def testBpodClass():
from BpodClass import BpodObject
bpodPort = AcademyUtils.findBpodUSBPort()
myBpod = BpodObject(bpodPort)
myBpod.set_subject('DummySubject')
myBpod.disconnect()
return None
def addPoint(valveNum, pulseTime, numPulses):
if numPulses > 200:
print('Max number of pulses is 200; changing numPulses to 200.')
numPulses = 200
#from Bpod_Gen2.Python_3.Modules.BpodClass import BpodObject # Import BpodObject
#from Bpod_Gen2_Python_3.Modules.StateMachineAssembler import stateMachine
#import run_MARFID as rm
pause = 0.3
valveTime = pulseTime / 1000
valveBin = 2**(valveNum - 1)
# Find name of port
portName = AcademyUtils.findBpodUSBPort()
myBpod = BpodObject(portName)
rc = myBpod.set_subject('Calibrator')
rc.currentProtocol = 'Calibrate'
calFolder = myBpod.calibrationFileFolder
calFile = "valve_calibration_%d.json" % valveNum
calPath = os.path.join(calFolder, calFile)
for pulse in range(numPulses):
sma = stateMachine(myBpod)
sma.addState('Name', 'FirstPause', 'Timer', pause,
'StateChangeConditions', ('Tup', 'Pulse'),
'OutputActions', ())
sma.addState('Name', 'Pulse', 'Timer', valveTime,
'StateChangeConditions', ('Tup', 'Pause'),
'OutputActions', ('ValveState', valveBin))
sma.addState('Name', 'Pause', 'Timer', pause, 'StateChangeConditions',
('Tup', 'exit'), 'OutputActions', ())
myBpod.sendStateMachine(sma)
RawEvents = myBpod.runStateMachine()
print('pulse:', pulse + 1)
myBpod.disconnect()
vol = input('How many ml?')
volume = float(vol)
val = truncate(volume / numPulses, 4)
pointDict = {str(float(pulseTime)): val}
return calPath, pointDict
This program is distributed WITHOUT ANY WARRANTY and without even the
implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
'''
import os, sys, time
sys.path.append(
os.path.join(os.path.dirname(__file__)[:-17],
"Modules")) # Add Bpod system files to Python path
# Initializing Bpod
from BpodClass import BpodObject # Import BpodObject
myBpod = BpodObject(
'COM13') # Create a new instance of a Bpod object on serial port COM13
myBpod.manualOverride(
'Output', 'Serial', 1,
65) # Send byte 65 on UART port 1 - by default, this is ASCII 'A'
time.sleep(1) # Wait 1s
myBpod.loadSerialMessage(1, 65, (
66, 67,
68)) # Set byte 65 ('A') on UART port 1 to trigger a 3-byte message: 'BCD'
myBpod.manualOverride('Output', 'Serial', 1,
65) # Now, the same command has a different result
time.sleep(1) # Wait 1s
myBpod.resetSerialMessages(
) # Reset the serial message library. Bytes will now pass through again.
myBpod.manualOverride('Output', 'Serial', 1, 65) # Back to 'A'
This program is distributed WITHOUT ANY WARRANTY and without even the
implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
'''
import os, sys
sys.path.append(os.path.join(os.path.dirname(__file__)[:-22], "Modules")) # Add Bpod system files to Python path
# Initializing Bpod
from BpodClass import BpodObject # Import BpodObject
from StateMachineAssembler import stateMachine # Import state machine assembler
myBpod = BpodObject('COM13') # Create a new instance of a Bpod object on serial port COM13
sma = stateMachine(myBpod) # Create a new state machine (events + outputs tailored for myBpod)
sma.setGlobalTimer('TimerID', 1, 'Duration', 3) # Set global timer 1 for 3 seconds
sma.addState('Name', 'TimerTrig', # Trigger global timer
'Timer', 0,
'StateChangeConditions', ('Tup', 'Port1Lit'),
'OutputActions', ('GlobalTimerTrig', 1))
sma.addState('Name', 'Port1Lit', # Infinite loop (with next state). Only a global timer can save us.
'Timer', .25,
'StateChangeConditions', ('Tup', 'Port3Lit', 'GlobalTimer1_End', 'exit'),
'OutputActions', ('PWM1', 255))
sma.addState('Name', 'Port3Lit',
'Timer', .25,
'StateChangeConditions', ('Tup', 'Port1Lit', 'GlobalTimer1_End', 'exit'),
'OutputActions', ('PWM3', 255))
myBpod.sendStateMachine(sma) # Send state machine description to Bpod device
This program is distributed WITHOUT ANY WARRANTY and without even the
implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
'''
import os, sys
sys.path.append(os.path.join(os.path.dirname(__file__)[:-22], "Modules")) # Add Bpod system files to Python path
from BpodClass import BpodObject # Import BpodObject
from StateMachineAssembler import stateMachine # Import state machine assembler
myBpod = BpodObject('COM13') # Create a new instance of a Bpod object on serial port COM13
sma = stateMachine(myBpod) # Create a new state machine (events + outputs tailored for myBpod)
sma.addState('Name', 'Port1Light', # Add a state
'Timer', 0,
'StateChangeConditions', ('Serial2_3', 'Port2Light'), # Go to Port2Light when byte 0x3 arrives on UART port 2
'OutputActions', ('PWM1', 255))
sma.addState('Name', 'Port2Light',
'Timer', 0,
'StateChangeConditions', ('Tup', 'exit'),
'OutputActions', ('PWM2', 255))
myBpod.sendStateMachine(sma) # Send state machine description to Bpod device
RawEvents = myBpod.runStateMachine() # Run state machine and return events
print RawEvents.__dict__ # Print events to console
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
'''
# Demonstration of AddTrialEvents used in a simple visual 2AFC session.
# AddTrialEvents formats each trial's data in a human-readable struct, and adds to myBpod.data (to save to disk later)
# Connect noseports to ports 1-3.
import os, sys, random
sys.path.append(
os.path.join(os.path.dirname(__file__)[:-17],
"Modules")) # Add Bpod system files to Python path
from BpodClass import BpodObject # Import BpodObject
from StateMachineAssembler import stateMachine # Import state machine assembler
myBpod = BpodObject(
'COM13') # Create a new instance of a Bpod object on serial port COM13
nTrials = 5
trialTypes = [1, 2] # 1 (rewarded left) or 2 (rewarded right)
for i in range(nTrials): # Main loop
print 'Trial: ' + str(i)
thisTrialType = random.choice(trialTypes) # Randomly choose trial type =
if thisTrialType == 1:
stimulus = 'PWM1' # set stimulus channel for trial type 1
leftAction = 'Reward'
rightAction = 'Punish'
rewardValve = 1
elif thisTrialType == 2:
stimulus = 'PWM3' # set stimulus channel for trial type 1
leftAction = 'Punish'
def runProtocol(bpodPort, reportCard):
# Initializing Bpod
from BpodClass import BpodObject # Import BpodObject
from StateMachineAssembler import stateMachine # Import state machine assembler
import random
import datetime
import time
myBpod = BpodObject(bpodPort)
myBpod.set_protocol('ProtocolTemplate')
import numpy as np
d = datetime.date.today()
d.strftime("%b%d_%y")
# Create a new instance of a Bpod object
subject = reportCard.mouseID
myBpod.set_subject(subject)
maxWater = reportCard.maxWater
rewardAmount = 4
timeout = 5
sessionDurationMinutes = 1
LeftPort = int(1)
CenterPort = int(2)
RightPort = int(3)
valveTimes = myBpod.getValveTimes(rewardAmount, [1, 2, 3])
LeftValveTime = valveTimes[0]
RightValveTime = valveTimes[2]
CenterValveTime = valveTimes[1]
LeftLED = 'PWM%d' % LeftPort
CenterLED = 'PWM%d' % CenterPort
RightLED = 'PWM%d' % RightPort
LeftPortBin = 1
CenterPortBin = 2
RightPortBin = 4
trialTypes = []
