Mathematica stuff
On this page I collected some Mathematicarelated projects. This page is still under construction until everything is migrated from the old site. If you are looking for content from the old page, also check out the Mathematicarelated blog posts!
Packages
MATLink
An advanced interface for seamlessly calling MATLAB functions from Mathematica. Please go to http://matlink.org/.
BoolEval
This is a package that allows a simple notation for doing MATLABstyle vectorized computations on numerical arrays. For example, to count the number of array elements greater than 0.5, one might write Count[arr, x_ /; x > 0.5]
. This is clean and readable, but there’s an orders of magnitude faster way to do the same thing when working with a large packed numerical array:
Total@UnitStep[0.5  arr]
Unfortunately this is not vey readable, and for complex conditions and comparisons it becomes very unwieldy to write. The package provides an alternative notation,
BoolCount[arr > 0.5]
There are functions for element selection, counting, and other similar operations, e.g.
BoolPick[arr, 0.5 < arr < 0.6]
which would take the much more complex Pick[arr, (1  UnitStep[0.5  arr]) UnitStep[0.6  arr], 1]
to write by hand.
Get the code here.
IGraphR
This package makes it easy to call the igraph graph manipulation library from Mathematica. This is useful both for graph operations that Mathematica doesn’t support and verifying results obtained with Mathematica.
Get the code here
Mathematica on the Notre Dame CRC cluster
This package greatly simplifies running parallel Mathematica jobs on Notre Dame’s HPC cluster. Just include the package, which autodetects the number of cores and hosts usable by the jobs and sets up Mathematica’s parallel tools appropriately.
Get the code here.
Links and tricks

See my blog posts tagged with
mathematica
. 
Mathematca at StackExchange — for help and questions about working with Mathematica.

These are some of my favourite programming tricks and techniques, recommended for the intermediate Mathematica programmer:

The “VillegasGayley trick” is a clever way for wrapping builtin functions to add arbitrary functionality.

How to transform parts of held expressions using replacement rules? Use the TrottStrzebonski inplace evaluation technique.

Creating closures, functions with an internal state.


Mathematica plugin for IntelliJ IDEA — this makes IntelliJ IDEA into an excellent Mathematica code editor with smart syntax highlighting, autocompletion and source navigation.

The Spelunking package makes it very easy to read the definitions of inmemory symbols. It can be used to see how some builtin or package functions work. I often use it on package functions even when the package source is available.

SciDraw by Mark Caprio is a package for creating publication quality figures. It makes it easy to create figure grids and subfigures and provides fine grained control over many aspects of the figure. The tradeoff is that it takes more code to create figures than standard Mathematica and it takes a while to learn the syntax. Highly recommended for publication figures or situations where output quality is important, but not for everyday visualization.

One of the first things I do when installing or upgrading Mathematica is set up shortcut keys for typing 〚 and 〛. Find the file
SystemFiles/FrontEnd/TextResources/Macintosh/KeyEventTranslations.tr
and add the following right after the lineEventTranslations[{
. Do make a backup before editing this file!Item[KeyEvent["[", Modifiers > {Command}], FrontEndExecute[{FrontEnd`NotebookWrite[FrontEnd`InputNotebook[], "\[LeftDoubleBracket]", After]}]], Item[KeyEvent["]", Modifiers > {Command}], FrontEndExecute[{FrontEnd`NotebookWrite[FrontEnd`InputNotebook[], "\[RightDoubleBracket]", After]}]],
Now it’s possible to type 〚 and 〛 using Command[ and Command]. Using these special brackets makes the code much easier to read than [[
and ]]
. On Windows or Linux replace Command
with Control
.