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= LES python seminar series (Thursday, 10:30 - 12:00) = = LES python seminar series (Thursday, 10:30 - 12:00, Geomatikum, 1729) =
contact: Alex Loew, Julia Pongratz
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Python related announcements and questions:''' python-friends@lists.zmaw.de '''
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contact: Alex Loew, Julia Pongratz Join the list by sending: ''' python-friends-join@lists.zmaw.de '''
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== Seminar outline == = Seminar outline =
== Part 1 ==
=== Working with arrays (Gernot, Michael) (19.07.2012) ===
 . [[PythonCourse/PythonLES/SeminarLog1|Commented examples from the seminar]]
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=== Working with arrays (Gernot,Michael) (19.07.2012) ===
 * numpy arrays (indexing, slicing, views ...)		  * general information on [[http://docs.python.org/reference/datamodel.html|python data model]] ([[http://docs.python.org/library/copy.html|copy, references, deepcopy]])
 * [[http://docs.python.org/library/functions.html#map|map]] and [[http://docs.python.org/tutorial/controlflow.html#lambda-forms|lambda]] functions
 * [[http://docs.scipy.org/doc/numpy/reference/arrays.ndarray.html|numpy arrays]] (indexing, slicing, views ...)
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 * general information on python data model (copy, references, deepcopy)
 * masked arrays		   * data type conversions
  * [[http://docs.scipy.org/doc/numpy/reference/routines.math.html|elementwise functions]]
  * [[http://docs.scipy.org/doc/numpy/reference/routines.linalg.html|linear algebra]]
  * [[http://docs.scipy.org/doc/numpy/reference/routines.statistics.html|array statistics]]
 * [[http://docs.scipy.org/doc/numpy/reference/maskedarray.generic.html|masked arrays]]
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 * map and lambda functions
 * pickle, cPickle		   * [[http://docs.scipy.org/doc/numpy/reference/routines.io.html|numpy input and output]]
  * general input and output ([[http://docs.python.org/library/functions.html#open|opening a file]] and [[http://docs.python.org/library/stdtypes.html#file-objects|working with a file]])
 * [[http://docs.python.org/library/pickle.html|pickle]], cPickle
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 * subplots, figure, axis objects
 * a brief tour through matplotlib gallery		 [[PythonCourse/PythonLES/SeminarLog2|Course material for plotting]]

* subplots, figure, axis objects; easy and more sophisticated appraoches

 * always use figure/ax
 * a brief tour through [[http://matplotlib.sourceforge.net/gallery.html|matplotlib gallery]]
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  * fill between   * fill_between
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 * working with different axes in a single plot; twinx()
 * saving figures
  * fitting to actual content
 * [[http://matplotlib.sourceforge.net/users/tight_layout_guide.html|tight_layout]]
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=== Geospatial data format handling and vizualization (Mikhail) (09.08.2012) ===
 * Nio - handling netCDF		 === Geospatial data format handling and vizualization (Mikhail) (16.08.2012) ===
[[IoBasemapNgl|Lesson code examples]]

 * [[http://www.pyngl.ucar.edu/Nio.shtml|PyNio]] - handling netCDF
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 * GDAL: the door to all available data formats ?
 * Basemap
 * pyNGL
 		    * data type conversion
    * how to write a numpy array (double) in a float netcdf variable?
    * how to store data as scaled integers?
 * [[http://www.gdal.org/|GDAL]]: the door to a huge number of different file formats. [[http://www.gdal.org/gdal_tutorial.html|GDAL (Python) API tutorial]]
 * [[http://matplotlib.github.com/basemap/|Basemap]]
 * [[http://www.pyngl.ucar.edu/|PyNGL]] [[http://www.pyngl.ucar.edu/Tutorial/|Tutorial]]
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 * replacing BASH: working with os adn system objects [[PythonCourse/PythonLES/SeminarLog4|Commented examples from the seminar]]

