def V_sampchan(self, chan, gain, data_rate=RATE):
'''
This routine returns a single reading of the voltage for the channel.
Returns a tuple of the following 5 objects:
V -- float, the measured voltage
time_stamp -- float, the time of the measurement in seconds since
the beginning of the epoch (OS dependent begin time)
ref -- float, the reference voltage (Vdd) collected
simultaneously.
:param int chan: the channel number (0, 1, 2, 3, 4, 5, 6, 7,
8). NOTE: channel 8 returns a measurement of Vdd.
:param gain: ignored by board. Defaults to 1.
:param int data_rate: ignored by board.
:returns: V_avg, stdev, stdev_avg, time_stamp, Vdd_avg
:return float V:
:return float time_stamp:
:return float ref:
'''
start = time.time()
value = DAQC2plate.getADC(self.addr, chan)
ref = DAQC2plate.getADC(self.addr, 8)
end = time.time()
time_stamp = (start + end) / 2
return value, time_stamp, ref
def V_oversampchan_stats(self, chan, gain, avg_sec, data_rate=RATE):
'''
This routine returns the average voltage for the channel
averaged at the maximum rate for the board. The standard
deviation and the estimated deviation of the mean are also
returned.
Returns a tuple of the following 5 objects:
V_avg -- float, the averaged voltage
stdev -- float, the standard deviation of the measured values
during the averaging interval
stdev_avg -- float, the estimated standard deviation of the
returned average
time_stamp -- float, the time at halfway through the averaging
interval in seconds since the beginning of the epoch (OS
dependent begin time)
Vdd_avg -- float, the reference voltage (Vdd) collected
simultaneously.
:param int chan: the channel number (0, 1, 2, 3, 4, 5, 6, 7,
8). NOTE: channel 8 returns a measurement of Vdd.
:param gain: ignored by board. Defaults to 1.
:param int data_rate: ignored by board.
:param float avg_sec: seconds to average for, actual
averaging interval will be as close as possible for an integer
number of samples
:returns: V_avg, stdev, stdev_avg, time_stamp, Vdd_avg
:return float V_avg: description
:return float stdev:
:return float stdev_avg:
:return float time_stamp:
:return float Vdd_avg:
'''
value = []
ref = []
starttime = time.time()
endtime = starttime + avg_sec
while time.time() < endtime:
value.append(DAQC2plate.getADC(self.addr, chan))
ref.append(DAQC2plate.getADC(self.addr, 8))
time_stamp = (starttime + endtime) / 2
ndata = len(value)
logging.debug('channel:' + str(chan) + ', starttime:' +
str(starttime) + ', '
'endtime:' + str(endtime) + ', ndata:' + str(ndata) +
'.')
V_avg = sum(value) / ndata
Vdd_avg = sum(ref) / ndata
stdev = np.std(value, ddof=1, dtype=np.float64)
stdev_avg = stdev / np.sqrt(float(ndata))
return V_avg, stdev, stdev_avg, time_stamp, Vdd_avg
def V_oversampchan(self, chan, gain, avg_sec, data_rate=RATE):
"""
This routine returns the average voltage for the channel
averaged at the default rate for the board and returns an
average and observed range.
Returns a tuple of the following 5 objects:
V_avg -- float, the averaged voltage
V_min -- float, the minimum voltage read during
the interval
V_max -- float, the maximum voltage read during the
interval
time_stamp -- float, the time at halfway through the averaging
interval in seconds since the beginning of the epoch (OS
dependent begin time)
Vdd_avg -- float, the reference voltage (Vdd) collected
simultaneously.
:param int chan: the channel number (0, 1, 2, 3, 4, 5, 6, 7,
8). NOTE: channel 8 returns a measurement of Vdd.
:param gain: ignored by board. Defaults to 1.
:param int data_rate: ignored by board.
:param float avg_sec: seconds to average for, actual
averaging interval will be as close as possible for an integer
number of samples
:returns: V_avg, V_min, V_max, time_stamp, Vdd_avg
:return float V_avg: description
:return float V_min:
:return float V_max:
:return float time_stamp:
:return float Vdd_avg:
"""
value = []
ref = []
starttime = time.time()
endtime = starttime + avg_sec
while time.time() < endtime:
value.append(DAQC2plate.getADC(self.addr, chan))
ref.append(DAQC2plate.getADC(self.addr, 8))
time_stamp = (endtime + endtime) / 2
ndata = len(value)
V_avg = sum(value) / ndata
Vdd_avg = sum(ref) / ndata
V_min = min(value)
V_max = max(value)
return V_avg, V_min, V_max, time_stamp, Vdd_avg
def exposeAndCollectData():
GPIO.output(methane_valve, GPIO.LOW)
GPIO.output(ethane_valve, GPIO.LOW)
GPIO.output(compressed_air_valve, GPIO.LOW)
GPIO.output(chamber_venting_valve, GPIO.LOW)
GPIO.output(mfc1_output_to_chamber_valve, GPIO.LOW)
GPIO.output(mfc2_output_to_chamber_valve, GPIO.LOW)
GPIO.output(mfc1_venting_valve, GPIO.LOW)
GPIO.output(mfc2_venting_valve, GPIO.LOW)
start_time = time.time() # capture the time at which the test began. All time values can use start_time as a reference
dataVector1 = [] # data values to be returned from sensor 1
dataVector2 = [] # data values to be returned from sensor 2
tempDataVector = []
humidityDataVector = []
timeVector = [] # time values associated with data values
sampling_time_index = 1 #sampling_time_index is used to ensure that sampling takes place every interval of sampling_time, without drifting.
