def _default__band_timer(self):
""" Create the default timer for the band state changes.
"""
timer = QTimer()
timer.setSingleShot(True)
timer.timeout.connect(self._on_band_timer)
return timer
def _postVisibilityChange(self, visible):
""" Post a visibility changed event for the dock item.
This method collapses the post on a timer and will not emit
the event when the visibility temporarily toggles bettwen
states.
Parameters
----------
visible : bool
True if the item was show, False if the item was hidden.
"""
area = self.rootDockArea()
if area is not None and area.dockEventsEnabled():
vis_changed = self._vis_changed
if vis_changed is None:
timer = QTimer()
timer.setSingleShot(True)
timer.timeout.connect(self._onVisibilityTimer)
self._vis_changed = (timer, visible)
timer.start()
else:
timer, old_visible = vis_changed
if old_visible != visible:
self._vis_changed = None
timer.stop()
def __init__(self):
self._reads = {}
self._writes = {}
self._notifiers = {}
self._timer = QTimer()
self._timer.setSingleShot(True)
self._timer.timeout.connect(self.iterate)
if QCoreApplication.instance() is None:
# Application Object has not been started yet
self.qApp = QCoreApplication([])
self._ownApp = True
else:
self.qApp = QCoreApplication.instance()
self._ownApp = False
self._blockApp = None
posixbase.PosixReactorBase.__init__(self)
def _postVisibilityChange(self, visible):
""" Post a visibility changed event for the dock item.
This method collapses the post on a timer and will not emit
the event when the visibility temporarily toggles bettwen
states.
Parameters
----------
visible : bool
True if the item was show, False if the item was hidden.
"""
area = self.rootDockArea()
if area is not None and area.dockEventsEnabled():
vis_changed = self._vis_changed
if vis_changed is None:
timer = QTimer()
timer.setSingleShot(True)
timer.timeout.connect(self._onVisibilityTimer)
self._vis_changed = (timer, visible)
timer.start()
else:
timer, old_visible = vis_changed
if old_visible != visible:
self._vis_changed = None
timer.stop()
def alert(self, level, on=250, off=250, repeat=4, persist=False):
""" Set the alert level on the dock item.
This will override any currently applied alert level.
Parameters
----------
level : unicode
The alert level token to apply to the dock item.
on : int
The duration of the 'on' cycle, in ms. A value of -1 means
always on.
off : int
The duration of the 'off' cycle, in ms. If 'on' is -1, this
value is ignored.
repeat : int
The number of times to repeat the on-off cycle. If 'on' is
-1, this value is ignored.
persist : bool
Whether to leave the alert in the 'on' state when the cycles
finish. If 'on' is -1, this value is ignored.
"""
if self._alert_data is not None:
self.clearAlert()
app = QApplication.instance()
app.focusChanged.connect(self._onAppFocusChanged)
timer = QTimer()
timer.setSingleShot(True)
timer.timeout.connect(self._onAlertTimer)
on, off, repeat = max(-1, on), max(0, off), max(1, repeat)
self._alert_data = _AlertData(timer, level, on, off, repeat, persist)
if on < 0:
self.alerted.emit(level)
else:
self._onAlertTimer()
def alert(self, level, on=250, off=250, repeat=4, persist=False):
""" Set the alert level on the dock item.
This will override any currently applied alert level.
Parameters
----------
level : unicode
The alert level token to apply to the dock item.
on : int
The duration of the 'on' cycle, in ms. A value of -1 means
always on.
off : int
The duration of the 'off' cycle, in ms. If 'on' is -1, this
value is ignored.
repeat : int
The number of times to repeat the on-off cycle. If 'on' is
-1, this value is ignored.
persist : bool
Whether to leave the alert in the 'on' state when the cycles
finish. If 'on' is -1, this value is ignored.
