Differences between revisions 1 and 50 (spanning 49 versions)

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

contact: Alex Loew, Julia Pongratz

Contents

LES python seminar series (Thursday, 10:30 - 12:00, Geomatikum, 1729)
1. What you should be able to do in advance
Seminar outline

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)

Commented examples from the seminar
general information on python data model (copy, references, deepcopy)
map and lambda functions
numpy arrays (indexing, slicing, views ...)
array functions (mean, sum etc. along axes)
- data type conversions
- elementwise functions
- linear algebra
- array statistics
masked arrays
reading ASCII files etc.
- numpy input and output
- general input and output (opening a file and working with a file)
pickle, cPickle

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

Indexed arrays
Merging, aligning and restructuring timeseries
Reindexing timeseries
Video tutorial by Wes McKinney
Official site with documentation

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.)

cdo - python interface

Integration of other programming languages (Alex, 06.12)

R
f2py
C-code
matlab
http://wiki.python.org/moin/IntegratingPythonWithOtherLanguages

-  ⇤ ← Revision 1 as of 2012-07-05 16:10:43 → 
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+   ← Revision 50 as of 2012-11-13 06:50:50 → ⇥
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-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-= LES python seminar series =
+= LES python seminar series (Thursday, 10:30 - 12:00, Geomatikum, 1729) =
-Line 18:
+Line 17:
-== Seminar outline ==
+= Seminar outline =
== Part 1 ==
=== Working with arrays (Gernot, Michael) (19.07.2012) ===
 . [[PythonCourse/PythonLES/SeminarLog1|Commented examples from the seminar]]
-Line 20:
+Line 22:
-=== 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 ...)
-Line 23:
+Line 26:
- * 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]]
-Line 26:
+Line 32:
- * 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
-Line 30:
+Line 37:
- * 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]]
-Line 33:
+Line 44:
-  * fill between
+  * fill_between
-Line 36:
+Line 47:
+ * 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]]
-Line 37:
+Line 52:
-=== 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
-Line 41:
+Line 58:
- * 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]]
-Line 46:
+Line 66:
- * replacing BASH: working with os adn system objects
+[[PythonCourse/PythonLES/SeminarLog4|Commented examples from the seminar]]

 * replacing BASH: working with os and system objects
-Line 49:
+Line 71:
+ * how to debug a python program?
-Line 50:
+Line 73:
-=== 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]]
-Line 54:
+Line 76:
-----
+ * 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
-Line 56:
+Line 82:
-=== time series analysis: the Pandas module (Mikhail) ===
 * introduction to pandas timeseries analysis module
+== 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.) ===
 
[[/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.) ===

[[/Parallel_Programming | Lesson code ]]
[[/ParallelSlides | ... and slides ]]
-Line 60:
+Line 105:
+ * 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 ]]
-Line 61:
+Line 115:
-=== pyCMBS (Alex) (???? on a separate day BEFORE the summer break ???) ===
 * introduction to pyCMBS
 * cdo interfacing
 * anomaly calculations, hovmoeller plots etc
+=== python CDO interface (Ralf Mueller) (22.11.) ===
 * cdo - python interface
-Line 66:
+Line 118:
-=== Integration of other programming languages ===
+=== Integration of other programming languages (Alex, 06.12) ===
-Line 72:
+Line 123:
+ * http://wiki.python.org/moin/IntegratingPythonWithOtherLanguages
-Line 73:
+Line 125:
+----
-Line 74:
+Line 127:
-=== 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
-Line 90:
+Line 130:
- * GUI programming
+ * GUI programming (Alex, remon???)
-Line 93:
+Line 133:
-= projects to work on ... =
 * MPI-ESM in python (Christian) ;-)