data_date_and_time = time.asctime( time.localtime(time.time()) )
print("Starting data capture")
while (time.time() < (start_time + duration_of_signal)): # While time is less than duration of logged file
if (time.time() > (start_time + (sampling_time * sampling_time_index))): # if time since last sample is more than the sampling time, take another sample
dataVector1.append( DAQC.getADC(daqc_address, sensor_input_channel_1) ) # Perform analog to digital function, reading voltage from first sensor channel
dataVector2.append( DAQC.getADC(daqc_address, sensor_input_channel_2) ) # Perform analog to digital function, reading voltage from second sensor channel
timeVector.append( time.time() - start_time )
sampling_time_index += 1 # increment sampling_time_index to set awaited time for next data sample
if ((sampling_time_index - 1) % 10 == 0):
print(int(time.time() - start_time))
print(DAQC.getADC(daqc_address, linear_actuator_position_channel))
# If time is between 10-50 seconds and the Linear Actuator position sensor signal from DAQCplate indicates a retracted state, extend the sensor
## elif (time.time() >= (start_time + sensing_delay_time) and time.time() <= (sensing_retract_time + start_time) and DAQC.getADC(daqc_address, linear_actuator_position_channel) < extended_state ):
elif (time.time() >= (start_time + sensing_delay_time) and time.time() <= (start_time + sensing_delay_time + 10) ):
GPIO.output(linear_actuator_extend, GPIO.HIGH) # Actuate linear actuator to extended position
GPIO.output(linear_actuator_unlock_retract, GPIO.LOW)# Energizing both control wires causes linear actuator to extend
# If time is less than 10 seconds or greater than 50 seconds and linear actuator position sensor signal from DAQCplate indicates an extended state, retract the sensor
elif ( ((time.time() < (sensing_delay_time + start_time)) or (time.time() > (sensing_retract_time + start_time)) ) and DAQC.getADC(daqc_address, linear_actuator_position_channel) > retracted_state):
## elif ( ((time.time() < (sensing_retract_time + start_time + 10)) and (time.time() > (sensing_retract_time + start_time)) )):
GPIO.output(linear_actuator_unlock_retract, GPIO.HIGH) # Retract linear actuator to initial position. Energizing only the linear_actuator_unlock_retract wire causes the lineaer actuator to retract
GPIO.output(linear_actuator_extend, GPIO.LOW)
# Otherwise, keep outputs off else:
GPIO.output(linear_actuator_unlock_retract, GPIO.LOW)
GPIO.output(linear_actuator_extend, GPIO.LOW)
## print("blep")
return dataVector1, dataVector2, timeVector
def sample_data(self):
heading_indices = self.args['preferences']['headingString'].split(",")
data_string = ""
for idx in heading_indices:
if idx[:2] == "ch":
# Read the normal input pins
if self.args['preferences']['headerIndices'][
idx] == "Anemometer(km/h)": # 1 tick per second = 2.4km/h
data_string += "{:.1f},".format(self.args['anemometer'])
elif self.args['preferences']['headerIndices'][
idx] == "RainGauge(mm)": # 1 tick = 0.2794mm rain
data_string += "{:.4f},".format(self.args['rainGauge'])
# Relative humidity is calculated using the formula:
# RH = 0.0375 * Vout - 37.7
# Vout needs to be in mV and RH in %
elif self.args['preferences']['headerIndices'][
idx] == "RelativeHumidity(%)":
Vout = DAQC2.getADC(
int(idx[2]), int(idx[3])
) * 1000 # We have to convert voltage to mV as it is read in V
RH = 0.0375 * Vout - 37.7
data_string += "{:.4f},".format(RH)
elif self.args['preferences']['headerIndices'][
idx] == "RainGauge(mm)": # 1 tick = 0.2794mm rain
data_string += "{:.4f},".format(self.args['rainGauge'])
else:
data_string += "{:.5f},".format(
DAQC2.getADC(int(idx[2]), int(idx[3])))
data_string += "{},".format(datetime.now(timezone.utc).strftime('%Y'))
data_string += "{},".format(datetime.now(timezone.utc).strftime('%m'))
data_string += "{},".format(datetime.now(timezone.utc).strftime('%d'))
data_string += "{},".format(datetime.now(timezone.utc).strftime('%H'))
