def test(OD_data, temp_data, vials, elapsed_time, exp_name):
control = np.power(2, range(0, 32))
flow_rate = np.array([
1.01, 1.05, 1.06, 1.03, 1.05, 1.04, 1.07, 1.1, 1.03, 1.07, 1.02, 1,
0.99, 1.04, 1.05, 1
]) #ml/sec
volume = 30 #mL
lower_thresh = np.array([
0.25, 0.25, 0.25, 0.25, 0.25, 0.25, 0.25, 0.25, 0.25, 0.25, 0.25, 0.25,
9999, 9999, 9999, 9999
])
upper_thresh = np.array([
0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 9999, 9999,
9999, 9999
])
time_out = 20
pump_wait = 7
#wait between pumps (min)
for x in vials:
if OD_data[x] > upper_thresh[x]:
time_in = -(np.log(lower_thresh[x] / upper_thresh[x]) *
volume) / flow_rate[x]
MESSAGE = "%s,0,%d," % ("{0:b}".format(control[x] +
control[x + 16]), time_in)
eVOLVER_module.fluid_command(MESSAGE, x, elapsed_time,
pump_wait * 60, exp_name, time_in,
'n')
MESSAGE = "%s,0,%d," % ("{0:b}".format(control[x + 16]), time_out)
eVOLVER_module.fluid_command(MESSAGE, x, elapsed_time,
pump_wait * 60, exp_name, time_out,
'y')
def update_Graphs():
elapsed_time = round((time.time() - start_time), 0)
if OD_data == 'empty':
send_alert()
else:
print "Efflux ON for overflow check"
MESSAGE = "111111110000000000000000,0,20,"
eVOLVER_module.fluid_command(MESSAGE, 0, elapsed_time, 1, exp_name, 1,
'n')
MESSAGE = "11111111000000000000000000000000,0,20,"
eVOLVER_module.fluid_command(MESSAGE, 0, elapsed_time, 1, exp_name, 1,
'n')
print "Increasing stir rate to prevent biofilm"
global graph_exp
# eVOLVER_module.graph_data(vials, exp_name, 'OD')
# eVOLVER_module.graph_data(vials, exp_name, 'temp')
eVOLVER_module.calc_growth_rate(vials, exp_name, elapsed_time, .3)
MESSAGE = "20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,"
# MESSAGE = "0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0"
eVOLVER_module.stir_rate(MESSAGE)
print "Fast stirring!!!"
time.sleep(40)
MESSAGE = "0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,"
eVOLVER_module.stir_rate(MESSAGE)
time.sleep(10)
MESSAGE = "12,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,"
eVOLVER_module.stir_rate(MESSAGE)
print "Normal stirring"
time.sleep(20)
graph_exp = root.after(60000 * 60, update_Graphs)
print "Clean cycle completed!"
def turbidostat(OD_data, temp_data, vials, elapsed_time):
##### USER DEFINED VARIABLES #####
turbidostat_vials = vials #vials is all 16, can set to different range (ex. [0,1,2,3]) to only trigger tstat on those vials
stop_after_n_curves = np.inf #set to np.inf to never stop, or integer value to stop diluting after certain number of growth curves
lower_thresh = [0.2] * len(
vials) #to set all vials to the same value, creates 16-value list
upper_thresh = [0.4] * len(
vials) #to set all vials to the same value, creates 16-value list
#Alternatively, use 16 value list to set different thresholds, use 9999 for vials not being used
#lower_thresh = [0.2, 0.2, 0.3, 0.3, 9999, 9999, 9999, 9999, 9999, 9999, 9999, 9999, 9999, 9999, 9999, 9999]
#upper_thresh = [0.4, 0.4, 0.4, 0.4, 9999, 9999, 9999, 9999, 9999, 9999, 9999, 9999, 9999, 9999, 9999, 9999]
##### END OF USER DEFINED VARIABLES #####
##### Turbidostat Settings #####
#Tunable settings for overflow protection, pump scheduling etc. Unlikely to change between expts
time_out = 5 #(sec) additional amount of time to run efflux pump
pump_wait = 3 # (min) minimum amount of time to wait between pump events
##### End of Turbidostat Settings #####
control = np.power(2, range(0, 32)) #vial addresses
save_path = os.path.dirname(os.path.realpath(__file__)) #save path
flow_rate = eVOLVER_module.get_flow_rate() #read from calibration file
##### Turbidostat Control Code Below #####
for x in turbidostat_vials: #main loop through each vial
# Update turbidostat configuration files for each vial
# initialize OD and find OD path
file_name = "vial{0}_ODset.txt".format(x)
ODset_path = os.path.join(save_path, EXP_NAME, 'ODset', file_name)
data = np.genfromtxt(ODset_path, delimiter=',')
ODset = data[len(data) - 1][1]
ODsettime = data[len(data) - 1][0]
num_curves = len(data) / 2
file_name = "vial{0}_OD.txt".format(x)
OD_path = os.path.join(save_path, EXP_NAME, 'OD', file_name)
data = np.genfromtxt(OD_path, delimiter=',')
average_OD = 0
# Determine whether turbidostat dilutions are needed
enough_ODdata = (
len(data) > 7
) #logical, checks to see if enough data points (couple minutes) for sliding window
collecting_more_curves = (
num_curves <= (stop_after_n_curves + 2)
) #logical, checks to see if enough growth curves have happened
if enough_ODdata:
# Take median to avoid outlier
od_values_from_file = []
for n in range(1, 7):
od_values_from_file.append(data[len(data) - n][1])
average_OD = float(np.median(od_values_from_file))
#if recently exceeded upper threshold, note end of growth curve in ODset, allow dilutions to occur and growthrate to be measured
if (average_OD > upper_thresh[x]) and (ODset != lower_thresh[x]):
text_file = open(ODset_path, "a+")
text_file.write("{0},{1}\n".format(elapsed_time,
lower_thresh[x]))
text_file.close()
ODset = lower_thresh[x]
# calculate growth rate
eVOLVER_module.calc_growth_rate(x, ODsettime, elapsed_time)
#if have approx. reached lower threshold, note start of growth curve in ODset
if (average_OD < (lower_thresh[x] +
(upper_thresh[x] - lower_thresh[x]) / 3)) and (
ODset != upper_thresh[x]):
text_file = open(ODset_path, "a+")
text_file.write("{0},{1}\n".format(elapsed_time,
upper_thresh[x]))
text_file.close()
ODset = upper_thresh[x]
#if need to dilute to lower threshold, then calculate amount of time to pump
if average_OD > ODset and collecting_more_curves:
time_in = -(np.log(lower_thresh[x] / average_OD) *
VOLUME) / flow_rate[x]
if time_in > 20:
time_in = 20
time_in = round(time_in, 2)
save_path = os.path.dirname(os.path.realpath(__file__))
file_name = "vial{0}_pump_log.txt".format(x)
file_path = os.path.join(save_path, EXP_NAME, 'pump_log',
file_name)
data = np.genfromtxt(file_path, delimiter=',')
last_pump = data[len(data) - 1][0]
if (
(elapsed_time - last_pump) * 60
) >= pump_wait: # if sufficient time since last pump, send command to Arduino
MESSAGE = {
'pumps_binary': "{0:b}".format(control[x]),
'pump_time': time_in,
'efflux_pump_time': time_out,
'delay_interval': 0,
'times_to_repeat': 0,
'run_efflux': 1
}
eVOLVER_module.fluid_command(MESSAGE, x, elapsed_time,
pump_wait * 60, time_in, 'y')
def test(OD_data, temp_data, vials, elapsed_time, exp_name):
##### USER DEFINED VARIABLES #####
temp_input = 30 #degrees C, can be scalar or 16-value numpy array
stir_input = 8 #try 8,10,12; can be scalar or 16-value numpy array
lower_thresh = np.array([9999] * len(vials))
upper_thresh = np.array([9999] * len(vials))
# lower_thresh = np.array([0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2])
# upper_thresh = np.array([0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4])
##### END OF USER DEFINED VARIABLES #####
##### Calibration Values:
# Be sure to check that OD_cal.txt and temp_calibration.txt are up to date
# Additional calibration values below, remain the same between experiments
time_out = 15 #(sec) additional amount of time to run efflux pump
pump_wait = 3 # (min) minimum amount of time to wait between pump events
control = np.power(2, range(0, 32)) #vial addresses
flow_rate = np.array([
0.95, 1.1, 0.975, 0.85, 0.95, 1.05, 1.05, 1.05, 1.025, 1.125, 1.0, 1.0,
1.05, 1.15, 1.1, 1.025
]) #ml/sec, paste from pump calibration
volume = 30 #mL, determined by straw length
save_path = os.path.dirname(os.path.realpath(__file__)) #save path
##### End of Calibration Values
##### Turbidostat Control Code Below #####
for x in vials: #main loop through each vial
# Update temperature configuration files for each vial
file_name = "vial{0}_tempconfig.txt".format(x)
tempconfig_path = os.path.join(save_path, exp_name, 'temp_config',
file_name)
temp_config = np.genfromtxt(tempconfig_path, delimiter=',')
if (
len(temp_config) is 2
): #set temp at the beginning of the experiment, can clone for subsequent temp changes
if np.isscalar(temp_input):
temp_val = temp_input
else:
temp_val = temp_input[x]
text_file = open(tempconfig_path, "a+")
text_file.write("{0},{1}\n".format(elapsed_time, temp_val))
text_file.close()
# Update turbidostat configuration files for each vial
# initialize OD and find OD path
file_name = "vial{0}_ODset.txt".format(x)
ODset_path = os.path.join(save_path, exp_name, 'ODset', file_name)
data = np.genfromtxt(ODset_path, delimiter=',')
ODset = data[len(data) - 1][1]
file_name = "vial{0}_OD.txt".format(x)
OD_path = os.path.join(save_path, exp_name, 'OD', file_name)
data = np.genfromtxt(OD_path, delimiter=',')
average_OD = 0
# Determine whether turbidostat dilutions are needed
if len(data) > 7:
# Take median to avoid outlier
od_values_from_file = []
for n in range(1, 7):
od_values_from_file.append(data[len(data) - n][1])
average_OD = float(np.median(od_values_from_file))
if (average_OD > upper_thresh[x]) and (ODset != lower_thresh[x]):
text_file = open(ODset_path, "a+")
text_file.write("{0},{1}\n".format(elapsed_time,
lower_thresh[x]))
text_file.close()
ODset = lower_thresh[x]
if (average_OD < (lower_thresh[x] +
(upper_thresh[x] - lower_thresh[x]) / 2)) and (
ODset != upper_thresh[x]):
text_file = open(ODset_path, "a+")
text_file.write("{0},{1}\n".format(elapsed_time,
upper_thresh[x]))
text_file.close()
ODset = upper_thresh[x]
if average_OD > ODset:
time_in = -(np.log(lower_thresh[x] / average_OD) *
volume) / flow_rate[x]
if time_in > 20:
time_in = 20
save_path = os.path.dirname(os.path.realpath(__file__))
file_name = "vial{0}_pump_log.txt".format(x)
file_path = os.path.join(save_path, exp_name, 'pump_log',
file_name)
data = np.genfromtxt(file_path, delimiter=',')
last_pump = data[len(data) - 1][0]
if ((elapsed_time - last_pump) * 60) >= pump_wait:
MESSAGE = {
'pumps_binary': "{0:b}".format(control[x]),
'pump_time': time_in,
'efflux_pump_time': time_out,
'delay_interval': 0,
'times_to_repeat': 0,
'run_efflux': 1
}
eVOLVER_module.fluid_command(MESSAGE, x, elapsed_time,
pump_wait * 60, exp_name,
time_in, 'y')
def test (OD_data, temp_data, vials, elapsed_time, exp_name):
MESSAGE = "8,8,8,8,8,8,8,8,14,8,8,14,8,8,8,8,"
eVOLVER_module.stir_rate(MESSAGE)
control = np.power(2,range(0,32))
flow_rate = np.array([1.11,1.11,1.1,1.08,1.1,1.12,1.04,1.1,1.13,1.12,0.93,1.1,1.1,1.17,1.07,1.1])#ml/sec
volume = 30#mL
lower_thresh = np.array([.17,.17,.17,.17,.17,.17,.17,.17,.17,.17,.17,.17,.17,.17,.17,.17])
upper_thresh = np.array([.2,.2,.2,.2,.2,.2,.2,.2,.2,.2,.2,.2,.2,.2,.2,.2])
heat_shockdelay = 5.5 #hours
normal_temp = 30.0 #degrees C
temp_mag = np.array([30,33,33,33,36,36,36,36,39,39,39,39,42,42,42,42])
temp_period = np.array([9999,2,6,48,9999,2,6,48,9999,2,6,48,9999,2,6,48])
#temp_mag = np.array([42,42,42,42,39,39,39,39,36,36,36,36,33,33,33,30])
#temp_period = np.array([2,6,48,9999,2,6,48,9999,2,6,48,9999,2,6,48,9999])
time_out =5
pump_wait = 3; #wait between pumps (min)
save_path = os.path.dirname(os.path.realpath(__file__))
for x in vials:
if elapsed_time > heat_shockdelay:
tempconfig_path = "%s/%s/temp_config/vial%d_tempconfig.txt" % (save_path,exp_name,x)
temp_config = np.genfromtxt(tempconfig_path, delimiter=',')
last_tempset = temp_config[len(temp_config)-1][0]
if (len(temp_config) is 2):
text_file = open(tempconfig_path,"a+")
text_file.write("%f,%s\n" % (elapsed_time, temp_mag[x]))
text_file.close()
if ((elapsed_time - last_tempset) > (float(temp_period[x])/2)):
text_file = open(tempconfig_path,"a+")
if (len(temp_config) % 2 == 0):
text_file.write("%f,%s\n" % (elapsed_time, temp_mag[x]))
else:
text_file.write("%f,%s\n" % (elapsed_time, normal_temp))
text_file.close()
ODset_path = "%s/%s/ODset/vial%d_ODset.txt" % (save_path,exp_name,x)
data = np.genfromtxt(ODset_path, delimiter=',')
ODset = data[len(data)-1][1]
OD_path = "%s/%s/OD/vial%d_OD.txt" % (save_path,exp_name,x)
data = np.genfromtxt(OD_path, delimiter=',')
average_OD = 0
if len(data) > 15:
for n in range(1,6):
average_OD = average_OD + (data[len(data)-n][1]/5)
if (average_OD > upper_thresh[x]) and (ODset != lower_thresh[x]):
text_file = open(ODset_path,"a+")
text_file.write("%f,%s\n" % (elapsed_time, lower_thresh[x]))
text_file.close()
ODset = lower_thresh[x]
if (average_OD < (lower_thresh[x] + 0.005)) and (ODset != upper_thresh[x]):
text_file = open(ODset_path,"a+")
text_file.write("%f,%s\n" % (elapsed_time, upper_thresh[x]))
text_file.close()
ODset = upper_thresh[x]
if average_OD > ODset:
time_in = - (np.log(lower_thresh[x]/average_OD)*volume)/flow_rate[x]
if time_in > 20:
time_in = 20
MESSAGE = "%s,0,%d," % ("{0:b}".format(control[x]+control[x+16]) , time_in)
eVOLVER_module.fluid_command(MESSAGE, x, elapsed_time, pump_wait *60, exp_name, time_in, 'n')
MESSAGE = "%s,0,%d," % ("{0:b}".format(control[x+16]) , time_out)
#eVOLVER_module.fluid_command(MESSAGE, x, elapsed_time, pump_wait *60, exp_name, time_out,'n')
eVOLVER_module.fluid_command(MESSAGE, x, elapsed_time, pump_wait *60, exp_name, time_out,'y')
def valving(mux_command,
vial_num=0,
media_type=[0],
step_size=[5000],
vials=range(0, 16),
x=1,
elapsed_time=99999,
pump_wait=1,
exp_name='mux_test1',
time_in=1,
wash=3,
preflush=2000,
logging='n'):
## translates mux_command (formatted as string) to valving scheme
if mux_command == 'syringe':
y = vial_num
#preflush with air
path = list(set(media[0]))
bin_path = format(sum([binvals[i] for i in path]), '032b')
MESSAGE = "%s,0,%d," % (bin_path, preflush)
eVOLVER_module.fluid_command(MESSAGE, x, elapsed_time, pump_wait * 60,
exp_name, time_in, 'n')
#print(MESSAGE)
#draw media
for z in range(0, len(media_type)):
path = list(set(media[media_type[z]]))
bin_path = format(sum([binvals[i] for i in path]), '032b')
MESSAGE = "%s,0,%d," % (bin_path, step_size[z])
eVOLVER_module.fluid_command(MESSAGE, x, elapsed_time,
pump_wait * 60, exp_name, time_in,
'n')
#print(MESSAGE)
#dispense media
path = list(set(demux[y] + influx + efflux + mux[y] + peri))
bin_path = format(sum([binvals[i] for i in path]), '032b')
MESSAGE = "%s,0,%d," % (bin_path, (-1 * sum(step_size) - preflush))
eVOLVER_module.fluid_command(MESSAGE, x, elapsed_time, pump_wait * 60,
exp_name, time_in, 'n')
#print(MESSAGE)
if mux_command == 'precleaned_syringe':
y = vial_num
#preflush with air
path = list(set(media[0]))
bin_path = format(sum([binvals[i] for i in path]), '032b')
MESSAGE = "%s,0,%d," % (bin_path, preflush)
eVOLVER_module.fluid_command(MESSAGE, x, elapsed_time, pump_wait * 60,
exp_name, time_in, 'n')
#print(MESSAGE)
#draw wash
path = list(set(media[7]))
bin_path = format(sum([binvals[i] for i in path]), '032b')
MESSAGE = "%s,0,%d," % (bin_path, sum(step_size))
eVOLVER_module.fluid_command(MESSAGE, x, elapsed_time, pump_wait * 60,
exp_name, time_in, 'n')
#print(MESSAGE)
#dispense wash
path = list(set(demux[y] + bridge + mux[y] + peri))
bin_path = format(sum([binvals[i] for i in path]), '032b')
