def test_dataframe_roundtrip(self):
df = self.get_dataframe()
epochs = TimeIntervals.from_dataframe(df, name='test epochs')
obtained = epochs.to_dataframe()
self.assertIs(obtained.loc[3, 'timeseries'][1],
df.loc[3, 'timeseries'][1])
self.assertEqual(obtained.loc[2, 'foo'], df.loc[2, 'foo'])
def test_from_dataframe(self):
df = pd.DataFrame({'start_time': [1., 2., 3.], 'stop_time': [2., 3., 4.], 'label': ['a', 'b', 'c']},
columns=('start_time', 'stop_time', 'label'))
ti = TimeIntervals.from_dataframe(df, name='ti_name')
self.assertEqual(ti.colnames, ('start_time', 'stop_time', 'label'))
self.assertEqual(ti.columns[0].data, [1.0, 2.0, 3.0])
self.assertEqual(ti.columns[2].data, ['a', 'b', 'c'])
def inject_all(self, valid_times, nwb_content):
intervals = TimeIntervals(
name='mda_valid_times',
description='Valid times based on mda timestamps',
)
for single_interval in valid_times:
self.inject(single_interval, intervals)
nwb_content.add_time_intervals(intervals)
def test_create_custom_intervals(self):
df_words = pd.DataFrame({
'start_time': [.1, 2.],
'stop_time': [.8, 2.3],
'label': ['hello', 'there']
})
words = TimeIntervals.from_dataframe(df_words, name='words')
self.nwbfile.add_time_intervals(words)
self.assertEqual(self.nwbfile.intervals['words'], words)
def run_conversion(self,
nwbfile: NWBFile,
metadata: dict = None,
stub_test: bool = False):
conditions = intervals_from_traces(self.recording_extractor)
mech_stim = TimeIntervals(
name='MechanicalStimulus',
description=
"Activation times inferred from TTL commands for mechanical stimulus."
)
laser_stim = TimeIntervals(
name='LaserStimulus',
description=
"Activation times inferred from TTL commands for cortical laser stimulus."
)
for j, table in enumerate([mech_stim, laser_stim]):
for row in conditions[j]:
table.add_row(
dict(start_time=float(row[0]), stop_time=float(row[1])))
# TODO - these really should be IntervalSeries added to stimulus, rather than processing
check_module(nwbfile, 'stimulus',
"Contains stimuli data.").add(mech_stim)
check_module(nwbfile, 'stimulus',
"Contains stimuli data.").add(laser_stim)
if stub_test or self.subset_channels is not None:
recording = self.subset_recording(stub_test=stub_test)
else:
recording = self.recording_extractor
# Pressure values
nwbfile.add_stimulus(
TimeSeries(
name='MechanicalPressure',
data=H5DataIO(recording.get_traces(0), compression="gzip"),
unit=self.recording_extractor._channel_smrxinfo[0]['unit'],
conversion=recording.get_channel_property(0, 'gain'),
rate=recording.get_sampling_frequency(),
description=
"Pressure sensor attached to the mechanical stimulus used to repeatedly evoke spiking."
))
def textgriddf_converter(text_df):
"""Converts data into TimeIntervals
For a given DataFrame this function converts the data into TimeIntervals
Parameters
----------
text_df : pandas.DataFrame
Data related to an item
Returns
----------
pynwb.epoch.TimeIntervals
"""
textgrid_sentences = TimeIntervals(
name='sentences',
description='desc'
)
textgrid_sentences.add_column('label', 'text of sentences')
for i in text_df.index:
textgrid_sentences.add_interval(label=text_df.iloc[i]['text'], start_time=float(text_df.iloc[i]['xmin']),
stop_time=float(text_df.iloc[i]['xmax']))
return textgrid_sentences
def setUp(self):
super().setUp()
# add intervals to nwbfile
ti1 = TimeIntervals(name='intervals',
description='experimental intervals')
ti1.add_interval(start_time=0.0, stop_time=2.0)
ti1.add_interval(start_time=2.0, stop_time=4.0)
ti1.add_interval(start_time=4.0, stop_time=6.0)
ti1.add_interval(start_time=6.0, stop_time=8.0)
ti1.add_column(name='var1',
data=['a', 'b', 'a', 'b'],
description='no description')
self.nwbfile.add_time_intervals(ti1)
self.widget = ExtendedTimeIntervalSelector(
input_data=self.nwbfile.units)
class TestAlignMultiTraceTimeSeriesByTrials(unittest.TestCase):
