matplotlib-users Mailing List for matplotlib

On 08/30/2011 12:14 PM, Craig Finch wrote:
> I successfully built Python 2.7.2, NumPy 1.61, and Scipy 0.9.0 in my
> home directory on a Centos5 system. I am trying to build matplotlib
> 1.0.1 in my home directory, but I am having a problem with the GTK
> backends. I also built pycairo 1.2.2, pygobject 2.14.2, and pygtk 2.10.6
> in my home directory (using the libraries and headers installed in the
> default system locations). I downloaded a few pygtk examples from the
> tutorial section of their web site and ran them to verify that pygtk
> works correctly.
>
> Here is the error I get when I run a script that contains only the line
> "import matplotlib.pyplot":
>
> python2.7 test.py --verbose-helpful
> $HOME=/home/cfinch
> CONFIGDIR=/home/cfinch/.matplotlib
> matplotlib data path
> /home/cfinch/.local/lib/python2.7/site-packages/matplotlib/mpl-data
> loaded rc file
> /home/cfinch/.local/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc
> matplotlib version 1.0.1
> verbose.level helpful
> interactive is False
> units is False
> platform is linux2
> Using fontManager instance from /home/cfinch/.matplotlib/fontList.cache
> Traceback (most recent call last):
> File "test.py", line 1, in <module>
> import matplotlib.pyplot
> File
> "/home/cfinch/.local/lib/python2.7/site-packages/matplotlib/pyplot.py",
> line 95, in <module>
> new_figure_manager, draw_if_interactive, show = pylab_setup()
> File
> "/home/cfinch/.local/lib/python2.7/site-packages/matplotlib/backends/__init__.py",
> line 25, in pylab_setup
> globals(),locals(),[backend_name])
> File
> "/home/cfinch/.local/lib/python2.7/site-packages/matplotlib/backends/backend_gtkagg.py",
> line 10, in <module>
> from matplotlib.backends.backend_gtk import gtk, FigureManagerGTK,
> FigureCanvasGTK,\
> File
> "/home/cfinch/.local/lib/python2.7/site-packages/matplotlib/backends/backend_gtk.py",
> line 28, in <module>
> from matplotlib.backends.backend_gdk import RendererGDK, FigureCanvasGDK
> File
> "/home/cfinch/.local/lib/python2.7/site-packages/matplotlib/backends/backend_gdk.py",
> line 29, in <module>
> from matplotlib.backends._backend_gdk import pixbuf_get_pixels_array
> ImportError: No module named _backend_gdk
>
> Here is the beginning of my matplotlib build log, which shows that the
> build process is actually finding the GTK libraries:
>
> basedirlist is: ['/home/cfinch']
> ============================================================================
> BUILDING MATPLOTLIB
> matplotlib: 1.0.1
> python: 2.7.2 (default, Aug 30 2011, 12:57:00) [GCC 4.1.2
> 20080704 (Red Hat 4.1.2-50)]
> platform: linux2
>
> REQUIRED DEPENDENCIES
> numpy: 1.6.1
> freetype2: 9.10.3
> * WARNING: Could not find 'freetype2' headers in any
> * of '/home/cfinch/include', '.',
> * '/usr/include/freetype2'.

Freetype is a requirement, so my guess is that this is the origin of the 
problem, even though it is is showing up as a puzzling import error for 
_backend_gdk.

Eric


>
> OPTIONAL BACKEND DEPENDENCIES
> libpng: 1.2.10
> Tkinter: no
> * TKAgg requires Tkinter
> wxPython: no
> * wxPython not found
> Gtk+: gtk+: 2.10.4, glib: 2.12.3, pygtk: 2.10.6,
> pygobject: 2.14.2
> Mac OS X native: no
> Qt: no
> Qt4: no
> Cairo: 1.2.2
>
> OPTIONAL DATE/TIMEZONE DEPENDENCIES
> datetime: present, version unknown
> dateutil: 1.5
> pytz: 2010o
>
> OPTIONAL USETEX DEPENDENCIES
> dvipng: 1.5
> ghostscript: 8.70
> latex: 3.141592
> pdftops: 3.00
> ------------ SNIP -----------
>
> There are no errors in the build or install logs, but I can post the
> rest of it if necessary. Also, the library _backend_gdk.so is present in
> ~/lib/python2.7/site-packages/matplotlib/backends/.
>
> Any suggestions would be appreciated!
>

