matplotlib-users Mailing List for matplotlib (Page 15)

Ryan May wrote:
> 
> Right, the show() command starts the GUI's mainloop, which blocks 
> execution of the script until you close the figure.  What you probably 
> want is something like the dynamic_demo.py example.

...which barfes for me:

Traceback (most recent call last):
   File "dynamic_demo.py", line 3, in <module>
     import gobject
ImportError: No module named gobject

What does that mean?

Chris

-- 
Simplistix - Content Management, Zope & Python Consulting
            - http://www.simplistix.co.uk

Le Sunday 09 March 2008 14:32:05 Eric Firing, vous avez écrit :
> hu...@ya... wrote:
> > 				Hello,
> >
> > I have some stupid questions about how to use colorbar.
> >
> > 1) I would like to be able to put the colorbar where I went: top, bottom,
> > left, right. For what I see I can do only a vertical left and horizontal
> > bottom ones (with a simple use of the function).
> > I know that it's possible to do a colorbar only but it's difficult to
> > place them a little bit automatically and that bring my second question.
>
> This looks like a feature request: instead of specifying "horizontal" or
> "vertical", be able to specify "top", "bottom", "left", or "right".
> This is fairly easy in principle, but there are some wrinkles such that
> I am not sure it would be satisfactory in practice--some custom
> adjustments might usually be needed depending on whether the main axes
> have a title (in the case of "top") or an xlabel (in the case of
> "left").  You may be better off simply figuring out what main and
> colorbar axes positions work best for your particular case and then
> making those axes explicitly.

I agree it's more feature request. I'll look on how to implement your 
suggestion. 

> > 2) I would like that the colorbar with exactly the same size than the
> > image I plot with pcolor. It's working when I'm not using the
> > aspect='equal' in the subplot but not with this option. Naturally I want
> > to not change the aspect of my image and so it's a big problem for me.
> > The only solution I found is to manipulate the colorbar with the shrink
> > valu but it's a little bit painfull especially the value change for each
> > pcolor image (they doesn't have always the same size).
>
> This is a common request, and a reasonable one, but unfortunately it is
> not straightforward to implement automatically given mpl's internal
> structure.  Again, however, you get the desired result quite easily by
> creating your own axes explicitly.

This is what I was afraid... So I have a stupid question but how to do this, 
create the axes at the same place than the pcolor image?

I can see how I can recuperate the axes coordinates but I don't know how to 
use them:

im = pylab.pcolor(a)
ax = im.get_axes()
cs = pylab.colorbar()

but after I'm a little bit lost...

> > 3) I would like to give a label to the colorbar (ie if the colorbar is at
> > the bottom a label under the colorbar etc). To tell people what means the
> > colors but I didn't find anyway to do it. xlabel work for the pcolor
> > object (as expected) and there are no colorbar.xlabel function.
>
> Use the set_label() method.
> ...
> cbar = fig1.colorbar(im,orientation='horizontal')
> cbar.set_label('label')
> ...

Great thanks it's working perfectly.

> Eric

Thank you for your help,

N.

Alan G Isaac wrote:
> On Tue, 11 Mar 2008, Chris Withers apparently wrote:
>> the first time I call show()
> 
> http://matplotlib.sourceforge.net/faq.html#SHOW

Okay, that tells me that I prettymuch don't want to be using show(), but 
I don't think I want interactive mode either...

What I'm trying to do is run a script and plot-and-show as I go.
The script reads the data to be plotted, but each set of points takes up 
to 20 minutes to generate, so I want to see the points appear on the 
graph as they arrive.

Is this possible? If so, how?

cheers,

Chris

-- 
Simplistix - Content Management, Zope & Python Consulting
            - http://www.simplistix.co.uk

On Tue, 11 Mar 2008, Chris Withers apparently wrote:
> the first time I call show()

http://matplotlib.sourceforge.net/faq.html#SHOW

hth,
Alan Isaac

Matthias Michler wrote:
> plot([x1], [y1], "bo", [x2], [y2], "r+")

This didn't work :-S

- the first time I call show(), execution never comes back to my script 
so the code never gets to plot any further points

- if I put the "show" after the plotting loop (which means I don't get 
the "live plotting" I'm after) then there are no lines between the 
points (well, the points don't show at all, but I'm guessing it's 
because there's no lines between the points)

- looking at the example, I'm left wondering how to pass keyword 
parameters such as "label" or use other methods such as plot_date

Any help greatfully received!

