matplotlib-users Mailing List for matplotlib

>>>>> "Alan" == Alan G Isaac <ai...@am...> writes:

    Alan> On Sat, 06 Aug 2005, John Hunter apparently wrote:
    >> What version of dvipng are you using, Alan?  I haven't tested
    >> with anything < 1.5

    Alan> I have the version 1.6 distributed with MiKTeX.

    Alan> I have found a few things.  (This is TKAgg only; the
    Alan> backend_ps works fine!)

To keep things as simple as possible, test with the Agg backend

  import matplotlib
  matplotlib.use('Agg')
  import pylab as p
  p.rc('text', usetex=True)
  ...etc...
  p.savefig('test')
  p.show()

and post the complete script and output file (test.png).  Also include
the output of running your script with --verbose-debug-annoying.  That
way I can verify whether your problems are platform specific (win32)
or generic.

    Alan> Focusing on the example at
    Alan> http://www.scipy.org/wikis/topical_software/UsingTex

    Alan> - On the xlabel and ylabel, if I use \bf I get problems
    Alan> (same for \textbf) but with \it I can see the axis labels.
    Alan> It looks like a spacing problem?  - If I delete the
    Alan> \displaystyle command in the title, it almost displays, but
    Alan> all the superscripts are missing in the fraction.  If I then
    Alan> delete \frac I see everything.  Again, it looks like a
    Alan> spacing problem?

    Alan> So actually I am getting substantial functionality at this
    Alan> point, as long as I avoid all bold, all displaystyle math,
    Alan> and \frac.

If you include these commands in a pure latex document, do they work
as expected?  Just verifying that you have a complete LaTeX
installation....

    Alan> - Can I do the following (i.e., is the syntax right)?
    Alan> rc('text.tex', engine='latex') rc('font.latex',
    Alan> package='type1cm') Will this over-ride the settings in
    Alan> matplotlibrc?  

Yes they will; they look right.

    Alan> ~/.tex.cache for reuse between sessions.  Does the tilde
    Alan> here mean the .matplotlib directory *below* the home
    Alan> directory?  

In UNIX, ~ is an alias for HOME

    Alan> Because that's where I find tex.cache (i.e., not right below
    Alan> HOME).  (Note: that's tex.cache, no leading dot in conflict
    Alan> with the docs, but I assume that's ok because

It should be HOME/.matplotlib/tex.cache, where HOME is something like
c:\Documents and Settings\youacct\.matplotlib\tex.cache. I'm working
from memory here...
           
The new .matplotlib dir should have a leading "dot".  The subdirs and
files in this directory (eg matplotlibrc, tex.cache) should not.

If the docs are misleading, please provide a patch or a pointer to
where the docs are wrong.

    Alan> backend_ps works and I am getting some TKAgg functionality
    Alan> as well?)  - Finally, should the tex.cache directory remain
    Alan> full of old cached images?  Forever?

Currently it is forever.  You can always flush this directory if you
want to rebuild it.

JDH

	The problem seems to be alleviated for me now from you latest commit, John.

Thanks,

Fernando Perez wrote:
> Charles Moad wrote:
> 
>> 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.
> 
> 
> Since it's really a python bug, I'd rather see it fixed upstream than 
> adding (yet another) hack in ipython to defend against it.  But I also 
> don't want ipython to crash for users, that's for sure.
> 
> Let's see if John can get his pycxx animals to grow a __repr__, which 
> will fix the issue.  If that doesn't work, I'll go ahead and stick in a 
> version-specific defense layer into Prompts.py to at least help the 
> ipython users, while python fixes the problem upstream.
> 
> Cheers,
> 
> f

Hi,

I'm working with support from the Python Software Foundation to develop
an open source course on basic software development skills for people
with backgrounds in science and engineering.  I have a beta version of
the course notes ready for review, and would like to pull in people
in sci&eng to look it over and give me feedback.  If you know anyone
who fits this bill (particularly people who might be interested in
following along with a trial run of the course this fall), I'd be
grateful for pointers.

