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app.py
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app.py
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######### Chi.Bio Operating System V1.0 #########
#Import required python packages
import os
import random
import time
import math
from flask import Flask, render_template, jsonify
from threading import Thread, Lock
import threading
import numpy as np
from datetime import datetime, date
import Adafruit_GPIO.I2C as I2C
import Adafruit_BBIO.GPIO as GPIO
import time
import serial
import simplejson
import copy
import csv
import smbus2 as smbus
application = Flask(__name__)
application.config['SEND_FILE_MAX_AGE_DEFAULT'] = 0 #Try this https://stackoverflow.com/questions/23112316/using-flask-how-do-i-modify-the-cache-control-header-for-all-output/23115561#23115561
lock=Lock()
#Initialise data structures.
#Sysdata is a structure created for each device and contains the setup / measured data related to that device during an experiment. All of this information is passed into the user interface during an experiment.
sysData = {'M0' : {
'UIDevice' : 'M0',
'present' : 0,
'presentDevices' : { 'M0' : 0,'M1' : 0,'M2' : 0,'M3' : 0,'M4' : 0,'M5' : 0,'M6' : 0,'M7' : 0},
'Version' : {'value' : 'Turbidostat V3.0','LED' : 1},
'DeviceID' : '',
'time' : {'record' : []},
'LEDA' : {'WL' : '395', 'default': 0.1, 'target' : 0.0, 'max': 1.0, 'min' : 0.0,'ON' : 0},
'LEDB' : {'WL' : '457', 'default': 0.1, 'target' : 0.0, 'max': 1.0, 'min' : 0.0,'ON' : 0},
'LEDC' : {'WL' : '500', 'default': 0.1, 'target' : 0.0, 'max': 1.0, 'min' : 0.0,'ON' : 0},
'LEDD' : {'WL' : '523', 'default': 0.1, 'target' : 0.0, 'max': 1.0, 'min' : 0.0,'ON' : 0},
'LEDE' : {'WL' : '595', 'default': 0.1, 'target' : 0.0, 'max': 1.0, 'min' : 0.0,'ON' : 0},
'LEDF' : {'WL' : '623', 'default': 0.1, 'target' : 0.0, 'max': 1.0, 'min' : 0.0,'ON' : 0},
'LEDG' : {'WL' : '6500K', 'default': 0.1, 'target' : 0.0, 'max': 1.0, 'min' : 0.0,'ON' : 0},
'LEDH' : {'WL' : '600', 'default': 0.1, 'target' : 0.0, 'max': 1.0, 'min' : 0.0,'ON' : 0}, #80nm FWHM
'LEDI' : {'WL' : '550', 'default': 0.1, 'target' : 0.0, 'max': 1.0, 'min' : 0.0,'ON' : 0}, #105nm FWHM
'LEDV' : {'WL' : 'White', 'default': 0.1, 'target' : 0.0, 'max': 1.0, 'min' : 0.0,'ON' : 0,'ScaleFactor' : 0.4}, #Virtual LED which mixes LEDB and LEDI. ScaleFactor is something to balance between the LED intensites being combined if you want to tune the spectra. Could tune this if you want to get a specific white spectrum blue balance.
'LASER650' : {'name' : 'LASER650', 'default': 0.5, 'target' : 0.0, 'max': 1.0, 'min' : 0.0,'ON' : 0},
'UV' : {'WL' : 'UV', 'default': 0.5, 'target' : 0.0, 'max': 1.0, 'min' : 0.0,'ON' : 0},
'Heat' : {'default': 0.0, 'target' : 0.0, 'max': 1.0, 'min' : 0.0,'ON' : 0,'record' : []},
'Thermostat' : {'default': 37.0, 'target' : 0.0, 'max': 50.0, 'min' : 0.0,'ON' : 0,'record' : [],'cycleTime' : 30.0, 'Integral' : 0.0,'last' : -1},
'Experiment' : {'indicator' : 'USR0', 'startTime' : 'Waiting', 'startTimeRaw' : 0, 'ON' : 0,'cycles' : 0, 'cycleTime' : 60.0,'threadCount' : 0},
'Terminal' : {'text' : ''},
'AS7341' : {
'spectrum' : {'nm410' : 0, 'nm440' : 0, 'nm470' : 0, 'nm510' : 0, 'nm550' : 0, 'nm583' : 0, 'nm620' : 0, 'nm670' : 0,'CLEAR' : 0, 'NIR' : 0,'DARK' : 0,'ExtGPIO' : 0, 'ExtINT' : 0, 'FLICKER' : 0},
'channels' : {'nm410' : 0, 'nm440' : 0, 'nm470' : 0, 'nm510' : 0, 'nm550' : 0, 'nm583' : 0, 'nm620' : 0, 'nm670' : 0,'CLEAR' : 0, 'NIR' : 0,'DARK' : 0,'ExtGPIO' : 0, 'ExtINT' : 0, 'FLICKER' : 0},
'current' : {'ADC0': 0,'ADC1': 0,'ADC2': 0,'ADC3': 0,'ADC4': 0,'ADC5' : 0}},
'ThermometerInternal' : {'current' : 0.0,'record' : []},
'ThermometerExternal' : {'current' : 0.0,'record' : []},
'ThermometerIR' : {'current' : 0.0,'record' : []},
'OD' : {'current' : 0.0,'target' : 0.5,'default' : 0.5,'max': 10, 'min' : 0,'record' : [],'targetrecord' : [],'Measuring' : 0, 'ON' : 0,'Integral' : 0.0,'Integral2' : 0.0,'device' : 'LASER650'},
'OD0' : {'target' : 0.0,'raw' : 0.0,'max' : 100000.0,'min': 0.0,'LASERb' : 1.833 ,'LASERa' : 0.226, 'LEDFa' : 0.673, 'LEDAa' : 7.0 },
'Chemostat' : {'ON' : 0, 'p1' : 0.0, 'p2' : 0.1},
'Zigzag': {'ON' : 0, 'Zig' : 0.04,'target' : 0.0,'SwitchPoint' : 0},
'GrowthRate': {'current' : 0.0,'record' : [],'default' : 2.0},
'Volume' : {'target' : 20.0,'max' : 50.0, 'min' : 0.0,'ON' : 0},
'Pump1' : {'target' : 0.0,'default' : 0.0,'max': 1.0, 'min' : -1.0, 'direction' : 1.0, 'ON' : 0,'record' : [], 'thread' : 0},
'Pump2' : {'target' : 0.0,'default' : 0.0,'max': 1.0, 'min' : -1.0, 'direction' : 1.0, 'ON' : 0,'record' : [], 'thread' : 0},
'Pump3' : {'target' : 0.0,'default' : 0.0,'max': 1.0, 'min' : -1.0, 'direction' : 1.0, 'ON' : 0,'record' : [], 'thread' : 0},