def setUp(self):
data = np.random.rand(100, 10)
timestamps = [0.0]
for _ in range(data.shape[0]):
timestamps.append(timestamps[-1] + 0.75 + 0.25 * np.random.rand())
self.ts_rate = TimeSeries(
name="test_timeseries_rate",
data=data,
unit="m",
starting_time=0.0,
rate=1.0,
)
self.ts_timestamps = TimeSeries(
name="test_timeseries_timestamps",
data=data,
unit="m",
timestamps=np.array(timestamps),
)
self.time_intervals = TimeIntervals(name="Test Time Interval")
n_intervals = 10
for start_time in np.linspace(0, 75, n_intervals + 1):
if start_time < 75:
stt = start_time + np.random.rand()
spt = stt + 7 - np.random.rand()
self.time_intervals.add_interval(start_time=stt, stop_time=spt)
self.time_intervals.add_column(
name="temp", description="desc", data=np.random.randint(2, size=n_intervals)
)
self.time_intervals.add_column(
name="temp2",
description="desc",
data=np.random.randint(10, size=n_intervals),
)
def test_align_by_timestamps(self):
amt = AlignMultiTraceTimeSeriesByTrialsVariable(
time_series=self.ts_timestamps, trials=self.time_intervals
)
gas = amt.controls['gas']
gas.group_dd.value = list(gas.categorical_columns.keys())[0]
gas.group_sm.value = (gas.group_sm.options[0],)
fig = amt.children[-1]
assert len(fig.data)==len(gas.group_sm.value)
def test_align_by_rate(self):
amt = AlignMultiTraceTimeSeriesByTrialsConstant(
time_series=self.ts_rate, trials=self.time_intervals
)
gas = amt.controls['gas']
gas.group_dd.value = list(gas.categorical_columns)[0]
gas.group_sm.value = (gas.group_sm.options[0],)
fig = amt.children[-1]
assert len(fig.data) == len(gas.group_sm.value)
def addContainer(self, nwbfile):
""" Add the test epochs with TimeSeries objects to the given NWBFile """
tsa, tsb = [
TimeSeries(name='a',
data=np.arange(11),
unit='flubs',
timestamps=np.linspace(0, 1, 11)),
TimeSeries(name='b',
data=np.arange(13),
unit='flubs',
timestamps=np.linspace(0.1, 5, 13)),
]
nwbfile.add_acquisition(tsa)
nwbfile.add_acquisition(tsb)
nwbfile.epochs = TimeIntervals.from_dataframe(pd.DataFrame({
'foo': [1, 2, 3, 4],
'bar': ['fish', 'fowl', 'dog', 'cat'],
'start_time': [0.2, 0.25, 0.30, 0.35],
'stop_time': [0.25, 0.30, 0.40, 0.45],
'timeseries': [[(2, 1, tsa)], [(3, 1, tsa)], [(3, 1, tsa)],
[(4, 1, tsa)]],
'tags': [[''], [''], ['fizz', 'buzz'], ['qaz']]
}),
'epochs',
columns=[
{
'name':
'foo',
'description':
'a column of integers'
},
{
'name':
'bar',
'description':
'a column of strings'
},
])
# reset the thing
self.container = nwbfile.epochs
def out_close(self, val):
self.value = val
if val == 1: # finished auto-detection of events
self.stimTimes = self.thread.stimTimes
self.respTimes = self.thread.respTimes
fname = self.parent.model.fullpath
with NWBHDF5IO(fname, 'r+', load_namespaces=True) as io:
nwb = io.read()
# Speaker stimuli times
ti_stim = TimeIntervals(name='TimeIntervals_speaker')
times = self.stimTimes.reshape((-1, 2)).astype('float')
for start, stop in times:
ti_stim.add_interval(start, stop)
# Microphone responses times
ti_resp = TimeIntervals(name='TimeIntervals_mic')
times = self.respTimes.reshape((-1, 2)).astype('float')
for start, stop in times:
ti_resp.add_interval(start, stop)
# Add both to file
nwb.add_time_intervals(ti_stim)
nwb.add_time_intervals(ti_resp)
# Write file
io.write(nwb)
self.accept()
class SpatialSeriesTrialsAlign(unittest.TestCase):
def setUp(self) -> None:
data = np.random.rand(100, 3)
timestamps = [0.0]
for _ in range(data.shape[0]):
timestamps.append(timestamps[-1] + 0.75 + 0.25 * np.random.rand())
self.spatial_series_rate = SpatialSeries(
name="position_rate",
data=data,
starting_time=0.0,
rate=1.0,
reference_frame="starting gate",
)
self.spatial_series_ts = SpatialSeries(
name="position_ts",
data=data,
timestamps=np.array(timestamps),
reference_frame="starting gate",
)
