def calibrate_pumps(pump_type, vials=None, dt=10):
'''
Routine that runs all pumps sequentially assuming the outlet is sitting on
on a balance. after running a pump for dt seconds, the user is prompted for the weight
until all 15 pumps have been run
'''
if vials is None:
vials = range(15)
calibration_morb = morb.morbidostat()
print("Upon pressing enter, each pump will be run for " + str(dt) +
" seconds.")
print(
"Before each pump, you will be prompted for the weight of the current set-up."
)
s = input("press enter to start, q to stop: ")
if len(s) > 0:
print("Aborting calibration")
return
# loop over vials, prompt for weight
weight = np.zeros(len(vials) + 1)
for vi, vial in enumerate(vials):
no_weight = True
while no_weight:
s = input('current weight: ')
try:
weight[vi] = float(s)
no_weight = False
except:
print("invalid weight")
calibration_morb.run_pump(pump_type, vial, run_time=dt)
# get final weight
no_weight = True
while no_weight:
s = input('final weight: ')
try:
weight[-1] = float(s)
no_weight = False
except:
print("invalid weight")
# calculate pump_rate and save to file
pump_rate = np.diff(weight) / dt
np.savetxt(morb.pump_calibration_file_base + '_' + pump_type + '.dat',
pump_rate)
def calibrate_pumps(pump_type, vials = None, dt = 10):
'''
Routine that runs all pumps sequentially assuming the outlet is sitting on
on a balance. after running a pump for dt seconds, the user is prompted for the weight
until all 15 pumps have been run
'''
if vials is None:
vials = range(15)
calibration_morb = morb.morbidostat()
print("Upon pressing enter, each pump will be run for "+str(dt)+" seconds.")
print("Before each pump, you will be prompted for the weight of the current set-up.")
s = raw_input("press enter to start, q to stop: ")
if len(s)>0:
print("Aborting calibration")
return
# loop over vials, prompt for weight
weight = np.zeros(len(vials)+1)
for vi,vial in enumerate(vials):
no_weight = True
while no_weight:
s = raw_input('current weight: ')
try:
weight[vi] =float(s)
no_weight = False
except:
print("invalid weight")
calibration_morb.run_pump(pump_type, vial,run_time=dt)
# get final weight
no_weight = True
while no_weight:
s = raw_input('final weight: ')
try:
weight[-1] =float(s)
no_weight = False
except:
print("invalid weight")
# calculate pump_rate and save to file
pump_rate = np.diff(weight)/dt
np.savetxt(morb.pump_calibration_file_base+'_'+pump_type+'.dat', pump_rate)
def __init__(self,
vials=range(15),
experiment_duration=2 * 60 * 60,
target_OD=0.1,
dilution_factor=0.9,
bug='tbd',
drugA='tbd',
drugB='tbd',
drugA_concentration=0.3,
drugB_concentration=2.0,
OD_dt=30,
cycle_dt=600):
# the default experiment is a morbidostat measurement
self.experiment_type = MORBIDOSTAT_EXPERIMENT
# all times in seconds, define parameter second to speed up for testing
self.second = 1.0
# set up the morbidostat
self.morb = morb.morbidostat()
self.morbidostat_port = self.morb.connect()
if not self.morb.morbidostat_OK:
print("Trouble setting up morbidostat")
# sync time units
self.morb.second = self.second
# experiment parameters
self.OD_dt = OD_dt
self.cycle_dt = cycle_dt
self.experiment_duration = experiment_duration
if (np.max(vials) < 15):
self.vials = copy.copy(vials)
else:
print(
"Morbidostat set-up: all vial numbers must be between 0 and 14"
)
self.vials = []
self.target_OD = target_OD
self.culture_volume = 18 # target volume in milliliters
self.dilution_factor = dilution_factor
self.dilution_threshold = 0.03
self.extra_suction = 2 # extra volume that is being sucked out of the vials [ml]
self.drugA = drugA
self.drugB = drugB
self.experiment_name = 'tbd'
self.bug = bug
self.drugA_concentration = drugA_concentration
self.drugB_concentration = drugB_concentration
# data acqusition specifics
self.n_reps = 8
self.buffer_time = 10
# counters
self.OD_measurement_counter = 0
self.cycle_counter = 0
self.restart_from_file = None # if a directory name, resume from there.
