def __init__(self):
super().__init__()
self._name = 'BaseTrialExperiment'
self.experiment_finished = False
self._event = None
self._print_check = False
self._current_trial = None
self._result_list = []
self._success_count = 0
self._parameter_dict = dict(TRIGGER='str',
PROCESS='str',
INTERTRIAL_TIME='int',
TRIAL_NAME='str',
TRIAL_TRIGGER='str',
TRIAL_TIME='int',
STIMULUS_TIME='int',
RESULT_FUNC='str',
EXP_LENGTH='int',
EXP_COMPLETION='int',
EXP_TIME='int')
self._settings_dict = get_experiment_settings(self._name,
self._parameter_dict)
self._process = setup_process(self._settings_dict['PROCESS'])
self._init_trigger = setup_trigger(self._settings_dict['TRIGGER'])
self._trials_list = self.generate_trials_list(
self._trials, self._settings_dict['EXP_LENGTH'])
self._trial_timer = Timer(self._settings_dict['TRIAL_TIME'])
self._exp_timer = Timer(self._settings_dict['EXP_TIME'])
self._intertrial_timer = Timer(self._settings_dict['INTERTRIAL_TIME'])
def __init__(self):
super().__init__()
self.experiment_finished = False
self._name = 'BaseOptogeneticExperiment'
#loading settings
self._exp_parameter_dict = dict(TRIGGER='str',
INTERTRIAL_TIME='int',
MAX_STIM_TIME='int',
MIN_STIM_TIME='int',
MAX_TOTAL_STIM_TIME='int',
EXP_TIME='int',
PROCESS='str')
self._settings_dict = get_experiment_settings(self._name,
self._exp_parameter_dict)
self._process = setup_process(self._settings_dict['PROCESS'])
self._intertrial_timer = Timer(self._settings_dict['INTERTRIAL_TIME'])
self._exp_timer = Timer(self._settings_dict['EXP_TIME'])
self._event = False
self._event_start = None
#setting limits
self._max_trial_time = self._settings_dict['MAX_STIM_TIME']
self._min_trial_time = self._settings_dict['MIN_STIM_TIME']
self._max_total_time = self._settings_dict['MAX_TOTAL_STIM_TIME'] if self._settings_dict['MAX_TOTAL_STIM_TIME']\
is not None else self._settings_dict['EXP_TIME'] + 1
#keeping count
self._results = []
self._total_time = 0
self._trial_time = 0
#trigger
self._trigger = setup_trigger(self._settings_dict['TRIGGER'])
def __init__(self):
super().__init__()
self._name = "BaseTrialExperiment"
self.experiment_finished = False
self._event = None
self._print_check = False
self._current_trial = None
self._result_list = []
self._success_count = 0
self._parameter_dict = dict(
TRIGGER="str",
PROCESS="str",
INTERTRIAL_TIME="int",
TRIAL_NAME="str",
TRIAL_TRIGGER="str",
TRIAL_TIME="int",
STIMULUS_TIME="int",
RESULT_FUNC="str",
EXP_LENGTH="int",
EXP_COMPLETION="int",
EXP_TIME="int",
)
self._settings_dict = get_experiment_settings(self._name,
self._parameter_dict)
self._process = setup_process(self._settings_dict["PROCESS"])
self._init_trigger = setup_trigger(self._settings_dict["TRIGGER"])
self._trials_list = self.generate_trials_list(
self._trials, self._settings_dict["EXP_LENGTH"])
self._trial_timer = Timer(self._settings_dict["TRIAL_TIME"])
self._exp_timer = Timer(self._settings_dict["EXP_TIME"])
self._intertrial_timer = Timer(self._settings_dict["INTERTRIAL_TIME"])
def __init__(self):
self._name = 'BaseExperiment'
self._settings_dict = {}
self.experiment_finished = False
self._process = None
self._event = None
self._current_trial = None
self._exp_timer = Timer(10)
class BaseExperiment:
"""
Base class for standard experiments"""
def __init__(self):
self._name = 'BaseExperiment'
self._settings_dict = {}
self.experiment_finished = False
self._process = None
self._event = None
self._current_trial = None
self._exp_timer = Timer(10)
def check_skeleton(self, frame, skeleton):
"""
Checking each passed animal skeleton for a pre-defined set of conditions
Outputting the visual representation, if exist
Advancing trials according to inherent logic of an experiment
:param frame: frame, on which animal skeleton was found
:param skeleton: skeleton, consisting of multiple joints of an animal
"""
pass
def check_exp_timer(self):
"""
Checking the experiment timer
"""
if not self._exp_timer.check_timer():
print("Experiment is finished")
print("Time ran out.")
