matplotlib-users Mailing List for matplotlib

Dear matplotlib-users,
I would appreciate some help installing matplotlib on fedora core 3.
After an initial unsuccessful build using gtk I decided to try to avoid
the pygtk 2.4 problem http://matplotlib.sourceforge.net/faq.html#PYGTK24
I therefore changed two lines in setup.py so that it now reads
BUILD_GTKAGG = 0
#BUILD_GTKAGG = 'auto'
#BUILD_GTK = 'auto'
BUILD_GTK = 0
After that the build and install went smoothly. But now if I try to
import pylab I get the following error:
>>> import pylab
Traceback (most recent call last):
 File "<stdin>", line 1, in ?
 File "/usr/lib/python2.3/site-packages/pylab.py", line 1, in ?
 from matplotlib.pylab import *
 File "/usr/lib/python2.3/site-packages/matplotlib/pylab.py", line 196,
in ?
 import backends
 File "/usr/lib/python2.3/site-
packages/matplotlib/backends/__init__.py", line 19, in ?
 globals(),locals(),[backend_name])
 File "/usr/lib/python2.3/site-
packages/matplotlib/backends/backend_gtkagg.py", line 10, in ?
 from backend_gtk import gtk, FigureManagerGTK, FigureCanvasGTK,\
 File "/usr/lib/python2.3/site-
packages/matplotlib/backends/backend_gtk.py", line 20, in ?
 from backend_gdk import RendererGDK
 File "/usr/lib/python2.3/site-
packages/matplotlib/backends/backend_gdk.py", line 44, in ?
 from matplotlib._nc_backend_gdk import pixbuf_get_pixels_array
ImportError: No module named _nc_backend_gdk
>>>
As far as I can see it is still trying to use some gtk-stuff?
I have tried removing the site-packages/matplotlib directory completely
and also do a new build and install from a fresh tarball with only the
above mentioned two changes in setup.py, but still I get the error.
 
Any help would be appreciated.
Karsten.

>>>>> "ravi" == ravi <ra...@gm...> writes:
 ravi> Hi, I just upgraded to 0.80 from 0.73.1 on a Fedora Core 3
 ravi> machine. I am (and have been) using ipython 0.6.13 as my
 ravi> shell. After the upgrade, plots from scripts are no longer
 ravi> interactive - I need an explicit call to pylab.show() to
 ravi> show the plots.
 ravi> Do I need to update some settings? I am using the GTKAgg
 ravi> backend with all default parameters (no user-specific
 ravi> .matplotlibrc) and I compiled matplotlib from sources. Here
 ravi> is a simple script that no longer updates 100 times but just
 ravi> shows once:
Fernando and I made a conscious choice to turn off interactive mode
when running scripts from ipython, since this is usually what people
want and has better performance. To override this, to need to
explicitly turn on/and off interactive mode where desired, and
possibly explicitly call draw in the animation loop where you want the
figure to be refreshed.
 import scipy
 import matplotlib
 from matplotlib import pylab
 pylab.ion() # turn on interactive mode
 for x in scipy.arange(100):
 pylab.plot(scipy.randn(1000)+x)
 pylab.show()
You can turn interactive mode on and off where desired with pylab.ion
and pylab.ioff (to suppress draws for a sequence of figure updates)
and explicitly draw where desired with pylab.draw. Details at
http://matplotlib.sf.net/interactive.html.
JDH

Hi,
 I just upgraded to 0.80 from 0.73.1 on a Fedora Core 3 machine. I am (and=
=20
have been) using ipython 0.6.13 as my shell. After the upgrade, plots from=
=20
scripts are no longer interactive - I need an explicit call to pylab.show()=
=20
to show the plots.=20
Do I need to update some settings? I am using the GTKAgg backend with all=20
default parameters (no user-specific .matplotlibrc) and I compiled matplotl=
ib=20
from sources. Here is a simple script that no longer updates 100 times but=
=20
just shows once:
import scipy
import matplotlib
from matplotlib import pylab
#matplotlib.interactive(True)
for x in scipy.arange(100):
 pylab.plot(scipy.randn(1000)+x)
=46rom the ipython prompt, I issued the command
 run scriptAbove.py
where ipython was invoked as follows:
 ipython -pylab -p scipy
Is this an ipython issue or a matplotlib issue? Any help greatly appreciate=
d.
Regards,
Ravi