#feedback parameters
self.max_growth_fraction = 0.05 # increase antibiotics with 5% OD increase per cycle
self.AB_switch_conc = 0.3 # use high concentration if culture conc is 30% of drug A
self.feedback_time_scale = 12 # compare antibiotic concentration to that x cycles ago
self.saturation_threshold = 0.22 # threshold beyond which OD can't be reliable measured
self.anticipation_threshold = 0.7 # fraction of target_OD, at which increasing antibiotics is first considered
# diagnostic variables
self.max_AB_fold_increase = 1.1 # maximum amount by which the antibiotic concentration is allowed to increase within the feed back time scale
self.mic_kd = 0.25 # fraction of the mic to which is added to low drug concentrations when calculating the AB_fold_increase
self.stopped = True
self.interrupted = False
self.running = False
self.override = False
self.n_cycles = self.experiment_duration // self.cycle_dt
self.n_vials = len(self.vials)
self.calculate_derived_values()
self.ODs_per_cycle = int(self.cycle_dt - self.morb.mixing_time -
self.pump_time -
self.buffer_time) // self.OD_dt
def calibrate_OD(vials=None):
'''
measure OD of OD standard, calculate regression coefficients
'''
import matplotlib.pyplot as plt
if vials is None:
vials = range(15)
calibration_morb = morb.morbidostat()
no_valid_standard = True
ODs = []
voltages = []
all_cycles_measured = False
while all_cycles_measured == False:
while no_valid_standard:
s = input("Enter OD of standard [q to quit]: ")
if s == 'q':
print("Aborting calibration")
all_cycles_measured = True
break
try:
cur_OD = float(s)
no_valid_standard = False
except:
print("invalid entry")
if not all_cycles_measured: # prompt user for 15 measurements while q is not pressed
ODs.append(cur_OD)
voltages.append(np.zeros(len(vials)))
for vi, vial in enumerate(vials):
OKstr = input("Place OD standard in receptible " +
str(vial + 1) + ", press enter when done")
time.sleep(
0.001
) #delay for 1 second to allow for heating of the diode
voltages[-1][vi] = calibration_morb.measure_voltage(
vial, switch_light_off=True)[0]
print(vial, "measurement ", voltages[-1][vi])
no_valid_standard = True
if len(ODs) > 1:
print("Collected " + str(len(ODs)) +
" OD voltage pairs, calculating voltage -> OD conversion")
ODs = np.array(ODs)
voltages = np.array(voltages).T
fit_parameters = np.zeros((len(vials), 2))
for vi, vial in enumerate(vials):
good_measurements = voltages[vi, :] < 900
if good_measurements.sum() > 1:
slope, intercept, r, p, stderr = linregress(
ODs[good_measurements], voltages[vi, good_measurements])
else:
print(
"less than 2 good measurements, also using saturated measurements for vial"
+ str(vial))
slope, intercept, r, p, stderr = linregress(
ODs, voltages[vi, :])
fit_parameters[vi, :] = [1.0 / slope, -intercept / slope]
np.savetxt(morb.OD_calibration_file_name, fit_parameters)
tmp_time = time.localtime()
# make figure showing calibration
plt.plot(ODs, voltages.T, 'o', ls='-')
plt.xlabel('OD standard')
plt.ylabel('measured signal (0-1023)')
# save calibration measurements
date_string = "".join([
format(v, '02d')
for v in [tmp_time.tm_year, tmp_time.tm_mon, tmp_time.tm_mday]
])
with open(
morb.morb_path + 'data/voltage_measurements_' + date_string +
'.txt', 'w') as volt_file:
for oi in range(len(ODs)):
volt_file.write(str(ODs[oi]))
for vi in range(len(vials)):
volt_file.write('\t' + str(voltages[vi, oi]))
volt_file.write('\n')
else:
print("need measurements for at least two OD standards")
return fit_parameters, ODs, voltages
import arduino_interface as M
import time
# initialize an instance of the morbidostat.
morb = M.morbidostat()
# if it was found on the serial port, loop over all
# pumps and switch them on for a few seconds
if morb.morbidostat_OK:
m,v,c = morb.measure_voltage(1, 10, 10)
for pump_type in ['medium','drug A', 'drug B']:
for pin in range(15):
morb.run_pump(pump_type, pin, 1)
time.sleep(1.2)
else:
print("Initializing morbidostat failed")
# run the waste pump for 4 seconds
morb.run_waste_pump(4)
# close the serial port
morb.disconnect()
def __init__(self, vials = range(15), experiment_duration = 2*60*60,
target_OD = 0.1, dilution_factor = 0.9, bug = 'tbd', drugA ='tbd',drugB ='tbd',
drugA_concentration = 0.3, drugB_concentration = 2.0, OD_dt = 30, cycle_dt = 600):
# the default experiment is a morbidostat measurement
self.experiment_type = MORBIDOSTAT_EXPERIMENT
# all times in seconds, define parameter second to speed up for testing
self.second = 1.0
# set up the morbidostat
self.morb = morb.morbidostat()
self.morbidostat_port = self.morb.connect()
if not self.morb.morbidostat_OK:
print("Trouble setting up morbidostat")
# sync time units
self.morb.second = self.second
# experiment parameters
self.OD_dt = OD_dt
self.cycle_dt = cycle_dt
self.experiment_duration = experiment_duration
if (np.max(vials)<15):
self.vials = copy.copy(vials)
else:
print("Morbidostat set-up: all vial numbers must be between 0 and 14")
self.vials = []
self.target_OD = target_OD
self.culture_volume = 18 # target volume in milliliters
self.dilution_factor = dilution_factor
self.dilution_threshold = 0.03
self.extra_suction = 2 # extra volume that is being sucked out of the vials [ml]
self.drugA = drugA
self.drugB = drugB
self.experiment_name = 'tbd'
self.bug = bug
self.drugA_concentration = drugA_concentration
self.drugB_concentration = drugB_concentration
# data acqusition specifics
self.n_reps=8
self.buffer_time = 10
# counters
self.OD_measurement_counter = 0
self.cycle_counter = 0
self.restart_from_file=None # if a directory name, resume from there.
