def adaptiveIMF(minpoints, r2lim):
#Starts with flush
global interface
devno = 0
ch1 = 16
Popen(["py", "-3", lib_p + os.sep + "Pump.py", "1", "0", "1"])
while True:
print("Flush started: " + time.strftime("%Y-%m-%d %H:%M:%S"))
filehandling.SetperiodStart(int(time.time()), ft)
exp = filehandling.TjekRun()
if not exp: break
filehandling.PrintPeriod("F")
while True:
# # # # # # #check flush dpo2 / dt
pass
# Stop flushing - wait is always nescessary
Popen(["py", "-3", lib_p + os.sep + "Pump.py", "0", "0", "1"])
print("Chamber closed: " + time.strftime("%Y-%m-%d %H:%M:%S"))
filehandling.SetperiodStart(int(time.time()), 30)
filehandling.PrintPeriod("W")
time.sleep(tw)
# # # # # #Start new calculator, pass on minpoints
while True:
# check file for flush command
if dpo2 > setp_dpo2: break # true -> end
#Waiting one second
time.sleep(1)
def ConventionalIMF(tf, tw, tm):
#Experimental control for IMF starting with flush period.
#Having only 1 channel to control the entire setup
global interface
devno = 0
ch1 = 16
exp = True
while exp:
Popen(["py", "-3", lib_p + os.sep + "Pump.py", "1", "0", "1"])
print("Flush started: " + time.strftime("%Y-%m-%d %H:%M:%S"))
filehandling.SetperiodStart(int(time.time()), ft)
exp = filehandling.TjekRun()
if not exp: break
filehandling.PrintPeriod("F")
time.sleep(tf)
Popen(["py", "-3", lib_p + os.sep + "oxygenserver.py"])
Popen(["py", "-3", lib_p + os.sep + "Pump.py", "0", "0", "1"])
print("Waiting period started: " + time.strftime("%Y-%m-%d %H:%M:%S"))
filehandling.SetperiodStart(int(time.time()), wt)
filehandling.PrintPeriod("W")
exp = filehandling.TjekRun()
if not exp: break
time.sleep(tw)
print("Measurement period started: " +
time.strftime("%Y-%m-%d %H:%M:%S"))
filehandling.SetperiodStart(int(time.time()), mt)
filehandling.PrintPeriod("M")
exp = filehandling.TjekRun()
if not exp: break
time.sleep(tm)
Popen(["python", lib_p + os.sep + "Pump.py", "1", "0", "1"])
print("Experiment End")
def closedrespirometry_uhuh(mo2interval):
global interface
devno = 0
ch1 = 16
# Popen(["py","-3", lib_p + os.sep +"pump control"+os.sep+"FlushCle.py"])
Popen(["python", lib_p + os.sep + "Pump.py", "1", "0", "1"])
print("Experiment starting in 60s, time is now " +
time.strftime("%H:%M:%S"))
filehandling.PrintPeriod("W")
time.sleep(60)
# Stop flushing - wait is always nescessary
Popen(["python", lib_p + os.sep + "Pump.py", "0", "0", "1"])
print("Experiment started, time is now " + time.strftime("%H:%M:%S"))
#init calculator and experiment time
filehandling.PrintPeriod("W")
# call calculator
Popen(["python", lib_p + os.sep + "oxygenserver.py"])
filehandling.SetperiodStart(int(time.time()), mo2interval)
#wait one period before starting
time.sleep(mo2interval)
while True:
exp = filehandling.TjekRun()
if not exp: break
#Start measuring
filehandling.PrintPeriod("M")
filehandling.SetperiodStart(int(time.time()), mo2interval)
#wait interval
time.sleep(mo2interval)
#Set status to wait period to stop calculator
filehandling.PrintPeriod("W")
# A little wait period of 5 seconds to avoid using the same sensor values for following mo2 calculations
time.sleep(5)
# call calculator
Popen(["python", lib_p + os.sep + "oxygenserver.py"])
# And another one to be sure
time.sleep(5)
print("Experiment ended: flushing starts")
global interface
devno = 0
ch1 = 16
Popen(["python", lib_p + os.sep + "Pump.py", "1", "0", "1"])
def Slave():
#Aquaresp acting as slave, listens to filehandling.TjekRun() for external setting of FWM status
# Flushy.EmergencyFlush()
exp = True
while exp:
whatperiod = filehandling.TjekPeriod()
exp = filehandling.TjekRun()
if not exp: break
if whatperiod == "W":
print("Wait period started")
# Popen(["python", lib_p + os.sep +"oxygenserver.py"])
exp = filehandling.TjekRun()
if not exp: break
if whatperiod == "M":
print("Measurement period registered")
exp = filehandling.TjekRun()
if not exp: break
print("Experiment End")
def ClosedStartIMF(tf, tw, tm):
#Experimental control for IMF starting with closed periods.