self.stop_experiment()
def start_experiment(self):
"""
Start the experiment
"""
if self._process is not None:
self._process.start()
if not self.experiment_finished:
self._exp_timer.start()
def stop_experiment(self):
"""
Stop the experiment and reset the timer
"""
self.experiment_finished = True
print('Experiment completed!')
self._exp_timer.reset()
# don't forget to end the process!
if self._process is not None:
self._process.end()
def get_settings(self):
return self._settings_dict
def get_name(self):
return self._name
def __init__(self):
super().__init__()
self._name = 'BaseConditionalExperiment'
self._parameter_dict = dict(TRIGGER='str',
PROCESS='str',
INTERTRIAL_TIME='int',
EXP_LENGTH='int',
EXP_TIME='int')
self._settings_dict = get_experiment_settings(self._name,
self._parameter_dict)
self.experiment_finished = False
self._process = setup_process(self._settings_dict['PROCESS'])
self._event = None
self._event_count = 0
self._current_trial = None
self._exp_timer = Timer(self._settings_dict['EXP_TIME'])
self._intertrial_timer = Timer(self._settings_dict['INTERTRIAL_TIME'])
self._trigger = setup_trigger(self._settings_dict['TRIGGER'])
def _trials(self):
trigger = setup_trigger(self._settings_dict['TRIAL_TRIGGER'])
if self._settings_dict['RESULT_FUNC'] == 'all':
result_func = all
elif self._settings_dict['RESULT_FUNC'] == 'any':
result_func = any
else:
raise ValueError(
f'Result function can only be "all" or "any", not {self._settings_dict["RESULT_FUNC"]}.'
)
trials = {
self._settings_dict['TRIAL_NAME']:
dict(stimulus_timer=Timer(self._settings_dict['STIMULUS_TIME']),
success_timer=Timer(self._settings_dict['TRIAL_TIME']),
trigger=trigger,
result_func=result_func)
}
return trials
def __init__(self):
super().__init__()
self._name = "BaseConditionalExperiment"
self._parameter_dict = dict(
TRIGGER="str",
PROCESS="str",
INTERTRIAL_TIME="int",
EXP_LENGTH="int",
EXP_TIME="int",
)
self._settings_dict = get_experiment_settings(self._name,
self._parameter_dict)
self.experiment_finished = False
self._process = setup_process(self._settings_dict["PROCESS"])
self._event = None
self._event_count = 0
self._current_trial = None
self._exp_timer = Timer(self._settings_dict["EXP_TIME"])
self._intertrial_timer = Timer(self._settings_dict["INTERTRIAL_TIME"])
self._trigger = setup_trigger(self._settings_dict["TRIGGER"])
def __init__(self):
super().__init__()
self.experiment_finished = False
self._name = "BaseOptogeneticExperiment"
# loading settings
self._exp_parameter_dict = dict(
TRIGGER="str",
INTERTRIAL_TIME="int",
MAX_STIM_TIME="int",
MIN_STIM_TIME="int",
MAX_TOTAL_STIM_TIME="int",
EXP_TIME="int",
PROCESS="str",
)
self._settings_dict = get_experiment_settings(self._name,
self._exp_parameter_dict)
self._process = setup_process(self._settings_dict["PROCESS"])
self._intertrial_timer = Timer(self._settings_dict["INTERTRIAL_TIME"])
self._exp_timer = Timer(self._settings_dict["EXP_TIME"])
self._event = False
self._event_start = None
# setting limits
self._max_trial_time = self._settings_dict["MAX_STIM_TIME"]
self._min_trial_time = self._settings_dict["MIN_STIM_TIME"]
self._max_total_time = (self._settings_dict["MAX_TOTAL_STIM_TIME"]
if self._settings_dict["MAX_TOTAL_STIM_TIME"]
is not None else
self._settings_dict["EXP_TIME"] + 1)
# keeping count
self._results = []
self._total_time = 0
self._trial_time = 0
# trigger
self._trigger = setup_trigger(self._settings_dict["TRIGGER"])
class BaseTrialExperiment(BaseExperiment):
def __init__(self):
super().__init__()
self._name = 'BaseTrialExperiment'
self.experiment_finished = False
self._event = None
self._print_check = False
self._current_trial = None
self._result_list = []
self._success_count = 0
self._parameter_dict = dict(TRIGGER='str',
PROCESS='str',
INTERTRIAL_TIME='int',
TRIAL_NAME='str',
TRIAL_TRIGGER='str',
TRIAL_TIME='int',
STIMULUS_TIME='int',
RESULT_FUNC='str',
EXP_LENGTH='int',
EXP_COMPLETION='int',
EXP_TIME='int')
self._settings_dict = get_experiment_settings(self._name,
self._parameter_dict)
self._process = setup_process(self._settings_dict['PROCESS'])
self._init_trigger = setup_trigger(self._settings_dict['TRIGGER'])
self._trials_list = self.generate_trials_list(
self._trials, self._settings_dict['EXP_LENGTH'])
self._trial_timer = Timer(self._settings_dict['TRIAL_TIME'])
self._exp_timer = Timer(self._settings_dict['EXP_TIME'])
self._intertrial_timer = Timer(self._settings_dict['INTERTRIAL_TIME'])
def check_skeleton(self, frame, skeleton):
status, trial = self._process.get_status()
if status:
current_trial = self._trials[trial]
condition, response = current_trial['trigger'].check_skeleton(
skeleton)
self._process.put(condition)
result = self._process.get_result()
if result is not None:
self.process_result(result, trial)
self._current_trial = None
# check if all trials were successful until completion
if self._success_count >= self._settings_dict['EXP_COMPLETION']:
print("Experiment is finished")
print("Trial reached required amount of successes")
self.stop_experiment()
# if not continue
print(' Going into Intertrial time.')