data_string += "{},".format(datetime.now(timezone.utc).strftime('%M'))
data_string += "{}\n".format(datetime.now(timezone.utc).strftime('%S'))
print(data_string, end='')
self.filemanager.save_to_file(self.args['preferences']['savePath'],
self.args['filename'], data_string)
self.previous_time = self.current_time
def animate(i):
# Left shift data
data[0:-1] = data[1:]
# Record current time
data[-1] = v_to_dbm(DAQC2.getADC(0, 0), laser_cw * 1e-3)
line.set_ydata(data)
return [line]
def photoTest():
elapsedTime = 0
tMax = 25
startReadTime = time.time()
onVolt = []
offVolt = []
## tRead = 0
while (tMax >= elapsedTime):
DAQC2.setDOUTbit(0, 7) #turn laser on
time.sleep(1)
tempVolt1 = []
tEnd1 = time.time() + 1
while (time.time() < tEnd1):
tempVolt1.append(DAQC2.getADC(0, 0))
DAQC2.clrDOUTbit(0, 7)
anaVolt = sum(tempVolt1) / len(tempVolt1)
print("number of reads: ", len(tempVolt1))
print("Voltage('ON'): ", anaVolt)
onVolt.append(anaVolt)
tempVolt2 = []
tEnd2 = time.time() + 1
while (time.time() < tEnd2):
tempVolt2.append(DAQC2.getADC(0, 0))
anaVolt = sum(tempVolt2) / len(tempVolt2)
print("number of reads: ", len(tempVolt2))
print("Voltage('OFF'): ", anaVolt)
offVolt.append(anaVolt)
elapsedTime = time.time() - startReadTime
print()
avgON = sum(onVolt) / len(onVolt)
avgOFF = sum(offVolt) / len(offVolt)
print("average ON volt: ", avgON)
print("avgerage OFF volt: ", avgOFF)
print()
def read_rain_gauge(self):
current_time = time.time()
elapsed_time = current_time - self.gauges['rainGauge']['previousTime']
if elapsed_time >= 1:
self.args['rainGauge'] = (self.gauges['rainGauge']['numberTicks'] *
self.args['preferences']['rainConstant'])
self.gauges['rainGauge']['numberTicks'] = 0
self.gauges['rainGauge']['previousTime'] = current_time
temp_val = DAQC2.getADC(int(self.gauges['rainGauge']['channel'][2]),
int(self.gauges['rainGauge']['channel'][3]))
if temp_val > 4:
if not self.gauges['rainGauge']['recordedTick']:
self.gauges['rainGauge']['numberTicks'] += 1
self.gauges['rainGauge']['recordedTick'] = True
else:
self.gauges['rainGauge']['recordedTick'] = False
def readOD():
DAQC2.setDOUTbit(0, 7)
time.sleep(1)
rowVolts = []
j = 0
k = 0
num = 1
while (k <= 5):
tempVolt = []
tEnd = time.time() + .5
while (time.time() < tEnd):
tempVolt.append(DAQC2.getADC(j, k))
currAvgVolt = sum(tempVolt) / len(tempVolt)
rowVolts.append(currAvgVolt)
print("Avg voltage for ", num, ": ", currAvgVolt)
k = k + 1
num = num + 1
if (k == 6 and j == 0):
j = 1
k = 0
elif (k == 2 and j == 1):
k = 10
DAQC2.clrDOUTbit(0, 7)
"Failed to import library from parent folder")
####### zet de LED uit
DAQC.setLED(0, 'off')
####### stuur de analoge output aan
DAQC.setDAC(0, 1, 2.64) # DAQ 0, adres analog-output 1, voltage 2.64 V
###### stuur 0, 1, 2, 3 volt naar analog-output 1
for i in range(10):
volt = i % 4 # i modulo 4
DAQC.setDAC(0, 1, volt)
time.sleep(0.1)
####### Lees data van Analoge Input
val = DAQC.getADC(0, 1) # DAQC 0, adres Analog-Input 1
print(val)
val8 = DAQC.getADCall(0) # lees alle 8 Analog-Inputs
print(val8)
######## Lees meerdere data punten
data = get_data.readPiPlate(DAQC, 3) # kanaal 0, 1000 punten, ADC 0
# maak een (unieke) filenaam aan
filename = 'meting_test1_%s.txt' % (int(time.time()))
write_data.saveArray(data, filename)
def readPressureMC():
voltage = DAQ.getADC(0, 2) - DAQ.getADC(0, 3)
vadj = 1.004029 * voltage - 0.000386 # Calibrated for Pi Plate Error
return 10**(1.66666667 * vadj - 11.46) #Pressure in Torr returned
def chemostat(timeL, pumpPeriod):
elapsedTime = 0
tMax = timeL + 11
min = timeL / 60
pumpTime = pumpPeriod
startReadTime = time.time()
tStart = 0
tPump = time.time()
volts = np.zeros(shape=(min + 1, 8))
counter = 0
currTime = time.time()
print("\n")
while (tMax >= elapsedTime):
if (currTime - tStart >
60): #58 b/c lose two seconds with sleep and measure
tStart = time.time()
readTimeS = (tStart - startReadTime) / 60
print("Read ", counter, " at ", readTimeS, " min.")
