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map-mock-data.py
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#! /usr/bin/env python
import os
import re
import sys
import pathlib
from importlib import reload
# pipeline_path = pathlib.Path('..').resolve()
# if pipeline_path.exists():
# print(pipeline_path.absolute())
# sys.path.insert(0, str(pipeline_path))
import datajoint as dj
from pipeline import lab
from pipeline import ccf
from pipeline import experiment
from pipeline import ephys
from pipeline import publication
from pipeline import report
from pipeline import foraging_analysis
from pipeline import histology
from pipeline import tracking
from pipeline import psth
from pipeline import get_schema_name
from pipeline import shell
def usage_exit():
print("usage: {p} [{c}]"
.format(p=os.path.basename(sys.argv[0]),
c='|'.join(list(actions.keys()))))
sys.exit(0)
def dropdbs():
print('dropping databases')
if 'nuclear_option' not in dj.config:
print('skipping database drop')
else:
try:
shell.nuke_all()
lab.schema.drop()
except Exception as e:
print(".... couldn't drop database {} : {}".format(d, repr(e)))
def mockdata():
print('populating with mock data')
reload(lab)
reload(ccf)
reload(experiment)
reload(ephys)
reload(histology)
reload(tracking)
try:
lab.Person().insert1({
'username': 'unknown',
'fullname': 'Unknown'},
skip_duplicates=True
)
lab.Person().insert1({
'username': 'daveliu',
'fullname': 'Dave Liu'},
skip_duplicates=True
)
lab.Person().insert1({
'username': 'susu',
'fullname': 'Susu Chen'},
skip_duplicates=True
)
lab.Person().insert1({
'username': 'tn',
'fullname': 'Thinh Nguyen'},
skip_duplicates=True
)
lab.ModifiedGene().insert1({
'gene_modification': 'VGAT-Chr2-EYFP Jax',
'gene_modification_description': 'VGAT'},
skip_duplicates=True
)
lab.ModifiedGene().insert1({
'gene_modification': 'PV-ires-Cre X Ai32',
'gene_modification_description': 'PV'},
skip_duplicates=True
)
lab.ModifiedGene().insert1({
'gene_modification': 'Rosa26 Cag lsl reachR-citrine 1A4 X PV-ires-Cre',
'gene_modification_description': 'reachR PV'},
skip_duplicates=True
)
# Subject 399752 / dl7
lab.Subject().insert1({
'subject_id': 399752,
'username': 'daveliu',
'cage_number': 145375,
'date_of_birth': '2017-08-03',
'sex': 'M',
'animal_source': 'Jackson labs'},
skip_duplicates=True
)
lab.Subject.GeneModification().insert1({
'subject_id': 399752,
'gene_modification': 'VGAT-Chr2-EYFP Jax'},
skip_duplicates=True
)
lab.Surgery().insert1({
'subject_id': 399752,
'surgery_id': 1,
'username': 'daveliu',
'start_time': '2017-11-03',
'end_time': '2017-11-03',
'surgery_description': 'Headbar anterior'},
skip_duplicates=True
)
lab.Surgery.Procedure().insert1({
'subject_id': 399752,
'surgery_id': 1,
'procedure_id': 1,
'skull_reference': 'Bregma',
'ml_location': 0,
'ap_location': -4,
'surgery_procedure_description': 'Fiducial marker'},
skip_duplicates=True
)
lab.WaterRestriction().insert1({
'subject_id': 399752,
'water_restriction_number': 'dl7',
'cage_number': 148861,
'wr_start_date': '2017-11-07',
'wr_start_weight': 25},
skip_duplicates=True
)
# Subject 397853 / dl14
lab.Subject().insert1({
'subject_id': 397853,
'username': 'daveliu',
'cage_number': 144545,
'date_of_birth': '2017-07-15',
'sex': 'M',
'animal_source': 'Allen Institute'},
skip_duplicates=True
)
lab.Subject.GeneModification().insert1({
