class SessionManager(object):
sessionmgr_version = Ver('0.0.1')
name = ''
def __init__(self, **kwargs):
if not kwargs:
pass
elif 'data' in kwargs:
self = self.load_from_dict(kwargs['data]'])
else:
pass
def load_from_dict(self, data):
self.sessionmgr_version = Ver(data['sessionmgr_version'])
self.name = data['name']
def save_to_dict(self):
data = dict()
data['sessionmgr_version'] = self.sessionmgr_version.__str__()
data['name'] = self.name
return data
def __repr__(self):
return "SessionManager object with name:%s" % (self.name)
def check_schedule(self):
return False
class NoTimeOff(SessionManager):
notimeoff_version = Ver('0.0.1')
def __init__(self, **kwargs):
super(NoTimeOff, self).__init__(**kwargs)
if not kwargs:
pass
elif 'data' in kwargs:
self = self.load_from_dict(kwargs['data]'])
else:
pass
def load_from_dict(self, data):
self.notimeoff_version = Ver(data['notimeoff_version'])
def save_to_dict(self):
data = super(NoTimeOff, self).save_to_dict()
data['notimeoff_version'] = self.notimeoff_version.__str__()
return data
def __repr__(self):
return "NoTimeOff object"
def check_schedule(self, **kwargs):
# Returns keep_doing_trials, secs_remaining_until_state_flip
keep_doing_trials = True
secs_remaining_until_state_flip = 0
return keep_doing_trials, secs_remaining_until_state_flip
class TimeRange(SessionManager):
timerange_version = Ver('0.0.1')
time_start = None
time_stop = None
def __init__(self, **kwargs):
super(TimeRange, self).__init__(**kwargs)
if not kwargs:
pass
elif 'data' in kwargs:
self = self.load_from_dict(kwargs['data]'])
else:
pass
def load_from_dict(self, data):
self.timerange_version = Ver(data['timerange_version'])
self.time_start = data['time_start']
self.time_stop = data['time_stop']
def save_to_dict(self):
data = super(TimeRange, self).save_to_dict()
data['timerange_version'] = self.timerange_version.__str__()
data['time_start'] = self.time_start
data['time_stop'] = self.time_stop
return data
def __repr__(self):
return "TimeRange object"
def check_schedule(self):
return NotImplementedError()
def __init__(self):
self.ver = Ver('0.0.1') # Feb 28 2014
name = "DemoGratingsProtocol"
training_steps = [
TrainingStep(
name="DemoGratingStepNum1",
trial_manager=gratings.GratingsAFC(
name='DemoAFCGratingsTrialManager',
deg_per_cycs={
'L': [0.20],
'R': [0.20]
},
durations={
'L': [1.],
'R': [1.]
},
reinforcement_manager=reinfmgr.ConstantReinforcement()),
# trial_manager=Gratings(name='DemoAFCGratingsTrialManager',
# deg_per_cycs=[0.1], #degrees
# orientations=[45,-45,], #degrees
# contrasts=[1],
# durations=[1], #seconds
# radii=[400], #degrees
# iti=1, #seconds
# itl=0., #inter trial luminance,
# ),
session_manager=sessmgr.NoTimeOff(),
criterion=crit.RepeatIndefinitely())
]
super(DemoAFCGratingsProtocol, self).__init__(training_steps,
name=name)
class MinutesPerSession(SessionManager):
minutespersession_version = Ver('0.0.1')
minutes = None
hours_between_sessions = None
def __init__(self, **kwargs):
super(MinutesPerSession, self).__init__(**kwargs)
if not kwargs:
pass
elif 'data' in kwargs:
self = self.load_from_dict(kwargs['data]'])
else:
pass
def load_from_dict(self, data):
self.minutespersession_version = Ver(data['minutespersession_version'])
self.minutes = data['minutes']
self.hours_between_sessions = data['hours_between_sessions']
def save_to_dict(self):
data = super(MinutesPerSession, self).save_to_dict()
data[
'minutespersession_version'] = self.minutespersession_version.__str__(
)
data['minutes'] = self.minutes
data['hours_between_sessions'] = self.hours_between_sessions
return data
def __repr__(self):
return "MinutesPerSession object, %s minutes with %s hrs between sessions" % (
self.minutes, self.hours_between_sessions)
def check_schedule(self):
return NotImplementedError()
def __init__(self,
trials_per_minute=10,
consecutive_minutes=5,
name='Unknown'):
super(PerformanceCriterion, self).__init__(name)
self.ver = Ver('0.0.1')
