calculate_volume2.py

from pathlib import Path
import csv
from datetime import datetime


FLOW_COLUMN = "Flow Unit #1 [Flowboard (1384)]"

THRESHOLD_UL_MIN = 0.4
STOP_AFTER_BELOW_THRESHOLD_SECONDS = 1.0
USE_ABSOLUTE_FLOW = True


def parse_time(t):
    return datetime.strptime(t, "%Y-%m-%d %H:%M:%S.%f")


def main():
    print("RUNNING NEW VERSION - sustained stop + trapezoidal integration")

    script_dir = Path(__file__).resolve().parent
    csv_files = sorted(script_dir.glob("*.csv"))

    if not csv_files:
        raise FileNotFoundError(f"No CSV files found in: {script_dir}")

    csv_path = csv_files[0]
    print(f"Using CSV file: {csv_path.name}")

    rows = []

    with open(csv_path, newline="", encoding="utf-8-sig") as f:
        reader = csv.DictReader(f, delimiter=";")

        for row in reader:
            time = parse_time(row["Time"])
            flow = float(row[FLOW_COLUMN].replace(",", "."))
            rows.append((time, flow))

    rows.sort(key=lambda x: x[0])

    if len(rows) < 2:
        raise ValueError("Need at least two rows to calculate volume.")

    start_index = None

    for i, (_, flow) in enumerate(rows):
        if abs(flow) > THRESHOLD_UL_MIN:
            start_index = i
            break

    if start_index is None:
        print(f"No flow above {THRESHOLD_UL_MIN} µL/min found.")
        return

    below_start_index = None
    stop_index = None

    for i in range(start_index, len(rows)):
        time, flow = rows[i]

        if abs(flow) < THRESHOLD_UL_MIN:
            if below_start_index is None:
                below_start_index = i

            below_duration = (rows[i][0] - rows[below_start_index][0]).total_seconds()

            if below_duration >= STOP_AFTER_BELOW_THRESHOLD_SECONDS:
                stop_index = below_start_index
                break
        else:
            below_start_index = None

    if stop_index is None:
        stop_index = len(rows) - 1
        print("Warning: no sustained stop found; integrating until end of file.")

    total_volume_ul = 0.0

    for i in range(start_index + 1, stop_index + 1):
        previous_time, previous_flow = rows[i - 1]
        current_time, current_flow = rows[i]

        dt_seconds = (current_time - previous_time).total_seconds()

        if USE_ABSOLUTE_FLOW:
            f1 = abs(previous_flow)
            f2 = abs(current_flow)
        else:
            f1 = previous_flow
            f2 = current_flow

        average_flow_ul_min = (f1 + f2) / 2.0
        total_volume_ul += average_flow_ul_min * dt_seconds / 60.0

    start_time = rows[start_index][0]
    stop_time = rows[stop_index][0]
    active_duration_s = (stop_time - start_time).total_seconds()

    print(f"Number of samples: {len(rows)}")
    print(f"Start threshold: {THRESHOLD_UL_MIN} µL/min")
    print(f"Stop delay below threshold: {STOP_AFTER_BELOW_THRESHOLD_SECONDS} s")
    print(f"Use absolute flow: {USE_ABSOLUTE_FLOW}")
    print(f"Pumping start time: {start_time}")
    print(f"Pumping stop time: {stop_time}")
    print(f"Integrated pumping time: {active_duration_s:.3f} s")
    print(f"Total pumped volume: {total_volume_ul:.6f} µL")
    print(f"Total pumped volume: {total_volume_ul / 1000.0:.9f} mL")


if __name__ == "__main__":
    main()