timewriter: Time protocol writer
In PaolaCognigni/CTraxHelper: CTrax Helper

Description Usage Arguments Details Value

Creates and collates time protocol data given minimal information (light pattern and protocol steps)

1	timewriter(lit, prot, sec3 = 0)

`lit`	a boolean or 0-1 integer vector indicating frames with lights on or off
`prot`	a list of protocol steps, in order; it can contain 0's and 1's, but only 2-5 are actually used
`sec3`	an optional section 3 add-on to stick the last 2s back onto the protocol (input in frames!!!)

Protocol steps are assumed to follow the scheme:

0: no video (disregarded)
1: no light (disregarded)
2: lights constantly on
3: lights on in a blinking pattern
4: quadrants on, NE and SW
5: quadrants on, NW and SE

This is primarily for the collapse of 4 and 5 into a single chunk.

There is currently no data cleanup. The underlying noise therefore shows up in frame variability (~4 frame jitter).

A data frame containing the columns time (frame number), lit (lights on or off, 0-1 integer), chunk (broad section definer including on frames and surrounding off frames), section (narrow section definer attributing values to each on and off time separately), rept (repeat: used in conjunction with section to uniquely identify each lights-on event) and various timers centered at the appropriate light-on time (chunktimer, sectiontimer, and lighttimer).