Add ROI masks to get_matches & recalculate r values with zero mask
Add ROI masks to get_matches & recalculate r values with zero mask

* Apply ROI mask on the whole section image before computing
  matches.
* To counter the effect of zeros in the correlogram calculation,
  reorganize get_match to recompute the correlation coefficient
  for the first peak & the three secondary peaks that we use for
  filtering. This ensures that r_max and r_delta are within a range
  comparable to matches that do not have zero-value pixels.

seung-lab/Julimaps,seung-lab/Julimaps