Category: Python

• Memory management in gnumpy

  I’m working on a project using gnumpy, which is a wrapper for CUDAmat, a toolbox for GPU computation in Python. I was having memory management issues, where the script would crash after the memory on the graphics card would fill up. I kept trying to delete the variables via del but this seemed to have…

  April 21, 2013

• ipython and ipython notebook for Matlab users

  Following my post on IDEs for scientific Python, several commenters mentioned using some combination of their favorite text editor and ipython rather than a dedicated IDE. ipython is an interactive Python interpreter that offers a much enhanced user experience over the regular Python interpreter: with features such as: Integration with matplotlib Autocompletion Syntax highlighting at…

  April 19, 2013

• Evaluating IDEs for scientific Python

  Updated March 2023. In my book, VSCode is the only game in town. It’s free, open, fast and full-featured. What’s not to like? Python is a general purpose scripting language that can be used for statistical analysis, numeric work, machine learning, and much more. If you’re coming from other scientific computing environments like Matlab, Mathematica…

  April 17, 2013

• NumPy uses the wrong BLAS libraries – solution

  I’ve been transferring some code from Matlab to NumPy and my first tests on my Ubuntu 12.10 installation were very disappointing – slow as molasses. Specifically, numpy.dot was taking forever. I figured this might have something to do with BLAS libraries, a subject which is completely beyond mere mortals to understand. Is something wrong with…

  April 12, 2013

• Setting up a cluster for the analysis of neural array data

  As I’ve mentioned before, we’ve been recording from a Utah array for more than a year now. We use a custom Plexon MAP system that allows for the recording of wideband data at 10 kHz over 96 channels. This custom configuration was requested so that we can get spike-free LFPs by preprocessing wideband data with…

  January 17, 2012

• Reading .plx files in Mac/Linux: a Python script

  Update (12/10/2011): Huang Xin has written better Python script based on ctypes, part of RealTimeElectrophy. I posted a few days ago on solutions for reading .plx files on Mac/Linux, and was kind of bummed out that in spite of doing a thorough background search I couldn’t find a really satisfying solution to the problem. So…

  September 12, 2011