self.time_intervals = TimeIntervals(name="Test Time Interval")
n_intervals = 10
for start_time in np.linspace(0, 75, n_intervals + 1):
if start_time < 75:
stt = start_time + np.random.rand()
spt = stt + 7 - np.random.rand()
self.time_intervals.add_interval(start_time=stt, stop_time=spt)
self.time_intervals.add_column(name="temp",
description="desc",
data=np.random.randint(
2, size=n_intervals))
self.time_intervals.add_column(
name="temp2",
description="desc",
data=np.random.randint(10, size=n_intervals),
)
def test_spatial_series_trials_align_rate(self):
trial_align_spatial_series(self.spatial_series_rate,
self.time_intervals)
def test_spatial_series_trials_align_ts(self):
trial_align_spatial_series(self.spatial_series_ts, self.time_intervals)
def test_align_by_time_intervals_Nonetrials_select(self):
time_intervals = TimeIntervals(name='Test Time Interval')
time_intervals.add_interval(start_time=21.0, stop_time=28.0)
time_intervals.add_interval(start_time=22.0, stop_time=26.0)
time_intervals.add_interval(start_time=22.0, stop_time=28.4)
ati = align_by_time_intervals(self.nwbfile.units,
index=1,
intervals=time_intervals,
stop_label=None,
before=20.,
after=30.)
compare_to_ati = [
np.array([-18.8, -18., 4., 5.]),
np.array([-19.8, -19., 3., 4.]),
np.array([-19.8, -19., 3., 4.])
]
np.testing.assert_array_equal(ati, compare_to_ati)
def test_align_by_time_intervals(self):
time_intervals = TimeIntervals(name='Test Time Interval')
time_intervals.add_interval(start_time=21.0, stop_time=28.0)
time_intervals.add_interval(start_time=22.0, stop_time=26.0)
time_intervals.add_interval(start_time=22.0, stop_time=28.4)
ATI = align_by_time_intervals(self.nwbfile.units,
index=1,
intervals=time_intervals,
stop_label=None,
before=20.,
after=30.,
rows_select=[0, 1])
ComparedtoATI = [
np.array([-18.8, -18., 4., 5.]),
np.array([-19.8, -19., 3., 4.])
]
np.testing.assert_array_equal(ATI, ComparedtoATI)
def test_align_by_time_intervals(self):
time_intervals = TimeIntervals(name="Test Time Interval")
time_intervals.add_interval(start_time=21.0, stop_time=28.0)
time_intervals.add_interval(start_time=22.0, stop_time=26.0)
time_intervals.add_interval(start_time=22.0, stop_time=28.4)
ati = align_by_time_intervals(
self.nwbfile.units,
index=1,
intervals=time_intervals,
stop_label=None,
start=-20.0,
end=30.0,
rows_select=[0, 1],
)
compare_to_ati = [
np.array([-18.8, -18.0, 4.0, 5.0]),
np.array([-19.8, -19.0, 3.0, 4.0]),
]
np.testing.assert_array_equal(ati, compare_to_ati)
from pynwb import NWBHDF5IO, NWBFile
from datetime import datetime
from pynwb.epoch import TimeIntervals
from ndx_speech import Transcription
import pandas as pd
words = TimeIntervals.from_dataframe(pd.DataFrame({
'start_time': [.1, 2.],
'stop_time': [.8, 2.3],
'label': ['hello', 'there']
}),
name='words')
nwbfile = NWBFile('aa', 'aa', datetime.now().astimezone())
nwbfile.add_acquisition(Transcription(words=words))
with NWBHDF5IO('test_transcription.nwb', 'w') as io:
io.write(nwbfile, cache_spec=True)
with NWBHDF5IO('test_transcription.nwb', 'r', load_namespaces=True) as io:
nwbfile2 = io.read()
assert (nwbfile.acquisition['transcription'].words.to_dataframe().equals(
nwbfile2.acquisition['transcription'].words.to_dataframe()))
def setUpContainer(self):
""" Return placeholder epochs object. Tested epochs are added directly to the NWBFile in addContainer """
return TimeIntervals('epochs')
def setUpContainer(self):
# this will get ignored
return TimeIntervals('epochs')
def test_align_by_time_intervals(self):
intervals = TimeIntervals(name='Time Intervals')
np.testing.assert_array_equal(
align_by_time_intervals(timeseries=self.ts,
intervals=intervals,
stop_label=None), np.array([]))
def nwb_copy_file(old_file, new_file, cp_objs={}):
"""
Copy fields defined in 'obj', from existing NWB file to new NWB file.
Parameters
----------
old_file : str, path
String such as '/path/to/old_file.nwb'.
new_file : str, path
String such as '/path/to/new_file.nwb'.
cp_objs : dict
Name:Value pairs (Group:Children) listing the groups and respective
children from the current NWB file to be copied. Children can be:
- Boolean, indicating an attribute (e.g. for institution, lab)
- List of strings, containing several children names
Example:
{'institution':True,
'lab':True,
'acquisition':['microphone'],
'ecephys':['LFP','DecompositionSeries']}
"""
manager = get_manager()
# Open original signal file
with NWBHDF5IO(old_file, 'r', manager=manager,
load_namespaces=True) as io1:
nwb_old = io1.read()
# Creates new file
nwb_new = NWBFile(session_description=str(nwb_old.session_description),
identifier='',
session_start_time=datetime.now(tzlocal()))
with NWBHDF5IO(new_file, mode='w', manager=manager,
load_namespaces=False) as io2:
# Institution name ------------------------------------------------
if 'institution' in cp_objs:
nwb_new.institution = str(nwb_old.institution)
# Lab name --------------------------------------------------------
if 'lab' in cp_objs:
nwb_new.lab = str(nwb_old.lab)
# Session id ------------------------------------------------------
if 'session' in cp_objs:
nwb_new.session_id = nwb_old.session_id
# Devices ---------------------------------------------------------
if 'devices' in cp_objs:
for aux in list(nwb_old.devices.keys()):
dev = Device(nwb_old.devices[aux].name)
nwb_new.add_device(dev)
# Electrode groups ------------------------------------------------
if 'electrode_groups' in cp_objs:
for aux in list(nwb_old.electrode_groups.keys()):
nwb_new.create_electrode_group(
name=str(nwb_old.electrode_groups[aux].name),
description=str(nwb_old.electrode_groups[
aux].description),
location=str(nwb_old.electrode_groups[aux].location),
device=nwb_new.get_device(
nwb_old.electrode_groups[aux].device.name)
)
# Electrodes ------------------------------------------------------
if 'electrodes' in cp_objs:
nElec = len(nwb_old.electrodes['x'].data[:])
for aux in np.arange(nElec):
nwb_new.add_electrode(
x=nwb_old.electrodes['x'][aux],
y=nwb_old.electrodes['y'][aux],
z=nwb_old.electrodes['z'][aux],
imp=nwb_old.electrodes['imp'][aux],
location=str(nwb_old.electrodes['location'][aux]),
filtering=str(nwb_old.electrodes['filtering'][aux]),
group=nwb_new.get_electrode_group(
nwb_old.electrodes['group'][aux].name),
group_name=str(nwb_old.electrodes['group_name'][aux])
)
# if there are custom variables
new_vars = list(nwb_old.electrodes.colnames)
default_vars = ['x', 'y', 'z', 'imp', 'location', 'filtering',
'group', 'group_name']
[new_vars.remove(var) for var in default_vars]
for var in new_vars:
if var == 'label':
var_data = [str(elem) for elem in nwb_old.electrodes[
var].data[:]]
else:
var_data = np.array(nwb_old.electrodes[var].data[:])
nwb_new.add_electrode_column(name=str(var),
description=
str(nwb_old.electrodes[
var].description),
data=var_data)
# Epochs ----------------------------------------------------------
if 'epochs' in cp_objs:
nEpochs = len(nwb_old.epochs['start_time'].data[:])
for i in np.arange(nEpochs):
nwb_new.add_epoch(
start_time=nwb_old.epochs['start_time'].data[i],
stop_time=nwb_old.epochs['stop_time'].data[i])
# if there are custom variables
new_vars = list(nwb_old.epochs.colnames)