MESSAGE = "%s,0,%d," % (bin_path, (-1 * sum(step_size) - preflush))
eVOLVER_module.fluid_command(MESSAGE, x, elapsed_time, pump_wait * 60,
exp_name, time_in, 'n')
#print(MESSAGE)
#preflush again
path = list(set(media[0]))
bin_path = format(sum([binvals[i] for i in path]), '032b')
MESSAGE = "%s,0,%d," % (bin_path, preflush)
eVOLVER_module.fluid_command(MESSAGE, x, elapsed_time, pump_wait * 60,
exp_name, time_in, 'n')
#print(MESSAGE)
#draw media
for z in range(0, len(media_type)):
path = list(set(media[media_type[z]]))
bin_path = format(sum([binvals[i] for i in path]), '032b')
MESSAGE = "%s,0,%d," % (bin_path, step_size[z])
eVOLVER_module.fluid_command(MESSAGE, x, elapsed_time,
pump_wait * 60, exp_name, time_in,
'n')
#print(MESSAGE)
#dispense media
path = list(set(demux[y] + influx + efflux + mux[y] + peri))
bin_path = format(sum([binvals[i] for i in path]), '032b')
MESSAGE = "%s,0,%d," % (bin_path, (-1 * sum(step_size) - preflush))
eVOLVER_module.fluid_command(MESSAGE, x, elapsed_time, pump_wait * 60,
exp_name, time_in, 'n')
#print(MESSAGE)
if mux_command == 'flush': #set vials in function call in order to not wash all lines, otherwise range(0,16)
for y in vials: #wash using peristaltic
path = list(
set(media[media_type[0]] + demux[y] + mux[y] + bridge + peri))
bin_path = format(sum([binvals[i] for i in path]), '032b')
MESSAGE = "%s,1,%d," % (bin_path, wash)
eVOLVER_module.fluid_command(MESSAGE, x, elapsed_time,
pump_wait * 60, exp_name, time_in,
'n')
#print(MESSAGE)
if mux_command == 'efflux': #set vials in function call in order to not clear all efflux lines, otherwise range(0,16)
for y in vials:
path = list(set(mux[y] + efflux + peri))
bin_path = format(sum([binvals[i] for i in path]), '032b')
MESSAGE = "%s,1,%d," % (bin_path, wash)
eVOLVER_module.fluid_command(MESSAGE, x, elapsed_time,
pump_wait * 60, exp_name, time_in,
logging)
import time
import pickle
import numpy as np
import numpy.matlib
import requests
import eVOLVER_module
import custom_script
x = 1 #why is this needed?
elapsed_time = 99999 #ensures fluidic commands not stopped by timing
pump_wait = 1 #ensures fluidic commands not stopped by timing
exp_name = 'mux_test1' #match with main_eVOLVER.py
time_in = 1 #also not needed
eVOLVER_module.fluid_command('clear', x, elapsed_time, pump_wait * 60,
exp_name, time_in, 'n')
exp_continue = raw_input('Conduct pump test (y/n): ')
while exp_continue == 'y':
custom_script.pump(3, [7], [5000], logging='n')
print('Testing...')
exp_continue = raw_input('Conduct test again(y/n): ')
exp_continue = raw_input('Conduct pump test with precleaning (y/n): ')
while exp_continue == 'y':
custom_script.precleaned_pump(3, [7], [5000], logging='n')
print('Testing...')
exp_continue = raw_input('Conduct test again(y/n): ')
exp_continue = raw_input('Conduct wash (y/n): ')
while exp_continue == 'y':
custom_script.valving('flush', vials=[3], media_type=[7])
def test (OD_data, temp_data, vials, elapsed_time, exp_name):
MESSAGE = "15,15,15,15,15,15,15,15,15,15,15,15,15,15,12,15,"
eVOLVER_module.stir_rate(MESSAGE)
control = np.power(2,range(0,32))
flow_rate = np.array([1.07,1,1.15,1.05,0.96,1.11,1.18,1.01,1.07,1.04,1.1,1.03,1.1,1.1,0.95,1.07])#ml/sec
volume = 15 #mL
lower_thresh = np.array([0.05, 0.05,9999999,0.1,0.05,9999999,0.1,9999999,0.15,0.05,0.1,0.15,0.2,0.05,0.1,0.15])
upper_thresh = np.array([0.1,0.15,9999999,0.15,0.2,9999999,0.2,9999999,0.2,0.25,0.25,0.25,0.25,0.3,0.3,0.3])
#lower_thresh = np.array([.05,.05,.05,.05,.05,.05,.05,.05,.05,.05,.05,.05,.05,.05,.05,.05])
#upper_thresh = np.array([.1,.1,.1,.1,.1,.1,.1,.1,.1,.1,.1,.1,.1,.1,.1,.1])
#lower_thresh = np.array([.6,.6,.6,.6,.6,.6,.6,.6,.6,.6,.6,.6,.6,.6,.6,.6])
