File list: 1. ps_main: main code 2. ps_tran: identifying transitions 3. repackage: separate contours into 2 level sets and construct graph 4. drawBare: make the plots 5. plotByPieces: plot contours with breaks for NaNs 6. contoursep: change MATLAB contour format into NaN-separated 7. smush: bring PS list into format for tracking 8. drawGraph: display the graph at a certain frame 9. diff2, fitDiff, and fastDiff - not used for differentiation (at the moment) 10. drawOnly – not currently used 11. sideBySide – not currently used Auxiliary functions 1. opread 2. intersections 3. track Tunable variables: ps_main: 1. opts.mode – which level sets to use 2. opts.exp – which kind of recording 3. opts.fou – which kind of smoothing of distance functions 4. st – start frame of analysis 5. L – length of analysis 6. de – number of frequencies thrown out in high-pass filter 7. deltat – minimum distance between peaks 8. MPP (mode 1) or MPP1, MPP2 (mode 2) – minimum peak prominence 9. sig – vector sigma for smoothing of high-passed data 10a. sig2 - vector sigma for smoothing of derivatives of smoothed data 10b. twind - size of time window for fit differentiation 11. rad (fou 1 only) – radius of Fourier mask 12. sigD (fou not 1) – sigma of 2D Gaussian 13. dis – minimum allowable distance of PS from edge/mask 14. record – whether movie of analysis is made 15. trQ – whether to rerun tracking 16. param.mem – how long a PS may disappear 17. sv - velocity scaling factor in tracking ps_tran: 18. md – max distance between paired created/annihilated PSs 19. lm - minimum length of a PS track used 20. timeout – how far back we go to attempt to classify transition 21. l – ratio of ad to dist that is too "long" repackage: 22. dmax – max jump along contour loop