matplotlib-users Mailing List for matplotlib (Page 4)

sparkplot is a short Python module I wrote that uses matplotlib to
create sparklines. For details see:

http://agiletesting.blogspot.com/2005/04/sparkplot-creating-sparklines-with.html

Kudos to everybody working on matplotlib, of course first of all to
John Hunter. I was really impressed with the functionality and
versatility of matplotlib. I'll keep trying my hand at it while
enhancing sparkplot.

Grig

Tim Leslie wrote:

>On Sun, 24 Apr 2005, Jeff Whitaker <js...@fa...> wrote...
>
>  
>
>>Tim Leslie wrote:
>>
>>    
>>
>>>Hi all,
>>>
>>>I use matplotlib for looking at EEG (brainwave) data and I was looking for
>>>a good way to do headmap plots of various things. I was wondering if
>>>anyone has done this before. The basemap toolkit looks like it's done a
>>>lot of the hard work, so I was planning on hacking on that to get it to do
>>>what I need but I figured I should check here first to see that I'm not
>>>reinventing a wheel that someone might have lying around. John, I know
>>>you've done EEG stuff, any pointers?
>>>
>>>Cheers,
>>>
>>>Tim Leslie
>>>
>>>
>>>      
>>>
>>What's a headma?
>>    
>>
>
>A headmap is visualisation where you plot certain values such as signal
>power over the scalp. When you do an EEG recording you're often interested
>in how certain values vary with location across the head and a headmap is
>a way to view this.
>
>If you think of the head as a perfect sphere, then I'd like to plot values
>at certain locations in the same way that using the basemap toolkit you
>can plot values of say, temperature, at different locations on the earth.
>
>Tim
>
>  
>
>

Thanks for the explanation Tim.  Sounds like it should work out of the 
box, provided that the map projection you need is supported.  If not, 
I'll try adding it.  Obviously, you don't need to plot coastlines and 
political boundaries, but is there something you would like to plot in 
their stead? 

-Jeff


-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
NOAA/OAR/CDC  R/CDC1        Email  : Jef...@no...
325 Broadway                Office : Skaggs Research Cntr 1D-124
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

I use python org. I already uninstalled the matplotlib from windows
add/remove program and verify that no matplotlib directory in
site-packages.
After that I reinstall the matplotlib again I use version 0.80

I can't import the matplotlib even in the minimum condition.
For example I go to python shell and type import pylab, this raise the
same error.

I create your myscript.py and run it, but before it finished it shows
the same message in windows forms like I send before, and I have to
stop it.

This processed is stop because I have to cancel the program (due to
error message I sent).

D:\>python myscript.py --verbose-helpful
matplotlib data path c:\python24\share\matplotlib
loaded rc file c:\python24\share\matplotlib\.matplotlibrc
matplotlib version 0.80
verbose.level helpful
interactive is False
platform is win32
numerix Numeric 23.8
font search path ['c:\\python24\\share\\matplotlib']

my os is Windows XP Home Edition.

Betriebssystemname      Microsoft Windows XP Home Edition
Version 5.1.2600 Service Pack 2 Build 2600
Betriebssystemhersteller        Microsoft Corporation
Systemname      MARLIN
Systemhersteller        MEDIONPC
Systemmodell    MS-7091
Systemtyp       X86-based PC
Prozessor       x86 Family 15 Model 3 Stepping 4 GenuineIntel ~3391 Mhz
Prozessor       x86 Family 15 Model 3 Stepping 4 GenuineIntel ~3391 Mhz
BIOS-Version/-Datum     Phoenix Technologies, LTD 6.00 PG, 12.10.2004
SMBIOS-Version  2.3
Windows-Verzeichnis     C:\WINDOWS
Systemverzeichnis       C:\WINDOWS\system32
Startger=E4t      \Device\HarddiskVolume1
Gebietsschema   =D6sterreich
Hardwareabstraktionsebene       Version =3D "5.1.2600.2180
(xpsp_sp2_rtm.040803-2158)"
Benutzername    MARLIN\Pujo
Zeitzone        Westeurop=E4ische Normalzeit
Gesamter realer Speicher        511,48 MB
Verf=FCgbarer realer Speicher     201,06 MB
Gesamter virtueller Speicher    2,00 GB
Verf=FCgbarer virtueller Speicher 1,96 GB
Gr=F6=DFe der Auslagerungsdatei     1,22 GB

