matplotlib-users Mailing List for matplotlib

I would consider this a python bug, and I just added a quick fix for me.
Changed line 511 in Prompts.py to say
	if self.Pprint and hasattr(arg, '__repr__'):
instead of
	if self.Pprint:
You probably don't want to add this for everything, but would it be possible to 
override the display method of the CachedOutput when the pylab option is 
specified? Further, you could only do this for python v.2.4.
- Charlie
Fernando Perez wrote:
> Charles Moad wrote:
> 
>> I found this link, 
>> http://mail.python.org/pipermail/python-bugs-list/2004-November/026192.html. 
>> I am guessing Jon and I are using python2.4 and you are using 2.3?
> 
> 
> That's correct. I have 2.4 lying around, but matplotlib isn't built for 
> it, nor are any of its dependencies. So I can only do mpl tests with 
> 2.3, I'm afraid.
> 
> Cheers,
> 
> f

Charles Moad wrote:
> I found this link, 
> http://mail.python.org/pipermail/python-bugs-list/2004-November/026192.html. I 
> am guessing Jon and I are using python2.4 and you are using 2.3?
That's correct. I have 2.4 lying around, but matplotlib isn't built for it, 
nor are any of its dependencies. So I can only do mpl tests with 2.3, I'm afraid.
Cheers,
f

I found this link, 
http://mail.python.org/pipermail/python-bugs-list/2004-November/026192.html. I 
am guessing Jon and I are using python2.4 and you are using 2.3?
- Charlie
Fernando Perez wrote:
> Charles Moad wrote:
> 
>> FYI, turning off pprint gets rid of the error. Will look into it more.
> 
> 
> OK, that's a start. Try running the following at a command line, via 
> plain python:
> 
> import pprint
> 
> from matplotlib.transforms import unit_bbox
> b = unit_bbox()
> print pprint.pformat(b)
> 
> 
> This is what I get:
> 
> planck[~/test]> python pprint_bug.py
> <Bbox object at 0x8f3c99c>
> 
> If you get a segfault, it means that there's a problem with those 
> objects triggered by pprint.
> 
> As a temporary workaround, you can permanently disable pprint in your 
> ipython sessions by setting
> 
> pprint 0
> 
> in your ~/.ipython/ipythonrc file.
> 
> Cheers,
> 
> f

Charles Moad wrote:
> FYI, turning off pprint gets rid of the error. Will look into it more.
OK, that's a start. Try running the following at a command line, via plain 
python:
import pprint
from matplotlib.transforms import unit_bbox
b = unit_bbox()
print pprint.pformat(b)
This is what I get:
planck[~/test]> python pprint_bug.py
<Bbox object at 0x8f3c99c>
If you get a segfault, it means that there's a problem with those objects 
triggered by pprint.
As a temporary workaround, you can permanently disable pprint in your ipython 
sessions by setting
pprint 0
in your ~/.ipython/ipythonrc file.
Cheers,
f

I am not aware of any specific mesh plotting routines, so you may have 
to write your own by specifying which lines you want drawn for the mesh 
- sort of like specifying the vertices of polygons in VTK.
x=[0,0,1,1,0]
y=[0,1,1,0,0]
pylab.plot(x,y,'bo-')
pylab.ylim((-0.1,1.1))
pylab.xlim((-0.1,1.1))
pylab.show()
Ryan
Henry Proudhon wrote:
> Yes two dimensional mesh only of course... for 3D I already use Vtk
> 
> The biggest potential problem is that matplotlib is exclusively a 2D
> plotting program (for now). Is the mesh that you want to plot two
> dimensional?
> 
> Ryan
> 
> 
> --Henry
> 
> 
> -------------------------------------------------------
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> 