myBpod.updateSettings({"Reward Amount": rewardAmount,
"Timeout": timeout,
"Session Duration (min)": sessionDurationMinutes})
currentTrial = 0
exitPauseTime = 1
sessionWater = 0
maxWater = reportCard.maxWater
waterToday = reportCard.getWaterToday()
startTime = time.time()
elapsed_time = 0
while elapsed_time < sessionDurationMinutes*60:
sma = stateMachine(myBpod) # Create a new state machine (events + outputs tailored for myBpod)
#choose random decimal between 0 and 1
randomDec = random.random()
if randomDec > 0.5:
trialType = 'Left'
else:
trialType = 'Right'
#update list of trial types to save to file
trialTypes = trialTypes + [trialType]
print('Trial %d, %s' % (currentTrial, trialType))
if trialType == 'Left':
leftCorrect = 'RewardLeft'
rightCorrect = 'Timeout'
displayLED = 'PWM1'
rewardState = 'RewardLeft'
else:
leftCorrect = 'Timeout'
rightCorrect = 'RewardRight'
displayLED = 'PWM3'
rewardState = 'RewardRight'
sma.addState('Name', 'WaitForPoke',
'Timer', 0,
'StateChangeConditions', ('Port1In', leftCorrect, 'Port3In', rightCorrect),
'OutputActions', (displayLED, 200))
sma.addState('Name', 'RewardLeft',
'Timer', LeftValveTime,
'StateChangeConditions', ('Tup', 'ExitPause'),
'OutputActions', ('ValveState', 1))
sma.addState('Name', 'RewardRight',
'Timer', RightValveTime,
'StateChangeConditions', ('Tup', 'ExitPause'),
'OutputActions', ('ValveState', 4))
sma.addState('Name', 'Timeout',
'Timer', timeout,
'StateChangeConditions', ('Tup', 'exit'),
'OutputActions', ())
sma.addState('Name', 'ExitPause',
'Timer', exitPauseTime,
'StateChangeConditions', ('Tup','exit'),
'OutputActions', ())
myBpod.sendStateMachine(sma) # Send state machine description to Bpod device
RawEvents = myBpod.runStateMachine() # Run state machine and return events
myBpod.addTrialEvents(RawEvents)
rawEventsDict = myBpod.structToDict(RawEvents)
#Find reward times to update session water
rewardTimes = getattr(myBpod.data.rawEvents.Trial[currentTrial].States, rewardState)
rewarded = rewardTimes[0][0]>0
#if correct and water rewarded, update water and reset streak
if rewarded:
sessionWater += 0.001*rewardAmount
elapsed_time = time.time()-startTime
currentTrial = currentTrial+1
if sessionWater+waterToday >= maxWater:
print('reached maxWater (%d)' % maxWater)
break
print('Session water:', sessionWater)
myBpod.updateSettings({'Trial Types':trialTypes})
myBpod.saveSessionData()
reportCard.drankWater(sessionWater, myBpod.currentDataFile)
reportCard.save()
# Disconnect Bpod
myBpod.disconnect() # Sends a termination byte and closes the serial port. PulsePal stores current params to its EEPROM.
return myBpod, reportCard
This program is distributed WITHOUT ANY WARRANTY and without even the
implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
'''
import os, sys, time
sys.path.append(
os.path.join(os.path.dirname(__file__)[:-17],
"Modules")) # Add Bpod system files to Python path
# Initializing Bpod
from BpodClass import BpodObject # Import BpodObject
myBpod = BpodObject(
'COM13') # Create a new instance of a Bpod object on serial port COM13
myBpod.manualOverride('Output', 'PWM', 2,
255) # Set LED of port 2 to max intensity
time.sleep(0.25) # Wait 250ms
myBpod.manualOverride('Output', 'PWM', 2,
8) # Set LED of port 2 to lower intensity
time.sleep(0.25) # Wait 250ms
myBpod.manualOverride('Output', 'PWM', 2,
0) # Set LED of port 2 to zero intensity
time.sleep(1) # Wait 1s
myBpod.manualOverride('Output', 'Valve', 1, 1) # Set valve of port 1 to "open"
time.sleep(0.25) # Wait 250ms
myBpod.manualOverride('Output', 'Valve', 1,