def add_ragged_data_to_dynamic_table(table,
data,
column_name,
column_description=""):
""" Builds the index and data vectors required for writing ragged array data to a pynwb dynamic table
Parameters
----------
table : pynwb.core.DynamicTable
table to which data will be added (as VectorData / VectorIndex)
data : dict
each key-value pair describes some grouping of data
column_name : str
used to set the name of this column
column_description : str, optional
used to set the description of this column
Returns
-------
nwbfile : pynwb.NWBFile
"""
idx, values = dict_to_indexed_array(data, table.id.data)
del data
table.add_column(name=column_name,
description=column_description,
data=values,
index=idx)
def add_trials(nwbfile, trials, description_dict={}):
order = list(trials.index)
for _, row in trials[['start_time', 'stop_time']].iterrows():
row_dict = row.to_dict()
nwbfile.add_trial(**row_dict)
for c in trials.columns:
if c in ['start_time', 'stop_time']:
continue
index, data = dict_to_indexed_array(trials[c].to_dict(), order)
if data.dtype == '<U1': # data type is composed of unicode characters
data = trials[c].tolist()
if not len(data) == len(order):
if len(data) == 0:
data = ['']
nwbfile.add_trial_column(name=c,
description=description_dict.get(
c, 'NOT IMPLEMENTED: %s' % c),
data=data,
index=index)
else:
nwbfile.add_trial_column(name=c,
description=description_dict.get(
c, 'NOT IMPLEMENTED: %s' % c),
data=data)
def to_nwb(self, nwbfile: NWBFile) -> NWBFile:
trials = self.value
order = list(trials.index)
for _, row in trials[['start_time', 'stop_time']].iterrows():
row_dict = row.to_dict()
nwbfile.add_trial(**row_dict)
for c in trials.columns:
if c in ['start_time', 'stop_time']:
continue
index, data = dict_to_indexed_array(trials[c].to_dict(), order)
if data.dtype == '<U1': # data type is composed of unicode
# characters
data = trials[c].tolist()
if not len(data) == len(order):
if len(data) == 0:
data = ['']
nwbfile.add_trial_column(name=c,
description='NOT IMPLEMENTED: %s' % c,
data=data,
index=index)
else:
nwbfile.add_trial_column(name=c,
description='NOT IMPLEMENTED: %s' % c,
data=data)
return nwbfile