#upper_thresh = np.array([.65,.65,.65,.65,.65,.65,.65,.65,.65,.65,.65,.65,.65,.65,.65,.65])
time_out =5
pump_wait = 2; #wait between pumps (min)
save_path = os.path.dirname(os.path.realpath(__file__))
for x in vials:
ODset_path = "%s/%s/ODset/vial%d_ODset.txt" % (save_path,exp_name,x)
data = np.genfromtxt(ODset_path, delimiter=',')
ODset = data[len(data)-1][1]
OD_path = "%s/%s/OD/vial%d_OD.txt" % (save_path,exp_name,x)
data = np.genfromtxt(OD_path, delimiter=',')
average_OD = 0
if len(data) > 15:
for n in range(1,6):
average_OD = average_OD + (data[len(data)-n][1]/5)
if (average_OD > upper_thresh[x]) and (ODset != lower_thresh[x]):
text_file = open(ODset_path,"a+")
text_file.write("%f,%s\n" % (elapsed_time, lower_thresh[x]))
text_file.close()
ODset = lower_thresh[x]
if (average_OD < (lower_thresh[x] + 0.005)) and (ODset != upper_thresh[x]):
text_file = open(ODset_path,"a+")
text_file.write("%f,%s\n" % (elapsed_time, upper_thresh[x]))
text_file.close()
ODset = upper_thresh[x]
if average_OD > ODset:
time_in = - (np.log((lower_thresh[x]-0.005)/average_OD)*volume)/flow_rate[x]
if time_in > 30:
time_in = 30
MESSAGE = "%s,0,%d," % ("{0:b}".format(control[x]+control[x+16]) , time_in)
eVOLVER_module.fluid_command(MESSAGE, x, elapsed_time, pump_wait *60, exp_name, time_in, 'n')
MESSAGE = "%s,0,%d," % ("{0:b}".format(control[x+16]) , time_out)
#eVOLVER_module.fluid_command(MESSAGE, x, elapsed_time, pump_wait *60, exp_name, time_out,'n')
eVOLVER_module.fluid_command(MESSAGE, x, elapsed_time, pump_wait *60, exp_name, time_out,'y')
def test(OD_data, temp_data, vials, elapsed_time, exp_name):
### Set Stir Rate
#### Message Stir Rates
MESSAGE = ""
for x in vials:
stir_rate_path = "%s/%s/stir_rate/vial%d_stir_rate.txt" % (save_path,
exp_name, x)
data = np.genfromtxt(stir_rate_path, delimiter=',')
stir_set = data[len(data) - 1][1]
MESSAGE += str(stir_set)
MESSAGE += ","
eVOLVER_module.stir_rate(MESSAGE)
control = np.power(2, range(0, 32))
#flow_rate = np.array([1.11,1.11,1.1,1.08,1.1,1.12,1.04,1.1,1.13,1.12,0.93,1.1,1.1,1.17,1.07,1.1])#ml/sec
volume = 35 #mL
#lower_thresh = np.array([.25,.25,.25,.25,.25,.25,.25,.25,.25,.25,.25,.25,.25,.25,.25,.25])
#upper_thresh = np.array([.3,.3,.3,.3,.3,.3,.3,.3,.3,.3,.3,.3,.3,.3,.3,.3])
lower_thresh = np.array([
.25, .25, 9999, 9999, 9999, 9999, 9999, 9999, 9999, 9999, 9999, 9999,
9999, 9999, 9999, 9999
])
upper_thresh = np.array([
.3, .3, 9999, 9999, 9999, 9999, 9999, 9999, 9999, 9999, 9999, 9999,
9999, 9999, 9999, 9999
])
time_out = 5
pump_wait = 10
#wait between pumps (min)
save_path = os.path.dirname(os.path.realpath(__file__))
drug_dose_start = 10 #hours
vial2vial_timeThresh = 14 #hours
#### Change media based on before or after drug dose
if elapsed_time > drug_dose_start:
media = np.array([0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
else:
media = np.array([1, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
#media 0- YPD
#media 1- YPD + chx
#media 2- YPD + keto
#media 3- YPD + chx + keto
#media 4- YPD + 20x chx
#media 5- YPD + 20x keto
#media 7- YPD + 20x keto + 20x chx
###### Make decision to dilute or not ################
for x in vials:
ODset_path = "%s/%s/ODset/vial%d_ODset.txt" % (save_path, exp_name, x)
data = np.genfromtxt(ODset_path, delimiter=',')
ODset = data[len(data) - 1][1]
OD_path = "%s/%s/OD/vial%d_OD.txt" % (save_path, exp_name, x)
data = np.genfromtxt(OD_path, delimiter=',')
average_OD = 0
if len(data) > 15:
## Averages last 5 data points
for n in range(1, 6):
average_OD = average_OD + (data[len(data) - n][1] / 5)
######### Set OD thresholds ########
#### Set to lower target growth rate for dilutions
if (average_OD > upper_thresh[x]) and (ODset != lower_thresh[x]):
text_file = open(ODset_path, "a+")