I successfully built Python 2.7.2, NumPy 1.61, and Scipy 0.9.0 in my home directory on a Centos5 system.  I am trying to build matplotlib 1.0.1 in my home directory, but I am having a problem with the GTK backends.  I also built pycairo 1.2.2, pygobject 2.14.2, and pygtk 2.10.6 in my home directory (using the libraries and headers installed in the default system locations).  I downloaded a few pygtk examples from the tutorial section of their web site and ran them to verify that pygtk works correctly.

Here is the error I get when I run a script that contains only the line "import matplotlib.pyplot":

python2.7 test.py --verbose-helpful
$HOME=/home/cfinch
CONFIGDIR=/home/cfinch/.matplotlib
matplotlib data path /home/cfinch/.local/lib/python2.7/site-packages/matplotlib/mpl-data
loaded rc file /home/cfinch/.local/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc
matplotlib version 1.0.1
verbose.level helpful
interactive is False
units is False
platform is linux2
Using fontManager instance from /home/cfinch/.matplotlib/fontList.cache
Traceback (most recent call last):
  File "test.py", line 1, in <module>
    import matplotlib.pyplot
  File "/home/cfinch/.local/lib/python2.7/site-packages/matplotlib/pyplot.py", line 95, in <module>
    new_figure_manager, draw_if_interactive, show = pylab_setup()
  File "/home/cfinch/.local/lib/python2.7/site-packages/matplotlib/backends/__init__.py", line 25, in pylab_setup
    globals(),locals(),[backend_name])
  File "/home/cfinch/.local/lib/python2.7/site-packages/matplotlib/backends/backend_gtkagg.py", line 10, in <module>
    from matplotlib.backends.backend_gtk import gtk, FigureManagerGTK, FigureCanvasGTK,\
  File "/home/cfinch/.local/lib/python2.7/site-packages/matplotlib/backends/backend_gtk.py", line 28, in <module>
    from matplotlib.backends.backend_gdk import RendererGDK, FigureCanvasGDK
  File "/home/cfinch/.local/lib/python2.7/site-packages/matplotlib/backends/backend_gdk.py", line 29, in <module>
    from matplotlib.backends._backend_gdk import pixbuf_get_pixels_array
ImportError: No module named _backend_gdk


Here is the beginning of my matplotlib build log, which shows that the build process is actually finding the GTK libraries:

basedirlist is: ['/home/cfinch']
============================================================================
BUILDING MATPLOTLIB
            matplotlib: 1.0.1
                python: 2.7.2 (default, Aug 30 2011, 12:57:00)  [GCC 4.1.2
                        20080704 (Red Hat 4.1.2-50)]
              platform: linux2

REQUIRED DEPENDENCIES
                 numpy: 1.6.1
             freetype2: 9.10.3
                        * WARNING: Could not find 'freetype2' headers in any
                        * of '/home/cfinch/include', '.',
                        * '/usr/include/freetype2'.

OPTIONAL BACKEND DEPENDENCIES
                libpng: 1.2.10
               Tkinter: no
                        * TKAgg requires Tkinter
              wxPython: no
                        * wxPython not found
                  Gtk+: gtk+: 2.10.4, glib: 2.12.3, pygtk: 2.10.6,
                        pygobject: 2.14.2
       Mac OS X native: no
                    Qt: no
                   Qt4: no
                 Cairo: 1.2.2

OPTIONAL DATE/TIMEZONE DEPENDENCIES
              datetime: present, version unknown
              dateutil: 1.5
                  pytz: 2010o

OPTIONAL USETEX DEPENDENCIES
                dvipng: 1.5
           ghostscript: 8.70
                 latex: 3.141592
               pdftops: 3.00
------------ SNIP -----------

There are no errors in the build or install logs, but I can post the rest of it if necessary.  Also, the library _backend_gdk.so is present in ~/lib/python2.7/site-packages/matplotlib/backends/.

