def pumping_operation(day,hour,minute,frequency_sampling,num_samples,operate_arduino_object,starting_well=0):
  samplingObject=CFlow.sampleHandling()

  click_object=CFlow.click(sample_counter=starting_well)
  click_object.set_measuring_times(day,hour,minute,frequency_sampling,num_samples)		#Set input correctly. day,hour,minute,frequency,num_samples

  read_fcs_object=CFlow.read_fcs('C:\\Users\\localadmin\\Desktop\\Results','ecoli')

  while click_object.set_waiting_time()==0:
    time.sleep(click_object.waiting_time)
    logging.info('waiting time until next measurement is: %f',click_object.waiting_time)
    samplingObject.bring_sample(operate_arduino_object,sample=click_object.measuring_times[click_object.time_counter][1])
    click_object.sample()
    click_object.run(click_object.measuring_times[click_object.time_counter][1])
    click_object.export()
    time.sleep(1)
    click_object.moveFiles('C:\\Users\\localadmin\\Desktop','C:\\Users\\localadmin\\Desktop\\Results')###THIS CHANGES FROM COMPUTER TO COMPUTER. THE OUTPUT FOLDER MUST BE CREATED BEFOREHAND
    time.sleep(1)
    ##PERFORM FEEDBACK
    ##
    click_object.backflush()
    operate_arduino_object.push_to_cytometer(2)
    operate_arduino_object.cytometer_to_waste(2)
    operate_arduino_object.push_to_cytometer(2)
    operate_arduino_object.cytometer_to_waste(2)
    operate_arduino_object.push_to_cytometer(2)
    operate_arduino_object.cytometer_to_waste(2)
  return
Beispiel #2
0
def pumping_operation(day,
                      hour,
                      minute,
                      frequency,
                      num_samples,
                      operate_arduino_object,
                      starting_well=0):
    click_object = CFlow.click(sample_counter=starting_well)
    click_object.set_measuring_times(
        day, hour, minute, frequency, num_samples
    )  #Set input correctly. day,hour,minute,frequency,num_samples
    read_fcs_object = CFlow.read_fcs('C:\\Users\\rumarc\\Desktop\\Results',
                                     'ecoli')
    operate_arduino_object.operate_led(1, 256)  ####
    operate_arduino_object.operate_led(2, 0 * 256)  ####
    ##Feedback constants
    I = 0
    P = 0
    kp = 0.8
    ki = 0.08
    ref = 0.66  #Reference value for controller
    ##
    while click_object.set_waiting_time() == 0:
        time.sleep(click_object.waiting_time)
        logging.info('waiting time until next measurement is: %f',
                     click_object.waiting_time)
        bring_sample(operate_arduino_object)
        click_object.sample()
        click_object.run()
        click_object.export()
        time.sleep(1)
        click_object.moveFiles(
            'C:\\Users\\rumarc\\Desktop', 'C:\\Users\\rumarc\\Desktop\\Results'
        )  ###THIS CHANGES FROM COMPUTER TO COMPUTER. THE OUTPUT FOLDER MUST BE CREATED BEFOREHAND
        time.sleep(1)
        ##PERFORM FEEDBACK
        GFP_mean = read_fcs_object.get_last_data(click_object)
        logging.info('GFP mean is: %f', GFP_mean)
        print(GFP_mean)
        I = ki * (ref - GFP_mean) + I
        print(I)
        logging.info('Integral parameter value is: %f', I)
        P = kp * (ref - GFP_mean)
        print(P)
        logging.info('Proportional parameter value is: %f', P)
        LED_signal = P + I
        if LED_signal < 0:
            LED_signal = 0
        elif LED_signal > 1:
            LED_signal = 1
        logging.info('LED signal is: %f', LED_signal)
        print(LED_signal)
        LED_signal = LED_signal * 256
        operate_arduino_object.operate_led(2, LED_signal)
        ##
        click_object.backflush()
        operate_arduino_object.cytometer_to_waste(8)
    return
def pumping_operation(day,hour,minute,frequency,num_samples,operate_arduino_object,starting_well=0):
  click_object=CFlow.click(sample_counter=starting_well)
  click_object.set_measuring_times(day,hour,minute,frequency,num_samples)		#Set input correctly. day,hour,minute,frequency,num_samples
  read_fcs_object=CFlow.read_fcs('C:\\Users\\rumarc\\Desktop\\Results','ecoli')
  operate_arduino_object.operate_led(1,256)####
  operate_arduino_object.operate_led(2,0*256)####
  ##Feedback constants
  I=0
  P=0
  kp=6.8
  ki=0.5
  ref=0.07									#Reference value for controller
  ##
  while click_object.set_waiting_time()==0:
    time.sleep(click_object.waiting_time)
    logging.info('waiting time until next measurement is: %f',click_object.waiting_time)
    bring_sample(operate_arduino_object)
    click_object.sample()
    click_object.run()
    click_object.export()
    time.sleep(1)
    click_object.moveFiles('C:\\Users\\rumarc\\Desktop','C:\\Users\\rumarc\\Desktop\\Results')###THIS CHANGES FROM COMPUTER TO COMPUTER. THE OUTPUT FOLDER MUST BE CREATED BEFOREHAND
    time.sleep(1)
    ##PERFORM FEEDBACK
    GFP_variance=read_fcs_object.get_last_data(click_object,'variance')
    logging.info('GFP variance is: %f',GFP_variance)
    if GFP_variance>ref:
        kp=13.6
        ki=1.5
    if GFP_variance<ref*0.9:
        kp=6.8
        ki=0.5
    print(GFP_variance)
    I=ki*(ref-GFP_variance)+I
    if I<0:
        I=0
    print(I)
    logging.info('Integral parameter value is: %f',I)
    P=kp*(ref-GFP_variance)
    print(P)
    logging.info('Proportional parameter value is: %f',P)
    LED_signal=P+I
    if LED_signal<0:
        LED_signal=0
    elif LED_signal>1:
        LED_signal=1
    logging.info('LED signal is: %f',LED_signal)
    print(LED_signal)
    LED_signal=LED_signal*256
    operate_arduino_object.operate_led(2,LED_signal)
	##
    click_object.backflush()
    operate_arduino_object.cytometer_to_waste(8)
  return
Beispiel #4
0
def pumping_operation(day,
                      hour,
                      minute,
                      frequency,
                      num_samples,
                      operate_arduino_object,
                      starting_well=0):
    click_object = CFlow.click(sample_counter=starting_well)
    click_object.set_measuring_times(
        day, hour, minute, frequency, num_samples
    )  #Set input correctly. day,hour,minute,frequency,num_samples
    read_fcs_object = CFlow.read_fcs('C:\\Users\\rumarc\\Desktop\\Results',
                                     'ecoli')
    operate_arduino_object.operate_led(1, 256)  ####
    operate_arduino_object.operate_led(2, 0 * 256)  ####
    ##controller setup
    controller = CFlow.MPC()
    reference = np.zeros(shape=(1, (num_samples + 2))) + 0.66
    LED_signal = 0
    ####Need to add something to subtract initial offset from data!!!
    ##
    cycle = 0
    offset = 0  #This is the offset that will be applied to both the GFP mean and the reference value. This is because the model fitting was done subtracting the initial timepoint from all the data.
    while click_object.set_waiting_time() == 0:
        time.sleep(click_object.waiting_time)
        logging.info('waiting time until next measurement is: %f',
                     click_object.waiting_time)
        bring_sample(operate_arduino_object)
        click_object.sample()
        click_object.run()
        click_object.export()
        time.sleep(1)
        click_object.moveFiles(
            'C:\\Users\\rumarc\\Desktop', 'C:\\Users\\rumarc\\Desktop\\Results'
        )  ###THIS CHANGES FROM COMPUTER TO COMPUTER. THE OUTPUT FOLDER MUST BE CREATED BEFOREHAND
        time.sleep(1)
        ##PERFORM CONTTROL
        GFP_mean = read_fcs_object.get_last_data(click_object)
        logging.info('GFP mean is: %f', GFP_mean)
        print(GFP_mean)
        if cycle == 0:
            offset = GFP_mean
        controller.kalmanFilter(LED_signal, GFP_mean - offset)
        LED_signal = controller.multiPrediction(reference[0][cycle:cycle + 5] -
                                                offset)  ####!!!!
        logging.info('LED signal is: %f', LED_signal)
        logging.info('reference is: %f', reference[0][cycle])
        print(LED_signal)
        operate_arduino_object.operate_led(2, LED_signal * 256)
        ##
        click_object.backflush()
        operate_arduino_object.cytometer_to_waste(8)
        cycle += 1
    return
def pumping_operation(day, hour, minute, frequency, num_samples, operate_arduino_object, starting_well=0):
    click_object = CFlow.click(sample_counter=starting_well)
    click_object.set_measuring_times(
        day, hour, minute, frequency, num_samples
    )  # Set input correctly. day,hour,minute,frequency,num_samples
    read_fcs_object = CFlow.read_fcs("C:\\Users\\rumarc\\Desktop\\Results", "ecoli")
    operate_arduino_object.operate_led(1, 256)  ####
    operate_arduino_object.operate_led(2, 0 * 256)  ####
    ##controller setup
    controller = CFlow.newMPC(10)
    LED_signal = 0
    LED_signalTransformed = 0
    ####Need to add something to subtract initial offset from data!!!
    ##
    cycle = 0
    while click_object.set_waiting_time() == 0:
        time.sleep(click_object.waiting_time)
        logging.info("waiting time until next measurement is: %f", click_object.waiting_time)
        bring_sample(operate_arduino_object)
        click_object.sample()
        click_object.run()
        click_object.export()
        time.sleep(1)
        click_object.moveFiles(
            "C:\\Users\\rumarc\\Desktop", "C:\\Users\\rumarc\\Desktop\\Results"
        )  ###THIS CHANGES FROM COMPUTER TO COMPUTER. THE OUTPUT FOLDER MUST BE CREATED BEFOREHAND
        time.sleep(1)
        ##PERFORM CONTTROL
        GFP_mean = read_fcs_object.get_last_data(click_object)
        logging.info("GFP mean is: %f", GFP_mean)
        print(GFP_mean)
        if cycle == 0:
            controller.initialGFPreading = GFP_mean
            reference = np.zeros(shape=(1, (num_samples + 6))) + 4
        controller.kalmanFilter(LED_signalTransformed, GFP_mean / controller.initialGFPreading)
        LED_signalTransformed = controller.multiPrediction(reference[0][cycle : cycle + 5])
        LED_signal = controller.ledOutputTransformation(LED_signalTransformed)
        if LED_signal > 1:
            LED_signal = 1
        elif LED_signal < 0:
            LED_signal = 0
        logging.info("LED signal is: %f", LED_signal)
        logging.info("reference is: %f", reference[0][cycle])
        print(LED_signal)
        operate_arduino_object.operate_led(2, LED_signal * 256)
        ##
        click_object.backflush()
        operate_arduino_object.cytometer_to_waste(8)
        cycle += 1
    return
def led_operation(day,hour,minute,frequency,operate_arduino_object):#frequency is in seconds
  led=CFlow.led(operate_arduino_object)
  led.read_intensity_file(folder_path='C:\\Users\\rumarc\\Desktop\\Results',file_name='intensities.csv')			##ADD FOLDER
  led.scale_intensities()
  led.set_change_times(day,hour,minute,frequency)
  led.led_guide()
  return
def pumping_operation(day,hour,minute,frequency,num_samples,operate_arduino_object,starting_well=0):
  click_object=CFlow.click(sample_counter=starting_well)
  click_object.set_measuring_times(day,hour,minute,frequency,num_samples)		#Set input correctly. day,hour,minute,frequency,num_samples
  read_fcs_object=CFlow.read_fcs('C:\\Users\\rumarc\\Desktop\\Results','ecoli')
  operate_arduino_object.operate_led(1,256)####
  operate_arduino_object.operate_led(2,0*256)####
  ##controller setup
  controller=CFlow.newMPC(10)
  LED_signal=0
  LED_signalTransformed=0
  ####Need to add something to subtract initial offset from data!!!
  ##
  cycle=0
  while click_object.set_waiting_time()==0:
    time.sleep(click_object.waiting_time)
    logging.info('waiting time until next measurement is: %f',click_object.waiting_time)
    bring_sample(operate_arduino_object)
    click_object.sample()
    click_object.run()
    click_object.export()
    time.sleep(1)
    click_object.moveFiles('C:\\Users\\rumarc\\Desktop','C:\\Users\\rumarc\\Desktop\\Results')###THIS CHANGES FROM COMPUTER TO COMPUTER. THE OUTPUT FOLDER MUST BE CREATED BEFOREHAND
    time.sleep(1)
    ##PERFORM CONTTROL
    GFP_mean=read_fcs_object.get_last_data(click_object)
    logging.info('GFP mean is: %f',GFP_mean)
    print(GFP_mean)
    if cycle==0:
      controller.initialGFPreading=GFP_mean
      reference=np.zeros(shape=(1,(num_samples+6)))+4
    controller.kalmanFilter(LED_signalTransformed,GFP_mean/controller.initialGFPreading)
    LED_signalTransformed=controller.multiPrediction(reference[0][cycle:cycle+5])
    LED_signal=controller.ledOutputTransformation(LED_signalTransformed)
    if LED_signal>1:
        LED_signal=1
    elif LED_signal<0:
        LED_signal=0
    logging.info('LED signal is: %f',LED_signal)
    logging.info('reference is: %f',reference[0][cycle])
    print(LED_signal)
    operate_arduino_object.operate_led(2,LED_signal*256)
	##
    click_object.backflush()
    operate_arduino_object.cytometer_to_waste(8)
    cycle+=1
  return
Beispiel #8
0
def pumping_operation(day,hour,minute,frequency,num_samples,operate_arduino_object,starting_well=0):
  click_object=CFlow.click(sample_counter=starting_well)
  click_object.set_measuring_times(day,hour,minute,frequency,num_samples)		#Set input correctly. day,hour,minute,frequency,num_samples
  read_fcs_object=CFlow.read_fcs('C:\\Users\\rumarc\\Desktop\\Results','ecoli')
  operate_arduino_object.operate_led(1,0*256)####
  operate_arduino_object.operate_led(2,1*256)####
  ##Feedback constants
  I=0
  P=0
  kp=0.8
  ki=0.06
  ref=0.66
  ##
  while click_object.set_waiting_time()==0:
    time.sleep(click_object.waiting_time)
    logging.info('waiting time until next measurement is: %f',click_object.waiting_time)
    bring_sample(operate_arduino_object)
    click_object.sample()
    click_object.run()
    click_object.export()
    time.sleep(1)
    click_object.moveFiles('C:\\Users\\rumarc\\Desktop','C:\\Users\\rumarc\\Desktop\\Results')###THIS CHANGES FROM COMPUTER TO COMPUTER. THE OUTPUT FOLDER MUST BE CREATED BEFOREHAND
    time.sleep(1)
    ##PERFORM FEEDBACK
    GFP_mean=read_fcs_object.get_last_data(click_object)
    logging.info('GFP mean is: %f',GFP_mean)
#    print(GFP_mean)
#    I=ki*(ref-GFP_mean)+I
#    print(I)
#    logging.info('Integral parameter value is: %f',I)
#    P=kp*(ref-GFP_mean)
#    print(P)
#    logging.info('Proportional parameter value is: %f',P)
#    LED_signal=P+I
#    if LED_signal<0:
#        LED_signal=0
#    elif LED_signal>1:
#        LED_signal=1
#    logging.info('LED signal is: %f',LED_signal)
#    print(LED_signal)
#    LED_signal=LED_signal*256
#    operate_arduino_object.operate_led(2,LED_signal)
	##
    click_object.backflush()
    operate_arduino_object.cytometer_to_waste(7)
  return
def pumping_operation(day,
                      hour,
                      minute,
                      frequency_sampling,
                      num_samples,
                      operate_arduino_object,
                      starting_well=0):
    samplingObject = CFlow.sampleHandling()

    click_object = CFlow.click(sample_counter=starting_well)
    click_object.set_measuring_times(
        day, hour, minute, frequency_sampling, num_samples
    )  #Set input correctly. day,hour,minute,frequency,num_samples

    read_fcs_object = CFlow.read_fcs('C:\\Users\\localadmin\\Desktop\\Results',
                                     'ecoli')

    while click_object.set_waiting_time() == 0:
        time.sleep(click_object.waiting_time)
        logging.info('waiting time until next measurement is: %f',
                     click_object.waiting_time)
        samplingObject.bring_sample(
            operate_arduino_object,
            sample=click_object.measuring_times[click_object.time_counter][1])
        click_object.sample()
        click_object.run(
            click_object.measuring_times[click_object.time_counter][1])
        click_object.export()
        time.sleep(1)
        click_object.moveFiles(
            'C:\\Users\\localadmin\\Desktop',
            'C:\\Users\\localadmin\\Desktop\\Results'
        )  ###THIS CHANGES FROM COMPUTER TO COMPUTER. THE OUTPUT FOLDER MUST BE CREATED BEFOREHAND
        time.sleep(1)
        ##PERFORM FEEDBACK
        ##
        click_object.backflush()
        operate_arduino_object.push_to_cytometer(2)
        operate_arduino_object.cytometer_to_waste(2)
        operate_arduino_object.push_to_cytometer(2)
        operate_arduino_object.cytometer_to_waste(2)
        operate_arduino_object.push_to_cytometer(2)
        operate_arduino_object.cytometer_to_waste(2)
    return
Beispiel #10
0
def pumping_operation(day,hour,minute,frequency,num_samples,operate_arduino_object,starting_well=0):
  click_object=CFlow.click(sample_counter=starting_well)
  click_object.set_measuring_times(day,hour,minute,frequency,num_samples)		#Set input correctly. day,hour,minute,frequency,num_samples
  read_fcs_object=CFlow.read_fcs('C:\\Users\\rumarc\\Desktop\\Results','ecoli')
  operate_arduino_object.operate_led(1,256)####
  operate_arduino_object.operate_led(2,0*256)####
  ##controller setup
  controller=CFlow.MPC()
  reference=np.zeros(shape=(1,(num_samples+2)))+0.66
  LED_signal=0
  ####Need to add something to subtract initial offset from data!!!
  ##
  cycle=0
  offset=0	#This is the offset that will be applied to both the GFP mean and the reference value. This is because the model fitting was done subtracting the initial timepoint from all the data.
  while click_object.set_waiting_time()==0:
    time.sleep(click_object.waiting_time)
    logging.info('waiting time until next measurement is: %f',click_object.waiting_time)
    bring_sample(operate_arduino_object)
    click_object.sample()
    click_object.run()
    click_object.export()
    time.sleep(1)
    click_object.moveFiles('C:\\Users\\rumarc\\Desktop','C:\\Users\\rumarc\\Desktop\\Results')###THIS CHANGES FROM COMPUTER TO COMPUTER. THE OUTPUT FOLDER MUST BE CREATED BEFOREHAND
    time.sleep(1)
    ##PERFORM CONTTROL
    GFP_mean=read_fcs_object.get_last_data(click_object)
    logging.info('GFP mean is: %f',GFP_mean)
    print(GFP_mean)
    if cycle==0:
      offset=GFP_mean
    controller.kalmanFilter(LED_signal,GFP_mean-offset)
    LED_signal=controller.multiPrediction(reference[0][cycle:cycle+5]-offset)####!!!!
    logging.info('LED signal is: %f',LED_signal)
    logging.info('reference is: %f',reference[0][cycle])
    print(LED_signal)
    operate_arduino_object.operate_led(2,LED_signal*256)
	##
    click_object.backflush()
    operate_arduino_object.cytometer_to_waste(8)
    cycle+=1
  return
Beispiel #11
0
import CFlow, time, threading, logging

logging.basicConfig(
    filename='C:\\Users\\rumarc\\Desktop\\Results\\CFlow_execution.log',
    level=logging.INFO,
    filemode='w',
    format='%(asctime)s %(message)s',
    datefmt='%Y-%m-%d %H:%M')
operate_arduino_object = CFlow.operate_arduino()

day = 28  #starting day
hour = 17  #starting hour
minute = 37  #starting minute
frequency_sampling = 10  #frequency of cytometer measurements, in minutes
samples = 21  #number of cytometer measurements in total
frequency_light = 3600  #frequency of led changes, in seconds
start_sample_well = 0


