matplotlib-users Mailing List for matplotlib

Can matplotlib be used in scripts with multiple processes, such as
when using the multiprocessing module?

I had some difficulty getting code to work in which I was carrying out
some long computations and wanted to show intermediate results in a
separate process so as not to interrupt the main computation. The
problem distilled down to trying to use the multiprocessing module and
matplotlib together. This is a code snippet which I expected to work,
but doesn't. Is this a matplotlib issue, some intricate issue with
GUIs and processes, or something with my understanding of the subject?

Would you expect this code to work? Is there any easy workaround?

from pylab import *
import multiprocessing
class myclass(object):
    def plotter(self):
        plot([1,2,3,4])
        show()		
    def mainfunction(self):
        a = arange(1, 10, 0.1)
        newprocess = multiprocessing.Process(target=self.plotter)
        newprocess.start()
        newprocess.join()
        plot(a, sin(a))
        show()
if __name__== '__main__':
    a = myclass()	
    a.mainfunction()

Thanks,
Sameer

Hi,
I am trying to change the format of the tick labels in a loglog plot from
exponential to decimal.
Right now the labels are   10^2 10 1 10^-1 10^-2
and I would like them to be   100 10 1 0.1 0.01

I tried finding easy explanations in the web with no luck. By the way I have
no clue what a class is
and the word instantiation makes me crossed eyed

If any charitable soul would help me I would greatly appreciate it

gino

> On Sun, 31 Oct 2010, David Kremer wrote:
> >  File
> >  "/usr/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py",
> 
> python 2.7 ^^
> 
> > RuntimeError: Could not open facefile /usr/lib/python2.6/site-
> > packages/matplotlib/mpl-data/fonts/ttf/Vera.ttf; Cannot_Open_Resource
> 
> python 2.6 ^^
> 
> I believe this problem is fixed in the next matplotlib release.  A
> workaround is to remove a local font cache file:
> 
> rm ~/.matplotlib/fontList.cache
> 
> HTH,
> daryl
It worked. Thank you.

I also did a symbolic link, but your method worked, so I deleted it.

Thank you.

David

On Sun, 31 Oct 2010, David Kremer wrote:

>  File "/usr/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py",

python 2.7 ^^

> RuntimeError: Could not open facefile /usr/lib/python2.6/site-
> packages/matplotlib/mpl-data/fonts/ttf/Vera.ttf; Cannot_Open_Resource

python 2.6 ^^

I believe this problem is fixed in the next matplotlib release.  A 
workaround is to remove a local font cache file:

rm ~/.matplotlib/fontList.cache

HTH,
daryl

Hello, Im running the last matplotlib version.

I just want to plot an histogram. Here is the complete backtrace, complaining 
about the Vera.ttf font missing :

Any idea ?

Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/matplotlib/backends/backend_gtk.py", 
line 393, in expose_event
    self._render_figure(self._pixmap, w, h)
  File "/usr/lib/python2.7/site-packages/matplotlib/backends/backend_gtkagg.py", 
line 75, in _render_figure
    FigureCanvasAgg.draw(self)
  File "/usr/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py", 
line 394, in draw
    self.figure.draw(self.renderer)
  File "/usr/lib/python2.7/site-packages/matplotlib/artist.py", line 55, in 
draw_wrapper
    draw(artist, renderer, *args, **kwargs)
  File "/usr/lib/python2.7/site-packages/matplotlib/figure.py", line 798, in draw
    func(*args)
  File "/usr/lib/python2.7/site-packages/matplotlib/artist.py", line 55, in 
draw_wrapper
    draw(artist, renderer, *args, **kwargs)
  File "/usr/lib/python2.7/site-packages/matplotlib/axes.py", line 1934, in draw
    a.draw(renderer)
  File "/usr/lib/python2.7/site-packages/matplotlib/artist.py", line 55, in 
draw_wrapper
    draw(artist, renderer, *args, **kwargs)
  File "/usr/lib/python2.7/site-packages/matplotlib/axis.py", line 1017, in draw
    tick.draw(renderer)
  File "/usr/lib/python2.7/site-packages/matplotlib/artist.py", line 55, in 
draw_wrapper
    draw(artist, renderer, *args, **kwargs)
  File "/usr/lib/python2.7/site-packages/matplotlib/axis.py", line 234, in draw
    self.label1.draw(renderer)
  File "/usr/lib/python2.7/site-packages/matplotlib/artist.py", line 55, in 
draw_wrapper
    draw(artist, renderer, *args, **kwargs)
  File "/usr/lib/python2.7/site-packages/matplotlib/text.py", line 524, in draw
    bbox, info = self._get_layout(renderer)
  File "/usr/lib/python2.7/site-packages/matplotlib/text.py", line 298, in 
_get_layout
    ismath=False)
  File "/usr/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py", 
line 180, in get_text_width_height_descent
    font = self._get_agg_font(prop)
  File "/usr/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py", 
line 221, in _get_agg_font
    font = FT2Font(str(fname))
RuntimeError: Could not open facefile /usr/lib/python2.6/site-
packages/matplotlib/mpl-data/fonts/ttf/Vera.ttf; Cannot_Open_Resource

Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/matplotlib/backends/backend_gtk.py", 
line 393, in expose_event
    self._render_figure(self._pixmap, w, h)
  File "/usr/lib/python2.7/site-packages/matplotlib/backends/backend_gtkagg.py", 
line 75, in _render_figure
    FigureCanvasAgg.draw(self)
  File "/usr/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py", 
line 394, in draw
    self.figure.draw(self.renderer)
  File "/usr/lib/python2.7/site-packages/matplotlib/artist.py", line 55, in 
draw_wrapper
    draw(artist, renderer, *args, **kwargs)
  File "/usr/lib/python2.7/site-packages/matplotlib/figure.py", line 798, in draw
    func(*args)
  File "/usr/lib/python2.7/site-packages/matplotlib/artist.py", line 55, in 
draw_wrapper
    draw(artist, renderer, *args, **kwargs)
  File "/usr/lib/python2.7/site-packages/matplotlib/axes.py", line 1934, in draw
    a.draw(renderer)
  File "/usr/lib/python2.7/site-packages/matplotlib/artist.py", line 55, in 
draw_wrapper
    draw(artist, renderer, *args, **kwargs)
  File "/usr/lib/python2.7/site-packages/matplotlib/axis.py", line 1017, in draw
    tick.draw(renderer)
  File "/usr/lib/python2.7/site-packages/matplotlib/artist.py", line 55, in 
draw_wrapper
    draw(artist, renderer, *args, **kwargs)
  File "/usr/lib/python2.7/site-packages/matplotlib/axis.py", line 234, in draw
    self.label1.draw(renderer)
  File "/usr/lib/python2.7/site-packages/matplotlib/artist.py", line 55, in 
draw_wrapper
    draw(artist, renderer, *args, **kwargs)
  File "/usr/lib/python2.7/site-packages/matplotlib/text.py", line 524, in draw
    bbox, info = self._get_layout(renderer)
  File "/usr/lib/python2.7/site-packages/matplotlib/text.py", line 298, in 
_get_layout
    ismath=False)
  File "/usr/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py", 
line 180, in get_text_width_height_descent
    font = self._get_agg_font(prop)
  File "/usr/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py", 
line 221, in _get_agg_font
    font = FT2Font(str(fname))
RuntimeError: Could not open facefile /usr/lib/python2.6/site-
packages/matplotlib/mpl-data/fonts/ttf/Vera.ttf; Cannot_Open_Resource

On Wed, Oct 27, 2010 at 10:36 PM, Matthieu Huin
<mat...@wa...> wrote:
> Anyone knows of a comprehensive doc or tutorial on that subject ?