Any suggestions would be appreciated!

Hey Matplotlib users,

Im trying to use the tricontourf function in matplotlib to reduce the complexity of an unstructured dataset into contours.
The resulting contours are retrieved from the path by the to_polygon() function, but i have some trouble distinguishing inner boundaries on the 
polygons, while plot.show() clearly doesn't

Using Matplotlib 1.01, and the attached code, I get one level, consisting of 2 polygons, where the first is the outer boundary, and the second should 
be the inner boundary.
The figure shown by show() correctly displays a square with a inner square cut-out. However i cannot distinguish between inner and outer boundaries in 
the list of polygons that to_polygon() returns.

Is there a trick how the plot functions distinguish inner boundaries? Calculating for each polygon if it is contained in other polygons will become 
complicated with a large number of polygons: As far as i can tell this would be checking if the starting point of each polygon is contained in any of 
the other polygons. Is there a simpler method i missed?

Thanks in advance,
Tijs de Kler

On Mon, Aug 29, 2011 at 10:26 PM, Trevor J Christensen <
tr...@jc...> wrote:

> I have a number of questions, but I'll start with one.  Consider the
> following code:
>
> import matplotlib as mpl
> import matplotlib.pyplot as plt
> import numpy as np
> x = np.arange(1, 6)
> plt.plot(x, x*1.5)
> plt.show()
> s = raw_input('Enter anything to continue:')
> plt.show()
> print 'The end'
>
> Question:  The first plt.show() launches an interactive window.  Control
> returns to the script upon its close.  The second plt.show() does nothing
> that I can see.  Why?
>
> Ubuntu 11.04, Python 2.7.1, Matplotlib 0.99.3
>


That is because closing the figure destroys that object.  If you want full
interactive mode, I suggest updating to v1.0.1 (or the upcoming v1.1.0
release) and use plt.ion().  The show() will trigger the figures to appear,
but control immediately returns to the script.

Interactivity in earlier versions of mpl is a bit more hit-or-miss, so you
can try it out first before updating.  Also note that multiple calls to
plt.show() in earlier versions are not recommended, but are allowed in v1.0
and up.

I hope this helps,
Ben Root

I have a number of questions, but I'll start with one. Consider the following code: 

import matplotlib as mpl 
import matplotlib.pyplot as plt 
import numpy as np 
x = np.arange(1, 6) 
plt.plot(x, x*1.5) 
plt.show() 
s = raw_input('Enter anything to continue:') 
plt.show() 
print 'The end' 

Question: The first plt.show() launches an interactive window. Control returns to the script upon its close. The second plt.show() does nothing that I can see. Why? 

Ubuntu 11.04, Python 2.7.1, Matplotlib 0.99.3 

How about Numpy's loadtxt()?  Genfromtext is more of a specialty function.

Ben Root

On Monday, August 29, 2011, Alexa Villaume <ale...@gm...> wrote:
> Hi there,
> I have a 2d array that I'd like to contour. The plot isn't turning out
right and I think it's because the array isn't be read in correctly.
> It's a 25x41 array that is in a text file. I have tried using genfromtxt
and the asciitable module to read the data in and neither gives the correct
output.
> Does anyone know of any command either specific for reading in 2d arrays
or is able to handle 2d arrays?
> Thanks,
> Alexa

Hi there,

I have a 2d array that I'd like to contour. The plot isn't turning out right
and I think it's because the array isn't be read in correctly.

It's a 25x41 array that is in a text file. I have tried using genfromtxt and
the asciitable module to read the data in and neither gives the correct
output.

Does anyone know of any command either specific for reading in 2d arrays or
is able to handle 2d arrays?

Thanks,
Alexa