matplotlib-users Mailing List for matplotlib

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

Hello,
I am also interested in masking polygons and defining the polygon by 'clicking' on the image... but I do not know anything about GUI.... does anyone can help? Is there already something implemented?
Thanks!
Chiara
> Date: 2008年1月23日 13:50:15 +1300
> From: am...@gm...
> To: mat...@li...
> Subject: Re: [Matplotlib-users] Polygon masking possible?
> 
> Hi Søren,
> 
> I've put this back on the list in case it's useful to anyone else, or
> if there are better suggestions or improvements around. Hope you don't
> mind.
> 
> On 22/01/2008, Søren Nielsen <sor...@gm...> wrote:
> > Yeah i'd like to see your code if I can..
> 
> import numpy as n
> 
> def get_poly_pts(x, y, shape):
> """Creates convex polygon mask from list of corners.
> 
> Parameters
> ----------
> x : array_like
> x co-ordinates of corners
> y : array_like
> y co-ordinates of corners, in order corresponding to x
> shape : array_like
> dimension sizes of result
> 
> Returns
> -------
> build : ndarray
> 2-D array of shape shape with values True inside polygon
> 
> Notes
> -----
> Code is constrained to convex polygons by "inside"
> assessment criterion.
> 
> """
> x = n.asarray(x)
> y = n.asarray(y)
> shape = n.asarray(shape)
> npts = x.size # should probably assert x.size == y.size
> inds = n.indices( shape )
> xs = inds[0]
> ys = inds[1]
> xav = n.round(x.mean()).astype(int)
> yav = n.round(y.mean()).astype(int)
> for i in xrange(npts): # iterate over pairs of co-ordinates
> j = (i + 1) % npts
> m = (y[j] - y[i])/(x[j] - x[i])
> c = (x[j] * y[i] - x[i] * y[j])/(x[j] - x[i])
> thisone = ( ys > m * xs + c )
> if thisone[xav, yav] == False:
> thisone = ~thisone
> if i == 0:
> build = thisone
> else:
> build &= thisone
> return build
> 
> (released under BSD licence)
> 
> > I just needed the push over the edge to know how to draw on the canvas,
> > mapping clicks etc. since i'm still fairly new to matplotlib, so I think
> > your code will be helpfull.
> 
> I hope so. As you can see this code doesn't do any of the drawing or
> click collecting, but the cookbook page should be able to guide you
> there. Ask again on the list if you have any further questions and
> we'll see if we can help.
> 
> Also, the code assumes that the average co-ordinate is inside the
> shape - that's true for convex polygons, but not necessarily for
> arbitrary ones. I use if after taking a convex hull of a greater list
> of points (using the delaunay module in scipy (now in scikits, I
> hear)), which ensures convexity. You just need to be aware of that
> limitation.
> 
> Cheers,
> 
> A.
> -- 
> AJC McMorland, PhD candidate
> Physiology, University of Auckland
> 
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Ryan,
See examples/colorbar_only.py. I think it illustrates what you want.
Eric
Ryan May wrote:
> Hi,
> 
> In working on creating updating pcolor plots, I noticed that I can't 
> create colorbars (which should be static) without first displaying an 
> image. I have a fixed Normalize object and colormap, so I would think 
> that the colorbar wouldn't actually need any information from the image 
> itself.
> 
> Is there any to create a colorbar without first actually plotting an 
> image? If not, is there any reason colorbar couldn't be modified to 
> work using only a norm and a cmap?
> 
> Thanks,
> 
> Ryan
>