#feedback parameters
self.max_growth_fraction = 0.05 # increase antibiotics with 5% OD increase per cycle
self.AB_switch_conc = 0.3 # use high concentration if culture conc is 30% of drug A
self.feedback_time_scale = 12 # compare antibiotic concentration to that x cycles ago
self.saturation_threshold = 0.22 # threshold beyond which OD can't be reliable measured
self.anticipation_threshold = 0.7 # fraction of target_OD, at which increasing antibiotics is first considered
# diagnostic variables
self.max_AB_fold_increase = 1.1 # maximum amount by which the antibiotic concentration is allowed to increase within the feed back time scale
self.mic_kd = 0.25 # fraction of the mic to which is added to low drug concentrations when calculating the AB_fold_increase
self.stopped = True
self.interrupted = False
self.running = False
self.override = False
self.n_cycles = self.experiment_duration//self.cycle_dt
self.n_vials = len(self.vials)
self.calculate_derived_values()
self.ODs_per_cycle = int(self.cycle_dt-self.morb.mixing_time-self.pump_time - self.buffer_time)//self.OD_dt
def calibrate_OD(vials = None):
'''
measure OD of OD standard, calculate regression coefficients
'''
import matplotlib.pyplot as plt
if vials is None:
vials = range(15)
calibration_morb = morb.morbidostat()
no_valid_standard=True
ODs = []
voltages = []
all_cycles_measured = False
while all_cycles_measured==False:
while no_valid_standard:
s = raw_input("Enter OD of standard [q to quit]: ")
if s=='q':
print("Aborting calibration")
all_cycles_measured = True
break
try:
cur_OD = float(s)
no_valid_standard=False
except:
print("invalid entry")
if not all_cycles_measured: # prompt user for 15 measurements while q is not pressed
ODs.append(cur_OD)
voltages.append(np.zeros(len(vials)))
for vi,vial in enumerate(vials):
OKstr = raw_input("Place OD standard in receptible "+str(vial+1)+
", press enter when done")
time.sleep(0.001) #delay for 1 second to allow for heating of the diode
voltages[-1][vi] = calibration_morb.measure_voltage(vial, switch_light_off=True)[0]
print vial, "measurement ", voltages[-1][vi]
no_valid_standard=True
if len(ODs)>1:
print("Collected "+str(len(ODs))+" OD voltage pairs, calculating voltage -> OD conversion")
ODs = np.array(ODs)
voltages = np.array(voltages).T
fit_parameters = np.zeros((len(vials), 2))
for vi,vial in enumerate(vials):
good_measurements = voltages[vi,:]<900
if good_measurements.sum()>1:
slope, intercept, r,p,stderr = linregress(ODs[good_measurements], voltages[vi,good_measurements])
else:
print("less than 2 good measurements, also using saturated measurements for vial"+str(vial))
slope, intercept, r,p,stderr = linregress(ODs, voltages[vi,:])
fit_parameters[vi,:] = [1.0/slope, -intercept/slope]
np.savetxt(morb.OD_calibration_file_name, fit_parameters)
tmp_time = time.localtime()
# make figure showing calibration
plt.plot(ODs, voltages.T, 'o', ls='-')
plt.xlabel('OD standard')
plt.ylabel('measured signal (0-1023)')
# save calibration measurements
date_string = "".join([format(v,'02d') for v in
[tmp_time.tm_year, tmp_time.tm_mon, tmp_time.tm_mday]])
with open(morb.morb_path+'data/voltage_measurements_'+date_string+'.txt', 'w') as volt_file:
for oi in range(len(ODs)):
volt_file.write(str(ODs[oi]))
for vi in range(len(vials)):
volt_file.write('\t'+str(voltages[vi,oi]))
volt_file.write('\n')
else:
print("need measurements for at least two OD standards")
return fit_parameters, ODs, voltages