Bingo! One upgrade to the latest numarray and everything works fine.
Many thanks for your help.
Mike.
On 4/25/05, Jeff Whitaker <js...@fa...> wrote:
> Mike Elson wrote:
>=20
> >Hello Jeff,
> >
> >I tried loading the file etopo20.pickle by itself but got the same error=
:
> >
> >import cPickle
> >a =3D cPickle.load(open('etopo20.pickle','rb'))
> >
> >Traceback (most recent call last):
> > File "<stdin>", line 1, in ?
> > 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 0xb71e48b4>, (<class
> >'numarray.numarraycore.NumArray'>, {'_type': 'Floa\t32', '_itemsize':
> >4, '_shape': (1081,), '_bytestride': 4, '_byteoffset': 0, '_\version':
> >'1.1', '_byteorder': 'big', '_data': <memory at 082ee9a0 with
> >size:4324円 held by object 082ee980 aliasing object 00000000>,
> >'_strides': (4,)}))
> >
> >Looking at etopo20.pickle itself, the 4th line reads
> >'cnumarray.generic' - I'm guessing that means it is stored using
> >numarray.
> >Do I need a specific version of python or numarray to read it? I have
> >both Numeric (23.1) and numarray installed already.
> >
> >Mike.
> >
> >
> >
> Mike: Not that I know of. I'm puzzled by this one. You said in your
> first message that you are using numarray 0.8 - I think that might be
> too old. It's up to 1.3.1 now, and I'm sure I created that pickle with
> at least 1.1.
>=20
> -Jeff
>=20
> --
> 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
>=20
>

Daniel Wheeler wrote:
> Is there a way to obtain the version number of Matplotlib from the 
> python command line?
> Such as "pylab.__version__'" for example, but that does not seem to work.
matplotlib.__version__
-- 
Robert Kern
rk...@uc...
"In the fields of hell where the grass grows high
 Are the graves of dreams allowed to die."
 -- Richard Harter

>>>>> "Daniel" == Daniel Wheeler <dan...@ni...> writes:
 Daniel> Is there a way to obtain the version number of Matplotlib
 Daniel> from the python command line? Such as
 Daniel> "pylab.__version__'" for example, but that does not seem
 Daniel> to work.
You can do this:
 > python -c 'import matplotlib; print matplotlib.__version__'
Or you can run your matplotlib scripts with:
 > python myscript.py --verbose-helpful
to get the version info and more.
JDH

Is there a way to obtain the version number of Matplotlib from the 
python command line?
Such as "pylab.__version__'" for example, but that does not seem to 
work.
Thanks...
-------------------------------------
Daniel Wheeler
Telephone: (301) 975-8358

>>>>> "steve" == steve schmerler <el...@gm...> writes:
 steve> Hi all I'm new to this list (but an active SciPy user). I
 steve> just installed the latest matplotlib 0.80 on WinXP, Python
 steve> 2.3.4, Numeric 23.8. A while ago I used matplotlib 0.61
 steve> together with Numeric 23.1 which worked pretty well. But
 steve> now I get the following error:
Do you get the error when you simply import gzip w/o importing
matplotlib or zlib? If so, you've got a problem unrelated to
matplotlib. If not, then the error may have something to do with the
fact that we're statically linking in zlib.
You can safely comment this import out of pylab. It is only used for
transparently loading and saving zipped files. But please let me know
about the results of the gzip import test....
JDH