Thanks,
Greg Wilson

Steve Schmerler wrote:

> I upgraded to IPython 0.6.15 (installed from source), the former 0.6.13 
> was apt-get installed on Debian (sarge, stable).
> 
> Actually, it is a segfault, and it kills the IPython shell.
> 
> ###############################################################################
> 
> elcorto@bach:~/Install/IPython$ ipython -pylab
> /usr/lib/python2.3/site-packages/IPython/Shell.py:627: 
> GtkDeprecationWarning: gtk.timeout_add is deprecated, use 
> gobject.timeout_add instead
>    self.gtk.timeout_add(self.TIMEOUT, self.on_timer)
> Python 2.3.5 (#2, May  4 2005, 08:51:39)
> Type "copyright", "credits" or "license" for more information.
> 
> IPython 0.6.15 -- 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.
> 
>    Welcome to pylab, a matplotlib-based Python environment.
>    For more information, type 'help(pylab)'.
> 
> In [1]: plot([1,2,3])
> ---------------------------------------------------------------------------
> exceptions.SystemError                               Traceback (most 
> recent call last)
> 
> 
> SystemError: ../Objects/moduleobject.c:48: bad argument to internal function
> Speicherzugriffsfehler
> elcorto@bach:~/Install/IPython$
> 
> #################################################################################
> 
> At least "Speicherzugriffsfehler" is german for segfault :)
> 
> I still can plot as root, but not as user!? If it's some kind of 
> permission problem it would be good to know something about
> "../Objects/moduleobject.c". I there a way to get IPython to print the 
> full path?

No, unfortunately the string:

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

is being generated internally, so the path has already been truncated by 
somebody else.  IPython has no access to any more info than this, as that 
string is the value of the exception given to the ipython traceback handler. 
You can try setting '%xmode verbose' in ipython to produce more verbose 
tracebacks, but I doubt we'll see anything more meaningful in this particular 
case (since there don't seem to be any frames properly generated in the 
traceback).

This is really strange.  I can only suggest trying some of the other backends 
(QtAgg, TKAgg, WXAgg) and seeing what happens.  But we're really debugging in 
the dark here.

> BTW, Fernando mentioned earlier that this GtkDeprecationWarning would go 
> away if I upgrade to IPython 0.6.15 but unfortunately it's still there.

Sorry, I should have clarified that this change was made to SVN, _right after_ 
we released .15.  So only an SVN install would make it go away (or manually 
applying the relevant fix).  If it really bothers you, I can track down the 
exact changes needed for you.

Cheers,

f

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?

I upgraded to IPython 0.6.15 (installed from source), the former 0.6.13 
was apt-get installed on Debian (sarge, stable).

Actually, it is a segfault, and it kills the IPython shell.

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

elcorto@bach:~/Install/IPython$ ipython -pylab
/usr/lib/python2.3/site-packages/IPython/Shell.py:627: 
GtkDeprecationWarning: gtk.timeout_add is deprecated, use 
gobject.timeout_add instead
   self.gtk.timeout_add(self.TIMEOUT, self.on_timer)
Python 2.3.5 (#2, May  4 2005, 08:51:39)
Type "copyright", "credits" or "license" for more information.

IPython 0.6.15 -- 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.

   Welcome to pylab, a matplotlib-based Python environment.
   For more information, type 'help(pylab)'.

In [1]: plot([1,2,3])
---------------------------------------------------------------------------
exceptions.SystemError                               Traceback (most 
recent call last)


SystemError: ../Objects/moduleobject.c:48: bad argument to internal function
Speicherzugriffsfehler
elcorto@bach:~/Install/IPython$

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

At least "Speicherzugriffsfehler" is german for segfault :)

I still can plot as root, but not as user!? If it's some kind of 
permission problem it would be good to know something about
"../Objects/moduleobject.c". I there a way to get IPython to print the 
full path?

BTW, Fernando mentioned earlier that this GtkDeprecationWarning would go 
away if I upgrade to IPython 0.6.15 but unfortunately it's still there.

> 
> 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.
> 

This works, a window shows up.

