def add_mice(self):
try:
tagreader = TagReader(RFID_serialPort,
RFID_doCheckSum,
timeOutSecs=RFID_timeout,
kind=RFID_kind)
except Exception as e:
raise e
i = 0
print('Scan mice now')
while i < 1:
try:
tag = tagreader.readTag()
i += 1
print(tag)
except ValueError as e:
print(str(e))
tagreader.clearBuffer()
SPT_lvl = input('Enter SPT level for new mouse:')
SPT_Spout = input('Enter initial SPT spout for new mouse (R/L):')
temp = {tag: {'SPT_Pattern': SPT_Spout, 'SPT_level': int(SPT_lvl)}}
self.mice_config.update(temp)
values1 = [tag, timestamp, weight_float, 0, 'N', Cage]
cur1.execute(insert_statment, values)
else:
with open(record_filename, 'r') as csv1:
reader = csv.reader(csv1)
reader1 = list(reader)
Baseline_Weight = float(reader1[1][2])
not_valu = round((float(weight_float) - Baseline_Weight) /
Baseline_Weight * 100, 1)
print(str(not_valu))
if (float(weight_float) -
Baseline_Weight) / Baseline_Weight * 100 < -15.0:
CO = 'Y'
print('Mouse Underweight, Need supplment water')
else:
CO = 'N'
values = [
tag, timestamp, weight_float,
round((float(weight_float) - Baseline_Weight) /
Baseline_Weight * 100, 1), CO, Cage
]
with open(record_filename, "a") as file:
file.write(timestamp + "," + str(tag) + "," +
str(weight_float) + ',' + str(not_valu) + '%' +
',' + CO + ',' + Cage + "\n")
cur1.execute(insert_statment, values)
except ValueError as e:
print(str(e))
tagReader.clearBuffer()
print('Read ' + ' tags')
def htloop (cageSet, tagReader, headFixer, stimulator, expSettings):
"""
Presents a menu asking user to choose a bit of hardware to test, and runs the tests
If a test fails, a dialog is presented asking user to change the pin setup. The modified pinout
can be saved, overwriting the configuration in ./AHF_Config.jsn
Commands are:
t= tagReader: trys to read a tag and, if successful, monitors Tag in Range Pin until tag goes away
r = reward solenoid: Opens the reward solenoid for a 1 second duration, then closes it
c = contact check: Monitors the head contact pin until contact, and then while contact is maintained
f = head Fixer
e = Entry beam break
p = pistons solenoid: Energizes the pistons for a 2 second duration, and then de-energizes them
l = LED: Turns on the brain illumination LED for a 2 second duration, then off
h = sHow config settings: Prints out the current pinout in the AHF_CageSet object
v = saVe modified config file: Saves the the AHF_CageSet object to the file ./AHF_Config.jsn
q = quit: quits the program
"""
if cageSet.contactPolarity == 'RISING':
contactEdge = GPIO.RISING
noContactEdge = GPIO.FALLING
contactState = GPIO.HIGH
noContactState = GPIO.LOW
else:
contactEdge = GPIO.FALLING
noContactEdge = GPIO.RISING
contactState = GPIO.LOW
noContactState = GPIO.HIGH
try:
while (True):
inputStr = input ('t=tagReader, r=reward solenoid, c=contact check, e= entry beam break, f=head Fixer, l=LED, s=stimulator tester, h=sHow config, v= saVe config, q=quit:')
if inputStr == 't': # t for tagreader
if tagReader == None:
cageSet.serialPort = input ('First, set the tag reader serial port:')
try:
tagReader = TagReader (cageSet.serialPort, True)
inputStr = input ('Do you want to read a tag now?')
if inputStr[0] == 'n' or inputStr[0] == "N":
continue
except IOError as anError:
print ('Try setting the serial port again.')
tagReader = None
if tagReader is not None:
try:
if (tagReader.serialPort.inWaiting() < 16):
print ('No data in serial buffer')
tagError = True
else:
tagID = tagReader.readTag()
tagError = False
except (IOError, ValueError) as anError:
tagError = True
if tagError == True:
print ('Serial Port Tag-Read Error\n')
tagReader.clearBuffer()
inputStr = input ('Do you want to change the tag reader serial port (currently ' + cageSet.serialPort + ')?')
