A collection of small functions and MATLAB tools, some that I have written.
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README.md

mtools by srinivas.gs

This repository contains a bunch of useful scripts and functions that make working in MATLAB much easier. All my other MATLAB repositories depend on this. Feel free to do with functions that I have written what you will. Some functions written by others are also included here, with licenses and attribution where possible.

Contents

Functions in this repository are organized into:

  1. beta don't use this.
  2. figure-tools Tools to make better plots. For example, prettyFig makes pretty figures.
  3. file-tools tools for working with files on your computer. For example, abf2kontroller, which converts AutoSpike files into kontroller compatible files.
  4. image-tools tools to help you with working with images. For example, saturationPlane computes the saturation plane from a colour image.
  5. internet-tools to help you work over HTTP connections. install is my package manager that installs toolboxes from GitHub.
  6. maths-tools are functions for various mathematical operations. e.g., spear computes the Spearman rank correlation.
  7. matlab-tools MATLAB-specific tools, to work around various quirks and missing bits in MATLAB. For example, the excellent swap swaps two variable in place.
  8. neuro-tools tools specific to neuroscience. For example, raster2 plots a raster of spike times from two neurons.
  9. publish-tools This toolset is built around MATLAB's publish function. For details on what you can do with this, look at this repo.
  10. string-tools tools to work with strings. For example, randomString(100) spits out a 100 random characters.
  11. time-series-tools tools to work with time series. For example, fastFilter speeds up convolutions using GPUs and Fourier Transforms for long time series.

General Notes on Usage

All functions here have help above the function definition, and you can get help about any file using help:

>> help raster2

shows:

  raster2.m
  makes a raster plot of two different neurons. A (or B) can be either a logical matrix with 1 where a spike occurs, or long (zero padded) matrices of spike times. The time step is assumed to be 1e-4s
  This function is designed to be faster the the original raster


  created by Srinivas Gorur-Shandilya at 10:20 , 09 April 2014. Contact me at http://srinivas.gs/contact/

  This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. 
  To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/.

You can also call most functions with no arguments and it will return help, if at least one argument is required for that function. So raster2 is the same as help raster2

Installation

The reccomended way to install this is to use my package manager (which is included in this repo):

>> urlwrite('http://srinivas.gs/install.m','install.m');
>> install sg-s/srinivas.gs_mtools

or you can install using git

$ git clone https://github.com/sg-s/srinivas.gs_mtools.git

If you do the latter, make sure you get add the paths to the subfolders to your MATLAB path.

Detailed Notes

makePDF.m and cleanPublish.m

makePDF.m is a wrapper for MATLAB's publish function that accepts a script, and makes into a PDF directly. It works by first using publish to make a .tex file, then using pdflatex to compile that to a PDF. Assumes you are working on a Unix machine with pdflatex installed.

This repo has a detailed workflow built around makePDF, cleanPublish, and cache.

It uses cleanPublish.m to remove all the figures and log files after the PDF is compiled.

textbar.m

textbar is a text-based waitbar replacement. Drop it into long loops:

for i = 1:34
    textbar(i,34)
    % do some long computation
end

will show you a progress bar and how many loops have evaluated. For loops that run more than a hundred times, textbar intelligently switches to percent completed. The progress bar is erased when the loop completes.

oval.m

oval is a version of round that is meant for use in figure labels, etc. oval returns a rounded string to an arbitrary number of digits:

>> oval(pi,2)

3.14

oval can also handle fractions, if you tell it to:

>> oval(1/7,'frac')

1/7