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

elcorto@bach:~/Install/IPython$ python test.py --verbose-helpful
matplotlib data path /usr/share/matplotlib
$HOME=/home/elcorto
CONFIGDIR=/home/elcorto/.matplotlib
loaded rc file /usr/share/matplotlib/matplotlibrc
matplotlib version 0.83.2
verbose.level helpful
interactive is False
platform is linux2
numerix Numeric 23.8
font search path ['/usr/share/matplotlib']
loaded ttfcache file /home/elcorto/.matplotlib/ttffont.cache
backend GTKAgg version 2.6.1

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

> 
>     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&
> 

I can do that.

> 
> 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).
> 
> 

Debian sarge, stable. I'm not a Linux expert but it's a pretty fresh 
installation (on my computer at work) and I can't see what I should have 
done wrong. In fact I installed mpl on my (the same) Debian at home and 
it works fine there (OK it's mpl 0.81 and IPython 0.6.13).

> 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.
> 

Uh, I didn't build TkAgg, So I set BUILD_TKAGG = 'auto', but

	python setup.py build

fails:

[...]

src/_tkagg.cpp:26:19: tk.h: Datei oder Verzeichnis nicht gefunden (file
not found)

[...]

error: command 'gcc' failed with exit status 1

Do I have to install something besides python-tk?

> 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.
> 
> 

I hope we can sort this out.

cheers,
steve

Hi list,

I successefully draw and add a matplotlib figure in a notebook page.
Thanks to John Hunter and it's powerfull FigureCanvasGTK.

I add a navigationToolbar2GTK.
But now, i am stuck to have callbacks when a button is pressed. Even the 
selection drawned when we use the zoom is not displayed.

How can i easily used callbacks ever written instead of rewriting all of 
them?
Thanks a lot,
Philippe Collet

John Hunter wrote:
>>>>>>"Steve" == Steve Schmerler <el...@gm...> writes:
> 
> 
>     Steve> I still can plot as root, but not as user!? If it's some
> 
> That I find bizarre.  Could it be a PATH or an LD_LIBRARY_PATH issue;
> ie, you and root are using different libraries.  Have you customized
> either of these variables?  For example, if you do the following as
> yourself and root, do you get the same link information
> 
>   > ldd /usr/lib/python2.4/site-packages/matplotlib/_nc_transforms.so 

I'm using Python 2.3.5, but

no, both:

           libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0x4009e000)
           libm.so.6 => /lib/tls/libm.so.6 (0x40159000)
           libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x4017b000)
           libpthread.so.0 => /lib/tls/libpthread.so.0 (0x40184000)
           libc.so.6 => /lib/tls/libc.so.6 (0x40193000)
           /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x80000000)


>   > ldd /usr/lib/python2.4/site-packages/Numeric/_numpy.so

no, both:

           libpthread.so.0 => /lib/tls/libpthread.so.0 (0x40026000)
           libc.so.6 => /lib/tls/libc.so.6 (0x40036000)
           /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x80000000)


> 
>     Steve> kind of permission problem it would be good to know
>     Steve> something about "../Objects/moduleobject.c". I there a way
>     Steve> to get IPython to print the full path?
> 
> This is part of python -- if you install python-dev you should be able
> to find the header on your system, eg at
> 
>   /usr/include/python2.4/moduleobject.h
>

Yes, I have this one (/usr/include/python2.3/moduleobject.h).

> 
>     Steve> Uh, I didn't build TkAgg, So I set BUILD_TKAGG = 'auto',
>     Steve> but
> 
> 
>     Steve> Do I have to install something besides python-tk?
> 
> You need the tk8.4-dev and maybe the tcl8.4-dev headers.  You may have
> a different version number.
> 

Ah OK. That does it.

> 
>     Steve> I hope we can sort this out.
> 
> Two other things to try.
> 
>   1) See if we can narrow down where the segfault is occurring by trying
>      to import the matplotlib modules separately
> 
>       import matplotlib.ft2font
>       import matplotlib._transforms
>       import matplotlib._agg
>       import matplotlib.backends._backend_agg
>       
> 

I hope this was what you ment:

ipython -pylab and then

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

In [1]: import matplotlib.ft2font

In [2]: import matplotlib._transforms

In [3]: import matplotlib._agg

In [4]: import matplotlib.backends._backend_agg
---------------------------------------------------------------------------
exceptions.ImportError                               Traceback (most
recent call last)

/home/elcorto/Install/Matplotlib/matplotlib-0.83.2/<console>

ImportError: No module named _backend_agg

In [5]: import matplotlib.backends._gtkagg

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


>   2) Compile matplotlib with 
> 
>       VERBOSE =  True

OK this prints a lot. I did

	python setup.py build > build_log.txt

It then prints some additional output which I pasted into
build_log2.txt. I hope this helps in any way.