###
DAQC2.setDOUTbit(0, 7)
time.sleep(1)
rowVolts = []
j = 0
k = 0
num = 1
while (k <= 5):
tempVolt = []
tEnd = time.time() + .5
while (time.time() < tEnd):
tempVolt.append(DAQC2.getADC(j, k))
currAvgVolt = sum(tempVolt) / len(tempVolt)
rowVolts.append(currAvgVolt)
print("Avg voltage for ", num, ": ", currAvgVolt)
k = k + 1
num = num + 1
if (k == 6 and j == 0):
j = 1
k = 0
elif (k == 2 and j == 1):
k = 10
DAQC2.clrDOUTbit(0, 7)
print("\n")
volts[counter] = rowVolts
counter = counter + 1
###
measureTime = (tStart - startReadTime) / 60.0
measureDateTime = datetime.now().strftime('%Y-%m-%d %H:%M:%S')
dateTime.append(measureDateTime)
readTime.append(measureTime)
if ((currTime - tPump - 1) > pumpTime * 60):
print("pump on/valves open")
tPump = (time.time() - startReadTime) / 60
print("pump on at: ", tPump)
j = 0
i = 0
while (i <= 5):
DAQC2.setDOUTbit(j, i)
DAQC2.setDOUTbit(0, 6)
time.sleep(2)
DAQC2.clrDOUTbit(0, 6)
DAQC2.clrDOUTbit(j, i)
time.sleep(.5)
i = i + 1
if (i == 6 and j == 0):
j = 1
i = 0
elif (i == 2 and j == 1):
i = 10
tPump = time.time()
print("pump off \n")
currTime = time.time()
elapsedTime = time.time() - startReadTime
morbido1 = volts[:, 0].tolist()
morbido2 = volts[:, 1].tolist()
morbido3 = volts[:, 2].tolist()
morbido4 = volts[:, 3].tolist()
morbido5 = volts[:, 4].tolist()
morbido6 = volts[:, 5].tolist()
morbido7 = volts[:, 6].tolist()
morbido8 = volts[:, 7].tolist()
OD1 = (((np.log10(morbido1) / logBlankVolts[0]) - .71891) /
-2.1235).tolist()
OD2 = (((np.log10(morbido2) / logBlankVolts[1]) - .71891) /
-2.1235).tolist()
OD3 = (((np.log10(morbido3) / logBlankVolts[2]) - .71891) /
-2.1235).tolist()
OD4 = (((np.log10(morbido4) / logBlankVolts[3]) - .71891) /
-2.1235).tolist()
OD5 = (((np.log10(morbido5) / logBlankVolts[4]) - .71891) /
-2.1235).tolist()
OD6 = (((np.log10(morbido6) / logBlankVolts[5]) - .71891) /
-2.1235).tolist()
OD7 = (((np.log10(morbido7) / logBlankVolts[6]) - .71891) /
-2.1235).tolist()
OD8 = (((np.log10(morbido8) / logBlankVolts[7]) - .71891) /
-2.1235).tolist()
df = [
dateTime, readTime, morbido1, morbido2, morbido3, morbido4, morbido5,
morbido6, morbido7, morbido8, OD1, OD2, OD3, OD4, OD5, OD6, OD7, OD8
]
my_df = pd.DataFrame(df)
my_df = my_df.T
global globalDF
globalDF = my_df
csvTitle = datetime.now().strftime('%Y-%m-%d_%H-%M-%S') + '.csv'
my_df.to_csv(csvTitle,
index=True,
header=[
'DateTime', 'Time', 'V1', 'V2', 'V3', 'V4', 'V5', 'V6',
'V7', 'V8', 'OD1', 'OD2', 'OD3', 'OD4', 'OD5', 'OD6',
'OD7', 'OD8'
])
print(my_df)
print()
print("new csv file on Desktop: ", csvTitle)
fig = plt.figure()
ax1 = fig.add_subplot(111)
ax1.scatter(readTime, morbido1, s=10, c='b', marker="s", label='Culture#1')
ax1.scatter(readTime, morbido2, s=10, c='g', marker="o", label='Culture#2')
ax1.scatter(readTime, morbido3, s=10, c='r', marker="^", label='Culture#3')
ax1.scatter(readTime, morbido4, s=10, c='c', marker="p", label='Culture#4')
ax1.scatter(readTime, morbido5, s=10, c='m', marker="D", label='Culture#5')
ax1.scatter(readTime, morbido6, s=10, c='y', marker="v", label='Culture#6')
ax1.scatter(readTime, morbido7, s=10, c='k', marker="h", label='Culture#7')
ax1.scatter(readTime,
morbido8,
s=10,
c='violet',
marker="8",
label='Culture#8')
plt.ylabel('Voltage')
plt.xlabel('Time (min)')
Volttitle = datetime.now().strftime('%Y-%m-%d_%H-%M') + ' Voltage plot'
plt.title(Volttitle)
plt.legend(loc='upper right')
plt.show()
fig = plt.figure()
ax1 = fig.add_subplot(111)
ax1.scatter(readTime, OD1, s=10, c='b', marker="s", label='Culture#1')
ax1.scatter(readTime, OD2, s=10, c='g', marker="o", label='Culture#2')
ax1.scatter(readTime, OD3, s=10, c='r', marker="^", label='Culture#3')
ax1.scatter(readTime, OD4, s=10, c='c', marker="p", label='Culture#4')
ax1.scatter(readTime, OD5, s=10, c='m', marker="D", label='Culture#5')
ax1.scatter(readTime, OD6, s=10, c='y', marker="v", label='Culture#6')
ax1.scatter(readTime, OD7, s=10, c='k', marker="h", label='Culture#7')
ax1.scatter(readTime, OD8, s=10, c='violet', marker="8", label='Culture#8')
plt.ylabel('OD600')
plt.xlabel('Time (min)')
ODtitle = datetime.now().strftime('%Y-%m-%d_%H-%M') + ' OD plot'
plt.title(ODtitle)
plt.legend(loc='upper left')
plt.show()
def Turbido(timeL, pumpPeriod, NormVolt):
elapsedTime = 0
tMax = timeL + 45
min = timeL / 60
pumpTime = pumpPeriod
startReadTime = time.time()
tStart = 0
tPump = time.time()
volts = np.zeros(shape=(min + 1, 8))
setVolt = NormVolt
counter = 0
currTime = time.time()
print("\n")
currVolts = []
while (tMax >= elapsedTime):
if (currTime - tStart > 60):
tStart = time.time()
readTimeS = (currTime - startReadTime) / 60
print("Read ", counter, " at ", readTimeS, " min.")
