Thread: [Matplotlib-users] NetCDF input/output/plotting using Matplotlib w/ Basemap

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

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

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