2013 Summer Project Week:CLI Matlab

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  • Example thresholding CLI module implemented in Matlab.

  • Module for generating Matlab CLI module skeletons.

  • Matlabcommander2.png

    Helper module to run Matlab scripts.

  • Design: Matlab CLI module generation.

  • Design: Matlab CLI module execution.

Key Investigators

  • Queen's: Andras Lasso
  • PMH, Toronto: Kevin Wang
  • Isomics: Steve Pieper

Objective

Allow easy implementation of CLI modules in Matlab.

Approach, Plan

Implement a module that can run Matlab functions as a CLI. It should not require building of Slicer or a C++ compiler. Should be possible to install from an extension.

Create a Python script that generates the following scripts:

  • Proxy: a Python CLI module (with a .bat executer on Windows), it returns the CLI description XML to Slicer during module discovery, it calls the Matlab stub script when Slicer executes the module. It may also start the Matlab server, if it's not running already.
  • Stub: a Matlab function that performs the actual processing. It receives the same parameters as the CLI module (input and output file names, numerical values, etc.), it reads the data from files (with helper file I/O functions), performs the computations, and writes results to files.

Other necessary components:

  • Matlab server: Matlab script that executes commands that it receives through OpenIGTLink. Already exists, was developed during the last project week.
  • Helper Matlab functions: file I/O to read write image, model, transform, etc., maybe command-line parameter parsing (if the CLI parameters are all passed as a simple string; alternatively, the parameter string parsing may be done in the proxy script).

Progress

Matlab functions can now be called directly from Slicer as a CLI module!

  • Matlab module generator: the user specifies a module name, the generator creates a skeleton .m file, a CLI definition .xml file, and a CLI launcher .bat file from a template, then the user customize the .xml and .m files.
  • MatlabCommander: this module provides simple remote Matlab method execution for testing, this module is also used internally by the CLI launcher

Next steps:

  • Support more helper functions for reading/writing more file formats (images, fiducials, numbers, strings, etc. are already covered)
  • Provide launcher script for Linux/Mac (on request)

Demo: http://screencast.com/t/CQbbJ9bnw6f

Delivery Mechanism

This work will be delivered to the NA-MIC Kit as part of the SlicerRT extension.

References

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