Category: C programming

• Reading Plexon files in Linux or Mac

  Updates (12/10 /2011): Plexon now offers a mex extension for Matlab which compiles on Linux and Mac. I have a Python .plx file reader available, and Huang Xin has a better one based on ctypes, part of RealTimeElectrophy. Plexon hardware is meant to interface with Windows-only tools (including recording software). I think that for such…

  September 7, 2011

• Gibbs sampler in Matlab using mexme

  Darren Wilkinson has a nice post up comparing different programming languages (C, Java, scala, Python, and R) for writing Gibbs samplers. Unsurprisingly, C is fastest, although it is certainly not the easiest language to program in. In particular, I/O is a bitch. Others have suggested an interesting solution: write the core of the Gibbs sampler…

  July 16, 2011

• Speeding up numeric code: McFor and Theano

  Matlab has high-level language constructs that make it easy to express linear algebra computations in a terse, intuitive syntax. Its flexibility as a scripting language, however, means that it has underwhelming performance in some circumstances. While Matlab’s just-in-time (JIT) compiler helps quite a bit, research has shown that there is much space for performance improvements.…

  July 7, 2011

• Programming for multi-core environments

  CPUs with multiple cores are currently the norm. Getting optimal performance out of these systems is challenging. I recently read Parallel Programming in C with MPI and OpenMP by Michael Quinn, a book that, while released in 2004, remains relevant and actual. Dr. Quinn introduces two technologies which are available in C (and in Fortran…

  June 28, 2011

• Matlab code for 2D Gaussian surface fitting

  Updated 10/21/2011 I have some code on Matlab Central to automatically fit a 1D Gaussian to a curve and a 2D Gaussian or Gabor to a surface. The 2D Gaussian code can optionally  fit a tilted Gaussian. In its basic form curve/surface fitting is straightforward (a call to lsqcurvefit will do the trick), but the…

  May 19, 2011

• Is it practical to train an HMM for spike sorting with Baum-Welch?

  *The short version: at the end of the post there’s some fast code (Matlab with MEX) for training an HMM for spike sorting* Earlier, we evaluated different solutions for sorting spikes for our 96-electrode array. One solution we looked at was spike sorting with HMMs (Hidden Markov Model). While most spike sorters first detect spikes…

  May 7, 2011