FYI, turning off pprint gets rid of the error. Will look into it more.
Fernando Perez wrote:
> John Hunter wrote:
> 
>> but in ipython I get the segfault
>>
>> peds-pc311:~> ipython
>> Python 2.4.1 (#2, Mar 30 2005, 21:51:10)
>> Type "copyright", "credits" or "license" for more information.
>>
>> IPython 0.6.16_cvs -- An enhanced Interactive Python.
>> ? -> Introduction to IPython's features.
>> %magic -> Information about IPython's 'magic' % functions.
>> help -> Python's own help system.
>> object? -> Details about 'object'. ?object also works, ?? prints 
>> more.
>>
>> In [1]: from matplotlib.transforms import unit_bbox
>>
>> In [2]: b = unit_bbox()
>>
>> In [3]: b
>> Segmentation fault
> 
> 
> This one is going to be hard to track, since I can't reproduce it on my 
> system (Fedora 3):
> 
> planck[~]> ip
> Python 2.3.4 (#1, Feb 2 2005, 12:11:53)
> Type "copyright", "credits" or "license" for more information.
> 
> IPython 0.6.16_svn -- An enhanced Interactive Python.
> ? -> Introduction to IPython's features.
> %magic -> Information about IPython's 'magic' % functions.
> help -> Python's own help system.
> object? -> Details about 'object'. ?object also works, ?? prints more.
> 
> In [1]: from matplotlib.transforms import unit_bbox
> 
> In [2]: b = unit_bbox()
> 
> In [3]: b
> Out[3]: <Bbox object at 0x965d6d4>
> 
> In [4]:
> 
> In [4]:
> planck[~]> pylab
> 
> In [1]: from matplotlib.transforms import unit_bbox
> 
> In [2]: b = unit_bbox()
> 
> In [3]: b
> Out[3]: <Bbox object at 0x893866c>
> 
> So neither plain ipython nor 'ipython -pylab' show me any sign of 
> trouble here.
> 
> I'm afraid we'll have to debug this one by proxy, since I can't see any 
> problem here. The code which is executed when output is to be printed 
> is the __call__ method of the CachedOutput object. Look around line 476 
> in IPython/Prompts.py. Adding some print/debug statements to that 
> function might shed some light.
> 
> One thing you could try is toggling %Pprint back and forth. This is the 
> pretty printer used by ipython, which is part of the stdlib (module 
> pprint). It might be triggering some problem in the underlying pycxx 
> objects.
> 
> Cheers,
> 
> f

John Hunter wrote:
> but in ipython I get the segfault
> 
> peds-pc311:~> ipython
> Python 2.4.1 (#2, Mar 30 2005, 21:51:10)
> Type "copyright", "credits" or "license" for more information.
> 
> IPython 0.6.16_cvs -- An enhanced Interactive Python.
> ? -> Introduction to IPython's features.
> %magic -> Information about IPython's 'magic' % functions.
> help -> Python's own help system.
> object? -> Details about 'object'. ?object also works, ?? prints more.
> 
> In [1]: from matplotlib.transforms import unit_bbox
> 
> In [2]: b = unit_bbox()
> 
> In [3]: b
> Segmentation fault
This one is going to be hard to track, since I can't reproduce it on my system 
(Fedora 3):
planck[~]> ip
Python 2.3.4 (#1, Feb 2 2005, 12:11:53)
Type "copyright", "credits" or "license" for more information.
IPython 0.6.16_svn -- An enhanced Interactive Python.
? -> Introduction to IPython's features.
%magic -> Information about IPython's 'magic' % functions.
help -> Python's own help system.
object? -> Details about 'object'. ?object also works, ?? prints more.
In [1]: from matplotlib.transforms import unit_bbox
In [2]: b = unit_bbox()
In [3]: b
Out[3]: <Bbox object at 0x965d6d4>
In [4]:
In [4]:
planck[~]> pylab
In [1]: from matplotlib.transforms import unit_bbox
In [2]: b = unit_bbox()
In [3]: b
Out[3]: <Bbox object at 0x893866c>
So neither plain ipython nor 'ipython -pylab' show me any sign of trouble here.
I'm afraid we'll have to debug this one by proxy, since I can't see any 
problem here. The code which is executed when output is to be printed is the 
__call__ method of the CachedOutput object. Look around line 476 in 
IPython/Prompts.py. Adding some print/debug statements to that function might 
shed some light.
One thing you could try is toggling %Pprint back and forth. This is the 
pretty printer used by ipython, which is part of the stdlib (module pprint). 
It might be triggering some problem in the underlying pycxx objects.
Cheers,
f

Yes two dimensional mesh only of course... for 3D I already use Vtk
 The biggest potential problem is that matplotlib is exclusively a 2D
 plotting program (for now). Is the mesh that you want to plot two
 dimensional?
 Ryan
--Henry

Dear Matplotlib users,
I'm new to this list as well as matplot lib, but already really 
impressed by this library.
I was wondering if there was an easy way to plot a simple (or not) fem 
mesh in the deformed (or not) state
before starting to write such a function, I though it would be a good 
idea to ask to the list.
Any advice or idea would be appreciated, thanks !
-- 
Henry Proudhon
Postdoc Fellow
Materials Engineering
The University of British Columbia
309-3650 Stores Road
V6T-1Z4 Vancouver B.C. (Canada)

Hello, I'm using scatter to plot markers that I would like to be
transparent, so I use the keyword alpha = 0.2 to set transparency at
20%. But the markers are not transparent. I was informed by this list
prior that there is a bug with using plot() and the transparency does
not work. Is this the same bug for scatter as well?

