# ==================== subject ====================
fnames = np.hstack(
glob.glob(os.path.join(dir_files[0], '*.mat'))
for dir_files in os.walk(path) if len(dir_files[1]) == 0)
for fname in fnames:
mat = sio.loadmat(fname, struct_as_record=False, squeeze_me=True)
mat_units = mat['unit']
mat_trial_info = mat.get('trial_info')
this_sess = meta_data.loc[re.sub('_units.mat|_JRC_units', '',
os.path.split(fname)[-1])]
print(f'\nReading: {this_sess.name}')
subject_info = dict(
subject_id=this_sess.subject_id.lower(),
date_of_birth=utilities.parse_date(str(this_sess.date_of_birth)),
sex=this_sess.sex[0].upper(),
species='Mus musculus', # not available, hard-coded here
animal_source='N/A') # animal source not available from data
allele_dict = {
alias.lower(): allele
for alias, allele in subject.AlleleAlias.fetch()
}
regex_str = '|'.join([re.escape(alias) for alias in allele_dict.keys()])
alleles = [
allele_dict[s.lower()]
for s in re.findall(regex_str, this_sess.genotype, re.I)
]
with subject.Subject.connection.transaction:
path = os.path.join('.', 'data', 'data', 'L4FS_loose_seal_ION_cut')
fname = 'JY1589AAAA.nwb'
nwb = h5.File(os.path.join(path, fname), 'r')
subject_info = {
c: nwb['general']['subject'][c].value.decode('UTF-8')
for c in ('subject_id', 'description', 'sex', 'species', 'weight', 'age',
'genotype')
}
# force subject_id to be lower-case for consistency
subject_info['subject_id'] = subject_info['subject_id'].lower()
# dob and sex
subject_info['sex'] = subject_info['sex'][0].upper()
dob_str = re.search('(?<=Date of birth:\s)(.*)', subject_info['description'])
if utilities.parse_date(dob_str.group()) is not None:
subject_info['date_of_birth'] = utilities.parse_date(dob_str.group())
# allele
allele_str = re.search('(?<=Animal Strain:\s)(.*)',
subject_info['description']).group(
) # extract the information related to animal allele
allele_dict = {
alias.lower(): allele
for alias, allele in subject.AlleleAlias.fetch()
}
regex_str = '|'.join([re.escape(alias) for alias in allele_dict.keys()])
alleles = [
allele_dict[s.lower()] for s in re.findall(regex_str, allele_str, re.I)
]
# source
for fname in fnames:
print(f'Reading {fname}...')
nwb = h5.File(fname, 'r')
subject_info = {
c: nwb['general']['subject'][c].value.decode('UTF-8')
for c in ('description', 'sex', 'species', 'weight', 'age', 'genotype')
}
# force subject_id to be lower-case for consistency
subject_info['subject_id'] = os.path.split(fname)[-1].split('_')[0].lower()
# dob and sex
subject_info['sex'] = subject_info['sex'][0].upper()
dob_str = re.search('(?<=Date of birth:\s)(.*)',
subject_info['description'])
if utilities.parse_date(dob_str.group()) is not None:
subject_info['date_of_birth'] = utilities.parse_date(dob_str.group())
# allele
allele_str = re.search(
'(?<=Animal Strain:\s)(.*)', subject_info['description']).group(
) # extract the information related to animal allele
allele_dict = {
alias.lower(): allele
for alias, allele in subject.AlleleAlias.fetch()
}
regex_str = '|'.join([re.escape(alias) for alias in allele_dict.keys()])
alleles = [
allele_dict[s.lower()] for s in re.findall(regex_str, allele_str, re.I)
]
# source
subject_id, session_time = sess_meta.filename.replace(
'.mat', '').split('_')[-2:]
# --- Subject - No info on: animal sex, dob, source, strains
subject_info = dict(
subject_id=subject_id.lower(),
species='Mus musculus', # not available, hard-coded here
animal_source='N/A'
) # animal source not available from data, nor 'sex'
subject.Subject.insert1(subject_info, skip_duplicates=True)
# --- Session - no session types
session_info = dict(subject_id=subject_info['subject_id'],
session_id=sess_idx,
session_time=utilities.parse_date(session_time))
experimenters = ['Mike Economo'] # hard-coded here
with acquisition.Session.connection.transaction:
if session_info not in acquisition.Session.proj():
acquisition.Session.insert1(session_info,
ignore_extra_fields=True)
acquisition.Session.Experimenter.insert(
(dict(session_info, experimenter=k)
for k in experimenters),
ignore_extra_fields=True)
print(
f'\nCreating Session - Subject: {subject_info["subject_id"]} - Date: {session_info["session_time"]}'
)
for fname in fnames:
print(f'Reading {fname}...')
nwb = h5.File(fname, 'r')
subject_info = {
c: nwb['general']['subject'][c].value.decode('UTF-8')
for c in ('subject_id', 'description', 'sex', 'species', 'weight',
'age', 'genotype')
}
# force subject_id to be lower-case for consistency
subject_info['subject_id'] = subject_info['subject_id'].lower()
# dob and sex
subject_info['sex'] = subject_info['sex'][0].upper()
dob_str = re.search('(?<=Date of birth:\s)(.*)',
subject_info['description'])
if utilities.parse_date(dob_str.group()) is not None:
subject_info['date_of_birth'] = utilities.parse_date(dob_str.group())
# allele
allele_str = re.search(
'(?<=Animal Strain:\s)(.*)', subject_info['description']).group(
) # extract the information related to animal allele
allele_dict = {
alias.lower(): allele
for alias, allele in subject.AlleleAlias.fetch()
}
regex_str = '|'.join([re.escape(alias) for alias in allele_dict.keys()])
alleles = [
allele_dict[s.lower()] for s in re.findall(regex_str, allele_str, re.I)
]
# source