Matlab style guide

Here are some Matlab style guide combined from various sources. I added some changes based on personal preferences and consistency.

1. Kevin Murphy's style guide
2. http://www.datatool.com/downloads/matlab_style_guidelines.pdf

 Names

• Capitalize constants.
• Use camel back notation for vairables, as in hiddenMarkovModel. CamelBack always starts with a lower case letter, and then uses an upper case letter for each new word. Acronyms, such as GaussianHMM, also follow this convention, so would be written as gaussianHmm.
• Names of functions should be written in lower case. 
• It is clearest to have the function and its m-file names the same. Using lower case avoids potential filename problems in mixed operating system environments. 
• To improve readability, underscore may be used.
• Prefix variables denoting a number of elements with the letter n as in nValue for the number of values. 
• Suffix variables storing indices with Ndx as in dataNdx

Comments

• There is a convention that the first comment line after the function header will be searched by the lookfor command. Also, the first contiguous block of comments after the function header will be returned by the help and doc commands. 
• http://stackoverflow.com/questions/3840657/matlab-m-file-help-formatting

Matlab parallel computing

Capabilities

• Can run twelve workers locally on a multicore desktop

mmread.m

mmread.m is a Matlab function for reading different media files on different platforms (Linux, Windows and Macs). It is used in the sample code of 2011/2012 One-shot-learning gesture recognition challenge.

When I first run example.m in the sample code, it asks me to install libavbin.so and I clicked yes. However I got segmentation fault after the installation. I also tried to install libavbin.so from the version downloaded from https://code.google.com/p/avbin/, but this causes an error (undefined symbol: 
avbin_open_filename_with_format error) in FFGrab.mexa64. The author noted that he fixed this bug. So I downloaded mmread from the Matlab file exchange and replaced that in the sample code. Now mmread works.

Matlab save path

Matlab allows you to add paths to the search path and you are supposed to be able to save it so that you don't need to add the paths again the next time. However when I tried to save the paths, the new paths didn't show up when I restarted Matlab. I'm running MATLAB R2012a and Ubuntu 12.04.

This post helps me solve the problem. After saving the new paths, a new file is created in ~/Documents/MATLAB because I do not have write permission in the default installation location. However the new pathdef.m file is not read when Matlab starts. To solve this, you can add startup.m in ~/Documents/MATLAB if that's your urserpath. Add the following line to the file:

path(pathdef)

On Windows 7, when you set path through the dialog box, it will add the new paths to the pathdef.m file in the installation folder. This will affect other users' path. To add the paths so only you will see it, you can do the similar thing before by adding a startup.m file in C:\Users\[username]\Documents\MATLAB if that is your statup path. On Windows, it won't ask you to specifiy a new file to save the paths, so you need to copy the pathdef.m file from the installation folder (default is C:\Program Files\MATLAB\R2013a\toolbox\local\pathdef.m) to the userpath.

However, one problem I encountered when I start from the userpath is that some functions in the parallel computing toolbox no longer work. Turns that there seem to be some conflicts between the toolbox and the Bayesian Network Toolbox (BNT) I'm using. After moving the BNT to the bottom of the search path, everything works again.

Running Matlab in Awesome

Today I tried to run Matlab R2012a 64bit under Awesome, but I only got gray windows. After googling around, I found that X window integration in most modern Java virtual machine displays gray windows when used with non-re-parenting window manager such as Awesome. According to this post, Sun  JVM 7 shows this symptom for some Java applications, while OpenJDK may work. So I changed the Matlab Java directory to point to OpenJDK's jre and it works.

export MATLAB_JAVA="/usr/lib/jvm/java-7-openjdk-amd64/jre"

To run Matlab from command line, use:

matlab -desktop

To check the environment variables used by Matlab, use:

matlab -n

I found the solution from this forum post.