It’s a real pain to surf the Web when the batteries die in your wireless mouse or trackball. I use some old rechargeables that are no longer fit for digital camera service, so this happens to me fairly often. My batteries just died again, so I had to figure out how to configure X.org to […]
How to make two mice work with xwindows (x.org) Read More »
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 determined from experimental data, or if the equation can’t be algebraically solved for one variable.
Lookup tables and spline fitting in Python Read More »
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. Older versions of matplotlib had rudimentary 3D support, but this was removed in version 0.98.
3D Plotting Software for Python::Part 1::PyX Read More »
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 cases I load a pickle file containing a Python objext. What if I want to read in
The Python configparser: a way to read simple data files Read More »
I have released a new version of my Python class that generates VTK data files in the .vtu format, which is compatible with Paraview and other VTK applications. If you have downloaded the old one, please get the latest version, which incorporates some bug fixes and has been more thoroughly tested.
Updated Python class for writing Paraview (VTK) (.vtu) files Read More »
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: Test successful! Note that Javascript must be enabled to see the highlighting. Get the plugins here: Visual Code Editor SyntaxHighlighter Plus
How to put formatted, highlighted code in a WordPress post Read More »
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 have package managers that make it easy to find and install required components. But, what
Deploying Python applications on Windows Read More »
I recently found a solution to a problem that had been vexing me for about a year. In order to successfully import anything from scipy.integrate, I had edit the file scipy/integrate/__init__.py and comment out the line from odepack import * If not, I would get various import errors such as Traceback (most recent call last):
Scipy.integrate ODEPACK import error solved! Read More »
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 the speed improvements due to various changes. Keep in mind that the actual speed improvement in
Optimizing Python code for fast math Read More »
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 early development and debugging of Python programs, I use print statements to keep me informed
Redirecting standard output from Python: another example Read More »