'subject_id': 397853,
'gene_modification': 'PV-ires-Cre X Ai32'},
skip_duplicates=True
)
lab.Surgery().insert1({
'subject_id': 397853,
'surgery_id': 1,
'username': 'daveliu',
'start_time': '2017-11-20',
'end_time': '2017-11-20',
'surgery_description': 'Headbar posterior'},
skip_duplicates=True
)
lab.Surgery.Procedure().insert1({
'subject_id': 397853,
'surgery_id': 1,
'procedure_id': 1,
'skull_reference': 'Bregma',
'ml_location': 0,
'ap_location': -1.75,
'surgery_procedure_description': 'Fiducial marker'},
skip_duplicates=True
)
lab.WaterRestriction().insert1({
'subject_id': 397853,
'water_restriction_number': 'dl14',
'cage_number': 149595,
'wr_start_date': '2017-11-27',
'wr_start_weight': 24.1},
skip_duplicates=True
)
# Subject 400480 / dl15
lab.Subject().insert1({
'subject_id': 400480,
'username': 'daveliu',
'cage_number': 145700,
'date_of_birth': '2017-08-09',
'sex': 'M',
'animal_source': 'Allen Institute'},
skip_duplicates=True
)
lab.Subject.GeneModification().insert1({
'subject_id': 400480,
'gene_modification': 'PV-ires-Cre X Ai32'},
skip_duplicates=True
)
lab.Surgery().insert1({
'subject_id': 400480,
'surgery_id': 1,
'username': 'daveliu',
'start_time': '2017-11-21',
'end_time': '2017-11-21',
'surgery_description': 'Headbar posterior'},
skip_duplicates=True
)
lab.Surgery.Procedure().insert1({
'subject_id': 400480,
'surgery_id': 1,
'procedure_id': 1,
'skull_reference': 'Bregma',
'ml_location': 0,
'ap_location': -1.75,
'surgery_procedure_description': 'Fiducial marker'},
skip_duplicates=True
)
lab.WaterRestriction().insert1({
'subject_id': 400480,
'water_restriction_number': 'dl15',
'cage_number': 149598,
'wr_start_date': '2017-11-27',
'wr_start_weight': 27.6},
skip_duplicates=True
)
# Subject 406680 / dl20
lab.Subject().insert1({
'subject_id': 406680,
'username': 'daveliu',
'cage_number': 148859,
'date_of_birth': '2017-10-06',
'sex': 'F',
'animal_source': 'Jackson labs'},
skip_duplicates=True
)
lab.Subject.GeneModification().insert1({
'subject_id': 406680,
'gene_modification': 'VGAT-Chr2-EYFP Jax'},
skip_duplicates=True
)
lab.Surgery().insert1({
'subject_id': 406680,
'surgery_id': 1,
'username': 'daveliu',
'start_time': '2018-01-04',
'end_time': '2018-01-04',
'surgery_description': 'Headbar posterior'},
skip_duplicates=True
)
lab.Surgery.Procedure().insert1({
'subject_id': 406680,
'surgery_id': 1,
'procedure_id': 1,
'skull_reference': 'Bregma',
'ml_location': 0,
'ap_location': -1.75,
'surgery_procedure_description': 'Fiducial marker'},
skip_duplicates=True
)
lab.WaterRestriction().insert1({
'subject_id': 406680,
'water_restriction_number': 'dl20',
'cage_number': 151282,
'wr_start_date': '2018-01-10',
'wr_start_weight': 22.7},
skip_duplicates=True
)
# Subject 408022 / dl21
lab.Subject().insert1({
'subject_id': 408022,
'username': 'daveliu',
'cage_number': 148859,
'date_of_birth': '2017-10-19',
'sex': 'F',
'animal_source': 'Jackson labs'},
skip_duplicates=True
)
lab.Subject.GeneModification().insert1({
'subject_id': 408022,
'gene_modification': 'VGAT-Chr2-EYFP Jax'},
skip_duplicates=True
)
lab.Surgery().insert1({
'subject_id': 408022,
'surgery_id': 1,
'username': 'daveliu',
'start_time': '2018-01-05',
'end_time': '2018-01-05',
'surgery_description': 'Headbar posterior'},
skip_duplicates=True
)
lab.Surgery.Procedure().insert1({
'subject_id': 408022,
'surgery_id': 1,
'procedure_id': 1,
'skull_reference': 'Bregma',
'ml_location': 0,
'ap_location': -1.75,
'surgery_procedure_description': 'Fiducial marker'},
skip_duplicates=True
)
lab.WaterRestriction().insert1({
'subject_id': 408022,
'water_restriction_number': 'dl21',
'cage_number': 151283,
'wr_start_date': '2018-01-10',
'wr_start_weight': 21.1},
skip_duplicates=True
)
# Subject 408021 / dl22
lab.Subject().insert1({
'subject_id': 408021,
'username': 'daveliu',
'cage_number': 148859,
'date_of_birth': '2017-10-19',
'sex': 'F',
'animal_source': 'Jackson labs'},
skip_duplicates=True
)
lab.Subject.GeneModification().insert1({
'subject_id': 408021,
'gene_modification': 'VGAT-Chr2-EYFP Jax'},
skip_duplicates=True
)
lab.Surgery().insert1({
'subject_id': 408021,
'surgery_id': 1,
'username': 'daveliu',
'start_time': '2018-01-15',
'end_time': '2018-01-15',
'surgery_description': 'Headbar posterior'},
skip_duplicates=True
)
lab.Surgery.Procedure().insert1({
'subject_id': 408021,
'surgery_id': 1,
'procedure_id': 1,
'skull_reference': 'Bregma',
'ml_location': 0,
'ap_location': -1.75,
'surgery_procedure_description': 'Fiducial marker'},
skip_duplicates=True
)
lab.WaterRestriction().insert1({
'subject_id': 408021,
'water_restriction_number': 'dl22',
'cage_number': 151704,
'wr_start_date': '2018-01-19',
'wr_start_weight': 21},
skip_duplicates=True
)
# Subject 407512 / dl24
lab.Subject().insert1({
'subject_id': 407512,
'username': 'daveliu',
'cage_number': 151629,
'date_of_birth': '2017-10-13',
'sex': 'M',
'animal_source': 'Jackson labs'},
skip_duplicates=True
)
lab.Subject.GeneModification().insert1({
'subject_id': 407512,
'gene_modification': 'VGAT-Chr2-EYFP Jax'},
skip_duplicates=True
)
lab.Surgery().insert1({
'subject_id': 407512,
'surgery_id': 1,
'username': 'daveliu',
'start_time': '2018-01-16',
'end_time': '2018-01-16',
'surgery_description': 'Headbar posterior'},
skip_duplicates=True
)
lab.Surgery.Procedure().insert1({
'subject_id': 407512,
'surgery_id': 1,
'procedure_id': 1,
'skull_reference': 'Bregma',
'ml_location': 0,
'ap_location': -1.75,
'surgery_procedure_description': 'Fiducial marker'},
skip_duplicates=True
)
lab.WaterRestriction().insert1({
'subject_id': 407512,
'water_restriction_number': 'dl24',
'cage_number': 151793,
'wr_start_date': '2018-01-22',
'wr_start_weight': 26},
skip_duplicates=True
)
# 407513 / dl25
lab.Subject().insert1({
'subject_id': 407513,
'username': 'daveliu',
'cage_number': 148636,
'date_of_birth': '2017-10-13',
'sex': 'M',
'animal_source': 'Jackson labs'},
skip_duplicates=True
)
lab.Subject.GeneModification().insert1({
'subject_id': 407513,
'gene_modification': 'VGAT-Chr2-EYFP Jax'},
skip_duplicates=True
)
lab.Surgery().insert1({
'subject_id': 407513,
'surgery_id': 1,
'username': 'daveliu',
'start_time': '2018-01-17',
'end_time': '2018-01-17',
'surgery_description': 'Headbar posterior'},
skip_duplicates=True
)
lab.Surgery.Procedure().insert1({
'subject_id': 407513,
'surgery_id': 1,
'procedure_id': 1,
'skull_reference': 'Bregma',
'ml_location': 0,
'ap_location': -1.75,
'surgery_procedure_description': 'Fiducial marker'},
skip_duplicates=True
)
lab.WaterRestriction().insert1({
'subject_id': 407513,
'water_restriction_number': 'dl25',
'cage_number': 151794,
'wr_start_date': '2018-01-22',
'wr_start_weight': 25.5},
skip_duplicates=True
)
# Subject 407986 / dl28
lab.Subject().insert1({
'subject_id': 407986,
'username': 'daveliu',
'cage_number': 152268,
'date_of_birth': '2017-10-18',
'sex': 'F',
'animal_source': 'Jackson labs'},
skip_duplicates=True
)
lab.Subject.GeneModification().insert1({
'subject_id': 407986,
'gene_modification': 'VGAT-Chr2-EYFP Jax'},
skip_duplicates=True
)
lab.Surgery().insert1({
'subject_id': 407986,
'surgery_id': 1,
'username': 'daveliu',
'start_time': '2018-02-01',
'end_time': '2018-02-01',
'surgery_description': 'Headbar anterior'},
skip_duplicates=True
)
lab.Surgery.Procedure().insert1({
'subject_id': 407986,
'surgery_id': 1,
'procedure_id': 1,
'skull_reference': 'Bregma',
'ml_location': 0,
'ap_location': -4,
'surgery_procedure_description': 'Fiducial marker'},
skip_duplicates=True
)
lab.WaterRestriction().insert1({
'subject_id': 407986,
'water_restriction_number': 'dl28',
'cage_number': 152312,
'wr_start_date': '2018-02-05',
'wr_start_weight': 19.8},
skip_duplicates=True
)
# Subject 123457 / tw5
lab.Subject().insert1({
'subject_id': 123457,
'username': 'daveliu',
'cage_number': 145375,
'date_of_birth': '2017-08-03',
'sex': 'M',
'animal_source': 'Jackson labs'},
skip_duplicates=True
)
lab.WaterRestriction().insert1({
'subject_id': 123457,
'water_restriction_number': 'tw5',
'cage_number': 148861,
'wr_start_date': '2017-11-07',
'wr_start_weight': 20.5},
skip_duplicates=True
)
# Subject 412330 / tw34
lab.Subject().insert1({
'subject_id': 412330,
'username': 'daveliu',
'cage_number': 154522,
'date_of_birth': '2017-12-05',
'sex': 'M',
'animal_source': 'Jackson labs'},
skip_duplicates=True
)
lab.WaterRestriction().insert1({
'subject_id': 412330,
'water_restriction_number': 'tw34',
'cage_number': 154522,
'wr_start_date': '2018-03-18',
'wr_start_weight': 21.0},
skip_duplicates=True
)
# subject 432998 / dl55
lab.Subject().insert1({
'subject_id': 432998,
'username': 'daveliu',
'cage_number': 160920,
'date_of_birth': '2018-07-02',
'sex': 'M',
'animal_source': 'Jackson labs'},
skip_duplicates=True
)
lab.WaterRestriction().insert1({
'subject_id': 432998,
'water_restriction_number': 'dl55',
'cage_number': 160920,
'wr_start_date': '2018-09-05',
'wr_start_weight': 21.0},
skip_duplicates=True
)
# Subject 435884 / dl59
lab.Subject().insert1({
'subject_id': 435884,
'username': 'daveliu',
'cage_number': 161908,
'date_of_birth': '2018-08-06',
'sex': 'M',
'animal_source': 'Jackson labs'},
skip_duplicates=True
)
lab.WaterRestriction().insert1({
'subject_id': 435884,
'water_restriction_number': 'dl59',
'cage_number': 154522,
'wr_start_date': '2018-09-30',
'wr_start_weight': 21.0},
skip_duplicates=True
)
# Subject 432572 / dl56
lab.Subject().insert1({
'subject_id': 432572,
'username': 'daveliu',
'cage_number': 161125,
'date_of_birth': '2018-06-28',
'sex': 'M',
'animal_source': 'Jackson labs'},
skip_duplicates=True
)
lab.WaterRestriction().insert1({
'subject_id': 432572,
'water_restriction_number': 'dl56',
'cage_number': 161125,
'wr_start_date': '2018-09-10',
'wr_start_weight': 21.0},
skip_duplicates=True
)
# Subject 412753 / dl36
lab.Subject().insert1({
'subject_id': 412753,
'username': 'daveliu',
'cage_number': 154570,
'date_of_birth': '2017-12-07',
'sex': 'M',
'animal_source': 'Jackson labs'},
skip_duplicates=True
)
lab.WaterRestriction().insert1({
'subject_id': 412753,
'water_restriction_number': 'dl36',
