def __init__(self, send_trial_number = False, *args, **kwargs):
HasTraits.__init__(self, *args, **kwargs)
# events -- dispatched on UI thread
self.on_trait_event(self._handle_push_event, 'push_event', dispatch='fast_ui')
self.on_trait_event(self._handle_push_streaming, 'push_streaming', dispatch='fast_ui')
self.on_trait_change(self._handle_eot, 'eot', dispatch='ui')
# database
self.persistor = Persistor()
# config
# self.configFile = os.environ.get("voyeur_config")
self.configFile = os.path.join('/Users/Gottfried_Lab/PycharmProjects/PyOlfa/src/voyeur_rig_config.conf')
# serial
self.serial_queue1 = SerialCallThread(monitor=self, max_queue_size=1)
try:
if self.serial1 is None:
self.serial1 = SerialPort(self.configFile, board='board1', port='port1', send_trial_number = send_trial_number)
except SerialException as e:
print('Serial Port 1 Error')
print('Serial exception. Message: ', e.msg, ' Path: ', e.path)
self.protocol_name = self.serial1.request_protocol_name()
### Define monitor metadata. This metadata is consistent between all protocols.
self.metadata = {'arduino_protocol_name': self.protocol_name,
'start_date': time.mktime(time.localtime()),
#todo: add VOYEUR core version hash or version number lookup.
}
class Monitor(HasTraits):
"""Central manager for CPU-side of Voyeur system"""
# Client
persistor = Instance(object, factory=Persistor)
serial1 = Instance(
object
) #, factory=SerialPort, args=(os.environ['VOYEUR_CONFIG'], 'board1', 'port1'))
serial_queue1 = Instance(object)
protocol = Instance(object)
database_file = File(None)
user = Str(getpass.getuser())
session_number = Int(1)
protocol_number = Int(1)
animal_id = Int(1)
rig = Int(1)
experiment_notes = Str("")
voyeur_version = Float(1.0)
usercode_version = Float(1.0)
arduino_protocol_name = Str("")
user_protocol_name = Str("")
start_date = Float("")
timezone = Str("")
user_metadata = Str("")
# Internal
running = Bool(False)
recording = Bool(False)
paused = Bool(False)
eot = Event() # queue for dispatch on ui thread
push_event = Event() # dispatch immediately on ui thread
push_streaming = Event() # dispatch immediately on ui thread
current_session_group = Instance(object)
current_trial_group = Instance(object)
current_trial_parameters = Instance(object)
acquisition_thread = Instance(AcquisitionThread)
_iti_timer = Instance(QTimer)
processed = 0
acquired = 0
_acquiringlock = False
_eventlock = False
def __init__(self, send_trial_number=False, *args, **kwargs):
HasTraits.__init__(self, *args, **kwargs)
# events -- dispatched on UI thread
self.on_trait_event(self._handle_push_event,
'push_event',
dispatch='fast_ui')
self.on_trait_event(self._handle_push_streaming,
'push_streaming',
dispatch='fast_ui')
self.on_trait_change(self._handle_eot, 'eot', dispatch='ui')
# database
self.persistor = Persistor()
# config
self.configFile = os.environ.get("VOYEUR_CONFIG")
# serial
self.serial_queue1 = SerialCallThread(monitor=self, max_queue_size=1)
try:
if self.serial1 is None:
self.serial1 = SerialPort(self.configFile,
board='board1',
port='port1',
send_trial_number=send_trial_number)
except SerialException as e:
print('Serial Port 1 Error')
print('Serial exception. Message: ', e.msg, ' Path: ', e.path)
self.protocol_name = self.serial1.request_protocol_name()
### Define monitor metadata. This metadata is consistent between all protocols.
self.metadata = {
'arduino_protocol_name': self.protocol_name,
'start_date': time.mktime(time.localtime()),
#todo: add VOYEUR core version hash or version number lookup.