Sorry it is in German, I live in Austria

Sincerely Yours,
Pujo Aji

On 4/23/05, John Hunter <jd...@gm...> wrote:
> On 4/22/05, Pujo Aji <aj...@gm...> wrote:
>=20
> >  Error message:
> > Microsoft Visual C++ Runtime Library
> > Assertion failed!
> > Program:c\python24\python.exe
> > File:CXX/cxx_extentions.cxx
> > Line:1031
> >
> > Expression: ob_refcnt =3D=3D 0
> > For information on how your program can cause an assertion
> > failure, see the Visual C++ documentation on asserts
> >
> > First I install in new computer python 2.4.1
> > then the error comes out.
> >
> > So I tried to reinstall with python 2.4
> > The problem still comes.
>=20
> Hmm, that's a strange one.  We've seen this once before
>=20
> http://sourceforge.net/mailarchive/message.php?msg_id=3D8789882
>=20
> and I can't remember what the solution was (the thread doesn't mention
> it) but it was resolved.  I've CCd Gregory on this email to see if he
> can remember, since he once saw the same problem .
>=20
> Are you using the python from python.org?  Does it help if you remove
> site-packages/matplotlib and then reinstall?  Please create this
> simple test script
>=20
>   import pylab
>   pylab.plot([1,2,3])
>   pylab.show()
>=20
> and run it with
>=20
> > c:\python24\python myscript.py --verbose-helpful
>=20
> and paste in all the output and errors in your response after doing a
> clean reinstall, as well as your OS information ....
>=20
> JDH
>

On 4/23/05, John Hunter <jd...@gm...> wrote:
> On 4/22/05, Pujo Aji <aj...@gm...> wrote:
>=20
> >  Error message:
> > Microsoft Visual C++ Runtime Library
> > Assertion failed!
> > Program:c\python24\python.exe
> > File:CXX/cxx_extentions.cxx
> > Line:1031
> >
> > Expression: ob_refcnt =3D=3D 0
> > For information on how your program can cause an assertion
> > failure, see the Visual C++ documentation on asserts
> >
> > First I install in new computer python 2.4.1
> > then the error comes out.
> >
> > So I tried to reinstall with python 2.4
> > The problem still comes.
>=20
> Hmm, that's a strange one.  We've seen this once before
>=20
> http://sourceforge.net/mailarchive/message.php?msg_id=3D8789882
>=20
> and I can't remember what the solution was (the thread doesn't mention
> it) but it was resolved.  I've CCd Gregory on this email to see if he
> can remember, since he once saw the same problem .
>=20
> Are you using the python from python.org?  Does it help if you remove
> site-packages/matplotlib and then reinstall?  Please create this
> simple test script
>=20
>   import pylab
>   pylab.plot([1,2,3])
>   pylab.show()
>=20
> and run it with
>=20
> > c:\python24\python myscript.py --verbose-helpful
>=20
> and paste in all the output and errors in your response after doing a
> clean reinstall, as well as your OS information ....
>=20
> JDH
>

Travis Brady wrote:

>Thanks, John.
>That worked, but Matplotlib is now spitting out the error below and I
>can't even find the rc file in the location it lists:
>
>/System/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site-packages/matplotlib/__init__.py:642:
>UserWarning: Bad val "error" on line #200
>        "verbose.level  : error     # one of silent, error, helpful,
>        debug, debug-annoying"
>        in file
>        "/System/Library/Frameworks/Python.framework/Versions/2.3/share/matplotlib/.matplotlibrc"
>        Illegal verbose string "error".  Legal values are ('silent',
>        'helpful', 'debug', 'debug-annoying')
>  warnings.warn('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s'
>  % (val, cnt, line, fname, msg))
>/System/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site-packages/matplotlib/__init__.py:630:
>UserWarning: Bad key "verbose.erro" on line 202 in
>/System/Library/Frameworks/Python.framework/Versions/2.3/share/matplotlib/.matplotlibrc
>  warnings.warn('Bad key "%s" on line %d in %s' % (key, cnt, fname))
>Bus error
>
>  
>