Unfortunately there is no such things as far as I know.

The agg_filter itself has relatively simple api (from the
documentation of backend_agg.stop_filter).

        """
        Save the plot in the current canvas as a image and apply
        the *post_processing* function.

           def post_processing(image, dpi):
             # ny, nx, depth = image.shape
             # image (numpy array) has RGBA channels and has a depth of 4.
             ...
             # create a new_image (numpy array of 4 channels, size can be
             # different). The resulting image may have offsets from
             # lower-left corner of the original image
             return new_image, offset_x, offset_y

        The saved renderer is restored and the returned image from
        post_processing is plotted (using draw_image) on it.
        """

So, any callable object with above api can be used as a filter. And
the classes in the above example describes just one way to create such
filters.

The agg_filter functionality is a very experimental feature. While I
contributed the example code, I myself rarely use this feature. And
I'm afraid that I may not be able to find enough time to maintain
and/or improve the code.

Regards,

-JJ

On 10/31/10 5:44 AM, John wrote:
> Jeff,
>
> I just built netcdf with the following script:
>
> #!/bin/bash
>
> ./configure --enable-netcdf-4 --enable-hdf4 --enable-hdf4-file-tests
> --enable-pnetcdf --enable-cxx-4 --with-hdf5=/flex_wrk/lib64
> --enable-shared --prefix=/flex_wrk/lib64
> make
> make install

John:  You forget --with-hdf4=<where hdf4 is installed>.

-Jeff
>
> Everything seemed to work fine.
>
> I then rebuilt netcdf4-python and got no errors.
> IE:
> export HDF5_DIR=/flex_wrk/lib64
> export NETCDF4_DIR=/flex_wrk/lib64
> python setup.py build
> python setup.py install --prefix=/custom...
>
> However, when I try to read a hdf4 file in Ipython I get:
> In [1]: from netCDF4 import Dataset as NetCDFFile
>
> In [2]: nci = NetCDFFile('scia_200910.hdf')
> ---------------------------------------------------------------------------
> RuntimeError                              Traceback (most recent call last)
>
> /xnilu_wrk/flex_wrk/EMISSIONS/<ipython console>  in<module>()
>
> /xnilu_wrk/flex_wrk/bin64/site-packages/netCDF4.so in
> netCDF4.Dataset.__init__ (netCDF4.c:6336)()
>
> RuntimeError: Attempt to use feature that was not turned on when
> netCDF was built.
>
>
> What is it that I need to do to 'build' netCDF and netcdf4-python with
> the support?
>
> Thank you,
> john
>
>
> On Sun, Oct 31, 2010 at 2:53 AM, Jeff Whitaker<js...@fa...>  wrote:
>> On 10/30/10 5:05 PM, John wrote:
>>> Thank you. I didn't think they used it, I just wanted to know if it
>>> was safe to do what you suggested to try. It does seem to work.
>>>
>>> Another question, can netcd4-python READ HDF files? Or is it just that
>>> it creates files that are readable? If it's the latter, does anyone
>>> have a suggestion for a python module that can read both hdf4 and
>>> hdf5??
>>>
>>> Thank you,
>>> john
>>>
>>>
>>> PS: Jeff, this module seems to work very well! And I am very thankful
>>> for the introduction of compression.
>> John: If you enabled hdf4 support when you built the netcdf lib, it will
>> read hdf4 files in 'scientific dataset' files.
>>
>> -Jeff
>>>
>>> On Sat, Oct 30, 2010 at 2:55 PM, Jeff Whitaker<js...@fa...>    wrote:
>>>>   On 10/30/10 3:41 AM, John wrote:
>>>>> I've searched through the netcdf4-python trunk, but I find no
>>>>> reference of NetCDFFile as in how the basemap or Scientific.IO.NetCDF
>>>>> modules use it.
>>>>>
>>>>> For compatibility with my old scripts, is it safe to simply:
>>>>>
>>>>> from netCDF4 import Dataset as NetCDFFile
>>>>>
>>>>> ??
>>>>>
>>>>> Thanks,
>>>>> john
>>>>>
>>>> John:  Neither basemap or Scientific.IO.NetCDF uses it.  What gave you
>>>> the impression they did?  There is a 'NetCDFFile' in function in
>>>> basemap, but it is based on the pure-python netCDF module pupynere. It
>>>> doesn't support netcdf-4 and I only recommend using it for the
>>>> occasional light use.
>>>>
>>>> The netcdf4-python API is mostly compatible with Scientific.IO.NetCDF,
>>>> so if you have old script that use the latter, you can try:
>>>>
>>>> from netCDF4 import Dataset as NetCDFFile
>>>>
>>>> The docs for netcdf4-python are at
>>>>
>>>> http://netcdf4-python.googlecode.com/svn/trunk/docs/netCDF4-module.html
>>>>
>>>>
>>>> -Jeff
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Nokia and AT&T present the 2010 Calling All Innovators-North America
>>>> contest
>>>> Create new apps&    games for the Nokia N8 for consumers in  U.S. and
>>>> Canada
>>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in
>>>> marketing
>>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>>>> http://p.sf.net/sfu/nokia-dev2dev
>>>> _______________________________________________
>>>> Matplotlib-users mailing list
>>>> Mat...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>>>
>>>
>>
>
>

