config.yaml

# Configuration for the KBarn RFID mouse-colony analysis.
# Edit the assumptions here to match your facility; the pipeline reads this file.

paths:
  raw_dir: data                 # folder of raw exported CSVs
  out_dir: outputs              # processed data + figures land here

# --- Timezone / lighting -------------------------------------------------
# Timestamps in the raw files are naive local time. Set the light cycle so
# circadian analysis can label day vs. night. Lights-on at 07:00, off at 19:00
# is a common 12:12 cycle -- CHANGE to your vivarium's schedule.
light_cycle:
  lights_on_hour: 7             # hour (0-23) lights turn ON  (start of "day")
  lights_off_hour: 19           # hour (0-23) lights turn OFF (start of "night")

# --- Zone normalization --------------------------------------------------
# Some exports label zones "1".."10", others "usb1".."usb9". We strip the
# "usb" prefix so usbN == zone N. If your USB port numbering does NOT match
# the physical zone numbering, override the mapping here (raw_label: zone).
zones:
  strip_usb_prefix: true
  overrides: {}                 # e.g. {usb7: 3} if usb port 7 is physically zone 3

# --- Noise filtering -----------------------------------------------------
# Real animal tags share the UID prefix "000C12" and carry an assigned tag_no.
# Reads failing these checks are misreads/electrical noise and are dropped
# (but counted in the QC report).
cleaning:
  valid_uid_regex: '^000C12[0-9A-Fa-f]{6}$'
  require_tag_no: true          # drop reads with an empty tag_no
  min_reads_per_animal: 100     # animals below this are flagged (likely strays/misreads), not dropped

# --- Contact / co-location detection -------------------------------------
# Two animals are "in contact" when read at the same zone within this many
# seconds of each other.
social:
  contact_window_seconds: 30

# --- Animal roster -------------------------------------------------------
# Left empty => the roster (tag_no -> uid, and optional metadata) is inferred
# from the data. Fill this in to attach sex / genotype / cage, and to pin the
# canonical tag<->uid mapping. Example:
# roster:
#   133: {uid: '000C1203302D', sex: F, genotype: WT,  cage: A}
roster: {}