Travis:  The matplotlib package in fink (http://fink.sf.net) is up to 
date, and includes basemap-0.3.2.  First, you'll need to install the 
developer tools.  After running the fink installer, enable the unstable 
tree by editing /sw/etc/fink.conf (add 'unstable/main' and 
'unstable/crypto' to the 'Trees:' line).  Then run "fink selfupdate", 
and when that is done "fink install matplotlib-py24".  Go get several 
cups of coffee as fink downloads and builds a whole bunch of depedencies 
(including python 2.4.1).  The fink installed python distribution will 
live entirely independently of your apple system python.  I keep the 
matplotlib package up to date, so all that will be needed to get the 
latest version will be to run "fink update matplotlib-py24" 
occasionally.  The disadvantage of the fink route is that you'll have to 
use X11 to run matplotlib with the gtk-agg backend, since fink python is 
a unix build and doesn't support using the native wx or tk toolkits.  
Right now I actually think of this an advantage, since as you've seen 
these toolkits are a bit buggy (the gtk-agg backend is better tested, 
since I believe it is the default under linux and windows).

-Jeff

P.S.  If you decide to go this route, be sure to read section 2.3 of the 
fink user's guide 
(http://fink.sourceforge.net/doc/users-guide/install.php?phpLang=en#setup).

-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/CDC1        FAX   : (303)497-6449
325 Broadway                Web   : http://www.cdc.noaa.gov/~jsw
Boulder, CO, USA 80305-3328 Office: Skaggs Research Cntr 1D-124

Thanks, John.
That worked, but Matplotlib is now spitting out the error below and I
can't even find the rc file in the location it lists:

/System/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site-packages/matplotlib/__init__.py:642:
UserWarning: Bad val "error" on line #200
        "verbose.level  : error     # one of silent, error, helpful,
        debug, debug-annoying"
        in file
        "/System/Library/Frameworks/Python.framework/Versions/2.3/share/matplotlib/.matplotlibrc"
        Illegal verbose string "error".  Legal values are ('silent',
        'helpful', 'debug', 'debug-annoying')
  warnings.warn('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s'
  % (val, cnt, line, fname, msg))
/System/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site-packages/matplotlib/__init__.py:630:
UserWarning: Bad key "verbose.erro" on line 202 in
/System/Library/Frameworks/Python.framework/Versions/2.3/share/matplotlib/.matplotlibrc
  warnings.warn('Bad key "%s" on line %d in %s' % (key, cnt, fname))
Bus error


Travis

On Sun, 24 Apr 2005 20:15:11 -0500, "John Hunter" <jd...@gm...>
said:
> On 4/24/05, Travis Brady <td...@fa...> wrote:
> > Excellent, thanks for the prompt response, Jeff.
> > 
> > I've just tried the ireland.py example and am at a complete loss as to
> > what to do about the following error.
> >  ...snip ....
> >   File "/platlib/matplotlib/lines.py", line 543, in _draw_dashed
> > TypeError: CXX: type error.
> > 
> > Any thoughts?
> 
> 
> You're going to need the latest matplotlib to run the latest basemap. 
> Robert Kern has a build in mac enthon -- check out
> http://download.enthought.com/MacEnthon (this also includes a slightly
> older basemap 0.1.2).  You can either install the entire macenthon
> package or selected subpacakges -- check out the readme on the site.
-- 
  Travis Brady
  td...@fa...

On Sun, 24 Apr 2005, Jeff Whitaker <js...@fa...> wrote...

> Tim Leslie wrote:
> 
> >Hi all,
> >
> >I use matplotlib for looking at EEG (brainwave) data and I was looking for
> >a good way to do headmap plots of various things. I was wondering if
> >anyone has done this before. The basemap toolkit looks like it's done a
> >lot of the hard work, so I was planning on hacking on that to get it to do
> >what I need but I figured I should check here first to see that I'm not
> >reinventing a wheel that someone might have lying around. John, I know
> >you've done EEG stuff, any pointers?
> >
> >Cheers,
> >
> >Tim Leslie
> > 
> >
> What's a headma?

A headmap is visualisation where you plot certain values such as signal
power over the scalp. When you do an EEG recording you're often interested
in how certain values vary with location across the head and a headmap is
a way to view this.