DAQC2.setDOUTbit(0, 7)
time.sleep(1)
rowVolts = []
j = 0
k = 0
num = 1
while (k <= 5):
tempVolt = []
tEnd = time.time() + .5
while (time.time() < tEnd):
tempVolt.append(DAQC2.getADC(j, k))
currAvgVolt = sum(tempVolt) / len(tempVolt)
rowVolts.append(currAvgVolt)
print("Avg voltage for ", num, ": ", currAvgVolt)
k = k + 1
num = num + 1
if (k == 6 and j == 0):
j = 1
k = 0
elif (k == 2 and j == 1):
k = 10
DAQC2.clrDOUTbit(0, 7)
currVolts = rowVolts
volts[counter] = rowVolts
counter = counter + 1
measureTime = (tStart - startReadTime) / 60.0
measureDateTime = datetime.now().strftime('%Y-%m-%d %H:%M:%S')
dateTime.append(measureDateTime)
readTime.append(measureTime)
print("\n")
if ((currTime - tPump - .05) > pumpTime * 60):
tPump = time.time()
timePump = (currTime - startReadTime) / 60
print("pump check at: ", timePump)
tempLog = 0
currLogVolts = []
f = 0
while (f < 8):
print(f)
tempLog = np.log10(currVolts[f]) / logBlankVolts[f]
print(tempLog)
currLogVolts.append(tempLog)
f = f + 1
print("CurrLogVolts: ", currLogVolts)
j = 0
i = 0
iter = 0
currHighVolt = 10
while (iter < 8):
print("iter: ", iter)
currHighVolt = currLogVolts[iter]
if (currHighVolt < setVolt):
count = 0
while (currHighVolt < setVolt):
DAQC2.setDOUTbit(j, i)
DAQC2.setDOUTbit(0, 6)
DAQC2.setDOUTbit(0, 7)
time.sleep(.25)
count = count + 1
avgV = 0
currHighVolt = 0
tVolt = []
tEnd = time.time() + .25
## print("tmie read: ", tEnd)
while (time.time() < tEnd):
tVolt.append(DAQC2.getADC(j, i))
avgV = sum(tVolt) / len(tVolt)
print("avg. volt: ", avgV)
currHighVolt = np.log10(avgV) / logBlankVolts[iter]
print("New currHighVolt: ", currHighVolt)
print(count)
DAQC2.clrDOUTbit(0, 7)
DAQC2.clrDOUTbit(0, 6)
DAQC2.clrDOUTbit(j, i)
iter = iter + 1
i = i + 1
if (i == 6 and j == 0):
j = 1
i = 0
elif (i == 2 and j == 1):
i = 10
print("pump off \n")
currTime = time.time()
elapsedTime = time.time() - startReadTime
morbido1 = volts[:, 0].tolist()
morbido2 = volts[:, 1].tolist()
morbido3 = volts[:, 2].tolist()
morbido4 = volts[:, 3].tolist()
morbido5 = volts[:, 4].tolist()
morbido6 = volts[:, 5].tolist()
morbido7 = volts[:, 6].tolist()
morbido8 = volts[:, 7].tolist()
OD1 = (((np.log10(morbido1) / logBlankVolts[0]) - .71891) /
-2.1235).tolist()
OD2 = (((np.log10(morbido2) / logBlankVolts[1]) - .71891) /
-2.1235).tolist()
OD3 = (((np.log10(morbido3) / logBlankVolts[2]) - .71891) /
-2.1235).tolist()
OD4 = (((np.log10(morbido4) / logBlankVolts[3]) - .71891) /
-2.1235).tolist()
OD5 = (((np.log10(morbido5) / logBlankVolts[4]) - .71891) /
-2.1235).tolist()
OD6 = (((np.log10(morbido6) / logBlankVolts[5]) - .71891) /
-2.1235).tolist()
OD7 = (((np.log10(morbido7) / logBlankVolts[6]) - .71891) /
-2.1235).tolist()
OD8 = (((np.log10(morbido8) / logBlankVolts[7]) - .71891) /
-2.1235).tolist()
df = [
dateTime, readTime, morbido1, morbido2, morbido3, morbido4, morbido5,
morbido6, morbido7, morbido8, OD1, OD2, OD3, OD4, OD5, OD6, OD7, OD8
]
my_df = pd.DataFrame(df)
my_df = my_df.T
global globalDF
globalDF = my_df
csvTitle = datetime.now().strftime('%Y-%m-%d_%H-%M-%S') + '.csv'
my_df.to_csv(csvTitle,
index=True,
header=[
'DateTime', 'Time', 'V1', 'V2', 'V3', 'V4', 'V5', 'V6',
'V7', 'V8', 'OD1', 'OD2', 'OD3', 'OD4', 'OD5', 'OD6',
'OD7', 'OD8'
])
print(my_df)
print()
print("new csv file on Desktop: ", csvTitle)
fig = plt.figure()
ax1 = fig.add_subplot(111)
ax1.scatter(readTime, morbido1, s=10, c='b', marker="s", label='Culture#1')
