class BpodObject(object):
def __init__(self, serialPortName):
self.initTime = datetime.datetime.now()
self.connectTime = 0
self.sentDateTime = 0
self.serialObject = 0
self.firmwareVersion = 0
self.currentFirmwareVersion = 16
self.machineType = 0
self.HW = Struct()
self.HW.n = Struct()
self.HW.Pos = Struct()
self.data = Struct()
self.softCodeMod = None
self.HW.inputsEnabled = 0
self.eventNames = ()
self.stateMachineInfo = Struct()
self.stateMachineInfo.Pos = Struct()
self.stateMachineInfo.nEvents = 0
self.stateMachineInfo.eventNames = ()
self.stateMachineInfo.inputChannelNames = ()
self.stateMachineInfo.nOutputChannels = 0
self.stateMachineInfo.outputChannelNames = ()
self.calibrationFileFolder = AcademyUtils.getCalibrationDir()
self.subject = 'DummySubject'
self.protocol = ''
self.protocolFolder = ''
self.date = datetime.date.today().strftime("%b%d_%y")
self.dataFolder = AcademyUtils.getDataDir()
if not os.path.exists(self.dataFolder):
os.mkdir(self.dataFolder)
self.remoteDataFolder = "C:\Data"
self.currentDataFolder = os.path.join(self.dataFolder, self.subject,
self.protocol, 'Session Data')
self.session = 1
self.currentDataFile = '%s_%s_%s_Session%d.json' % (
self.subject, self.protocol, self.date, self.session)
self.stateMachine = Struct()
self.modules = Struct()
self.status = Struct()
self.settings = {}
self.syncConfig = [
255, 1
] # [Channel,Mode] 255 = no sync, otherwise set to a hardware channel number. Mode 0 = flip logic every trial, 1 = every state
self.connect(serialPortName)
self.getModuleInfo()
self.setup()
def updateSettings(self, data):
self.settings.update(data)
def updateCurrentDataFile(self):
dataFile = '%s_%s_%s_Session%d.json' % (self.subject, self.protocol,
self.date, self.session)
self.currentDataFile = dataFile
return dataFile
def updateCurrentDataFolder(self):
df = os.path.join(self.dataFolder, self.subject, self.protocol,
'Session Data')
self.currentDataFolder = df
if not os.path.exists(df):
os.makedirs(df)
return self.currentDataFolder
def updateSession(self):
oldSession = os.path.exists(
os.path.join(self.currentDataFolder, self.currentDataFile))
while oldSession:
self.session = self.session + 1
dataFile = self.updateCurrentDataFile()
oldSession = os.path.exists(
os.path.join(self.currentDataFolder, dataFile))
def set_subject(self, subStr):
self.subject = subStr
self.updateCurrentDataFolder()
self.updateCurrentDataFile()
self.updateSession()
from ReportCardClass import ReportCard
rc = ReportCard(self.subject)
self.protocol = rc.currentProtocol
print('Subject: ', self.subject, '\nDate: ', self.date, '\nSession: ',
self.session)
return rc
def set_protocol(self, protStr):
self.protocol = protStr
self.updateCurrentDataFolder()
self.updateCurrentDataFile()
protocolFolder = importlib.import_module(protStr, package=None)
try:
softCodeHandlerStr = "SoftCodeHandler_" + self.protocol
self.softCodeMod = importlib.import_module(softCodeHandlerStr,
package=protStr)
except Exception as e:
self.disconnect()
print(e)
raise ImportError("SoftCodeHandler_%s.py not found." %
self.protocol)
try:
self.softCodeHandler = self.softCodeMod.SoftCodeHandler()
except ImportError as e:
raise BpodError(e)
def structToDict(self, st):
import BpodClass
d = st.__dict__
for key, val in d.items():
if isinstance(val, BpodClass.Struct):
d.update({key: self.structToDict(val)})
elif isinstance(val, list):
if isinstance(val[0], BpodClass.Struct):
newIter = [{} for x in range(len(val))]
for i, item in enumerate(val):
newIter[i].update({key: self.structToDict(item)})
d.update({key: newIter})
return d
def saveSessionData(self):
dataFolder = self.currentDataFolder
self.updateCurrentDataFolder()
self.updateCurrentDataFile()
if not os.path.exists(self.currentDataFolder):
os.mkdir(self.currentDataFolder)
print("current data folder: %s" % self.currentDataFolder)
print("current data file: %s" % self.currentDataFile)
fullPath = os.path.join(self.currentDataFolder, self.currentDataFile)
dataDict = self.structToDict(self.data)
dataDict.update({'Settings': self.settings})
with open(fullPath, 'a+') as f:
f.write(
json.dumps(dataDict,
sort_keys=True,
indent=2,
separators=(',', ': '),
default=AcademyUtils.json_serial))
f.write('\n')
return fullPath
def connect(self, serialPortName):
from ArCOM import ArCOMObject # Import ArCOMObject
self.serialObject = ArCOMObject(
serialPortName,
115200) # Create a new instance of an ArCOM serial port's
#self.resetSerialMessages()
#self.serialObject.resetSerial()
self.connectTime = datetime.datetime.now()
self.serialObject.write('6', 'char') # Test connectivity
OK = self.serialObject.read(1, 'char') # Receive response
if OK != '5':
raise BpodError(
'Error: Bpod failed to confirm connectivity. Please reset Bpod and try again.'
)
# Get firmware version
self.serialObject.write(ord('F'), 'uint8') # Request firmware version
self.firmwareVersion = self.serialObject.read(1, 'uint16')
self.machineType = self.serialObject.read(1, 'uint16')
if self.firmwareVersion < self.currentFirmwareVersion:
raise BpodError(
'Error: Old firmware detected. Please update state machine firmware and try again.'
)
elif self.firmwareVersion > self.currentFirmwareVersion:
raise BpodError(
'Error: Future firmware detected. Please update the Bpod python software.'
)
# Get state machine hardware description
self.serialObject.write(ord('H'), 'uint8')
maxStates = self.serialObject.read(1, 'uint16')
self.HW.cyclePeriod = self.serialObject.read(1, 'uint16')
self.HW.cycleFrequency = 1000000 / self.HW.cyclePeriod
self.HW.n.MaxSerialEvents = self.serialObject.read(1, 'uint8')
self.HW.n.GlobalTimers = self.serialObject.read(1, 'uint8')
self.HW.n.GlobalCounters = self.serialObject.read(1, 'uint8')
self.HW.n.Conditions = self.serialObject.read(1, 'uint8')
self.HW.n.Inputs = self.serialObject.read(1, 'uint8')
self.HW.Inputs = self.serialObject.read(self.HW.n.Inputs, 'char')
self.HW.n.Outputs = self.serialObject.read(1, 'uint8')
self.HW.Outputs = self.serialObject.read(self.HW.n.Outputs,
'char') + 'GGG'
self.status.newStateMachineSent = 0
self.stateMachineInfo.nOutputChannels = self.HW.n.Outputs + 3
self.stateMachineInfo.maxStates = maxStates
self.HW.n.UARTSerialChannels = 0
for i in range(self.HW.n.Inputs):
if self.HW.Inputs[i] == 'U':
self.HW.n.UARTSerialChannels += 1
# Set input channel enable/disable
self.HW.inputsEnabled = [0] * self.HW.n.Inputs
PortsFound = 0
for i in range(self.HW.n.Inputs):
if self.HW.Inputs[i] == 'B':
self.HW.inputsEnabled[i] = 1
elif self.HW.Inputs[i] == 'W':
self.HW.inputsEnabled[i] = 1
if PortsFound == 0 and self.HW.Inputs[
i] == 'P': # Enable ports 1-3 by default
PortsFound = 1
self.HW.inputsEnabled[i] = 1
self.HW.inputsEnabled[i + 1] = 1
self.HW.inputsEnabled[i + 2] = 1
self.serialObject.write([ord('E')] + self.HW.inputsEnabled, 'uint8')
Confirmed = self.serialObject.read(1, 'uint8')
if (not Confirmed):
raise BpodError('Error: Failed to enable Bpod inputs.')