If you think of the head as a perfect sphere, then I'd like to plot values
at certain locations in the same way that using the basemap toolkit you
can plot values of say, temperature, at different locations on the earth.

Tim

> 
> -Jeff
> 
> -- 
> Jeffrey S. Whitaker         Phone : (303)497-6313
> NOAA/OAR/CDC  R/CDC1        FAX   : (303)497-6449
> 325 Broadway                Web   : http://www.cdc.noaa.gov/~jsw
> Boulder, CO, USA 80305-3328 Office: Skaggs Research Cntr 1D-124
> 
`-

Excellent, thanks for the prompt response, Jeff.

I've just tried the ireland.py example and am at a complete loss as to
what to do about the following error.

Traceback (most recent call last):
  File "ireland.py", line 21, in ?
    show()
  File "/platlib/matplotlib/backends/backend_wx.py", line 1156, in show
  File "/platlib/matplotlib/backends/backend_wxagg.py", line 52, in draw
  File "/platlib/matplotlib/backends/backend_agg.py", line 319, in draw
  File "/platlib/matplotlib/figure.py", line 338, in draw
  File "/platlib/matplotlib/axes.py", line 1296, in draw
  File "/platlib/matplotlib/lines.py", line 283, in draw
  File "/platlib/matplotlib/lines.py", line 543, in _draw_dashed
TypeError: CXX: type error.

Any thoughts?

Travis
On Sun, 24 Apr 2005 18:30:21 -0600, "Jeff Whitaker" <js...@fa...>
said:
> Travis Brady wrote:
> 
> >Has anyone successfully installed and run matplotlib from the .dmg here:
> > http://sda.iu.edu/projects.html ?
> >I'm able to install just fine and I can import pylab and create a plot,
> >but using "pylab.show()" crashes Python and returns "Segmentation Fault"
> >and nothing else.
> >
> >
> >Also has anyone successfully installed BaseMap on OS X?
> >I've attempted to install the latest BaseMap package (I believe it's
> >0.3.2) and receive the following error:
> >error: could not create
> >'/System/Library/Frameworks/Python.framework/Versions/2.3/share/basemap-py23':
> >Permission denied
> >
> >I'm running the stock Python 2.3 and Matplotlib 0.72.1 from the link
> >above.
> >
> >Thanks,
> >
> >Travis Brady
> >  
> >
> Travis:  Regarding the basemap install - you need admin privileges on 
> your mac to install using "python setup.py install", so either run it as 
> sudo, or if you don't have admin access try "python setup.py install 
> --home=~" (this will install it in your home directory).  If you do the 
> latter, you'll have to add ~/lib/python to your PYTHONPATH.
> 
> 
> -Jeff
> 
> -- 
> Jeffrey S. Whitaker         Phone : (303)497-6313
> NOAA/OAR/CDC  R/CDC1        FAX   : (303)497-6449
> 325 Broadway                Web   : http://www.cdc.noaa.gov/~jsw
> Boulder, CO, USA 80305-3328 Office: Skaggs Research Cntr 1D-124
> 
-- 
  Travis Brady
  td...@fa...

Travis Brady wrote:

>Has anyone successfully installed and run matplotlib from the .dmg here:
> http://sda.iu.edu/projects.html ?
>I'm able to install just fine and I can import pylab and create a plot,
>but using "pylab.show()" crashes Python and returns "Segmentation Fault"
>and nothing else.
>
>
>Also has anyone successfully installed BaseMap on OS X?
>I've attempted to install the latest BaseMap package (I believe it's
>0.3.2) and receive the following error:
>error: could not create
>'/System/Library/Frameworks/Python.framework/Versions/2.3/share/basemap-py23':
>Permission denied
>
>I'm running the stock Python 2.3 and Matplotlib 0.72.1 from the link
>above.
>
>Thanks,
>
>Travis Brady
>  
>
Travis:  Regarding the basemap install - you need admin privileges on 
your mac to install using "python setup.py install", so either run it as 
sudo, or if you don't have admin access try "python setup.py install 
--home=~" (this will install it in your home directory).  If you do the 
latter, you'll have to add ~/lib/python to your PYTHONPATH.


