention my import lines:
>
> import numpy as np
> from numpy import sum, zeros, less, where
> import scipy as sp
>
> import matplotlib.pyplot as plt
> from matplotlib import collections
> from matplotlib.colors import colorConverter
>
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by the 2008 JavaOne(SM) Conference 
> Don't miss this year's exciting event. There's still time to save $100. 
> Use priority code J8TL2D2. 
> http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone
> _______________________________________________
> 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

Sorry about that; it turns out it is GSview rendering extra whitspace. The bounding box is, in fact, fine. 
Now I feel silly ;-). 

----- Original Message ----
From: izak marais <iza...@ya...>
To: mat...@li...
Sent: Friday, May 2, 2008 12:03:44 PM
Subject: eps bounding box broken

Hi

I have recently upgraded to 0.91.2 (from 0.8<something>). Firstof all: thanks to the developers for the improved documentation andexcellent software.

However, now my eps saving appears to be broken:

plot([1,2,3])
savefig('test.eps')

results in a massive whitespace borders in the saved eps figure. Fidgeting with ps.papersize in the rc file only makes it worse or introduces clipping. (The new ability to save to pdf works nicely though and produces the correct, tight, bounding box.)

Is this behavior normal? Any ideas on how to fix it?

Thanks 
Izak




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      ____________________________________________________________________________________
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Hi

I have recently upgraded to 0.91.2 (from 0.8<something>). Firstof all: thanks to the developers for the improved documentation andexcellent software.

However, now my eps saving appears to be broken:

plot([1,2,3])
savefig('test.eps')

results in a massive whitespace borders in the saved eps figure. Fidgeting with ps.papersize in the rc file only makes it worse or introduces clipping. (The new ability to save to pdf works nicely though and produces the correct, tight, bounding box.)

Is this behavior normal? Any ideas on how to fix it?

Thanks 
Izak





      ____________________________________________________________________________________
Be a better friend, newshound, and 
know-it-all with Yahoo! Mobile.  Try it now.  http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

On Thu, May 1, 2008 at 4:32 PM, Michael Hearne <mh...@us...> wrote:
>  legend(('s1','s2'))
>
>  The resulting legend shows the symbols twice (two little red dots and
>  two blue ones).  Does anyone else get this, and if so, do you know
>  what the problem is?

You can tell the legend how many points to draw using the numpoints
kwarg.  See the docs at
http://matplotlib.sourceforge.net/matplotlib.legend.html#Legend

Check out the example code below -- in addition tomaking the numpoints
setting, it also fixes the tick format overlap problem

import datetime
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.dates as mpldates
import matplotlib.ticker as ticker

date1 = datetime.date( 1952, 1, 1 )
date2 = datetime.date( 2004, 4, 12 )
delta = datetime.timedelta(days=100)
dates = mpldates.drange(date1, date2, delta)
s1 = np.random.rand(len(dates))

fig = plt.figure()
ax = fig.add_subplot(111)
ax.plot_date(dates, s1,'r.')
ax.hold(True)
s2 = np.random.rand(len(dates))
ax.plot_date(dates, s2,'bo')
ax.legend(('s1','s2'), numpoints=1)

# only write ticklabels on the decades
def fmtticks(x, pos=None):
    dt = mpldates.num2date(x)
    if dt.year%10: return ''
    return dt.strftime('%Y')

# this fizes yhe tick labels
ax.xaxis.set_major_formatter(ticker.FuncFormatter(fmtticks))

# this fixes the toolbar x coord
ax.fmt_xdata = mpldates.DateFormatter('%Y-%m-%d')

# this rotates the ticklabels to help with overlapping
fig.autofmt_xdate()
plt.show()

JDH

Michael Hearne wrote:
> Jeff (or anyone) - I recently reinstalled all of my numpy/scipy 
> related packages, including matplotlib, from a Mac OS X installer 
> called the SciPy SuperPack.
>
> (http://macinscience.org/?page_id=6)
>
> All of the packages he includes work really well.
>
> However, after I used easy_install to grab Basemap, I found I can't 
> import it.  I was wondering if you could give me a pointer on how to 
> tell Python where to look for Basemap?
>
> Thanks,
>
> Mike Hearne

Mike:  Unfortunately, if matplotlib was installed as an egg, you can't 
install Basemap.  This bug has been fixed in 0.98pre, but that won't 
help you unless you compile matplotlib and Basemap from svn.  I think 
you can manually fix it by adding some symbolic links manually in the 
egg directory structure, but I don't remember the details.