if inputStr == 'y' or inputStr == "Y":
cageSet.serialPort = input ('Enter New Serial Port:')
# remake tagReader and open serial port
tagReader = TagReader (cageSet.serialPort, True)
else:
print ("Tag ID =", tagID)
# now check Tag-In-Range pin function
if (GPIO.input (cageSet.tirPin)== GPIO.LOW):
print ('Tag was never registered as being "in range"')
tagError = True
else:
startTime = time()
GPIO.wait_for_edge (cageSet.tirPin, GPIO.FALLING, timeout= 10000)
if (time () > startTime + 10.0):
print ('Tag stayed in range for over 10 seconds')
tagError = True
else:
print ('Tag no longer in range')
tagError = False
if (tagError == True):
inputStr = input ('Do you want to change the tag-in-range Pin (currently ' + str (cageSet.tirPin) + ')?')
if inputStr[0] == 'y' or inputStr[0] == "Y":
cageSet.tirPin = int (input('Enter New tag-in-range Pin:'))
GPIO.setup (cageSet.tirPin, GPIO.IN)
elif inputStr == 'r': # r for reward solenoid
print ('Reward Solenoid opening for 3 sec')
GPIO.output(cageSet.rewardPin, 1)
sleep(3.0)
GPIO.output(cageSet.rewardPin, 0)
inputStr= input('Reward Solenoid closed.\nDo you want to change the Reward Solenoid Pin (currently ' + str (cageSet.rewardPin) + ')?')
if inputStr[0] == 'y' or inputStr[0] == "Y":
cageSet.rewardPin = int (input('Enter New Reward Solenoid Pin:' ))
GPIO.setup (cageSet.rewardPin, GPIO.OUT, initial=GPIO.LOW)
elif inputStr == 'c': #c for contact on head fix
if GPIO.input (cageSet.contactPin)== contactState:
print ('Contact pin already indicates contact.')
err=True
else:
GPIO.wait_for_edge (cageSet.contactPin, contactEdge, 100)
if GPIO.input (cageSet.contactPin)== noContactState:
print ('No Contact after 10 seconds.')
err = True
else:
print ('Contact Made.')
GPIO.wait_for_edge (cageSet.contactPin, noContactEdge, 100)
if GPIO.input (cageSet.contactPin)== contactState:
print ('Contact maintained for 10 seconds.')
err = True
else:
print ('Contact Broken')
err = False
if err == True:
inputStr= input ('Do you want to change Contact settings (currently pin=' + str (cageSet.contactPin) + ', polarity=' + str(cageSet.contactPolarity) + ', pull up/down =' + str (cageSet.contactPUD) + ')?')
if inputStr[0] == 'y' or inputStr[0] == "Y":
cageSet.contactPin= int (input ('Enter the GPIO pin connected to the headbar contacts or IR beam-breaker:'))
contactInt = int (input ('Enter the contact polarity, 0=FALLING for IR beam-breaker or falling polarity electrical contacts, 1=RISING for rising polarity elctrical contacts:'))
if contactInt == 0:
cageSet.contactPolarity = 'FALLING'
else:
cageSet.contactPolarity = 'RISING'
contactInt = int (input('Enter desired resistor on contact pin, 0=OFF if external resistor present, else 1=DOWN if rising polarity electrical contact or 2 = UP if IR beam-breaker or falling polarity electrical contacts:'))
if contactInt ==0:
cageSet.contactPUD = 'OFF'
elif contactInt == 1:
cageSet.contactPUD = 'DOWN'
else:
cageSet.contactPUD='UP'
GPIO.setup (cageSet.contactPin, GPIO.IN, pull_up_down=getattr (GPIO, "PUD_" + cageSet.contactPUD))
if cageSet.contactPolarity =='RISING':
contactEdge = GPIO.RISING
noContactEdge = GPIO.FALLING
contactState = GPIO.HIGH
noContactState = GPIO.LOW
else:
contactEdge = GPIO.FALLING
noContactEdge = GPIO.RISING
contactState = GPIO.LOW
noContactState = GPIO.HIGH
elif inputStr == 'e': # beam break at enty
if GPIO.input (cageSet.entryBBpin)== GPIO.LOW:
print ('Entry beam break is already broken')
err=True
else:
GPIO.wait_for_edge (cageSet.entryBBpin, GPIO.FALLING, timeout= 10000)
if GPIO.input (cageSet.entryBBpin)== GPIO.HIGH:
print ('Entry beam not broken after 10 seconds.')
err = True
else:
print ('Entry Beam Broken.')