self.trials_per_minute = trials_per_minute
self.consecutive_minutes = consecutive_minutes
def __init__(self,
num_trials=100,
num_trials_mode='global',
name='Unknown'):
super(NumTrialsDoneCriterion, self).__init__(name)
self.ver = Ver('0.0.1')
self.num_trials = num_trials
self.num_trials_mode = num_trials_mode
def load_from_dict(self, data):
self.svbstation_version = Ver(data['svbstation_version'])
self.sound_on = data['sound_on']
self.io_type = data['io_type']
self.parallel_port = data['parallel_port']
self.parallel_port_address = data['parallel_port_address']
self.display_name = data['display_name']
self.display_type = data['display_type']
return self
def __init__(self, draw_stim_onset_rect=False, iti=1.0, itl=(0., 0., 0.)):
self.ver = Ver('0.0.2')
self.draw_stim_onset_rect = draw_stim_onset_rect
self.iti = iti
if np.isscalar(itl):
self.itl = itl * np.asarray(
[1, 1, 1]) # inter trial luminance as gray scale
else:
self.itl = np.asarray(itl) #itl as color
def __init__(self,
pct_correct=0.8,
num_trials=200,
num_trials_mode='global',
name='Unknown'):
super(PerformanceCriterion, self).__init__(name)
self.ver = Ver('0.0.1')
self.pct_correct = pct_correct
self.num_trials = num_trials
self.num_trials_mode = num_trials_mode
def load_from_dict(self, data):
self.version = Ver(data['version']) # needed
self.server_id = data['server_id'] # needed
self.server_data_path = data['server_data_path'] # needed
self.creation_time = datetime.datetime.strptime(
data['creation_time'],
DATETIME_TO_STR) # Month-dd-YYYY::Hr:Min:Sec
for sub in data['subjects']:
self.subjects.append(Subject.load_from_dict(sub))
for stn in data['stations']:
self.stations.append(Station.load_from_dict(stn))
self.assignments = data['assignemnts']
return self
def load_from_dict(self, data):
self.station_version = Ver(data['station_version'])
self.creation_time = datetime.datetime.strptime(
data['creation_time'], DATETIME_TO_STR)
self.station_id = data['station_id']
self.station_name = data['station_name']
self.station_path = os.path.join(get_base_path(), 'BCoreData',
'StationData', str(self.station_id))
self.station_location = data['station_location']
self.mac_address = get_mac_address()
self.ip_address = get_ip_addr()
self.port = get_port()
return self
def __init__(
self,
name,
reinforcement_manager=reinfmgr.ConstantReinforcement(),
min_run_speed=50, # sets_trigger on arduino
run_duration_distribution=2., # seconds
iti=1.,
itl=(
0.,
0.,
0.,
),
**kwargs):
super(RunForReward, self).__init__(iti=iti, itl=itl)
self.ver = Ver('0.0.1')
self.reinforcement_manager = reinforcement_manager
self.name = name
self.run_speed = run_speed
self.run_duration_distribution = delay_distribution
self._verify_params_ok()
def __init__(self,
name='DefaultCC_ConstantDelay_1s',
delay_distribution=('Constant', 1.),
go_signal=None,
response_duration=2.,
iti=1.,
itl=(
0.,
0.,
0.,
),
**kwargs):
super(ClassicalConditioning, self).__init__(iti=iti, itl=itl)
self.ver = Ver('0.0.2')
self.reinforcement_manager = reinforcement_manager
self.name = name
self.delay_distribution = delay_distribution
self.go_signal = go_signal
self.response_duration = response_duration
# check if values are ok
self._verify_params_ok()
def __init__(self,
name='DefaultAuditory_Go_ConstantDelay_2s',
reinforcement_manager=reinfmgr.ConstantReinforcement(),
delay_distribution=('Constant', 2.),
go_signal=None,
response_duration=2.,
iti=1.,
itl=(
0.,
0.,
0.,
),
**kwargs):
super(AuditoryGoOnly, self).__init__(iti=iti, itl=itl)
self.ver = Ver('0.0.1')
self.reinforcement_manager = reinforcement_manager
self.name = name
self.delay_distribution = delay_distribution
self.go_signal = go_signal
self.response_duration = response_duration
# check if values are ok
self._verify_params_ok()
class BServer(object):
"""
BSERVER keeps track of all the stations that it commands,
which subjects are allowed in which station and data storage locations.