-Jeff

-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/CDC1        FAX   : (303)497-6449
325 Broadway                Web   : http://www.cdc.noaa.gov/~jsw
Boulder, CO, USA 80305-3328 Office: Skaggs Research Cntr 1D-124

Mike Elson wrote:

>I'm having trouble running some of the examples that come with basemap
>- any th\at use the file etopo20.pickle fail with an error similar to:
>
>Traceback (most recent call last):
>  File "test.py", line 12, in ?
>    topodict = cPickle.load(open('etopo20.pickle','rb'))
>  File "/usr/lib/python2.3/site-packages/numarray/generic.py", line
>159, in Cla\ssicUnpickler
>    self.__setstate__(state)
>  File "/usr/lib/python2.3/site-packages/numarray/numarraycore.py",
>line 463, i\n __setstate__
>    self._type      = state["_type"]
>AttributeError: ("'str' object has no attribute 'name'", <function
>ClassicUnpic\kler at 0xb7b08e9c>, (<class
>'numarray.numarraycore.NumArray'>, {'_type': 'Floa\t32', '_itemsize':
>4, '_shape': (1081,), '_bytestride': 4, '_byteoffset': 0, '_\version':
>'1.1', '_byteorder': 'big', '_data': <memory at 082f8798 with
>size:43\24 held by object 082f8778 aliasing object 00000000>,
>'_strides': (4,)}))
>
>Can anyone tell me how to fix this?
>I'm using python 2.3.4, matplotlib 0.80, basemap 0.3.2, proj 4.4.8 and
>have the Python libraries numeric 23.1 and numarray 0.8 installed.
>
>Thanks in advance,
>Mike.
>
>  
>
Mike:  My guess is I saved the data as a pickle Numeric (not numarray) object.  You can either install Numeric, or I can re-pickle it for you with numarray.

-Jeff


---
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/CDC1        FAX   : (303)497-6449
325 Broadway                Web   : http://www.cdc.noaa.gov/~jsw
Boulder, CO, USA 80305-3328 Office: Skaggs Research Cntr 1D-124

Has anyone successfully installed and run matplotlib from the .dmg here:
 http://sda.iu.edu/projects.html ?
I'm able to install just fine and I can import pylab and create a plot,
but using "pylab.show()" crashes Python and returns "Segmentation Fault"
and nothing else.


Also has anyone successfully installed BaseMap on OS X?
I've attempted to install the latest BaseMap package (I believe it's
0.3.2) and receive the following error:
error: could not create
'/System/Library/Frameworks/Python.framework/Versions/2.3/share/basemap-py23':
Permission denied

I'm running the stock Python 2.3 and Matplotlib 0.72.1 from the link
above.

Thanks,

Travis Brady
-- 
  Travis Brady
  td...@fa...

I'm having trouble running some of the examples that come with basemap
- any th\at use the file etopo20.pickle fail with an error similar to:

Traceback (most recent call last):
  File "test.py", line 12, in ?
    topodict =3D cPickle.load(open('etopo20.pickle','rb'))
  File "/usr/lib/python2.3/site-packages/numarray/generic.py", line
159, in Cla\ssicUnpickler
    self.__setstate__(state)
  File "/usr/lib/python2.3/site-packages/numarray/numarraycore.py",
line 463, i\n __setstate__
    self._type      =3D state["_type"]
AttributeError: ("'str' object has no attribute 'name'", <function
ClassicUnpic\kler at 0xb7b08e9c>, (<class
'numarray.numarraycore.NumArray'>, {'_type': 'Floa\t32', '_itemsize':
4, '_shape': (1081,), '_bytestride': 4, '_byteoffset': 0, '_\version':
'1.1', '_byteorder': 'big', '_data': <memory at 082f8798 with
size:43\24 held by object 082f8778 aliasing object 00000000>,
'_strides': (4,)}))

Can anyone tell me how to fix this?
I'm using python 2.3.4, matplotlib 0.80, basemap 0.3.2, proj 4.4.8 and
have the Python libraries numeric 23.1 and numarray 0.8 installed.

Thanks in advance,
Mike.