'Pump4' : {'target' : 0.0,'default' : 0.0,'max': 1.0, 'min' : -1.0, 'direction' : 1.0, 'ON' : 0,'record' : [], 'thread' : 0},
'Stir' : {'target' : 0.0,'default' : 0.5,'max': 1.0, 'min' : 0.0, 'ON' : 0},
'Light' : {'target' : 0.0,'default' : 0.5,'max': 1.0, 'min' : 0.0, 'ON' : 0, 'Excite' : 'LEDD', 'record' : []},
'Custom' : {'Status' : 0.0,'default' : 0.0,'Program': 'C1', 'ON' : 0,'param1' : 0, 'param2' : 0, 'param3' : 0.0, 'record' : []},
'FP1' : {'ON' : 0 ,'LED' : 0,'BaseBand' : 0, 'Emit1Band' : 0,'Emit2Band' : 0,'Base' : 0, 'Emit1' : 0,'Emit2' : 0,'BaseRecord' : 0, 'Emit1Record' : 0,'Emit2Record' : 0 ,'Gain' : 0},
'FP2' : {'ON' : 0 ,'LED' : 0,'BaseBand' : 0, 'Emit1Band' : 0,'Emit2Band' : 0,'Base' : 0, 'Emit1' : 0,'Emit2' : 0,'BaseRecord' : 0, 'Emit1Record' : 0,'Emit2Record' : 0 ,'Gain' : 0},
'FP3' : {'ON' : 0 ,'LED' : 0,'BaseBand' : 0, 'Emit1Band' : 0,'Emit2Band' : 0,'Base' : 0, 'Emit1' : 0,'Emit2' : 0,'BaseRecord' : 0, 'Emit1Record' : 0,'Emit2Record' : 0 ,'Gain' : 0},
'biofilm' : {'LEDA' : {'nm410' : 0, 'nm440' : 0, 'nm470' : 0, 'nm510' : 0, 'nm550' : 0, 'nm583' : 0, 'nm620' : 0, 'nm670' : 0,'CLEAR' : 0,'NIR' : 0},
'LEDB' : {'nm410' : 0, 'nm440' : 0, 'nm470' : 0, 'nm510' : 0, 'nm550' : 0, 'nm583' : 0, 'nm620' : 0, 'nm670' : 0,'CLEAR' : 0,'NIR' : 0},
'LEDC' : {'nm410' : 0, 'nm440' : 0, 'nm470' : 0, 'nm510' : 0, 'nm550' : 0, 'nm583' : 0, 'nm620' : 0, 'nm670' : 0,'CLEAR' : 0,'NIR' : 0},
'LEDD' : {'nm410' : 0, 'nm440' : 0, 'nm470' : 0, 'nm510' : 0, 'nm550' : 0, 'nm583' : 0, 'nm620' : 0, 'nm670' : 0,'CLEAR' : 0,'NIR' : 0},
'LEDE' : {'nm410' : 0, 'nm440' : 0, 'nm470' : 0, 'nm510' : 0, 'nm550' : 0, 'nm583' : 0, 'nm620' : 0, 'nm670' : 0,'CLEAR' : 0,'NIR' : 0},
'LEDF' : {'nm410' : 0, 'nm440' : 0, 'nm470' : 0, 'nm510' : 0, 'nm550' : 0, 'nm583' : 0, 'nm620' : 0, 'nm670' : 0,'CLEAR' : 0,'NIR' : 0},
'LEDG' : {'nm410' : 0, 'nm440' : 0, 'nm470' : 0, 'nm510' : 0, 'nm550' : 0, 'nm583' : 0, 'nm620' : 0, 'nm670' : 0,'CLEAR' : 0,'NIR' : 0},
'LASER650' : {'nm410' : 0, 'nm440' : 0, 'nm470' : 0, 'nm510' : 0, 'nm550' : 0, 'nm583' : 0, 'nm620' : 0, 'nm670' : 0,'CLEAR' : 0,'NIR' : 0}}
}}
#SysDevices is unique to each device and is responsible for storing information required for the digital communications, and various automation funtions. These values are stored outside sysData since they are not passable into the HTML interface using the jsonify package.
sysDevices = {'M0' : {
'AS7341' : {'device' : 0},
'ThermometerInternal' : {'device' : 0},
'ThermometerExternal' : {'device' : 0},
'ThermometerIR' : {'device' : 0,'address' :0},
'DAC' : {'device' : 0},
'Pumps' : {'device' : 0,'startup' : 0, 'frequency' : 0},
'PWM' : {'device' : 0,'startup' : 0, 'frequency' : 0},
'Pump1' : {'thread' : 0,'threadCount' : 0, 'active' : 0},
'Pump2' : {'thread' : 0,'threadCount' : 0, 'active' : 0},
'Pump3' : {'thread' : 0,'threadCount' : 0, 'active' : 0},
'Pump4' : {'thread' : 0,'threadCount' : 0, 'active' : 0},
'Experiment' : {'thread' : 0},
'Thermostat' : {'thread' : 0,'threadCount' : 0},
}}
for M in ['M1','M2','M3','M4','M5','M6','M7']:
sysData[M]=copy.deepcopy(sysData['M0'])
sysDevices[M]=copy.deepcopy(sysDevices['M0'])
#sysItems stores information about digital addresses which is used as a reference for all devices.
sysItems = {
'Multiplexer' : {'device' : 0 , 'M0' : '00000001','M1' : '00000010','M2' : '00000100','M3' : '00001000','M4' : '00010000','M5' : '00100000','M6' : '01000000','M7' : '10000000'},
'UIDevice' : 'M0',
'Watchdog' : {'pin' : 'P8_11','thread' : 0,'ON' : 1},
'FailCount' : 0,
'All' : {'ONL' : 0xFA, 'ONH' : 0xFB, 'OFFL' : 0xFC, 'OFFH' : 0xFD},
'Stir' : {'ONL' : 0x06, 'ONH' : 0x07, 'OFFL' : 0x08, 'OFFH' : 0x09},
'Heat' : {'ONL' : 0x3E, 'ONH' : 0x3F, 'OFFL' : 0x40, 'OFFH' : 0x41},
'UV' : {'ONL' : 0x42, 'ONH' : 0x43, 'OFFL' : 0x44, 'OFFH' : 0x45},
'LEDA' : {'ONL' : 0x0E, 'ONH' : 0x0F, 'OFFL' : 0x10, 'OFFH' : 0x11},# Only Led1
'LEDB' : {'ONL' : 0x16, 'ONH' : 0x17, 'OFFL' : 0x18, 'OFFH' : 0x19},#Both LEDs common
'LEDC' : {'ONL' : 0x0A, 'ONH' : 0x0B, 'OFFL' : 0x0C, 'OFFH' : 0x0D},#Both LEDs common
'LEDD' : {'ONL' : 0x1A, 'ONH' : 0x1B, 'OFFL' : 0x1C, 'OFFH' : 0x1D},#Both LEDs Common
'LEDE' : {'ONL' : 0x22, 'ONH' : 0x23, 'OFFL' : 0x24, 'OFFH' : 0x25},#Only Led1
'LEDF' : {'ONL' : 0x1E, 'ONH' : 0x1F, 'OFFL' : 0x20, 'OFFH' : 0x21},#Both LEDs Common
'LEDG' : {'ONL' : 0x12, 'ONH' : 0x13, 'OFFL' : 0x14, 'OFFH' : 0x15},#Only Led1
'LEDH' : {'ONL' : 0x26, 'ONH' : 0x27, 'OFFL' : 0x28, 'OFFH' : 0x29},#Only Led2
'LEDI' : {'ONL' : 0x2E, 'ONH' : 0x2F, 'OFFL' : 0x30, 'OFFH' : 0x31},#Only Led2
'LEDJ' : {'ONL' : 0x36, 'ONH' : 0x37, 'OFFL' : 0x38, 'OFFH' : 0x39},#Only Led2 - same colour as LEDI so current not used.