}
def _database_file_changed(self):
initial_metadata = dict(self.metadata.items() +
self.protocol.metadata.items()
) # combine protocol and monitor metadata
if self.serial1 != None:
#self.serial_queue1.enqueue(self.persistor.close_database)
self.current_session_group = self.persistor.create_database(
self.database_file, initial_metadata)
self.persistor.create_trials(
self.protocol.protocol_parameters_definition(),
self.protocol.controller_parameters_definition(),
self.protocol.event_definition(), self.current_session_group,
'')
def _protocol_changed(self, name, old, new):
"""
Update protocol number.
If self.protocol.__class__ == new.__class__ don't update
"""
"""if new != None and old.__class__ != new.__class__:
self.protocol_number += 1
self.user_protocol_name = self.protocol.protocol_name
self.persistor.create_trials(new.protocol_parameters_definition(),
new.controller_parameters_definition(),
new.event_definition(),
self.current_session_group,
'')"""
# For Debugging
"""self.persistor.create_trials(new.protocol_parameters_definition(),
new.controller_parameters_definition(),
new.event_definition(),
self.current_session_group,
'')"""
pass
def start_acquisition(self):
self.running = True
self.recording = True
self.paused = False
self.start_new_trial()
def stop_acquisition(self):
"""Stops acquisition"""
if self._iti_timer:
self._iti_timer.stop()
self._iti_timer.deleteLater()
self._iti_timer = None
self.recording = False
self.running = False
self.paused = False
self.setup_complete = False
if self.serial1 != None:
self._eventlock = True
self.serial_queue1.enqueue(self.serial1.end_trial)
self._eventlock = False
#self.serial_queue1.enqueue(self.persistor.close_database)
#self.serial_queue1.enqueue(self.serial1.close)
self.persistor.close_database()
def pause_acquisition(self, graceful=False):
"""Pauses acquisition"""
self.paused = True
if self._iti_timer:
self._iti_timer.stop()
self._iti_timer.deleteLater()
self._iti_timer = None
if graceful:
if self.serial1 != None:
self._eventlock = True
self.serial_queue1.enqueue(self.serial1.end_trial)
self._eventlock = False
if self.running:
self.recording = False
def unpause_acquisition(self):
"""Unpauses acquisition"""
self.paused = False
if self.running:
self.recording = True
self.start_new_trial()
def send_command(self, command):
""" Sends a user command to arduino """
if not self.serial_queue1.isRunning():
self.serial_queue1.start()
if self.serial1 != None:
self._eventlock = True
self.serial_queue1.enqueue(self.serial1.user_def_command, command)
self._eventlock = False
"""if not sent:
raise ProtocolException(self.protocol.protocol_description(),
"Sending user defined command failed")"""
def start_new_trial(self, ):
"""Start New Trial"""
# Get parameters for next trial
if self.running and self.recording:
trial_parameters = self.protocol.trial_parameters()
# Create the trial group
self.current_trial_group = self.persistor.add_trial(
self.protocol.trialNumber, trial_parameters.protocolParameters,
trial_parameters.controllerParameters,
self.protocol.stream_definition(), self.current_session_group,
self.protocol.protocol_description())
self.protocol.start_of_trial()
self._start_acquisition(trial_parameters.controllerParameters)
if not self.serial_queue1.isRunning():
self.serial_queue1.start()
self._start_acquisition_thread()
def acquire_events(self):
"""Run event acquisition"""
event = self.serial1.request_event(self.protocol.event_definition())
if event:
self.push_event = (event, self.recording)
else:
raise ProtocolException(self.protocol.protocol_description(),
"Event is null")
def acquire_stream(self):
"""Run stream acquisition"""
try:
stream = self.serial1.request_stream(
self.protocol.stream_definition())
#print "Stream acquired from serial: ", stream
if stream:
self._acquiringlock = True
self.push_streaming = (stream, self.recording)
self.acquired += 1
#print "Total streams acquired: ", self.acquired
else:
raise ProtocolException(self.protocol.protocol_description(),
"Stream data is null.")
