CorrectOD.py

"""
Calculate OD values of an old experiment using the original raw data and a given calibration
by Daniel Garcia Ruano (dani14-96)
SyntheCell Team
"""

import json
import numpy as np
import os

# Custom variables
PATH_TO_CALIBRATIONS_JSON = "calibrations.json"
CALIBRATION_NAME = "OD_01_01_2000"
FIT_NAME = "OD_01_01_2000"
EXPT_PATH = "/Users/evolver/dpu/experiment/test/test_cp_expt"

# Load initial calibration curve
calibrations = json.load(open(PATH_TO_CALIBRATIONS_JSON, "r"))
for c, cal in enumerate(calibrations):  # Iterate over calibrations list
	if cal["calibrationType"] == "od":
		if cal["name"] == CALIBRATION_NAME:
			calibration = cal
			for f in calibration["fits"]:
				if f["name"] == FIT_NAME:
					fit = f  # Extract fit for the coefficients

# Iterate through vials
for vial in range(0,16):
	print(f"Recalculating ODs for vial {vial}...")
	# Read Raw data files
	raw_file = os.path.join(EXPT_PATH, "od_135_raw", f"vial{vial}_od_135_raw.txt")  # Change for od_90 if needed
	new_od_file = os.path.join(EXPT_PATH, "NewOD", f"vial{vial}_OD.txt")  # You need to manually create a folder NewOD inside your experiment
	header = open(raw_file, "r").readlines()[0]
	data = np.genfromtxt(raw_file, delimiter=",", skip_header=1)

	od_coefficients = fit["coefficients"][vial]
	for i in range(len(data)):
		# Get OD using calibration curve
		data[i,1] = np.real(od_coefficients[2] -
							((np.log10((od_coefficients[1] -
							od_coefficients[0]) /
							(float(data[i,1]) -
							od_coefficients[0])-1)) /
							od_coefficients[3]))

		# Here, substract blank if needed

		if not np.isfinite(data[i,1]):
			data[i,1] = "NaN"

	# Log data in datafiles
	np.savetxt(new_od_file, data, delimiter=",", fmt='%.4f', header=header)

	print("Done")