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.pass_condition(condition)
result = self._process.get_result()
if result is not None:
self.process_result(result, trial)
self._chosen_trial = None
print(self._completion_counter)
# check if all trials were successful until completion
if all(self._completion_counter.values()):
print("Experiment is finished")
print("All trials reached required amount of successes")
self.stop_experiment()
# if not continue
self._iti_duration = next(self._iti_list, False)
self._intertrial_timer = Timer(self._iti_duration)
print(" Going into InterTrialTime for " +
str(self._iti_duration) + " sec.")
self._intertrial_timer.start()
result = None
plot_triggers_response(frame, response)
# elif not self._intertrial_timer.check_timer() and not self._penalty_timer.check_timer():
elif not self._intertrial_timer.check_timer():
# chosen_trial = random.choice(list(self._experiment['possible_trials'].keys()))
if self._chosen_trial is None:
self._chosen_trial = next(self._trials_list, False)
elif not self._chosen_trial:
print("Experiment is finished due to max. trial number.")
print(self._result_list)
self.stop_experiment()
elif self._counter["result"][("Greenbar_whiteback", True)] >= 20:
print("Reached max amount of CS+ trial successes!")
print(self._result_list)
self.stop_experiment()
else:
# if self._counter['trial']['Greenbar_whiteback'] >= 10:
# # check if 10 green trials have passed and change trigger stage
# self._stage = 2
if self.check_triggers(skeleton):
# check trial start triggers
self._process.set_trial(self._chosen_trial)
self._print_check = False
elif not self._print_check:
print("Next trial: #" + str(len(self._result_list) + 1) +
" " + self._chosen_trial)
print(
"Animal is not meeting trial start criteria, the start of trial is delayed."
)
self._print_check = True
# self._penalty_timer.reset()
# self._penalty_timer.start()
# if experimental time ran out, finish experiments
self.check_exp_timer()
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_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
for trial in self._trial_count:
# checking if any trial hit a predefined cap
if self._trial_count[trial] >= 10:
self.stop_experiment()
if not self.experiment_finished:
result, response = False, None
for trial in self._trials:
# check for all trials if condition is met
result, response = self._trials[trial]["trigger"](
skeleton=skeleton)
plot_triggers_response(frame, response)
if result:
if self._current_trial is None:
if not self._trial_timers[trial].check_timer():
self._current_trial = trial
self._trial_timers[trial].reset()
self._trial_count[trial] += 1
print(trial, self._trial_count[trial])
else:
if self._current_trial == trial:
self._current_trial = None
self._trial_timers[trial].start()
self._process.set_trial(self._current_trial)
return result, response
def start_videoanalyser():
print("Starting DeepLabCut")
model = load_model(
r"D:\DeepPoseKit-Data-master\datasets\fly\best_model_densenet.h5")
experiment_enabled = False
video_output = True
if experiment_enabled:
print("Initializing experiment")
experiment = ExampleExperiment()
experiment.start_experiment()
# some variables initialization
all_rows = []
index = 0
while video.isOpened():
ret, frame = video.read()
if ret:
scmap, locref, pose = get_pose(frame, config, sess, inputs,
outputs)
peaks = find_local_peaks_new(scmap, locref, ANIMALS_NUMBER, config)
skeletons = calculate_skeletons(peaks, ANIMALS_NUMBER)
if skeletons:
for skeleton in skeletons:
if experiment_enabled:
result, response = experiment.check_skeleton(
frame, skeleton)
plot_triggers_response(frame, response)
out_frame = plot_bodyparts(frame, skeletons)
else:
out_frame = frame
cv2.imshow('stream', out_frame)
if video_output:
video_file.write(out_frame)
if experiment_enabled:
all_rows.append(
create_row(index, skeletons, experiment_enabled,
experiment.get_trial()))
else:
all_rows.append(
create_row(index, skeletons, experiment_enabled, None))
index += 1
else:
break
if cv2.waitKey(1) & 0xFF == ord('q'):
break
if experiment_enabled:
experiment.stop_experiment()
if video_output:
print('Saving analyzed video for {}'.format(video_name))
video_file.release()
video.release()
create_dataframes(all_rows)
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 check_skeleton(self, frame, skeletons):
"""
Checking passed animal skeletons 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 skeletons: skeletons, consisting of multiple joints of an animal
"""
self.check_exp_timer() # checking if experiment is still on
for trial in self._trial_count:
# checking if any trial hit a predefined cap
if self._trial_count[trial] >= self._max_reps:
self.stop_experiment()
if not self.experiment_finished:
result, response = False, None
#checking if enough animals were detected
if len(skeletons) >= self._min_animals:
for trial in self._trials:
# check if social interaction trigger is true
result, response = self._trials[trial]['trigger'](
skeletons=skeletons)
plot_triggers_response(frame, response)
if result:
if self._current_trial is None:
if not self._trial_timers[trial].check_timer():
self._current_trial = trial
self._trial_timers[trial].reset()
self._trial_count[trial] += 1
print(trial, self._trial_count[trial])
else:
if self._current_trial == trial:
self._current_trial = None
self._trial_timers[trial].start()
self._process.set_trial(self._current_trial)
else:
pass
return result, response
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 not self.experiment_finished:
result, response = self._trigger.check_skeleton(skeleton=skeleton)
plot_triggers_response(frame, response)
if result:
laser_switch(True)
self._event_count += 1
print(self._event_count)
print("Light on")
else:
laser_switch(False)
print("Light off")
return result, response