9032957364

Committed 10 May 2024 01:25PM UTC coverage: 48.538% (+1.7%) from 46.79%

Build # 9032957364

Build Type

Pull #643

github

Specific Base 74d2ec

Committed by

web-flow

Commit Message

Merge aebf2c9af into ec2d8e4fe

Pull Request Pull Request #643: 8.19.0

Run Details

377 of 1074 new or added lines in 38 files covered. (35.1%)

977 existing lines in 19 files now uncovered.

3253 of 6702 relevant lines covered (48.54%)

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69.44

/iblrig/ephys.py

import argparse
import string

import numpy as np

from iblatlas import atlas
from iblrig.base_tasks import EmptySession
from iblrig.transfer_experiments import EphysCopier
from iblutil.util import setup_logger


def prepare_ephys_session_cmd():
    parser = argparse.ArgumentParser(prog='start_video_session', description='Prepare video PC for video recording session.')
    parser.add_argument('subject_name', help='name of subject')
    parser.add_argument('nprobes', help='number of probes', type=int, default=2)
    parser.add_argument('--debug', action='store_true', help='enable debugging mode')
    args = parser.parse_args()
    setup_logger(name='iblrig', level='DEBUG' if args.debug else 'INFO')
    prepare_ephys_session(args.subject_name, args.nprobes)


def prepare_ephys_session(subject_name: str, nprobes: int = 2):
    """
    Setup electrophysiology recordings.

    Parameters
    ----------
    subject_name : str
        A subject name.
    nprobes : int
        Number of probes to be used
    """
    # Initialize a session for paths and settings
    session = EmptySession(subject=subject_name, interactive=False)
    session_path = session.paths.SESSION_FOLDER
    copier = EphysCopier(session_path=session_path, remote_subjects_folder=session.paths.REMOTE_SUBJECT_FOLDER)
    copier.initialize_experiment(nprobes=nprobes)


def neuropixel24_micromanipulator_coordinates(ref_shank, pname, ba=None, shank_spacings_um=(0, 200, 400, 600)):
    """
    Provided the micro-manipulator coordinates of the first shank, this function
    returns the relative coordinates of all shanks, labeled as probe01a, probe01b, etc.
    :param ref_shank: dictionary with keys x, y, z, phi, theta, depth, roll
    example: {'x': 2594.2, 'y': -3123.7, 'z': -711, 'phi': 0 + 15, 'theta': 15, 'depth': 1250.4, 'roll': 0}
    :param pname: str
    :param ba: brain atlas object
    :param shank_spacings_um: list of shank spacings in micrometers
    :return:
    """
    # this only works if the roll is 0, ie. the probe is facing upwards
    assert ref_shank['roll'] == 0
    ba = atlas.NeedlesAtlas() if ba is None else ba
    trajectories = {}
    for i, d in enumerate(shank_spacings_um):
        x = ref_shank['x'] + np.sin(ref_shank['phi'] / 180 * np.pi) * d
        y = ref_shank['y'] - np.cos(ref_shank['phi'] / 180 * np.pi) * d
        shank = {
            'x': x,
            'y': y,
            'z': np.NaN,
            'phi': ref_shank['phi'],
            'theta': ref_shank['theta'],
            'depth': ref_shank['depth'],
            'roll': 0,
        }
        insertion = atlas.Insertion.from_dict(shank, brain_atlas=ba)
        xyz_entry = atlas.Insertion.get_brain_entry(insertion.trajectory, ba)
        if i == 0:
            xyz_ref = xyz_entry
        shank['z'] = xyz_entry[2] * 1e6
        shank['depth'] = ref_shank['depth'] + (xyz_entry[2] - xyz_ref[2]) * 1e6
        trajectories[f'{pname}{string.ascii_lowercase[i]}'] = shank
    return trajectories

1	import argparse	2✔
2	import string	2✔
3
4	import numpy as np	2✔
5
6	from iblatlas import atlas	2✔
7	from iblrig.base_tasks import EmptySession	2✔
8	from iblrig.transfer_experiments import EphysCopier	2✔
9	from iblutil.util import setup_logger	2✔
10
11
12	def prepare_ephys_session_cmd():	2✔
NEW 13	parser = argparse.ArgumentParser(prog='start_video_session', description='Prepare video PC for video recording session.')	×
14	parser.add_argument('subject_name', help='name of subject')	×
15	parser.add_argument('nprobes', help='number of probes', type=int, default=2)	×
16	parser.add_argument('--debug', action='store_true', help='enable debugging mode')	×
17	args = parser.parse_args()	×
18	setup_logger(name='iblrig', level='DEBUG' if args.debug else 'INFO')	×
19	prepare_ephys_session(args.subject_name, args.nprobes)	×
20
21
22	def prepare_ephys_session(subject_name: str, nprobes: int = 2):	2✔
23	"""
24	Setup electrophysiology recordings.
25
26	Parameters
27	----------
28	subject_name : str
29	A subject name.
30	nprobes : int
31	Number of probes to be used
32	"""
33	# Initialize a session for paths and settings
34	session = EmptySession(subject=subject_name, interactive=False)	×
35	session_path = session.paths.SESSION_FOLDER	×
NEW 36	copier = EphysCopier(session_path=session_path, remote_subjects_folder=session.paths.REMOTE_SUBJECT_FOLDER)	×
37	copier.initialize_experiment(nprobes=nprobes)	×
38
39
40	def neuropixel24_micromanipulator_coordinates(ref_shank, pname, ba=None, shank_spacings_um=(0, 200, 400, 600)):	2✔
41	"""
42	Provided the micro-manipulator coordinates of the first shank, this function
43	returns the relative coordinates of all shanks, labeled as probe01a, probe01b, etc.
44	:param ref_shank: dictionary with keys x, y, z, phi, theta, depth, roll
45	example: {'x': 2594.2, 'y': -3123.7, 'z': -711, 'phi': 0 + 15, 'theta': 15, 'depth': 1250.4, 'roll': 0}
46	:param pname: str
47	:param ba: brain atlas object
48	:param shank_spacings_um: list of shank spacings in micrometers
49	:return:
50	"""
51	# this only works if the roll is 0, ie. the probe is facing upwards
52	assert ref_shank['roll'] == 0	2✔
53	ba = atlas.NeedlesAtlas() if ba is None else ba	2✔
54	trajectories = {}	2✔
55	for i, d in enumerate(shank_spacings_um):	2✔
56	x = ref_shank['x'] + np.sin(ref_shank['phi'] / 180 * np.pi) * d	2✔
57	y = ref_shank['y'] - np.cos(ref_shank['phi'] / 180 * np.pi) * d	2✔
58	shank = {	2✔
59	'x': x,
60	'y': y,
61	'z': np.NaN,
62	'phi': ref_shank['phi'],
63	'theta': ref_shank['theta'],
64	'depth': ref_shank['depth'],
65	'roll': 0,
66	}
67	insertion = atlas.Insertion.from_dict(shank, brain_atlas=ba)	2✔
68	xyz_entry = atlas.Insertion.get_brain_entry(insertion.trajectory, ba)	2✔
69	if i == 0:	2✔
70	xyz_ref = xyz_entry	2✔
71	shank['z'] = xyz_entry[2] * 1e6	2✔
72	shank['depth'] = ref_shank['depth'] + (xyz_entry[2] - xyz_ref[2]) * 1e6	2✔
73	trajectories[f'{pname}{string.ascii_lowercase[i]}'] = shank	2✔
74	return trajectories	2✔

int-brain-lab / iblrig / 9032957364

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