HitLd sets pixel register bits on enabled pixels

(regardless of whether the pixel is triggered).

Bits are set on pixels that have been hit-enabled. Injection and HitOr enabling
does not affect the HitLd.
Fix HitLd. Now it works!

Bare minimum working version. Not optimized or clean.
Fixed by pausing between all commands issued to chip. This allows noise to die
down, which would otherwise trigger HitLd to write a 1 to the shift register.
Reduce pause between commands to ~0.

The pause created by reading and writing the output from the chip is sufficient
to keep startup noise from affecting the output.
Combine run_seq and get_sr_output into run.

run() calls run_seq, get_sr_output, and reset_seq in order, then returns the
output. run_seq and get_sr_output have been made private (i.e. prefixed with
_).
Change scan_injecct.py to primitive source scan.

Almost functional. Issue in _reset_hit_configuration.
Scan one column at a time.
Working scan!
Add scan_analysis.py to plot real-time results.