'cage_number': 154570,
'wr_start_date': '2017-03-30',
'wr_start_weight': 21.0},
skip_duplicates=True
)
# Subject 440010 / dl62
lab.Subject().insert1({
'subject_id': 440010,
'username': 'daveliu',
'cage_number': 163782,
'date_of_birth': '2018-09-24',
'sex': 'M',
'animal_source': 'Jackson labs'},
skip_duplicates=True
)
lab.WaterRestriction().insert1({
'subject_id': 440010,
'water_restriction_number': 'dl62',
'cage_number': 163782,
'wr_start_date': '2018-11-24',
'wr_start_weight': 23.0},
skip_duplicates=True
)
# Subject 55004 / DL004
lab.Subject().insert1({
'subject_id': 550004,
'username': 'daveliu',
'cage_number': 163782,
'date_of_birth': '2018-09-24',
'sex': 'M',
'animal_source': 'Jackson labs'},
skip_duplicates=True
)
lab.WaterRestriction().insert1({
'subject_id': 550004,
'water_restriction_number': 'DL004',
'cage_number': 163782,
'wr_start_date': '2018-11-24',
'wr_start_weight': 23.0},
skip_duplicates=True
)
# Subject 550009 / DL009
lab.Subject().insert1({
'subject_id': 550009,
'username': 'daveliu',
'cage_number': 163782,
'date_of_birth': '2018-09-24',
'sex': 'M',
'animal_source': 'Jackson labs'},
skip_duplicates=True
)
lab.WaterRestriction().insert1({
'subject_id': 550009,
'water_restriction_number': 'DL009',
'cage_number': 163782,
'wr_start_date': '2018-11-24',
'wr_start_weight': 23.0},
skip_duplicates=True
)
# Subject 550010 / DL010
lab.Subject().insert1({
'subject_id': 550010,
'username': 'daveliu',
'cage_number': 163782,
'date_of_birth': '2018-09-24',
'sex': 'M',
'animal_source': 'Jackson labs'},
skip_duplicates=True
)
lab.WaterRestriction().insert1({
'subject_id': 550010,
'water_restriction_number': 'DL010',
'cage_number': 163782,
'wr_start_date': '2018-11-24',
'wr_start_weight': 23.0},
skip_duplicates=True
)
# Subject 550022 / DL022
lab.Subject().insert1({
'subject_id': 550022,
'username': 'daveliu',
'cage_number': 163782,
'date_of_birth': '2018-09-24',
'sex': 'M',
'animal_source': 'Jackson labs'},
skip_duplicates=True
)
lab.WaterRestriction().insert1({
'subject_id': 550022,
'water_restriction_number': 'DL022',
'cage_number': 163782,
'wr_start_date': '2018-11-24',
'wr_start_weight': 23.0},
skip_duplicates=True
)
# Subject 440959 / SC011
lab.Subject().insert1({
'subject_id': 440959,
'username': 'susu',
'cage_number': 440959,
'date_of_birth': '2018-10-09',
'sex': 'M',
'animal_source': 'Jackson labs'},
skip_duplicates=True
)
lab.WaterRestriction().insert1({
'subject_id': 440959,
'water_restriction_number': 'SC011',
'cage_number': 440959,
'wr_start_date': '2018-12-21',
'wr_start_weight': 22.8},
skip_duplicates=True
)
# Subject 442571 / SC022
lab.Subject().insert1({
'subject_id': 442571,
'username': 'susu',
'cage_number': 442571,
'date_of_birth': '2018-10-29',
'sex': 'M',
'animal_source': 'Jackson labs'},
skip_duplicates=True
)
lab.WaterRestriction().insert1({
'subject_id': 442571,
'water_restriction_number': 'SC022',
'cage_number': 442571,
'wr_start_date': '2019-01-02',
'wr_start_weight': 26.5},
skip_duplicates=True
)
# Subject 460432 / SC030
lab.Subject().insert1({
'subject_id': 456773,
'username': 'susu',
'cage_number': 171857,
'date_of_birth': '2019-05-29',
'sex': 'M',
'animal_source': 'Jackson Labs'},
skip_duplicates=True
)
lab.WaterRestriction().insert1({
'subject_id': 456773,
'water_restriction_number': 'SC030',
'cage_number': 171857,