Jeff,

I just built netcdf with the following script:

#!/bin/bash

./configure --enable-netcdf-4 --enable-hdf4 --enable-hdf4-file-tests
--enable-pnetcdf --enable-cxx-4 --with-hdf5=/flex_wrk/lib64
--enable-shared --prefix=/flex_wrk/lib64
make
make install


Everything seemed to work fine.

I then rebuilt netcdf4-python and got no errors.
IE:
export HDF5_DIR=/flex_wrk/lib64
export NETCDF4_DIR=/flex_wrk/lib64
python setup.py build
python setup.py install --prefix=/custom...

However, when I try to read a hdf4 file in Ipython I get:
In [1]: from netCDF4 import Dataset as NetCDFFile

In [2]: nci = NetCDFFile('scia_200910.hdf')
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)

/xnilu_wrk/flex_wrk/EMISSIONS/<ipython console> in <module>()

/xnilu_wrk/flex_wrk/bin64/site-packages/netCDF4.so in
netCDF4.Dataset.__init__ (netCDF4.c:6336)()

RuntimeError: Attempt to use feature that was not turned on when
netCDF was built.


What is it that I need to do to 'build' netCDF and netcdf4-python with
the support?

Thank you,
john


On Sun, Oct 31, 2010 at 2:53 AM, Jeff Whitaker <js...@fa...> wrote:
> On 10/30/10 5:05 PM, John wrote:
>>
>> Thank you. I didn't think they used it, I just wanted to know if it
>> was safe to do what you suggested to try. It does seem to work.
>>
>> Another question, can netcd4-python READ HDF files? Or is it just that
>> it creates files that are readable? If it's the latter, does anyone
>> have a suggestion for a python module that can read both hdf4 and
>> hdf5??
>>
>> Thank you,
>> john
>>
>>
>> PS: Jeff, this module seems to work very well! And I am very thankful
>> for the introduction of compression.
>
> John: If you enabled hdf4 support when you built the netcdf lib, it will
> read hdf4 files in 'scientific dataset' files.
>
> -Jeff
>>
>>
>> On Sat, Oct 30, 2010 at 2:55 PM, Jeff Whitaker<js...@fa...>  wrote:
>>>
>>>  On 10/30/10 3:41 AM, John wrote:
>>>>
>>>> I've searched through the netcdf4-python trunk, but I find no
>>>> reference of NetCDFFile as in how the basemap or Scientific.IO.NetCDF
>>>> modules use it.
>>>>
>>>> For compatibility with my old scripts, is it safe to simply:
>>>>
>>>> from netCDF4 import Dataset as NetCDFFile
>>>>
>>>> ??
>>>>
>>>> Thanks,
>>>> john
>>>>
>>> John:  Neither basemap or Scientific.IO.NetCDF uses it.  What gave you
>>> the impression they did?  There is a 'NetCDFFile' in function in
>>> basemap, but it is based on the pure-python netCDF module pupynere. It
>>> doesn't support netcdf-4 and I only recommend using it for the
>>> occasional light use.
>>>
>>> The netcdf4-python API is mostly compatible with Scientific.IO.NetCDF,
>>> so if you have old script that use the latter, you can try:
>>>
>>> from netCDF4 import Dataset as NetCDFFile
>>>
>>> The docs for netcdf4-python are at
>>>
>>> http://netcdf4-python.googlecode.com/svn/trunk/docs/netCDF4-module.html
>>>
>>>