# Set sync channel config
self.serialObject.write([ord('K')] + self.syncConfig, 'uint8')
Confirmed = self.serialObject.read(1, 'uint8')
if (not Confirmed):
raise BpodError('Error: Failed to configure Sync channel.')
def getModuleInfo(self):
# Get module info
nModules = 0
for i in range(self.HW.n.Inputs):
if self.HW.Inputs[i] == 'U':
nModules += 1
self.modules.nModules = nModules
# Get self-descriptions from modules
self.modules.connected = np.array([0] * nModules)
self.modules.name = [''] * nModules
self.modules.firmwareVersion = [0] * nModules
self.modules.nSerialEvents = [0] * nModules
for i in range(nModules):
self.modules.nSerialEvents[i] = int(self.HW.n.MaxSerialEvents /
(nModules + 1))
self.modules.eventNames = []
for i in range(nModules):
self.modules.eventNames.append([])
self.modules.relayActive = np.array([0] * nModules)
self.serialObject.write(ord('M'), 'uint8')
time.sleep(0.1)
moduleEventsRequested = np.array([0] * nModules)
messageLength = self.serialObject.bytesAvailable()
if messageLength > 1:
for i in range(nModules):
self.modules.connected[i] = self.serialObject.read(1, 'uint8')
if (self.modules.connected[i] == 1):
self.modules.firmwareVersion[i] = self.serialObject.read(
1, 'uint32')
nameLength = self.serialObject.read(1, 'uint8')
nameString = self.serialObject.read(nameLength, 'char')
sameModuleCount = 1
for j in range(nModules):
thisModuleName = self.modules.name[j]
if thisModuleName[:-1] == nameString:
sameModuleCount += 1
self.modules.name[i] = nameString + str(sameModuleCount)
moreInfoFollows = self.serialObject.read(1, 'uint8')
if moreInfoFollows == 1:
while moreInfoFollows == 1:
paramType = self.serialObject.read(1, 'uint8')
if paramType == ord('#'):
moduleEventsRequested[
i] = self.serialObject.read(1, 'uint8')
elif paramType == ord('E'):
nEventNames = self.serialObject.read(
1, 'uint8')
for j in range(nEventNames):
nCharInThisString = self.serialObject.read(
1, 'uint8')
thisEventName = self.serialObject.read(
nCharInThisString, 'char')
self.modules.eventNames[i].append(
thisEventName)
moreInfoFollows = self.serialObject.read(
1, 'uint8')
nEventsRequested = moduleEventsRequested.sum()
nUSBSerialEvents = int(self.HW.n.MaxSerialEvents / (nModules + 1))
if nEventsRequested + nUSBSerialEvents > self.HW.n.MaxSerialEvents:
raise BpodError(
'Error: Connected modules requested too many events.')
for i in range(nModules):
if self.modules.connected[i] == 1:
if moduleEventsRequested[i] > self.modules.nSerialEvents[i]:
nToReassign = moduleEventsRequested[
i] - self.modules.nSerialEvents[i]
self.modules.nSerialEvents[i] = moduleEventsRequested[
i] # Assign events
else:
nToReassign = 0
Pos = nModules - 1
while nToReassign > 0:
if (self.modules.nSerialEvents[Pos] >
0) and (self.modules.connected[Pos] == 0):
if self.modules.nSerialEvents[Pos] >= nToReassign:
self.modules.nSerialEvents[
Pos] = self.modules.nSerialEvents[
Pos] - nToReassign
nToReassign = 0
else:
nToReassign = nToReassign - self.modules.nSerialEvents[
Pos]
self.modules.nSerialEvents[Pos] = 0
Pos -= 1
self.HW.n.SoftCodes = self.HW.n.MaxSerialEvents - sum(
self.modules.nSerialEvents)
self.serialObject.write([ord('%')] + self.modules.nSerialEvents +
[self.HW.n.SoftCodes], 'uint8')
Confirmed = self.serialObject.read(1, 'uint8')
if (not Confirmed):
raise BpodError(
'Error: Failed to configure module event assignment.')
def setup(self):
# Generate event and input channel names
inputChannelNames = ()
eventNames = ()
Pos = 0
nUSB = 0
nUART = 0
nBNCs = 0
nWires = 0
nPorts = 0
for i in range(self.HW.n.Inputs):
if self.HW.Inputs[i] == 'U':
nUART += 1
moduleName = 'Serial' + str(nUART)
if self.modules.connected[nUART - 1] == 1:
moduleName = self.modules.name[nUART - 1]
inputChannelNames += (moduleName, )
else:
inputChannelNames += ('Serial' + str(nUART), )
nModuleEventNames = len(self.modules.eventNames[nUART - 1])
for j in range(self.modules.nSerialEvents[nUART - 1]):
if j < nModuleEventNames:
eventNames += (moduleName + '_' +
self.modules.eventNames[nUART - 1][j], )
else:
eventNames += (moduleName + '_' + str(j + 1), )
Pos += 1
elif self.HW.Inputs[i] == 'X':
if nUSB == 0:
self.HW.Pos.Event_USB = Pos
nUSB += 1
inputChannelNames += ('USB' + str(nUSB), )
for j in range(
int(self.HW.n.MaxSerialEvents /
(self.modules.nModules + 1))):
eventNames += ('SoftCode' + str(j + 1), )
Pos += 1
elif self.HW.Inputs[i] == 'P':
if nPorts == 0:
self.HW.Pos.Event_Port = Pos
nPorts += 1
inputChannelNames += ('Port' + str(nPorts), )
eventNames += (inputChannelNames[-1] + 'In', )
Pos += 1
eventNames += (inputChannelNames[-1] + 'Out', )
Pos += 1
elif self.HW.Inputs[i] == 'B':
if nBNCs == 0:
self.HW.Pos.Event_BNC = Pos
nBNCs += 1
inputChannelNames += ('BNC' + str(nBNCs), )
eventNames += (inputChannelNames[-1] + 'In', )
Pos += 1
eventNames += (inputChannelNames[-1] + 'Out', )
Pos += 1
elif self.HW.Inputs[i] == 'W':
if nWires == 0:
self.HW.Pos.Event_Wire = Pos
nWires += 1
inputChannelNames += ('Wire' + str(nWires), )
eventNames += (inputChannelNames[-1] + 'In', )
Pos += 1
eventNames += (inputChannelNames[-1] + 'Out', )
Pos += 1
self.stateMachineInfo.Pos.globalTimerStart = Pos
for i in range(self.HW.n.GlobalTimers):
eventNames += ('GlobalTimer' + str(i + 1) + '_Start', )
Pos += 1
self.stateMachineInfo.Pos.globalTimerEnd = Pos
for i in range(self.HW.n.GlobalTimers):
eventNames += ('GlobalTimer' + str(i + 1) + '_End', )
Pos += 1
self.stateMachineInfo.Pos.globalCounter = Pos
for i in range(self.HW.n.GlobalCounters):
eventNames += ('GlobalCounter' + str(i + 1) + '_End', )
Pos += 1
self.stateMachineInfo.Pos.condition = Pos
for i in range(self.HW.n.Conditions):
eventNames += ('Condition' + str(i + 1), )
Pos += 1
self.stateMachineInfo.Pos.jump = Pos
for i in range(self.HW.n.UARTSerialChannels):
eventNames += ('Serial' + str(i + 1) + 'Jump', )
Pos += 1
eventNames += ('SoftJump', )
Pos += 1
eventNames += ('Tup', )
self.stateMachineInfo.Pos.Tup = Pos
Pos += 1
self.stateMachineInfo.inputChannelNames = inputChannelNames