'wr_start_date': '2019-08-08',
'wr_start_weight': 25.700},
skip_duplicates=True
)
# Subject 460432 / SC032
lab.Subject().insert1({
'subject_id': 460432,
'username': 'susu',
'cage_number': 173167,
'date_of_birth': '2019-07-15',
'sex': 'M',
'animal_source': 'Jackson labs'},
skip_duplicates=True
)
lab.WaterRestriction().insert1({
'subject_id': 460432,
'water_restriction_number': 'SC032',
'cage_number': 173167,
'wr_start_date': '2019-09-20',
'wr_start_weight': 22.8},
skip_duplicates=True
)
for num in range(1, 20):
lab.Subject().insert1({
'subject_id': 777000 + num,
'username': 'tn',
'cage_number': 173167,
'date_of_birth': '2019-07-15',
'sex': 'M',
'animal_source': 'Jackson labs'},
skip_duplicates=True
)
lab.WaterRestriction().insert1({
'subject_id': 777000 + num,
'water_restriction_number': 'FOR' + f'{num:02}',
'cage_number': 173167,
'wr_start_date': '2019-09-20',
'wr_start_weight': 22.8},
skip_duplicates=True
)
# Rig
lab.Rig().insert1({
'rig': 'TRig1',
'room': '2w.334',
'rig_description': 'Training rig 1'},
skip_duplicates=True
)
lab.Rig().insert1({
'rig': 'TRig2',
'room': '2w.334',
'rig_description': 'Training rig 2'},
skip_duplicates=True
)
lab.Rig().insert1({
'rig': 'TRig3',
'room': '2w.334',
'rig_description': 'Training rig 3'},
skip_duplicates=True
)
lab.Rig().insert1({
'rig': 'RRig',
'room': '2w.334',
'rig_description': 'Recording rig'},
skip_duplicates=True
)
lab.Rig().insert1({
'rig': 'RRig2',
'room': '2w.334',
'rig_description': 'Recording rig2'},
skip_duplicates=True
)
lab.Rig().insert1({
'rig': 'RRig3',
'room': '2w.334',
'rig_description': 'Recording rig3 for multi-target-licking'},
skip_duplicates=True
)
lab.Rig().insert1({
'rig': 'Ephys1',
'room': '2w.334',
'rig_description': 'Recording computer'},
skip_duplicates=True
)
lab.ProbeType.create_neuropixels_probe()
except Exception as e:
print("error creating mock data: {e}".format(e=e), file=sys.stderr)
raise
def post_ephys(*args):
from pipeline.ingest import ephys as ephys_ingest
for ef in ephys_ingest.EphysIngest.EphysFile().fetch(as_dict=True):
fname = ef['ephys_file']
print('attempting Probe InsertionLocation for fname: {}'.format(fname),
end=' ')
if re.match('.*20181207.*dl59.*.mat', fname):
rec_locs = [{
'subject_id': 435884,
'session': 1,
'insertion_number': 1,
'skull_reference': 'bregma',
'ml_location': 1500,
'ap_location': 2500,
'depth': -1668.9,
'theta': 0,
'phi': 0,
'beta': 0
}]
rec_brain = [{
'subject_id': 435884,
'session': 1,
'insertion_number': 1,
'brain_area': 'ALM',
'hemisphere': 'right'
}]
print('match!: {} - {}'.format(rec_brain, rec_locs))
elif re.match('.*20180716.*tw34.*.mat', fname):
rec_locs = [{
'subject_id': 412330,
'session': 1,
'insertion_number': 1,
'skull_reference': 'Bregma',
'ml_location': 1500,
'ap_location': 2500,
'depth': -2103.2,
'theta': 0,
'phi': 0,
'beta': 0
}, {
'subject_id': 412330,
'session': 1,
'insertion_number': 2,
'skull_reference': 'Bregma',
'ml_location': 1000,
'ap_location': 6500,
'depth': -5237.5,
'theta': 0,
'phi': 0,
'beta': 0
}]
rec_brain = [{
'subject_id': 412330,
'session': 1,
'insertion_number': 1,
'brain_area': 'ALM',
'hemisphere': 'right'
}, {
'subject_id': 412330,
'session': 1,
'insertion_number': 2,
'brain_area': 'Medulla',
'hemisphere': 'right'
}
]
print('match!: {} - {}'.format(rec_brain, rec_locs))
elif re.match('.*SC022/20190303.*', fname):