"""
if self._alert_data is not None:
self.clearAlert()
app = QApplication.instance()
app.focusChanged.connect(self._onAppFocusChanged)
timer = QTimer()
timer.setSingleShot(True)
timer.timeout.connect(self._onAlertTimer)
on, off, repeat = max(-1, on), max(0, off), max(1, repeat)
self._alert_data = _AlertData(timer, level, on, off, repeat, persist)
if on < 0:
self.alerted.emit(level)
else:
self._onAlertTimer()
def start_timer(self, name, duration, callback):
log.debug('Starting %f sec. timer %s', duration, name)
timer = QTimer()
timer.timeout.connect(callback)
timer.setSingleShot(True)
timer.start(duration * 1e3)
self._timers[name] = timer
def _start_timer(self, duration, event):
# The duration can be specified as a string naming the context variable
# to extract.
if isinstance(duration, basestring):
duration = self.context.get_value(duration)
log.debug('Timer for {} with duration {}'.format(event, duration))
receiver = partial(self.handle_event, event)
if duration == 0:
deferred_call(receiver)
else:
self.timer = QTimer()
self.timer.timeout.connect(receiver) # set up new callback
self.timer.setSingleShot(True) # call only once
self.timer.start(duration*1e3)
def start_timer(self, name, duration, callback):
try:
timer = QTimer()
timer.timeout.connect(callback)
timer.setSingleShot(True)
timer.start(int(duration * 1e3))
self._timers[name] = timer
except Exception as e:
log.error(
f'Attempt to start timer {name} with duration {duration} sec failed'
)
raise
class QtReactor(posixbase.PosixReactorBase):
implements(IReactorFDSet)
def __init__(self):
self._reads = {}
self._writes = {}
self._notifiers = {}
self._timer = QTimer()
self._timer.setSingleShot(True)
self._timer.timeout.connect(self.iterate)
if QCoreApplication.instance() is None:
# Application Object has not been started yet
self.qApp = QCoreApplication([])
self._ownApp = True
else:
self.qApp = QCoreApplication.instance()
self._ownApp = False
self._blockApp = None
posixbase.PosixReactorBase.__init__(self)
def _add(self, xer, primary, type):
"""
Private method for adding a descriptor from the event loop.
It takes care of adding it if new or modifying it if already added
for another state (read -> read/write for example).
"""
if xer not in primary:
primary[xer] = TwistedSocketNotifier(None, self, xer, type)
def addReader(self, reader):
"""
Add a FileDescriptor for notification of data available to read.
"""
self._add(reader, self._reads, QSocketNotifier.Read)
def addWriter(self, writer):
"""
Add a FileDescriptor for notification of data available to write.
"""
self._add(writer, self._writes, QSocketNotifier.Write)
def _remove(self, xer, primary):
"""
Private method for removing a descriptor from the event loop.
It does the inverse job of _add, and also add a check in case of the fd
has gone away.
"""
if xer in primary:
notifier = primary.pop(xer)
notifier.shutdown()
def removeReader(self, reader):
"""
Remove a Selectable for notification of data available to read.
"""
self._remove(reader, self._reads)
def removeWriter(self, writer):
"""
Remove a Selectable for notification of data available to write.
"""
self._remove(writer, self._writes)
def removeAll(self):
"""
Remove all selectables, and return a list of them.
"""
rv = self._removeAll(self._reads, self._writes)
return rv
def getReaders(self):
return self._reads.keys()
def getWriters(self):
return self._writes.keys()
def callLater(self, howlong, *args, **kargs):
rval = super(QtReactor, self).callLater(howlong, *args, **kargs)
self.reactorInvocation()
return rval
def reactorInvocation(self):
self._timer.stop()
self._timer.setInterval(0)
self._timer.start()
def _iterate(self, delay=None, fromqt=False):
"""
See twisted.internet.interfaces.IReactorCore.iterate.
"""
self.runUntilCurrent()
self.doIteration(delay, fromqt)
iterate = _iterate
def doIteration(self, delay=None, fromqt=False):
"""
This method is called by a Qt timer or by network activity
on a file descriptor
"""
if not self.running and self._blockApp:
self._blockApp.quit()
self._timer.stop()
delay = max(delay, 1)
if not fromqt:
self.qApp.processEvents(QEventLoop.AllEvents, delay * 1000)
if self.timeout() is None:
timeout = 0.1
elif self.timeout() == 0:
timeout = 0
else:
timeout = self.timeout()
self._timer.setInterval(timeout * 1000)
self._timer.start()
def runReturn(self, installSignalHandlers=True):
self.startRunning(installSignalHandlers=installSignalHandlers)
self.reactorInvocation()
def run(self, installSignalHandlers=True):
if self._ownApp:
self._blockApp = self.qApp
else:
self._blockApp = QEventLoop()
self.runReturn()
self._blockApp.exec_()
class AppetitivePlugin(BasePlugin):
'''
Plugin for controlling appetitive experiments that are based on a reward.
Eventually this may become generic enough that it can be used with aversive
experiments as well (it may already be sufficiently generic).
'''
lock = Typed(object)
# Current trial
trial = Int(0)
# Current number of consecutive nogos
consecutive_nogo = Int(0)
# Used by the trial sequence selector to randomly select between go/nogo.
rng = Typed(np.random.RandomState)
trial_type = Unicode()
trial_info = Typed(dict, ())
trial_state = Typed(TrialState)
timer = Typed(QTimer)
event_map = {
('rising', 'nose_poke'): Event.np_start,
('falling', 'nose_poke'): Event.np_end,
('rising', 'reward_contact'): Event.reward_start,
('falling', 'reward_contact'): Event.reward_end,
}
score_map = {
('nogo', 'reward'): TrialScore.false_alarm,
('nogo', 'poke'): TrialScore.correct_reject,
('nogo', 'no response'): TrialScore.correct_reject,
('go', 'reward'): TrialScore.hit,
('go', 'poke'): TrialScore.miss,
('go', 'no response'): TrialScore.miss,
}
def next_selector(self):
'''
Determine next trial type
'''
try:
max_nogo = self.context.get_value('max_nogo')
go_probability = self.context.get_value('go_probability')
score = self.context.get_value('score')
except KeyError:
self.trial_type = 'go_remind'
return 'remind'
if self._remind_requested:
self.trial_type = 'go_remind'
return 'remind'
elif self.consecutive_nogo >= max_nogo:
self.trial_type = 'go_forced'
return 'go'
elif score == TrialScore.false_alarm:
self.trial_type = 'nogo_repeat'
return 'nogo'
else:
if self.rng.uniform() <= go_probability:
self.trial_type = 'go'
return 'go'
else:
self.trial_type = 'nogo'
return 'nogo'
def start_experiment(self):
self.lock = threading.RLock()
try:
self.trial += 1
#self.context.apply_changes()
#self.core.invoke_command('psi.data.prepare')
#self.start_engines()
#log.debug('Done starting engines')
self.rng = np.random.RandomState()
self.context.next_setting(self.next_selector(), save_prior=False)
self.experiment_state = 'running'
self.trial_state = TrialState.waiting_for_np_start
# Evaluates remaining values in context
self.context.get_values()
self.invoke_actions('experiment_start', self.get_ts())
except Exception as e:
# TODO - provide user interface to notify of errors. How to
# recover?
raise
def start_trial(self):
self.invoke_actions('trial_start', self.get_ts())
# TODO - the hold duration will include the update delay. Do we need
# super-precise tracking of hold period or can it vary by a couple 10s
# to 100s of msec?
self.trial_state = TrialState.waiting_for_hold_period
self.start_timer('hold_duration', Event.hold_duration_elapsed)
def end_trial(self, response):
log.debug('Animal responded by {}, ending trial'.format(response))
self.stop_timer()
trial_type = self.trial_type.split('_', 1)[0]
score = self.score_map[trial_type, response]
self.consecutive_nogo = self.consecutive_nogo + 1 \
if trial_type == 'nogo' else 0
response_ts = self.trial_info.setdefault('response_ts', np.nan)
target_start = self.trial_info.setdefault('target_start', np.nan)
np_end = self.trial_info.setdefault('np_end', np.nan)
np_start = self.trial_info.setdefault('np_start', np.nan)
self.trial_info.update({
'response': response,
'trial_type': self.trial_type,
'score': score.value,
'correct': score in (TrialScore.correct_reject, TrialScore.hit),
'response_time': response_ts-target_start,
'reaction_time': np_end-np_start,
})
if score == TrialScore.false_alarm:
self.invoke_actions('timeout_start', self.get_ts())
self.trial_state = TrialState.waiting_for_to
self.start_timer('to_duration', Event.to_duration_elapsed)
else:
if score == TrialScore.hit:
if not self.context.get_value('training_mode'):
self.invoke_actions('deliver_reward', self.get_ts())
self.trial_state = TrialState.waiting_for_iti
self.start_timer('iti_duration', Event.iti_duration_elapsed)
self.context.set_values(self.trial_info)
parameters ={'results': self.context.get_values()}
self.core.invoke_command('psi.data.process_trial', parameters)
log.debug('Setting up for next trial')
