Differences between revisions 1 and 11 (spanning 10 versions)

Python at KlimaCampus

This page shall be a central help for ZMAW/KlimaCampus users of Python. Contact LarsKaleschke for permission to edit this page. Please help to fill this page with useful information about Python for climate research and data analysis.

Contents

Python at KlimaCampus
1. ZMAW Settings
2. Courses
Documentation and further reading
Modules for Scientific Computing and Visualization
Topical Modules
Python and Climate
Download (try this at home)
Literature

ZMAW Settings

Python2.6.2 requires

module load R/2.7.0
module load Python/2.6.2

More ZMAW specific settings

Courses

Open Source Scripting for Geo-Scientific Data Processing and Analysis by LarsKaleschke KlimaCampus Lecture

Documentation and further reading

http://www.python.org/doc/ Standard documentation
NumPy for IDL users
NumPy for Matlab users
SciPy tutorial
Software Carpentry

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

Import the Basemap module

from mpl_toolkits.basemap import Basemap

GDAL

GDAL - Geospatial Data Abstraction Library for various satellite data formats

PyNGL PyNio

PyNGL/PyNIO Python interface to NCAR Command Language
Scientific visualization and data formats (netCDF, HDF, GRIB etc.)

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!

Fortran to Python

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

Python and Climate

Download (try this at home)

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.

Literature

Python Scripting for Computational Science, Hans Petter Langtangen, Springer (available in the ZMAW library)
Matplotlib for Python Developers - Build remarkable publication quality plots the easy way, Sandro Tosi, Packt Publishing, Birmingham - Mumbai, 2009

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-== Lectures ==
+This page shall be a central help for ZMAW/KlimaCampus users of Python. Contact LarsKaleschke for permission to edit this page. Please help to fill this page with useful information about Python for climate research and data analysis.
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- * [[http://wiki.zmaw.de/lehre/OpenSource2010|Open Source Scripting for Geo-Scientific Data Processing and Analysis]] by LarsKaleschke
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-== Documentation ==
+<<TableOfContents(2)>>
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- * 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]]
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-== Modules for Scientific Computing and Visualization ==
+== ZMAW Settings ==
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+Line 16:
-=== 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):
+Python2.6.2 requires
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+Line 22:
-In Python you can import the Basemap module by
+[[/ZMAW|More ZMAW specific settings]]

== Courses ==

 * [[http://wiki.zmaw.de/lehre/OpenSource2010|Open Source Scripting for Geo-Scientific Data Processing and Analysis]] by LarsKaleschke '''KlimaCampus Lecture'''
 
= Documentation and further reading =

 * http://www.python.org/doc/ Standard documentation
 * [[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]]
 * [[http://software-carpentry.org/|Software Carpentry]]


= 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

Import the Basemap module
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-=== GDAL ===
+== GDAL ==
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+Line 56:
-To enable GDAL use
{{{
module load gdal
}}}
+== PyNGL PyNio ==
-Line 50:
+Line 58:
-{{{
from osgeo import gdal
}}}


=== PyNGL PyNio ===
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+Line 61:
-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 ===
+== Python Interface to GrADS ==
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-=== RPy ===
+== RPy ==
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-=== F2PY: Fortran to Python interface generator ===
+== F2PY: Fortran to Python interface generator ==
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+Line 68:
-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
}}}
+Calling Fortran code from python is easy!
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+Line 70:
-Run
{{{f2py -c -m hello hello.f}}}
+[[/F2PY|Fortran to Python]]
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+Line 72:
-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 ==
+= Topical Modules =
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+= Python and Climate =
 
 * [[http://geosci.uchicago.edu/~rtp1/ClimateBook/ClimateBook.html|Principles of Planetary Climate (RAYMOND T. PIERREHUMBERT)]]
 * [[http://maths.ucd.ie/~rca/climt/|CliMT: An object-oriented Climate Modeling and diagnostics Toolkit]]
 * [[http://www2-pcmdi.llnl.gov/cdat|Climate Data Analysis Tools (CDAT)]]
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-=== 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 ==
+= Download (try this at home) =
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+Line 96:
+= Literature =
 
 * Python Scripting for Computational Science, Hans Petter Langtangen, Springer (available in the ZMAW library)
 * Matplotlib for Python Developers - Build remarkable publication quality plots the easy way, Sandro Tosi, Packt Publishing, Birmingham - Mumbai, 2009