#print "Stream empty exception raised: ", time.clock()
except NonOperationException:
raise ProtocolException(self.protocol.protocol_description(),
"NonOperationException.")
except EndOfTrialException as ex:
stream = ex.last_read
if stream:
self._acquiringlock = True
self.push_streaming = (stream, self.recording)
#self.acquired += 1
#print "Total streams acquired: ", self.acquired
raise ex
while (self._acquiringlock):
if self.running == False or self._eventlock:
break
continue
return
def _handle_eot(self):
self.protocol.end_of_trial()
self._eventlock = True
self.serial_queue1.enqueue(self.acquire_events)
self._eventlock = False
def _run_iti(self, continuation):
"""Starts a timer with Protocol-supplied inter-trial interval. Timer
calls continuation when fired
ITI timer is an object that can be modified and queried. To check if timer is active,
use _iti_timer.is_active() method. To cancel timer, call _iti_timer.cancel()
"""
iti_ms = self.protocol.trial_iti_milliseconds()
#print "next start iti = ", iti_ms
if self._iti_timer:
self._iti_timer.stop()
self._iti_timer.deleteLater()
self._iti_timer = QTimer()
self._iti_timer.timeout.connect(continuation)
self._iti_timer.setSingleShot(True)
self._iti_timer.start(iti_ms)
return
def _start_acquisition_thread(self):
"""Spawns the acquisition thread"""
self.acquisition_thread = AcquisitionThread()
self.acquisition_thread.serial_queue = self.serial_queue1
self.acquisition_thread.monitor = self
self.acquisition_thread.start()
def _start_acquisition(self, trial_parameters):
"""Starts acquisition. Called by AcquisitionThread.run"""
if self.protocol != None:
self._eventlock = True
self.serial_queue1.enqueue(self.serial1.start_trial,
trial_parameters)
self._eventlock = False
def _handle_push_event(self, event_tuple):
event, persist = event_tuple
self.persistor.insert_event(event, self.current_session_group)
self.protocol.process_event_request(event)
if not self.paused:
self._run_iti(self.start_new_trial)
def _handle_push_streaming(self, streaming_tuple):
#print "processing stream....", time.clock()
if not self.running:
return
stream, persist = streaming_tuple
if persist:
self.persistor.insert_stream(stream, self.current_trial_group)
self.protocol.process_stream_request(stream)
self.processed += 1
#print "stream processed: ", time.clock(), ". Total processed: ", self.processed
self._acquiringlock = False
return
class Monitor(HasTraits):
"""Central manager for CPU-side of Voyeur system"""
# Client
persistor = Instance(object, factory=Persistor)
serial1 = Instance(object)
serial_queue1 = Instance(object)
protocol = Instance(object)
database_file = File(None)
user = Str(getpass.getuser())
session_number = Int(1)
protocol_number = Int(1)
animal_id = Int(1)
rig = Int(1)
experiment_notes = Str("")
voyeur_version = Float(1.0)
usercode_version = Float(1.0)
arduino_protocol_name = Str("")
user_protocol_name = Str("")
start_date = Float("")
timezone = Str("")
user_metadata = Str("")
# Internal
running = Bool(False)
recording = Bool(False)
paused = Bool(False)
eot = Event() # queue for dispatch on ui thread
push_event = Event() # dispatch immediately on ui thread
push_streaming = Event() # dispatch immediately on ui thread
current_session_group = Instance(object)
current_trial_group = Instance(object)
current_trial_parameters = Instance(object)
acquisition_thread = Instance(AcquisitionThread)
_iti_timer = Instance(QTimer)
processed = 0
acquired = 0
_acquiringlock = False
_eventlock = False
def __init__(self, send_trial_number = False, *args, **kwargs):
HasTraits.__init__(self, *args, **kwargs)
# events -- dispatched on UI thread
self.on_trait_event(self._handle_push_event, 'push_event', dispatch='fast_ui')
self.on_trait_event(self._handle_push_streaming, 'push_streaming', dispatch='fast_ui')
self.on_trait_change(self._handle_eot, 'eot', dispatch='ui')
# database
self.persistor = Persistor()
# config
# self.configFile = os.environ.get("voyeur_config")
self.configFile = os.path.join('/Users/Gottfried_Lab/PycharmProjects/PyOlfa/src/voyeur_rig_config.conf')
# serial
self.serial_queue1 = SerialCallThread(monitor=self, max_queue_size=1)
try:
if self.serial1 is None:
self.serial1 = SerialPort(self.configFile, board='board1', port='port1', send_trial_number = send_trial_number)
except SerialException as e:
print('Serial Port 1 Error')
print('Serial exception. Message: ', e.msg, ' Path: ', e.path)
self.protocol_name = self.serial1.request_protocol_name()