self.stateMachineInfo.eventNames = eventNames
self.stateMachineInfo.nEvents = Pos
# Generate output channel names
outputChannelNames = ()
Pos = 0
nUSB = 0
nUART = 0
nSPI = 0
nBNCs = 0
nWires = 0
nPorts = 0
for i in range(self.HW.n.Outputs):
if self.HW.Outputs[i] == 'U':
nUART += 1
outputChannelNames += ('Serial' + str(nUART), )
Pos += 1
if self.HW.Outputs[i] == 'X':
if nUSB == 0:
self.HW.Pos.output_USB = Pos
nUSB += 1
outputChannelNames += ('SoftCode', )
Pos += 1
if self.HW.Outputs[i] == 'S':
if nSPI == 0:
self.HW.Pos.output_SPI = Pos
nSPI += 1
outputChannelNames += (
'ValveState',
) # Assume an SPI shift register mapping bits of a byte to 8 valves
Pos += 1
if self.HW.Outputs[i] == 'B':
if nBNCs == 0:
self.HW.Pos.output_BNC = Pos
nBNCs += 1
outputChannelNames += (
'BNC' + str(nBNCs),
) # Assume an SPI shift register mapping bits of a byte to 8 valves
Pos += 1
if self.HW.Outputs[i] == 'W':
if nWires == 0:
self.HW.Pos.output_Wire = Pos
nWires += 1
outputChannelNames += (
'Wire' + str(nWires),
) # Assume an SPI shift register mapping bits of a byte to 8 valves
Pos += 1
if self.HW.Outputs[i] == 'P':
if nPorts == 0:
self.HW.Pos.output_PWM = Pos
nPorts += 1
outputChannelNames += (
'PWM' + str(nPorts),
) # Assume an SPI shift register mapping bits of a byte to 8 valves
Pos += 1
outputChannelNames += ('GlobalTimerTrig', )
Pos += 1
outputChannelNames += ('GlobalTimerCancel', )
Pos += 1
outputChannelNames += ('GlobalCounterReset', )
Pos += 1
self.stateMachineInfo.outputChannelNames = outputChannelNames
self.stateMachineInfo.nOutputChannels = Pos
# try importing softcode module
def refreshModules(self):
self.getModuleInfo()
self.setup()
def startModuleRelay(self, moduleID):
if isinstance(moduleID, str):
if moduleID in self.modules.name:
moduleID = self.modules.name.index(moduleID)
else:
raise BpodError('Error: Module' + moduleID + 'not found')
else:
moduleID = moduleID - 1
if self.modules.relayActive.sum() == 0:
if moduleID <= self.modules.nModules:
self.serialObject.write([ord('J'), moduleID, 1], 'uint8')
self.modules.relayActive[moduleID] = 1
else:
raise BpodError('Error: Module' + self.modules.name[moduleID] +
'not found')
else:
raise BpodError(
'Error: You must disable the active module relay before starting another one.'
)
def stopModuleRelay(self):
for i in range(self.modules.nModules):
self.serialObject.write([ord('J'), i, 0], 'uint8')
self.modules.relayActive[i] = 0
time.sleep(0.1)
if self.serialObject.bytesAvailable() > 0:
self.serialObject.read(self.serialObject.bytesAvailable(), 'uint8')
def moduleWrite(self, moduleID, message, *args):
if isinstance(moduleID, str):
if moduleID in self.modules.name:
moduleID = self.modules.name.index(moduleID) + 1
else:
raise BpodError('Error: Module' + moduleID + 'not found')
else:
moduleID = moduleID
if isinstance(message, int):
message = [message]
nValues = len(message)
dataType = 'uint8'
if len(args) > 0:
dataType = args[0]
if dataType == 'uint8':
nBytes = nValues
elif dataType == 'uint16':
nBytes = nValues * 2
elif dataType == 'uint32':
nBytes = nValues * 4
elif dataType == 'int8':
nBytes = nValues
elif dataType == 'int16':
nBytes = nValues * 2
elif dataType == 'int32':
nBytes = nValues * 4
elif dataType == 'char':
nBytes = nValues
else:
raise BpodError(
'Error: datatype must be one of: uint8 uint16 uint32 int8 int16 int32'
)
if nBytes > 64:
raise BpodError(
'Error: module messages must be under 64 bytes per transmission'
)
self.serialObject.write([ord('T'), moduleID, nBytes], 'uint8', message,
dataType)
def moduleRead(self, moduleID, nValues, *args):
if isinstance(moduleID, str):
if moduleID in self.modules.name:
moduleID = self.modules.name.index(moduleID) + 1
else:
raise BpodError('Error: Module' + moduleID + 'not found')
else:
moduleID = moduleID
if not self.modules.relayActive[moduleID - 1]:
raise BpodError(
'Error: you must start the module relay with startModuleRelay() before you can read bytes from a module'
)
dataType = 'uint8'
if len(args) > 0:
dataType = args[0]
return self.serialObject.read(nValues, dataType)
def sendStateMachine(self, sma):
# Replace undeclared states (at the time they were referenced) with actual state numbers
for i in range(len(sma.undeclared)):
undeclaredStateNumber = i + 10000
thisStateNumber = sma.manifest.index(sma.undeclared[i])
for j in range(sma.nStates):
if sma.stateTimerMatrix[j] == undeclaredStateNumber:
sma.stateTimerMatrix[j] = thisStateNumber
inputTransitions = sma.inputMatrix[j]
for k in range(0, len(inputTransitions)):
thisTransition = inputTransitions[k]
if thisTransition[1] == undeclaredStateNumber:
inputTransitions[k] = (thisTransition[0],
thisStateNumber)
sma.inputMatrix[j] = inputTransitions
inputTransitions = sma.globalTimers.startMatrix[j]
for k in range(0, len(inputTransitions)):
thisTransition = inputTransitions[k]
if thisTransition[1] == undeclaredStateNumber:
inputTransitions[k] = (thisTransition[0],
thisStateNumber)
sma.globalTimers.startMatrix[j] = inputTransitions
inputTransitions = sma.globalTimers.endMatrix[j]
for k in range(0, len(inputTransitions)):
thisTransition = inputTransitions[k]
if thisTransition[1] == undeclaredStateNumber:
inputTransitions[k] = (thisTransition[0],
thisStateNumber)
sma.globalTimers.endMatrix[j] = inputTransitions
inputTransitions = sma.globalCounters.matrix[j]
for k in range(0, len(inputTransitions)):
thisTransition = inputTransitions[k]
if thisTransition[1] == undeclaredStateNumber:
inputTransitions[k] = (thisTransition[0],
thisStateNumber)
sma.globalCounters.matrix[j] = inputTransitions
inputTransitions = sma.conditions.matrix[j]
for k in range(0, len(inputTransitions)):
thisTransition = inputTransitions[k]
if thisTransition[1] == undeclaredStateNumber:
inputTransitions[k] = (thisTransition[0],
thisStateNumber)
sma.conditions.matrix[j] = inputTransitions
# Check to make sure all states in manifest exist
if len(sma.manifest) > sma.nStates:
raise BpodError(
'Error: Could not send state machine - some states were referenced by name, but not subsequently declared.'
)
Message = ()
Message += (sma.nStates, )
for i in range(
sma.nStates): # Send state timer transitions (for all states)
if math.isnan(sma.stateTimerMatrix[i]):
Message += (sma.nStates, )
else:
Message += (sma.stateTimerMatrix[i], )
for i in range(
sma.nStates
): # Send event-triggered transitions (where they are different from default)
currentStateTransitions = sma.inputMatrix[i]
nTransitions = len(currentStateTransitions)
Message += (nTransitions, )
for j in range(nTransitions):
thisTransition = currentStateTransitions[j]
Message += (thisTransition[0], )
destinationState = thisTransition[1]
if math.isnan(destinationState):
Message += (sma.nStates, )
else:
Message += (destinationState, )
for i in range(
sma.nStates
): # Send hardware states (where they are different from default)
currentHardwareState = sma.outputMatrix[i]
nDifferences = len(currentHardwareState)
Message += (nDifferences, )
for j in range(nDifferences):
thisHardwareConfig = currentHardwareState[j]
Message += (thisHardwareConfig[0], )
Message += (thisHardwareConfig[1], )
for i in range(
sma.nStates
): # Send global timer-start triggered transitions (where they are different from default)
currentStateTransitions = sma.globalTimers.startMatrix[i]
nTransitions = len(currentStateTransitions)
Message += (nTransitions, )
for j in range(nTransitions):
thisTransition = currentStateTransitions[j]
Message += (thisTransition[0] -
self.stateMachineInfo.Pos.globalTimerStart, )
destinationState = thisTransition[1]
if math.isnan(destinationState):
Message += (sma.nStates, )
else:
Message += (destinationState, )
for i in range(
sma.nStates
): # Send global timer-end triggered transitions (where they are different from default)
currentStateTransitions = sma.globalTimers.endMatrix[i]
nTransitions = len(currentStateTransitions)
Message += (nTransitions, )
for j in range(nTransitions):
thisTransition = currentStateTransitions[j]
Message += (thisTransition[0] -
self.stateMachineInfo.Pos.globalTimerEnd, )
destinationState = thisTransition[1]
if math.isnan(destinationState):
Message += (sma.nStates, )
else:
Message += (destinationState, )
for i in range(
sma.nStates
): # Send global counter triggered transitions (where they are different from default)
currentStateTransitions = sma.globalCounters.matrix[i]
nTransitions = len(currentStateTransitions)
Message += (nTransitions, )
for j in range(nTransitions):
thisTransition = currentStateTransitions[j]
Message += (thisTransition[0] -
self.stateMachineInfo.Pos.globalCounter, )
destinationState = thisTransition[1]
if math.isnan(destinationState):
Message += (sma.nStates, )
else:
Message += (destinationState, )
for i in range(
sma.nStates
): # Send condition triggered transitions (where they are different from default)
currentStateTransitions = sma.conditions.matrix[i]
nTransitions = len(currentStateTransitions)
Message += (nTransitions, )
for j in range(nTransitions):
thisTransition = currentStateTransitions[j]
Message += (thisTransition[0] -
self.stateMachineInfo.Pos.condition, )
destinationState = thisTransition[1]
if math.isnan(destinationState):
Message += (sma.nStates, )
else:
Message += (destinationState, )
for i in range(self.HW.n.GlobalTimers):
Message += (sma.globalTimers.channels[i], )
for i in range(self.HW.n.GlobalTimers):
Message += (sma.globalTimers.onMessages[i], )
for i in range(self.HW.n.GlobalTimers):
Message += (sma.globalTimers.offMessages[i], )
for i in range(self.HW.n.GlobalTimers):
Message += (sma.globalTimers.loopMode[i], )
for i in range(self.HW.n.GlobalTimers):
Message += (sma.globalTimers.sendEvents[i], )
for i in range(self.HW.n.GlobalCounters):
Message += (sma.globalCounters.attachedEvents[i], )
for i in range(self.HW.n.Conditions):
Message += (sma.conditions.channels[i], )
for i in range(self.HW.n.Conditions):
Message += (sma.conditions.values[i], )
sma.stateTimers = sma.stateTimers[:sma.nStates]
ThirtyTwoBitMessage = [
i * self.HW.cycleFrequency for i in sma.stateTimers
] + [i * self.HW.cycleFrequency for i in sma.globalTimers.timers] + [
i * self.HW.cycleFrequency for i in sma.globalTimers.onsetDelays
] + [
i * self.HW.cycleFrequency for i in sma.globalTimers.loopIntervals
] + sma.globalCounters.thresholds
nSMbytes = len(Message) + (len(ThirtyTwoBitMessage)) * 4
sentDateTime = datetime.datetime.now()
self.sentDateTime = datetime.datetime.now()
self.serialObject.write(ord('C'), 'uint8', nSMbytes, 'uint16', Message,
'uint8', ThirtyTwoBitMessage, 'uint32')
self.stateMachine = sma
self.status.newStateMachineSent = 1
def runStateMachine(self):
self.stateMachineStartTime = datetime.datetime.now()
RawEvents = Struct()
eventPos = 0
currentState = 0
StateChangeIndexes = []
RawEvents.Events = []
RawEvents.EventTimestamps = []
RawEvents.States = [currentState]
RawEvents.StateTimestamps = [0]
RawEvents.TrialStartTimestamp = 0
self.serialObject.write(ord('R'), 'uint8')
if self.status.newStateMachineSent == 1:
confirmed = self.serialObject.read(1, 'uint8')
if not confirmed:
raise BpodError(
'Error: The last state machine sent was not acknowledged by the Bpod device.'
)
self.status.newStateMachineSent = 0
runningStateMachine = True
while runningStateMachine:
if self.serialObject.bytesAvailable() > 0:
opCodeBytes = self.serialObject.read(2, 'uint8')
opCode = opCodeBytes[0]
if opCode == 1: # Read events
nCurrentEvents = opCodeBytes[1]
CurrentEvents = self.serialObject.read(
nCurrentEvents, 'uint8')
if nCurrentEvents == 1:
CurrentEvents = [CurrentEvents]
TransitionEventFound = False
for i in range(nCurrentEvents):
thisEvent = CurrentEvents[i]
if thisEvent == 255:
runningStateMachine = False
else:
RawEvents.Events.append(thisEvent)
if not TransitionEventFound:
thisStateTransitions = self.stateMachine.inputMatrix[
currentState]
nTransitions = len(thisStateTransitions)
for j in range(nTransitions):
thisTransition = thisStateTransitions[j]
if thisTransition[0] == thisEvent:
currentState = thisTransition[1]
if not math.isnan(currentState):
RawEvents.States.append(
currentState)
StateChangeIndexes.append(
len(RawEvents.Events) - 1)
TransitionEventFound = True
if not TransitionEventFound:
thisStateTimerTransition = self.stateMachine.stateTimerMatrix[
currentState]
if thisEvent == self.stateMachineInfo.Pos.Tup:
if not (thisStateTimerTransition
== currentState):
currentState = thisStateTimerTransition
if not math.isnan(currentState):
RawEvents.States.append(
currentState)
StateChangeIndexes.append(
len(RawEvents.Events) - 1)
TransitionEventFound = True
if not TransitionEventFound:
thisGlobalTimerTransitions = self.stateMachine.globalTimers.startMatrix[
currentState]
nTransitions = len(thisGlobalTimerTransitions)
for j in range(nTransitions):
thisTransition = thisGlobalTimerTransitions[
j]
if thisTransition[0] == thisEvent:
currentState = thisTransition[1]
if not math.isnan(currentState):
RawEvents.States.append(
currentState)
StateChangeIndexes.append(
len(RawEvents.Events) - 1)
TransitionEventFound = True
if not TransitionEventFound:
thisGlobalTimerTransitions = self.stateMachine.globalTimers.endMatrix[
currentState]
nTransitions = len(thisGlobalTimerTransitions)
for j in range(nTransitions):
thisTransition = thisGlobalTimerTransitions[
j]
if thisTransition[0] == thisEvent:
currentState = thisTransition[1]
if not math.isnan(currentState):
RawEvents.States.append(
currentState)
StateChangeIndexes.append(
len(RawEvents.Events) - 1)
TransitionEventFound = True
elif opCode == 2: # Handle soft code
SoftCode = opCodeBytes[1]
self.softCodeHandler.handleSoftCode(SoftCode)
RawEvents.TrialStartTimestamp = float(
self.serialObject.read(
1, 'uint32')) / 1000 # Start-time of the trial in milliseconds
RawEvents.TrialSentTimestamp = self.sentDateTime.timestamp(
) # Start-time of the trial in milliseconds
nTimeStamps = self.serialObject.read(1, 'uint16')
TimeStamps = self.serialObject.read(nTimeStamps, 'uint32')
if nTimeStamps == 1:
TimeStamps = (TimeStamps, )
RawEvents.EventTimestamps = [
i / float(self.HW.cycleFrequency) for i in TimeStamps
]
for i in range(len(StateChangeIndexes)):
RawEvents.StateTimestamps.append(
RawEvents.EventTimestamps[StateChangeIndexes[i]])
RawEvents.StateTimestamps.append(RawEvents.EventTimestamps[-1])
return RawEvents
def addTrialEvents(self, RawEvents):
if not hasattr(self.data, 'nTrials'):
self.data.nTrials = 0
self.data.info = Struct()
self.data.info.BpodFirmwareVersion = self.firmwareVersion
self.data.sessionDateTime = self.connectTime
self.data.sessionStartTime = str(self.connectTime)
self.data.trialStartTimestamp = []
self.data.trialSentTimestamp = []
self.data.rawData = []
self.data.rawEvents = Struct()
self.data.rawEvents.Trial = []
self.data.rawEvents.Trial.append(Struct())
self.data.rawEvents.Trial[self.data.nTrials].Events = Struct()
self.data.rawEvents.Trial[self.data.nTrials].States = Struct()
self.data.trialStartTimestamp.append(RawEvents.TrialStartTimestamp)
self.data.trialSentTimestamp.append(RawEvents.TrialSentTimestamp)
self.data.rawData.append(RawEvents)
states = RawEvents.States
events = RawEvents.Events
nStates = len(states)
nEvents = len(events)
nPossibleStates = self.stateMachine.nStates
visitedStates = [0] * nPossibleStates
# determine unique states while preserving visited order
uniqueStates = []
nUniqueStates = 0
uniqueStateIndexes = [0] * nStates
for i in range(nStates):
if states[i] in uniqueStates:
uniqueStateIndexes[i] = uniqueStates.index(states[i])
else:
uniqueStateIndexes[i] = nUniqueStates
nUniqueStates += 1
uniqueStates.append(states[i])
visitedStates[states[i]] = 1
uniqueStateDataMatrices = [[] for i in range(nStates)]
# Create a 2-d matrix for each state in a list
for i in range(nStates):
uniqueStateDataMatrices[uniqueStateIndexes[i]] += [
(RawEvents.StateTimestamps[i],
RawEvents.StateTimestamps[i + 1])
]
# Append one matrix for each unique state
for i in range(nUniqueStates):
thisStateName = self.stateMachine.stateNames[uniqueStates[i]]
setattr(self.data.rawEvents.Trial[self.data.nTrials].States,
thisStateName, uniqueStateDataMatrices[i])
for i in range(nPossibleStates):
thisStateName = self.stateMachine.stateNames[i]
if not visitedStates[i]:
setattr(self.data.rawEvents.Trial[self.data.nTrials].States,
thisStateName, [(float('NaN'), float('NaN'))])
for i in range(nEvents):
thisEvent = events[i]
thisEventName = self.stateMachineInfo.eventNames[thisEvent]
thisEventIndexes = [
j for j, k in enumerate(events) if k == thisEvent
]
thisEventTimestamps = []
for i in thisEventIndexes:
thisEventTimestamps.append(RawEvents.EventTimestamps[i])
setattr(self.data.rawEvents.Trial[self.data.nTrials].Events,
thisEventName, thisEventTimestamps)
self.data.nTrials += 1
def manualOverride(self, channelType, channelName, channelNumber, value):
if channelType.lower() == 'input':
raise BpodError(
'Manually overriding a Bpod input channel is not yet supported in Python.'
)
elif channelType.lower() == 'output':
if channelName == 'Valve':
if value > 0:
value = math.pow(2, channelNumber - 1)
channelNumber = self.HW.Pos.output_SPI
byteString = (ord('O'), channelNumber, value)
elif channelName == 'Serial':
byteString = (ord('U'), channelNumber, value)
else:
try:
channelNumber = self.stateMachineInfo.outputChannelNames.index(
channelName + str(channelNumber))
byteString = (ord('O'), channelNumber, value)
except:
raise BpodError('Error using manualOverride: ' +
channelName +
' is not a valid channel name.')
self.serialObject.write(byteString, 'uint8')
else:
raise BpodError(
'Error using manualOverride: first argument must be "Input" or "Output".'
)
def loadSerialMessage(self, serialChannel, messageID, message):
nMessages = 1
messageLength = len(message)
if messageLength > 3:
raise BpodError(
'Error: Serial messages cannot be more than 3 bytes in length.'
)
if (messageID > 255) or (messageID < 1):
raise BpodError(
'Error: Bpod can only store 255 serial messages (indexed 1-255).'
)
ByteString = (ord('L'), serialChannel - 1, nMessages, messageID,
messageLength) + message
print(ByteString)
self.serialObject.write(ByteString, 'uint8')
Confirmed = self.serialObject.read(1, 'uint8')
if (not Confirmed):
raise BpodError('Error: Failed to set serial message.')
def resetSerialMessages(self):
self.serialObject.write(ord('>'), 'uint8')
Confirmed = self.serialObject.read(1, 'uint8')
if (not Confirmed):
raise BpodError('Error: Failed to reset serial message library.')
def getValveTimes(self, rewardAmount, targetValves):
times = [0 for valve in targetValves]
for i, valve in enumerate(targetValves):
filename = os.path.join(self.calibrationFileFolder,
'valve_calibration_%d.json' % valve)
try:
with open(filename, 'r') as f:
s = f.read()
d = json.loads(s)
except FileNotFoundError:
raise BpodError('Error: valve calibration file not found.')
#calibration point values string to float
invcoeffs = [float(c) for c in d["invcoeffs"]]
p = np.poly1d(invcoeffs)
times[i] = np.polyval(p, rewardAmount) / 1000
return times
def disconnect(self):
self.serialObject.write(ord('Z'), 'uint8')
self.serialObject.close()
class BpodObject(object):
def __init__(self, serialPortName):
self.serialObject = 0
self.firmwareVersion = 0
self.HW = Struct()
self.HW.n = Struct()
self.HW.Pos = Struct()
self.data = Struct()
self.HW.inputsEnabled = 0
self.eventNames = ()
self.stateMachineInfo = Struct()
self.stateMachineInfo.Pos = Struct()
self.stateMachineInfo.nEvents = 0
self.stateMachineInfo.eventNames = ()
self.stateMachineInfo.inputChannelNames = ()
self.stateMachineInfo.nOutputChannels = 0
self.stateMachineInfo.outputChannelNames = ()
self.stateMachine = Struct()
self.status = Struct()
self.syncConfig = [
255, 1
] # [Channel,Mode] 255 = no sync, otherwise set to a hardware channel number. Mode 0 = flip logic every trial, 1 = every state
self.connect(serialPortName)
self.setup()
def connect(self, serialPortName):
from ArCOM import ArCOMObject # Import ArCOMObject
self.serialObject = ArCOMObject(
serialPortName,
115200) # Create a new instance of an ArCOM serial port
self.serialObject.write('6', 'char') # Test connectivity
OK = self.serialObject.read('char') # Receive response
if (OK != '5'):
raise BpodError(
'Error: Bpod failed to confirm connectivity. Please reset Bpod and try again.'
)
self.serialObject.write(ord('F'), 'uint8') # Request firmware version
self.firmwareVersion = self.serialObject.read('uint32')
if (self.firmwareVersion < 8):
raise BpodError(
'Error: Old firmware detected. Please update Bpod 0.7+ firmware and try again.'
)
# Get hardware description
self.serialObject.write(ord('H'), 'uint8')
maxStates = self.serialObject.read('uint16')
self.HW.cyclePeriod = self.serialObject.read('uint16')
self.HW.cycleFrequency = 1000000 / self.HW.cyclePeriod
self.HW.n.EventsPerSerialChannel = self.serialObject.read('uint8')
self.HW.n.GlobalTimers = self.serialObject.read('uint8')
self.HW.n.GlobalCounters = self.serialObject.read('uint8')
self.HW.n.Conditions = self.serialObject.read('uint8')
self.HW.n.Inputs = self.serialObject.read('uint8')
self.HW.Inputs = self.serialObject.readArray(self.HW.n.Inputs, 'char')
self.HW.n.Outputs = self.serialObject.read('uint8')
self.HW.Outputs = self.serialObject.readArray(self.HW.n.Outputs,
'char') + 'GGG'
self.status.newStateMachineSent = 0
self.stateMachineInfo.nOutputChannels = self.HW.n.Outputs + 3
self.stateMachineInfo.maxStates = maxStates
self.HW.n.UARTSerialChannels = 0
for i in range(self.HW.n.Inputs):
if self.HW.Inputs[i] == 'U':
self.HW.n.UARTSerialChannels += 1
# Set input channel enable/disable
self.HW.inputsEnabled = [0] * self.HW.n.Inputs
PortsFound = 0
for i in range(self.HW.n.Inputs):
if self.HW.Inputs[i] == 'B':
self.HW.inputsEnabled[i] = 1
elif self.HW.Inputs[i] == 'W':
self.HW.inputsEnabled[i] = 1
if PortsFound == 0 and self.HW.Inputs[
i] == 'P': # Enable ports 1-3 by default
PortsFound = 1
self.HW.inputsEnabled[i] = 1
self.HW.inputsEnabled[i + 1] = 1
self.HW.inputsEnabled[i + 2] = 1
self.serialObject.write([ord('E')] + self.HW.inputsEnabled, 'uint8')
Confirmed = self.serialObject.read('uint8')
if (not Confirmed):
raise BpodError('Error: Failed to enable Bpod inputs.')
# Set sync channel config
self.serialObject.write([ord('K')] + self.syncConfig, 'uint8')
Confirmed = self.serialObject.read('uint8')
if (not Confirmed):
raise BpodError('Error: Failed to configure Sync channel.')
def setup(self):
# Generate event and input channel names
inputChannelNames = ()
eventNames = ()
Pos = 0
nUSB = 0
nUART = 0
nBNCs = 0
nWires = 0
nPorts = 0
for i in range(self.HW.n.Inputs):
if self.HW.Inputs[i] == 'U':
nUART += 1
inputChannelNames += ('Serial' + str(nUART), )
for j in range(self.HW.n.EventsPerSerialChannel):
eventNames += ('Serial' + str(nUART) + '_' + str(j + 1), )
Pos += 1
elif self.HW.Inputs[i] == 'X':
if nUSB == 0:
self.HW.Pos.Event_USB = Pos
nUSB += 1
inputChannelNames += ('USB' + str(nUSB), )
for j in range(self.HW.n.EventsPerSerialChannel):
eventNames += ('SoftCode' + str(j + 1), )
Pos += 1
elif self.HW.Inputs[i] == 'P':
if nPorts == 0:
self.HW.Pos.Event_Port = Pos
nPorts += 1
inputChannelNames += ('Port' + str(nPorts), )
eventNames += (inputChannelNames[-1] + 'In', )
Pos += 1
eventNames += (inputChannelNames[-1] + 'Out', )
Pos += 1
elif self.HW.Inputs[i] == 'B':
if nBNCs == 0:
self.HW.Pos.Event_BNC = Pos
nBNCs += 1
inputChannelNames += ('BNC' + str(nBNCs), )
eventNames += (inputChannelNames[-1] + 'In', )
Pos += 1
eventNames += (inputChannelNames[-1] + 'Out', )
Pos += 1
elif self.HW.Inputs[i] == 'W':
if nWires == 0:
self.HW.Pos.Event_Wire = Pos
nWires += 1
inputChannelNames += ('Wire' + str(nWires), )
eventNames += (inputChannelNames[-1] + 'In', )
Pos += 1
eventNames += (inputChannelNames[-1] + 'Out', )
Pos += 1
self.stateMachineInfo.Pos.globalTimerStart = Pos
for i in range(self.HW.n.GlobalTimers):
eventNames += ('GlobalTimer' + str(i + 1) + '_Start', )
Pos += 1
self.stateMachineInfo.Pos.globalTimerEnd = Pos
for i in range(self.HW.n.GlobalTimers):
eventNames += ('GlobalTimer' + str(i + 1) + '_End', )
Pos += 1
self.stateMachineInfo.Pos.globalCounter = Pos
for i in range(self.HW.n.GlobalCounters):
eventNames += ('GlobalCounter' + str(i + 1) + '_End', )
Pos += 1
self.stateMachineInfo.Pos.condition = Pos
for i in range(self.HW.n.Conditions):
eventNames += ('Condition' + str(i + 1), )
Pos += 1
self.stateMachineInfo.Pos.jump = Pos
for i in range(self.HW.n.UARTSerialChannels):
eventNames += ('Serial' + str(i + 1) + 'Jump', )
Pos += 1
eventNames += ('SoftJump', )
Pos += 1
eventNames += ('Tup', )
self.stateMachineInfo.Pos.Tup = Pos
Pos += 1
self.stateMachineInfo.inputChannelNames = inputChannelNames
self.stateMachineInfo.eventNames = eventNames
self.stateMachineInfo.nEvents = Pos
# Generate output channel names
outputChannelNames = ()
Pos = 0
nUSB = 0
nUART = 0
nSPI = 0
nBNCs = 0
nWires = 0
nPorts = 0
for i in range(self.HW.n.Outputs):
if self.HW.Outputs[i] == 'U':
nUART += 1
outputChannelNames += ('Serial' + str(nUART), )
Pos += 1
if self.HW.Outputs[i] == 'X':
if nUSB == 0:
self.HW.Pos.output_USB = Pos
nUSB += 1
outputChannelNames += ('SoftCode', )
Pos += 1
if self.HW.Outputs[i] == 'S':
if nSPI == 0:
self.HW.Pos.output_SPI = Pos
nSPI += 1
outputChannelNames += (
'ValveState',
) # Assume an SPI shift register mapping bits of a byte to 8 valves
Pos += 1
if self.HW.Outputs[i] == 'B':
if nBNCs == 0:
self.HW.Pos.output_BNC = Pos
nBNCs += 1
outputChannelNames += (
'BNC' + str(nBNCs),
) # Assume an SPI shift register mapping bits of a byte to 8 valves
Pos += 1
if self.HW.Outputs[i] == 'W':
if nWires == 0:
self.HW.Pos.output_Wire = Pos
nWires += 1
outputChannelNames += (
'Wire' + str(nWires),
) # Assume an SPI shift register mapping bits of a byte to 8 valves
Pos += 1
if self.HW.Outputs[i] == 'P':
if nPorts == 0:
self.HW.Pos.output_PWM = Pos
nPorts += 1
outputChannelNames += (
'PWM' + str(nPorts),
) # Assume an SPI shift register mapping bits of a byte to 8 valves
Pos += 1
outputChannelNames += ('GlobalTimerTrig', )
Pos += 1
outputChannelNames += ('GlobalTimerCancel', )
Pos += 1
outputChannelNames += ('GlobalCounterReset', )
Pos += 1
self.stateMachineInfo.outputChannelNames = outputChannelNames
self.stateMachineInfo.nOutputChannels = Pos
def sendStateMachine(self, sma):
# Replace undeclared states (at the time they were referenced) with actual state numbers
for i in range(len(sma.undeclared)):
undeclaredStateNumber = i + 10000
thisStateNumber = sma.manifest.index(sma.undeclared[i])
for j in range(sma.nStates):
if sma.stateTimerMatrix[j] == undeclaredStateNumber:
sma.stateTimerMatrix[j] = thisStateNumber