Hi all
I'm new to this list (but an active SciPy user).
I just installed the latest matplotlib 0.80 on WinXP, Python 2.3.4, Numeric 23.8. A while ago I used matplotlib 0.61 
together with Numeric 23.1 which worked pretty well. But now I get the following error:
In [1]: from pylab import *
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
C:\Dokumente und Einstellungen\user\Eigene Dateien\<console>
C:\PROGRA~1\Python23\Lib\site-packages\pylab.py
 -3 from matplotlib.pylab import *
C:\PROGRA~1\Python23\Lib\site-packages\matplotlib\pylab.py
 188 """
 189
--> 190 import gzip
 191 import cm
 192 import _pylab_helpers
C:\PROGRA~1\Python23\Lib\gzip.py
 7
 8 import struct, sys, time
----> 9 import zlib
 10 import __builtin__
 11
ImportError: dynamic module does not define init function (initzlib)
I've never seen this error message before. Any hints are appreciated. Many thanks.
Cheers,
Steve
-- 
Man is the best computer we can put aboard a spacecraft ... and the only one that can be
mass produced with unskilled labor. - Wernher von Braun

>>>>> "Michal" == Michal Kaukic <mi...@fr...> writes:
 Michal> Hi, John and all, is the recent patch for use of masked
 Michal> data in plotting lines (and contours) working? What is
 Michal> the simplest example of using it?
 Michal> I got this with recent CVS
I don't know how this bug crept into CVS (but I'm sure it's my fault),
but you need to edit the add_line function in Axes in the section
which reads
 xdata = l.get_xdata()
 ydata = l.get_ydata()
and replace it with
 xdata = l.get_xdata(valid_only=True)
 ydata = l.get_ydata(valid_only=True)
Also, FYI,
 > python examples/masked_demo.py -numarray
should be 
 > python examples/masked_demo.py --numarray
JDH

Hi, John and all,
 is the recent patch for use of masked data in plotting lines (and contours) working?
What is the simplest example of using it?
I got this with recent CVS 
 python examples/masked_demo.py -numarray :
 
Traceback (most recent call last):
 File "examples/masked_demo.py", line 19, in ?
 lines = plot(x, y, 'r', x, ym1, 'g', x, ym2, 'bo')
 File "/usr/lib/python2.3/site-packages/matplotlib/pylab.py", line 1930, in plot
 ret = gca().plot(*args, **kwargs)
 File "/usr/lib/python2.3/site-packages/matplotlib/axes.py", line 2411, in plot
 self.add_line(line)
 File "/usr/lib/python2.3/site-packages/matplotlib/axes.py", line 739, in add_line
 self.update_datalim_numerix( xdata, ydata )
 File "/usr/lib/python2.3/site-packages/matplotlib/axes.py", line 724, in update_datalim_numerix
 self.dataLim.update_numerix(x, y, not self.has_data())
TypeError: Bbox::update_numerix expected numerix array
This is independent from using Numeric or numarray. Some grepp-ing of source shows that this
"TypeError" message comes from src/_transforms.cpp (lines 439, 445). 
This short code fragment (lines 426-439 of src/_transforms.cpp) should make clear where the error occured: 
Py::Object
Bbox::update_numerix(const Py::Tuple &args) {
 //update the boox from the numerix arrays x and y
 _VERBOSE("Bbox::update_numerix");
 args.verify_length(3);
 Py::Object xo = args[0];
 Py::Object yo = args[1];
 PyArrayObject *x = (PyArrayObject *) PyArray_ContiguousFromObject(xo.ptr(), PyArray_DOUBLE, 1,1);
 if (x==NULL)
 throw Py::TypeError("Bbox::update_numerix expected numerix array");
---------------------------------------------------------------------------------------------------
So, the trouble is with converting class MaskedArray to (Numeric) array. Sorry, I am not able 
to help with the fix. I wonder, if someone can run the masked_demo.py successfully.
 Mike

Tim Leslie <ti...@cs...> writes:
> On 2005年4月24日, 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.
You might also want to have a look at Christopher James' topogs for matlab
<http://www.soton.ac.uk/~jamescj/research-downloads.html>
If you have matlab than rather than porting topogs you could just easily use
it access it from python through mlabwrap (<http://mlabwrap.sourceforge.net>)
-- as I did myself. Of course it would be even nicer to have somthing like it
available in plain python.
'as