>>> -Jeff
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Nokia and AT&T present the 2010 Calling All Innovators-North America
>>> contest
>>> Create new apps&  games for the Nokia N8 for consumers in  U.S. and
>>> Canada
>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in
>>> marketing
>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>>> http://p.sf.net/sfu/nokia-dev2dev
>>> _______________________________________________
>>> Matplotlib-users mailing list
>>> Mat...@li...
>>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>>
>>
>>
>
>



-- 
Configuration
``````````````````````````
Plone 2.5.3-final,
CMF-1.6.4,
Zope (Zope 2.9.7-final, python 2.4.4, linux2),
Python 2.6
PIL 1.1.6
Mailman 2.1.9
Postfix 2.4.5
Procmail v3.22 2001/09/10
Basemap: 1.0
Matplotlib: 1.0.0

On 10/30/10 5:05 PM, John wrote:
> Thank you. I didn't think they used it, I just wanted to know if it
> was safe to do what you suggested to try. It does seem to work.
>
> Another question, can netcd4-python READ HDF files? Or is it just that
> it creates files that are readable? If it's the latter, does anyone
> have a suggestion for a python module that can read both hdf4 and
> hdf5??
>
> Thank you,
> john
>
>
> PS: Jeff, this module seems to work very well! And I am very thankful
> for the introduction of compression.

John: If you enabled hdf4 support when you built the netcdf lib, it will 
read hdf4 files in 'scientific dataset' files.

-Jeff
>
>
> On Sat, Oct 30, 2010 at 2:55 PM, Jeff Whitaker<js...@fa...>  wrote:
>>   On 10/30/10 3:41 AM, John wrote:
>>> I've searched through the netcdf4-python trunk, but I find no
>>> reference of NetCDFFile as in how the basemap or Scientific.IO.NetCDF
>>> modules use it.
>>>
>>> For compatibility with my old scripts, is it safe to simply:
>>>
>>> from netCDF4 import Dataset as NetCDFFile
>>>
>>> ??
>>>
>>> Thanks,
>>> john
>>>
>> John:  Neither basemap or Scientific.IO.NetCDF uses it.  What gave you
>> the impression they did?  There is a 'NetCDFFile' in function in
>> basemap, but it is based on the pure-python netCDF module pupynere. It
>> doesn't support netcdf-4 and I only recommend using it for the
>> occasional light use.
>>
>> The netcdf4-python API is mostly compatible with Scientific.IO.NetCDF,
>> so if you have old script that use the latter, you can try:
>>
>> from netCDF4 import Dataset as NetCDFFile
>>
>> The docs for netcdf4-python are at
>>
>> http://netcdf4-python.googlecode.com/svn/trunk/docs/netCDF4-module.html
>>
>>
>> -Jeff
>>
>>
>> ------------------------------------------------------------------------------
>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>> Create new apps&  games for the Nokia N8 for consumers in  U.S. and Canada
>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>> http://p.sf.net/sfu/nokia-dev2dev
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>
>