This is an old revision of the document!
As can be expected, there is a lot of online python documentation available, and it's easy to get lost. You can always use google to find an answer to your problem, and you will probably end up looking at lots of answers on Stack Overflow or a similar site. But it's always better to know where you can find some good documentation… and to spend some time to read the documentation
This page tries to list some python for the scientist related resources, in a suggested reading order. Do not print anything (or at least not everything), but it's a good idea to download all the pdf files in the same place, so that you can easily open and search the documents
You can start using python by reading the Bien démarrer avec python tutorial that was used during a 2013 IPSL python class:
Once you have done your first steps, you should read Plus loin avec Python (start at page 39, the previous pages are an old version of what was covered in Part 1 above)
os.remove(file_name)
instead of rm $file_name
)You do not need to read all the python documentation at this step, but it is really well made and you should at least have a look at it. The Tutorial is very good, and you should have a look at the table of content of the Python Standard Library. There is a lot in the default library that can make your life easier
Summary: Python provides ordered objects (e.g. lists, strings, basic arrays, …) and some math operators, but you can't do real heavy computation with these. Numpy makes it possible to work with multi-dimensional data arrays, and using array syntax and masks (instead of explicit nested loops and tests) and the apropriate numpy functions will allow you to get performance similar to what you would get with a compiled program! Scipy adds more scientific functions
Where: html and pdf documentation
0
and that the last element of an array is at index -1
!'This document by JY is awesome!'[::-1]
and 'This document by JY is awesome!'[slice(None, None, -1)]
) That is not a problem when you only read the values, but if you change the values of the View, you change the values of the first array (and vice-versa)! If that is not what want, do not forget to make a copy of the data before working on it!
Views are a good thing most of the time, so only make a copy of your data when needed, because otherwise copying a big array will just be a waste of CPU and computer memory. Anyway, it is always better to understand what you are doing…
Check the example below and the copies and views part of the quickstart tutorial.
>>> import numpy as np >>> a = np.arange(30).reshape((3,10)) >>> a array([[ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9], [10, 11, 12, 13, 14, 15, 16, 17, 18, 19], [20, 21, 22, 23, 24, 25, 26, 27, 28, 29]]) >>> b = a[1, :] >>> b array([10, 11, 12, 13, 14, 15, 16, 17, 18, 19]) >>> b[3:7] = 0 >>> b array([10, 11, 12, 0, 0, 0, 0, 17, 18, 19]) >>> a array([[ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9], [10, 11, 12, 0, 0, 0, 0, 17, 18, 19], [20, 21, 22, 23, 24, 25, 26, 27, 28, 29]]) >>> a[:, 2:4] = -1 >>> a array([[ 0, 1, -1, -1, 4, 5, 6, 7, 8, 9], [10, 11, -1, -1, 0, 0, 0, 17, 18, 19], [20, 21, -1, -1, 24, 25, 26, 27, 28, 29]]) >>> b array([10, 11, -1, -1, 0, 0, 0, 17, 18, 19]) >>> c = a[1, :].copy() >>> c array([10, 11, -1, -1, 0, 0, 0, 17, 18, 19]) >>> c[:] = 9 >>> c array([9, 9, 9, 9, 9, 9, 9, 9, 9, 9]) >>> b array([10, 11, -1, -1, 0, 0, 0, 17, 18, 19]) >>> a array([[ 0, 1, -1, -1, 4, 5, 6, 7, 8, 9], [10, 11, -1, -1, 0, 0, 0, 17, 18, 19], [20, 21, -1, -1, 24, 25, 26, 27, 28, 29]])
There is a good chance that your input array data will come from a file in the NetCDF format. Depending on which python distribution you are using, you can use the cdms2 or or netCDF4 modules to read the data.
Note: the NetCDF file format is self-documented, and the metadata of climate date files often follows the CF (Climate and Forecast) Metadata Conventions
Summary: cdms2 can read/write netCDF files (and read grads dat+ctl files) and provides a higher level interface than netCDF4. Unfortunately, cdms2 is only available in the UV-CDAT distribution, and distributions where somebody has installed some version of cdat-lite. When you can use cdms2, you also have access to cdtime, that is very useful for handling time axis data.
How to get started:
Summary: netCDF4 can read/write netCDF files and is available in most python distributions
Summary: there are lots of python libraries that you can use for plotting, but Matplotlib has become a de facto standard
Where: Matplotlib web site
The documentation is good, but not always easy to use. A good way to start with matplotlib is to:
Summary: Basemap is an extension of Matplotlib that you can use for plotting maps, using different projections
Where: Basemap web site
How to use basemap?
Summary: One document to learn numerics, science, and data with Python
This is a really nice document that is regularly updated and used for the EuroScipy tutorials. You will learn more things about python, numpy and matplotlib, debugging and optimizing scripts, and also learn about using python for statistics, image processing, machine learning, washing dishes (this is just to check if you have read this page), etc…
You can already get a very efficient script by checking the following:
If your script is still not fast enough, there is a lot you can do to improve it, without resorting to parallelization (that may introduce extra bugs rather that extra performance). See the sections below
Hint: before optimizing your script, you should spent some time profiling it, in order to only spend time improving the slow parts of your script
The official Porting Python 2 Code to Python 3 page gives the required information to make the transition from python 2 to python 3. It is still safe to use Python 2.7, so there is no rush to change to Python 3.
You can do a lot more with python! But if you have read at least a part of this page, you should be able to find and use the modules you need. Make sure you do not reinvent the wheel! Use existing packages when possible, and make sure to report bugs or errors in the documentations when you find some
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