# FIXME: 15deg dv angle -> ?
# FIXME: 'you should add 175um to the note depths
# 'because where I used as zero reference is where the 1st tip
# enters the dura' ...
kbase = {'subject_id': 888888, 'session': 1}
rec_locs = [{
**kbase,
'insertion_number': 1,
'skull_reference': 'Bregma',
'ml_location': 1500,
'ap_location': 2500,
'depth': -2900,
'theta': 0,
'phi': 0,
'beta': 0
},{
**kbase,
'insertion_number': 2,
'skull_reference': 'Bregma',
'ml_location': 1500,
'ap_location': 2500,
'depth': -2900,
'theta': 0,
'phi': 0,
'beta': 0
},{
**kbase,
'insertion_number': 3,
'skull_reference': 'Bregma',
'ml_location': 1000,
'ap_location': 2800,
'depth': -4500,
'theta': 0,
'phi': 0,
'beta': 0
},{
**kbase,
'insertion_number': 4,
'skull_reference': 'Bregma',
'ml_location': 1000,
'ap_location': 2800,
'depth': -4500,
'theta': 0,
'phi': 0,
'beta': 0
}]
rec_brain = [{
**kbase,
'insertion_number': 1,
'brain_area': 'ALM',
'hemisphere': 'left'
}, {
**kbase,
'insertion_number': 2,
'brain_area': 'ALM',
'hemisphere': 'right'
}, {
**kbase,
'insertion_number': 3,
'brain_area': 'striatum',
'hemisphere': 'left'
}, {
**kbase,
'insertion_number': 4,
'brain_area': 'striatum',
'hemisphere': 'right'
}
]
print('match!: {} - {}'.format(rec_brain, rec_locs))
elif re.match('.*2018-07-10.*dl36.*.mat', fname):
kbase = {'subject_id': 412753, 'session': 1}
rec_locs = [{
**kbase,
'insertion_number': 1,
'skull_reference': 'Bregma',
'ml_location': 1000,
'ap_location': 2500,
'depth': -2019.4,
'theta': 0,
'phi': 0,
'beta': 0
}, {
**kbase,
'insertion_number': 2,
'skull_reference': 'Bregma',
'ml_location': 1000,
'ap_location': 1750,
'depth': -4954.8,
'theta': 0,
'phi': 0,
'beta': 0
}]
rec_brain = [{
**kbase,
'insertion_number': 1,
'brain_area': 'ALM',
'hemisphere': 'left'
}, {
**kbase,
'insertion_number': 2,
'brain_area': 'Thalamus',
'hemisphere': 'right'
}
]
print('match!: {} - {}'.format(rec_brain, rec_locs))
elif re.match('.*20181125.*dl56.*.mat', fname):
kbase = {'subject_id': 432572, 'session': 1}
rec_locs = [{
**kbase,
'insertion_number': 1,
'skull_reference': 'Bregma',
'ml_location': -1500,
'ap_location': 2500,