I attached my setup.py and the *.txt files.


BTW, I installed the .debs (mpl 0.82)

	from http://anakonda.altervista.org (on the mpl website)

and this works!


cheers,
steve

Hi all:

I've added a new cookbook wiki item on plotting data on map projections 
with the basemap toolkit.

http://www.scipy.org/wikis/topical_software/Maps

Comments are welcome.

-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

Charles Moad wrote:
> 	The problem seems to be alleviated for me now from you latest commit, John.

OK, thanks for the info.  I'll leave Prompts.py alone for now then.

Cheers,

f

John Hunter wrote:
>>>>>>"Steve" == Steve Schmerler <el...@gm...> writes:
> 
> 
>     Steve> I still can plot as root, but not as user!? If it's some
> 
> That I find bizarre.  Could it be a PATH or an LD_LIBRARY_PATH issue;
> ie, you and root are using different libraries.  Have you customized
> either of these variables?  For example, if you do the following as
> yourself and root, do you get the same link information
> 
>   > ldd /usr/lib/python2.4/site-packages/matplotlib/_nc_transforms.so 

I'm using Python 2.3.5, but

no, both:

          libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0x4009e000)
          libm.so.6 => /lib/tls/libm.so.6 (0x40159000)
          libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x4017b000)
          libpthread.so.0 => /lib/tls/libpthread.so.0 (0x40184000)
          libc.so.6 => /lib/tls/libc.so.6 (0x40193000)
          /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x80000000)


>   > ldd /usr/lib/python2.4/site-packages/Numeric/_numpy.so

no, both:

          libpthread.so.0 => /lib/tls/libpthread.so.0 (0x40026000)
          libc.so.6 => /lib/tls/libc.so.6 (0x40036000)
          /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x80000000)


> 
>     Steve> kind of permission problem it would be good to know
>     Steve> something about "../Objects/moduleobject.c". I there a way
>     Steve> to get IPython to print the full path?
> 
> This is part of python -- if you install python-dev you should be able
> to find the header on your system, eg at
> 
>   /usr/include/python2.4/moduleobject.h
>

Yes, I have this one (/usr/include/python2.3/moduleobject.h).

> 
>     Steve> Uh, I didn't build TkAgg, So I set BUILD_TKAGG = 'auto',
>     Steve> but
> 
> 
>     Steve> Do I have to install something besides python-tk?
> 
> You need the tk8.4-dev and maybe the tcl8.4-dev headers.  You may have
> a different version number.
> 

Ah OK. That does it.

> 
>     Steve> I hope we can sort this out.
> 
> Two other things to try.
> 
>   1) See if we can narrow down where the segfault is occurring by trying
>      to import the matplotlib modules separately
> 
>       import matplotlib.ft2font
>       import matplotlib._transforms
>       import matplotlib._agg
>       import matplotlib.backends._backend_agg
>       
> 

I hope this was what you ment:

ipython -pylab and then

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

In [1]: import matplotlib.ft2font

In [2]: import matplotlib._transforms

In [3]: import matplotlib._agg

In [4]: import matplotlib.backends._backend_agg
---------------------------------------------------------------------------
exceptions.ImportError                               Traceback (most
recent call last)

/home/elcorto/Install/Matplotlib/matplotlib-0.83.2/<console>

ImportError: No module named _backend_agg

In [5]: import matplotlib.backends._gtkagg

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


>   2) Compile matplotlib with 
> 
>       VERBOSE =  True

OK this prints a lot. I did

	python setup.py build > build_log.txt

It then prints some additional output which I pasted into
build_log2.txt. I hope this helps in any way.

I attached my setup.py and the *.txt files.


BTW, I installed the .debs (mpl 0.82)

	from http://anakonda.altervista.org (on the mpl website)

and this works!


cheers,
steve