Chris

-- 
Simplistix - Content Management, Zope & Python Consulting
            - http://www.simplistix.co.uk

I suspect there is an .afm font file on your new system that is untested 
with matplotlib and exhibiting something "new".

I would first try to track down which font file it is, and then send it 
to me off list and I'll have a look at what might be tripping up matplotlib.

Cheers,
Mike

Rich Shepard wrote:
>    I upgraded my notebook to Slackware-12.0 (which includes python-2.5) and
> discovered that the application I'm developing no longer ran. Turns out that
> matplotlib went missing during the upgrade.
>
>    So, I just built matplotlib-0.91.2 using the same matplotlib.Slackbuild
> script I used on my workstation/server, but this time it failed. The font
> manager seems to be the issue; the error message repeatedly is: "Found an
> unknown keyword in AFM header (was Underline)". Specifically, the error is
> in File "/usr/lib/Python2.5/site-packages/matplotlib/afm.py", line 166, in
> _parse_char_metrics
>  	name=vals[2].split()[1]
> IndexError: List index out of range
>
>    Is this unique to me? What do I do to fix the problem?
>
> TIA,
>
> Rich
>
>   

-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

I'm getting a nonsensical error when attempting to make a simple plot
with a date axis. Googling shows this similar errors, but none with a
date axis. What could be causing this?

>>> import datetime
>>> from pylab import figure, show
>>> fig = figure()
>>> ax = fig.add_subplot(111)
>>> dates = [datetime.date(2008, 1, 30),datetime.date(2008, 1, 31)]
>>> values = [10.25, 10.0]
>>> ax.plot_date(dates, values)#, '-')
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python2.5/site-packages/matplotlib/axes.py", line
2585, in plot_date
    ret = self.plot(x, y, fmt, **kwargs)
  File "/usr/lib/python2.5/site-packages/matplotlib/axes.py", line 2535, in plot
    for line in self._get_lines(*args, **kwargs):
  File "/usr/lib/python2.5/site-packages/matplotlib/axes.py", line
428, in _grab_next_args
    for seg in self._plot_3_args(remaining, **kwargs):
  File "/usr/lib/python2.5/site-packages/matplotlib/axes.py", line
404, in _plot_3_args
    func(x[:,j], y[:,j])
  File "/usr/lib/python2.5/site-packages/matplotlib/axes.py", line
385, in makeline
    axes=self.axes,
  File "/usr/lib/python2.5/site-packages/matplotlib/lines.py", line
226, in __init__
    self.set_data(xdata, ydata)
  File "/usr/lib/python2.5/site-packages/matplotlib/lines.py", line
315, in set_data
    self.recache()
  File "/usr/lib/python2.5/site-packages/matplotlib/lines.py", line
320, in recache
    x = ma.asarray(self.convert_xunits(self._xorig), Float)
  File "/usr/lib/python2.5/site-packages/numpy/core/ma.py", line 2122,
in asarray
    return array(data, dtype=dtype, copy=0)
  File "/usr/lib/python2.5/site-packages/numpy/core/ma.py", line 573,
in __init__
    self._data = c.astype(tc)
TypeError: a float is required

Hi Michael,

Michael Droettboom wrote:
> Well, that was a good puzzle!

Glad I got your neurons firing.

> This seems like a safe fix to me, but anyone who currently extends the 
> Wx Frame (meaning the whole window etc.) and is unknowingly compensating 
> for this effect may have problems after my change.

Many thanks for looking at this. I applied your fix and it works for me.

Gary R.

For what it's worth, the standalone agg 2.4 library compiles just fine  
on my system -- this problem seems to be some sort of matplotlib / agg  
interaction.