Tim Leslie wrote:

>Hi all,
>
>I use matplotlib for looking at EEG (brainwave) data and I was looking for
>a good way to do headmap plots of various things. I was wondering if
>anyone has done this before. The basemap toolkit looks like it's done a
>lot of the hard work, so I was planning on hacking on that to get it to do
>what I need but I figured I should check here first to see that I'm not
>reinventing a wheel that someone might have lying around. John, I know
>you've done EEG stuff, any pointers?
>
>Cheers,
>
>Tim Leslie
>  
>
What's a headma?

-Jeff

-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/CDC1        FAX   : (303)497-6449
325 Broadway                Web   : http://www.cdc.noaa.gov/~jsw
Boulder, CO, USA 80305-3328 Office: Skaggs Research Cntr 1D-124

Hi all,

I use matplotlib for looking at EEG (brainwave) data and I was looking for
a good way to do headmap plots of various things. I was wondering if
anyone has done this before. The basemap toolkit looks like it's done a
lot of the hard work, so I was planning on hacking on that to get it to do
what I need but I figured I should check here first to see that I'm not
reinventing a wheel that someone might have lying around. John, I know
you've done EEG stuff, any pointers?

Cheers,

Tim Leslie

Jim,

 >Using matplotlib 0.74.
 >The default linestyle for contour lines representing values less than
 >zero should be dashed.
 >I have used this in the past ( I guess prior to 0.74) but now the
 >behavior is different.
 >The default appears to be a greyscale color map - all solid lines.
 >Looking at the code - line 768 of contour.py, the negative lines are
 >dashed if Ncolors == 1.
 >As far as I can tell, there is no way for this to be true. The code
 >change to rectify this is trivial,
 >but I may be missing something.

I made the change to which you refer, that is, adding the condition 
"Ncolors == 1" to the test for changing to dashed lines.  My rationale 
is that the default is to color the lines with the default colormap, in 
which case the level information is in the colors, and making the 
negative values dashed just adds clutter.  If the intent is to use 
simple black (or any other single color) lines, then one uses the kwarg 
"colors=('k',)" (for example), in which case Ncolors == 1, and the 
negative lines are dashed.  This is illustrated in the attached script.

If you don't specify a colormap, the default is taken from your 
.matplotlibrc file if it exists, otherwise from the system default 
.matplotlibrc: specifically, the line

image.cmap   : jet               # gray | jet

The present system default is jet, not gray, so I presume it is your own 
.matplotlibrc file that is changing the default to gray.

Note that contour returns two arguments: a list of contour levels, and a 
corresponding list of LineCollections, which make it quite easy to 
change the line properties.  If you want multicolored lines dashed for 
negative levels, you can do something like this:

levs, colls = contour(Z, cmap=hot())
for lev, coll in zip(levs, colls):
     if lev < 0:
         coll.set_linestyle((0, (6.,6.)),)

My inclination is to keep the default behavior rather simple, and let 
people customize as above. It is debatable whether the default even for 
single-color lines at negative levels should be dashed; I think a better 
design, more consistent with matlab and with the spirit of matplotlib, 
would be to leave this out.

We could also add support for a linestyles kwarg, similar to the 
linewidths kwarg that contour already accepts.

Eric

On 4/22/05, Pujo Aji <aj...@gm...> wrote:

>  Error message:
> Microsoft Visual C++ Runtime Library
> Assertion failed!
> Program:c\python24\python.exe
> File:CXX/cxx_extentions.cxx
> Line:1031
>=20
> Expression: ob_refcnt =3D=3D 0
> For information on how your program can cause an assertion
> failure, see the Visual C++ documentation on asserts
>=20
> First I install in new computer python 2.4.1
> then the error comes out.
>=20
> So I tried to reinstall with python 2.4
> The problem still comes.

Hmm, that's a strange one.  We've seen this once before

http://sourceforge.net/mailarchive/message.php?msg_id=3D8789882

and I can't remember what the solution was (the thread doesn't mention
it) but it was resolved.  I've CCd Gregory on this email to see if he
can remember, since he once saw the same problem .

Are you using the python from python.org?  Does it help if you remove
site-packages/matplotlib and then reinstall?  Please create this
simple test script

  import pylab
  pylab.plot([1,2,3])
  pylab.show()

and run it with

> c:\python24\python myscript.py --verbose-helpful

and paste in all the output and errors in your response after doing a
clean reinstall, as well as your OS information ....