version : string identifier
server_id : string Identifier
server_data_path : allowed data storage location
server_ip : IPV4 value
creation_time : time.time()
stations : list of stations
subjects : list of subjects
assignments : dictionary with keys being subjectID
and values being list of stationIDs
"""
version = Ver('0.0.1') # Feb 5, 2014
server_id = ''
server_ip = ''
server_data_path = ''
creation_time = None
stations = []
subjects = []
assignments = dict()
server_connection = []
station_connections = []
def __init__(self, **kwargs):
if not kwargs:
self.creation_time = datetime.datetime.now()
elif 'data' in kwargs:
self = self.load_from_dict(kwargs['data'], convert=False)
else:
pass
def load_from_dict(self, data):
self.version = Ver(data['version']) # needed
self.server_id = data['server_id'] # needed
self.server_data_path = data['server_data_path'] # needed
self.creation_time = datetime.datetime.strptime(
data['creation_time'],
DATETIME_TO_STR) # Month-dd-YYYY::Hr:Min:Sec
for sub in data['subjects']:
self.subjects.append(Subject.load_from_dict(sub))
for stn in data['stations']:
self.stations.append(Station.load_from_dict(stn))
self.assignments = data['assignemnts']
return self
def save_to_dict(self):
data = dict()
data['version'] = self.version.__str__()
data['server_id'] = self.server_id
data['server_data_path'] = self.server_data_path
data['creation_time'] = datetime.datetime.strftime(
self.creation_time, DATETIME_TO_STR)
subjects = []
for sub in self.subjects:
subjects.append(sub.save_to_dict())
data['subjects'] = subjects
stations = []
for stn in self.stations:
stations.append(stn.save_to_dict())
data['stations'] = stations
data['assignments'] = self.assignments
def __repr__(self):
return "BServer with id:%s, name:%s, created on:%s)" % (
self.server_id, self.server_name,
time.strftime("%b-%d-%Y", self.creation_time))
def run(server, **kwargs):
# should expose the ZMQ context. and allow connections
raise NotImplementedError()
@staticmethod
def load():
"""
Alias for server.loadServer
"""
return BServer.load_server()
@staticmethod
def load_server():
# use standard location for path,
# make sure to never modify server here:
dbLoc = os.path.join(get_base_path(), 'BCoreData', 'ServerData',
'db.BServer')
if os.path.isfile(dbLoc):
with open(dbLoc, 'rb') as f:
server = json.load(f)
print('BServer loaded')
else:
raise RuntimeError(
'db.Server not found. Ensure it exists before calling loadServer'
)
return server
def save(self):
"""
Alias for server.saveServer
"""
self.save_server()
def save_server(self):
srcDir = os.path.join(get_base_path(), 'BCoreData', 'ServerData')
desDir = os.path.join(get_base_path(), 'BCoreData', 'ServerData',
'backupDBs')
if not os.path.isdir(self.server_data_path):
# assume that these are never made alone...
self._setup_paths()
if os.path.isfile(os.path.join(srcDir, 'db.BServer')): # old db exists
print(('Old db.Bserver found. moving to backup'))
old = BServer() # standardLoad to old
des_name = 'db_' + get_time_stamp(old.creation_time) + '.BServer'
shutil.copyfile(os.path.join(srcDir, 'db.BServer'),
os.path.join(desDir, des_name))
print(('Moved to backup... deleting old copy'))
os.remove(os.path.join(srcDir, 'db.BServer'))
# there might be some attributes that need to be deleted
# delete them here before continuing
print(('Cleaning and pickling object'))
cleanedBServer = copy.deepcopy(self)
cleanedBServer.station_connections = {}
with open(os.path.join(srcDir, 'db.BServer'), 'wb') as f:
pickle.dump(cleanedBServer, f)
def load_backup(self):
"""
Use this only if you specifically require the deletion of current
db.BServer and replacement with an older backup. Only the latest
back up is used.
"""
desDir = os.path.join(get_base_path(), 'BCoreData', 'ServerData')
srcDir = os.path.join(get_base_path(), 'BCoreData', 'ServerData',
'backupDBs')
# delete the original database
os.remove(os.path.join(desDir, 'db.BServer'))
# find the latest file in the backupDBs
newestBkup = max(os.listdir(srcDir), key=os.path.getctime)
shutil.copyfile(
os.path.join(srcDir, newestBkup), # source
os.path.join(desDir, 'db.BServer') # destination
)
# delete the newest backup
os.remove(os.path.join(srcDir, newestBkup))
def _setup_paths(server):
# create 'BServerData'
os.mkdir(os.path.join(get_base_path(), 'BCoreData'))
# create 'ServerData','Stations','PermanentTrialRecordStore' in
# BServerData
os.mkdir(os.path.join(get_base_path(), 'BCoreData', 'ServerData'))
os.mkdir(os.path.join(get_base_path(), 'BCoreData', 'StationData'))
os.mkdir(os.path.join(get_base_path(), 'BCoreData', 'SubjectData'))
os.mkdir(os.path.join(get_base_path(), 'BCoreData', 'ChangeParams'))
# create 'replacedDBs' in 'ServerData'
os.mkdir(
os.path.join(get_base_path(), 'BCoreData', 'ServerData',
'backupDBs'))
# create 'Full' and 'Compiled' in 'SubjectData'
os.mkdir(
os.path.join(get_base_path(), 'BCoreData', 'SubjectData',
'SessionRecords'))
os.mkdir(
os.path.join(get_base_path(), 'BCoreData', 'SubjectData',
'CompiledTrialRecords'))
def add_station(self, new_station):
if (new_station.station_id in self.get_station_ids()
or new_station.station_name in self.get_station_names()):
raise ValueError('Station IDs and Station Names have to be unique')
self.stations.append(new_station)
# now enable station specific data
self.save()
def add_subject(self, new_subject):
if new_subject in self.subjects:
raise ValueError('Cannot add replica of subjects to BServer')
self.subjects.append(new_subject)
self.save()
def change_assignment(self, subject, new_assignment):
if subject not in self.subjects:
raise ValueError('Cannot change assignment on a subject \
that is not on Bserver')
if not (any(new_assignment in self.get_station_ids())):
raise ValueError('Cannot assign subject to non existent stations')
self.assignments[subject.subject_id] = new_assignment
self.save()
def get_station_ids(self):
station_ids = []
for station in self.stations:
station_ids.append(station.station_id)
return station_ids
def get_station_names(self):
station_names = []
for station in self.stations:
station_names.append(station.station_name)
return station_names
def get_subject_ids(self):
subject_ids = []
for subject in self.subjects:
subject_ids.append(subject.subject_id)
return subject_ids
def __init__(self):
self.ver = Ver('0.0.1')
name = 'DemoNoStimulusProtocol'
class StandardKeyboardStation(StandardVisionBehaviorStation):
"""
STANDARDKEYBOARDSTATION(SKBS) defines a subclass of
STANDARDVISIONBEHAVIORSTATION(SVBS).