>>>>> "Charles" == Charles Moad <cm...@in...> writes:
Setting followups to matplotlib-devel
 Charles> I get segfaults with ipython -pylab (and without the
 Charles> flag) quite a bit as well. They usually seem pretty
 Charles> random and frequent, but I found one way to reproduce.
 Charles> gentoo-linux ipython-0.6.15 matplotlib-cvs
 Charles> plot(rand(10)) a = gca() a.bbox<return> Segmentation
 Charles> fault
 Charles> This may not be a practical example, but it is the only
 Charles> consistent one I can find right now.
Hey Charles,
Thanks for reporting this. I'm not sure this is related to Steve's
bug, but it's good to know about. 
I can reproduce your crash on ubuntu, and only in ipython. This is
independent of backends and can be reproduced with this minimal script
 peds-pc311:~> python
 Python 2.4.1 (#2, Mar 30 2005, 21:51:10)
 [GCC 3.3.5 (Debian 1:3.3.5-8ubuntu2)] on linux2
 Type "help", "copyright", "credits" or "license" for more information.
 >>> from matplotlib.transforms import unit_bbox
 >>> b = unit_bbox()
 >>> b
 <Bbox object at 0x81e3a6c>
 >>>
but in ipython I get the segfault
 peds-pc311:~> ipython
 Python 2.4.1 (#2, Mar 30 2005, 21:51:10)
 Type "copyright", "credits" or "license" for more information.
 IPython 0.6.16_cvs -- An enhanced Interactive Python.
 ? -> Introduction to IPython's features.
 %magic -> Information about IPython's 'magic' % functions.
 help -> Python's own help system.
 object? -> Details about 'object'. ?object also works, ?? prints more.
 In [1]: from matplotlib.transforms import unit_bbox
 In [2]: b = unit_bbox()
 In [3]: b
 Segmentation fault
bbox is a pycxx extension object defined in src/_transforms.cpp
Something ipython is doing to represent the object is causing the
crash. I can do the following in ipython
 In [1]: from matplotlib.transforms import unit_bbox
 In [2]: b = unit_bbox()
 In [3]: print b
 <Bbox object at 0x82601c4>
 In [4]: str(b)
 Out[4]: '<Bbox object at 0x82601c4>'
Fernando, what kind of whacky magic are you doing when I type
 In [5]: b
 Segmentation fault
We've seen segfault's before when doing type inspection in pycxx; I've
reported this but haven't gotten any resolution
http://sourceforge.net/tracker/index.php?func=detail&aid=1210007&group_id=3180&atid=103180
JDH

I get segfaults with ipython -pylab (and without the flag) quite a bit as well. 
 They usually seem pretty random and frequent, but I found one way to reproduce.
gentoo-linux
ipython-0.6.15
matplotlib-cvs
plot(rand(10))
a = gca()
a.bbox<return>
Segmentation fault
This may not be a practical example, but it is the only consistent one I can 
find right now.
- Charlie
John Hunter wrote:
>>>>>>"Steve" == Steve Schmerler <el...@gm...> writes:
> 
> 
> Steve> Hi I recently posted something about segfaults I get when
> Steve> plotting. Now here is a little update and I really hope
> Steve> someone has an idea how I can solve this problem.
> 
> Steve> I'm running IPython 0.6.13 on a Debian box, installed the
> Steve> recent mpl 0.83.2 from source, GTKAgg backend.
> 
> Steve> 1)
> 
> Steve> When I start ipython (as normal user) with the -pylab
> Steve> option and then say
> 
> Steve> 	plot([1,2,3])
> 
> Steve> I get
> 
> Steve> In [1]: plot([1,2,3])
> Steve> ---------------------------------------------------------------------------
> Steve> exceptions.SystemError Traceback (most recent call last)
> 
> 
> Steve> SystemError: ../Objects/moduleobject.c:48: bad argument to
> Steve> internal function
> 
> You say this is a segfault, but it looks like an exception. Does this
> actually kill the ipython shell? Is this a full posting of the
> traceback?
> 
> What happens if you run the following script outside of ipython
> 
> from pylab import plot, show
> plot([1,2,3])
> show()
> 
> with 
> 
> > python test.py --verbose-helpful 
> 
> Does this create a proper figure window -- please post all output from
> the script.
> 
> 
> Steve> 2)
> 
> Steve> However when I change to root
> 
> Steve> 	su <pwd>
> 
> Steve> 	ipython -pylab
> 
> Steve> then plotting works fine!?
> 
> Perhaps this has something to do with having permission to connect to
> the X11 server? As a normal user, can you launch graphical apps from
> the shell, eg 
> 
> > gedit&
> 
> 
> Have you done anything unusual with your system, changed the default
> permission bits, done a chroot, etc? What linux distro are you
> running?
> 
> 
> Steve> I have no idea where this moduleobject.c lives or to which
> Steve> application it belongs.
> 
> Steve> 2)
> 
> Steve> If I try the same with the normal python interpreter
> 
> Steve> 	python
> 
> Steve> 	from pylab import *; ion() plot([1,2,3])
> 
> Steve> a plot window pops up but shows no picture (no matter if
> Steve> I'm root or not).
> 
> 
> GTKAgg is not expected to work unless you are in a special threaded
> environment like ipython with -gthread or -pylab. Try the same with
> the TkAgg backend (edit your rc file) and let me know what happens.
> 
> The last thing I'd advise is upgrading your ipython to the latest.
> 
> I've never seen this one before so I'm flying by the seat of my pants.
> 
> 
> JDH
> 
> 
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference & EXPO
> September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices
> Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA
> Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

