'''
----------------------------------------------------------------------------
This file is part of the Sanworks ArCOM repository
Copyright (C) 2016 Sanworks LLC, Sound Beach, New York, USA
----------------------------------------------------------------------------
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, version 3.
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/>.
'''
# To use this code, load the example Arduino sketch in /ArCOM/Arduino
# Update the serial port string below ('COM3') to your actual port.
from ArCOM import ArCOMObject # Import ArCOMObject
serialPort = ArCOMObject(
'COM3', 115200) # Create a new instance of an ArCOM serial port
serialPort.write([5] * 100, 'uint16', [500] * 100, 'uint32')
myVoltages, myTimes = serialPort.read(100, 'uint16', 100, 'uint32')
print myVoltages
print myTimes
class BpodHiFi(object):
def __init__(self, PortName):
self.Port = ArCOMObject(PortName, 115200)
self.Port.write(ord('I'), 'uint8'); # Get current parameters
InfoParams8Bit = self.Port.read(4, 'uint8')
InfoParams32Bit = self.Port.read(3, 'uint32')
self.isHD = InfoParams8Bit[0] # HiFi Module Model (0=base,1=HD)
self._samplingRate = InfoParams32Bit[0] # use H.samplingRate = X. Underscored version does not support get and set callbacks
self.bitDepth = InfoParams8Bit[1] # Bits per sample (fixed in firmware)
self.maxWaves = InfoParams8Bit[2] # Number of sounds the device can store
digitalAttBits = InfoParams8Bit[3]
self._digitalAttenuation_dB = np.double(digitalAttBits)*-0.5
self._synthAmplitude = 0; # 0 = synth off, 1 = max
self._synthAmplitudeFade = 0; # Number of samples over which to ramp changes in synth amplitude (0 = instant change)
self._synthWaveform = 'WhiteNoise'; # WhiteNoise or Sine
self._synthFrequency = 1000; # Frequency of waveform (if sine)
self.Port.write(ord('F'), 'uint8', self._synthFrequency*1000, 'uint32') # Force SynthFrequency
confirm = self.Port.read(1, 'uint8')
self._headphoneAmpEnabled = 0;
self._headphoneAmpGain = 15;
self.Port.write((ord('G'), 15), 'uint8'); # Set gain to non-painful initial level (range = 0-63)
self.Port.read(1, 'uint8');
self.maxSamplesPerWaveform = InfoParams32Bit[1]*192000
self.maxEnvelopeSamples = InfoParams32Bit[2]
self.validSamplingRates = (44100,48000,96000,192000)
self.minAttenuation_Pro = -103
self.minAttenuation_HD = -120
@property
def samplingRate(self):
return self._samplingRate
@samplingRate.setter
def samplingRate(self, value):
if not value in self.validSamplingRates:
raise HiFiError('Error: Invalid Sampling Rate.')
self.Port.write(ord('S'), 'uint8', value, 'uint32');
confirm = self.Port.read(1, 'uint8');
if confirm != 1:
raise HiFiError('Error setting sampling rate: Confirm code not returned.')
self._samplingRate = value
@property
def digitalAttenuation_dB(self):
return self._digitalAttenuation_dB
@digitalAttenuation_dB.setter
def digitalAttenuation_dB(self, value):
minAttenuation = self.minAttenuation_Pro
if self.isHD:
minAttenuation = self.minAttenuation_HD
if (value > 0) or (value < minAttenuation):
raise HiFiError('Error: Invalid digitalAttenuation_dB. Value must be in range: [' + str(minAttenuation) + ',0]')
attenuationBits = value*-2;
self.Port.write((ord('A'),attenuationBits), 'uint8')
confirm = self.Port.read(1, 'uint8');
if confirm != 1:
raise HiFiError('Error setting digitalAttenuation: Confirm code not returned.')
self._digitalAttenuation_dB = value
@property
def synthAmplitude(self):
return self._synthAmplitude
@synthAmplitude.setter
def synthAmplitude(self, value):
if not ((value >= 0) and (value <= 1)):
raise HiFiError('Error: Synth amplitude values must range between 0 and 1.')
amplitudeBits = round(value*32767);
self.Port.write(ord('N'), 'uint8', amplitudeBits, 'uint16')
confirm = self.Port.read(1, 'uint8');
if confirm != 1:
raise HiFiError('Error setting synthAmplitude: Confirm code not returned.')
self._synthAmplitude = value
@property
def synthAmplitudeFade(self):
return self._synthAmplitudeFade
@synthAmplitudeFade.setter
def synthAmplitudeFade(self, value):
if not ((value >= 0) and (value <= 1920000)):
raise HiFiError('Error: Synth amplitude fade must range between 0 and 1920000 samples.')
self.Port.write(ord('Z'), 'uint8', value, 'uint32')
confirm = self.Port.read(1, 'uint8');
if confirm != 1:
raise HiFiError('Error setting synthAmplitudeFade: Confirm code not returned.')
self._synthAmplitudeFade = value
@property
def synthWaveform(self):
return self._synthWaveform
@synthWaveform.setter
def synthWaveform(self, value):
validWaveforms = ['WhiteNoise','Sine']
if not value in validWaveforms:
raise HiFiError('Invalid value for synthWaveform: Valid values are WhiteNoise or Sine.')
waveformIndex = validWaveforms.index(value)
self.Port.write((ord('W'),waveformIndex), 'uint8')
confirm = self.Port.read(1, 'uint8');
if confirm != 1:
raise HiFiError('Error setting synthWaveform: Confirm code not returned.')