 * replacing BASH: working with os and system objects
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 * how to debug a python program?
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=== structuring a program (Mikhail) (13.9.2012) ===
 * python functions with optional and kwargs
 * python object oriented programming (classes etc)		 === Structuring a program (Mikhail) (13.9.2012) ===
[[PythonCourse/PythonLES/SeminarLog5|Commented program from the seminar]]

 * general structure of python scripts
 * writing python functions, what are the keyworded and the non-keyworded arguments
 * writing modules and classes, why and how to create custom objects
 * naming convention
 * how to parse command line input for options and arguments

== Part 2 ==
=== pyCMBS (Alex) (31.10. as part of the Wednsday seminar) ===
 * introduction to pyCMBS
 * cdo interfacing
 * anomaly calculations, hovmoeller plots etc ...
 * EOF, SVD analysis

=== time series analysis: the Pandas module (Mikhail) (25.10.) ===
[[PythonCourse/PythonLES/Pandas|Lesson code]]

 * Indexed arrays
 * Merging, aligning and restructuring timeseries
 * Reindexing timeseries
 * [[http://www.youtube.com/watch?v=w26x-z-BdWQ|Video tutorial by Wes McKinney]]
 * [[http://pandas.pydata.org/pandas-docs/dev/api.html|Official site with documentation]]

=== parallel programming (Heinrich Widmann) (08.11.) ===
[[PythonCourse/PythonLES/Parallel_Programming|Lesson code]] [[PythonCourse/PythonLES/ParallelSlides|... and slides]]

 * Threading vs. multiprocessing
  * The GIL issue
 * ParallelPython module (pp)
 * Processing module
 * Further approaches and techniques ...
 * Not (really) addressed :
  * openMP, MPI
  * more sophuisticated clustering, scheduling and load balancing ....
 * [[https://github.com/ianozsvald/ParallelPython_EuroSciPy2012|Ian Ozsvald's lesson at SciPy2012]]

=== python CDO interface (Ralf Mueller) (22.11.) ===
 * [[https://code.zmaw.de/projects/cdo/wiki/Cdo{rbpy}|cdo - python/ruby interface]]

=== Integration of other programming languages (Nikolay Koldunov, Mikhail Itkin, 06.12) ===
 * Ipython Notebook [[https://wiki.zmaw.de/lehre/PythonCourse/PythonLES?action=AttachFile&do=get&target=map.ipynb|Ipython lesson notebook]]
 * f2py | [[PythonCourse/PythonLES/F2Py|f2py lesson code]]
 * R and Python tutorials:
  * [[http://www.r-bloggers.com/accessing-r-from-python-using-rpy2/|rpy2: Accessing R from Python video tutorial]]
  * [[http://rpy.sourceforge.net/rpy2/doc-dev/html/introduction.html|Gentle RPY2 tutorial]]
 * [[http://wiki.python.org/moin/IntegratingPythonWithOtherLanguages|Python integration with other languages]]
 * Bonus: [[http://code.google.com/p/pyresample/|Pyresample]]- reprojection of geospatial data


= Tips and Tricks =
 * Spearman rank correlation revisited in python [[attachment:Spearman.pdf | Documentation how to do it (PDF)]], [[ attachment:TestSpearman.py | script ]]
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=== time series analysis: the Pandas module (Mikhail) ===
 * introduction to pandas timeseries analysis module



=== pyCMBS (Alex) (???? on a separate day BEFORE the summer break ???) ===
 * introduction to pyCMBS
 * cdo interfacing
 * anomaly calculations, hovmoeller plots etc


=== Integration of other programming languages ===
 * R
 * f2py
 * C-code
 * matlab





=== scientific data analysis in python ===
 * EOF, SVD analysis

=== running JSBACH offline in a python environment (Gernot) ===

=== parallel programming (Heinrich Widmann) ===
 * openMP, MPI, subprocesses, threads

=== statistics in python (???) ===
 * statistical analysis of large data sets

=== other topics ===		 == other topics ==
 * statistical analysis of large data sets
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 * GUI programming  * GUI programming (Alex, remon???)
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= projects to work on ... =
 * MPI-ESM in python (Christian) ;-)



 