# Apply pending changes that way any parameters (such as repeat_FA or
# go_probability) are reflected in determining the next trial type.
if self._apply_requested:
self._apply_changes()
selector = self.next_selector()
self.context.next_setting(selector, save_prior=True)
self.trial += 1
self.trial_info = {}
def request_resume(self):
super(AppetitivePlugin, self).request_resume()
self.trial_state = TrialState.waiting_for_np_start
def ao_callback(self, name):
log.debug('Updating output {}'.format(name))
self._outputs[name].update()
def ai_callback(self, name, data):
parameters = {'name': name, 'data': data}
self.core.invoke_command('psi.data.process_ai', parameters)
def di_callback(self, name, data):
pass
def et_callback(self, name, edge, event_time):
if edge == 'processed':
# sort of a hack ...
parameters = {'name': 'event_log', 'timestamp': event_time}
self.core.invoke_command('psi.data.set_current_time', parameters)
else:
log.debug('Detected {} on {} at {}'.format(edge, name, event_time))
event = self.event_map[edge, name]
self.handle_event(event, event_time)
def stop_experiment(self):
self.stop_engines()
self.experiment_state = 'stopped'
self.invoke_actions('experiment_end', self.get_ts())
self.core.invoke_command('psi.data.finalize')
def pause_experiment(self):
if self.trial_state == TrialState.waiting_for_np_start:
deferred_call(self._pause_experiment)
def _pause_experiment(self):
self.experiment_state = 'paused'
self._pause_requested = False
def apply_changes(self):
if self.trial_state == TrialState.waiting_for_np_start:
deferred_call(self._apply_changes)
def _apply_changes(self):
self.context.apply_changes()
self._apply_requested = False
log.debug('applied changes')
def handle_event(self, event, timestamp=None):
# Ensure that we don't attempt to process several events at the same
# time. This essentially queues the events such that the next event
# doesn't get processed until `_handle_event` finishes processing the
# current one.
# Only events generated by NI-DAQmx callbacks will have a timestamp.
# Since we want all timing information to be in units of the analog
# output sample clock, we will capture the value of the sample clock
# if a timestamp is not provided. Since there will be some delay
# between the time the event occurs and the time we read the analog
# clock, the timestamp won't be super-accurate. However, it's not
# super-important since these events are not reference points around
# which we would do a perievent analysis. Important reference points
# would include nose-poke initiation and withdraw, reward contact,
# sound onset, lights on, lights off. These reference points will
# be tracked via NI-DAQmx or can be calculated (i.e., we know
# exactly when the target onset occurs because we precisely specify
# the location of the target in the analog output buffer).
try:
if timestamp is None:
timestamp = self.get_ts()
log.debug('{} at {}'.format(event, timestamp))
log.trace('Emitting handle_event signal')
deferred_call(self._handle_event, event, timestamp)
except Exception as e:
log.exception(e)
raise
def _handle_event(self, event, timestamp):
'''
Give the current experiment state, process the appropriate response for
the event that occured. Depending on the experiment state, a particular
event may not be processed.
'''
log.debug('Recieved handle_event signal')
self.invoke_actions(event.name, timestamp)
if self.experiment_state == 'paused':
# If the experiment is paused, don't do anything.
return
if self.trial_state == TrialState.waiting_for_np_start:
if event == Event.np_start:
# Animal has nose-poked in an attempt to initiate a trial.
self.trial_state = TrialState.waiting_for_np_duration
self.start_timer('np_duration', Event.np_duration_elapsed)
# If the animal does not maintain the nose-poke long enough,
# this value will be deleted.
self.trial_info['np_start'] = timestamp
elif self.trial_state == TrialState.waiting_for_np_duration:
if event == Event.np_end:
# Animal has withdrawn from nose-poke too early. Cancel the
# timer so that it does not fire a 'event_np_duration_elapsed'.
log.debug('Animal withdrew too early')
self.stop_timer()
self.trial_state = TrialState.waiting_for_np_start
del self.trial_info['np_start']
elif event == Event.np_duration_elapsed:
log.debug('Animal initiated trial')
self.start_trial()