It defines a station with a standard display, sounds settings
which can only be turned on or off, three sensor pins
[connected to the keyboard]. Only allows stand alone running
Attributes allowed are:
station_id : numeric ID to be sent to STATION
station_path : DO NOT SEND - STATION WILL SET IT
display : dictionary containing details about the
display unit
soundOn : True/False
For the StandardKeyboardStation:
K+1 : Left Sensor
K+2 : Center Sensor
K+3 : Right Sensor
K+Q : Quit
"""
skstation_version = Ver('0.0.1')
def __init__(self, **kwargs):
super(StandardKeyboardStation, self).__init__(**kwargs)
if not kwargs:
pass
elif 'data' in kwargs:
self = self.load_from_dict(kwargs['data]'])
else:
pass
def load_from_dict(self, data):
self.skstation_version = Ver(data['skstation_version'])
return self
def save_to_dict(self):
data = super(StandardKeyboardStation, self).save_to_dict()
data['skstation_version'] = self.skstation_version
return data
def __repr__(self):
return "StandardKeyboardStation object with id:%s, location:%s and ip:%s" % (
self.station_id, self.station_location, self.ip_address)
@property
def num_ports(self):
return 3
def read_ports(self):
key = psychopy.event.getKeys(keyList=['1', '2', '3', 'k'])
ports = np.asarray([False, False, False])
if key:
if not key[0] in self._key_pressed:
self._key_pressed.append(key[0])
if 'k' in self._key_pressed and '1' in self._key_pressed:
ports = np.bitwise_or(ports, [True, False, False])
psychopy.event.clearEvents()
print(self._key_pressed)
self._key_pressed.remove('k')
self._key_pressed.remove('1')
if 'k' in self._key_pressed and '2' in self._key_pressed:
ports = np.bitwise_or(ports, [False, True, False])
psychopy.event.clearEvents()
print(self._key_pressed)
self._key_pressed.remove('k')
self._key_pressed.remove('2')
if 'k' in self._key_pressed and '3' in self._key_pressed:
ports = np.bitwise_or(ports, [False, False, True])
psychopy.event.clearEvents()
print(self._key_pressed)
self._key_pressed.remove('k')
self._key_pressed.remove('3')
return self.get_ports()[ports]
def open_valve(self, valve):
print('Opening valve', valve)
def close_valve(self, valve):
print('Closing valve', valve)
def flush_valves(self, dur=1):
pass
def close_all_valves(self):
print('Closing all valves')
def initialize(self):
self.initialize_display(display=self.display)
self.initialize_sounds()
self.close_all_valves()
def load_from_dict(self, data):
self.notimeoff_version = Ver(data['notimeoff_version'])
def __init__(self, name='DefaultProtocol'):
self.ver = Ver('0.0.1') # Feb 28 2014
self.name = name
def load_from_dict(self, data):
self.sessionmgr_version = Ver(data['sessionmgr_version'])
self.name = data['name']
def load_from_dict(self, data):
self.timerange_version = Ver(data['timerange_version'])
self.time_start = data['time_start']
self.time_stop = data['time_stop']
class Station(object):
"""
STATION contains all the relevant details and interfaces to run
trials from a particular station. This is an abstract class.
Do not instantiate.