'Pump1' : {
'In1' : {'ONL' : 0x06, 'ONH' : 0x07, 'OFFL' : 0x08, 'OFFH' : 0x09},
'In2' : {'ONL' : 0x0A, 'ONH' : 0x0B, 'OFFL' : 0x0C, 'OFFH' : 0x0D},
},
'Pump2' : {
'In1' : {'ONL' : 0x0E, 'ONH' : 0x0F, 'OFFL' : 0x10, 'OFFH' : 0x11},
'In2' : {'ONL' : 0x12, 'ONH' : 0x13, 'OFFL' : 0x14, 'OFFH' : 0x15},
},
'Pump3' : {
'In1' : {'ONL' : 0x16, 'ONH' : 0x17, 'OFFL' : 0x18, 'OFFH' : 0x19},
'In2' : {'ONL' : 0x1A, 'ONH' : 0x1B, 'OFFL' : 0x1C, 'OFFH' : 0x1D},
},
'Pump4' : {
'In1' : {'ONL' : 0x1E, 'ONH' : 0x1F, 'OFFL' : 0x20, 'OFFH' : 0x21},
'In2' : {'ONL' : 0x22, 'ONH' : 0x23, 'OFFL' : 0x24, 'OFFH' : 0x25},
},
'AS7341' : {
'0x00' : {'A' : 'nm470', 'B' : 'U'},
'0x01' : {'A' : 'U', 'B' : 'nm410'},
'0x02' : {'A' : 'U', 'B' : 'U'},
'0x03' : {'A' : 'nm670', 'B' : 'U'},
'0x04' : {'A' : 'U', 'B' : 'nm583'},
'0x05' : {'A' : 'nm510', 'B' : 'nm440'},
'0x06' : {'A' : 'nm550', 'B' : 'U'},
'0x07' : {'A' : 'U', 'B' : 'nm620'},
'0x08' : {'A' : 'CLEAR', 'B' : 'U'},
'0x09' : {'A' : 'nm550', 'B' : 'U'},
'0x0A' : {'A' : 'U', 'B' : 'nm620'},
'0x0B' : {'A' : 'U', 'B' : 'U'},
'0x0C' : {'A' : 'nm440', 'B' : 'U'},
'0x0D' : {'A' : 'U', 'B' : 'nm510'},
'0x0E' : {'A' : 'nm583', 'B' : 'nm670'},
'0x0F' : {'A' : 'nm470', 'B' : 'U'},
'0x10' : {'A' : 'ExtGPIO', 'B' : 'nm410'},
'0x11' : {'A' : 'CLEAR', 'B' : 'ExtINT'},
'0x12' : {'A' : 'DARK', 'B' : 'U'},
'0x13' : {'A' : 'FLICKER', 'B' : 'NIR'},
}
}
# This section of code is responsible for the watchdog circuit. The circuit is implemented in hardware on the control computer, and requires the watchdog pin be toggled low->high each second, otherwise it will power down all connected devices. This section is therefore critical to operation of the device.
def runWatchdog():
#Watchdog timing function which continually runs in a thread.
global sysItems;
if (sysItems['Watchdog']['ON']==1):
#sysItems['Watchdog']['thread']
toggleWatchdog();
time.sleep(0.15)
sysItems['Watchdog']['thread']=Thread(target = runWatchdog, args=())
sysItems['Watchdog']['thread'].setDaemon(True)
sysItems['Watchdog']['thread'].start();
def toggleWatchdog():
#Toggle the watchdog
global sysItems;
GPIO.output(sysItems['Watchdog']['pin'], GPIO.HIGH)
time.sleep(0.05)
GPIO.output(sysItems['Watchdog']['pin'], GPIO.LOW)
GPIO.setup(sysItems['Watchdog']['pin'], GPIO.OUT)
print(str(datetime.now()) + ' Starting watchdog')
sysItems['Watchdog']['thread']=Thread(target = runWatchdog, args=())
sysItems['Watchdog']['thread'].setDaemon(True)
sysItems['Watchdog']['thread'].start();
GPIO.setup('P8_15', GPIO.OUT) #This output connects to the RESET pin on the I2C Multiplexer.
GPIO.output('P8_15', GPIO.HIGH)
GPIO.setup('P8_17', GPIO.OUT) #This output connects to D input of the D-Latch
GPIO.output('P8_17', GPIO.HIGH)
def initialise(M):
#Function that initialises all parameters / clears stored values for a given device.
#If you want to record/add values to sysData, recommend adding an initialisation line in here.
