9031936551

Committed 10 May 2024 12:05PM UTC coverage: 48.538% (+1.7%) from 46.79%

Build # 9031936551

Build Type

Pull #643

github

Specific Base 53c3e3

Committed by

web-flow

Commit Message

Merge 3c8214f78 into ec2d8e4fe

Pull Request Pull Request #643: 8.19.0

Run Details

377 of 1073 new or added lines in 38 files covered. (35.14%)

977 existing lines in 19 files now uncovered.

3253 of 6702 relevant lines covered (48.54%)

0.97 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

43.08

/iblrig_tasks/_iblrig_tasks_passiveChoiceWorld/task.py

import logging
import sys
import time
from pathlib import Path

import pandas as pd

import iblrig.misc
from iblrig.base_choice_world import ChoiceWorldSession

log = logging.getLogger('iblrig.task')


class Session(ChoiceWorldSession):
    protocol_name = '_iblrig_tasks_passiveChoiceWorld'

    def __init__(self, *args, session_template_id=0, **kwargs):
        self.extractor_tasks = ['PassiveRegisterRaw', 'PassiveTask']
        super(ChoiceWorldSession, self).__init__(**kwargs)
        self.task_params.SESSION_TEMPLATE_ID = session_template_id
        all_trials = pd.read_parquet(Path(__file__).parent.joinpath('passiveChoiceWorld_trials_fixtures.pqt'))
        self.trials_table = all_trials[all_trials['session_id'] == self.task_params.SESSION_TEMPLATE_ID].copy()
        self.trials_table['reward_valve_time'] = self.compute_reward_time(amount_ul=self.trials_table['reward_amount'])

    @staticmethod
    def extra_parser():
        """:return: argparse.parser()"""
        parser = super(Session, Session).extra_parser()
        parser.add_argument(
            '--session_template_id',
            option_strings=['--session_template_id'],
            dest='session_template_id',
            default=0,
            type=int,
            help='pre-generated session index (zero-based)',
        )
        return parser

    def start_hardware(self):
        if not self.is_mock:
            self.start_mixin_frame2ttl()
            self.start_mixin_bpod()
            self.start_mixin_valve()
            self.start_mixin_sound()
            self.start_mixin_bonsai_cameras()
            self.start_mixin_bonsai_microphone()
            self.start_mixin_rotary_encoder()

    def get_state_machine_trial(self, *args, **kwargs):
        pass

    def next_trial(self):
        pass

    def _run(self):
        """
        This is the method that runs the task with the actual state machine
        :return:
        """
        self.trigger_bonsai_cameras()
        log.info('Starting spontaneous activity followed by receptive field mapping')
        # Run the passive part i.e. spontaneous activity and RFMapping stim
        self.run_passive_visual_stim(sa_time='00:10:00')
        # Then run the replay of task events: V for valve, T for tone, N for noise, G for gratings
        log.info('Starting replay of task stims')

        action_show_stim = self.bpod.actions['bonsai_show_stim'][1]
        action_hide_stim = self.bpod.actions['bonsai_hide_stim'][1]
        byte_show_stim = self.bpod.serial_messages[action_show_stim]['message'][-1]
        byte_hide_stim = self.bpod.serial_messages[action_hide_stim]['message'][-1]

        if not self.is_mock:
            self.start_mixin_bonsai_visual_stimulus()
        for trial_num, trial in self.trials_table.iterrows():
            self.trial_num = trial_num
            log.info(f'Delay: {trial.stim_delay}; ID: {trial.stim_type}; Count: {self.trial_num}/300')
            sys.stdout.flush()
            time.sleep(trial.stim_delay)
            if trial.stim_type == 'V':
                self.valve_open(self.reward_time)
            elif trial.stim_type == 'T':
                self.sound_play_tone(state_timer=0.102)
            elif trial.stim_type == 'N':
                self.sound_play_noise(state_timer=0.510)
            elif trial.stim_type == 'G':
                # this will send the current trial info to the visual stim
                # we need to make sure Bonsai is in a state to display stimuli
                self.send_trial_info_to_bonsai()
                self.bonsai_visual_udp_client.send_message(r'/re', byte_show_stim)
                time.sleep(0.3)
                self.bonsai_visual_udp_client.send_message(r'/re', byte_hide_stim)
            if self.paths.SESSION_FOLDER.joinpath('.stop').exists():
                self.paths.SESSION_FOLDER.joinpath('.stop').unlink()
                break


if __name__ == '__main__':  # pragma: no cover
    # python .\iblrig_tasks\_iblrig_tasks_spontaneous\task.py --subject mysubject
    kwargs = iblrig.misc.get_task_arguments(parents=[Session.extra_parser()])
    sess = Session(**kwargs)
    sess.run()