#Having only 1 channel to control the entire setup
global interface
devno = 0
ch1 = 16
# Flushy.EmergencyFlush()
while True:
Popen(["py", "-3", lib_p + os.sep + "oxygenserver.py"])
Popen(["py", "-3", lib_p + os.sep + "Pump.py", "0", "0", "1"])
# Flushy.FlipOff(interface,devno,ch1)
print("Waiting period started: " + time.strftime("%Y-%m-%d %H:%M:%S"))
filehandling.SetperiodStart(int(time.time()), wt)
exp = filehandling.TjekRun()
if not exp: break
filehandling.PrintPeriod("W")
time.sleep(tw)
print("Measurement period started: " +
time.strftime("%Y-%m-%d %H:%M:%S"))
filehandling.SetperiodStart(int(time.time()), mt)
filehandling.PrintPeriod("M")
exp = filehandling.TjekRun()
if not exp: break
time.sleep(tm)
Popen(["py", "-3", lib_p + os.sep + "Pump.py", "1", "0", "1"])
print("Flush started: " + time.strftime("%Y-%m-%d %H:%M:%S"))
filehandling.SetperiodStart(int(time.time()), ft)
exp = filehandling.TjekRun()
if not exp: break
filehandling.PrintPeriod("F")
time.sleep(tf)
def MeasurementPeriod(mainpath):
# fn = oxygenpath + "firesting.txt"
# presentfolder
pf, slopefolder, expfolder = filehandling.presentfolderFunc()
#Datacollection when it is measuring time
measurementperiod1 = []
measurementperiod2 = []
measurementperiod3 = []
measurementperiod4 = []
timesec = []
timeabs = []
timeunix = []
pO2_1, pO2_2, pO2_3, pO2_4, oxtime = ["", "", "", "", ""]
oxtimeold = datetime.datetime.strptime(time.strftime("%H:%M:%S"),
"%H:%M:%S")
unixtime = int(time.time())
unixtime2 = int(time.time())
timestartmeasurement = datetime.datetime.strptime(
time.strftime("%H:%M:%S"), "%H:%M:%S")
timestartmeasurement2 = datetime.datetime.strptime(
time.strftime("%Y-%m-%d %H:%M:%S"), "%Y-%m-%d %H:%M:%S")
datadict = {
1: measurementperiod1,
2: measurementperiod2,
3: measurementperiod3,
4: measurementperiod4
}
print("Start Data Acquisition - MO2")
while 1:
try:
pO2_1, pO2_2, pO2_3, pO2_4, oxtime1 = aqdev.uniformoxygen()
except:
pO2_1, pO2_2, pO2_3, pO2_4, oxtime1 = [
0, 0, 0, 0,
datetime.datetime.strptime(time.strftime("%H:%M:%S"),
"%H:%M:%S")
]
# filehandling.ox2file(pO2_1,pO2_2,pO2_3,pO2_4,oxtime1)
unixtime = int(time.time())
# Standard sampling rate for Aquaresp is .25 second
time.sleep(.25)
po2dict = {1: pO2_1, 2: pO2_2, 3: pO2_3, 4: pO2_4}
try:
oxtime = datetime.datetime.strptime(oxtime1, "%H:%M:%S")
except:
print("Missed a reading.")
dtime = oxtime - oxtimeold
stime = oxtime - timestartmeasurement
if not dtime.total_seconds() == 0:
# samplingrate in aquaresp is to high compared to the oxygenmeter. So if there is no time difference
# between the samples, they are not logged.
for i in range(1, 5):
# inuse, volume, animalmass = filehandling.readrespirometerinfo(i)
# if inuse =="y":
try:
datadict[i].append(float(po2dict[i]))
except ValueError:
datadict[i].append(float(9999))
except:
datadict[i].append(float(9998))
timesec.append(float(stime.total_seconds()))
timeabs.append(oxtime1)
timeunix.append(unixtime)
filehandling.ox2file(pO2_1, pO2_2, pO2_3, pO2_4, oxtime1)
# print("her?",filehandling.TjekPeriod() )
oxtimeold = oxtime
#When measurement period ends
if filehandling.TjekPeriod() != "M": break
#
exp = filehandling.TjekRun()
if not exp: break
#Get measurement period duration
duration = int(time.time()) - unixtime2
#Handle save data, and MO2 Calculation etc
numfiles = len([
name for name in os.listdir(slopefolder)
if os.path.isfile(os.path.join(slopefolder, name))
])
with open(slopefolder + "Cycle_" + str(numfiles + 1) + ".txt", 'w') as f:
f.write(
"Time;Seconds from start for linreg;Unix Time;ch1 po2;ch2 po2;ch3 po2;ch4 po2;\n"
)
for ii, l in enumerate(timesec):
f.write("%s;%s;%s;%s;%s;%s;%s;\n" %
(timeabs[ii], l, timeunix[ii], measurementperiod1[ii],
measurementperiod2[ii], measurementperiod3[ii],
