How to use the toolkit in Clojure

The Java code from this toolkit can easily be used in Clojure -- the project jar has been deployed to maven as me.lizier/jidt for automated inclusion in clojure projects (see further details below).

Here we give only a brief overview of calling Java code from Clojure; several longer examples of using the JIDT toolkit in Clojure can be viewed at Clojure_Examples.

No special installations are required to begin using Java objects in Clojure, these are supported natively as described here.

You can run your Java code in Clojure as follows:

1. Add the ["LATEST"](me.lizier/jidt) for the latest version (or name a specific version) to the :dependencies vector of your project.clj file (this automatically references the JIDT jar from the leiningen repository and pulls it in). See our sample project.clj file in our Clojure_Examples.
2. Import the classes you wish to use, e.g. (import infodynamics.measures.discrete.TransferEntropyCalculatorDiscrete).
3. Create an instance of the calculator you wish to use, e.g. (def teCalc (TransferEntropyCalculatorDiscrete. 2 1))
4. Call methods on the object, e.g. (.addObservations teCalc sourceArray destArray).

Array conversion -- is generally straightforward -- see some details at the Clojure-Java interoperability documentation, and the use of int-array, into-array and map in our Clojure_Examples.

A big thank you to Matthew Chadwick for showing me how to do this and getting things up and running with clojure and leiningen.