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[[OpenSource2010|Open Source Scripting for Geo-Scientific Data Processing and Analysis]]

== Documentation ==

 * http://www.python.org/doc/
 * [[http://www.cfa.harvard.edu/~jbattat/computer/python/science/idl-numpy.html|NumPy for IDL users]]
 * [[http://www.scipy.org/NumPy_for_Matlab_Users|NumPy for Matlab users]]
 * [[http://www.tau.ac.il/~kineret/amit/scipy_tutorial/|SciPy tutorial]]

== Modules for Scientific Computing and Visualization ==

=== SciPy/NumPy ===
 * http://www.scipy.org/

=== pylab ===
 * [[http://matplotlib.sourceforge.net/|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 Python2.4.4:
{{{
module load Python/2.4.4
}}}
or to start Python2.6.2 (recommended):
{{{
module load R/2.7.0
module load Python/2.6.2
}}}

In Python you can import the Basemap module by
{{{
from mpl_toolkits.basemap import Basemap
}}}
=== GDAL ===
 * [[http://www.gdal.org/|GDAL - Geospatial Data Abstraction Library]] for various satellite data formats

To enable GDAL use
{{{
module load gdal
}}}

{{{
from osgeo import gdal
}}}


=== PyNGL PyNio ===
 * [[http://www.pyngl.ucar.edu/|PyNGL/PyNIO]] Python interface to [[http://www.ncl.ucar.edu/ | 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
}}}

Please note, that Nio should be on the top of the list, e.g.

{{{
import Nio
from osgeo import gdal
import pylab as pl
}}}


=== Python Interface to GrADS ===
 * http://opengrads.org/wiki/index.php?title=Python_Interface_to_GrADS
=== RPy ===
 * [[http://rpy.sourceforge.net/| 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

 * [[http://cens.ioc.ee/projects/f2py2e/|F2PY: Fortran to Python interface generator]]

== Topical Modules ==

 * [[http://www.imr.no/~bjorn/python/seawater/index.html|Seawater]] is a package for computing properties of seawater (UNESCO 1981 and UNESCO 1983).
 * [[https://launchpad.net/escript-finley/|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

 * [[http://python.org/download/|Python interpreter]]
 * [[http://ipython.scipy.org/moin/Download|IPython shell]]
 * [[http://www.scipy.org/Download| SciPy]]
 * [[http://matplotlib.sourceforge.net/|Matplotlib/pylab]]
 * [[http://www.crimsoneditor.com/| Editor]] (a nice editor for Windows user, if you don't like to install xemacs)

The [[http://www.pythonxy.com/foreword.php|python(x,y)]] distribution contains all that above.