matplotlib-users Mailing List for matplotlib

Hi list,
Recently, a VISA library was released (http://pyvisa.sourceforge.net/),
and I would like to get it and matplotlib working nicely together.=20
VISA is a generic interface for data logging from scientific instruments.
Currently, I'm running these things from an ipython window by exec'ing a
file object, which refers to some data taking script.

Unfortuantely, there seem to be some circumstances under which the plot
window will not update. Often (awlays?) it has stopped updating after som=
e
ui event has occured in the plot window. I've checked the pages on
"interactive plotting", and tried wxagg and tkagg backends, but to no ava=
il.

Hopefully this is a stupid, easily answered question, as I'd rather get o=
n
with my experiments than trawl through code, but it would be great to get=
 this
working. I feel that python+numpy+matplot+VISA may be a far superior alte=
rnative
to the frequently used Labview commerical software, and any
hints that would save me from reinventing the wheel would be much appreci=
ated.

BTW: Developers, thank you indeed for matplotlib. It's one of the great
libraries for a great language.

Marc

Rafael Perez Pascual wrote:
> I have a Debian  Ubuntu 5.10 Breeze system in an amd64  machine  with
> python2.4. I install numpy, scipy and matplotlib without troubles, but
> when I treat to import pylab  I get a segmentation fault  and python 
> breaks.
> I treat lots of thinks but nothing works, some one have an idea  about
> these?

How did you install those packages? What versions? What code did you run that
segfaulted? Can you isolate a small, self-contained example that segfaults so we
can examine it? If it's a numpy or scipy problem (likely), we will be happy to
answer your questions on the appropriate list to avoid cluttering the matplotlib
list.

-- 
Robert Kern
rob...@gm...

"In the fields of hell where the grass grows high
 Are the graves of dreams allowed to die."
  -- Richard Harter

I have a Debian  Ubuntu 5.10 Breeze system in an amd64  machine  with
python2.4. I install numpy, scipy and matplotlib without troubles, but
when I treat to import pylab  I get a segmentation fault  and python 
breaks.
I treat lots of thinks but nothing works, some one have an idea  about
these?

Thanks

Rafael Perez

>>>>> "Charlie" == Charlie Moad <cw...@gm...> writes:

    Charlie>      You could use html image maps to accomplish this.
    Charlie> Obviously this would be in the context of a web page.  I
    Charlie> think frontpage or dreamweaver has some nice tools for
    Charlie> creating these.  Just google "html image maps" for more
    Charlie> info.

Andrew Dalke has a tutorial on creating html image maps with
matplotlib

http://www.dalkescientific.com/writings/diary/archive/2005/04/24/interactive_html.html

JDH

     You could use html image maps to accomplish this.  Obviously this
would be in the context of a web page.  I think frontpage or
dreamweaver has some nice tools for creating these.  Just google "html
image maps" for more info.

On 2/15/06, Julius Lucks <jul...@gm...> wrote:
> Is it possible to embed clickable URLs, associated with data points or
> plot features, into PNGs or JPEGs produced by matplotlib?
>
> Thank you for your help,
>
> Julius
>
>
> -------------------------------------------------------
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>

Is it possible to embed clickable URLs, associated with data points or
plot features, into PNGs or JPEGs produced by matplotlib?

Thank you for your help,

Julius

On Feb 15, 2006, at 10:42 AM, J.B...@if... wrote:

> I 've to change line 736 in mplot3d.py too but then it works...
>
> Line 736:
>
> - if z:
> + if z is None: --> correct or not?

Your logic is backwards, I think.  This is what I think is correct:

     def auto_scale_xyz(self, X,Y,Z=None,had_data=None):
         x,y,z = X,Y,Z
         try:
             x,y = X.flat,Y.flat
             if Z is not None:
                 z = Z.flat
         except AttributeError:
             pass

         self.xy_dataLim.update_numerix(x, y, not had_data)
         if z is not None:
             self.zz_dataLim.update_numerix(z, z, not had_data)
         self.autoscale_view()

The PNG I get from python surface.py is attached.

Cheers,

-- Paul

--
Dr. Paul S. Ray              E-mail: Pau...@nr...
Naval Research Laboratory    WWW   : http://xweb.nrl.navy.mil/ 
personnel/paulr/
Code 7655                    Phone : (202) 404-1619
Washington, DC 20375         AIM   : NRLPSR

Hi,

>With that change, the demos both work for me.

I 've to change line 736 in mplot3d.py too but then it works...

Line 736:

- if z:
+ if z is None: --> correct or not?

>"python surface.py" makes a nice surface plot.

No, for me it looks rather strange...

Thanks

Jens

On Feb 15, 2006, at 7:12 AM, J.B...@if... wrote:

> for a better understanding please could someone explain this for  
> the actual
> problem?

Arrays are no longer allowed as truth values in numpy, because the  
"truth" of an array (except one with exactly one element) is ambiguous.

> It was about simple surface plots in matplotlib... I took the 3D  
> package
> from  http://matplotlib.sourceforge.net/mpl3d.zip and I changed the
> following in 'mplot3d.py':
>
> line 729:
>
> - if Z:
> + if Z is None: --> correct or not?

Yes, that is corect.

> Now I get this 'The truth value of an array with more than one  
> element is
>   ambiguous. Use a.any() or a.all()' ValueError in line 680 ...
>
> line 680:
>
> - M = M or self.M
> + ???