1	import logging	2✔
2	import sys	2✔
3	import time	2✔
4	from pathlib import Path	2✔
5
6	import pandas as pd	2✔
7
8	import iblrig.misc	2✔
9	from iblrig.base_choice_world import ChoiceWorldSession	2✔
10
11	log = logging.getLogger('iblrig.task')	2✔
12
13
14	class Session(ChoiceWorldSession):	2✔
15	protocol_name = '_iblrig_tasks_passiveChoiceWorld'	2✔
16
17	def __init__(self, args, session_template_id=0, *kwargs):	2✔
18	self.extractor_tasks = ['PassiveRegisterRaw', 'PassiveTask']	2✔
19	super(ChoiceWorldSession, self).__init__(**kwargs)	2✔
20	self.task_params.SESSION_TEMPLATE_ID = session_template_id	2✔
21	all_trials = pd.read_parquet(Path(__file__).parent.joinpath('passiveChoiceWorld_trials_fixtures.pqt'))	2✔
22	self.trials_table = all_trials[all_trials['session_id'] == self.task_params.SESSION_TEMPLATE_ID].copy()	2✔
23	self.trials_table['reward_valve_time'] = self.compute_reward_time(amount_ul=self.trials_table['reward_amount'])	2✔
24
25	@staticmethod	2✔
26	def extra_parser():	2✔
27	""":return: argparse.parser()"""
28	parser = super(Session, Session).extra_parser()	2✔
29	parser.add_argument(	2✔
30	'--session_template_id',
31	option_strings=['--session_template_id'],
32	dest='session_template_id',
33	default=0,
34	type=int,
35	help='pre-generated session index (zero-based)',
36	)
37	return parser	2✔
38
39	def start_hardware(self):	2✔
UNCOV 40	if not self.is_mock:	×
UNCOV 41	self.start_mixin_frame2ttl()	×
42	self.start_mixin_bpod()	×
43	self.start_mixin_valve()	×
UNCOV 44	self.start_mixin_sound()	×
45	self.start_mixin_bonsai_cameras()	×
UNCOV 46	self.start_mixin_bonsai_microphone()	×
47	self.start_mixin_rotary_encoder()	×
48
49	def get_state_machine_trial(self, args, *kwargs):	2✔
50	pass	2✔
51
52	def next_trial(self):	2✔
53	pass	2✔
54
55	def _run(self):	2✔
56	"""
57	This is the method that runs the task with the actual state machine
58	:return:
59	"""
60	self.trigger_bonsai_cameras()	×
61	log.info('Starting spontaneous activity followed by receptive field mapping')	×
62	# Run the passive part i.e. spontaneous activity and RFMapping stim
63	self.run_passive_visual_stim(sa_time='00:10:00')	×
64	# Then run the replay of task events: V for valve, T for tone, N for noise, G for gratings
65	log.info('Starting replay of task stims')	×
66
UNCOV 67	action_show_stim = self.bpod.actions['bonsai_show_stim'][1]	×
UNCOV 68	action_hide_stim = self.bpod.actions['bonsai_hide_stim'][1]	×
UNCOV 69	byte_show_stim = self.bpod.serial_messages[action_show_stim]['message'][-1]	×
UNCOV 70	byte_hide_stim = self.bpod.serial_messages[action_hide_stim]['message'][-1]	×
71
UNCOV 72	if not self.is_mock:	×
UNCOV 73	self.start_mixin_bonsai_visual_stimulus()	×
NEW 74	for trial_num, trial in self.trials_table.iterrows():	×
NEW 75	self.trial_num = trial_num	×
UNCOV 76	log.info(f'Delay: {trial.stim_delay}; ID: {trial.stim_type}; Count: {self.trial_num}/300')	×
UNCOV 77	sys.stdout.flush()	×
UNCOV 78	time.sleep(trial.stim_delay)	×
UNCOV 79	if trial.stim_type == 'V':	×
UNCOV 80	self.valve_open(self.reward_time)	×
UNCOV 81	elif trial.stim_type == 'T':	×
UNCOV 82	self.sound_play_tone(state_timer=0.102)	×
UNCOV 83	elif trial.stim_type == 'N':	×
UNCOV 84	self.sound_play_noise(state_timer=0.510)	×
UNCOV 85	elif trial.stim_type == 'G':	×
86	# this will send the current trial info to the visual stim
87	# we need to make sure Bonsai is in a state to display stimuli
UNCOV 88	self.send_trial_info_to_bonsai()	×
UNCOV 89	self.bonsai_visual_udp_client.send_message(r'/re', byte_show_stim)	×
UNCOV 90	time.sleep(0.3)	×
UNCOV 91	self.bonsai_visual_udp_client.send_message(r'/re', byte_hide_stim)	×
UNCOV 92	if self.paths.SESSION_FOLDER.joinpath('.stop').exists():	×
UNCOV 93	self.paths.SESSION_FOLDER.joinpath('.stop').unlink()	×
UNCOV 94	break	×
95
96
97	if __name__ == '__main__': # pragma: no cover
98	# python .\iblrig_tasks\_iblrig_tasks_spontaneous\task.py --subject mysubject
99	kwargs = iblrig.misc.get_task_arguments(parents=[Session.extra_parser()])
100	sess = Session(**kwargs)
101	sess.run()

int-brain-lab / iblrig / 9031936551

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous