process_flir_aryballe.py

from pathlib import Path
import csv
import numpy as np

root = Path(r"...")
odors = {"CH4", "NH3", "TBP", "TEP", "Air", "Humidity"}
odors = list(sorted(odors))
confusents = {"None", "Diesel", "Gasoline", "Roundup", "Tobacco", "Smoke", "Vanilla"}
confusents = list(sorted(confusents))


def get_item(name):
    odor = "Air"
    confusent = "None"
    for o in odors:
        if o.lower() in name.lower():
            odor = o
            break
    for c in confusents:
        if c.lower() in name.lower():
            confusent = c
            break
    return odor, confusent


toc = [("Filename", "Record ID", "Run ID", "Device ID", "Analyte", "Confusant", "Trial")]
counts = np.zeros((len(odors), len(confusents)))
files = list(sorted(root.glob("*.csv"), key=lambda x: int(x.name.split(" - ")[0])))

for file in files:
    with open(file, "r") as fh:
        reader = csv.reader(fh, delimiter=",")
        next(reader)
        line = next(reader)
        name = line[6]
        sensor = line[5]

    odor, confusent = get_item(name)
    counts[odors.index(odor), confusents.index(confusent)] += 1
    with open(file, "r") as fh:
        contents = fh.read()

    contents = contents.replace(",item,", ",Analyte,Confusant,")
    contents = contents.replace(f",{name},", f",{odor},{confusent},")
    print(f"{name} -> {odor} / {confusent}")
    
    rec, run, *_, trial = file.name.split(" - ")
    rec = int(rec)
    run = run[4:]
    trial = int(trial.split(" ")[1])
    new_name = f"item_{rec:03}_run_{run}_trial_{trial}.csv"
    
    with open(file.parent / new_name, "w") as fh:
        fh.write(contents)
    
    toc.append((new_name, str(rec), run, sensor, odor, confusent, str(trial)))

np.savetxt(root / "summary.csv", counts, delimiter=",", fmt="%d")
with open(root / "table_of_contents.csv", "w", newline='') as fh:
    writer = csv.writer(fh, delimiter=",")
    writer.writerows(toc)