NA-MIC Project Weeks

Conversion of Matlab Bridge modules to integrated 3DSlicer modules

Key Investigators

Sharon Peled (Brigham and Women’s, USA)
Andras Lasso (Queen’s University, Canada)
Anyone else that is interested

Project Description

Matlab Bridge is a very quick and convenient way to combine the display features of 3DSlicer with Matlab analysis code. A straightforward way of exporting Matlab modules to Python and incorporation of the code in 3DSlicer may allow Matlab programmers to make their modules available to the Slicer community.

Objective

Create tutorial about the process of translating a Matlab Bridge module to a Slicer Python scripted module.

Approach and Plan

Investigate freeware to convert Matlab code to Python.
Document a complete pipeline for Matlab-proficient non-developers on the process of creating a Python module.

Progress and Next Steps

Progress

A couple of examples of Matlab Bridge modules with all their dependent functions were collected here: https://www.dropbox.com/sh/36vvhsi90z90arq/AACTInsRPBkQdhaH8jf_qml9a?dl=0
It was concluded that conversion needs to be done manually - Matlab to Python converters would not work well for this purpose.
The tutorial “Programming in Slicer4” by Sonia Pujol and Steve Pieper (https://www.dropbox.com/s/wrhrvvmplosiis1/Slicer4_ProgrammingTutorial_SPujol-SPieper_Nightly.pdf?dl=0#) was worked through and summarized in the following document for quick reference: https://www.dropbox.com/s/0wukoaesndf3ug4/SlicerPython.pdf?dl=0

Next steps:

Add a summary of the tutorial “Developing and contributing extensions for 3D Slicer” by Andrey Fedorov, Jean-Christophe Fillion-Robin, and Steve Pieper (https://docs.google.com/presentation/d/1JXIfs0rAM7DwZAho57Jqz14MRn2BIMrjB17Uj_7Yztc/edit#slide=id.g420896289_0216) to the document.
Summarize essential Python for Matlab users and add to the document.

https://bastibe.de/2013-01-20-a-python-primer-for-matlab-users.html

https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html

Convert the example Matlab Bridge modules to Python and add a two column comparison of the Python code versus the Matlab code to the document.