default_vars = ['start_time', 'stop_time', 'tags',
'timeseries']
[new_vars.remove(var) for var in default_vars if
var in new_vars]
for var in new_vars:
nwb_new.add_epoch_column(name=var,
description=nwb_old.epochs[
var].description,
data=nwb_old.epochs[var].data[:])
# Invalid times ---------------------------------------------------
if 'invalid_times' in cp_objs:
nInvalid = len(nwb_old.invalid_times['start_time'][:])
for aux in np.arange(nInvalid):
nwb_new.add_invalid_time_interval(
start_time=nwb_old.invalid_times['start_time'][aux],
stop_time=nwb_old.invalid_times['stop_time'][aux])
# Trials ----------------------------------------------------------
if 'trials' in cp_objs:
nTrials = len(nwb_old.trials['start_time'])
for aux in np.arange(nTrials):
nwb_new.add_trial(
start_time=nwb_old.trials['start_time'][aux],
stop_time=nwb_old.trials['stop_time'][aux])
# if there are custom variables
new_vars = list(nwb_old.trials.colnames)
default_vars = ['start_time', 'stop_time']
[new_vars.remove(var) for var in default_vars]
for var in new_vars:
nwb_new.add_trial_column(name=var,
description=nwb_old.trials[
var].description,
data=nwb_old.trials[var].data[:])
# Intervals -------------------------------------------------------
if 'intervals' in cp_objs:
all_objs_names = list(nwb_old.intervals.keys())
for obj_name in all_objs_names:
obj_old = nwb_old.intervals[obj_name]
# create and add TimeIntervals
obj = TimeIntervals(name=obj_old.name,
description=obj_old.description)
nInt = len(obj_old['start_time'])
for ind in np.arange(nInt):
obj.add_interval(start_time=obj_old['start_time'][ind],
stop_time=obj_old['stop_time'][ind])
# Add to file
nwb_new.add_time_intervals(obj)
# Stimulus --------------------------------------------------------
if 'stimulus' in cp_objs:
all_objs_names = list(nwb_old.stimulus.keys())
for obj_name in all_objs_names:
obj_old = nwb_old.stimulus[obj_name]
obj = TimeSeries(name=obj_old.name,
description=obj_old.description,
data=obj_old.data[:],
rate=obj_old.rate,
resolution=obj_old.resolution,
conversion=obj_old.conversion,
starting_time=obj_old.starting_time,
unit=obj_old.unit)
nwb_new.add_stimulus(obj)
# Processing modules ----------------------------------------------
if 'ecephys' in cp_objs:
if cp_objs['ecephys'] is True:
interfaces = nwb_old.processing[
'ecephys'].data_interfaces.keys()
else: # list of items
interfaces = [
nwb_old.processing['ecephys'].data_interfaces[key]
for key in cp_objs['ecephys']
]
# Add ecephys module to NWB file
ecephys_module = ProcessingModule(
name='ecephys',
description='Extracellular electrophysiology data.'
)
nwb_new.add_processing_module(ecephys_module)
for interface_old in interfaces:
obj = copy_obj(interface_old, nwb_old, nwb_new)
if obj is not None:
ecephys_module.add_data_interface(obj)
# Acquisition -----------------------------------------------------
if 'acquisition' in cp_objs:
if cp_objs['acquisition'] is True:
all_acq_names = list(nwb_old.acquisition.keys())
else: # list of items
all_acq_names = cp_objs['acquisition']
for acq_name in all_acq_names:
obj_old = nwb_old.acquisition[acq_name]
obj = copy_obj(obj_old, nwb_old, nwb_new)
if obj is not None:
nwb_new.add_acquisition(obj)
# Subject ---------------------------------------------------------
if 'subject' in cp_objs:
try:
cortical_surfaces = CorticalSurfaces()
