def set_electrode_areas(proj, el_in_gc={}):
exp_info = proj._exp_info
for i, row in exp_info.iterrows():
name = row['exp_name']
if name not in el_in_gc.keys():
continue
exp = blechpy.load_experiment(row['exp_dir'])
ingc = el_in_gc[name]
if ingc is 'right':
el = np.arange(8, 24)
elif ingc is 'left':
el = np.concatenate([np.arange(0, 8), np.arange(24, 32)])
elif ingc is 'none':
el = np.arange(0, 32)
else:
el = None
for rec in exp.recording_dirs:
dat = load_dataset(rec)
print('Fixing %s...' % dat.data_name)
em = dat.electrode_mapping
em['area'] = 'GC'
if el is not None:
em.loc[em['Channel'].isin(el), 'area'] = 'STR'
h5io.write_electrode_map_to_h5(dat.h5_file, em)
dat.save()
return
def clustering(exp):
# TODO Actually I now cluster 1 recording at a time
if isinstance(exp, str):
fd = exp
exp = blechpy.load_experiment(fd)
if exp is None:
exp = blechpy.experiment(fd)
dat = blechpy.load_dataset(exp.recording_dirs[0])
clustering_params = dat.clustering_params.copy()
clustering_params['clustering_params']['Max Number of Clusters'] = 15
exp.cluster_spikes(custom_params=clustering_params, umap=True)
for fd in exp.recording_dirs:
dat = blechpy.load_dataset(fd)
dat.cleanup_clustering()
def fix_palatability(proj, pal_map=None):
'''Goes through all datasets in project and fixes palatability rankings
'''
if pal_map is None:
pal_map = PAL_MAP
exp_dirs = proj._exp_info.exp_dir.to_list()
for exp_dir in tqdm(exp_dirs):
exp = blechpy.load_experiment(exp_dir)
for rd in exp.recording_dirs:
dat = load_dataset(rd)
dat.dig_in_mapping[
'palatability_rank'] = dat.dig_in_mapping.name.map(pal_map)
h5io.write_digital_map_to_h5(dat.h5_file, dat.dig_in_mapping, 'in')
dat.save()
def get_all_units(proj):
# Columns:
# - exp_name, exp_group, rec_name, rec_group, rec_dir, unit_num,
# - electrode, area, single, unit_type
all_units = pd.DataFrame(columns=[
'exp_name', 'exp_group', 'rec_name', 'rec_group', 'rec_dir',
'unit_name', 'unit_num', 'electrode', 'area', 'single_unit',
'regular_spiking', 'fast_spiking'
])
for i, row in proj._exp_info.iterrows():
exp_name = row['exp_name']
exp_group = row['exp_group']
exp_dir = row['exp_dir']
exp = blechpy.load_experiment(exp_dir)
for rec_name, rec_dir in exp.rec_labels.items():
if 'preCTA' in rec_name:
rec_group = 'preCTA'
elif 'postCTA' in rec_name:
rec_group = 'postCTA'
elif 'Train' in rec_name:
rec_group = 'ctaTrain'
elif 'Test' in rec_name:
rec_group = 'ctaTest'
else:
# TODO: Make more elegant, ask for input
raise ValueError('Rec %s does not fit into a group' % rec_name)
dat = load_dataset(rec_dir)
units = dat.get_unit_table().copy()
units['exp_name'] = exp_name
units['exp_group'] = exp_group
units['rec_name'] = rec_name
units['rec_group'] = rec_group
units['rec_dir'] = rec_dir
em = dat.electrode_mapping.copy().set_index('Electrode')
units['area'] = units['electrode'].map(em['area'])
units = units[all_units.columns]
all_units = all_units.append(units).reset_index(drop=True)
return all_units
def exp_name(ed):
exp = load_experiment(ed)
return exp.data_name