GPIO.wait_for_edge (cageSet.entryBBpin, GPIO.RISING, timeout= 10000)
if GPIO.input (cageSet.entryBBpin)== GPIO.LOW:
print ('Entry Beam Broken maintained for 10 seconds.')
err = True
else:
print ('Entry Beam Intact Again.')
err = False
if err == True:
inputStr= input ('Do you want to change the Entry Beam Break Pin (currently pin=' + str (cageSet.entryBBpin)+ '?')
if inputStr[0] == 'y' or inputStr[0] == "Y":
cageSet.entryBBpin= int (input ('Enter the GPIO pin connected to the tube entry IR beam-breaker:'))
GPIO.setup (cageSet.entryBBpin, GPIO.IN, pull_up_down=GPIO.PUD_UP)
elif inputStr == 'f': # head Fixer, run test from headFixer class
headFixer.test(cageSet)
elif inputStr == 'l': # l for LED trigger
print ('LED turning ON for 2 seconds.')
GPIO.output(cageSet.ledPin, 1)
sleep (2)
GPIO.output(cageSet.ledPin, 0)
inputStr=input ('LED turned OFF\nDo you want to change the LED Pin (currently ' + str(cageSet.ledPin) + ')?')
if inputStr == 'y' or inputStr == "Y":
cageSet.ledPin = int (input('Enter New LED Pin:'))
GPIO.setup (cageSet.ledPin, GPIO.OUT, initial = GPIO.LOW)
elif inputStr == 's':
for i,j in enumerate(expSettings.stimulator):
print('\t'+str(i)+': '+str(j))
inputStr = input ('Which stimulator tester would you like to run?')
try:
stimulator[int(inputStr)].tester(expSettings)
except:
print('Input is not a valid number!')
elif inputStr == 'h':
cageSet.show()
elif inputStr=='v':
cageSet.save()
elif inputStr == 'q':
break
except KeyboardInterrupt:
print ("quitting.")
finally:
if __name__ == '__main__':
GPIO.cleanup() # this ensures a clean exit
def main():
"""
The main function for the AutoHeadFix program.
It initializes or loads settings and configurations, then endlessly loops running entries and head fix trials
Ctrl-C is used to enter a menu-driven mode where settings can be altered.
"""
try:
# load general settings for this cage, mostly hardware pinouts
# things not expected to change often - there is only one AHFconfig.jsn file, in the enclosing folder
cageSettings = AHF_CageSet()
#print (cageSettings)
# get settings that may vary by experiment, including rewarder, camera parameters, and stimulator
# More than one of these files can exist, and the user needs to choose one or make one
# we will add some other variables to expSettings so we can pass them as a single argument to functions
# logFP, statsFP, dateStr, dayFolderPath, doHeadFix,
# configFile can be specified if launched from command line, eg, sudo python3 myconfig or sudo python3 AHFexp_myconfig.jsn
configFile = None
if argv.__len__() > 1:
configFile = argv[1]
expSettings = AHF_Settings(configFile)
# nextDay starts tomorrow at KDAYSTARTHOUR
#nextDay = (int((time() - timezone)/KSECSPERDAY) + 1) * KSECSPERDAY + timezone + (KDAYSTARTHOUR * KSECSPERHOUR)
nextDay = ((int(
(time() - timezone + localtime().tm_isdst * 3600) / KSECSPERDAY)) *
KSECSPERDAY) + timezone - (localtime().tm_isdst * 3600
) + KSECSPERDAY + KDAYSTARTHOUR
# Create folders where the files for today will be stored
makeDayFolderPath(expSettings, cageSettings)
# initialize mice with zero mice
mice = Mice()
# make daily Log files and quick stats file
makeLogFile(expSettings, cageSettings)
makeQuickStatsFile(expSettings, cageSettings, mice)
#Generate h5 file to store mouse-individual data
makeH5File(expSettings, cageSettings, mice)
updateStats(expSettings.statsFP, mice)
backup_H5(expSettings, cageSettings)
