matplotlib

Hi Eric,

On Tuesday 21 June 2005 11:16 am, Eric Emsellem wrote:
> for some reason I have now (with the new matplotlib) problems with ps
> files saving figures with savefig.
> (it works with gif, jpg, etc).
>
> [I am running Python 2.3.4, IPython 0.6.12, matplotlib 0.82
> and =A0verbose.level helpful, interactive is False, platform is linux2,
> numerix numarray 1.3.0]
>
> So here is what I get with a simple example:
>
> scatter(arange(0,10,1), arange(10,20,1))
> savefig('toto.ps')

I didnt have any trouble with this example. Your traceback shows backend_ag=
g=20
cant import FigureCanvasPS. Does this work in ipython?

from matplotlib.backends.backend_ps import FigureCanvasPS

Did you try to removing the matplotlib directory in site-packages, and=20
reinstalling?

=2D-=20
Darren S. Dale

Bard Hall
Department of Materials Science and Engineering
Cornell University
Ithaca, NY. 14850

dd55@...
http://people.ccmr.cornell.edu/~dd55/

>>>>> "Eric" == Eric Emsellem <emsellem@...> writes:

 
    Eric> /usr/lib/python2.3/site-packages/matplotlib/backends/backend_agg.py
    Eric> in print_figure(self, filename, dpi, facecolor, edgecolor,
    Eric> orientation) 458 svg.print_figure(filename, dpi, facecolor,
    Eric> edgecolor, orientation) 459 elif ext.find('ps')>=0 or
    Eric> ext.find('ep')>=0:
    --> 460 from backend_ps import FigureCanvasPS # lazy import
    Eric>     461 ps = self.switch_backends(FigureCanvasPS) 462
    Eric> ps.print_figure(filename, dpi, facecolor, edgecolor,
    Eric> orientation)

    Eric> ImportError: cannot import name FigureCanvasPS

This looks you might have a bad install.  I would remove
site-packages/matplotlib and try re-installing cleanly.  If the error
persists, make sure that you don't have a copy of backend_ps.py
anywhere in your PYTHONPATH (do 'locate backend_ps' to find out if
there are any errant copies lying around.).

Your example runs fine on my system.

JDH

Thanks for the tip, but as you and John suggested I tried a new clean 
installation (both for matplotlib - removing the site-packages and 
/usr/share matplotlib dir - and ipython) but the small test I sent you 
still react the same. 
The specific import command:

from matplotlib.backends.backend_ps import FigureCanvasPS

does indeed give an ImportError:

ImportError: cannot import name FigureCanvasPS

not sure what to do now. Thanks for any input there!

Eric

Darren Dale wrote:

>Hi Eric,
>
>On Tuesday 21 June 2005 11:16 am, Eric Emsellem wrote:
>  
>
>>for some reason I have now (with the new matplotlib) problems with ps
>>files saving figures with savefig.
>>(it works with gif, jpg, etc).
>>
>>[I am running Python 2.3.4, IPython 0.6.12, matplotlib 0.82
>>and  verbose.level helpful, interactive is False, platform is linux2,
>>numerix numarray 1.3.0]
>>
>>So here is what I get with a simple example:
>>
>>scatter(arange(0,10,1), arange(10,20,1))
>>savefig('toto.ps')
>>    
>>
>
>I didnt have any trouble with this example. Your traceback shows backend_agg 
>cant import FigureCanvasPS. Does this work in ipython?
>
>from matplotlib.backends.backend_ps import FigureCanvasPS
>
>Did you try to removing the matplotlib directory in site-packages, and 
>reinstalling?
>
>  
>

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===============================================================

>>>>> "Eric" == Eric Emsellem <emsellem@...> writes:

    Eric> Thanks for the tip, but as you and John suggested I tried a
    Eric> new clean installation (both for matplotlib - removing the
    Eric> site-packages and /usr/share matplotlib dir - and ipython)
    Eric> but the small test I sent you still react the same. The
    Eric> specific import command:

    Eric> from matplotlib.backends.backend_ps import FigureCanvasPS

    Eric> does indeed give an ImportError:

    Eric> ImportError: cannot import name FigureCanvasPS

    Eric> not sure what to do now. Thanks for any input there!

