Scientific Programming with Python

Documentation

• http://www.python.org/doc/

• NumPy for IDL users

• NumPy for Matlab users

• SciPy tutorial

Modules for Scientific Computing and Visualization

SciPy/NumPy

• http://www.scipy.org/

pylab

• Matplotlib/pylab Plotting functions with a high degree of Matlab compatibility

• http://matplotlib.sourceforge.net/basemap/doc/html/ Matplotlib Basemap

To enable Basemap (on ZMAW Linux ia32/x64 and solaris10) you have to type before starting Python

module load Python/2.4.4

or

module unload Python
module load ncl/5.0.0-bin
module load R/2.7.0
module load Python/2.6
module load gdal

In Python you can import the Basemap module by

from mpl_toolkits.basemap import Basemap

GDAL

• GDAL - Geospatial Data Abstraction Library for various satellite data formats

PyNGL

• PyNGL/PyNIO Python interface to NCAR Command Language

• Scientific visualization and data formats (netCDF, HDF, GRIB etc.)

To enable PyNGL (on ZMAW Linux ia32/x64 and solaris10) you have to type

module load PyNGL/1.2.0

Python Interface to GrADS

• http://opengrads.org/wiki/index.php?title=Python_Interface_to_GrADS

RPy

• RPy (R from Python) Statistical computing and graphics

F2PY: Fortran to Python interface generator

Calling Fortran code from python is easy! Create a file hello.f:

C File hello.f
      subroutine foo (a)
      integer a
      print*, "Hello from Fortran!"
      print*, "a=",a
      end

Run f2py -c -m hello hello.f

Now in IPython try:

In [1]: import hello
In [2]: hello.foo(4)
 Hello from Fortran!
 a=           4

Example taken from

• F2PY: Fortran to Python interface generator

Topical Modules

• Seawater is a package for computing properties of seawater (UNESCO 1981 and UNESCO 1983).

• Escript/Finley: Fast Finite Elements for Partial Differential Equations

More topical software can be found at http://scipy.org/Topical_Software

Installation in the home directory

The seawater module is installed on the ZMAW machines for Python 2.6. Use

module load Python/2.6.2

to set up the environment. In the following it is explained how to install the module for the case if it would be not available or if a different version of python has to be used.

Installation of module seawater in directory ~/modules

python setup.py install --prefix=~/modules/

Usage

import sys,os
home=os.getenv('HOME')
genpath=home+'/modules/lib/python2.4/site-packages/'
if not sys.path.__contains__(genpath):
    sys.path.append(genpath)
from seawater import *

Download

A basic system for scientific computing consists of Python, ipython, numpy/scipy, pylab, and an editor of your choice

• Python interpreter

• IPython shell

• SciPy

• Matplotlib/pylab

• Editor (a nice editor for Windows user, if you don't like to install xemacs)

The python(x,y) distribution contains all that above.