Simple MATLAB script to automate all components of Clack Whisker Tracker
Uses version 1.1.0d of Whisk (https://openwiki.janelia.org/wiki/display/MyersLab/Whisker+Tracking+Downloads), Python 2.7, and a 64-bit distribution of MATLAB.
WhiskerTracking should be installed on the Desktop for convenience but not neccessary and movies to be analyzed can exist in any directory as long as the path can be added to the analysis computer.
The user can select any directory and "click" will batch process all tif files within that directory and all it's subdirectories. Movies within the data directory folder are first processed using the parallel batch trace processor provided with the Whisker Tracker. Then all data files are analyzed, matrix files created for each movie with individual and average whisker figures which are then output to the source data directory folder. In order to recieve precise analysis and minimal tracking issues, the expected number of whiskers per a folder to be analyzed is needed as an argument. This way "click" can process each directory and subdirectory with it's respective whisker information.
If there exists a gap in the data from the whisker tracker being unable to identify whiskers, figures will be created indicating an error per the respective movie and the gap will be replaced with NaN. Also included is a function called "redo" which you can run after filling in the gaps in data via the Whisker Tracker GUI to remake the figures and data with the updated whisker information. "redo" will only run the analysis end of "click" and will only correct the files that have ERROR figures. If you wish to re-run the analysis on all files "redoall" will do the same thing as redo but to all files within the directory.
Also included is the "rdir" function written by Thomas Vanaret and Gus Brown, which allows click and redo to process all appropriate files in all subdirectories within the starting directory.