Zach


On Mar 9, 2008, at 11:35 PM, Zachary Pincus wrote:

> Hello,
>
> I just tried to compile the SVN head of matplotlib (r4994) from source
> on OS X 10.5.2 (with source builds of python 2.5.2 and the SVN head of
> numpy), and ran into an "internal compiler error" in the agg code.
> (pkgconfig 0.23 and wxPython 2.8.7.1 also present and accounted for.)
>
> Here's the compile line and error:
>> building 'matplotlib.backends._backend_agg' extension
>> gcc -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-
>> madd -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-
>> prototypes -I/Library/Frameworks/Python.framework/Versions/2.5/lib/
>> python2.5/site-packages/numpy/core/include -I/usr/X11/include/
>> libpng12 -I/usr/local/include -I/usr/include -I/usr/X11R6/include -
>> I. -I/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/
>> site-packages/numpy/core/include -Isrc -Iagg24/include -I. -I/usr/
>> X11/include/freetype2 -I/usr/X11/include -I/usr/local/include -I/usr/
>> include -I/usr/X11R6/include -I. -I/Library/Frameworks/
>> Python.framework/Versions/2.5/include/python2.5 -c src/_image.cpp -o
>> build/temp.macosx-10.4-i386-2.5/src/_image.o
>> cc1plus: warning: command line option "-Wstrict-prototypes" is valid
>> for C/ObjC but not for C++
>> src/_image.cpp: In member function ‘Py::Object
>> _image_module::from_images(const Py::Tuple&)’:
>> src/_image.cpp:842: error: insn does not satisfy its constraints:
>> (insn 2573 1070 2574 126 agg24/include/agg_color_rgba.h:268 (set
>> (mem:QI (plus:SI (reg/f:SI 6 bp)
>>               (const_int -280 [0xfffffffffffffee8])) [0 SR.2969+0
>> S1 A8])
>>       (reg:QI 5 di)) 56 {*movqi_1} (nil)
>>   (nil))
>> src/_image.cpp:842: internal compiler error: in
>> reload_cse_simplify_operands, at postreload.c:391
>> Please submit a full bug report, with preprocessed source if
>> appropriate.
>> See <URL:http://developer.apple.com/bugreporter> for instructions.
>
> This seems to be an agg and OS X error; it's cropped up here:
> http://trac.osgeo.org/mapserver/ticket/2368
> and John Hunter reported it on the agg list here:
> http://article.gmane.org/gmane.comp.graphics.agg/3963
>
> Unfortunately, the error appears to either not have been fixed by the
> 10.5.1 update, as suggested in the email thread cited above, or the
> error re-appeared in 10.5.2.
>
> Changing the optimization flag from -O3 to -Os and compiling
> _image.cpp manually (along with copying src/_image.cpp to src/
> image.cpp and compiling that manually in the same way) allowed me to
> finish building matplotlib, but clearly an optimized agg image library
> is pretty important... (-O2 didn't work...)
>
> Anyone have any idea at all about this error? Or is just turning off -
> O3 for this file the best thing to do until Apple fixes the compiler
> bug? Does anyone who knows more about agg than I want to try to reduce
> this to a test case?
>
>
> Zach Pincus
>
> Postdoctoral Fellow
> Molecular, Cellular, and Developmental Biology
> Yale University
>
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

   I upgraded my notebook to Slackware-12.0 (which includes python-2.5) and
discovered that the application I'm developing no longer ran. Turns out that
matplotlib went missing during the upgrade.

   So, I just built matplotlib-0.91.2 using the same matplotlib.Slackbuild
script I used on my workstation/server, but this time it failed. The font
manager seems to be the issue; the error message repeatedly is: "Found an
unknown keyword in AFM header (was Underline)". Specifically, the error is
in File "/usr/lib/Python2.5/site-packages/matplotlib/afm.py", line 166, in
_parse_char_metrics
 	name=vals[2].split()[1]
IndexError: List index out of range

   Is this unique to me? What do I do to fix the problem?

TIA,

Rich

-- 
Richard B. Shepard, Ph.D.               |  Integrity            Credibility
Applied Ecosystem Services, Inc.        |            Innovation
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863

Well, that was a good puzzle!

It turns out that in the Wx backends, the figure is created at the 
correct (requested) size, and then immediately the height is shrunk by 
25 pixels (at least on my platform) when the status bar is added to the 
window.  By creating the status bar before the figure canvas I was able 
to prevent this from happening.