self._intertrial_timer.reset()
self._intertrial_timer.start()
result = None
plot_triggers_response(frame, response)
elif not self._intertrial_timer.check_timer():
if self._current_trial is None:
self._current_trial = next(self._trials_list, False)
elif not self._current_trial:
print("Experiment is finished due to max. trial repetition.")
print(self._result_list)
self.stop_experiment()
else:
init_result, response_body = self._init_trigger.check_skeleton(
skeleton)
if init_result:
# check trial start triggers
self._process.put_trial(self._trials[self._current_trial],
self._current_trial)
self._print_check = False
elif not self._print_check:
print('Next trial: #' + str(len(self._result_list) + 1) +
' ' + self._current_trial)
print(
'Animal is not meeting trial start criteria, the start of trial is delayed.'
)
self._print_check = True
# if experimental time ran out, finish experiments
super().check_exp_timer()
def process_result(self, result, trial):
"""
Will add result if TRUE or reset comp_counter if FALSE
:param result: bool if trial was successful
:param trial: str name of the trial
:return:
"""
self._result_list.append((trial, result))
if result is True:
self._success_count += 1
print('Trial successful!')
else:
print('Trial failed.')
#
@staticmethod
def generate_trials_list(trials: dict, length: int):
trials_list = []
for trial in range(length):
trials_list.append(random.choice(list(trials.keys())))
return iter(trials_list)
@property
def _trials(self):
trigger = setup_trigger(self._settings_dict['TRIAL_TRIGGER'])
if self._settings_dict['RESULT_FUNC'] == 'all':
result_func = all
elif self._settings_dict['RESULT_FUNC'] == 'any':
result_func = any
else:
raise ValueError(
f'Result function can only be "all" or "any", not {self._settings_dict["RESULT_FUNC"]}.'
)
trials = {
self._settings_dict['TRIAL_NAME']:
dict(stimulus_timer=Timer(self._settings_dict['STIMULUS_TIME']),
success_timer=Timer(self._settings_dict['TRIAL_TIME']),
trigger=trigger,
result_func=result_func)
}
return trials
class BaseOptogeneticExperiment(BaseExperiment):
"""Standard implementation of an optogenetic experiment"""
def __init__(self):
super().__init__()
self.experiment_finished = False
self._name = 'BaseOptogeneticExperiment'
#loading settings
self._exp_parameter_dict = dict(TRIGGER='str',
INTERTRIAL_TIME='int',
MAX_STIM_TIME='int',
MIN_STIM_TIME='int',
MAX_TOTAL_STIM_TIME='int',
EXP_TIME='int',
PROCESS='str')
self._settings_dict = get_experiment_settings(self._name,
self._exp_parameter_dict)
self._process = setup_process(self._settings_dict['PROCESS'])
self._intertrial_timer = Timer(self._settings_dict['INTERTRIAL_TIME'])
self._exp_timer = Timer(self._settings_dict['EXP_TIME'])
self._event = False
self._event_start = None
#setting limits
self._max_trial_time = self._settings_dict['MAX_STIM_TIME']
self._min_trial_time = self._settings_dict['MIN_STIM_TIME']
self._max_total_time = self._settings_dict['MAX_TOTAL_STIM_TIME'] if self._settings_dict['MAX_TOTAL_STIM_TIME']\
is not None else self._settings_dict['EXP_TIME'] + 1
#keeping count
self._results = []
self._total_time = 0
self._trial_time = 0
#trigger
self._trigger = setup_trigger(self._settings_dict['TRIGGER'])
def check_skeleton(self, frame, skeleton):
if self._exp_timer.check_timer():
if self._total_time >= self._max_total_time:
# check if total time to stimulate per experiment is reached
print("Ending experiment, total event time ran out")
self.stop_experiment()
else:
# if not continue
if not self._intertrial_timer.check_timer():
# check if there is an intertrial time running right now, if not continue
# check if the trigger is true
result, _ = self._trigger.check_skeleton(skeleton)
if result:
if not self._event:
# if a stimulation event wasn't started already, start one
print("Starting Stimulation")
self._event = True
# and activate the laser, start the timer and reset the intertrial timer
self._event_start = time.time()