#CFLOW STARTUP
#PUMP CALIBRATION
#PUMP STARTUP
def bring_sample(operate_arduino_object):
    operate_arduino_object.sample_to_cytometer(
        1.25)  ##How much sample to take. 1.2
    operate_arduino_object.air_to_cytometer(1)  #2
    operate_arduino_object.cytometer_to_waste(3)  #3
    operate_arduino_object.push_to_cytometer(2.5)  #2
    operate_arduino_object.cytometer_to_waste(3)  #3
    operate_arduino_object.push_to_cytometer(2.5)  #2
    operate_arduino_object.cytometer_to_waste(3)  #3
Beispiel #12
0
import CFlow, time, threading, logging
'''for multisampling'''
logging.basicConfig(
    filename='C:\\Users\\localadmin\\Desktop\\Results\\CFlow_execution.log',
    level=logging.INFO,
    filemode='w',
    format='%(asctime)s %(message)s',
    datefmt='%Y-%m-%d %H:%M')
operate_arduino_object = CFlow.multiOperate_arduino()

day = 7  #starting day
hour = 14  #starting hour
minute = 49  #starting minute
frequency_sampling = [6, 0, 6,
                      6]  #frequency of cytometer measurements, in minutes
num_samples = [2, 0, 2, 2]  #number of cytometer measurements in total
starting_well = 72


def pumping_operation(day,
                      hour,
                      minute,
                      frequency_sampling,
                      num_samples,
                      operate_arduino_object,
                      starting_well=0):
    samplingObject = CFlow.sampleHandling()

    click_object = CFlow.click(sample_counter=starting_well)
    click_object.set_measuring_times(
        day, hour, minute, frequency_sampling, num_samples
Beispiel #13
0
import CFlow,time,threading,logging
'''for multisampling'''
logging.basicConfig(filename='C:\\Users\\localadmin\\Desktop\\Results\\CFlow_execution.log', level=logging.INFO,filemode='w',format='%(asctime)s %(message)s',datefmt='%Y-%m-%d %H:%M')
operate_arduino_object=CFlow.multiOperate_arduino()

day=7#starting day
hour=14#starting hour
minute=49#starting minute
frequency_sampling=[6,0,6,6]#frequency of cytometer measurements, in minutes
num_samples=[2,0,2,2]#number of cytometer measurements in total
starting_well=72

def pumping_operation(day,hour,minute,frequency_sampling,num_samples,operate_arduino_object,starting_well=0):
  samplingObject=CFlow.sampleHandling()

  click_object=CFlow.click(sample_counter=starting_well)
  click_object.set_measuring_times(day,hour,minute,frequency_sampling,num_samples)		#Set input correctly. day,hour,minute,frequency,num_samples

  read_fcs_object=CFlow.read_fcs('C:\\Users\\localadmin\\Desktop\\Results','ecoli')

  while click_object.set_waiting_time()==0:
    time.sleep(click_object.waiting_time)
    logging.info('waiting time until next measurement is: %f',click_object.waiting_time)
    samplingObject.bring_sample(operate_arduino_object,sample=click_object.measuring_times[click_object.time_counter][1])
    click_object.sample()
    click_object.run(click_object.measuring_times[click_object.time_counter][1])
    click_object.export()
    time.sleep(1)
    click_object.moveFiles('C:\\Users\\localadmin\\Desktop','C:\\Users\\localadmin\\Desktop\\Results')###THIS CHANGES FROM COMPUTER TO COMPUTER. THE OUTPUT FOLDER MUST BE CREATED BEFOREHAND
    time.sleep(1)
    ##PERFORM FEEDBACK
import CFlow,time,threading,logging

logging.basicConfig(filename='C:\\Users\\rumarc\\Desktop\\Results\\CFlow_execution.log', level=logging.INFO,filemode='w',format='%(asctime)s %(message)s',datefmt='%Y-%m-%d %H:%M')
operate_arduino_object=CFlow.operate_arduino()

day=24#starting day
hour=18#starting hour
minute=10#starting minute
frequency_sampling=10#frequency of cytometer measurements, in minutes
samples=57#number of cytometer measurements in total
frequency_light=3600#frequency of led changes, in seconds
start_sample_well=0