global sysData;
global sysItems;
global sysDevices
for LED in ['LEDA','LEDB','LEDC','LEDD','LEDE','LEDF','LEDG','LEDH','LEDI','LEDV']:
sysData[M][LED]['target']=sysData[M][LED]['default']
sysData[M][LED]['ON']=0
sysData[M]['UV']['target']=sysData[M]['UV']['default']
sysData[M]['UV']['ON']=0
sysData[M]['LASER650']['target']=sysData[M]['LASER650']['default']
sysData[M]['LASER650']['ON']=0
FP='FP1'
sysData[M][FP]['ON']=0
sysData[M][FP]['LED']="LEDB"
sysData[M][FP]['Base']=0
sysData[M][FP]['Emit1']=0
sysData[M][FP]['Emit2']=0
sysData[M][FP]['BaseBand']="CLEAR"
sysData[M][FP]['Emit1Band']="nm510"
sysData[M][FP]['Emit2Band']="nm550"
sysData[M][FP]['Gain']="x10"
sysData[M][FP]['BaseRecord']=[]
sysData[M][FP]['Emit1Record']=[]
sysData[M][FP]['Emit2Record']=[]
FP='FP2'
sysData[M][FP]['ON']=0
sysData[M][FP]['LED']="LEDD"
sysData[M][FP]['Base']=0
sysData[M][FP]['Emit1']=0
sysData[M][FP]['Emit2']=0
sysData[M][FP]['BaseBand']="CLEAR"
sysData[M][FP]['Emit1Band']="nm583"
sysData[M][FP]['Emit2Band']="nm620"
sysData[M][FP]['BaseRecord']=[]
sysData[M][FP]['Emit1Record']=[]
sysData[M][FP]['Emit2Record']=[]
sysData[M][FP]['Gain']="x10"
FP='FP3'
sysData[M][FP]['ON']=0
sysData[M][FP]['LED']="LEDE"
sysData[M][FP]['Base']=0
sysData[M][FP]['Emit1']=0
sysData[M][FP]['Emit2']=0
sysData[M][FP]['BaseBand']="CLEAR"
sysData[M][FP]['Emit1Band']="nm620"
sysData[M][FP]['Emit2Band']="nm670"
sysData[M][FP]['BaseRecord']=[]
sysData[M][FP]['Emit1Record']=[]
sysData[M][FP]['Emit2Record']=[]
sysData[M][FP]['Gain']="x10"
for PUMP in ['Pump1','Pump2','Pump3','Pump4']:
sysData[M][PUMP]['default']=0.0;
sysData[M][PUMP]['target']=sysData[M][PUMP]['default']
sysData[M][PUMP]['ON']=0
sysData[M][PUMP]['direction']=1.0
sysDevices[M][PUMP]['threadCount']=0
sysDevices[M][PUMP]['active']=0
sysData[M]['Heat']['default']=0;
sysData[M]['Heat']['target']=sysData[M]['Heat']['default']
sysData[M]['Heat']['ON']=0
sysData[M]['Thermostat']['default']=37.0;
sysData[M]['Thermostat']['target']=sysData[M]['Thermostat']['default']
sysData[M]['Thermostat']['ON']=0
sysData[M]['Thermostat']['Integral']=0
sysData[M]['Thermostat']['last']=-1
sysData[M]['Stir']['target']=sysData[M]['Stir']['default']
sysData[M]['Stir']['ON']=0
sysData[M]['Light']['target']=sysData[M]['Light']['default']
sysData[M]['Light']['ON']=0
sysData[M]['Light']['Excite']='LEDD'
sysData[M]['Custom']['Status']=sysData[M]['Custom']['default']
sysData[M]['Custom']['ON']=0
sysData[M]['Custom']['Program']='C1'
sysData[M]['Custom']['param1']=0.0
sysData[M]['Custom']['param2']=0.0
sysData[M]['Custom']['param3']=0.0
sysData[M]['OD']['current']=0.0
sysData[M]['OD']['target']=sysData[M]['OD']['default'];
sysData[M]['OD0']['target']=65000.0
sysData[M]['OD0']['raw']=65000.0
sysData[M]['OD']['device']='LASER650'
sysData[M]['Volume']['target']=20.0
clearTerminal(M)
addTerminal(M,'System Initialised')
sysData[M]['Experiment']['ON']=0
sysData[M]['Experiment']['cycles']=0
sysData[M]['Experiment']['threadCount']=0
sysData[M]['Experiment']['startTime']=' Waiting '
sysData[M]['Experiment']['startTimeRaw']=0
sysData[M]['OD']['ON']=0
sysData[M]['OD']['Measuring']=0
sysData[M]['OD']['Integral']=0.0
sysData[M]['OD']['Integral2']=0.0
sysData[M]['Zigzag']['ON']=0
sysData[M]['Zigzag']['target']=0.0
sysData[M]['Zigzag']['SwitchPoint']=0
sysData[M]['GrowthRate']['current']=sysData[M]['GrowthRate']['default']
sysDevices[M]['Thermostat']['threadCount']=0
channels=['nm410','nm440','nm470','nm510','nm550','nm583','nm620', 'nm670','CLEAR','NIR','DARK','ExtGPIO', 'ExtINT' , 'FLICKER']
for channel in channels:
sysData[M]['AS7341']['channels'][channel]=0
sysData[M]['AS7341']['spectrum'][channel]=0
DACS=['ADC0', 'ADC1', 'ADC2', 'ADC3', 'ADC4', 'ADC5']
for DAC in DACS:
sysData[M]['AS7341']['current'][DAC]=0
sysData[M]['ThermometerInternal']['current']=0.0
sysData[M]['ThermometerExternal']['current']=0.0
sysData[M]['ThermometerIR']['current']=0.0
sysData[M]['time']['record']=[]
sysData[M]['OD']['record']=[]
sysData[M]['OD']['targetrecord']=[]
sysData[M]['Pump1']['record']=[]
sysData[M]['Pump2']['record']=[]
sysData[M]['Pump3']['record']=[]
sysData[M]['Pump4']['record']=[]
sysData[M]['Heat']['record']=[]
sysData[M]['Light']['record']=[]
sysData[M]['ThermometerInternal']['record']=[]
sysData[M]['ThermometerExternal']['record']=[]
sysData[M]['ThermometerIR']['record']=[]
sysData[M]['Thermostat']['record']=[]
sysData[M]['GrowthRate']['record']=[]
sysDevices[M]['ThermometerInternal']['device']=I2C.get_i2c_device(0x18,2) #Get Thermometer on Bus 2!!!
sysDevices[M]['ThermometerExternal']['device']=I2C.get_i2c_device(0x1b,2) #Get Thermometer on Bus 2!!!
sysDevices[M]['DAC']['device']=I2C.get_i2c_device(0x48,2) #Get DAC on Bus 2!!!
sysDevices[M]['AS7341']['device']=I2C.get_i2c_device(0x39,2) #Get OD Chip on Bus 2!!!!!
sysDevices[M]['Pumps']['device']=I2C.get_i2c_device(0x61,2) #Get OD Chip on Bus 2!!!!!
sysDevices[M]['Pumps']['startup']=0
sysDevices[M]['Pumps']['frequency']=0x1e #200Hz PWM frequency
sysDevices[M]['PWM']['device']=I2C.get_i2c_device(0x60,2) #Get OD Chip on Bus 2!!!!!
sysDevices[M]['PWM']['startup']=0
sysDevices[M]['PWM']['frequency']=0x03# 0x14 = 300hz, 0x03 is 1526 Hz PWM frequency for fan/LEDs, maximum possible. Potentially dial this down if you are getting audible ringing in the device!
#There is a tradeoff between large frequencies which can make capacitors in the 6V power regulation oscillate audibly, and small frequencies which result in the number of LED "ON" cycles varying during measurements.
sysDevices[M]['ThermometerIR']['device']=smbus.SMBus(bus=2) #Set up SMBus thermometer
sysDevices[M]['ThermometerIR']['address']=0x5a
# This section of commented code is used for testing I2C communication integrity.
# sysData[M]['present']=1
# getData=I2CCom(M,'ThermometerInternal',1,16,0x05,0,0)
# i=0
# while (1==1):
# i=i+1
# if (i%1000==1):
# print(str(i))
# sysDevices[M]['ThermometerInternal']['device'].readU8(int(0x05))
# getData=I2CCom(M,which,1,16,0x05,0,0)
scanDevices(M)
if(sysData[M]['present']==1):
turnEverythingOff(M)
V1_Present=0
V2_Present=0
# Now we will detect LED version FIrst checking for version 2
out=GetLight(M,['nm583'],10,10) #Measure with maximum gain (10) and for short period.