This seems like a safe fix to me, but anyone who currently extends the 
Wx Frame (meaning the whole window etc.) and is unknowingly compensating 
for this effect may have problems after my change.

Committed on the maintenance branch in r4997.

http://matplotlib.svn.sourceforge.net/viewvc/matplotlib?view=rev&revision=4997

BTW, I also committed the fix for the range of values in 
figure.subplot.* here:

<http://www.nabble.com/Re%3A-pylab-axis-query-and-possible-bug-p14459682.html>

to the maintenance branch (it was previously only made to the trunk.)

Cheers,
Mike

Gary Ruben wrote:
> Gary Ruben wrote:
>> The attached test.py
> Oops. Here it is.
> Gary R.
> ------------------------------------------------------------------------
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> ------------------------------------------------------------------------
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

Hello,

I'm not sure if there is a nicer way to do what you want and I understand 
correctly what you want to do, but as a workaround I would recommand you the 
following:

use the mainloop-mode after show and an event to rearch a function, which 
includes a "raw_input" to input text from the shell like

import pylab 

def myfunc(event):
    txt = raw_input(" input a string : ")
    print "The string >%s< was recognized and will be executed" % (txt)
    exec(txt)
    pylab.draw()

pylab.figure()
pylab.axes()
pylab.connect("key_press_event", myfunc)        
# call "myfunc" after a key press event
pylab.show()

you can end the mainloop by closing the figure.

best regards
Matthias

On Sunday 02 March 2008 13:31, linzhenhua wrote:
>  Hello,all
>       I have a problem with matplotlib. The numpy and matplotlib versions
> are all the newest versions. First,if I want to plot a figure,I can type
> several command,finally use the show() command,everything seems well,but I
> have to use the Ctrl+c to stop the show() to go further. And I know I can
> use the interactive mode.So first I use ion(),then use the plot command to
> plot figure and draw() command to update the figure,but in this case ,the
> figure toolbar is not visible on the figure and I can not use it.However if
> I run the show() command then the figure toolbar appear and I can control
> the figure using the toolbar. I wonder whether I can take advantage of the
> figure toolbar and the command line at the same time or not ? Best wishes.

Hello Chris,

you may try something like 

plot([x1], [y1], "bo", [x2], [y2], "r+")

or you have to iterate through your data.

best regards
Matthias

On Friday 07 March 2008 10:11, Chris Withers wrote:
> Hi All,
>
> Apologies if I'm missing anything obvious...
>
> How do I plot lines point-by-point as opposed to by passing arrays?
>
> I'm guessing something like:
>
> plot([x],[y])
>
> ...but that feels a bit weird to me.
>
> In any case, using that, I don't know how to plot more than one line at
> a time, so thought I'd ask here...
>
> Hope you can help!
>
> cheers,
>
> Chris

Hello,

I just tried to compile the SVN head of matplotlib (r4994) from source  
on OS X 10.5.2 (with source builds of python 2.5.2 and the SVN head of  
numpy), and ran into an "internal compiler error" in the agg code.  
(pkgconfig 0.23 and wxPython 2.8.7.1 also present and accounted for.)

Here's the compile line and error:
> building 'matplotlib.backends._backend_agg' extension
> gcc -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused- 
> madd -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict- 
> prototypes -I/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
> python2.5/site-packages/numpy/core/include -I/usr/X11/include/ 
> libpng12 -I/usr/local/include -I/usr/include -I/usr/X11R6/include - 
> I. -I/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ 
> site-packages/numpy/core/include -Isrc -Iagg24/include -I. -I/usr/ 
> X11/include/freetype2 -I/usr/X11/include -I/usr/local/include -I/usr/ 
> include -I/usr/X11R6/include -I. -I/Library/Frameworks/ 
> Python.framework/Versions/2.5/include/python2.5 -c src/_image.cpp -o  
> build/temp.macosx-10.4-i386-2.5/src/_image.o
> cc1plus: warning: command line option "-Wstrict-prototypes" is valid  
> for C/ObjC but not for C++
> src/_image.cpp: In member function ‘Py::Object  
> _image_module::from_images(const Py::Tuple&)’:
> src/_image.cpp:842: error: insn does not satisfy its constraints:
> (insn 2573 1070 2574 126 agg24/include/agg_color_rgba.h:268 (set  
> (mem:QI (plus:SI (reg/f:SI 6 bp)
>                (const_int -280 [0xfffffffffffffee8])) [0 SR.2969+0  
> S1 A8])
>        (reg:QI 5 di)) 56 {*movqi_1} (nil)
>    (nil))
> src/_image.cpp:842: internal compiler error: in  
> reload_cse_simplify_operands, at postreload.c:391
> Please submit a full bug report, with preprocessed source if  
> appropriate.
> See <URL:http://developer.apple.com/bugreporter> for instructions.