Strange indeed.  Issue these commands and let me know what you find

    >>> import matplotlib.backends.backend_ps
    >>> matplotlib.__file__
    '/usr/lib/python2.4/site-packages/matplotlib/__init__.pyc'
    >>> matplotlib.backends.backend_ps.__file__
    '/usr/lib/python2.4/site-packages/matplotlib/backends/backend_ps.pyc'

    >>> import matplotlib
    >>> matplotlib.__version__
    '0.82'
    >>> matplotlib.__file__
    '/usr/lib/python2.4/site-packages/matplotlib/__init__.pyc'


Also, what do these commands from the unix shell return (substituting
in your path to backend_ps.py)

    peds-pc311:~> md5sum /usr/lib/python2.4/site-packages/matplotlib/backends/backend_ps.py
    2bb2161d70c11f56e803d7749b4fe05a  /usr/lib/python2.4/site-packages/matplotlib/backends/backend_ps.py
    peds-pc311:~> grep '^class FigureCanvas' /usr/lib/python2.4/site-packages/matplotlib/backends/backend_ps.py
    class FigureCanvasPS(FigureCanvasBase):

The only things I can think of are 

 1) you have an errant copy of matplotlib.backends.backend_ps
    somewhere in your path

 2) you have a corrupted backend_ps (hence the md5sum check)

 3) You did not successfully remove site-packages/matplotlib and have
    a corrupt install.

JDH

followed what you suggested, everything was fine until the 'grep' : for 
some obscure reason every new install produced an empty (0 byte) 
backend_ps.py file (I think this may have come from a previously 
interrupted 'build'). I therefore erased the original matplotlib source 
dir (as well as the installed ones), and redetared the archive starting 
from scratch..
It works...

thanks a lot for the support!!!!

Eric

John Hunter wrote:

>>>>>>"Eric" == Eric Emsellem <emsellem@...> writes:
>>>>>>            
>>>>>>
>
>    Eric> Thanks for the tip, but as you and John suggested I tried a
>    Eric> new clean installation (both for matplotlib - removing the
>    Eric> site-packages and /usr/share matplotlib dir - and ipython)
>    Eric> but the small test I sent you still react the same. The
>    Eric> specific import command:
>
>    Eric> from matplotlib.backends.backend_ps import FigureCanvasPS
>
>    Eric> does indeed give an ImportError:
>
>    Eric> ImportError: cannot import name FigureCanvasPS
>
>    Eric> not sure what to do now. Thanks for any input there!
>
>Strange indeed.  Issue these commands and let me know what you find
>
>    >>> import matplotlib.backends.backend_ps
>    >>> matplotlib.__file__
>    '/usr/lib/python2.4/site-packages/matplotlib/__init__.pyc'
>    >>> matplotlib.backends.backend_ps.__file__
>    '/usr/lib/python2.4/site-packages/matplotlib/backends/backend_ps.pyc'
>
>    >>> import matplotlib
>    >>> matplotlib.__version__
>    '0.82'
>    >>> matplotlib.__file__
>    '/usr/lib/python2.4/site-packages/matplotlib/__init__.pyc'
>
>
>Also, what do these commands from the unix shell return (substituting
>in your path to backend_ps.py)
>
>    peds-pc311:~> md5sum /usr/lib/python2.4/site-packages/matplotlib/backends/backend_ps.py
>    2bb2161d70c11f56e803d7749b4fe05a  /usr/lib/python2.4/site-packages/matplotlib/backends/backend_ps.py
>    peds-pc311:~> grep '^class FigureCanvas' /usr/lib/python2.4/site-packages/matplotlib/backends/backend_ps.py
>    class FigureCanvasPS(FigureCanvasBase):
>
>The only things I can think of are 
>
> 1) you have an errant copy of matplotlib.backends.backend_ps
>    somewhere in your path
>
> 2) you have a corrupted backend_ps (hence the md5sum check)
>
> 3) You did not successfully remove site-packages/matplotlib and have
>    a corrupt install.
>
>JDH
>
>  
>

-- 
===============================================================
Observatoire de Lyon                 emsellem@...
9 av. Charles-Andre                      tel: +33 4 78 86 83 84
69561 Saint-Genis Laval Cedex            fax: +33 4 78 86 83 86
France               http://www-obs.univ-lyon1.fr/eric.emsellem
===============================================================

>>>>> "Eric" == Eric Emsellem <emsellem@...> writes:

    Eric> followed what you suggested, everything was fine until the
    Eric> 'grep' : for some obscure reason every new install produced
    Eric> an empty (0 byte) backend_ps.py file (I think this may have
    Eric> come from a previously interrupted 'build'). I therefore
    Eric> erased the original matplotlib source dir (as well as the
    Eric> installed ones), and redetared the archive starting from
    Eric> scratch..  It works...

Oh -- both Darren and I forgot to suggest rm -rf "build" in addition
to site-packages/matplotlib.  This is, however, suggested in
http://matplotlib.sourceforge.net/faq.html#FAILURE

   The first thing to try is to remove site-packages/matplotlib and
   reinstall. If you are running the windows installer or using some
   other package, that is all you need to do. If you are compiling
   matplotlib yourself, you also need to remove the build subdirectory
   of the matplotlib src tree you are compiling from. It is not enough
   to do python setup.py clean. Try rebuilding and reinstalling
   matplotlib after removing these two directories and see if that
   helps. If 

Glad you found and fixed the problem!

JDH

Hi,
a short report on 2 minor problems I face with matplotlib:

- I tried to save a figure in gif. It gave me back an error message 
saying that basically this is not supported. This is fine of course. 
However, then the plot window crashed, and then the whole Ipython 
session. It would be useful then to have this error not affecting the 
session in this way if possible.

- I also noticed recently that when I had a plot made with matplotlib, 
and changing desktop (I am running under Linux and KDE), when I come 
back to the panel where my matplotlib session is, the plot is often (but 
not every time) "perturbed": the figure is zoomed in some corner, or 
offseted. I am not sure why this occurs, and this could be something 
specific to my setting, but just to report the problem, if this is a 
more general item (I have no clue what triggers this since it does not 
occur systematically, which I understand does not ease the debugging...:-)

Cheers
Eric
(and thanks for all this hard work. to repeat myself once more, 
matplotlib is just amazing!)

-- 
===============================================================
Observatoire de Lyon                 emsellem@...
9 av. Charles-Andre                      tel: +33 4 78 86 83 84
69561 Saint-Genis Laval Cedex            fax: +33 4 78 86 83 86
France               http://www-obs.univ-lyon1.fr/eric.emsellem
===============================================================

Hi again,

regarding the problem of "perturbed plot" I mentioned, I found out some 
systematic behaviour:

- I plot something
- I save it into a jpg
- I get the cursor into the window and there it gets nuts...

scatter([0,1],[0,1])
savefig('toto.jpg')

==> then put the cursor in the plot window....

and this is systematic (so this does not seem linked to a change in the 
desktop finally)

Eric

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===============================================================
Observatoire de Lyon                 emsellem@...
9 av. Charles-Andre                      tel: +33 4 78 86 83 84
69561 Saint-Genis Laval Cedex            fax: +33 4 78 86 83 86
France               http://www-obs.univ-lyon1.fr/eric.emsellem
===============================================================

Eric Emsellem wrote:
> Hi,
> a short report on 2 minor problems I face with matplotlib:
> 
> - I tried to save a figure in gif. It gave me back an error message 
> saying that basically this is not supported. This is fine of course. 
> However, then the plot window crashed, and then the whole Ipython 
> session. It would be useful then to have this error not affecting the 
> session in this way if possible.