# set up the GPIO pins for each for their respective functionalities.
GPIO.setmode(GPIO.BCM)
GPIO.setwarnings(False)
GPIO.setup(cageSettings.ledPin, GPIO.OUT,
initial=GPIO.LOW) # turns on brain illumination LED
GPIO.setup(cageSettings.led2Pin, GPIO.OUT,
initial=GPIO.LOW) # turns on masking stim LED2
GPIO.setup(cageSettings.tirPin,
GPIO.IN) # Tag-in-range output from RFID tag reader
GPIO.setup(cageSettings.contactPin,
GPIO.IN,
pull_up_down=getattr(GPIO,
"PUD_" + cageSettings.contactPUD))
if cageSettings.contactPolarity == 'RISING':
expSettings.contactEdge = GPIO.RISING
expSettings.noContactEdge = GPIO.FALLING
expSettings.contactState = GPIO.HIGH
expSettings.noContactState = GPIO.LOW
else:
expSettings.contactEdge = GPIO.FALLING
expSettings.noContactEdge = GPIO.RISING
expSettings.contactState = GPIO.LOW
expSettings.noContactState = GPIO.HIGH
# make head fixer - does its own GPIO initialization from info in cageSettings
headFixer = AHF_HeadFixer.get_class(
cageSettings.headFixer)(cageSettings)
# make a rewarder
rewarder = AHF_Rewarder(30e-03, cageSettings.rewardPin)
rewarder.addToDict('entrance', expSettings.entranceRewardTime)
rewarder.addToDict('task', expSettings.taskRewardTime)
# make a notifier object
if expSettings.hasTextMsg == True:
notifier = AHF_Notifier(cageSettings.cageID, expSettings.phoneList)
else:
notifier = None
# make RFID reader
tagReader = TagReader(cageSettings.serialPort, False, None)
# configure camera
camera = AHF_Camera(expSettings.camParamsDict)
# make UDP Trigger
if expSettings.hasUDP == True:
UDPTrigger = AHF_UDPTrig(expSettings.UDPList)
print(UDPTrigger)
else:
UDPTrigger = None
# make a lick detector
simpleLogger = Simple_Logger(expSettings.logFP)
lickDetector = AHF_LickDetector((0, 1), 26, simpleLogger)
sleep(1)
lickDetector.start_logging()
# make stimulator(s)
stimulator = [
AHF_Stimulator.get_class(i)(cageSettings, expSettings, rewarder,
lickDetector, camera)
for i in expSettings.stimulator
]
#Stimdict is chosen from the first stimulator
expSettings.stimDict = stimulator[0].configDict
# Entry beam breaker
if cageSettings.hasEntryBB == True:
GPIO.setup(cageSettings.entryBBpin,
GPIO.IN,
pull_up_down=GPIO.PUD_UP)
GPIO.add_event_detect(cageSettings.entryBBpin, GPIO.BOTH,
entryBBCallback)
#GPIO.add_event_callback (cageSettings.entryBBpin, entryBBCallback)
gTubePanicTime = time() + 25920000 # a month from now.
gTubeMaxTime = expSettings.inChamberTimeLimit
except Exception as anError:
print('Unexpected error starting AutoHeadFix:', str(anError))
raise anError
exit(0)
try:
print('Waiting for a mouse...')
