By Geo. Dylan Dickerson gdicker1@uwyo.edu
For UWyo Ind. Study in Genetic Algorithms Spring 2018
Approximates the file 'VM_runner.m' provided by Srinu Yershwant written in Matlab while changing to accomodate the implementation of a Covariance Matrix Adaptation - Evolution Strategy to find 12 lines (24 points) that create an ablation set to try to fix Multi-wavelet Re-entry and provide support for theories about MWR.
NOTE: This project was developed on Ubuntu 16.04 and no guarantees of functionality are made. However, if Singularity 2.3.2 can be installed on your system, this project should work.
The Batchtool simulator. This was developed by another group and permission will need to be obtained before it can be provided.
homg_runner.py: Python process to execute the evolutionary strategy using the 'VisEp_BatchTool_1' on a tissue generated by hom_fileMake.py.
heter_runner: Python process to execute the evolutionary strategy using the 'VisEp_BatchTool_1' on a tissue generated by hom_fileMake.py modified to have a patch.
CMAES_evolStrat.py: Contains extra functions to carry out the evolutionary strategy (e.g. find fitnesses).
CMAES_fileWrite.py: Contains utilities to write the files necessary to change the ADP and Intercellular Resistances of the reference file *.vepxml file to run the strategy.
CMAES_xmlMake.py: Contains the utilities to create the relevant Extensible Markup Language (XML) files to run 'VisEp_BatchTool_1' on or to find runtime for a tissue given a series of stimulation events.
createAblation.py: Contains functions that create ablation files based on CMAES solutions.
hom_fileMake.py: Creates apd and resistance files offline for homogeneous tissue.
afib.singularity: Bootstrap file to create a Singularity version 2.3.2 container using an Ubuntu 16.04 base image. Can also use versions of the instructions in the post section to attempt to have the correct dependencies for this project.
afib_hom.sh: Bash file with instructions to start the respective *_runner.py files.
Tissues/ : Directory containing the reference 80x80_RC10.vepxml tissue and a sub-directory of the tissue files used for the data collection in Spring of 2018.
multiFigMake.py: Creates gifs and graphs of data generated by the *_runner.py files as well as some statistical tests.