hpos-data/scripts/serial_qc.py

import serial
import pandas as pd
import os.path
from datetime import datetime
import math
import time
from tqdm import tqdm

class Device:
    def __init__(self, accuracy, precision):
        self.accuracy = accuracy
        self.precision = precision

def perform_hpos_test(repeat_no):
    try:
        data_file = 'data.xlsx'
        if os.path.exists(data_file):
            df = pd.read_excel('data.xlsx')
        else:
            df = pd.DataFrame(columns=["sol", "427_buffer_intensity", "555_buffer_intensity", "427_sample_intensity", "555_sample_intensity", "427_absorbance", "555_absorbance", "absorbance_ratio", "time"])
        
        time.sleep(5)

        with serial.Serial('/dev/cu.usbserial-1420', 115200, timeout=1, parity=serial.PARITY_NONE) as ser:
            x = ser.read()
            s = ser.read(10)
            line = ser.readline()
            print(x)
            print(s)
            print(line)

            # perform_blanking = input("Do you want to perform blanking?(Y/N)")
            
            ser.write(b'B')
            while True:
                x = ser.read()
                b = ser.read(100) 
                line = ser.readline()
                print(b)
                if 'Buffer Completed' in b.decode("utf-8"):
                    ser.write(b'S')
                    while True:
                        x = ser.read()
                        s = ser.read(100) 
                        line = ser.readline()
                        print(s)
                        if 'Sample Completed' in s.decode("utf-8"):
                            ser.write(b'P')
                            while True:
                                x = ser.read()
                                r = ser.read(100) 
                                line = ser.readline()
                                print(r)
                                if 'RESULT' in r.decode("utf-8") or 'REND' in r.decode('utf-8'):
                                    result = r.decode("utf-8").split(' ')
                                    df = pd.concat([df, pd.DataFrame([{"sol": solution + '-' + str(repeat_no), "427_buffer_intensity": result[3], "555_buffer_intensity": result[3], "427_sample_intensity": result[5], "555_sample_intensity": result[6], "427_absorbance": math.log10(float(result[3]) / float(result[5])), "555_absorbance": math.log10(float(result[4]) / float(result[6])), "absorbance_ratio": math.log10(float(result[3]) / float(result[5])) / math.log10(float(result[4]) / float(result[6])), "time": datetime.today().strftime('%d-%m-%y %H:%M:%S')}])], ignore_index = True)
                                    print(df)
                                    writer = pd.ExcelWriter(data_file, engine = 'openpyxl')
                                    df.to_excel(writer, sheet_name = 'data', index=False)
                                    writer.close()
                                    break
                            break
                    break

    except serial.serialutil.SerialException:
        print("device is not connected!")
        exit()
    except Exception as err:
        print("error!", err)
        exit()


if __name__ == "__main__":

    d = Device(0.01, 0.001)

    solution = input("solution name: ")
    repeats = int(input("number of repeats: "))
    for repeat in tqdm(range(0, repeats)):
        perform_hpos_test(repeat)