while True: #start main loop
try:
# wait for mouse entry, with occasional timeout to catch keyboard interrupt
GPIO.wait_for_edge(
cageSettings.tirPin, GPIO.RISING, timeout=kTIMEOUTmS
) # wait for entry based on Tag-in-range pin
if (GPIO.input(cageSettings.tirPin) == GPIO.HIGH):
try:
tag = tagReader.readTag()
except (IOError, ValueError):
tagReader.clearBuffer()
continue
entryTime = time()
if cageSettings.hasEntryBB == True:
GPIO.remove_event_detect(cageSettings.entryBBpin)
thisMouse = mice.getMouseFromTag(tag)
if thisMouse is None:
# try to open mouse config file to initialize mouse data
thisMouse = Mouse(tag, 1, 0, 0, 0, 0, 0)
mice.addMouse(thisMouse, expSettings.statsFP)
writeToLogFile(expSettings.logFP, thisMouse, 'entry')
thisMouse.entries += 1
# if we have entrance reward, first wait for entrance reward or first head-fix, which countermands entry reward
if thisMouse.entranceRewards < expSettings.maxEntryRewards:
giveEntranceReward = True
expSettings.doHeadFix = expSettings.propHeadFix > random(
)
while GPIO.input(
cageSettings.tirPin) == GPIO.HIGH and time(
) < (entryTime + expSettings.entryRewardDelay):
GPIO.wait_for_edge(cageSettings.contactPin,
expSettings.contactEdge,
timeout=kTIMEOUTmS)
if (GPIO.input(cageSettings.contactPin) ==
expSettings.contactState):
runTrial(thisMouse, expSettings, cageSettings,
rewarder, headFixer,
stimulator[thisMouse.stimType],
UDPTrigger)
giveEntranceReward = False
break
if (GPIO.input(cageSettings.tirPin)
== GPIO.HIGH) and giveEntranceReward == True:
thisMouse.reward(
rewarder, 'entrance'
) # entrance reward was not countermanded by an early headfix
writeToLogFile(expSettings.logFP, thisMouse,
'entryReward')
# wait for contacts and run trials till mouse exits or time in chamber exceeded
expSettings.doHeadFix = expSettings.propHeadFix > random()
while GPIO.input(
cageSettings.tirPin) == GPIO.HIGH and time(
) < entryTime + expSettings.inChamberTimeLimit:
if (GPIO.input(cageSettings.contactPin) ==
expSettings.noContactState):
GPIO.wait_for_edge(cageSettings.contactPin,
expSettings.contactEdge,
timeout=kTIMEOUTmS)
if (GPIO.input(cageSettings.contactPin) ==
expSettings.contactState):
runTrial(thisMouse, expSettings, cageSettings,
rewarder, headFixer,
stimulator[thisMouse.stimType],
UDPTrigger)
expSettings.doHeadFix = expSettings.propHeadFix > random(
) # set doHeadFix for next contact
# either mouse left the chamber or has been in chamber too long
if GPIO.input(cageSettings.tirPin) == GPIO.HIGH and time(
) > entryTime + expSettings.inChamberTimeLimit:
# explictly turn off pistons, though they should be off at end of trial
headFixer.releaseMouse()
if expSettings.hasTextMsg == True:
notifier.notify(thisMouse.tag,
(time() - entryTime), True)
# wait for mouse to leave chamber, with no timeout, unless it left while we did last 3 lines
if GPIO.input(cageSettings.tirPin) == GPIO.HIGH:
GPIO.wait_for_edge(cageSettings.tirPin,
GPIO.FALLING)
if expSettings.hasTextMsg == True:
notifier.notify(thisMouse.tag,
(time() - entryTime), False)
tagReader.clearBuffer()
if cageSettings.hasEntryBB == True:
#GPIO.setup (cageSettings.entryBBpin, GPIO.IN, pull_up_down = GPIO.PUD_UP)
GPIO.add_event_detect(cageSettings.entryBBpin,
GPIO.BOTH, entryBBCallback)
# after exit, update stats
writeToLogFile(expSettings.logFP, thisMouse, 'exit')
updateH5File(expSettings, cageSettings, mice, stimulator)
updateStats(expSettings.statsFP, mice, thisMouse)
# after each exit check for a new day
if time() > nextDay:
# stop lick logging so we dont write to file when it is closed
lickDetector.stop_logging()
mice.show()
writeToLogFile(expSettings.logFP, None, 'SeshEnd')
expSettings.logFP.close()
expSettings.statsFP.close()
makeDayFolderPath(expSettings, cageSettings)
makeLogFile(expSettings, cageSettings)
simpleLogger.logFP = expSettings.logFP
makeQuickStatsFile(expSettings, cageSettings, mice)
for i in stimulator:
i.nextDay(expSettings.logFP)
nextDay += KSECSPERDAY
mice.clear()
updateH5File(expSettings, cageSettings, mice,
stimulator)
updateStats(expSettings.statsFP, mice)
backup_H5(expSettings, cageSettings)
# reinitialize lick detector because it can lock up if too many licks when not logging
lickDetector.__init__((0, 1), 26, simpleLogger)
lickDetector.start_logging()
print('Waiting for a mouse...')
