Python/CDAT for Earth Scientists: Tips and Examples

Introduction

This is a collection of tips and examples on using Python in the earth sciences, with an emphasis on climate science. We focus solely on standard Python, Numerical Python, and the analysis and plotting routines in the Climate Data Analysis Tools (CDAT) suite. This collection of tips/examples is neither "official" nor comprehensive.

A note from June 2017: While a number of the tips on this site are still useful, this site hasn't really been updated much since the first decade of the 2000's. The community has also moved on: NumPy and not Numerical Python is the array package of choice and CDAT has become UV-CDAT. Python is also now at version 3. Some more recent Python-for-the-atmospheric sciences resources are available or listed at the PyAOS blog.

General Python references (some referenced herein) that have helped me include:

• Martelli, Alex (2003): Python in a Nutshell, Sebastopol, CA: O'Reilly and Associates, Inc., 636 pp.
• van Rossum, Guido (2003): Python Tutorial, Ed. Fred L. Drake, Jr.

If you have any comments, questions, additions, and corrections for this page, please send me (Johnny Lin) email.

Advertisement: In 2012, I published the book A Hands-On Introduction to Using Python in the Atmospheric and Oceanic Sciences. If you're new to Python, you may find it useful!

Index

Array Manipulation Color File Input/Output General CDAT

Graphics: General Graphics: 2-D Masked Arrays & Variables Mathematics Python Language

Acknowledgements Copyright and Licensing

WWW www.johnny-lin.com

Array Manipulation

• How does Python reference and store array elements?
• How do you reverse the elements in a sequence or along one dimensions in an array?
• How do you concatenate Numeric arrays? Can you concatenate along "extra" dimensions like you can in IDL?
• How do you "search-and-replace" elements in an array (like where in IDL and find in MATLAB)?
• How do you find the minimum or maximum of an array?
• How do you sum all the elements in an array?
• How do you do element-wise and and or operations on arrays?
• What order are array elements printed out by the print command?
• How do IDL commands translate into Numeric/numarray functions?

Color

• What are color maps and how are they structured?
• What colors are the "permanent" color indices assigned to?
• How do you show what color maps are available?
• What do the predefined color maps look like?
• How do you create and use your own color maps?
• How do you use the vcs.getcolors function?
• Have you made any color maps? I'm looking for a rainbow color map or a blue-scale color map.

File Input/Output

• How do you read/write a binary file into/from a Numeric array?
• Why is Ferret sometimes unable to properly read a netCDF file written in Python?
• How do you open/set up an existing netCDF file so that you can append data to it?

General CDAT

• Does it matter that CDAT is an object-oriented package? How does that affect how I use it?

Graphics: General

• Why doesn't VCS recognize my custom graphics method or other VCS object?
• What is a graphics method and template?
• How do you show what graphics methods are available?
• How do you show what already defined VCS objects are available?
• How do you list what a VCS object's attribute settings are?

• How do you make levels spanning a range?
• How do I simulate the MATLAB imagesc function and make plots with color bars that are scaled over the same range?
• How do I make nicely formatted labels, such as for axis tick marks?

• Has anyone written any front-ends to simplify graphing with CDAT?

Graphics: 2-D

• How do you do an x-y line plot?
• Why doesn't the plot method x|yrev keyword work to reverse the axis?

• How do you change line styles?
• What line styles are available?
• How do you change plot symbols and symbol size?
• What plot symbols are available?
• How do you add a block of text to a plot?
• How do I change style attributes of the text passed via plot keyword name?
• How do you reference plot coordinates?
• What units is font height in?
• How do you create and use color maps in plotting?

• Example: A simple x-y line plot
• Example: A complex x-y line plot
• Example: A simple latitude-longitude filled contour plot
• Example: A complex latitude-longitude filled contour plot

Masked Arrays & Variables

• Why do I sometimes get incorrect results when I compare one mask to another?
• Are indexing and slicing treated differently in MA vs. Numeric?
• Does MA have a default missing value?

Mathematics

• How do you sum all the elements in an array?
• How do you do simple interpolation?
• How do IDL commands translate into Numeric/numarray functions?

Python Language

• Is there any way in Python to stop program execution in the middle of the code?
• How do I run a script from the command line but keep the interpreter session open after the script is done?
• Why are some floating point values not represented exactly in Python?
• How do you append directories to your Python path?
• How can you make user customized settings to Python (e.g. path settings, package imports, etc.)?
• How do IDL commands translate into Numeric/numarray functions?