Tag: Python

• Calling R from Matlab – flat file communication

  I showed earlier how to fit a Bayesian hierarchical model in R to estimate experimental parameters. Our main data analysis pipeline uses Matlab, and we’d like to integrate these two environments for the purpose of analysis.So how can you pipe your data from Matlab to R and back? Flat file communication There are a variety of…

  April 6, 2015

• Theano: numerical computation in Python

  Theano is a very interesting numeric library for Python that I covered briefly a few years ago. Coming from the machine learning group at Université de Montréal – i.e. Yoshua Bengio et al. – it is well adapted to the kinds of numerical tasks that frequently occur in machine learning problems, in particular deep neural…

  January 26, 2014

• Load pickle files in Matlab

  Updated March 2020 It’s easy enough to load .mat files in Python via the scipy.io.loadmat function. But what about loading .pickle files into Matlab? You need to do a little more work! It’s a bit roundabout, but if python is installed and on your path, you can call it from Matlab to save the data…

  June 12, 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

• 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