### Define monitor metadata. This metadata is consistent between all protocols.
self.metadata = {'arduino_protocol_name': self.protocol_name,
'start_date': time.mktime(time.localtime()),
#todo: add VOYEUR core version hash or version number lookup.
}
def _database_file_changed(self):
initial_metadata = dict(self.metadata.items() + self.protocol.metadata.items()) # combine protocol and monitor metadata
if self.serial1 != None:
#self.serial_queue1.enqueue(self.persistor.close_database)
self.current_session_group = self.persistor.create_database(self.database_file, initial_metadata)
self.persistor.create_trials(self.protocol.protocol_parameters_definition(),
self.protocol.controller_parameters_definition(),
self.protocol.event_definition(),
self.current_session_group,
'')
def _protocol_changed(self, name, old, new):
"""
Update protocol number.
If self.protocol.__class__ == new.__class__ don't update
"""
"""if new != None and old.__class__ != new.__class__:
self.protocol_number += 1
self.user_protocol_name = self.protocol.protocol_name
self.persistor.create_trials(new.protocol_parameters_definition(),
new.controller_parameters_definition(),
new.event_definition(),
self.current_session_group,
'')"""
# For Debugging
"""self.persistor.create_trials(new.protocol_parameters_definition(),
new.controller_parameters_definition(),
new.event_definition(),
self.current_session_group,
'')"""
pass
def start_acquisition(self):
self.running = True
self.recording = True
self.paused = False
self.start_new_trial()
def stop_acquisition(self):
"""Stops acquisition"""
if self._iti_timer:
self._iti_timer.stop()
self._iti_timer.deleteLater()
self._iti_timer = None
self.recording = False
self.running = False
self.paused = False
self.setup_complete = False
if self.serial1 != None:
self._eventlock = True
self.serial_queue1.enqueue(self.serial1.end_trial)
self._eventlock = False
#self.serial_queue1.enqueue(self.persistor.close_database)
#self.serial_queue1.enqueue(self.serial1.close)
self.persistor.close_database()
def pause_acquisition(self, graceful = False):
"""Pauses acquisition"""
self.paused = True
if self._iti_timer:
self._iti_timer.stop()
self._iti_timer.deleteLater()
self._iti_timer = None
if graceful:
if self.serial1 != None:
self._eventlock = True
self.serial_queue1.enqueue(self.serial1.end_trial)
self._eventlock = False
if self.running:
self.recording = False
def unpause_acquisition(self):
"""Unpauses acquisition"""
self.paused = False
if self.running:
self.recording = True
self.start_new_trial()
def send_command(self, command):
""" Sends a user command to arduino """
if not self.serial_queue1.isRunning():
self.serial_queue1.start()
if self.serial1 != None:
self._eventlock = True
self.serial_queue1.enqueue(self.serial1.user_def_command, command)
self._eventlock = False
"""if not sent:
raise ProtocolException(self.protocol.protocol_description(),
"Sending user defined command failed")"""
def start_new_trial(self, ):
"""Start New Trial"""
# Get parameters for next trial
if self.running and self.recording:
trial_parameters = self.protocol.trial_parameters()
# Create the trial group
self.current_trial_group = self.persistor.add_trial(self.protocol.trialNumber,
trial_parameters.protocolParameters,
trial_parameters.controllerParameters,
self.protocol.stream_definition(),
