def main(sign, label):
"""
show group sizes in h5files
"""
files = h5files(os.getcwd())
n_arti_total = 0
for fname in files:
man = Combinato(fname, sign, label)
if not man.initialized:
continue
groups = man.get_groups(times=False, spikes=False)
if 0 in groups.keys():
n_unassigned = len(groups[0])
if -1 in groups.keys():
n_arti = len(groups[-1])
else:
n_arti = 0
print('{} {} groups, {} artifacts'.
format(os.path.basename(fname), len(groups), n_arti))
n_arti_total += n_arti
return n_arti_total
def parse_args():
"""
standard command line parsing
"""
from argparse import ArgumentParser
parser = ArgumentParser()
parser.add_argument('--label', required=True)
parser.add_argument('--h5file')
parser.add_argument('--neg', action='store_true', default=False)
parser.add_argument('--no-info', action='store_true', default=False)
parser.add_argument('--drop-artifacts', action='store_true', default=False)
args = parser.parse_args()
label = args.label
sign = 'neg' if args.neg else 'pos'
do_info = not args.no_info
drop_artifacts = args.drop_artifacts
if args.h5file is None:
rel_h5files = h5files(os.getcwd())
else:
rel_h5files = [args.h5file]
# for cluster_info.mat:
all_info = [[None] * len(rel_h5files), [None] * len(rel_h5files)]
if do_info:
session_name = os.path.dirname(rel_h5files[0])
date = time.strftime('%Y-%m-%d_%H:%M:%S')
csvfile = open('cluster_info.csv', 'w')
writer = csv.writer(csvfile)
writer.writerow(
['# Session: {}, Converted: {}'.format(session_name, date)])
writer.writerow([
'# For Artifacts, 0 means there are none, 1 means '
'they are included as clusters (type -1), 2 means '
'they are included as unassigned (type 0)'
])
writer.writerow([
'# For Unassigned, 1 means they exist, 0 means they '
'do not exist.'
])
writer.writerow([
'# For Clusters, 1 means multi-unit, 2 means '
'single-unit, -1 means artifact'
])
writer.writerow([
'ChannelNumber', 'ChannelName', 'Artifacts', 'Unassigned',
'Cluster1', 'Cluster2', '...'
])
for dfile in rel_h5files:
basedir = os.path.dirname(dfile)
basename = os.path.basename(dfile)
sorting_path = os.path.join(basedir, label)
outfname = basename[5:-3]
info = main(dfile, sorting_path, sign, outfname, drop_artifacts)
if do_info and (info is not None):
writer.writerow(info)
all_info[0][rel_h5files.index(dfile)] = info[4:]
all_info[1][rel_h5files.index(dfile)] = info[1]
if do_info:
info_dict = {
'cluster_info':
all_info,
'label_info':
' 1 = MU\n 2 = SU\n-1 = Artif.\nRefers to '
'"cluster_class"-values 1 and up.\nIgnores Unassigned '
'(value 0)'
}
info_fname = "cluster_info.mat"
savemat(info_fname, info_dict)
def parse_args():
"""
standard command line parsing
"""
from argparse import ArgumentParser
parser = ArgumentParser()
parser.add_argument('--label', required=True)
parser.add_argument('--h5file' )
parser.add_argument('--neg', action='store_true', default=False)
parser.add_argument('--no-info', action='store_true', default=False)
parser.add_argument('--drop-artifacts', action='store_true',
default=False)
args = parser.parse_args()
label = args.label
sign = 'neg' if args.neg else 'pos'
do_info = not args.no_info
drop_artifacts = args.drop_artifacts
if args.h5file is None:
rel_h5files = h5files(os.getcwd())
else:
rel_h5files = [args.h5file]
# for cluster_info.mat:
all_info = [[None]*len(rel_h5files), [None]*len(rel_h5files)]
if do_info:
session_name = os.path.dirname(rel_h5files[0])
date = time.strftime('%Y-%m-%d_%H:%M:%S')
csvfile = open('cluster_info.csv', 'w')
writer = csv.writer(csvfile)
writer.writerow(['# Session: {}, Converted: {}'.
format(session_name, date)])
writer.writerow(['# For Artifacts, 0 means there are none, 1 means '
'they are included as clusters (type -1), 2 means '
'they are included as unassigned (type 0)'])
writer.writerow(['# For Unassigned, 1 means they exist, 0 means they '
'do not exist.'])
writer.writerow(['# For Clusters, 1 means multi-unit, 2 means '
'single-unit, -1 means artifact'])
writer.writerow(['ChannelNumber', 'ChannelName', 'Artifacts',
'Unassigned', 'Cluster1', 'Cluster2', '...'])
for dfile in rel_h5files:
basedir = os.path.dirname(dfile)
basename = os.path.basename(dfile)
sorting_path = os.path.join(basedir, label)
outfname = basename[5:-3]
info = main(dfile, sorting_path, sign, outfname, drop_artifacts)
if do_info and (info is not None):
writer.writerow(info)
all_info[0][rel_h5files.index(dfile)] = info[4:]
all_info[1][rel_h5files.index(dfile)] = info[1]
if do_info:
info_dict = {'cluster_info': all_info, 'label_info':
' 1 = MU\n 2 = SU\n-1 = Artif.\nRefers to '
'"cluster_class"-values 1 and up.\nIgnores Unassigned '
'(value 0)'}
info_fname = "cluster_info"
savemat(info_fname, info_dict)