def open_klusters(filename):
indices = find_indices(filename)
triplet = filename_to_triplet(filename)
filenames_shanks = {}
for index in indices:
filenames_shanks[index] = triplet_to_filename(triplet[:2] + (index, ))
klusters_data = {
index: open_klusters_oneshank(filename)
for index, filename in filenames_shanks.iteritems()
}
shanks = filenames_shanks.keys()
# Find the dataset filenames and load the metadata.
filenames = find_filenames(filename)
# Metadata common to all shanks.
metadata = read_xml(filenames['xml'], 1)
# Metadata specific to each shank.
metadata.update(
{shank: read_xml(filenames['xml'], shank)
for shank in shanks})
metadata['shanks'] = sorted(shanks)
metadata['has_masks'] = (
('mask' in filenames and filenames['mask'] is not None)
or ('fmask' in filenames and filenames['fmask'] is not None))
klusters_data['name'] = triplet[0]
klusters_data['metadata'] = metadata
klusters_data['shanks'] = shanks
klusters_data['filenames'] = filenames
# Load probe file.
filename_probe = filenames['probe']
# It no probe file exists, create a default, linear probe with the right
# number of channels per shank.
if not filename_probe:
# Generate a probe filename.
filename_probe = find_filename_or_new(filename,
'default.probe',
have_file_index=False)
shanks = {
shank: klusters_data[shank]['nchannels']
for shank in filenames_shanks.keys()
}
probe_python = generate_probe(shanks, 'complete')
# with open(filename_probe, 'w') as f:
# f.write(probe_python)
# save_probe(filename_probe, probe_python)
klusters_data['prb'] = probe_python
else:
probe_ns = {}
execfile(filename_probe, {}, probe_ns)
klusters_data['probe'] = probe_ns
return klusters_data
def open_klusters(filename):
indices = find_indices(filename)
triplet = filename_to_triplet(filename)
filenames_shanks = {}
for index in indices:
filenames_shanks[index] = triplet_to_filename(triplet[:2] + (index,))
klusters_data = {index: open_klusters_oneshank(filename)
for index, filename in filenames_shanks.iteritems()}
shanks = filenames_shanks.keys()
# Find the dataset filenames and load the metadata.
filenames = find_filenames(filename)
# Metadata common to all shanks.
metadata = read_xml(filenames['xml'], 1)
# Metadata specific to each shank.
metadata.update({shank: read_xml(filenames['xml'], shank)
for shank in shanks})
metadata['shanks'] = sorted(shanks)
metadata['has_masks'] = (('mask' in filenames
and filenames['mask'] is not None) or (
'fmask' in filenames
and filenames['fmask'] is not None
))
klusters_data['name'] = triplet[0]
klusters_data['metadata'] = metadata
klusters_data['shanks'] = shanks
klusters_data['filenames'] = filenames
# Load probe file.
filename_probe = filenames['probe']
# It no probe file exists, create a default, linear probe with the right
# number of channels per shank.
if not filename_probe:
# Generate a probe filename.
filename_probe = find_filename_or_new(filename, 'default.probe',
have_file_index=False)
shanks = {shank: klusters_data[shank]['nchannels']
for shank in filenames_shanks.keys()}
probe_python = generate_probe(shanks, 'complete')
# with open(filename_probe, 'w') as f:
# f.write(probe_python)
# save_probe(filename_probe, probe_python)
klusters_data['prb'] = probe_python
else:
probe_ns = {}
execfile(filename_probe, {}, probe_ns)
klusters_data['probe'] = probe_ns
return klusters_data
def open_klusters_oneshank(filename):
filenames = find_filenames(filename)
fileindex = find_index(filename)
# Open small Klusters files.
data = {}
metadata = read_xml(filenames['xml'], fileindex)
data['clu'] = read_clusters(filenames['clu'])
# Read .aclu data.
if 'aclu' in filenames and os.path.exists(filenames['aclu']):
data['aclu'] = read_clusters(filenames['aclu'])
else:
data['aclu'] = data['clu']
# Read .acluinfo data.
if 'acluinfo' in filenames and os.path.exists(filenames['acluinfo']):
data['acluinfo'] = read_cluster_info(filenames['acluinfo'])
# If the ACLUINFO does not exist, try CLUINFO (older file extension)
elif 'cluinfo' in filenames and os.path.exists(filenames['cluinfo']):
data['acluinfo'] = read_cluster_info(filenames['cluinfo'])
else:
data['acluinfo'] = default_cluster_info(np.unique(data['aclu']))
# Read group info.
if 'groupinfo' in filenames and os.path.exists(filenames['groupinfo']):
data['groupinfo'] = read_group_info(filenames['groupinfo'])
else:
data['groupinfo'] = default_group_info()
# Find out the number of columns in the .fet file.
with open(filenames['fet'], 'r') as f:
f.readline()
# Get the number of non-empty columns in the .fet file.
data['fetcol'] = len(
[col for col in f.readline().split(' ') if col.strip() != ''])
metadata['nspikes'] = len(data['clu'])
data['fileindex'] = fileindex
# Open big Klusters files.
data['fet'] = MemMappedText(filenames['fet'], np.int64, skiprows=1)
if 'spk' in filenames and os.path.exists(filenames['spk'] or ''):
data['spk'] = MemMappedBinary(filenames['spk'],
np.int16,
rowsize=metadata['nchannels'] *
metadata['nsamples'])
if 'uspk' in filenames and os.path.exists(filenames['uspk'] or ''):
data['uspk'] = MemMappedBinary(filenames['uspk'],
np.int16,
rowsize=metadata['nchannels'] *
metadata['nsamples'])
if 'mask' in filenames and os.path.exists(filenames['mask'] or ''):
data['mask'] = MemMappedText(filenames['mask'], np.float32, skiprows=1)
# data['metadata'] = metadata
data.update(metadata)
return data
def open_klusters_oneshank(filename):
filenames = find_filenames(filename)
fileindex = find_index(filename)
# Open small Klusters files.
data = {}
metadata = read_xml(filenames['xml'], fileindex)
data['clu'] = read_clusters(filenames['clu'])
# Read .aclu data.
if 'aclu' in filenames and os.path.exists(filenames['aclu']):
data['aclu'] = read_clusters(filenames['aclu'])
else:
data['aclu'] = data['clu']
# Read .acluinfo data.
if 'acluinfo' in filenames and os.path.exists(filenames['acluinfo']):
data['acluinfo'] = read_cluster_info(filenames['acluinfo'])
# If the ACLUINFO does not exist, try CLUINFO (older file extension)
elif 'cluinfo' in filenames and os.path.exists(filenames['cluinfo']):
data['acluinfo'] = read_cluster_info(filenames['cluinfo'])
else:
data['acluinfo'] = default_cluster_info(np.unique(data['aclu']))
# Read group info.
if 'groupinfo' in filenames and os.path.exists(filenames['groupinfo']):
data['groupinfo'] = read_group_info(filenames['groupinfo'])
else:
data['groupinfo'] = default_group_info()
# Find out the number of columns in the .fet file.
with open(filenames['fet'], 'r') as f:
f.readline()
# Get the number of non-empty columns in the .fet file.
data['fetcol'] = len([col for col in f.readline().split(' ') if col.strip() != ''])
metadata['nspikes'] = len(data['clu'])
data['fileindex'] = fileindex
# Open big Klusters files.
data['fet'] = MemMappedText(filenames['fet'], np.int64, skiprows=1)
if 'spk' in filenames and os.path.exists(filenames['spk'] or ''):
data['spk'] = MemMappedBinary(filenames['spk'], np.int16,
rowsize=metadata['nchannels'] * metadata['nsamples'])
if 'uspk' in filenames and os.path.exists(filenames['uspk'] or ''):
data['uspk'] = MemMappedBinary(filenames['uspk'], np.int16,
rowsize=metadata['nchannels'] * metadata['nsamples'])
if 'mask' in filenames and os.path.exists(filenames['mask'] or ''):
data['mask'] = MemMappedText(filenames['mask'], np.float32, skiprows=1)
# data['metadata'] = metadata
data.update(metadata)
return data