self._synthWaveform = value
@property
def synthFrequency(self):
return self._synthFrequency
@synthFrequency.setter
def synthFrequency(self, value):
if not ((value >= 20) and (value <= 80000)):
raise HiFiError('Error: Synth frequency must range between 0 and 80000 Hz.')
self.Port.write(ord('F'), 'uint8', value*1000, 'uint32')
confirm = self.Port.read(1, 'uint8')
if confirm != 1:
raise HiFiError('Error setting synthFrequency: Confirm code not returned.')
self._synthFrequency = value
@property
def headphoneAmpEnabled(self):
return self._headphoneAmpEnabled
@headphoneAmpEnabled.setter
def headphoneAmpEnabled(self, value):
validValues = (0,1)
if not value in validValues:
raise HiFiError('Error: headphoneAmpEnabled must be 0 (disabled) or 1 (enabled)')
self.Port.write((ord('H'),value), 'uint8')
confirm = self.Port.read(1, 'uint8');
if confirm != 1:
raise HiFiError('Error setting headphone amp: Confirm code not returned.')
self._headphoneAmpEnabled = value
@property
def headphoneAmpGain(self):
return self._headphoneAmpGain
@headphoneAmpGain.setter
def headphoneAmpGain(self, value):
if not ((value >= 0) and (value <= 63)):
raise HiFiError('Error: Headphone amp gain values must range between 0 and 63.')
self.Port.write((ord('G'),value), 'uint8')
confirm = self.Port.read(1, 'uint8');
if confirm != 1:
raise HiFiError('Error setting headphone amp gain: Confirm code not returned.')
self._headphoneAmpGain = value
def play(self, SoundIndex):
self.Port.write((ord('P'),SoundIndex), 'uint8')
def stop(self):
self.Port.write(ord('X'), 'uint8')
def push(self):
self.Port.write(ord('*'), 'uint8')
confirm = self.Port.read(1, 'uint8')
if confirm != 1:
raise HiFiError('Error: Confirm code not returned.')
def setAMEnvelope(self, envelope):
if not envelope.ndim == 1:
raise HiFiError('Error: AM Envelope must be a 1xN array.')
nEnvelopeSamples = envelope.shape[0]
if nEnvelopeSamples > self.maxEnvelopeSamples:
raise HiFiError('Error: AM Envelope cannot contain more than ' + str(self.maxEnvelopeSamples) + ' samples.')
if not ((envelope >= 0).all() and (envelope <= 1).all()):
raise HiFiError('Error: AM Envelope values must range between 0 and 1.')
self.Port.write((ord('E'), 1, ord('M')), 'uint8', nEnvelopeSamples, 'uint16', envelope, 'single')
confirm = self.Port.read(2, 'uint8')
def load(self, soundIndex, waveform):
# waveform must be a 1xN or 2xN numpy array in range [-1, 1]
isStereo = 1 # Default to stereo
isLooping = 0 # Default loop mode = off
loopDuration = 0 # Default loop duration = 0
if (soundIndex < 0) or (soundIndex > self.maxWaves-1):
raise HiFiError('Error: Invalid sound index (' + str(soundIndex) + '). The HiFi module supports up to ' + str(self.maxWaves) + ' sounds.')
if waveform.ndim == 1:
isStereo = 0
nChannels = 1
nSamples = waveform.shape[0]
formattedWaveform = waveform
else:
(nChannels,nSamples) = waveform.shape
formattedWaveform = np.ravel(waveform, order='F')
if self.bitDepth == 16:
formattedWaveform = formattedWaveform*32767
self.Port.write((ord('L'),soundIndex,isStereo, isLooping), 'uint8', (loopDuration, nSamples), 'uint32', formattedWaveform, 'int16')
confirm = self.Port.read(1, 'uint8')
if confirm != 1:
raise HiFiError('Error: Confirm code not returned.')
def __repr__ (self): # Self description when the object is entered into the IPython console with no properties or methods specified
return ('\nBpodHiFi with user properties:' + '\n\n'
'Port: ArCOMObject(' + self.Port.serialObject.port + ')' + '\n'
'samplingRate: ' + str(self.samplingRate) + '\n'
'digitalAttenuation_dB: ' + str(self.digitalAttenuation_dB) + '\n'
'synthAmplitude: ' + str(self.synthAmplitude) + '\n'
'synthAmplitudeFade: ' + str(self.synthAmplitudeFade) + '\n'
'synthWaveform: ' + str(self.synthWaveform) + '\n'
'synthFrequency: ' + str(self.synthFrequency) + '\n'
'headphoneAmpEnabled: ' + str(self.headphoneAmpEnabled) + '\n'
'headphoneAmpGain: ' + str(self.headphoneAmpGain) + '\n'
)
def __del__(self):
self.Port.close()
'''
----------------------------------------------------------------------------
This file is part of the Sanworks ArCOM repository
Copyright (C) 2016 Sanworks LLC, Sound Beach, New York, USA
----------------------------------------------------------------------------
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, version 3.
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/>.
'''
# To use this code, load the example Arduino sketch in /ArCOM/Arduino
# Update the serial port string below ('COM3') to your actual port.
from ArCOM import ArCOMObject # Import ArCOMObject
serialPort = ArCOMObject('COM3', 115200) # Create a new instance of an ArCOM serial port
serialPort.write([5]*100, 'uint16', [500]*100, 'uint32')
myVoltages, myTimes = serialPort.read(100, 'uint16', 100, 'uint32')
print myVoltages
print myTimes
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')