Baseline=out[0]
SetOutputOn(M,'LEDH',1) #Turn on LEDH at default level - should only be present in version 2
out=GetLight(M,['nm583'],10,10)
NewLevel=out[0]
SetOutputOn(M,'LEDH',0) #Turn off LEDH at default level - should only be present in version 2
if (NewLevel>Baseline*3+20):
V2_Present = 1
#print(str(datetime.now()) + ' Baseline: ' + str(Baseline) + ' New Level: ' + str(NewLevel))
# Now we will detect for Version 1
out=GetLight(M,['nm583'],10,10) #Measure with maximum gain (10) and for short period.
Baseline=out[0]
SetOutputOn(M,'LEDG',1) #Turn on LEDG at default level - should only be present in version 1
out=GetLight(M,['nm583'],10,10)
NewLevel=out[0]
SetOutputOn(M,'LEDG',0) #Turn off LEDG at default level - should only be present in version 1
#print(str(datetime.now()) + ' Baseline: ' + str(Baseline) + ' New Level: ' + str(NewLevel))
if (NewLevel>Baseline*3+20):
V1_Present = 1
if (V1_Present==1 and V2_Present==0):
sysData[M]['Version']['LED']=1
elif (V1_Present==0 and V2_Present==1):
sysData[M]['Version']['LED']=2
else:
sysData[M]['Version']['LED']=1 #We have messed up somehow in this case and stuff isn't going to work well
print(str(datetime.now()) + " ERROR on " + str(M) +', this device has an unknown LED version. Defaulting to version 1.')
print(str(datetime.now()) + " Initialised " + str(M) +', LED Version: ' + str(sysData[M]['Version']['LED']) + ', Device ID: ' + sysData[M]['DeviceID'])
def initialiseAll():
# Initialisation function which runs at when software is started for the first time.
sysItems['Multiplexer']['device']=I2C.get_i2c_device(0x74,2)
sysItems['FailCount']=0
time.sleep(2.0) #This wait is to allow the watchdog circuit to boot.
print(str(datetime.now()) + ' Initialising devices')
for M in ['M0','M1','M2','M3','M4','M5','M6','M7']:
initialise(M)
scanDevices("all")
def turnEverythingOff(M):
# Function which turns off all actuation/hardware.
for LED in ['LEDA','LEDB','LEDC','LEDD','LEDE','LEDF','LEDG','LEDH','LEDI','LEDV']:
sysData[M][LED]['ON']=0
sysData[M]['LASER650']['ON']=0
sysData[M]['Pump1']['ON']=0
sysData[M]['Pump2']['ON']=0
sysData[M]['Pump3']['ON']=0
sysData[M]['Pump4']['ON']=0
sysData[M]['Stir']['ON']=0
sysData[M]['Heat']['ON']=0
sysData[M]['UV']['ON']=0
I2CCom(M,'DAC',0,8,int('00000000',2),int('00000000',2),0)#Sets all DAC Channels to zero!!!
setPWM(M,'PWM',sysItems['All'],0,0)
setPWM(M,'Pumps',sysItems['All'],0,0)
SetOutputOn(M,'Stir',0)
SetOutputOn(M,'Thermostat',0)
SetOutputOn(M,'Heat',0)
SetOutputOn(M,'UV',0)
SetOutputOn(M,'Pump1',0)
SetOutputOn(M,'Pump2',0)
SetOutputOn(M,'Pump3',0)
SetOutputOn(M,'Pump4',0)
@application.route('/')
def index():
#Function responsible for sending appropriate device's data to user interface.
global sysData
global sysItems
outputdata=sysData[sysItems['UIDevice']]
for M in ['M0','M1','M2','M3','M4','M5','M6','M7']:
if sysData[M]['present']==1:
outputdata['presentDevices'][M]=1
else:
outputdata['presentDevices'][M]=0
return render_template('index.html',**outputdata)
@application.route('/getSysdata/')
def getSysdata():
#Similar to function above, packages data to be sent to UI.
global sysData
global sysItems
outputdata=sysData[sysItems['UIDevice']]
for M in ['M0','M1','M2','M3','M4','M5','M6','M7']:
if sysData[M]['present']==1:
outputdata['presentDevices'][M]=1
else:
outputdata['presentDevices'][M]=0
return jsonify(outputdata)
@application.route('/changeDevice/<M>',methods=['POST'])
def changeDevice(M):
#Function responsible for changin which device is selected in the UI.
global sysData
global sysItems
M=str(M)
if sysData[M]['present']==1:
for Mb in ['M0','M1','M2','M3','M4','M5','M6','M7']:
sysData[Mb]['UIDevice']=M
sysItems['UIDevice']=M
return ('', 204)
@application.route('/scanDevices/<which>',methods=['POST'])
def scanDevices(which):
#Scans to decide which devices are plugged in/on. Does this by trying to communicate with their internal thermometers (if this communication failes, software assumes device is not present)
global sysData
which=str(which)
if which=="all":
for M in ['M0','M1','M2','M3','M4','M5','M6','M7']:
sysData[M]['present']=1
I2CCom(M,'ThermometerInternal',1,16,0x05,0,0) #We arbitrarily poll the thermometer to see if anything is plugged in!
sysData[M]['DeviceID']=GetID(M)
else:
sysData[which]['present']=1
I2CCom(which,'ThermometerInternal',1,16,0x05,0,0)
sysData[which]['DeviceID']=GetID(which)
return ('', 204)
def GetID(M):
#Gets the CHi.Bio reactor's ID, which is basically just the unique ID of the infrared thermometer.
global sysData
M=str(M)
ID=''
if sysData[M]['present']==1:
pt1=str(I2CCom(M,'ThermometerIR',1,0,0x3C,0,1))
pt2=str(I2CCom(M,'ThermometerIR',1,0,0x3D,0,1))
pt3=str(I2CCom(M,'ThermometerIR',1,0,0x3E,0,1))
pt4=str(I2CCom(M,'ThermometerIR',1,0,0x3F,0,1))
ID = pt1+pt2+pt3+pt4
return ID
def addTerminal(M,strIn):
#Responsible for adding a new line to the terminal in the UI.
global sysData
now=datetime.now()
timeString=now.strftime("%Y-%m-%d %H:%M:%S ")
sysData[M]['Terminal']['text']=timeString + ' - ' + str(strIn) + '</br>' + sysData[M]['Terminal']['text']
@application.route("/ClearTerminal/<M>",methods=['POST'])
def clearTerminal(M):
#Deletes everything from the terminal.
global sysData
M=str(M)
if (M=="0"):
M=sysItems['UIDevice']
sysData[M]['Terminal']['text']=''
addTerminal(M,'Terminal Cleared')
return ('', 204)
@application.route("/SetFPMeasurement/<item>/<Excite>/<Base>/<Emit1>/<Emit2>/<Gain>",methods=['POST'])
def SetFPMeasurement(item,Excite,Base,Emit1,Emit2,Gain):
#Sets up the fluorescent protein measurement in terms of gain, and which LED / measurement bands to use.