JDH

On 4/22/05, ch...@ll... <ch...@ol...> wrote:
  > There is beginning interest in this quality library=20
  > on AIX 5.x.  Is a port planned, and when might it be
  > available?


I've never worked on AIX, but the steps there should be the same as
elsewhere -- mpl has been compiled on a number of UNIX boxes.  Make
sure you have the dependencies on your system (zlib, libpng and
freetype with development headers).  Add an entry in setupext.py in
the basedirs dictionary, where the key is your sys.platform and the
value is a list of paths in which matplotlib should search for
dependencies (eg /opt, /usr/local, whatever).   You will probably have
the best luck trying to compile with gcc but this may not be an
option.  If your compiler is C++ standards compliant, and the
matplotlib compile fails because of some noncompliant code, I'll treat
this as a bug and try and fix it.  Unfortunately, I don't have access
to an AIX system which makes it a little slower to find and fix these
problems.  Perhaps there is an AIX system on the sourceforge compile
farm -- anyone want to volunteer into looking into the compile farm
options :-) ?

Basically, I suggest you try following the instructions at
http://matplotlib.sf.net/installing.html and see how far you get, and
report the errors you get when tyring to compile as well as the
compiler you are using and other relevant information.

Good luck!
JDH

Pietro,

Are you sure it is savefig() that is using memory?  Try
commenting out close().  In my case it solved a memory
problem with batch processing.  See recent list postings
for more details.  You may need to add clf() or cla() to
avoid overplotting.

Please let the list know if it works for you without
close() and your matplotlib version to help developers
track down memory leaks or related issues.

Good Luck,

-- David

>Date: Thu, 21 Apr 2005 07:32:13 -0700 (PDT)
>From: Pietro Speroni di Fenizio <pie...@ya...>
>To: mat...@li...
>Subject: [Matplotlib-users] Memory problem with savefig

>Hello, I have been using Matplotlib lately for some
>academic research. It seem to work just fine. The only
>serious problem is a problem with memory. When I run

.
.
.

>def PlotAreaOrganization(data,filename):
>    keys=symbol2color.keys()
>    keys.sort()
>    colors=[]
>    for key in keys:  colors.append(symbol2color[key])
>    fig=figure(dpi=75)
>    area(data,colors)
>    savefig(filename)
>    close(fig)


>Any suggestion? Is there any other way to save a
>picture that might work better?


+_+_+_+_+_+_+_+_+_+_+_+_+_+_+_+_+

__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 

There is beginning interest in this quality library
on AIX 5.x.  Is a port planned, and when might it be
available?
Thanks,
Lila
lc...@ll...

Using matplotlib 0.74.
The default linestyle for contour lines representing values less than 
zero should be dashed.
I have used this in the past ( I guess prior to 0.74) but now the 
behavior is different.
The default appears to be a greyscale color map - all solid lines.
Looking at the code - line 768 of contour.py, the negative lines are 
dashed if Ncolors == 1.
As far as I can tell, there is no way for this to be true. The code 
change to rectify this is trivial,
but I may be missing something.

I could easily be doing something really dumb - but it seems pretty 
straightforward.

Thanks for any help.

--Jim

I found this error message when I import pylab.

from pylab import *

Error message:
Microsoft Visual C++ Runtime Library
Assertion failed!
Program:c\python24\python.exe
File:CXX/cxx_extentions.cxx
Line:1031

Expression: ob_refcnt =3D=3D 0
For information on how your program can cause an assertion
failure, see the Visual C++ documentation on asserts

First I install in new computer python 2.4.1
then the error comes out.

So I tried to reinstall with python 2.4
The problem still comes.

Please help

Pujo

  > So, i create an instance of the class like this:
  >   a=3D Arrow(0,0,5,5,2.0)
  > The problem is i don"t know how to draw the arrow on a figure.
=20
You can add the arrow to the Axes with=20

   ax.add_artist(arrow)
 =20
Is this what you are looking for.    The Axes will implicitly assume
the arrow is in data coordinates, unless you set the transform
instance of the arrow edxplicitly.  Eg, if you do

  arrow.set_transform(ax.transAxes)

where ax is a matplotlib.axes.Axes instance.


