def _prepend_db_root(cls, protocols_root, index):
"""
Prepends the protocols_root onto elements of index that contain the basename of protocols_root and look
like paths.
"""
protocols_basename = os.path.basename(protocols_root)
for k, v in list(index.items()):
if isinstance(v, dict):
cls._prepend_db_root(protocols_root, v)
elif isinstance(v, string_types):
v_path = pathlib.Path(str(v))
root = str(v_path.parts[0])
if root == protocols_basename:
index[k] = os.path.join(protocols_root,
str(v_path.parts[1:]))
def read_matlab(self):
"""
Reads Matlab event file and returns corresponging np.recarray. Path to the eegfile is changed
w.r.t original Matlab code to account for the following:
1. /data dir of the database might have been mounted under different mount point e.g. /Users/m/data
2. use_reref_eeg is set to True in which case we replaces 'eeg.reref' with 'eeg.noreref' in eegfile path
:return: np.recarray representing events
"""
# extract matlab matrix (called 'events') as numpy structured array
struct_array = read_single_matlab_matrix_as_numpy_structured_array(
self.filename, 'events')
evs = struct_array
if 'eegfile' in evs.dtype.names:
if self.eliminate_events_with_no_eeg:
# eliminating events that have no eeg file
indicator = np.empty(len(evs), dtype=bool)
indicator[:] = False
for i, ev in enumerate(evs):
# MAKE THIS CHECK STRONGER
indicator[i] = (len(str(evs[i].eegfile)) > 3)
# indicator[i] = (type(evs[i].eegfile).__name__.startswith('unicode')) & (len(str(evs[i].eegfile)) > 3)
evs = evs[indicator]
# determining data_dir_prefix in case rhino /data filesystem was mounted under different root
if self.normalize_eeg_path:
data_dir_prefix = self.find_data_dir_prefix()
for i, ev in enumerate(evs):
ev.eegfile = join(
data_dir_prefix,
str(pathlib.Path(str(ev.eegfile)).parts[1:]))
evs = self.normalize_paths(evs)
# if not self.use_reref_eeg:
if self._alter_eeg_path_flag:
evs = self.modify_eeg_path(evs)
if self.eliminate_nans:
# this is
evs = self.replace_nans(evs)
return evs