ax1.scatter(readTime, morbido2, s=10, c='g', marker="o", label='Culture#2')
ax1.scatter(readTime, morbido3, s=10, c='r', marker="^", label='Culture#3')
ax1.scatter(readTime, morbido4, s=10, c='c', marker="p", label='Culture#4')
ax1.scatter(readTime, morbido5, s=10, c='m', marker="D", label='Culture#5')
ax1.scatter(readTime, morbido6, s=10, c='y', marker="v", label='Culture#6')
ax1.scatter(readTime, morbido7, s=10, c='k', marker="h", label='Culture#7')
ax1.scatter(readTime,
morbido8,
s=10,
c='violet',
marker="8",
label='Culture#8')
plt.ylabel('Voltage')
plt.xlabel('Time (min)')
Volttitle = datetime.now().strftime('%Y-%m-%d_%H-%M') + ' Voltage plot'
plt.title(Volttitle)
plt.legend(loc='upper right')
plt.show()
fig = plt.figure()
ax1 = fig.add_subplot(111)
ax1.scatter(readTime, OD1, s=10, c='b', marker="s", label='Culture#1')
ax1.scatter(readTime, OD2, s=10, c='g', marker="o", label='Culture#2')
ax1.scatter(readTime, OD3, s=10, c='r', marker="^", label='Culture#3')
ax1.scatter(readTime, OD4, s=10, c='c', marker="p", label='Culture#4')
ax1.scatter(readTime, OD5, s=10, c='m', marker="D", label='Culture#5')
ax1.scatter(readTime, OD6, s=10, c='y', marker="v", label='Culture#6')
ax1.scatter(readTime, OD7, s=10, c='k', marker="h", label='Culture#7')
ax1.scatter(readTime, OD8, s=10, c='violet', marker="8", label='Culture#8')
plt.ylabel('OD600')
plt.xlabel('Time (min)')
ODtitle = datetime.now().strftime('%Y-%m-%d_%H-%M') + ' OD plot'
plt.title(ODtitle)
plt.legend(loc='upper left')
plt.show()
def sysTest():
print("testing parts")
i = 0
while (i < 1):
print("\n")
print("quit: 0")
print("pumps: 1")
print("valves:2")
print("Photodiodes: 3")
print("lasers: 4")
var = input(": ")
currInput = int(var)
print("current input: ", currInput)
if (currInput == 0):
print(
"turning off pump, closing all valves, turning off lasers, quitting"
)
DAQC2.clrDOUTbit(0, 6) #turn off pump1
DAQC2.clrDOUTbit(1, 6) #turn off pump2
DAQC2.clrDOUTbit(0, 0) #turn off valves
DAQC2.clrDOUTbit(0, 1)
DAQC2.clrDOUTbit(0, 2)
DAQC2.clrDOUTbit(0, 3)
DAQC2.clrDOUTbit(0, 4)
DAQC2.clrDOUTbit(0, 5)
DAQC2.clrDOUTbit(1, 0)
DAQC2.clrDOUTbit(1, 1)
DAQC2.clrDOUTbit(1, 2)
DAQC2.clrDOUTbit(1, 3)
DAQC2.clrDOUTbit(1, 4)
DAQC2.clrDOUTbit(1, 5)
DAQC2.clrDOUTbit(0, 7) #turn off lasers
i = 5
print("quitting")
break
elif (currInput == 1):
print("pumps")
j = 0
while (j < 1):
print("\n")
print("to go back: 0")
print("turn on pump#1: 1")
print("turn on pump#2: 2")
print("turn off pump#1: 3")
print("turn off pump#2: 4")
var = input(": ")
currInput1 = int(var)
print("current input: ", currInput1)
if (currInput1 == 0):
print("back to main test menu")
j = 5
elif (currInput1 == 1):
print("turning on pump#1")
DAQC2.setDOUTbit(0, 6)
elif (currInput1 == 2):
print("turning on pump#2")
DAQC2.setDOUTbit(1, 6)
elif (currInput1 == 3):
print("turning off pump#1")
DAQC2.clrDOUTbit(0, 6)
elif (currInput1 == 4):
print("turning off pump#1")
DAQC2.clrDOUTbit(1, 6)
elif (currInput == 4):
print("Lasers")
j = 0
while (j < 1):
print("\n")
print("turn lasers on: 1")
print("turn lasers off: 2")
print("go back to test menu: 0")
var = input(": ")
currInput2 = int(var)
print("current input: ", currInput2)
if (currInput2 == 0):
print("back to main test menu")
j = 5
elif (currInput2 == 1):
print("lasers on")
DAQC2.setDOUTbit(0, 7)
elif (currInput2 == 2):
print("lasers off")
DAQC2.clrDOUTbit(0, 7)
elif (currInput == 2):
print("Valves")
j = 0
while (j < 1):
print("\n")