I can see the problem in the GTK backend, but all other backends I tried under 
linux (TkAgg, QtAgg and WXAgg) all behave correctly.  This seems like a bug in 
the GTK backend to me: it puts out to the screen an error message box, but the 
OK button in that box is unresponsive.  Eventually the window manager just 
kills the window, which brings the whole python process down with it.

I don't know the backends enough to know what the right solution should be here.


Cheers,

f

Hi,

I know this may be a question for scipy or numarray but since matplotlib 
is using something close to what I wish to have..., here is the question:

- I would like to use some 2D interpolation of a set of x, y, z points 
(not regularly positioned). If possible I would like to test various 
interpolation schemes (bilinear, splines, etc), and have a FLAG to tell 
me if I am trying to EXTRAPOLATE (so that I can control the output). I 
looked at scipy but this is really bad: as far as I understand the doc 
mentions that it takes 1D array (what I want), but in fact works on 2D 
arrays (NOT what I want).... (and it only provides splines)

I know that imshow has this built in with many different options for the 
visualisation. So how is this done? Is it hard coded in one of the 
matplotlib routine ? Could not find it there...

thanks for the help

Eric Emsellem

-- 
===============================================================
Observatoire de Lyon                 emsellem@...
9 av. Charles-Andre                      tel: +33 4 78 86 83 84
69561 Saint-Genis Laval Cedex            fax: +33 4 78 86 83 86
France               http://www-obs.univ-lyon1.fr/eric.emsellem
===============================================================

On Jul 19, 2005, at 2:17 AM, Eric Emsellem wrote:

> - I would like to use some 2D interpolation of a set of x, y, z points 
> (not regularly positioned). If possible I would like to test various 
> interpolation schemes (bilinear, splines, etc), and have a FLAG to 
> tell me if I am trying to EXTRAPOLATE (so that I can control the 
> output). I looked at scipy but this is really bad: as far as I 
> understand the doc mentions that it takes 1D array (what I want), but 
> in fact works on 2D arrays (NOT what I want).... (and it only provides 
> splines)

You have at least 2 general approaches: Delaunay triangulation and 
splines. Straight Delaunay triangulation would be linear interpolation, 
but can be embellished with fancier interpolation techniques.  As far 
as I know, Delaunay triangulation and associated interpolation routines 
are not (yet) available in scipy. Surface splines are available in 
scipy -- check out bisplrep/bisplev.

As far as a FLAG to tell if you want to EXTRAPOLATE, I don't know.  
They may not be in ALL CAPS, either, so read the fine print. :)

> I know that imshow has this built in with many different options for 
> the visualisation. So how is this done? Is it hard coded in one of the 
> matplotlib routine ? Could not find it there...

I don't think imshow does anything as fancy as what you suggest.  The 
contour routines are more sophisticated and may be useful to you, but I 
haven't followed how they work.

Hi
thanks for the input, however scipy interpolation scheme is on a regular 
grid.

The positions I have are not even on an ORTHOGONAL grid: they are 
randomly distributed!
So I have a set of x,y random positions with Z values and I wish to know 
the interpolated value
at a new position xnew, ynew...

It seems that this does not exist in scipy. Someone pointed out 
Scientific Python but this again does not work
(using irregular but orthogonal grids)...

This would be pretty bad if I cannot do this in python!!!

Any help welcome!