#CFLOW STARTUP
#PUMP CALIBRATION
#PUMP STARTUP
def bring_sample(operate_arduino_object):
  operate_arduino_object.sample_to_cytometer(1.25)##How much sample to take. 1.2
  operate_arduino_object.air_to_cytometer(1)#2
  operate_arduino_object.cytometer_to_waste(3)#3
  operate_arduino_object.push_to_cytometer(2.5)#2
  operate_arduino_object.cytometer_to_waste(3)#3
  operate_arduino_object.push_to_cytometer(2.5)#2
  operate_arduino_object.cytometer_to_waste(3)#3
  operate_arduino_object.push_to_cytometer(2)#2
  operate_arduino_object.cytometer_to_waste(3)#3
  operate_arduino_object.push_to_cytometer(0.4)##Critical time step. 2
  operate_arduino_object.push_to_cytometer(0)##0.3
  operate_arduino_object.cytometer_to_waste(7)#7
  operate_arduino_object.push_to_cytometer(1)##How much sample to introduce into cytometer. 1
  operate_arduino_object.air_to_cytometer(1.5)#2.5
def pumping_operation(day,hour,minute,frequency,num_samples,operate_arduino_object,starting_well=0):
  click_object=CFlow.click(sample_counter=starting_well)
  click_object.set_measuring_times(day,hour,minute,frequency,num_samples)		#Set input correctly. day,hour,minute,frequency,num_samples
  read_fcs_object=CFlow.read_fcs('C:\\Users\\localadmin\\Desktop\\Results','ecoli')
  ##Initial light conditions
  LED_signal=0#initial green light
  LED_signalTransformed=0
  operate_arduino_object.operate_led(1,256)
  operate_arduino_object.operate_led(2,LED_signal*256)
  ##Start up Matlab
  matlab = matlab_wrapper.MatlabSession()
  matlab.eval("parpool")
  matlab.eval("cd('C:\\Users\\localadmin\\Desktop\\Particle Filter')")
  ##Controller setup
  P=5000#number of particles
  MPChorizon=3#number of steps that the MPC looks ahead for the optimization
  reference=[4,]*(num_samples+MPChorizon)
  GFP_measurements=[1]
  LEDapplied=[0]#Needs to be from 0 to 4.5!!
  ##Dose-response Sigmoidal
  a=5.828
  b=3.353
  c=-0.05946
  d=-1.3388
  ##
  cycle=0
  while click_object.set_waiting_time()==0:
    time.sleep(click_object.waiting_time)
    logging.info('waiting time until next measurement is: %f',click_object.waiting_time)
    bring_sample(operate_arduino_object)
    click_object.sample()
    click_object.run()
    click_object.export()
    time.sleep(1)
    click_object.moveFiles('C:\\Users\\localadmin\\Desktop','C:\\Users\\localadmin\\Desktop\\Results')###THIS CHANGES FROM COMPUTER TO COMPUTER. THE OUTPUT FOLDER MUST BE CREATED BEFOREHAND
    time.sleep(1)
    ##PERFORM CONTTROL
    GFP_mean=read_fcs_object.get_last_data(click_object)
    logging.info('GFP mean is: %f',GFP_mean)
    print(GFP_mean)
    if cycle==0:
      initialGFPreading=GFP_mean
    GFP_measurements.append(GFP_mean/initialGFPreading)
    matlabCommand="LED=MPC_loop(%i,%i,%i,%s,%s,%s)"%(P,frequency,MPChorizon,str(GFP_measurements),str(reference),str(LEDapplied))#!!!Don't apply on the first cycle.
    matlab.eval(matlabCommand)
    LED_signalTransformed=matlab.get('LED')
    LEDapplied.append(LED_signalTransformed)
    LED_signal=np.log(a/(b*(LED_signalTransformed-d))-1/b)/(c*100)
    if LED_signal>1:
        LED_signal=1
    elif LED_signal<0:
        LED_signal=0
    logging.info('LED signal is: %f',LED_signal)
    logging.info('reference is: %f',reference[cycle])
    print(LED_signal)
    operate_arduino_object.operate_led(2,LED_signal*256)