self._intertrial_timer.reset()
else:
if time.time(
) - self._event_start <= self._max_trial_time:
# if the total event time has not reached the maximum time per event
pass
else:
# if the maximum event time was reached, reset the event,
# turn off the laser and start inter-trial time
print(
"Ending Stimulation, Stimulation time ran out"
)
self._event = False
trial_time = time.time() - self._event_start
self._total_time += trial_time
self._results.append(trial_time)
print("Stimulation duration", trial_time)
self._intertrial_timer.start()
else:
# if the trigger is false
if self._event:
# but the stimulation is still going
if time.time(
) - self._event_start < self._min_trial_time:
# check if the minimum event time was not reached, then pass
pass
else:
# if minumum event time has been reached, reset the event,
# turn of the laser and start intertrial time
print("Ending Stimulation, Trigger is False")
self._event = False
trial_time = time.time() - self._event_start
self._total_time += trial_time
self._results.append(trial_time)
print("Stimulation duration", trial_time)
self._intertrial_timer.start()
self._process.put(self._event)
else:
# if maximum experiment time was reached, stop experiment
print("Ending experiment, timer ran out")
self.stop_experiment()
def start_experiment(self):
self._exp_timer.start()
def stop_experiment(self):
self.experiment_finished = True
print('Experiment completed!')
print("Total event duration", sum(self._results))
print(self._results)
def get_trial(self):
return self._event
class BaseConditionalExperiment(BaseExperiment):
"""
Simple class to contain all of the experiment properties
Uses multiprocess to ensure the best possible performance and
to showcase that it is possible to work with any type of equipment, even timer-dependent
"""
def __init__(self):
super().__init__()
self._name = 'BaseConditionalExperiment'
self._parameter_dict = dict(TRIGGER='str',
PROCESS='str',
INTERTRIAL_TIME='int',
EXP_LENGTH='int',
EXP_TIME='int')
self._settings_dict = get_experiment_settings(self._name,
self._parameter_dict)
self.experiment_finished = False
self._process = setup_process(self._settings_dict['PROCESS'])
self._event = None
self._event_count = 0
self._current_trial = None
self._exp_timer = Timer(self._settings_dict['EXP_TIME'])
self._intertrial_timer = Timer(self._settings_dict['INTERTRIAL_TIME'])
self._trigger = setup_trigger(self._settings_dict['TRIGGER'])
def check_skeleton(self, frame, skeleton):
"""
Checking each passed animal skeleton for a pre-defined set of conditions
Outputting the visual representation, if exist
Advancing trials according to inherent logic of an experiment
:param frame: frame, on which animal skeleton was found
:param skeleton: skeleton, consisting of multiple joints of an animal
"""
self.check_exp_timer() # checking if experiment is still on
if self._event_count >= self._settings_dict['EXP_LENGTH']:
self.stop_experiment()
elif not self.experiment_finished:
if not self._intertrial_timer.check_timer():
# check if condition is met
result, response = self._trigger.check_skeleton(
skeleton=skeleton)
if result:
self._event_count += 1
print('Stimulation #{self._event_count}'.format())
self._intertrial_timer.reset()
self._intertrial_timer.start()
plot_triggers_response(frame, response)
self._process.put(result)
def check_exp_timer(self):
"""
Checking the experiment timer
"""
if not self._exp_timer.check_timer():
print("Time ran out.")
self.stop_experiment()
def start_experiment(self):
"""
Start the experiment
"""
self._process.start()
if not self.experiment_finished:
self._exp_timer.start()
def stop_experiment(self):
"""
Stop the experiment and reset the timer
"""
self.experiment_finished = True
print('Experiment completed!')
self._exp_timer.reset()
# don't forget to end the process!
self._process.end()
def get_trial(self):
"""
Check which trial is going on right now
"""
return self._current_trial