FP=str(item)
Excite=str(Excite)
Base=str(Base)
Emit1=str(Emit1)
Emit2=str(Emit2)
Gain=str(Gain)
M=sysItems['UIDevice']
if sysData[M][FP]['ON']==1:
sysData[M][FP]['ON']=0
return ('', 204)
else:
sysData[M][FP]['ON']=1
sysData[M][FP]['LED']=Excite
sysData[M][FP]['BaseBand']=Base
sysData[M][FP]['Emit1Band']=Emit1
sysData[M][FP]['Emit2Band']=Emit2
sysData[M][FP]['Gain']=Gain
return ('', 204)
@application.route("/SetOutputTarget/<item>/<M>/<value>",methods=['POST'])
def SetOutputTarget(M,item, value):
#General function used to set the output level of a particular item, ensuring it is within an acceptable range.
global sysData
item = str(item)
value = float(value)
M=str(M)
if (M=="0"):
M=sysItems['UIDevice']
print(str(datetime.now()) + " Set item: " + str(item) + " to value " + str(value) + " on " + str(M))
if (value<sysData[M][item]['min']):
value=sysData[M][item]['min']
if (value>sysData[M][item]['max']):
value=sysData[M][item]['max']
sysData[M][item]['target']=value
if(sysData[M][item]['ON']==1 and not(item=='OD' or item=='Thermostat')): #Checking to see if our item is already running, in which case
SetOutputOn(M,item,0) #we turn it off and on again to restart at new rate.
SetOutputOn(M,item,1)
return ('', 204)
@application.route("/SetOutputOn/<item>/<force>/<M>",methods=['POST'])
def SetOutputOn(M,item,force):
#General function used to switch an output on or off.
global sysData
item = str(item)
force = int(force)
M=str(M)
if (M=="0"):
M=sysItems['UIDevice']
#The first statements are to force it on or off it the command is called in force mode (force implies it sets it to a given state, regardless of what it is currently in)
if (force==1):
sysData[M][item]['ON']=1
SetOutput(M,item)
return ('', 204)
elif(force==0):
sysData[M][item]['ON']=0;
SetOutput(M,item)
return ('', 204)
#Elsewise this is doing a flip operation (i.e. changes to opposite state to that which it is currently in)
if (sysData[M][item]['ON']==0):
sysData[M][item]['ON']=1
SetOutput(M,item)
return ('', 204)
else:
sysData[M][item]['ON']=0;
SetOutput(M,item)
return ('', 204)
def SetOutput(M,item):
#Here we actually do the digital communications required to set a given output. This function is called by SetOutputOn above as required.
global sysData
global sysItems
global sysDevices
M=str(M)
#We go through each different item and set it going as appropriate.
if(item=='Stir'):
#Stirring is initiated at a high speed for a couple of seconds to prevent the stir motor from stalling (e.g. if it is started at an initial power of 0.3)
if (sysData[M][item]['target']*float(sysData[M][item]['ON'])>0):
setPWM(M,'PWM',sysItems[item],1.0*float(sysData[M][item]['ON']),0) # This line is to just get stirring started briefly.
time.sleep(1.5)
if (sysData[M][item]['target']>0.4 and sysData[M][item]['ON']==1):
setPWM(M,'PWM',sysItems[item],0.5*float(sysData[M][item]['ON']),0) # This line is to just get stirring started briefly.
time.sleep(0.75)
if (sysData[M][item]['target']>0.8 and sysData[M][item]['ON']==1):
setPWM(M,'PWM',sysItems[item],0.7*float(sysData[M][item]['ON']),0) # This line is to just get stirring started briefly.
time.sleep(0.75)
setPWM(M,'PWM',sysItems[item],sysData[M][item]['target']*float(sysData[M][item]['ON']),0)
elif(item=='Heat'):
setPWM(M,'PWM',sysItems[item],sysData[M][item]['target']*float(sysData[M][item]['ON']),0)
elif(item=='UV'):
setPWM(M,'PWM',sysItems[item],sysData[M][item]['target']*float(sysData[M][item]['ON']),0)
elif (item=='Thermostat'):
sysDevices[M][item]['thread']=Thread(target = Thermostat, args=(M,item))
sysDevices[M][item]['thread'].setDaemon(True)
sysDevices[M][item]['thread'].start();
elif (item=='Pump1' or item=='Pump2' or item=='Pump3' or item=='Pump4'):
if (sysData[M][item]['target']==0):
sysData[M][item]['ON']=0
sysDevices[M][item]['thread']=Thread(target = PumpModulation, args=(M,item))
sysDevices[M][item]['thread'].setDaemon(True)
sysDevices[M][item]['thread'].start();
elif (item=='OD'):
SetOutputOn(M,'Pump1',0)
SetOutputOn(M,'Pump2',0) #We turn pumps off when we switch OD state
elif (item=='Zigzag'):
sysData[M]['Zigzag']['target']=5.0
sysData[M]['Zigzag']['SwitchPoint']=sysData[M]['Experiment']['cycles']
elif (item=='LEDA' or item=='LEDC' or item=='LEDD' or item=='LEDE' or item=='LEDF' or item=='LEDG' or item == 'LEDH'):
setPWM(M,'PWM',sysItems[item],sysData[M][item]['target']*float(sysData[M][item]['ON']),0)
elif (item=='LEDB' or item == 'LEDI'): #We must handle these differently in case they are simultaneously being used to mix with LEDV
if (sysData[M]['LEDV']['target']*float(sysData[M]['LEDV']['ON'])>0): #If LEDV is on, we need to make up the difference in these other LEDs.
# First determine what is the intensity for this LED required to maintain current LEDV level. Note we have alreayd checked that LEDV is on.
if (item=='LEDB'):
LEDV_Intensity = sysData[M]['LEDV']['target']*sysData[M]['LEDV']['ScaleFactor']
elif (item == 'LEDI'):
LEDV_Intensity = sysData[M]['LEDV']['target']
NewIntensity = sysData[M][item]['target']*float(sysData[M][item]['ON']) + LEDV_Intensity #Add on whatever extra intensity is required to maintain LEDV level.
if (NewIntensity>1.0):
NewIntensity=1.0
setPWM(M,'PWM',sysItems[item],NewIntensity,0)
else:
setPWM(M,'PWM',sysItems[item],sysData[M][item]['target']*float(sysData[M][item]['ON']),0)
elif (item=='LEDV'): #This is the virtual white LED which is made by combinng LEDB and LEDI
LEDB_Intensity = sysData[M]['LEDV']['target']*float(sysData[M]['LEDV']['ON'])*sysData[M]['LEDV']['ScaleFactor'] #This is the intensity of the blue we want mixed into our white light
LEDB_Intensity = LEDB_Intensity + sysData[M]['LEDB']['target']*float(sysData[M]['LEDB']['ON']) #This adds the intensity of the blue we already have on
LEDI_Intensity = sysData[M]['LEDV']['target']*float(sysData[M]['LEDV']['ON']) #This is the intensity of the Lime, similar to above.
LEDI_Intensity = LEDI_Intensity + sysData[M]['LEDI']['target']*float(sysData[M]['LEDI']['ON'])
if (LEDB_Intensity>1.0): #If we are exceeding the maximum intensity, we are going to force a saturation.
LEDB_Intensity=1.0
if (LEDI_Intensity>1.0):
LEDI_Intensity=1.0
setPWM(M,'PWM',sysItems['LEDB'],LEDB_Intensity,0)
setPWM(M,'PWM',sysItems['LEDI'],LEDI_Intensity,0)
elif(item == 'LASER650'): #This is if we are setting the Laser
value=sysData[M][item]['target']*float(sysData[M][item]['ON'])
if (value==0):
value=0
else:
value=(value+0.00)/1.00
sf=0.303 #This factor is scaling down the maximum voltage being fed to the laser, preventing its photodiode current (and hence optical power) being too large.
value=value*sf
binaryValue=bin(int(value*4095.9)) #Bit of a dodgy method for ensuring we get an integer in [0,4095]
toWrite=str(binaryValue[2:].zfill(16))
toWrite1=int(toWrite[0:8],2)
toWrite2=int(toWrite[8:16],2)
I2CCom(M,'DAC',0,8,toWrite1,toWrite2,0)
def PumpModulation(M,item):
#Responsible for turning pumps on/off with an appropriate duty cycle. They are turned on for a fraction of each ~1minute cycle to achieve low pump rates.
global sysData
global sysItems
global sysDevices
sysDevices[M][item]['threadCount']=(sysDevices[M][item]['threadCount']+1)%100 #Index of the particular thread running.
currentThread=sysDevices[M][item]['threadCount']
while (sysDevices[M][item]['active']==1): #Idea is we will wait here if a previous thread on this pump is already running. Potentially all this 'active' business could be removed from this fuction.
time.sleep(0.02)
if (abs(sysData[M][item]['target']*sysData[M][item]['ON'])!=1 and currentThread==sysDevices[M][item]['threadCount']): #In all cases we turn things off to begin
sysDevices[M][item]['active']=1
setPWM(M,'Pumps',sysItems[item]['In1'],0.0*float(sysData[M][item]['ON']),0)
setPWM(M,'Pumps',sysItems[item]['In2'],0.0*float(sysData[M][item]['ON']),0)
setPWM(M,'Pumps',sysItems[item]['In1'],0.0*float(sysData[M][item]['ON']),0)
setPWM(M,'Pumps',sysItems[item]['In2'],0.0*float(sysData[M][item]['ON']),0)
sysDevices[M][item]['active']=0
if (sysData[M][item]['ON']==0):
return
Time1=datetime.now()
cycletime=sysData[M]['Experiment']['cycleTime']*1.05 #We make this marginally longer than the experiment cycle time to avoid too much chaos when you come back around to pumping again.
Ontime=cycletime*abs(sysData[M][item]['target'])
# Decided to remove the below section in order to prevent media buildup in the device if you are pumping in very rapidly. This check means that media is removed, then added. Removing this code means these happen simultaneously.
#if (item=="Pump1" and abs(sysData[M][item]['target'])<0.3): #Ensuring we run Pump1 after Pump2.
# waittime=cycletime*abs(sysData[M]['Pump2']['target']) #We want to wait until the output pump has stopped, otherwise you are very inefficient with your media since it will be pumping out the fresh media fromthe top of the test tube right when it enters.
# time.sleep(waittime+1.0)
if (sysData[M][item]['target']>0 and currentThread==sysDevices[M][item]['threadCount']): #Turning on pumps in forward direction
sysDevices[M][item]['active']=1
setPWM(M,'Pumps',sysItems[item]['In1'],1.0*float(sysData[M][item]['ON']),0)
setPWM(M,'Pumps',sysItems[item]['In2'],0.0*float(sysData[M][item]['ON']),0)
sysDevices[M][item]['active']=0
elif (sysData[M][item]['target']<0 and currentThread==sysDevices[M][item]['threadCount']): #Or backward direction.
sysDevices[M][item]['active']=1
setPWM(M,'Pumps',sysItems[item]['In1'],0.0*float(sysData[M][item]['ON']),0)
setPWM(M,'Pumps',sysItems[item]['In2'],1.0*float(sysData[M][item]['ON']),0)
sysDevices[M][item]['active']=0
time.sleep(Ontime)
if(abs(sysData[M][item]['target'])!=1 and currentThread==sysDevices[M][item]['threadCount']): #Turning off pumps at appropriate time.
sysDevices[M][item]['active']=1
setPWM(M,'Pumps',sysItems[item]['In1'],0.0*float(sysData[M][item]['ON']),0)
setPWM(M,'Pumps',sysItems[item]['In2'],0.0*float(sysData[M][item]['ON']),0)
setPWM(M,'Pumps',sysItems[item]['In1'],0.0*float(sysData[M][item]['ON']),0)
setPWM(M,'Pumps',sysItems[item]['In2'],0.0*float(sysData[M][item]['ON']),0)
sysDevices[M][item]['active']=0
Time2=datetime.now()
elapsedTime=Time2-Time1
elapsedTimeSeconds=round(elapsedTime.total_seconds(),2)
Offtime=cycletime-elapsedTimeSeconds
if (Offtime>0.0):
time.sleep(Offtime)
if (sysData[M][item]['ON']==1 and sysDevices[M][item]['threadCount']==currentThread): #If pumps need to keep going, this starts a new pump thread.
sysDevices[M][item]['thread']=Thread(target = PumpModulation, args=(M,item))
sysDevices[M][item]['thread'].setDaemon(True)
sysDevices[M][item]['thread'].start();
def Thermostat(M,item):
#Function that implements thermostat temperature control using MPC algorithm.
global sysData
global sysItems
global sysDevices
ON=sysData[M][item]['ON']
sysDevices[M][item]['threadCount']=(sysDevices[M][item]['threadCount']+1)%100
currentThread=sysDevices[M][item]['threadCount']
if (ON==0):
SetOutputOn(M,'Heat',0)
return
MeasureTemp(M,'IR') #Measures temperature - note that this may be happening DURING stirring.
CurrentTemp=sysData[M]['ThermometerIR']['current']
TargetTemp=sysData[M]['Thermostat']['target']
LastTemp=sysData[M]['Thermostat']['last']
#MPC Controller Component
MediaTemp=sysData[M]['ThermometerExternal']['current']
MPC=0
if (MediaTemp>0.0):
Tdiff=CurrentTemp-MediaTemp
Pumping=sysData[M]['Pump1']['target']*float(sysData[M]['Pump1']['ON'])*float(sysData[M]['OD']['ON'])
Gain=2.5
MPC=Gain*Tdiff*Pumping
#PI Controller Component
e=TargetTemp-CurrentTemp
dt=sysData[M]['Thermostat']['cycleTime']
I=sysData[M]['Thermostat']['Integral']
if (abs(e)<2.0):
I=I+0.0005*dt*e
P=0.25*e
else:
P=0.5*e;
if (abs(TargetTemp-LastTemp)>2.0): #This resets integrator if we make a big jump in set point.
I=0.0
elif(I<0.0):
I=0.0
elif (I>1.0):
I=1.0
sysData[M]['Thermostat']['Integral']=I
U=P+I+MPC
if(U>1.0):
U=1.0
sysData[M]['Heat']['target']=U
sysData[M]['Heat']['ON']=1
elif(U<0):
U=0
sysData[M]['Heat']['target']=U
sysData[M]['Heat']['ON']=0
else:
sysData[M]['Heat']['target']=U
sysData[M]['Heat']['ON']=1
sysData[M]['Thermostat']['last']=sysData[M]['Thermostat']['target']
SetOutput(M,'Heat')
time.sleep(dt)
if (sysData[M][item]['ON']==1 and sysDevices[M][item]['threadCount']==currentThread):
sysDevices[M][item]['thread']=Thread(target = Thermostat, args=(M,item))
sysDevices[M][item]['thread'].setDaemon(True)
sysDevices[M][item]['thread'].start();
else:
sysData[M]['Heat']['ON']=0
sysData[M]['Heat']['target']=0
SetOutput(M,'Heat')
@application.route("/Direction/<item>/<M>",methods=['POST'])
def direction(M,item):
#Flips direction of a pump.
global sysData
M=str(M)
if (M=="0"):
M=sysItems['UIDevice']
sysData[M][item]['target']=-1.0*sysData[M][item]['target']
if (sysData[M]['OD']['ON']==1):
sysData[M][item]['direction']=-1.0*sysData[M][item]['direction']
return ('', 204)
def AS7341Read(M,Gain,ISteps,reset):
#Responsible for reading data from the spectrometer.
global sysItems
global sysData
reset=int(reset)
ISteps=int(ISteps)
if ISteps>255:
ISteps=255 #255 steps is approx 0.71 seconds.
elif (ISteps<0):
ISteps=0
if Gain>10:
Gain=10 #512x
elif (Gain<0):
Gain=0 #0.5x
I2CCom(M,'AS7341',0,8,int(0xA9),int(0x04),0) #This sets us into BANK mode 0, for accesing registers 0x80+. The 4 means we have WTIMEx16
if (reset==1):
I2CCom(M,'AS7341',0,8,int(0x80),int(0x00),0) #Turns power down
time.sleep(0.01)
I2CCom(M,'AS7341',0,8,int(0x80),int(0x01),0) #Turns power on with spectral measurement disabled
else:
I2CCom(M,'AS7341',0,8,int(0x80),int(0x01),0) #Turns power on with spectral measurement disabled
I2CCom(M,'AS7341',0,8,int(0xAF),int(0x10),0) #Tells it we are going to now write SMUX configuration to RAM
#I2CCom(M,'AS7341',0,100,int(0x00),int(0x00),0) #Forces AS7341SMUX to run since length is 100.
AS7341SMUX(M,'AS7341',0,0)
I2CCom(M,'AS7341',0,8,int(0x80),int(0x11),0) #Runs SMUX command (i.e. cofigures SMUX with data from ram)
time.sleep(0.001)
I2CCom(M,'AS7341',0,8,int(0x81),ISteps,0) #Sets number of integration steps of length 2.78ms Max ISteps is 255
I2CCom(M,'AS7341',0,8,int(0x83),0xFF,0) #Sets maxinum wait time of 0.7mS (multiplex by 16 due to WLONG)
I2CCom(M,'AS7341',0,8,int(0xAA),Gain,0) #Sets gain on ADCs. Maximum value of Gain is 10 and can take values from 0 to 10.
#I2CCom(M,'AS7341',0,8,int(0xA9),int(0x14),0) #This sets us into BANK mode 1, for accessing 0x60 to 0x74. The 4 means we have WTIMEx16
#I2CCom(M,'AS7341',0,8,int(0x70),int(0x00),0) #Sets integration mode SPM (normal mode)
#Above is default of 0x70!
I2CCom(M,'AS7341',0,8,int(0x80),int(0x0B),0) #Starts spectral measurement, with WEN (wait between measurements feature) enabled.
time.sleep((ISteps+1)*0.0028 + 0.2) #Wait whilst integration is done and results are processed.
ASTATUS=int(I2CCom(M,'AS7341',1,8,0x94,0x00,0)) #Get measurement status, including saturation details.
C0_L=int(I2CCom(M,'AS7341',1,8,0x95,0x00,0))
C0_H=int(I2CCom(M,'AS7341',1,8,0x96,0x00,0))
C1_L=int(I2CCom(M,'AS7341',1,8,0x97,0x00,0))
C1_H=int(I2CCom(M,'AS7341',1,8,0x98,0x00,0))
C2_L=int(I2CCom(M,'AS7341',1,8,0x99,0x00,0))
C2_H=int(I2CCom(M,'AS7341',1,8,0x9A,0x00,0))
C3_L=int(I2CCom(M,'AS7341',1,8,0x9B,0x00,0))
C3_H=int(I2CCom(M,'AS7341',1,8,0x9C,0x00,0))
C4_L=int(I2CCom(M,'AS7341',1,8,0x9D,0x00,0))
C4_H=int(I2CCom(M,'AS7341',1,8,0x9E,0x00,0))
C5_L=int(I2CCom(M,'AS7341',1,8,0x9F,0x00,0))
C5_H=int(I2CCom(M,'AS7341',1,8,0xA0,0x00,0))
I2CCom(M,'AS7341',0,8,int(0x80),int(0x01),0) #Stops spectral measurement, leaves power on.
#Status2=int(I2CCom(M,'AS7341',1,8,0xA3,0x00,0)) #Reads system status at end of spectral measursement.
#print(str(ASTATUS))
#print(str(Status2))
sysData[M]['AS7341']['current']['ADC0']=int(bin(C0_H)[2:].zfill(8)+bin(C0_L)[2:].zfill(8),2)
sysData[M]['AS7341']['current']['ADC1']=int(bin(C1_H)[2:].zfill(8)+bin(C1_L)[2:].zfill(8),2)