surfaces = nwb_old.subject.cortical_surfaces.surfaces
for sfc in list(surfaces.keys()):
cortical_surfaces.create_surface(
name=surfaces[sfc].name,
faces=surfaces[sfc].faces,
vertices=surfaces[sfc].vertices)
nwb_new.subject = ECoGSubject(
cortical_surfaces=cortical_surfaces,
subject_id=nwb_old.subject.subject_id,
age=nwb_old.subject.age,
description=nwb_old.subject.description,
genotype=nwb_old.subject.genotype,
sex=nwb_old.subject.sex,
species=nwb_old.subject.species,
weight=nwb_old.subject.weight,
date_of_birth=nwb_old.subject.date_of_birth)
except:
nwb_new.subject = Subject(age=nwb_old.subject.age,
description=nwb_old.subject.description,
genotype=nwb_old.subject.genotype,
sex=nwb_old.subject.sex,
species=nwb_old.subject.species,
subject_id=nwb_old.subject.subject_id,
weight=nwb_old.subject.weight,
date_of_birth=nwb_old.subject.date_of_birth)
# Write new file with copied fields
io2.write(nwb_new, link_data=False)
def test_frorm_dataframe_missing_supplied_col(self):
with self.assertRaises(ValueError):
df = pd.DataFrame({'start_time': [1., 2., 3.], 'stop_time': [2., 3., 4.], 'label': ['a', 'b', 'c']})
TimeIntervals.from_dataframe(df, name='ti_name', columns=[{'name': 'not there'}])
def test_from_dataframe_missing_required_cols(self):
with self.assertRaises(ValueError):
df = pd.DataFrame({'start_time': [1., 2., 3.], 'label': ['a', 'b', 'c']})
TimeIntervals.from_dataframe(df, name='ti_name')
])
nwbfile.add_epoch(6.0, 8.0, ['second', 'example'], [
test_ts,
])
####################
# Other time intervals
# ~~~~~~~~~~~~~~~~~~~~~~
# Both ``epochs`` and ``trials`` are of of data type :py:class:`~pynwb.epoch.TimeIntervals`, which is a type of
# ``DynamicTable`` for storing information about time intervals. ``"epochs"`` and ``"trials"``
# are the two default names for :py:class:`~pynwb.base.TimeIntervals` objects, but you can also add your own
from pynwb.epoch import TimeIntervals
sleep_stages = TimeIntervals(
name="sleep_stages",
description="intervals for each sleep stage as determined by EEG",
)
sleep_stages.add_column(name="stage", description="stage of sleep")
sleep_stages.add_column(name="confidence",
description="confidence in stage (0-1)")
sleep_stages.add_row(start_time=0.3, stop_time=0.5, stage=1, confidence=.5)
sleep_stages.add_row(start_time=0.7, stop_time=0.9, stage=2, confidence=.99)
sleep_stages.add_row(start_time=1.3, stop_time=3.0, stage=3, confidence=0.7)
nwbfile.add_time_intervals(sleep_stages)
####################
# .. _basic_units:
#
def nwb_copy_file(old_file, new_file, cp_objs={}, save_to_file=True):
"""
Copy fields defined in 'obj', from existing NWB file to new NWB file.
Parameters
----------
old_file : str, path, nwbfile
String or path to nwb file '/path/to/old_file.nwb'. Alternatively, the
nwbfile object.
new_file : str, path
String such as '/path/to/new_file.nwb'.
cp_objs : dict
Name:Value pairs (Group:Children) listing the groups and respective
children from the current NWB file to be copied. Children can be:
- Boolean, indicating an attribute (e.g. for institution, lab)
- List of strings, containing several children names
Example:
{'institution':True,
'lab':True,
'acquisition':['microphone'],
'ecephys':['LFP','DecompositionSeries']}
save_to_file: Boolean
If True, saves directly to new_file.nwb. If False, only returns nwb_new.
