UDAS_FCNS_Module.py

##UDAS Functions File_MS202_Spring_2022
#Contains functions to run the various sensors configured to the UDAS system

import numpy as np
import serial
from datetime import datetime
import time
import csv
import board
import busio
import adafruit_gps
import io
import pynmea2



# Fucnction to retrieve the TSG sensor Data
# TSG sensor provides data for Temperature (C), conductivity, and salinity (PSU)
def getTSG(TSG_sensor):
    '''Obtain temperature, conducivity, and practical salinity measurments from TSG sensor.
        
        INPUTS:
           TSG_sensor - a serial object
        
        RETURNS:
        temperature (Celsius)
        conductivity
        salinity
        '''
    try:
        data = TSG_sensor.readline().decode()
        split = data.split(',')
        data_T = float(split[0])
        data_C = float(split[1])
        data_S = float(split[2])
        
        return(data_T,data_C,data_S)
            
    except:
        print('No data collected')
        data_T = 'nan'
        data_C = 'nan'
        data_S = 'nan'
        return (data_T, data_C, data_S)


#=========================================================
# Function to Retrive SUNA sensor data
# SUNA sensor provides nitrate data (NO3)
def getSUNA(suna,nsample):
    '''
    Obtain nitrate measurement from SUNA sensor operating in polled mode.
    
    This version has been tested on Python 3 only.
    
    INPUTS:
    suna - a Serial object
    nsample - number of light samples to average
    
    RETURNS
    nitrate_uM (umol/L)
    nitrogen (mg/L)
    '''
    
    try:
        print('Connected to SUNA'+'\n')
        
        suna.write(b'Waking up SUNA\n')
        wake1 = suna.readline().decode()
        #print('wake1: ' + wake1+'\n')
        wake2 = suna.readline().decode()
        #print('wake2: ' + wake2+'\n')
        #print('Woken up SUNA, exit from command line'+'\n')
        suna.write(b'exit\n')
        
        #wait a few secs
        time.sleep(10)
        
        #SATSDF: SUNA Dark Full: blank dark reading
        #SATSLF: this has the data in it. Check SUNA hardware manual pg 58 for column headers
        #... full ascii column
        
        #Request data, take samples and average them together
        sample_command = 'measure '+str(nsample)+'\n'
        try:
            suna.write(sample_command)
        except:
            suna.write(str.encode(sample_command))
            
        nitrate_list=[]
        nitrogen_list = []
                
        count = 1
        # Loop through until done, limit to nsample*10 to avoid infinite loop
        for i in range(nsample*2):
            try:
                line=suna.readline().decode()
            except:
                line=suna.readline()
            #print('Line: '+line+'\n')
            if 'SATSL' in line:
                #Only average the light counts
                data = line.split(',')
                nitrate_list.append(float(data[3]))
                nitrogen_list.append(float(data[4]))
                count = count+1
            if count > nsample:
                break
        
        suna.close()
        
        
        
        data = line.split(',')
        nitrate_uM = np.mean(nitrate_list)
        nitrogen = np.mean(nitrogen_list)
        
        
        print ('*****************************************\n')
        print ('Nitrate (uM): '+str(nitrate_uM)+'\n')
        print ('Nitrogen (mg/L): '+str(nitrogen)+'\n')
        print ('*****************************************\n')
        
        
        return (nitrate_uM, nitrogen)

    
    except:
        
        print ('No data received from SUNA.'+'\n')
        return ('NA','NA')

#==================================================================================
# Function to retrieve data from the transmissometer sensor
# Transmissometer sensor provides data for beam attenuation
def get_Transmissometer(TM_Sensor):
    '''Obtain transmisometer data from transmissometer sensor.
        Inputs:
            TMSensor - a serial object
        
        Outputs:
            Beam_Attenuation
        '''
    try:
        data = TM_Sensor.readline().decode()
        index = data.split()
        Beam_Attenuation = float(index[4])
        return Beam_Attenuation
    
    except:
        print('No data collected')
        Beam_Attenuation = 'nan'
        return Beam_Attenuation
    
#===============================================================
#Chlorophyll 
def get_chla(chla_sensor):
    ''' Obtain Chlorophyl a and turbidity measurments.
        
        INPUTS:
           chla_sensor - a serial object
        
        RETURNS:
        Chl_a (chlorophyll a)
        turb (Turbidity)
    '''
    try:
        data = chla_sensor.readline().decode()
        split = data.split()
        chl_a = float(split[3])
        turb = float(split[4])
        return chl_a,turb
    
    except:
        print('No data collected')
        chl_a = 'nan'
        turb = 'nan'
        return chl_a,turb
    
#=================================================================
# GPS
def get_gps(sio):

    timestamp = time.monotonic()
    try:
        line = sio.readline()
        msg= pynmea2.parse(line)
        lat = msg.lat
        lon = msg.lon
        return repr(msg.lat), repr(msg.lon)
    except serial.SerialException as e:
        lat = 'nan'
        lon = 'nan'
        #error = str('Device error: {}'.format(e))
        return lat,lon
    except pynmea2.ParseError as e:
        lat = 'nan'
        lon = 'nan'
        #rror = str('Parse error: {}'.format(e))
        return lat,lon
    except AttributeError as e:
        lat = 'nan'
        lon = 'nan'
        #error = str('Attribute error: {}'.format(e))
        return lat,lon
    except:
        lat = 'nan'
        lon = 'nan'
        return lat,lon