from os import listdir
from os.path import isfile, join
import serial 

import numpy as np
import pandas as pd 
import time 
from scipy.integrate import trapz

#step1: be sure to the address of the files that the ftir data is exported is matching to line 11 (mypath)
mypath = "C:\\Users\Admin\Desktop\Dnya\\Exp 20230714"
onlyfiles = [f for f in listdir(mypath) if isfile(join(mypath, f))]


#step2: make sure that pump and the potentiostat is correctly addressed in the line 16 and 17
pump_1 = serial.serial_for_url("socket://169.254.1.51:10001",9600) #HPLC Pump LAN
port = serial.Serial("COM1",115200)
pump_2 = serial.Serial("COM5",9600) #HPLC Pump
printer = serial.Serial("COM6", 115200, timeout=1)

#step 3: grab the lines from 22 to 90 and presss f9 
def area_under(data,start,end):
    x = np.flip(data.iloc[start:end,0].to_numpy())
    y = np.flip(data.iloc[start:end,1].to_numpy())
    area = trapz(y,x)
    return np.abs(area)

def file_namer(num):
    str1 = str(num)
    length = int(len((str1)))
    empt = ''
    for i in range(5-length):
        empt = empt+'0'
        
    return empt+str1

        
def ftir_extract(filename,init,end):

    filename = filename

    temp_df = pd.read_csv(filename)
    # nump_df = temp_df.to_numpy()
    area = area_under(temp_df, init, end)
    # max_peak = np.max(nump_df[90:120,1])
    print(area)

    return area


def function(flowrate_1,flowrate_2,v,i):
    
     #set the pumps with the flowrate as the desired flowrate for the function

    fr_1 = flowrate_1*1000   #ml/min
    pump_1.write(('flow:'+ str(fr_1) + '\r').encode())
    
    time.sleep(0.1)
    fr_2=flowrate_2*1000 #converting ml/min to ul/min as pump takes this as input val
    pump_2.write(('flow:'+ str(fr_2) + '\r').encode())
    
    #set the com port for potentiostat and set the voltage and current    
    vol = v
    curr = i
    port.write(('VOLT '+str(vol)+'\r\n').encode())     #to change the voltge we need to use "VOLT 1" command 
    port.write(('CURR '+str(curr)+'\r\n').encode())    #to change the current we need to use "CURR 1" command

    
    #pumps run
    pump_1.write(b'on\r')
    time.sleep(0.1)
    pump_2.write(b'on\r')
    
    time.sleep(480)
    
def function2():
    time.sleep(180) # Last 3 minutes
    files = [f for f in listdir(mypath) if isfile(join(mypath, f))]

    val = 0
    
    #change wavelengths as per product here.
    f_row=19 #first row of range for wavelength as per IR CSV
    l_row=24 #last row of range for wavelength as per IR CSV
    
    val += ftir_extract(files[-1],f_row,l_row)
    val += ftir_extract(files[-2],f_row,l_row)
    val += ftir_extract(files[-3],f_row,l_row)

    avg_val = val/3
    
    return avg_val


#step 4:grab the line 93 and f9
from skopt.optimizer import Optimizer


#step5:in line 96 we have to define the range that (flowrate,voltage,current) (from,to) and after (anytime) appllying changes you need to grab the line 96 and f9
#flowrates are in ml/min, voltage in V, Current in Ampere
bounds = [(0.2,2.0),(10.0,15.0),(4.4,4.5)]
#step 6: grab the line 100 and f9
opter =Optimizer(bounds,base_estimator='gp',n_initial_points=3,acq_func="EI",random_state=np.random.randint(3326))


#step7: to selecte number of the cycles that you have to do the experiment and then grab the line 104 to 121 and f9: the closed loop experimentation is initiated
number_of_cycles =160
results = []
flowrates_1 = []
flowrates_2 = []
vs = []
currents = []

product_wavelength=True #set to true if product wavelengths being monitored

if product_wavelength == True:
    val=1
else:
    val=-1

# Step 8: Test Tubes on Printer
USE_PRINTER = True
REST_HEIGHT = 200
X_HOME = -5
Y_HOME = 20
Z_HOME = 175
DEFAULT_PUMP_TIME="1"
# Distance between test tubes
X_SPACING=20
Y_SPACING=20
# Number of test tubes
X_ROWS = 11
Y_COLUMNS = 4

def send_cmd(cmd):
    print(cmd)
    printer.write(f"{cmd}\n".encode("ASCII"))

def move(x=None, y=None, z=None):
    s = "G0"
    if x is not None:
        s += f"X{x}"
    if y is not None:
        s += f"Y{y}"
    if z is not None:
        s += f"Z{z}"
    
    s+= "F5000"
    send_cmd(s)

def printer_positions():
    for j in range(Y_COLUMNS):
        for i in range(X_ROWS):
            if j%2==1:
                yield (X_HOME + (X_ROWS - 1 - i) * X_SPACING, Y_HOME + j * Y_SPACING, Z_HOME)
            else:
                yield (X_HOME + i * X_SPACING, Y_HOME + j * Y_SPACING, Z_HOME)

# Run this.
tube_location = list(printer_positions())

try:
    for i in range(number_of_cycles):
        move(*tube_location[2*i])
        asked = opter.ask()
        function(asked[0],asked[0],asked[1],asked[2])
        
        move(*tube_location[2*i+1])
        told= function2()
        
        print(f"area under the curve in the round {i:.2f} = {told:.2f}")
        opter.tell(asked,-told*val)
        results.append(told)
        flowrates_1.append(asked[0])
        flowrates_2.append(asked[0])
        vs.append(asked[1])
        currents.append(asked[2])
    
        dict1 = {"flowrate_1":flowrates_1,"flowrate_2":flowrates_2,"voltages":vs, "currents":currents,"area-results":results}
        df2 = pd.DataFrame(dict1)
        df2.to_csv("output round "+str(i)+".csv")
finally:
    pump_1.write(b'off\r')        
    pump_2.write(b'off\r')