measurementperiod4[ii]))
measurementperiod1 = np.array(measurementperiod1)
measurementperiod2 = np.array(measurementperiod2)
measurementperiod3 = np.array(measurementperiod3)
measurementperiod4 = np.array(measurementperiod4)
datadict = {
1: measurementperiod1,
2: measurementperiod2,
3: measurementperiod3,
4: measurementperiod4
}
timesec = np.array(timesec)
sensor, AD, ExpType, ft, wt, mt, temperature, salinity, o2sol, UNIXtime, Dateime, IsSlave = filehandling.GetExperimentInfo(
)
filehandling.updateLastmo2file(2, "-", "-")
for ik in range(1, 5):
inuse, volume, animalmass = filehandling.readrespirometerinfo(ik)
if inuse == "y":
slope, intercept, rr, p_value, std_err, avgpo2, medianpo2, minpo2, maxpo2 = AA.sloper(
timesec, datadict[ik])
in_hours, in_minutes, in_seconds, in_days = filehandling.GetTimeStartExperiment(
)
MO2, beta, rRespFish, MO2_TOT = AA.mo2maker(
slope, float(temperature), float(salinity), 760,
float(animalmass), float(volume))
print("Respirometer ", str(ik), "MO2: ", str(MO2), " r-squared: ",
str(rr**2))
filehandling.updateLastmo2file(0, MO2, rr**2)
filehandling.MO2Save(timestartmeasurement2, in_hours, unixtime,
MO2, slope, intercept, rr, rr**2, p_value,
std_err, duration, avgpo2, medianpo2, minpo2,
maxpo2, maxpo2 - minpo2, beta, rRespFish,
in_hours, in_minutes, in_seconds, in_days, ik)
filehandling.MO2Save_TOT(timestartmeasurement, in_hours, unixtime,
MO2_TOT, slope, intercept, rr, rr**2,
p_value, ik)
try:
# AquaPlot.fakeJSdatasource()
#Create copy data for data viewer
# Popen(["python", mainpath +os.sep +"lib" + os.sep +"copytoGD.py"])
Popen([
"python", mainpath + os.sep + "lib" + os.sep + "Plotz.py"
])
except:
pass
filehandling.updateLastmo2file(1, "-", "-")
Popen(["python", lib_p + os.sep + "Pump.py", "1", "0", "1"])
def deltaPO2IMF(setp_dpo2, tf):
#Starts with flush
global interface
devno = 0
ch1 = 16
Popen(["py", "-3", lib_p + os.sep + "Pump.py", "1", "0", "1"])
while True:
#Popen(["py","-3", lib_p + os.sep +"pump control"+ os.sep+"FlushCle.py"])
print("Flush started: " + time.strftime("%Y-%m-%d %H:%M:%S"))
filehandling.SetperiodStart(int(time.time()), ft)
exp = filehandling.TjekRun()
if not exp: break
filehandling.PrintPeriod("F")
lf = 0
while lf < int(tf):
time.sleep(1)
if filehandling.FORCEMEASUREMENTEND_REQ(): break
lf += 1
lf = 0
# call calculator
Popen(["py", "-3", lib_p + os.sep + "oxygenserver.py"])
exp = filehandling.TjekRun()
if not exp: break
# Stop flushing
mandatorywait = 60
Popen(["py", "-3", lib_p + os.sep + "Pump.py", "0", "0", "1"])
print("Chamber closed: " + time.strftime("%Y-%m-%d %H:%M:%S"))
filehandling.SetperiodStart(int(time.time()), mandatorywait)
filehandling.PrintPeriod("W")
time.sleep(mandatorywait - 30)
print("Collecting data for start po2 - 30 sek to measurement start")
# read po2 flush for 30 sec
lf = 0
sumpo2 = 0.0
while lf < 30:
# readpo2
# readpo2,readpo22,readpo23,readpo24,oxtime = filehandling.GetLastOxygen()
try:
readpo2, readpo22, readpo23, readpo24, oxtime = aqdev.uniformoxygen(
)
except:
pass
sumpo2 = sumpo2 + float(readpo2)
time.sleep(1)
lf += 1
# get last wait po2 value
po2flush = sumpo2 / 30.0
print("Start pO2: ", po2flush)
print("Flush On at pO2: ", po2flush - setp_dpo2)
exp = filehandling.TjekRun()
if not exp: break
#change to po2 percent
filehandling.SetperiodStart(int(time.time()), mt)
filehandling.PrintPeriod("M")
while True:
# readpo2
try:
po2chamber, readpo22, readpo23, readpo24, oxtime = aqdev.uniformoxygen(
)
except:
pass
#calc dpo2
dpo2 = po2flush - float(po2chamber)
# check if dpo2 > setpoint
if dpo2 > setp_dpo2: break
# true -> end
#Waiting one second
time.sleep(1)
if filehandling.FORCEMEASUREMENTEND_REQ(): break
exp = filehandling.TjekRun()
if not exp: break
filehandling.PrintPeriod("F")