LES python seminar series (Thursday, 10:30 - 12:00, Geomatikum, 1729)

contact: Alex Loew, Julia Pongratz

Python related announcements and questions: python-friends@lists.zmaw.de

Join the list by sending: python-friends-join@lists.zmaw.de

Contents

  1. LES python seminar series (Thursday, 10:30 - 12:00, Geomatikum, 1729)
    1. What you should be able to do in advance
  2. Seminar outline
    1. Part 1
      1. Working with arrays (Gernot, Michael) (19.07.2012)
      2. Plotting (1D,2D,3D) (Alex) (2.8.2012)
      3. Geospatial data format handling and vizualization (Mikhail) (16.08.2012)
      4. system operations (Michael) (30.8.2012)
      5. Structuring a program (Mikhail) (13.9.2012)
    2. Part 2
      1. pyCMBS (Alex) (31.10. as part of the Wednsday seminar)
      2. time series analysis: the Pandas module (Mikhail) (25.10.)
      3. parallel programming (Heinrich Widmann) (08.11.)
      4. python CDO interface (Ralf Mueller) (22.11.)
      5. Integration of other programming languages (Nikolay Koldunov, Mikhail Itkin, 06.12)
  3. Tips and Tricks
    1. other topics

What you should be able to do in advance

  • python programming structures
  • if clauses
  • function calling
  • print statements
  • well, running python scripts (in python shell and interactive shell like ipython)
  • edit python scripts in the editor of your choice
  • ...

Seminar outline

Part 1

Working with arrays (Gernot, Michael) (19.07.2012)

Plotting (1D,2D,3D) (Alex) (2.8.2012)

Course material for plotting

* subplots, figure, axis objects; easy and more sophisticated appraoches

  • always use figure/ax

  • a brief tour through matplotlib gallery

    • lineplots
    • fill_between
    • contour plots
  • nice colorbars, colormaps handling etc.
  • working with different axes in a single plot; twinx()
  • saving figures
    • fitting to actual content

  • tight_layout

Geospatial data format handling and vizualization (Mikhail) (16.08.2012)

Lesson code examples

  • PyNio - handling netCDF

    • read netCDF
    • write netCDF
      • data type conversion
        • how to write a numpy array (double) in a float netcdf variable?
        • how to store data as scaled integers?

  • GDAL: the door to a huge number of different file formats. GDAL (Python) API tutorial

  • Basemap

  • PyNGL Tutorial

system operations (Michael) (30.8.2012)

Commented examples from the seminar

  • replacing BASH: working with os and system objects
  • os.system, subprocess etc.
  • python as a replacement for bash
  • how to debug a python program?

Structuring a program (Mikhail) (13.9.2012)

Commented program from the seminar

  • general structure of python scripts
  • writing python functions, what are the keyworded and the non-keyworded arguments
  • writing modules and classes, why and how to create custom objects
  • naming convention
  • how to parse command line input for options and arguments

Part 2

pyCMBS (Alex) (31.10. as part of the Wednsday seminar)

  • introduction to pyCMBS
  • cdo interfacing
  • anomaly calculations, hovmoeller plots etc ...
  • EOF, SVD analysis

time series analysis: the Pandas module (Mikhail) (25.10.)

Lesson code

parallel programming (Heinrich Widmann) (08.11.)

Lesson code ... and slides

  • Threading vs. multiprocessing
    • The GIL issue

  • ParallelPython module (pp)

  • Processing module
  • Further approaches and techniques ...
  • Not (really) addressed :
    • openMP, MPI
    • more sophuisticated clustering, scheduling and load balancing ....

  • Ian Ozsvald's lesson at SciPy2012

python CDO interface (Ralf Mueller) (22.11.)

Integration of other programming languages (Nikolay Koldunov, Mikhail Itkin, 06.12)

Tips and Tricks

other topics

  • statistical analysis of large data sets
  • animations
  • GUI programming (Alex, remon???)
  • H5PY - simple access to HDF5 files
  • python2.x or python3.x (does it make a difference?)

LehreWiki: PythonCourse/PythonLES (last edited 2012-12-19 13:14:36 by AlexanderLoew)