Cheers
Eric

Eric Emsellem wrote:

> Hi,
>
> I know this may be a question for scipy or numarray but since 
> matplotlib is using something close to what I wish to have..., here is 
> the question:
>
> - I would like to use some 2D interpolation of a set of x, y, z points 
> (not regularly positioned). If possible I would like to test various 
> interpolation schemes (bilinear, splines, etc), and have a FLAG to 
> tell me if I am trying to EXTRAPOLATE (so that I can control the 
> output). I looked at scipy but this is really bad: as far as I 
> understand the doc mentions that it takes 1D array (what I want), but 
> in fact works on 2D arrays (NOT what I want).... (and it only provides 
> splines)
>
> I know that imshow has this built in with many different options for 
> the visualisation. So how is this done? Is it hard coded in one of the 
> matplotlib routine ? Could not find it there...
>
> thanks for the help
>
> Eric Emsellem
>
>On Jul 19, 2005, at 2:17 AM, Eric Emsellem wrote:
> 
> > - I would like to use some 2D interpolation of a set of x, y, z points 
> > (not regularly positioned). If possible I would like to test various 
> > interpolation schemes (bilinear, splines, etc), and have a FLAG to 
> > tell me if I am trying to EXTRAPOLATE (so that I can control the 
> > output). I looked at scipy but this is really bad: as far as I 
> > understand the doc mentions that it takes 1D array (what I want), but 
> > in fact works on 2D arrays (NOT what I want).... (and it only provides 
> > splines)
> 
> You have at least 2 general approaches: Delaunay triangulation and 
> splines. Straight Delaunay triangulation would be linear interpolation, 
> but can be embellished with fancier interpolation techniques.  As far 
> as I know, Delaunay triangulation and associated interpolation routines 
> are not (yet) available in scipy. Surface splines are available in 
> scipy -- check out bisplrep/bisplev.
> 
> As far as a FLAG to tell if you want to EXTRAPOLATE, I don"t know.  
> They may not be in ALL CAPS, either, so read the fine print. :)
> 
> > I know that imshow has this built in with many different options for 
> > the visualisation. So how is this done? Is it hard coded in one of the 
> > matplotlib routine ? Could not find it there...
> 
> I don"t think imshow does anything as fancy as what you suggest.  The 
> contour routines are more sophisticated and may be useful to you, but I 
> haven"t followed how they work.
> 
>  
>

-- 
===============================================================
Observatoire de Lyon                 emsellem@...
9 av. Charles-Andre                      tel: +33 4 78 86 83 84
69561 Saint-Genis Laval Cedex            fax: +33 4 78 86 83 86
France               http://www-obs.univ-lyon1.fr/eric.emsellem
===============================================================

I do this in python/matplotlib using hardy's multiquadric 
interpolation.... I've posted here before promising to attach some code, 
but haven't done so yet, since really need  to clean things up a little. 
Will try to get it done on my 10 hour flight tonight... and post within 
the next few days...

Cheers,
Peter

Eric Emsellem wrote:

> Hi
> thanks for the input, however scipy interpolation scheme is on a 
> regular grid.
>
> The positions I have are not even on an ORTHOGONAL grid: they are 
> randomly distributed!
> So I have a set of x,y random positions with Z values and I wish to 
> know the interpolated value
> at a new position xnew, ynew...
>
> It seems that this does not exist in scipy. Someone pointed out 
> Scientific Python but this again does not work
> (using irregular but orthogonal grids)...
>
> This would be pretty bad if I cannot do this in python!!!
>
> Any help welcome!
>
> Cheers
> Eric
>
> Eric Emsellem wrote:
>
>> Hi,
>>
>> I know this may be a question for scipy or numarray but since 
>> matplotlib is using something close to what I wish to have..., here 
>> is the question:
>>
>> - I would like to use some 2D interpolation of a set of x, y, z 
>> points (not regularly positioned). If possible I would like to test 
>> various interpolation schemes (bilinear, splines, etc), and have a 
>> FLAG to tell me if I am trying to EXTRAPOLATE (so that I can control 
>> the output). I looked at scipy but this is really bad: as far as I 
>> understand the doc mentions that it takes 1D array (what I want), but 
>> in fact works on 2D arrays (NOT what I want).... (and it only 
>> provides splines)
>>
>> I know that imshow has this built in with many different options for 
>> the visualisation. So how is this done? Is it hard coded in one of 
>> the matplotlib routine ? Could not find it there...
>>
>> thanks for the help
>>
>> Eric Emsellem
>>
>> On Jul 19, 2005, at 2:17 AM, Eric Emsellem wrote:
>>
>> > - I would like to use some 2D interpolation of a set of x, y, z 
>> points > (not regularly positioned). If possible I would like to test 
>> various > interpolation schemes (bilinear, splines, etc), and have a 
>> FLAG to > tell me if I am trying to EXTRAPOLATE (so that I can 
>> control the > output). I looked at scipy but this is really bad: as 
>> far as I > understand the doc mentions that it takes 1D array (what I 
>> want), but > in fact works on 2D arrays (NOT what I want).... (and it 
>> only provides > splines)
>>
>> You have at least 2 general approaches: Delaunay triangulation and 
>> splines. Straight Delaunay triangulation would be linear 
>> interpolation, but can be embellished with fancier interpolation 
>> techniques.  As far as I know, Delaunay triangulation and associated 
>> interpolation routines are not (yet) available in scipy. Surface 
>> splines are available in scipy -- check out bisplrep/bisplev.
>>
>> As far as a FLAG to tell if you want to EXTRAPOLATE, I don"t know.  
>> They may not be in ALL CAPS, either, so read the fine print. :)
>>
>> > I know that imshow has this built in with many different options 
>> for > the visualisation. So how is this done? Is it hard coded in one 
>> of the > matplotlib routine ? Could not find it there...
>>
>> I don"t think imshow does anything as fancy as what you suggest.  The 
>> contour routines are more sophisticated and may be useful to you, but 
>> I haven"t followed how they work.
>>
>>  
>>
>


-- 
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Tel: +1 808 9742509       670 N. A'ohoku Place
Fax: +1 808 9359235       Hilo, Hawai'i 96720, USA

Andrew Straw wrote:

> You have at least 2 general approaches: Delaunay triangulation and 
> splines. Straight Delaunay triangulation would be linear interpolation, 
> but can be embellished with fancier interpolation techniques.  As far as 
> I know, Delaunay triangulation and associated interpolation routines are 
> not (yet) available in scipy.

I don't think they are. I've been planning to write python wrappers for
Jonathan Shewchuk's triangle code, but if someone wanted to beat me to
it....

http://www-2.cs.cmu.edu/~quake/triangle.html

> Surface splines are available in scipy -- 
> check out bisplrep/bisplev.

Can you do surface splines with irregularly spaced points?

> The
> contour routines are more sophisticated and may be useful to you, but I 
> haven't followed how they work.

I'm pretty sure they require regularly spaced points as well. Or at
least  "logically Cartesian" points.

-Chris




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Chris.Barker@...

Eric Emsellem wrote:

> Hi,
>
> I know this may be a question for scipy or numarray but since 
> matplotlib is using something close to what I wish to have..., here is 
> the question:
>
> - I would like to use some 2D interpolation of a set of x, y, z points 
> (not regularly positioned). If possible I would like to test various 
> interpolation schemes (bilinear, splines, etc), and have a FLAG to 
> tell me if I am trying to EXTRAPOLATE (so that I can control the 
> output). I looked at scipy but this is really bad: as far as I 
> understand the doc mentions that it takes 1D array (what I want), but 
> in fact works on 2D arrays (NOT what I want).... (and it only provides 
> splines)
>
> I know that imshow has this built in with many different options for 
> the visualisation. So how is this done? Is it hard coded in one of the 
> matplotlib routine ? Could not find it there...
>
> thanks for the help
>
> Eric Emsellem
>
Eric:  There are a couple of modules in CDAT (http://cdat.sf.net) to do 
this.  See

http://rainbow.llnl.gov/software/cdat/support/cdat_utilities/cdat_utilities-3.php

Look for the 'ngmath' module.  I've found that ngmath.natgrid works 
quite well.  Here's a quick description from the docstring:

"natgrid - a two-dimensional random data interpolation package based on 
Dave Watson's nngridr."

-Jeff


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