inputTransitions = sma.inputMatrix[j]
for k in range(0, len(inputTransitions)):
thisTransition = inputTransitions[k]
if thisTransition[1] == undeclaredStateNumber:
inputTransitions[k] = (thisTransition[0],
thisStateNumber)
sma.inputMatrix[j] = inputTransitions
inputTransitions = sma.globalTimers.startMatrix[j]
for k in range(0, len(inputTransitions)):
thisTransition = inputTransitions[k]
if thisTransition[1] == undeclaredStateNumber:
inputTransitions[k] = (thisTransition[0],
thisStateNumber)
sma.globalTimers.startMatrix[j] = inputTransitions
inputTransitions = sma.globalTimers.endMatrix[j]
for k in range(0, len(inputTransitions)):
thisTransition = inputTransitions[k]
if thisTransition[1] == undeclaredStateNumber:
inputTransitions[k] = (thisTransition[0],
thisStateNumber)
sma.globalTimers.endMatrix[j] = inputTransitions
inputTransitions = sma.globalCounters.matrix[j]
for k in range(0, len(inputTransitions)):
thisTransition = inputTransitions[k]
if thisTransition[1] == undeclaredStateNumber:
inputTransitions[k] = (thisTransition[0],
thisStateNumber)
sma.globalCounters.matrix[j] = inputTransitions
inputTransitions = sma.conditions.matrix[j]
for k in range(0, len(inputTransitions)):
thisTransition = inputTransitions[k]
if thisTransition[1] == undeclaredStateNumber:
inputTransitions[k] = (thisTransition[0],
thisStateNumber)
sma.conditions.matrix[j] = inputTransitions
# Check to make sure all states in manifest exist
if len(sma.manifest) > sma.nStates:
raise BpodError(
'Error: Could not send state machine - some states were referenced by name, but not subsequently declared.'
)
Message = (ord('C'), )
Message += (sma.nStates, )
for i in range(
sma.nStates): # Send state timer transitions (for all states)
if math.isnan(sma.stateTimerMatrix[i]):
Message += (sma.nStates, )
else:
Message += (sma.stateTimerMatrix[i], )
for i in range(
sma.nStates
): # Send event-triggered transitions (where they are different from default)
currentStateTransitions = sma.inputMatrix[i]
nTransitions = len(currentStateTransitions)
Message += (nTransitions, )
for j in range(nTransitions):
thisTransition = currentStateTransitions[j]
Message += (thisTransition[0], )
destinationState = thisTransition[1]
if math.isnan(destinationState):
Message += (sma.nStates, )
else:
Message += (destinationState, )
for i in range(
sma.nStates
): # Send hardware states (where they are different from default)
currentHardwareState = sma.outputMatrix[i]
nDifferences = len(currentHardwareState)
Message += (nDifferences, )
for j in range(nDifferences):
thisHardwareConfig = currentHardwareState[j]
Message += (thisHardwareConfig[0], )
Message += (thisHardwareConfig[1], )
for i in range(
sma.nStates
): # Send global timer-start triggered transitions (where they are different from default)
currentStateTransitions = sma.globalTimers.startMatrix[i]
nTransitions = len(currentStateTransitions)
Message += (nTransitions, )
for j in range(nTransitions):
thisTransition = currentStateTransitions[j]
Message += (thisTransition[0] -
self.stateMachineInfo.Pos.globalTimerStart, )
destinationState = thisTransition[1]
if math.isnan(destinationState):
Message += (sma.nStates, )
else:
Message += (destinationState, )
for i in range(
sma.nStates
): # Send global timer-end triggered transitions (where they are different from default)
currentStateTransitions = sma.globalTimers.endMatrix[i]
nTransitions = len(currentStateTransitions)
Message += (nTransitions, )
for j in range(nTransitions):
thisTransition = currentStateTransitions[j]
Message += (thisTransition[0] -
self.stateMachineInfo.Pos.globalTimerEnd, )
destinationState = thisTransition[1]
if math.isnan(destinationState):
Message += (sma.nStates, )
else:
Message += (destinationState, )
for i in range(
sma.nStates
): # Send global counter triggered transitions (where they are different from default)
currentStateTransitions = sma.globalCounters.matrix[i]
nTransitions = len(currentStateTransitions)
Message += (nTransitions, )
for j in range(nTransitions):
thisTransition = currentStateTransitions[j]
Message += (thisTransition[0] -
self.stateMachineInfo.Pos.globalCounter, )
destinationState = thisTransition[1]
if math.isnan(destinationState):
Message += (sma.nStates, )
else:
Message += (destinationState, )
for i in range(
sma.nStates
): # Send condition triggered transitions (where they are different from default)
currentStateTransitions = sma.conditions.matrix[i]
nTransitions = len(currentStateTransitions)
Message += (nTransitions, )
for j in range(nTransitions):
thisTransition = currentStateTransitions[j]
Message += (thisTransition[0] -
self.stateMachineInfo.Pos.condition, )
destinationState = thisTransition[1]
if math.isnan(destinationState):
Message += (sma.nStates, )
else:
Message += (destinationState, )
for i in range(self.HW.n.GlobalTimers):
Message += (sma.globalTimers.channels[i], )
for i in range(self.HW.n.GlobalTimers):
Message += (sma.globalTimers.onMessages[i], )
for i in range(self.HW.n.GlobalTimers):
Message += (sma.globalTimers.offMessages[i], )
for i in range(self.HW.n.GlobalCounters):
Message += (sma.globalCounters.attachedEvents[i], )
for i in range(self.HW.n.Conditions):
Message += (sma.conditions.channels[i], )
for i in range(self.HW.n.Conditions):
Message += (sma.conditions.values[i], )
sma.stateTimers = sma.stateTimers[:sma.nStates]
ThirtyTwoBitMessage = [
i * self.HW.cycleFrequency for i in sma.stateTimers
] + [i * self.HW.cycleFrequency for i in sma.globalTimers.timers] + [
i * self.HW.cycleFrequency for i in sma.globalTimers.onsetDelays
] + sma.globalCounters.thresholds
self.serialObject.write(Message, 'uint8', ThirtyTwoBitMessage,
'uint32')
self.stateMachine = sma
self.status.newStateMachineSent = 1
def runStateMachine(self):
from datetime import datetime
self.stateMachineStartTime = datetime.now()
RawEvents = Struct()
eventPos = 0
currentState = 0
StateChangeIndexes = []
RawEvents.Events = []
RawEvents.EventTimestamps = []
RawEvents.States = [currentState]
RawEvents.StateTimestamps = [0]
RawEvents.TrialStartTimestamp = 0
self.serialObject.write(ord('R'), 'uint8')
if self.status.newStateMachineSent == 1:
confirmed = self.serialObject.read('uint8')
if not confirmed:
raise BpodError(
'Error: The last state machine sent was not acknowledged by the Bpod device.'