  >  i"m trying to generate the smith chart which is very usefull in
electromagnetic domain.
  > In this purpose, i need to draw circle.
  > I try to find in the polar function the way circles are drawn but
i didn"t find it.
  >  Can you told me John how did you draw circles in the polar figure?
=20
You can create an instance of matplotlib.patches.Circle, and add it to
the Axes with ax.add_patch(circ).  Same rules about the transform
applies above.

If you want to create a circular Axes, like polar does, you may want
to add the circle instance to the figure.  I suggest looking at the
code for matplotlib.axes.PolarAxes, where I create the axes background
"circle" with

        self.thetas =3D linspace(0,2*math.pi, self.RESOLUTION)
        verts =3D zip(self.thetas, ones(self.RESOLUTION))
        self.axesPatch =3D Polygon(
            verts,
            facecolor=3Dself._axisbg,
            edgecolor=3DrcParams['axes.edgecolor'],
            )

If you succeed in creating the smith chart, lpease post a patch or an
example, and feel free to ask if you have more questions.  I
understand those are tough charts to create.

JDH

  >  I am trying to scale the y axis like this:
  >   a =3D axes(gca())

This is probably harmless but redundant.  gca creates a new axes if
none exists, so you can do
any of the foloowing
=20
  a =3D gca()
  a =3D subplot(111)
  a =3D axes([0.1, 0.1, 0.8, 0.8])

but I wouldn't do axes(gca())
=20
  >   a.set_ylim((-1.25, 1.25))
=20
  > This works fine when yticks is non-empty. However, if I do
  >    a.set_yticks([]])
  > either before or after the set_ylim call, the y axis is not scaled.
=20
  >  Any suggestions are appreciated.=20
=20
Make sure that you are updating the figure after you change the
properties.  The figure is automatically redrawn after pylab commands
if interactive is True, but afterr calling object setters, you need to
explicitly call draw (if working interactively)

Please post a complete example which exposes the problem, as well as
matplotlib version and backend information.  You can get the latter by
running your script with --verbose-helpful.

JDH

 Grig

  > Hello, I have been using Matplotlib lately for some
  > academic research. It seem to work just fine. The only
  > serious problem is a problem with memory. When I run
  > the following code, I get the memory increasing
  > linearly with the time. Soon (after around 20
  > generations, and 100 times is this part of the program
  > called) I get beyond the limits of my laptop, and the
  > simulation ends. Considering that I need to do at
  > least 200 generations, you can see that it is a
  > serious problem.

You need to give us a little more information, namely what backend you
are using.  Best if you run your script with --verbose-helpful and
post the output it generates,

There are no known signigicant leaks in the Agg backend proper.  If
you use TkAgg to create many new canvases (which the script you posted
does), there is a known leak, and it may be on the tk side.  The
solution is to reuse the same figure canvas rather than creating new
ones.  There is also a small amount of memory that is used up with the
caching of text layout information, which you can clear manually.

Try something like this (untested)

from matplotlib.text import Text
import gc
fig =3D figure()
for i in range(200):
    fig.clear()
    ax =3D fig.subplot(111)
    ax.plot(blah)
    fig.savefig('myfig')
    Text.cached =3D {}
    gc.collect()

See also the FAQ on memory leaks
http://matplotlib.sourceforge.net/faq.html#LEAKS and search the
mailing list archive for "leak" for more inspiration.

Let us know hwat you learn,
JDH

  > I"d like to be able to add text to various (x,y) coordinates. Currently
  > I specify a figsize of (1.3,0.3) and I add as text (via the text
  > method) the value of the last y, right next to that data point.
  > Depending on the actual value, sometimes the text does not fit within
  > the bounds of the figure.=20
=20
  > Is there any way I can enlarge just the figure so that the text can
  > fit, without enlarging the axes? Or is there a better way to solve my
  > problem?

There are a few parameters that affect the relative sizes of all the
figure elements and text

  figsize - passed to the figure command, width and height in inches
  dpi       - passed to the figure command, number of dots per inch
  fontsize - passed to the text command, size of text in points
  axes([l,b,w,h]) - create a custom axes with width and height as
fractions of figure size

By tweaking these parameters, you should be able to place your text
anywhere you want at any size you want.

If this doesn't help, post a complete example and describe what is
wrong and someone may be able to offer pointers