	##
    click_object.backflush()
    operate_arduino_object.cytometer_to_waste(8)
    cycle+=1
  return
Beispiel #16
0
def pumping_operation(day,
                      hour,
                      minute,
                      frequency,
                      num_samples,
                      operate_arduino_object,
                      starting_well=0):
    click_object = CFlow.click(sample_counter=starting_well)
    click_object.set_measuring_times(
        day, hour, minute, frequency, num_samples
    )  #Set input correctly. day,hour,minute,frequency,num_samples
    read_fcs_object = CFlow.read_fcs('C:\\Users\\localadmin\\Desktop\\Results',
                                     'ecoli')
    ##Initial light conditions
    LED_signal = 0  #initial green light
    LED_signalTransformed = 0
    operate_arduino_object.operate_led(1, 256)
    operate_arduino_object.operate_led(2, LED_signal * 256)
    ##Start up Matlab
    matlab = matlab_wrapper.MatlabSession()
    matlab.eval("parpool")
    matlab.eval("cd('C:\\Users\\localadmin\\Desktop\\Particle Filter')")
    ##Controller setup
    P = 5000  #number of particles
    MPChorizon = 3  #number of steps that the MPC looks ahead for the optimization
    reference = [
        4,
    ] * (num_samples + MPChorizon)
    GFP_measurements = [1]
    LEDapplied = [0]  #Needs to be from 0 to 4.5!!
    ##Dose-response Sigmoidal
    a = 5.828
    b = 3.353
    c = -0.05946
    d = -1.3388
    ##
    cycle = 0
    while click_object.set_waiting_time() == 0:
        time.sleep(click_object.waiting_time)
        logging.info('waiting time until next measurement is: %f',
                     click_object.waiting_time)
        bring_sample(operate_arduino_object)
        click_object.sample()
        click_object.run()
        click_object.export()
        time.sleep(1)
        click_object.moveFiles(
            'C:\\Users\\localadmin\\Desktop',
            'C:\\Users\\localadmin\\Desktop\\Results'
        )  ###THIS CHANGES FROM COMPUTER TO COMPUTER. THE OUTPUT FOLDER MUST BE CREATED BEFOREHAND
        time.sleep(1)
        ##PERFORM CONTTROL
        GFP_mean = read_fcs_object.get_last_data(click_object)
        logging.info('GFP mean is: %f', GFP_mean)
        print(GFP_mean)
        if cycle == 0:
            initialGFPreading = GFP_mean
        GFP_measurements.append(GFP_mean / initialGFPreading)
        matlabCommand = "LED=MPC_loop(%i,%i,%i,%s,%s,%s)" % (
            P, frequency, MPChorizon, str(GFP_measurements), str(reference),
            str(LEDapplied))  #!!!Don't apply on the first cycle.
        matlab.eval(matlabCommand)
        LED_signalTransformed = matlab.get('LED')
        LEDapplied.append(LED_signalTransformed)
        LED_signal = np.log(a /
                            (b *
                             (LED_signalTransformed - d)) - 1 / b) / (c * 100)
        if LED_signal > 1:
            LED_signal = 1
        elif LED_signal < 0:
            LED_signal = 0
        logging.info('LED signal is: %f', LED_signal)
        logging.info('reference is: %f', reference[cycle])
        print(LED_signal)
        operate_arduino_object.operate_led(2, LED_signal * 256)
        ##
        click_object.backflush()
        operate_arduino_object.cytometer_to_waste(8)
        cycle += 1
    return