I changed it to this:
     def tunit_cube(self,vals=None,M=None):
         if M is None:
             M = self.M
         xyzs = self.unit_cube(vals)

With that change, the demos both work for me.
"python surface.py" makes a nice surface plot.

Now, my question is: Is "mplot3d" planned for inclusion in future  
matplotlib releases?  It does exactly what I need for 3d surface  
plots without the huge baggage and complexity of the VTK-based  
solutions that allow interactive 3D and all that stuff I don't need.

Cheers,

-- Paul

--
Dr. Paul S. Ray              E-mail: Pau...@nr...
Naval Research Laboratory    WWW   : http://xweb.nrl.navy.mil/ 
personnel/paulr/
Code 7655                    Phone : (202) 404-1619
Washington, DC 20375         AIM   : NRLPSR

Hi,

for a better understanding please could someone explain this for the actual
problem?

It was about simple surface plots in matplotlib... I took the 3D package
from  http://matplotlib.sourceforge.net/mpl3d.zip and I changed the
following in 'mplot3d.py':

line 729:

- if Z:
+ if Z is None: --> correct or not?

Now I get this 'The truth value of an array with more than one element is
  ambiguous. Use a.any() or a.all()' ValueError in line 680 ...

line 680:

- M = M or self.M
+ ???

So, I do understand that the 'or' is the problem here but how would you
replace it???

Cheers

Jens

PS.: Maybe someone just send me a 'mplot3d.py' running under numpy... 

Curtis,

I have added support for the extent kwarg in the case with 
origin=None--that is, the case in which contour is being used alone, not 
superimposed on an image.

The intention is that extent = (x0,x1,y0,y1) with origin = None will 
make (x0,y0) the coordinates of Z[0,0] and (x1,y1) the coordinates of 
Z[-1,-1].  In other words, it provides an easy way to generate 
equally-spaced coordinates specified by the end points, and 
corresponding in a simple and unambiguous way to the Z array.  Beyond 
that, the orientation of the axes is determined in the usual way. This 
seems logical to me.



Curtis Cooper wrote:
>>But it does.  The X and Y arrays give the coordinates of the Z points.
>>If you want to reverse the Y axis, say to have Y increase downward, then
>>  you do something like this:
>>
>>a = gca()
>>a.set_ylim(a.get_ylim()[::-1])
>>
>>There are many other ways to do it, but the point is that the axes are
>>drawn with the first ylim value at the bottom and the second at the top,
>>  so to reverse the axis you simply reverse the order of the y limits.
>>Similarly for the x-axis.
>>
> 
> 
> Fair enough, but notice that if I use imshow(Z, extent=[xmin, xmax,
> ymax, min]), it displays the image with the ymax extent at the bottom and
> ymin at the top of the y-axis, as I intended.  For contour, the extent is
> always displayed in increasing order in each axis.
> 


With respect to the comparison to imshow: is there any circumstance 
under which the plotting the same data with the same origin and extent 
options on the same axes (as in contour_image.py) results in a 
mis-registration--any sort of mismatch between the image view and the 
contour view?

I still can't find anything wrong; but if you send me a script that 
illustrates incorrect behavior, I will certainly look at it.

Thanks.

Eric

>>>>> "Chris" == Chris Seberino <seb...@sp...> writes:

    Chris> I know this matplotlib code works.  I'm having trouble
    Chris> running it in a CGI script.  It appears some of modules
    Chris> matplotlib imports need certain X Window permissions or
    Chris> DISPLAY variable set?....

It looks like mpl is trying to load its default backend (eg GTKAgg)
and in CGI mode you'll likely want to use an image backend (eg Agg).
See the FAQ http://matplotlib.sourceforge.net/faq.html#APPSERVER and
links therein.  In particular, you'll likely want to set the backend
with

  backend : Agg

in your matplotlib rc file -- http://matplotlib.sf.net/matplotlibrc
or else in your CGI script with the *use* directive , eg

  import matplotlib
  matplotlib.use('Agg')
  import pylab

matplotlib.use must be called *before* importing pylab, and overrides
any rc or command line backend settings.

JDH

I know this matplotlib code works.  I'm having trouble
running it in a CGI script.  It appears some of modules
matplotlib imports need certain X Window permissions or=20
DISPLAY variable set?....

[seberino root /var/www] # tail /var/log/apache2/error.log
[Tue Feb 14 17:07:30 2006] [error] [client 127.0.0.1]
[Tue Feb 14 17:07:30 2006] [error] [client 127.0.0.1] import gtk; gdk =3D
gtk.gdk
[Tue Feb 14 17:07:30 2006] [error] [client 127.0.0.1]   File
"/usr/lib/python2.3/site-packages/gtk-2.0/gtk/__init__.py", line 37,
in ?
[Tue Feb 14 17:07:30 2006] [error] [client 127.0.0.1]
[Tue Feb 14 17:07:30 2006] [error] [client 127.0.0.1] from _gtk import *
[Tue Feb 14 17:07:30 2006] [error] [client 127.0.0.1] RuntimeError
[Tue Feb 14 17:07:30 2006] [error] [client 127.0.0.1] :
[Tue Feb 14 17:07:30 2006] [error] [client 127.0.0.1] could not open
display
[Tue Feb 14 17:07:30 2006] [error] [client 127.0.0.1]
[Tue Feb 14 17:07:30 2006] [error] [client 127.0.0.1] Premature end of
script headers: create_ssg.py