text_file.write("%f,%s\n" % (elapsed_time, lower_thresh[x]))
text_file.close()
ODset = lower_thresh[x]
########## Measure and record growth rate when hits OD threshold###########
growth_rate = measure_growthRate(x, save_path, exp_name)
growth_rate_path = "%s/%s/growth_rate/vial%d_growth_rate.txt" % (
save_path, exp_name, x)
text_file = open(growth_rate_path, "a+")
text_file.write("%f,%s\n" % (elapsed_time, growth_rate))
text_file.close()
if (average_OD <
(lower_thresh[x] + 0.005)) and (ODset != upper_thresh[x]):
text_file = open(ODset_path, "a+")
text_file.write("%f,%s\n" % (elapsed_time, upper_thresh[x]))
text_file.close()
ODset = upper_thresh[x]
### Average last three growth rates ######
growth_rate_path = "%s/%s/growth_rate/vial%d_growth_rate.txt" % (
save_path, exp_name, x)
rate_data = np.genfromtxt(growth_rate_path, delimiter=',')
average_rate = 0
num_averaged = 3
if len(rate_data) > num_averaged:
for n in range(1, num_averaged + 1):
average_rate = average_rate + (
rate_data[len(rate_data) - n][1] / num_averaged)
##### Make decision on growth rates #####
if elapsed_time > vial2vial_timeThresh:
rate_thresholds = np.array(
np.mat('0 99999; 1 99999; 0 99999; 1 99999')
) ## [vial_output, growth_rate threshold]
next_vial_0 = np.array(np.mat('2 4; 5 7; 8 10; 11 13'))
next_vail_1 = np.array(
np.mat('3 4; 6 7; 9 10; 12 13')) ## ['vial_in1, vial_in2']
for n in range(0, len(rate_thresholds)):
if x == rate_thresholds[n][
0]: ## checks to see if correct vial output
if average_rate > rate_thresholds[n][
1]: ## check to see what the rate threshold is
rate_thresh_path = "%s/%s/rate_thresh/vial%d_rate_thresh.txt" % (
save_path, exp_name, x)
data = np.genfromtxt(rate_thresh_path,
delimiter=',')
last_rate_thresh = data[len(data) - 1][1]
if rate_thresholds[n][1] > last_rate_thresh:
rate_thresh_path = "%s/%s/rate_thresh/vial%d_rate_thresh.txt" % (
save_path, exp_name, x)
text_file = open(rate_thresh_path, "a+")
text_file.write(
"%f,%s\n" %
(elapsed_time, rate_thresholds[n][1]))
text_file.close()
## media, vialOut, vialIn1, vialIn2
MESSAGE = "v2v_2x,%d,2000,0,%d,%d,%d,100,5,2000," % (
media[0], 0, next_vial_0[n][0],
next_vial_0[n][1])
eVOLVER_module.fluid_command(
MESSAGE, 0, elapsed_time, pump_wait * 60,
exp_name, time_out, 'y')
ODset_path = "%s/%s/ODset/vial%d_ODset.txt" % (
save_path, exp_name, 0)
text_file = open(ODset_path, "a+")
text_file.write(
"%f,%s\n" %
(elapsed_time, upper_thresh[0]))
text_file.close()
## media, vialOut, vialIn1, vialIn2
MESSAGE = "v2v_2x,%d,2000,0,%d,%d,%d,100,5,2000," % (
media[1], 1, next_vial_1[n][0],
next_vial_1[n][1])
eVOLVER_module.fluid_command(
MESSAGE, 1, elapsed_time, pump_wait * 60,
exp_name, time_out, 'y')
ODset_path = "%s/%s/ODset/vial%d_ODset.txt" % (
save_path, exp_name, 1)
text_file = open(ODset_path, "a+")
text_file.write(
"%f,%s\n" %
(elapsed_time, upper_thresh[1]))
text_file.close()
#### Make decision for stir rates if above a certain density then change stir rate
stir_thresh = .8
if average_OD > stir_thresh:
stir_rate_path = "%s/%s/stir_rate/vial%d_stir_rate.txt" % (
save_path, exp_name, x)
data = np.genfromtxt(stir_rate_path, delimiter=',')
stir_set = data[len(data) - 1][1]
if stir_set == 0:
stir_rate_path = "%s/%s/stir_rate/vial%d_stir_rate.txt" % (
save_path, exp_name, x)
text_file = open(stir_rate_path, "a+")
text_file.write("%f,%s\n" % (elapsed_time, 0))
text_file.close()
if average_OD > ODset:
time_in = 0
step_size = ((
(-1) * np.log(lower_thresh[x] / average_OD) * volume) +
.1) / (.0009)
if step_size < 1000:
step_size = 1000
MESSAGE = "dilute,%d,%d,0,%d,3,5,0,0,0," % (media[x],
step_size, x)
eVOLVER_module.fluid_command(MESSAGE, x, elapsed_time,
pump_wait * 60, exp_name,
time_out, 'y')
