Profiling memory usage of Python code
Friday, April 17th, 2009 Posted in Linux, Python, Scientific computing, Software development | 2 Comments »In a previous post, I explained how to use the Python profiler. The profile is great for finding out which parts of the code run the slowest, or are called most often. However, the profiler doesn't give any information about ...
Lookup tables and spline fitting in Python
Wednesday, April 8th, 2009 Posted in Python, Scientific computing, Software development | No Comments »Lookup tables and spline fitting are widely used by scientific programmers. A particular function may not have an analytic solution--in other words, it can't be expressed as an equation of elementary functions. This might happen if the function were empirically ...
3D Plotting Software for Python::Part 1::PyX
Friday, March 20th, 2009 Posted in Python, Scientific computing, Software development | 3 Comments »There are lots of good open-source tools that you can use to make high-resolution, publication-quality 2D plots. Personally, I like to use Python, numpy, and matplotlib. Unfortunately, it is much harder to find a good tools to make 3D plots. ...
The Python configparser: a way to read simple data files
Tuesday, February 3rd, 2009 Posted in Linux, Software development | 2 Comments »My simulation library, which is written mostly in Python, needs a lot of data and parameters in order to run. In some cases, I just hard-code the values in the script that calls the library, and in other ...
How to put formatted, highlighted code in a WordPress post
Saturday, January 17th, 2009 Posted in Software development, Web design | No Comments »I found two complementary plugins that enable me to put highlighted formatted code in a Wordpress page or post. Here's an example of what they do: [sourcecode language="python"] # Plot flux at continuum boundary pylab.figure() pylab.hold(True) pylab.plot(nd_times, Jl_BD, 'b-', label="Flux from BD simulation") pylab.plot(nd_times, Jl_BD+Jl_BD_std, 'b.', ...
Deploying Python applications on Windows
Thursday, January 15th, 2009 Posted in Linux, Python, Software development | No Comments »Writing applications in Python on a Linux system is almost too easy. Deploying Python apps on other Linux systems is not hard, because most Linux systems already have Python, with its core libraries and tools, installed. Most Linux systems also ...
Optimizing Python code for fast math
Friday, January 9th, 2009 Posted in Python, Scientific computing, Software development | 2 Comments »I spent some time today profiling a Brownian dynamics simulation written in Python to see how I could make it faster before starting some long runs on a Linux cluster. In the sections below, I have attempted to quantify ...
Redirecting standard output from Python: another example
Wednesday, January 7th, 2009 Posted in Python, Software development | No Comments »I wrote a previous post about how to redirect standard output from a Python script to a GUI window. In this post, I will give an even simpler example of to redirect standard output to a log file. During the ...
Tools for Python software development
Tuesday, January 6th, 2009 Posted in Linux, Python, Software development | No Comments »I have found a few tools over the years that I find extremely useful for developing software. Python is my language of choice at the moment, but I'm sure these tools will be handy for any language. Subversion is an ...
Using Python to generate XML files for visualization in Paraview
Thursday, November 13th, 2008 Posted in Linux, Python, Software development | No Comments »VTK is an open-source software system for "3D computer graphics, image processing, and visualization" developed by by Kitware. VTK is the foundation of Paraview, an industrial-strength CFD visualization tool that I have found to be very useful. I ...