# We want to deliver the reward immediately when in training
# mode so the food is already in the hopper. Not sure how
# *critical* this is?
if self.context.get_value('training_mode'):
if self.trial_type.startswith('go'):
self.invoke_actions('deliver_reward', self.get_ts())
elif self.trial_state == TrialState.waiting_for_hold_period:
# All animal-initiated events (poke/reward) are ignored during this
# period but we may choose to record the time of nose-poke withdraw
# if it occurs.
if event == Event.np_end:
# Record the time of nose-poke withdrawal if it is the first
# time since initiating a trial.
log.debug('Animal withdrew during hold period')
if 'np_end' not in self.trial_info:
log.debug('Recording np_end')
self.trial_info['np_end'] = timestamp
elif event == Event.hold_duration_elapsed:
log.debug('Animal maintained poke through hold period')
self.trial_state = TrialState.waiting_for_response
self.invoke_actions('response_start', self.get_ts())
self.start_timer('response_duration',
Event.response_duration_elapsed)
elif self.trial_state == TrialState.waiting_for_response:
# If the animal happened to initiate a nose-poke during the hold
# period above and is still maintaining the nose-poke, they have to
# manually withdraw and re-poke for us to process the event.
if event == Event.np_end:
# Record the time of nose-poke withdrawal if it is the first
# time since initiating a trial.
log.debug('Animal withdrew during response period')
if 'np_end' not in self.trial_info:
log.debug('Recording np_end')
self.trial_info['np_end'] = timestamp
elif event == Event.np_start:
log.debug('Animal repoked')
self.trial_info['response_ts'] = timestamp
self.end_trial(response='poke')
# At this point, trial_info should have been cleared by the
# `end_trial` function so that we can prepare for the next
# trial. Save the start of the nose-poke.
self.trial_info['np_start'] = timestamp
elif event == Event.reward_start:
log.debug('Animal went to reward')
self.trial_info['response_ts'] = timestamp
self.end_trial(response='reward')
elif event == Event.response_duration_elapsed:
log.debug('Animal provided no response')
self.trial_info['response_ts'] = np.nan
self.end_trial(response='no response')
elif self.trial_state == TrialState.waiting_for_to:
if event == Event.to_duration_elapsed:
# Turn the light back on
self.invoke_actions('timeout_end', self.get_ts())
self.trial_state = TrialState.waiting_for_iti
self.invoke_actions('iti_start', self.get_ts())
self.start_timer('iti_duration', Event.iti_duration_elapsed)
elif event in (Event.reward_start, Event.np_start):
log.debug('Resetting timeout duration')
self.stop_timer()
self.start_timer('to_duration', Event.to_duration_elapsed)
elif self.trial_state == TrialState.waiting_for_iti:
if event == Event.iti_duration_elapsed:
if self._pause_requested:
self.pause_experiment()
self.trial_state = TrialState.waiting_for_resume
elif 'np_start' in self.trial_info:
# The animal had initiated a nose-poke during the ITI.
# Allow this to contribute towards the start of the next
# trial by calculating how much is pending in the nose-poke
# duration.
self.trial_state = TrialState.waiting_for_np_duration
current_poke_duration = self.get_ts()-self.trial_info['np_start']
poke_duration = self.context.get_value('np_duration')
remaining_poke_duration = poke_duration-current_poke_duration
delta = max(0, remaining_poke_duration)
self.start_timer(delta, Event.np_duration_elapsed)
else:
self.trial_state = TrialState.waiting_for_np_start
elif event == Event.np_end and 'np_start' in self.trial_info:
del self.trial_info['np_start']
def start_timer(self, duration, event):
deferred_call(self._start_timer, duration, event)
def stop_timer(self):
deferred_call(self._stop_timer)
def _stop_timer(self):
if self.timer is not None:
self.timer.timeout.disconnect()
self.timer.stop()
def _start_timer(self, duration, event):
# The duration can be specified as a string naming the context variable
# to extract.
if isinstance(duration, basestring):
duration = self.context.get_value(duration)
log.debug('Timer for {} with duration {}'.format(event, duration))
receiver = partial(self.handle_event, event)
if duration == 0:
deferred_call(receiver)
else:
self.timer = QTimer()
self.timer.timeout.connect(receiver) # set up new callback
self.timer.setSingleShot(True) # call only once
self.timer.start(duration*1e3)