stationID : numeric ID
stationPath : string path to data storage location
MACAddress : unique mac address for the processor/ethernet
card. string identifier
"""
_subject = None
_key_pressed = []
_sounds = {}
_stims = {}
_clocks = {}
_parallel_port_conn = None
creation_time = ''
station_version = Ver('0.0.1')
station_id = None
station_name = ''
station_path = ''
station_location = None
def __init__(self, **kwargs):
if not kwargs:
pass
elif 'data' in kwargs:
self = self.load_from_dict(kwargs['data'])
else:
pass
def load_from_dict(self, data):
self.station_version = Ver(data['station_version'])
self.creation_time = datetime.datetime.strptime(
data['creation_time'], DATETIME_TO_STR)
self.station_id = data['station_id']
self.station_name = data['station_name']
self.station_path = os.path.join(get_base_path(), 'BCoreData',
'StationData', str(self.station_id))
self.station_location = data['station_location']
self.mac_address = get_mac_address()
self.ip_address = get_ip_addr()
self.port = get_port()
return self
def save_to_dict(self):
data = dict()
data['station_version'] = self.station_version.__str__()
data['station_id'] = self.station_id
data['station_name'] = self.station_name
data['station_location'] = self.station_location
data['creation_time'] = datetime.datetime.strftime(
self.creation_time, DATETIME_TO_STR)
return data
def __repr__(self):
return "Station object with id:%s, location:%s and ip:%s" % (
self.station_id, self.station_location, self.ip_address)
def register(self):
#
pass
def _setup_paths(self):
if not os.path.isdir(self.station_path):
os.makedirs(self.station_path)
def do_trials(self, **kwargs):
raise NotImplementedError('Run doTrials() on a subclass')
def initialize_sounds(self):
self._sounds['trial_start_sound'] = psychopy.sound.Sound(440,
stereo=0,
secs=1.,
hamming=True)
self._sounds['request_sound'] = psychopy.sound.Sound(493.88,
stereo=0,
secs=1.,
hamming=True)
self._sounds['stim_start_sound'] = psychopy.sound.Sound(493.88,
stereo=0,
secs=1.,
hamming=True)
self._sounds['go_sound'] = psychopy.sound.Sound(493.88,
stereo=0,
secs=1.,
hamming=True)
self._sounds['keep_going_sound'] = psychopy.sound.Sound(493.88,
stereo=0,
secs=1.,
hamming=True)
self._sounds['request_sound'] = psychopy.sound.Sound(493.88,
stereo=0,
secs=1.,
hamming=True)
self._sounds['correct_sound'] = psychopy.sound.Sound(523.25,
stereo=0,
secs=1.,
hamming=True)
self._sounds['reward_sound'] = psychopy.sound.Sound(523.25,
stereo=0,
secs=1.,
hamming=True)
self._sounds['trial_end_sound'] = psychopy.sound.Sound(523.25,
stereo=0,
secs=1.,
hamming=True)
sampleRate, secs, f_punishment = (44100, 2, [370, 440])
nSamples = int(secs * sampleRate)
phase = 2 * np.pi * np.linspace(0.0, 1.0, nSamples)
val = np.full_like(phase, 0.)
for f in f_punishment:
val += np.sin(f * phase)
val = np.matlib.repmat(val, 2, 1)
self._sounds['punishment_sound'] = psychopy.sound.Sound(val.T,
hamming=True)
val = 0.5 * np.random.randn(1, nSamples)
val = np.matlib.repmat(val, 2, 1)
self._sounds['try_something_else'] = psychopy.sound.Sound(val.T,
hamming=True)
self._sounds['trial_end_sound'] = psychopy.sound.Sound(587.33,
stereo=0,
secs=1.,
hamming=True)
def _rewind_sounds(self, time=0.):
for sound in self._sounds:
self._sounds[sound].seek(time)
def decache(self):
"""
Remove session specific details. ideal for pickling
"""
self._key_pressed = None
self._sounds = None
self._stims = None
self._clocks = None
def load_from_dict(self, data):
self.minutespersession_version = Ver(data['minutespersession_version'])
self.minutes = data['minutes']
self.hours_between_sessions = data['hours_between_sessions']
class StandardVisionBehaviorStation(Station):
"""
STANDARDVISIONBEHAVIORSTATION(SVBS) defines a subclass of STATION.
It defines a station with a standard display, a parallel port for i/o
with standard pin-out settings, sounds settings which can only be
turned on or off, three valve pins, three sensor pins. Only allows
stand alone running
Attributes allowed are:
station_id : numeric ID to be sent to STATION
station_path : DO NOT SEND - STATION WILL SET IT
display : dictionary containing details about the
display unit
soundOn : True/False
parallelPort : dictionary containing details about the parallel
port
For the StandardVisualBehaviorStation, with Rev 2/3 breakout boards
("The Bomb"), only certain ports are used and for specific purposes:
Pin 2 : Right Reward Valve
Pin 3 : Center Reward Valve
Pin 4 : Left Reward Valve
Pin 5 : LED1
Pin 6 : eyePuff
Pin 7 : LED2
Pin 8 : indexPulse
Pin 9 : framePulse
Pin 10 : Center Response Sensor
Pin 12 : Right Response Sensor
Pin 13 : Left Response Sensor
While, these values are not hard coded here, use these values if you
want your system to work :)
Use these defaults unless you know what you are doing
parallel_port = {}
parallel_port['right_valve'] = 2
parallel_port['center_valve'] = 3
parallel_port['left_valve'] = 4
parallel_port['valve_pins'] = (2, 3, 4)
parallel_port['center_port'] = 10
parallel_port['right_port'] = 12
parallel_port['left_port'] = 13
parallel_port['port_pins'] = (12, 10, 13)
parallel_port['index_pin'] = 8
parallel_port['frame_pin'] = 9
parallel_port['led_0'] = 5
parallel_port['led_1'] = 7
"""
_window = None
_session = None
_server_conn = None
svbstation_version = Ver('0.0.1')
sound_on = False
io_type = ''
parallel_port = None
parallel_port_address = ''
display_name = ''
display_type = ''
display = None
def __init__(self, **kwargs):
super(StandardVisionBehaviorStation, self).__init__(**kwargs)
if not kwargs:
pass
elif 'data' in kwargs:
self = self.load_from_dict(kwargs['data]'])
else:
pass
self.display = self.get_display()
self.parallel_port = self.get_parport_mappings()
def load_from_dict(self, data):
self.svbstation_version = Ver(data['svbstation_version'])
self.sound_on = data['sound_on']
self.io_type = data['io_type']
self.parallel_port = data['parallel_port']
self.parallel_port_address = data['parallel_port_address']
self.display_name = data['display_name']
self.display_type = data['display_type']
return self
def save_to_dict(self):
data = super(StandardVisionBehaviorStation, self).save_to_dict()
data['svbstation_version'] = self.svbstation_version
data['sound_on'] = self.sound_on
data['io_type'] = self.io_type
data['parallel_port'] = self.parallel_port
data['parallel_port_address'] = self.parallel_port_address
data['display_name'] = self.display_name
data['display_type'] = self.display_type
return data
def __repr__(self):
return "StandardVisionBehaviorStation object with id:%s, location:%s and ip:%s" % (
self.station_id, self.station_location, self.ip_address)
def get_display(self):
return displays.StandardDisplay()
def get_parport_mappings(self):
if self.parallel_port == 'standardVisionBehaviorDefault':
print(
'STANDARDVISIONBEHAVIORSTATION:INITIALIZE_PARALLEL_PORT::setting parallelport to standardVisionBehaviorDefault'
)
pPort = {}
pPort['right_valve'] = 2
pPort['center_valve'] = 3
pPort['left_valve'] = 4
pPort['valve_pins'] = [2, 3, 4]
pPort['center_port'] = 10
pPort['right_port'] = 12
pPort['left_port'] = 13
pPort['port_pins'] = [13, 10, 12]
pPort['index_pin'] = 8
pPort['frame_pin'] = 9
pPort['trial_pin'] = 6
pPort['led_0'] = 5
pPort['led_1'] = 7
return pPort
elif self.parallel_port == 'standardHeadfixBehaviorDefault':
print(
'STANDARDVISIONBEHAVIORSTATION:INITIALIZE_PARALLEL_PORT::setting parallelport to standardVisionHeadfixDefault'
)
pPort = {}
pPort['reward_valve'] = 3
pPort['valve_pins'] = [
3,
]
pPort['response_port'] = 10
pPort['running_port'] = 13
pPort['port_pins'] = [
10,
]
pPort['index_pin'] = 8
pPort['frame_pin'] = 9
pPort['trial_pin'] = 6
pPort['led_0'] = 5
pPort['led_1'] = 7
return pPort
else:
return None # need to write code that checks if allowable
def initialize(self):
self.initialize_display(display=self.display)
self.initialize_sounds()
self.initialize_parallel_port()
self.close_all_valves()
def run(self):
self.connect_to_server()
run_trials = False
while True:
# look for data from server
msg = self.get_server_msg()
quit = False
if run_trials and ~quit:
# get info anout session
self.get_session()
sub = self._session['subject']
tR = self._session['trial_record']
cR = self._session['compiled_record']
prot = self._session['protocol']
trial_num = self._session['trial_num']
def initialize_display(self, display=displays.StandardDisplay()):
self._window = psychopy.visual.Window(color=(0., 0., 0.),
fullscr=True,
winType='pyglet',
allowGUI=False,
units='deg',
screen=0,
viewScale=None,
waitBlanking=True,
allowStencil=True,
monitor=display)
self._window.flip()
def initialize_parallel_port(self):
self._parallel_port_conn = psychopy.parallel.ParallelPort(
address=self.parallel_port_address)
self.close_all_valves()
def connect_to_server(self):
"""
This is a somewhat complicated handshake. Initially, the
station acts as a server exposing its IP::port to the server.
Since the server knows this IP::port it can create a client
connection easily. Upon connection, BServer(currently client)
sends a connection info for a separate connection(BServer will
reserve the space for this connection) to the station and the
station will connect to the BServer now as a client. This way
new stations can be added to the server without any
station-side code modification. BServer can dynamically manage
its resources. Along with threaded TCP server connections on
the server side, this should provide scalable, TCP communications
with the server
"""
self._server_conn = TCPServerConnection(ipaddr=self.ip_address,
port=self.port)
self._server_conn.start()
server_connection_details = self._server_conn.recvData()
# use server_connection_details to connect to the BServer as a client
print(
'STANDARDVISIONBEHAVIORSTATION:CONNECT_TO_SERVER::Closing connection as server...'
)
self._server_conn.stop()
self._server_conn = BehaviorClientConnection(
ipaddr=server_connection_details['ipaddr'],
port=server_connection_details['port'])
print(
'STANDARDVISIONBEHAVIORSTATION:CONNECT_TO_SERVER::Starting connection as client...'
)
self._server_conn.start()
@property
def subject(self):
return self._subject
@subject.setter
def subject(self, value):
self._subject = value
@property
def session(self):
return self._session
@session.setter
def session(self, value):
self._session = value
def get_ports(self):
return np.asarray(['left_port', 'center_port', 'right_port'])
@property
def num_ports(self):
if self.parallel_port:
return len(self.parallel_port['port_pins'])
else:
return 0
def add_subject(self, sub):
self.subject = sub
#if sub.subject_id in self.get_subjects():
# RuntimeError("STATION:STANDARDVISIONBEHAVIORSTATION:ADD_SUBJECT:Subject "+ sub.subject_id + " already in station. Cannot add twice")
#
#print("STATION:STANDARDVISIONBEHAVIORSTATION:ADD_SUBJECT: Adding subject_id " + sub.subject_id +" to station_id " + str(self.station_id))
#self.subjects.append(sub)
def remove_subject(self, sub):
self.subject = None
#if sub.subject_id not in self.get_subjects():
# RuntimeError("STATION:STANDARDVISIONBEHAVIORSTATION:ADD_SUBJECT:Subject "+ sub.subject_id + " not in station. Cannot remove.")
#print("STATION:STANDARDVISIONBEHAVIORSTATION:REMOVE_SUBJECT: Removing subject_id " + sub.subject_id +" from station_id " + str(self.station_id))
#idx = [i for (i,x) in enumerate(self.get_subjects()) if x==sub.subject_id]
#self.subjects = self.subjects[:idx[0]]+self.subjects[idx[0]+1:]
def close_all_valves(self):
val = list('{0:08b}'.format(self._parallel_port_conn.readData()))
for valve in self.parallel_port['valve_pins']:
val[1 - valve] = '0'
self._parallel_port_conn.setData(int(''.join(val), 2))
def read_ports(self):
out = [False, False, False]
port_names = ['left_port', 'center_port', 'right_port']
for i, port in enumerate(self.parallel_port['port_pins']):
out[i] = self._parallel_port_conn.readPin(port)
active_ports = [x for x, y in zip(port_names, out) if not y]
return active_ports
def open_valve(self, valve):
valve_pin = self.parallel_port[valve]
self.set_pin_on(valve_pin)
def close_valve(self, valve):
valve_pin = self.parallel_port[valve]
self.set_pin_off(valve_pin)
def flush_valves(self, dur=1):
val = list('{0:08b}'.format(self._parallel_port_conn.readData()))
for valve in self.parallel_port['valve_pins']:
val[1 - valve] = '1'
self._parallel_port_conn.setData(int(''.join(val), 2))
time.sleep(dur)
for valve in self.parallel_port['valve_pins']:
val[1 - valve] = '0'
self._parallel_port_conn.setData(int(''.join(val), 2))
def set_index_pin_on(self):
index_pin = self.parallel_port['index_pin']
self.set_pin_on(index_pin)
def set_index_pin_off(self):
index_pin = self.parallel_port['index_pin']
self.set_pin_off(index_pin)
def set_frame_pin_on(self):
frame_pin = self.parallel_port['frame_pin']
self.set_pin_on(frame_pin)
def set_frame_pin_off(self):
frame_pin = self.parallel_port['frame_pin']
self.set_pin_off(frame_pin)
def set_trial_pin_on(self):
trial_pin = self.parallel_port['trial_pin']
self.set_pin_on(trial_pin)
def set_trial_pin_off(self):
trial_pin = self.parallel_port['trial_pin']
self.set_pin_off(trial_pin)
def set_pin_on(self, pin):
if pin < 2 or pin > 9:
ValueError('Cannot deal with this')
val = list('{0:08b}'.format(self._parallel_port_conn.readData()))
val[1 - pin] = '1'
self._parallel_port_conn.setData(int(''.join(val), 2))
def set_pin_off(self, pin):
if pin < 2 or pin > 9:
ValueError('Cannot deal with this')
val = list('{0:08b}'.format(self._parallel_port_conn.readData()))
val[1 - pin] = '0'
self._parallel_port_conn.setData(int(''.join(val), 2))
def get_display_size(self):
pass
def get_session(self):
"""
Connect to BServer and request session details to be loaded
"""
self._session = self._server_conn.client_to_server(
self._server_conn.SESSION_REQUESTED)
def decache(self):
"""
Remove session specific details. ideal for pickling
"""
self._window = None
self._session = None
self._server_conn = None
self._parallel_port_conn = None
self._clocks = None
def do_trials(self, **kwargs):
# first step in the running of trials. called directly by station
# or through the BServer
if __debug__:
pass
self.initialize()
# get the compiled_records for the animal. Compiled records will contain all the information that will be used in
# the course of running the experiment. If some stimulus parameter for a given trial is dependent on something in
# the previous trial, please add it to compiled records
compiled_record = self.subject.load_compiled_records()
quit = False
# session starts here
session_record = [] # just a list of tRs
session_number = compiled_record["session_number"][-1] + 1
# setup the clocks
self._clocks['session_clock'] = psychopy.core.MonotonicClock()
self._clocks['trial_clock'] = psychopy.core.Clock()
session_start_time = psychopy.core.getAbsTime()
while not quit:
# it loops in here every trial
trial_record = {}
# just assign relevant details here
trial_record["session_start_time"] = session_start_time
trial_record[
"trial_number"] = compiled_record["trial_number"][-1] + 1
trial_record["session_number"] = session_number
trial_record["station_id"] = self.station_id
trial_record["station_version_number"] = self.ver.__str__()
trial_record["station_name"] = self.station_name
trial_record["num_ports_in_station"] = self.num_ports
trial_record["trial_start_time"] = self._clocks[
'session_clock'].getTime()
# doTrial - only trial_record will be returned as its type will be changed
trial_record, quit = self.subject.do_trial(
station=self,
trial_record=trial_record,
compiled_record=compiled_record,
quit=quit)
trial_record["trial_stop_time"] = self._clocks[
'session_clock'].getTime()
# update sessionRecord and compiledRecord
compiled_record = compile_records(compiled_record, trial_record)
session_record.append(trial_record)
# save session records
self.subject.save_session_records(session_record)
# save compiled records
self.subject.save_compiled_records(compiled_record)
self.decache()
def close_session(self, **kwargs):
print("STANDARDVISIONBEHAVIORSTATION:CLOSE_SESSION::Closing Session")
def close_window(self):
self._window.close()
def check_manual_quit(self):
key = psychopy.event.getKeys(keyList=['k', 'q'])
if key:
if not key[0] in self._key_pressed:
self._key_pressed.append(key[0])
if 'k' in self._key_pressed and 'q' in self._key_pressed:
psychopy.event.clearEvents()
return True
else:
return False
def read_kb(self):
key, modifier = event.getKeys(keyList=['1', '2', '3', 'k'],
modifier=True)
ports = np.asarray([False, False, False])
if key:
if not key[0] in self._key_pressed:
self._key_pressed.append(key[0])
if 'k' in self._key_pressed and '1' in self._key_pressed:
self._key_pressed.remove('k')
self._key_pressed.remove('1')
if 'k' in self._key_pressed and '2' in self._key_pressed:
ports = np.bitwise_or(ports, [False, True, False])
psychopy.event.clearEvents()
print(self._key_pressed)
self._key_pressed.remove('k')
self._key_pressed.remove('2')
if 'k' in self._key_pressed and '3' in self._key_pressed:
ports = np.bitwise_or(ports, [False, False, True])
psychopy.event.clearEvents()
print(self._key_pressed)
self._key_pressed.remove('k')
self._key_pressed.remove('3')
return self.get_ports()[ports]
def __init__(self, name='Unknown'):
self.name = name
self.ver = Ver('0.0.1')
class StandardVisionHeadfixStation(StandardVisionBehaviorStation):
"""
STANDARDVISIONHEADFIXSTATION(SVHS) defines a subclass of SVBS.
It defines a station with a standard display, a parallel port for i/o
with standard pin-out settings, sounds settings which can only be
turned on or off, one valve pins, one sensor pins. Only allows
stand alone running
Attributes allowed are:
station_id : numeric ID to be sent to STATION
station_path : DO NOT SEND - STATION WILL SET IT
display : dictionary containing details about the
display unit
soundOn : True/False
parallelPort : dictionary containing details about the parallel
port
For the StandardVisualBehaviorStation, with Rev 2/3 breakout boards
("The Bomb"), only certain ports are used and for specific purposes:
Pin 3 : Center Reward Valve
Pin 8 : indexPulse
Pin 9 : framePulse
Pin 10 : Center Response Sensor
While, these values are not hard coded here, use these values if you
want your system to work :)
Use these defaults unless you know what you are doing
parallel_port = {}
parallel_port['center_valve'] = 3
parallel_port['valve_pins'] = (3)
parallel_port['center_port'] = 10
parallel_port['port_pins'] = (10)
parallel_port['index_pin'] = 8
parallel_port['frame_pin'] = 9
parallel_port['led_0'] = 5
parallel_port['led_1'] = 7
"""
svhfstation_version = Ver('0.0.1')
def __init__(self, **kwargs):
super(StandardVisionHeadfixStation, self).__init__(**kwargs)
if not kwargs:
pass
elif 'data' in kwargs:
self = self.load_from_dict(kwargs['data]'])
else:
pass
def load_from_dict(self, data):
self.svhfstation_version = Ver(data['svhfstation_version'])
return self
def save_to_dict(self):
data = super(StandardVisionHeadfixStation, self).save_to_dict()
data['svhfstation_version'] = self.svhfstation_version
return data
def __repr__(self):
return "StandardVisionHeadfixStation object with id:%s, location:%s and ip:%s" % (
self.station_id, self.station_location, self.ip_address)
def get_ports(self):
return np.asarray(['response_port'])
def read_ports(self):
port_names = ['response_port']
if self._parallel_port_conn.readPin(
self.parallel_port['port_pins'][0]):
return [] # when the lick port is high then it is empty.
else:
return ['response_port'
] # when the lick port is low, then there is licking
def open_valve(self, valve):
valve_pin = self.parallel_port[valve]
self.set_pin_on(valve_pin)
def close_valve(self, valve):
valve_pin = self.parallel_port[valve]
self.set_pin_off(valve_pin)
def close_all_valves(self):
self.close_valve('reward_valve')
def __init__(self, name='Unknown'):
self.ver = Ver('0.0.1')
super(RepeatIndefinitely, self).__init__(name)
def load_from_dict(self, data):
self.skstation_version = Ver(data['skstation_version'])
return self
def __init__(self, name, trial_manager, session_manager, criterion):
self.ver = Ver('0.0.1')
self.name = name
self.trial_manager = trial_manager
self.session_manager = session_manager
self.criterion = criterion