This seems to be an agg and OS X error; it's cropped up here:
http://trac.osgeo.org/mapserver/ticket/2368
and John Hunter reported it on the agg list here:
http://article.gmane.org/gmane.comp.graphics.agg/3963

Unfortunately, the error appears to either not have been fixed by the  
10.5.1 update, as suggested in the email thread cited above, or the  
error re-appeared in 10.5.2.

Changing the optimization flag from -O3 to -Os and compiling  
_image.cpp manually (along with copying src/_image.cpp to src/ 
image.cpp and compiling that manually in the same way) allowed me to  
finish building matplotlib, but clearly an optimized agg image library  
is pretty important... (-O2 didn't work...)

Anyone have any idea at all about this error? Or is just turning off - 
O3 for this file the best thing to do until Apple fixes the compiler  
bug? Does anyone who knows more about agg than I want to try to reduce  
this to a test case?


Zach Pincus

Postdoctoral Fellow
Molecular, Cellular, and Developmental Biology
Yale University

hu...@ya... wrote:
> 				Hello,
> 
> I have some stupid questions about how to use colorbar.
> 
> 1) I would like to be able to put the colorbar where I went: top, bottom, 
> left, right. For what I see I can do only a vertical left and horizontal 
> bottom ones (with a simple use of the function).
> I know that it's possible to do a colorbar only but it's difficult to place 
> them a little bit automatically and that bring my second question.

This looks like a feature request: instead of specifying "horizontal" or 
"vertical", be able to specify "top", "bottom", "left", or "right". 
This is fairly easy in principle, but there are some wrinkles such that 
I am not sure it would be satisfactory in practice--some custom 
adjustments might usually be needed depending on whether the main axes 
have a title (in the case of "top") or an xlabel (in the case of 
"left").  You may be better off simply figuring out what main and 
colorbar axes positions work best for your particular case and then 
making those axes explicitly.

> 
> 2) I would like that the colorbar with exactly the same size than the image I 
> plot with pcolor. It's working when I'm not using the aspect='equal' in the 
> subplot but not with this option. Naturally I want to not change the aspect 
> of my image and so it's a big problem for me. The only solution I found is to 
> manipulate the colorbar with the shrink valu but it's a little bit painfull 
> especially the value change for each pcolor image (they doesn't have always 
> the same size).

This is a common request, and a reasonable one, but unfortunately it is 
not straightforward to implement automatically given mpl's internal 
structure.  Again, however, you get the desired result quite easily by 
creating your own axes explicitly.

> 
> 3) I would like to give a label to the colorbar (ie if the colorbar is at the 
> bottom a label under the colorbar etc). To tell people what means the colors 
> but I didn't find anyway to do it. xlabel work for the pcolor object (as 
> expected) and there are no colorbar.xlabel function.

Use the set_label() method.
...
cbar = fig1.colorbar(im,orientation='horizontal')
cbar.set_label('label')
...

Eric

				Hello,

I have some stupid questions about how to use colorbar.

1) I would like to be able to put the colorbar where I went: top, bottom, 
left, right. For what I see I can do only a vertical left and horizontal 
bottom ones (with a simple use of the function).
I know that it's possible to do a colorbar only but it's difficult to place 
them a little bit automatically and that bring my second question.

2) I would like that the colorbar with exactly the same size than the image I 
plot with pcolor. It's working when I'm not using the aspect='equal' in the 
subplot but not with this option. Naturally I want to not change the aspect 
of my image and so it's a big problem for me. The only solution I found is to 
manipulate the colorbar with the shrink valu but it's a little bit painfull 
especially the value change for each pcolor image (they doesn't have always 
the same size).