self.current_session_group,
self.protocol.protocol_description())
self.protocol.start_of_trial()
self._start_acquisition(trial_parameters.controllerParameters)
if not self.serial_queue1.isRunning():
self.serial_queue1.start()
self._start_acquisition_thread()
def acquire_events(self):
"""Run event acquisition"""
event = self.serial1.request_event(self.protocol.event_definition())
if event:
self.push_event = (event, self.recording)
else:
raise ProtocolException(self.protocol.protocol_description(), "Event is null")
def acquire_stream(self):
"""Run stream acquisition"""
try:
stream = self.serial1.request_stream(self.protocol.stream_definition())
#print "Stream acquired from serial: ", stream
if stream:
self._acquiringlock = True
self.push_streaming = (stream, self.recording)
self.acquired += 1
#print "Total streams acquired: ", self.acquired
else:
raise ProtocolException(self.protocol.protocol_description(), "Stream data is null.")
#print "Stream empty exception raised: ", time.clock()
except NonOperationException:
raise ProtocolException(self.protocol.protocol_description(), "NonOperationException.")
except EndOfTrialException as ex:
stream = ex.last_read
if stream:
self._acquiringlock = True
self.push_streaming = (stream, self.recording)
#self.acquired += 1
#print "Total streams acquired: ", self.acquired
raise ex
while(self._acquiringlock):
if self.running == False or self._eventlock:
break
continue
return
def _handle_eot(self):
self.protocol.end_of_trial()
self._eventlock = True
self.serial_queue1.enqueue(self.acquire_events)
self._eventlock = False
def _run_iti(self, continuation):
"""Starts a timer with Protocol-supplied inter-trial interval. Timer
calls continuation when fired
ITI timer is an object that can be modified and queried. To check if timer is active,
use _iti_timer.is_active() method. To cancel timer, call _iti_timer.cancel()
"""
iti_ms = self.protocol.trial_iti_milliseconds()
#print "next start iti = ", iti_ms
if self._iti_timer:
self._iti_timer.stop()
self._iti_timer.deleteLater()
self._iti_timer = QTimer()
self._iti_timer.timeout.connect(continuation)
self._iti_timer.setSingleShot(True)
self._iti_timer.start(iti_ms)
return
def _start_acquisition_thread(self):
"""Spawns the acquisition thread"""
self.acquisition_thread = AcquisitionThread()
self.acquisition_thread.serial_queue = self.serial_queue1
self.acquisition_thread.monitor = self
self.acquisition_thread.start()
def _start_acquisition(self, trial_parameters):
"""Starts acquisition. Called by AcquisitionThread.run"""
if self.protocol != None:
self._eventlock = True
self.serial_queue1.enqueue(self.serial1.start_trial, trial_parameters)
self._eventlock = False
def _handle_push_event(self, event_tuple):
event, persist = event_tuple
self.persistor.insert_event(event, self.current_session_group)
self.protocol.process_event_request(event)
if not self.paused:
self._run_iti(self.start_new_trial)
def _handle_push_streaming(self, streaming_tuple):
#print "processing stream....", time.clock()
if not self.running:
return
stream, persist = streaming_tuple
if persist:
self.persistor.insert_stream(stream, self.current_trial_group)
self.protocol.process_stream_request(stream)
self.processed += 1
#print "stream processed: ", time.clock(), ". Total processed: ", self.processed
self._acquiringlock = False
return