def test(OD_data, temp_data, vials, elapsed_time, exp_name):
##### USER DEFINED VARIABLES #####
temp_input = 25 #degrees C, can be scalar or 16-value numpy array
stir_input = 11 #try 8,10,12; see paper for rpm conversion, can be scalar or 16-value numpy array
# lower_thresh = np.array([0.2] * len(vials))
lower_thresh = np.array([9999] * 16)
upper_thresh = np.array([9999] * 16)
##### END OF USER DEFINED VARIABLES #####
##### Calibration Values:
# Be sure to check that OD_cal.txt and temp_calibration.txt are up to date
# Additional calibration values below, remain the same between experiments
time_out = 5 #(sec) additional amount of time to run efflux pump
pump_wait = 15 # (min) minimum amount of time to wait between pump events
control = np.power(2, range(0, 32)) #vial addresses
flow_rate = np.array([
0.95, 1.1, 0.975, 0.85, 0.95, 1.05, 1.05, 1.05, 1.025, 1.125, 1.0, 1.0,
1.05, 1.15, 1.1, 1.025
]) #ml/sec, paste from pump calibration
volume = 25 #mL, determined by straw length
save_path = os.path.dirname(os.path.realpath(__file__)) #save path
##### End of Calibration Values
##### Turbidostat Control Code Below #####
for x in vials: #main loop through each vial
# Update temperature configuration files for each vial
tempconfig_path = "{0}/{1}/temp_config/vial{2}_tempconfig.txt".format(
save_path, exp_name, x)
temp_config = np.genfromtxt(tempconfig_path, delimiter=',')
if (
len(temp_config) is 2
): #set temp at the beginning of the experiment, can clone for subsequent temp changes
if np.isscalar(temp_input):
temp_val = temp_input
else:
temp_val = temp_input[x]
text_file = open(tempconfig_path, "a+")
text_file.write("{0},{1}\n".format(elapsed_time, temp_val))
text_file.close()
# Update turbidostat configuration files for each vial
# initialize OD and find OD path
ODset_path = "{0}/{1}/ODset/vial{2}_ODset.txt".format(
save_path, exp_name, x)
data = np.genfromtxt(ODset_path, delimiter=',')
ODset = data[len(data) - 1][1]
OD_path = "{0}/{1}/OD/vial{2}_OD.txt".format(save_path, exp_name, x)
data = np.genfromtxt(OD_path, delimiter=',')
average_OD = 0
# Determine whether turbidostat dilutions are needed
if len(data) > 7:
for n in range(1, 6):
average_OD = average_OD + (data[len(data) - n][1] / 5)
if (average_OD > upper_thresh[x]) and (ODset != lower_thresh[x]):
text_file = open(ODset_path, "a+")
text_file.write("{0},{1}\n".format(elapsed_time,
lower_thresh[x]))
text_file.close()
ODset = lower_thresh[x]
if (average_OD < (lower_thresh[x] +
(upper_thresh[x] - lower_thresh[x]) / 2)) and (
ODset != upper_thresh[x]):
text_file = open(ODset_path, "a+")
text_file.write("{0},{1}\n".format(elapsed_time,
upper_thresh[x]))
text_file.close()
ODset = upper_thresh[x]
if average_OD > ODset:
time_in = -(np.log(lower_thresh[x] / average_OD) *
volume) / flow_rate[x]
if time_in > 20:
time_in = 20
save_path = os.path.dirname(os.path.realpath(__file__))
file_path = "{0}/{1}/pump_log/vial{2}_pump_log.txt".format(
save_path, exp_name, x)
data = np.genfromtxt(file_path, delimiter=',')
last_pump = data[len(data) - 1][0]
if ((elapsed_time - last_pump) * 60) >= pump_wait:
MESSAGE = {
'pump_binary': "{0:b}".format(control[x]),
'pump_time': time_in,
'efflux_pump_time': time_out,
'delay_interval': 0,
'times_to_repeat': 0,
'run_efflux': 1
}
eVOLVER_module.fluid_command(MESSAGE, x, elapsed_time,
pump_wait * 60, exp_name,
time_in, 'y')
#Update stir rate for all vials
if np.isscalar(stir_input):
STIR_MESSAGE = [stir_input] * 16
else:
stir_val = np.array2string(stir_input, separator=',')
stir_val = stir_val.replace(' ', '')
stir_val = stir_val.replace('[', '')
stir_val = stir_val.replace(']', '')
STIR_MESSAGE = list(map(int, stir_val.split(',')))
eVOLVER_module.stir_rate(STIR_MESSAGE)