print("to go back: 0")
print("to open individual valves: 1-12")
print("to close individual valves 21-32")
print("to open all valves: 13")
print("to close all valves: 14")
var = input(": ")
currInput3 = int(var)
print("current input: ", currInput3)
if (currInput3 == 0):
print("back to main test menu")
j = 5
elif (currInput3 == 13):
print("opening all valves")
DAQC2.setDOUTbit(0, 0) #open all valves
DAQC2.setDOUTbit(0, 1)
DAQC2.setDOUTbit(0, 2)
DAQC2.setDOUTbit(0, 3)
DAQC2.setDOUTbit(0, 4)
DAQC2.setDOUTbit(0, 5)
DAQC2.setDOUTbit(1, 0)
DAQC2.setDOUTbit(1, 1)
DAQC2.setDOUTbit(1, 2)
DAQC2.setDOUTbit(1, 3)
DAQC2.setDOUTbit(1, 4)
DAQC2.setDOUTbit(1, 5)
elif (currInput3 == 14):
print("closing all valves")
DAQC2.clrDOUTbit(0, 0) #close all valves
DAQC2.clrDOUTbit(0, 1)
DAQC2.clrDOUTbit(0, 2)
DAQC2.clrDOUTbit(0, 3)
DAQC2.clrDOUTbit(0, 4)
DAQC2.clrDOUTbit(0, 5)
DAQC2.clrDOUTbit(1, 0)
DAQC2.clrDOUTbit(1, 1)
DAQC2.clrDOUTbit(1, 2)
DAQC2.clrDOUTbit(1, 3)
DAQC2.clrDOUTbit(1, 4)
DAQC2.clrDOUTbit(1, 5)
elif (currInput3 == 1):
print("opening valve #1")
DAQC2.setDOUTbit(0, 0)
elif (currInput3 == 2):
print("opening valve #2")
DAQC2.setDOUTbit(0, 1)
elif (currInput3 == 3):
print("opening valve #3")
DAQC2.setDOUTbit(0, 2)
elif (currInput3 == 4):
print("opening valve #4")
DAQC2.setDOUTbit(0, 3)
elif (currInput3 == 5):
print("opening valve #5")
DAQC2.setDOUTbit(0, 4)
elif (currInput3 == 6):
print("opening valve #6")
DAQC2.setDOUTbit(0, 5)
elif (currInput3 == 7):
print("opening valve #7")
DAQC2.setDOUTbit(1, 0)
elif (currInput3 == 8):
print("opening valve #8")
DAQC2.setDOUTbit(1, 1)
elif (currInput3 == 9):
print("opening valve #9")
DAQC2.setDOUTbit(1, 2)
elif (currInput3 == 10):
print("opening valve #10")
DAQC2.setDOUTbit(1, 3)
elif (currInput3 == 11):
print("opening valve #11")
DAQC2.setDOUTbit(1, 4)
elif (currInput3 == 12):
print("opening valve #12")
DAQC2.setDOUTbit(1, 5)
elif (currInput3 == 21):
print("closing valve #1")
DAQC2.clrDOUTbit(0, 0)
elif (currInput3 == 22):
print("closing valve #2")
DAQC2.clrDOUTbit(0, 1)
elif (currInput3 == 23):
print("closing valve #3")
DAQC2.clrDOUTbit(0, 2)
elif (currInput3 == 24):
print("closing valve #4")
DAQC2.clrDOUTbit(0, 3)
elif (currInput3 == 25):
print("closing valve #5")
DAQC2.clrDOUTbit(0, 4)
elif (currInput3 == 26):
print("closing valve #6")
DAQC2.clrDOUTbit(0, 5)
elif (currInput3 == 27):
print("closing valve #7")
DAQC2.clrDOUTbit(1, 0)
elif (currInput3 == 28):
print("closing valve #8")
DAQC2.clrDOUTbit(1, 1)
elif (currInput3 == 29):
print("closing valve #9")
DAQC2.clrDOUTbit(1, 2)
elif (currInput3 == 30):
print("closing valve #10")
DAQC2.clrDOUTbit(1, 3)
elif (currInput3 == 31):
print("closing valve #11")
DAQC2.clrDOUTbit(1, 4)
elif (currInput3 == 32):
print("closing valve #12")
DAQC2.clrDOUTbit(1, 5)
elif (currInput == 3):
print("Photodiodes")
j = 0
while (j < 1):
print("\n")
print("to go back: 0")
print("to take a reading from a single morbidostat: 1-12")
print("to take a reading from all morbidostats: 13")
var = input(": ")
currInput4 = int(var)
print("current input: ", currInput4)
if (currInput4 == 0):
print("back to main test menu")
j = 5
elif (currInput4 == 13):
print("reading from all morbidostats")
plate1 = DAQC2.getADCall(0)
plate2 = DAQC2.getADCall(1)
j = 0
k = 0
num = 1
while (k < 12):
if (k <= 5):
currVolt = plate1[k]
print(num, ": ", currVolt)
k = k + 1
num = num + 1
elif (k > 5):
a = k - 6
currVolt = plate2[a]
print(num, ": ", currVolt)