3) I would like to give a label to the colorbar (ie if the colorbar is at the 
bottom a label under the colorbar etc). To tell people what means the colors 
but I didn't find anyway to do it. xlabel work for the pcolor object (as 
expected) and there are no colorbar.xlabel function.

Thank you for any help.

N.

ps: i join a simple script to show my problem

#!/usr/bin/env python

import pylab
import numpy

a = numpy.arange(100).reshape((10,10))

fig1 = pylab.figure()

ax = fig1.add_subplot(141)
im = ax.pcolor(a)
fig1.colorbar(im,orientation='horizontal') 
pylab.xlabel('label')

ax = fig1.add_subplot(142)
im = ax.pcolor(a)
fig1.colorbar(im,orientation='vertical')
pylab.xlabel('label')

ax = fig1.add_subplot(143,aspect='equal')
im = ax.pcolor(a)
fig1.colorbar(im,orientation='vertical')
pylab.xlabel('label')

ax = fig1.add_subplot(144,aspect='equal')
im = ax.pcolor(a)
fig1.colorbar(im,orientation='horizontal')
pylab.xlabel('label')


pylab.show()

Hi ,

I am trying to plot a filled triangle (or if possible any filled
polygon) in 3D. I am afraid, I am missing something very basic here.

I'd like to do something like:
x=[0,1,1]   #coordintes of the three corners
y=[0,0,1]
z=[3,8,1]
ax.plane(x,y,z,facecolor='r')

So far I tried the "plot_surface", but this requires the points to be on
a rectangular grid. The solution proposed in "*Re: [Matplotlib-users] plot 3D with filled curves is similar to what i am searching for,
 but allows the planes to be only along one of the  main  x-y-z axes. I tried to write this myself by
extracting info from axes3d.plot_surface and the art3d, but unfortunately failed miserable.

Anyone go a clue?

Thanks a lot in advance!

Cheers,

Ulrich 

Gary Ruben wrote:
> The attached test.py
Oops. Here it is.
Gary R.

The attached test.py produces the attached png files with the Agg and 
WXAgg backends respectively. I've just started using the latest 
Enthought all-in-one beta which ships with matplotlib 0.91.2 and 
defaults to using WXAgg rather than TkAgg, so I've only just noticed 
this behaviour. I edited rcsetup.py, making the changes described in 
<http://www.nabble.com/Re%3A-pylab-axis-query-and-possible-bug-p14459682.html> 
to enable this to run.

The other backends I was able to test (PDF, PS, SVG, TkAgg) all produce 
correct output (same as test_Agg.png), so the scaling problem seems 
looks like it's specific to WXAgg.

Gary R.

I use the python-netcdf4 package in linux.

http://code.google.com/p/netcdf4-python/

You can make a netcdf3-compatible version of the library by installing 
with:

python setup-nc3.py install


Jordan

Hi Zane,

>This all seems to suggest to me, after a little poking around, that the 
>NetCDF file format would be good.  I've managed to get SciPy and 
>Matplotlib and Basemap installed and apparently working together 
>happily... but I can't seem to find any "official" module within that 
>structure for writing NetCDF files.  There are references to the old 
>Scientific.IO.NetCDF package, and I found something that had been 
>hanging around in the scipy.sandbox area... but which isn't there any 
>more.  There's quite a list of Python interfaces to NetCDF on the 
>Unidata website... but they don't make any recommendations as to which 
>is "best".

>If I'm going to be working within Matplotlib and Basemap and SciPy, does 
>anyone have a good recommendation for which NetCDF Python package to 
>use?  Or issues I should consider?

I have been very happy with PyNIO. The main reason I choose this package was
that it has support for other formats as well (e.g. GRIB) and is actively developed
and has great support. The next version of it will also be open source if that
matters.

Another package which I have been looking at is netcdf4-python. The interface
seems very similar to that of PyNIO and it has some nice features that are
not present in the PyNIO package. I really like the features that are handling
Climate and Forecast convention specialities. These are date conversion utilities
(which I am using in combination with the PyNIO package) and automatic packing
and unpacking.