>>>>> "Steve" == Steve Schmerler <el...@gm...> writes:
 Steve> Hi I recently posted something about segfaults I get when
 Steve> plotting. Now here is a little update and I really hope
 Steve> someone has an idea how I can solve this problem.
 Steve> I'm running IPython 0.6.13 on a Debian box, installed the
 Steve> recent mpl 0.83.2 from source, GTKAgg backend.
 Steve> 1)
 Steve> When I start ipython (as normal user) with the -pylab
 Steve> option and then say
 Steve> 	plot([1,2,3])
 Steve> I get
 Steve> In [1]: plot([1,2,3])
 Steve> ---------------------------------------------------------------------------
 Steve> exceptions.SystemError Traceback (most recent call last)
 Steve> SystemError: ../Objects/moduleobject.c:48: bad argument to
 Steve> internal function
You say this is a segfault, but it looks like an exception. Does this
actually kill the ipython shell? Is this a full posting of the
traceback?
What happens if you run the following script outside of ipython
 from pylab import plot, show
 plot([1,2,3])
 show()
with 
 > python test.py --verbose-helpful 
Does this create a proper figure window -- please post all output from
the script.
 Steve> 2)
 Steve> However when I change to root
 Steve> 	su <pwd>
 Steve> 	ipython -pylab
 Steve> then plotting works fine!?
Perhaps this has something to do with having permission to connect to
the X11 server? As a normal user, can you launch graphical apps from
the shell, eg 
 > gedit&
Have you done anything unusual with your system, changed the default
permission bits, done a chroot, etc? What linux distro are you
running?
 Steve> I have no idea where this moduleobject.c lives or to which
 Steve> application it belongs.
 Steve> 2)
 Steve> If I try the same with the normal python interpreter
 Steve> 	python
 Steve> 	from pylab import *; ion() plot([1,2,3])
 Steve> a plot window pops up but shows no picture (no matter if
 Steve> I'm root or not).
GTKAgg is not expected to work unless you are in a special threaded
environment like ipython with -gthread or -pylab. Try the same with
the TkAgg backend (edit your rc file) and let me know what happens.
The last thing I'd advise is upgrading your ipython to the latest.
I've never seen this one before so I'm flying by the seat of my pants.
JDH

Hi,
I have just fink-installed matplotlib-py24.
When I do the following, I get a 10 sec delay after the warning 
message until I can enter further text.
 >>> pylab.figure(1)
/sw/lib/python2.4/site-packages/matplotlib/backends/backend_gtk.py: 
960: GtkWarning: Could not find the icon 'gnome-fs-home'. The 
'hicolor' theme
was not found either, perhaps you need to install it.
You can get a copy from:
 http://freedesktop.org/Software/icon-theme/releases
 buttons, backend)
pylab.plot(x,y)
gnome-fs-home.png is in:
/sw/share/icons/{Flat-Blue, gnome, HighContrastLargePrint, 
HighContrastLargePrintInverse, LowContrastLargePrint}/48x48
hicolor exists as a directory at:
/sw/share/icons/hicolor
Am I missing some files?
regards,
Graeme

Hi
I recently posted something about segfaults I get when plotting. Now 
here is a little update and I really hope someone has an idea how I can 
solve this problem.
I'm running IPython 0.6.13 on a Debian box, installed the recent mpl 
0.83.2 from source, GTKAgg backend.
1)
When I start ipython (as normal user) with the -pylab option and then say
	plot([1,2,3])
I get
In [1]: plot([1,2,3])
---------------------------------------------------------------------------
exceptions.SystemError Traceback (most 
recent call last)
SystemError: ../Objects/moduleobject.c:48: bad argument to internal function
2)
However when I change to root
	su
	<pwd>
	ipython -pylab
then plotting works fine!?
I have no idea where this moduleobject.c lives or to which application 
it belongs.
2)
If I try the same with the normal python interpreter
	python
	from pylab import *; ion()
	plot([1,2,3])
a plot window pops up but shows no picture (no matter if I'm root or not).
I'll appreciate any hints. Thanx!!
cheers,
steve