k = k + 1
num = num + 1
elif (currInput4 == 1):
currVolt = DAQC2.getADC(0, 0)
print("Morbidostat#1: ", currVolt)
elif (currInput4 == 2):
currVolt = DAQC2.getADC(0, 1)
print("Morbidostat#2: ", currVolt)
elif (currInput4 == 3):
currVolt = DAQC2.getADC(0, 2)
print("Morbidostat#3: ", currVolt)
elif (currInput4 == 4):
currVolt = DAQC2.getADC(0, 3)
print("Morbidostat#4: ", currVolt)
elif (currInput4 == 5):
currVolt = DAQC2.getADC(0, 4)
print("Morbidostat#4: ", currVolt)
elif (currInput4 == 6):
currVolt = DAQC2.getADC(0, 5)
print("Morbidostat#6: ", currVolt)
elif (currInput4 == 7):
currVolt = DAQC2.getADC(1, 0)
print("Morbidostat#7: ", currVolt)
elif (currInput4 == 8):
currVolt = DAQC2.getADC(1, 1)
print("Morbidostat#8: ", currVolt)
elif (currInput4 == 9):
currVolt = DAQC2.getADC(1, 2)
print("Morbidostat#9: ", currVolt)
elif (currInput4 == 10):
currVolt = DAQC2.getADC(1, 3)
print("Morbidostat#10: ", currVolt)
elif (currInput4 == 11):
currVolt = DAQC2.getADC(1, 4)
print("Morbidostat#11: ", currVolt)
elif (currInput4 == 12):
currVolt = DAQC2.getADC(1, 5)
print("Morbidostat#12: ", currVolt)
index = -1
for i in range(photocurrent.size):
if (photocurrent[i] >= 0):
index = i
break
V_s = retarding_voltage[index][0]
print('V_s = {:.4f} V'.format(V_s))
return V_s
### MAIN ###
voltages = np.arange(0, 0.7, 0.001)
np.random.shuffle(voltages)
led_data = np.zeros((voltages.size, 3))
dark_current = 1.3e-03
for i in range(voltages.size):
Vr = voltages[i]
led_data[i, 0] = Vr
DAQC2.setDAC(0, 0, Vr)
Vp = DAQC2.getADC(0, 0) - DAQC2.getADC(0, 1)
led_data[i, 1] = Vp
led_data[i, 2] = dark_current
wavelength = 654.9
led_df = create_LED_df(led_data)
filename = "data/laser_{λ}nm.csv".format(λ=wavelength)
led_df.to_csv(filename, encoding='utf-8', index=False)
plot_LED_data(led_df, np.array(wavelength))
resp['bit'] = bit
resp['state'] = 0
elif (cmd == "toggleDOUTbit"):
bit = args['bit']
try:
DP.toggleDOUTbit(addr, bit)
except AssertionError:
DP2.toggleDOUTbit(addr, bit)
resp['bit'] = bit
resp['state'] = 'UNKNOWN'
elif (cmd == "getADC"):
channel = args['channel']
try:
voltage = DP.getADC(addr, channel)
except AssertionError:
voltage = DP2.getADC(addr, channel)
resp['channel'] = channel
resp['voltage'] = voltage
elif (cmd == "getTEMP"):
bit = args['bit']
scale = args['scale']
try:
temp = DP.getTEMP(addr, bit, scale)
except AssertionError:
temp = DP2.getTEMP(addr, bit, scale)
resp['temp'] = temp
resp['bit'] = bit
else:
sys.stderr.write("unknown daqc cmd: " + cmd)
print(json.dumps(resp))
elif (plate_type == "MOTOR"):
def get_value(self):
return DQ.getADC(self.piid, self.tid)
import piplates.DAQC2plate as DAQC2
import time
DAQC2.setDAC(0, 0, 2.5)
time.sleep(0.25)
AIN = DAQC2.getADC(0, 0)
time.sleep(0.25)
DAQC2.setDAC(0, 0, 0)
print("AIN =", AIN, "volts")
from tsl200 import laser_init
import numpy as np
import time
from matplotlib import pyplot as plt
import piplates.DAQC2plate as DAQC2
from v_to_dbm import v_to_dbm
from tsl_offset import tsl_offset
sleep = 50e-3
my_laser = laser_init()
my_laser.on()
N = 300
wavelength = np.linspace(1530,1600,N)
data = [None]*N
power = [None]*N
my_laser.set_wavelength(1530)
time.sleep(4)
for wn,w in enumerate(wavelength):
my_laser.set_wavelength(w)
time.sleep(sleep)
data[wn] = v_to_dbm(DAQC2.getADC(0,0),w*1e-3)
data[wn] = tsl_offset(data[wn],w)
power[wn] = my_laser.set_power_dBm(0)
print("Data recorded")
plt.figure()
plt.plot(wavelength,data)
plt.show()