else:
# check for entry beam break while idling between trials
if cageSettings.hasEntryBB == True and time(
) > gTubePanicTime:
print(
'Some one has been in the entrance of this tube for too long'
)
# explictly turn off pistons, though they should be off
headFixer.releaseMouse()
BBentryTime = gTubePanicTime - gTubeMaxTime
if expSettings.hasTextMsg == True:
notifier.notify(
0, (time() - BBentryTime), True
) # we don't have an RFID for this mouse, so use 0
# wait for mouse to leave chamber
while time() > gTubePanicTime:
sleep(kTIMEOUTmS / 1000)
print(
'looks like some one managed to escape the entrance of this tube'
)
if expSettings.hasTextMsg == True:
notifier.notify(0, (time() - BBentryTime), False)
except KeyboardInterrupt:
GPIO.output(cageSettings.ledPin, GPIO.LOW)
headFixer.releaseMouse()
GPIO.output(cageSettings.rewardPin, GPIO.LOW)
lickDetector.stop_logging()
if cageSettings.hasEntryBB == True:
sleep(1)
GPIO.remove_event_detect(cageSettings.entryBBpin)
print('removed BB event detect')
while True:
event = input(
'Enter:\nr to return to head fix trials\nq to quit\nv to run valve control\nh for hardware tester\nm for mice inspection\nc for camera configuration\ne for experiment configuration\n:'
)
if event == 'r' or event == "R":
lickDetector.start_logging()
sleep(1)
if cageSettings.hasEntryBB == True:
sleep(1)
print('Restarting entry bb')
GPIO.setup(cageSettings.entryBBpin,
GPIO.IN,
pull_up_down=GPIO.PUD_UP)
GPIO.add_event_detect(cageSettings.entryBBpin,
GPIO.BOTH, entryBBCallback)
break
elif event == 'q' or event == 'Q':
exit(0)
elif event == 'v' or event == "V":
valveControl(cageSettings)
elif event == 'h' or event == 'H':
hardwareTester(cageSettings, tagReader, headFixer,
stimulator, expSettings)
if cageSettings.contactPolarity == 'RISING':
expSettings.contactEdge = GPIO.RISING
expSettings.noContactEdge = GPIO.FALLING
expSettings.contactState = GPIO.HIGH
expSettings.noContactState = GPIO.LOW
else:
expSettings.contactEdge = GPIO.FALLING
expSettings.noContactEdge = GPIO.RISING
expSettings.contactState = GPIO.LOW
expSettings.noContactState = GPIO.HIGH
elif event == 'm' or event == 'M':
mice.show()
for i, j in enumerate(expSettings.stimulator):
print('\t' + str(i) + ': ' + str(j))
inputStr = input(
'Which stimulator-specific inspection method would you like to run?'
)
try:
stimulator[int(inputStr)].inspect_mice(
mice, cageSettings, expSettings)
except:
print("Stimulator doesn't exist.")
updateH5File(expSettings, cageSettings, mice,
stimulator)
elif event == 'c' or event == 'C':
camParams = camera.adjust_config_from_user()
elif event == 'e' or event == 'E':
modCode = expSettings.edit_from_user()
if modCode >= 2:
stimulator[modCode - 2] = AHF_Stimulator.get_class(
expSettings.stimulator[modCode - 2])(
cageSettings, expSettings.stimDict,
rewarder, lickDetector, expSettings.logFP,
camera)
if modCode & 1:
for stim in stimulator:
stim.change_config(expSettings.stimDict)
except Exception as anError:
print('AutoHeadFix error:' + str(anError))
raise anError
finally:
for stim in stimulator:
stim.quitting()
GPIO.output(cageSettings.ledPin, False)
headFixer.releaseMouse()
GPIO.output(cageSettings.rewardPin, False)
GPIO.cleanup()
writeToLogFile(expSettings.logFP, None, 'SeshEnd')
expSettings.logFP.close()
expSettings.statsFP.close()
camera.close()
print('AutoHeadFix Stopped')