SDSU Bioengineering Lab FTLE analysis code
The master script to rerun all of the studies is called 'runscripts.m' and is run from Matlab. It was written using Matlab 2011a on a Linux machine, and uses Linux file system commands. It expects velocity files to be stored under a file structure like "bin/bag name/LVAD speed/" where bag name and LVAD speed are written in the script. The conversion from the B00xxx.txt velocity files into binary files is done using the 'bin/ascii2binnC.py' file using Python 2.7. To change the settings used for flowVC, modify 'input/forward_template.in' and 'input/reverse_template.in'. These files will be read by 'bin/changelimits.py', which will create a 'input/forward.in' and 'input/reverse.in' updated to use the proper boundaries from the current velocity files. 'output/conversion.py' creates a series of .csv files from the flowVC output. 'visualize.m' will read the .csv files into Matlab, save the data as a series of .mat files, and creates FTLE field .tif images from the data. It can also turn the images into a video if that section of code isn't commented out.
Dependancies: Python 2.7, Matlab 2011a, Linux, flowVC version 1
This code makes use of flowVC. Shadden, S. C. (2010) FlowVC (Version 1) [Computer software]. Retrieved from http://shaddenlab.berkeley.edu/software/.