)
self.status.newStateMachineSent = 0
runningStateMachine = True
while runningStateMachine:
if self.serialObject.bytesAvailable() > 0:
opCodeBytes = self.serialObject.readArray(2, 'uint8')
opCode = opCodeBytes[0]
if opCode == 1: # Read events
nCurrentEvents = opCodeBytes[1]
CurrentEvents = self.serialObject.readArray(
nCurrentEvents, 'uint8')
TransitionEventFound = False
for i in range(nCurrentEvents):
thisEvent = CurrentEvents[i]
if thisEvent == 255:
runningStateMachine = False
else:
RawEvents.Events.append(thisEvent)
if not TransitionEventFound:
thisStateTransitions = self.stateMachine.inputMatrix[
currentState]
nTransitions = len(thisStateTransitions)
for j in range(nTransitions):
thisTransition = thisStateTransitions[j]
if thisTransition[0] == thisEvent:
currentState = thisTransition[1]
if not math.isnan(currentState):
RawEvents.States.append(
currentState)
StateChangeIndexes.append(
len(RawEvents.Events) - 1)
TransitionEventFound = True
if not TransitionEventFound:
thisStateTimerTransition = self.stateMachine.stateTimerMatrix[
currentState]
if thisEvent == self.stateMachineInfo.Pos.Tup:
if not (thisStateTimerTransition
== currentState):
currentState = thisStateTimerTransition
if not math.isnan(currentState):
RawEvents.States.append(
currentState)
StateChangeIndexes.append(
len(RawEvents.Events) - 1)
TransitionEventFound = True
if not TransitionEventFound:
thisGlobalTimerTransitions = self.stateMachine.globalTimers.startMatrix[
currentState]
nTransitions = len(thisGlobalTimerTransitions)
for j in range(nTransitions):
thisTransition = thisGlobalTimerTransitions[
j]
if thisTransition[0] == thisEvent:
currentState = thisTransition[1]
if not math.isnan(currentState):
RawEvents.States.append(
currentState)
StateChangeIndexes.append(
len(RawEvents.Events) - 1)
TransitionEventFound = True
if not TransitionEventFound:
thisGlobalTimerTransitions = self.stateMachine.globalTimers.endMatrix[
currentState]
nTransitions = len(thisGlobalTimerTransitions)
for j in range(nTransitions):
thisTransition = thisGlobalTimerTransitions[
j]
if thisTransition[0] == thisEvent:
currentState = thisTransition[1]
if not math.isnan(currentState):
RawEvents.States.append(
currentState)
StateChangeIndexes.append(
len(RawEvents.Events) - 1)
TransitionEventFound = True
elif opCode == 2: # Handle soft code
SoftCode = opCodeBytes[1]
RawEvents.TrialStartTimestamp = float(self.serialObject.read(
'uint32')) / 1000 # Start-time of the trial in milliseconds
nTimeStamps = self.serialObject.read('uint16')
TimeStamps = self.serialObject.readArray(nTimeStamps, 'uint32')
RawEvents.EventTimestamps = [
i / float(self.HW.cycleFrequency) for i in TimeStamps
]
for i in range(len(StateChangeIndexes)):
RawEvents.StateTimestamps.append(
RawEvents.EventTimestamps[StateChangeIndexes[i]])
RawEvents.StateTimestamps.append(RawEvents.EventTimestamps[-1])
return RawEvents
def addTrialEvents(self, RawEvents):
if not hasattr(self.data, 'nTrials'):
self.data.nTrials = 0
self.data.info = Struct()
if self.firmwareVersion < 7:
self.data.info.BpodVersion = 5
else:
self.data.info.BpodVersion = 7
self.data.sessionDateTime = self.stateMachineStartTime
self.data.sessionStartTime = str(self.stateMachineStartTime)
self.data.trialStartTimestamp = []
self.data.rawData = []
self.data.rawEvents = Struct()
self.data.rawEvents.Trial = []
self.data.rawEvents.Trial.append(Struct())
self.data.rawEvents.Trial[self.data.nTrials].Events = Struct()
self.data.rawEvents.Trial[self.data.nTrials].States = Struct()
self.data.trialStartTimestamp.append(RawEvents.TrialStartTimestamp)
self.data.rawData.append(RawEvents)
states = RawEvents.States
events = RawEvents.Events
nStates = len(states)
nEvents = len(events)
nPossibleStates = self.stateMachine.nStates
visitedStates = [0] * nPossibleStates
# determine unique states while preserving visited order
uniqueStates = []
nUniqueStates = 0
uniqueStateIndexes = [0] * nStates
for i in range(nStates):
if states[i] in uniqueStates:
uniqueStateIndexes[i] = uniqueStates.index(states[i])
else:
uniqueStateIndexes[i] = nUniqueStates
nUniqueStates += 1
uniqueStates.append(states[i])
visitedStates[states[i]] = 1
uniqueStateDataMatrices = [[] for i in range(nStates)]
# Create a 2-d matrix for each state in a list
for i in range(nStates):
uniqueStateDataMatrices[uniqueStateIndexes[i]] += [
(RawEvents.StateTimestamps[i],
RawEvents.StateTimestamps[i + 1])
]
# Append one matrix for each unique state
for i in range(nUniqueStates):
thisStateName = self.stateMachine.stateNames[uniqueStates[i]]
setattr(self.data.rawEvents.Trial[self.data.nTrials].States,
thisStateName, uniqueStateDataMatrices[i])
for i in range(nPossibleStates):
thisStateName = self.stateMachine.stateNames[i]
if not visitedStates[i]:
setattr(self.data.rawEvents.Trial[self.data.nTrials].States,
thisStateName, [(float('NaN'), float('NaN'))])
for i in range(nEvents):
thisEvent = events[i]
thisEventName = self.stateMachineInfo.eventNames[thisEvent]
thisEventIndexes = [
j for j, k in enumerate(events) if k == thisEvent
]
thisEventTimestamps = []
for i in thisEventIndexes:
thisEventTimestamps.append(RawEvents.EventTimestamps[i])
setattr(self.data.rawEvents.Trial[self.data.nTrials].Events,
thisEventName, thisEventTimestamps)
self.data.nTrials += 1
def manualOverride(self, channelType, channelName, channelNumber, value):
if channelType.lower() == 'input':
raise BpodError(
'Manually overriding a Bpod input channel is not yet supported in Python.'
)
elif channelType.lower() == 'output':
if channelName == 'Valve':
if value > 0:
value = math.pow(2, channelNumber - 1)
channelNumber = self.HW.Pos.output_SPI
byteString = (ord('O'), channelNumber, value)
elif channelName == 'Serial':
byteString = (ord('U'), channelNumber, value)
else:
try:
channelNumber = self.stateMachineInfo.outputChannelNames.index(
channelName + str(channelNumber))
byteString = (ord('O'), channelNumber, value)
except:
raise BpodError('Error using manualOverride: ' +
channelName +
' is not a valid channel name.')
self.serialObject.write(byteString, 'uint8')
else:
raise BpodError(
'Error using manualOverride: first argument must be "Input" or "Output".'
)
def loadSerialMessage(self, serialChannel, messageID, message):
nMessages = 1
messageLength = len(message)
if messageLength > 3:
raise BpodError(
'Error: Serial messages cannot be more than 3 bytes in length.'
)
if (messageID > 255) or (messageID < 1):
raise BpodError(
'Error: Bpod can only store 255 serial messages (indexed 1-255).'
)
ByteString = (ord('L'), serialChannel - 1, nMessages, messageID,
messageLength) + message
print ByteString
self.serialObject.write(ByteString, 'uint8')
Confirmed = self.serialObject.read('uint8')
if (not Confirmed):
raise BpodError('Error: Failed to set serial message.')
def resetSerialMessages(self):
self.serialObject.write(ord('>'), 'uint8')
Confirmed = self.serialObject.read('uint8')
if (not Confirmed):
raise BpodError('Error: Failed to reset serial message library.')
def disconnect(self):
self.serialObject.write(ord('Z'), 'uint8')