Hope this helps,
Jesper

Hi All,
  I am trying to solve the Hamiltonian of a linear chair of atoms using green’s function and I would like to do this using python.
  Does anyone know any pre-existing library functions and literature that will be helpful?
  Thanks
  EOF 


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Zane Selvans wrote:
> I have a model that calculates the tidal stress tensor (a symmetric 
> 2x2 matrix) on the surface of an icy satellite.  It's just two 
> orthogonal vector fields on the surface of the body.  I want to be 
> able to make pretty plots of the model output, including:
>
> * The magnitude of either one of the fields at any point
> * The magnitude and orientation of either or both fields, as a grid of 
> little arrows, whose colors correspond to whether the value is 
> positive or negative.
> * Animations of time (or other) series.
>
> I also want to be able to save the model output in a format that other 
> people can read and manipulate.  Ideally, model run results could also 
> be hosted on a web server, and other people could view them remotely.
>
> I just re-wrote the model in pure Python (it had been written in C 
> previously), and I've been using my own hacked together ASCII file 
> format and a Perl script that builds GMT plots based on them to make 
> figures and visualizations up until now... but I'm sick of that and 
> want something more flexible.
>
> This all seems to suggest to me, after a little poking around, that 
> the NetCDF file format would be good.  I've managed to get SciPy and 
> Matplotlib and Basemap installed and apparently working together 
> happily... but I can't seem to find any "official" module within that 
> structure for writing NetCDF files.  There are references to the old 
> Scientific.IO.NetCDF package, and I found something that had been 
> hanging around in the scipy.sandbox area... but which isn't there any 
> more.  There's quite a list of Python interfaces to NetCDF on the 
> Unidata website... but they don't make any recommendations as to which 
> is "best".
>
> If I'm going to be working within Matplotlib and Basemap and SciPy, 
> does anyone have a good recommendation for which NetCDF Python package 
> to use?  Or issues I should consider?
>
> Thanks for any insight,
>
> Zane
>

Zane:  Basemap already includes a NetCDFFile function that can read 
netCDF and opendap (http://opendap.org) datasets.  If you need to write 
netCDF, then netcdf4-python should do fine.

-Jeff

-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
325 Broadway                Boulder, CO, USA 80305-3328

Zane Selvans wrote:

 > If I'm going to be working within Matplotlib and Basemap and SciPy,
 > does anyone have a good recommendation for which NetCDF Python
 > package to use?  Or issues I should consider?

We're heavy users of netcdf4-python and it's working well.  

 http://code.google.com/p/netcdf4-python/

If you want to stick with netcdf3 until the official netcdf4 release, then
just run

python setup-nc3.py install

regards, Phil

I have a model that calculates the tidal stress tensor (a symmetric 2x2 
matrix) on the surface of an icy satellite.  It's just two orthogonal 
vector fields on the surface of the body.  I want to be able to make 
pretty plots of the model output, including:

* The magnitude of either one of the fields at any point
* The magnitude and orientation of either or both fields, as a grid of 
little arrows, whose colors correspond to whether the value is positive 
or negative.
* Animations of time (or other) series.

I also want to be able to save the model output in a format that other 
people can read and manipulate.  Ideally, model run results could also 
be hosted on a web server, and other people could view them remotely.

I just re-wrote the model in pure Python (it had been written in C 
previously), and I've been using my own hacked together ASCII file 
format and a Perl script that builds GMT plots based on them to make 
figures and visualizations up until now... but I'm sick of that and want 
something more flexible.

This all seems to suggest to me, after a little poking around, that the 
NetCDF file format would be good.  I've managed to get SciPy and 
Matplotlib and Basemap installed and apparently working together 
happily... but I can't seem to find any "official" module within that 
structure for writing NetCDF files.  There are references to the old 
Scientific.IO.NetCDF package, and I found something that had been 
hanging around in the scipy.sandbox area... but which isn't there any 
more.  There's quite a list of Python interfaces to NetCDF on the 
Unidata website... but they don't make any recommendations as to which 
is "best".

If I'm going to be working within Matplotlib and Basemap and SciPy, does 
anyone have a good recommendation for which NetCDF Python package to 
use?  Or issues I should consider?

Thanks for any insight,

Zane

-- 
Zane Selvans
Amateur Human
za...@id...
303/815-6866
PGP Key: 55E0815F