-Jeff
>
> My site-packages directory looks like this:
> -rw-rw-r--   1 root  admin     119 Oct  5  2007 README
> drwxr-xr-x  20 root  admin     680 Apr 30 16:43 
> basemap-0.9.9.1-py2.5-macosx-10.5-i386.egg
> -rw-r--r--   1 root  admin     555 Apr 30 16:43 easy-install.pth
> drwxr-xr-x   4 root  admin     136 Apr 30 16:49 
> ipython-0.8.3.svn.r3001-py2.5.egg
> drwxr-xr-x  12 root  admin     408 Apr 30 16:48 
> matplotlib-0.98pre-py2.5-macosx-10.3-i386.egg
> drwxr-xr-x  11 root  admin     374 Apr 17 15:03 
> matplotlib-0.98pre-py2.5-macosx-10.5-i386.egg
> drwxr-xr-x   5 root  admin     170 Apr 30 16:38 nose-0.10.1-py2.5.egg
> drwxr-xr-x   4 root  admin     136 Apr 17 15:03 
> numpy-1.0.5.dev4954-py2.5-macosx-10.5-i386.egg
> drwxr-xr-x   4 root  admin     136 Apr 30 16:48 
> numpy-1.1.0.dev5077-py2.5-macosx-10.3-i386.egg
> drwxr-xr-x   4 root  admin     136 Apr 17 15:04 
> pymc-2.0DEV_r686-py2.5-macosx-10.3-i386.egg
> drwxr-xr-x   4 root  admin     136 Apr 30 16:49 
> pymc-2.0DEV_r709-py2.5-macosx-10.3-i386.egg
> drwxr-xr-x   6 root  admin     204 Apr 17 15:04 
> readline-2.5.1-py2.5-macosx-10.5-i386.egg
> drwxr-xr-x   4 root  admin     136 Apr 17 15:04 
> scipy-0.7.0.dev4075-py2.5-macosx-10.5-i386.egg
> drwxr-xr-x   4 root  admin     136 Apr 30 16:48 
> scipy-0.7.0.dev4174-py2.5-macosx-10.3-i386.egg
> -rw-r--r--   1 root  admin  324858 Apr 17 15:03 
> setuptools-0.6c8-py2.5.egg
> -rw-r--r--   1 root  admin      29 Apr 30 16:41 setuptools.pth
>
> The easy-install.pth file looks like this:
> import sys; sys.__plen = len(sys.path)
> ./setuptools-0.6c8-py2.5.egg
> ./readline-2.5.1-py2.5-macosx-10.5-i386.egg
> ./ipython-0.8.3.svn.r3001-py2.5.egg
> ./numpy-1.1.0.dev5077-py2.5-macosx-10.3-i386.egg
> ./matplotlib-0.98pre-py2.5-macosx-10.3-i386.egg
> ./scipy-0.7.0.dev4174-py2.5-macosx-10.3-i386.egg
> ./pymc-2.0DEV_r709-py2.5-macosx-10.3-i386.egg
> ./nose-0.10.1-py2.5.egg
> ./basemap-0.9.9.1-py2.5-macosx-10.5-i386.egg
> import sys; new=sys.path[sys.__plen:]; del sys.path[sys.__plen:]; 
> p=getattr(sys,'__egginsert',0); sys.path[p:p]=new; sys.__egginsert = 
> p+len(new)
>
>


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

Jeff (or anyone) - I recently reinstalled all of my numpy/scipy  
related packages, including matplotlib, from a Mac OS X installer  
called the SciPy SuperPack.

(http://macinscience.org/?page_id=6)

All of the packages he includes work really well.

However, after I used easy_install to grab Basemap, I found I can't  
import it.  I was wondering if you could give me a pointer on how to  
tell Python where to look for Basemap?

Thanks,

Mike Hearne

My site-packages directory looks like this:
-rw-rw-r--   1 root  admin     119 Oct  5  2007 README
drwxr-xr-x  20 root  admin     680 Apr 30 16:43 basemap-0.9.9.1-py2.5- 
macosx-10.5-i386.egg
-rw-r--r--   1 root  admin     555 Apr 30 16:43 easy-install.pth
drwxr-xr-x   4 root  admin     136 Apr 30 16:49  
ipython-0.8.3.svn.r3001-py2.5.egg
drwxr-xr-x  12 root  admin     408 Apr 30 16:48 matplotlib-0.98pre- 
py2.5-macosx-10.3-i386.egg
drwxr-xr-x  11 root  admin     374 Apr 17 15:03 matplotlib-0.98pre- 
py2.5-macosx-10.5-i386.egg
drwxr-xr-x   5 root  admin     170 Apr 30 16:38 nose-0.10.1-py2.5.egg
drwxr-xr-x   4 root  admin     136 Apr 17 15:03 numpy-1.0.5.dev4954- 
py2.5-macosx-10.5-i386.egg
drwxr-xr-x   4 root  admin     136 Apr 30 16:48 numpy-1.1.0.dev5077- 
py2.5-macosx-10.3-i386.egg
drwxr-xr-x   4 root  admin     136 Apr 17 15:04 pymc-2.0DEV_r686-py2.5- 
macosx-10.3-i386.egg
drwxr-xr-x   4 root  admin     136 Apr 30 16:49 pymc-2.0DEV_r709-py2.5- 
macosx-10.3-i386.egg
drwxr-xr-x   6 root  admin     204 Apr 17 15:04 readline-2.5.1-py2.5- 
macosx-10.5-i386.egg
drwxr-xr-x   4 root  admin     136 Apr 17 15:04 scipy-0.7.0.dev4075- 
py2.5-macosx-10.5-i386.egg
drwxr-xr-x   4 root  admin     136 Apr 30 16:48 scipy-0.7.0.dev4174- 
py2.5-macosx-10.3-i386.egg
-rw-r--r--   1 root  admin  324858 Apr 17 15:03 setuptools-0.6c8- 
py2.5.egg
-rw-r--r--   1 root  admin      29 Apr 30 16:41 setuptools.pth

The easy-install.pth file looks like this:
import sys; sys.__plen = len(sys.path)
./setuptools-0.6c8-py2.5.egg
./readline-2.5.1-py2.5-macosx-10.5-i386.egg
./ipython-0.8.3.svn.r3001-py2.5.egg
./numpy-1.1.0.dev5077-py2.5-macosx-10.3-i386.egg
./matplotlib-0.98pre-py2.5-macosx-10.3-i386.egg
./scipy-0.7.0.dev4174-py2.5-macosx-10.3-i386.egg
./pymc-2.0DEV_r709-py2.5-macosx-10.3-i386.egg
./nose-0.10.1-py2.5.egg
./basemap-0.9.9.1-py2.5-macosx-10.5-i386.egg
import sys; new=sys.path[sys.__plen:]; del sys.path[sys.__plen:];  
p=getattr(sys,'__egginsert',0); sys.path[p:p]=new; sys.__egginsert = p 
+len(new)