Returns:
--------
nwb_new : nwbfile object
"""
manager = get_manager()
# Get from nwbfile object in memory or from file
if isinstance(old_file, NWBFile):
nwb_old = old_file
io1 = False
else:
io1 = NWBHDF5IO(str(old_file),
'r',
manager=manager,
load_namespaces=True)
nwb_old = io1.read()
# Creates new file
nwb_new = NWBFile(
session_description=str(nwb_old.session_description),
identifier=id_generator(),
session_start_time=nwb_old.session_start_time,
)
with NWBHDF5IO(new_file, mode='w', manager=manager,
load_namespaces=False) as io2:
# Institution name ------------------------------------------------
if 'institution' in cp_objs:
nwb_new.institution = str(nwb_old.institution)
# Lab name --------------------------------------------------------
if 'lab' in cp_objs:
nwb_new.lab = str(nwb_old.lab)
# Session id ------------------------------------------------------
if 'session' in cp_objs:
nwb_new.session_id = nwb_old.session_id
# Devices ---------------------------------------------------------
if 'devices' in cp_objs:
for aux in list(nwb_old.devices.keys()):
dev = Device(nwb_old.devices[aux].name)
nwb_new.add_device(dev)
# Electrode groups ------------------------------------------------
if 'electrode_groups' in cp_objs and nwb_old.electrode_groups is not None:
for aux in list(nwb_old.electrode_groups.keys()):
nwb_new.create_electrode_group(
name=str(nwb_old.electrode_groups[aux].name),
description=str(nwb_old.electrode_groups[aux].description),
location=str(nwb_old.electrode_groups[aux].location),
device=nwb_new.get_device(
nwb_old.electrode_groups[aux].device.name))
# Electrodes ------------------------------------------------------
if 'electrodes' in cp_objs and nwb_old.electrodes is not None:
nElec = len(nwb_old.electrodes['x'].data[:])
for aux in np.arange(nElec):
nwb_new.add_electrode(
x=nwb_old.electrodes['x'][aux],
y=nwb_old.electrodes['y'][aux],
z=nwb_old.electrodes['z'][aux],
imp=nwb_old.electrodes['imp'][aux],
location=str(nwb_old.electrodes['location'][aux]),
filtering=str(nwb_old.electrodes['filtering'][aux]),
group=nwb_new.get_electrode_group(
nwb_old.electrodes['group'][aux].name),
group_name=str(nwb_old.electrodes['group_name'][aux]))
# if there are custom variables
new_vars = list(nwb_old.electrodes.colnames)
default_vars = [
'x', 'y', 'z', 'imp', 'location', 'filtering', 'group',
'group_name'
]
[new_vars.remove(var) for var in default_vars]
for var in new_vars:
if var == 'label':
var_data = [
str(elem) for elem in nwb_old.electrodes[var].data[:]
]
else:
var_data = np.array(nwb_old.electrodes[var].data[:])
nwb_new.add_electrode_column(
name=str(var),
description=str(nwb_old.electrodes[var].description),
data=var_data)
# If Bipolar scheme for electrodes
for v in nwb_old.lab_meta_data.values():
if isinstance(v, EcephysExt) and hasattr(
v, 'bipolar_scheme_table'):
bst_old = v.bipolar_scheme_table
bst_new = BipolarSchemeTable(
name=bst_old.name, description=bst_old.description)
ecephys_ext = EcephysExt(name=v.name)
ecephys_ext.bipolar_scheme_table = bst_new
nwb_new.add_lab_meta_data(ecephys_ext)
# Epochs ----------------------------------------------------------
if 'epochs' in cp_objs and nwb_old.epochs is not None:
nEpochs = len(nwb_old.epochs['start_time'].data[:])
for i in np.arange(nEpochs):
nwb_new.add_epoch(
start_time=nwb_old.epochs['start_time'].data[i],
stop_time=nwb_old.epochs['stop_time'].data[i])
# if there are custom variables
new_vars = list(nwb_old.epochs.colnames)
default_vars = ['start_time', 'stop_time', 'tags', 'timeseries']
[new_vars.remove(var) for var in default_vars if var in new_vars]
for var in new_vars:
nwb_new.add_epoch_column(
name=var,
description=nwb_old.epochs[var].description,
data=nwb_old.epochs[var].data[:])
# Invalid times ---------------------------------------------------
if 'invalid_times' in cp_objs and nwb_old.invalid_times is not None:
nInvalid = len(nwb_old.invalid_times['start_time'][:])
for aux in np.arange(nInvalid):
nwb_new.add_invalid_time_interval(
start_time=nwb_old.invalid_times['start_time'][aux],
stop_time=nwb_old.invalid_times['stop_time'][aux])
# Trials ----------------------------------------------------------
if 'trials' in cp_objs and nwb_old.trials is not None:
nTrials = len(nwb_old.trials['start_time'])
for aux in np.arange(nTrials):
nwb_new.add_trial(start_time=nwb_old.trials['start_time'][aux],
stop_time=nwb_old.trials['stop_time'][aux])
# if there are custom variables
new_vars = list(nwb_old.trials.colnames)
default_vars = ['start_time', 'stop_time']
[new_vars.remove(var) for var in default_vars]
for var in new_vars:
nwb_new.add_trial_column(
name=var,
description=nwb_old.trials[var].description,
data=nwb_old.trials[var].data[:])
# Intervals -------------------------------------------------------
if 'intervals' in cp_objs and nwb_old.intervals is not None:
all_objs_names = list(nwb_old.intervals.keys())
for obj_name in all_objs_names:
obj_old = nwb_old.intervals[obj_name]
# create and add TimeIntervals
obj = TimeIntervals(name=obj_old.name,
description=obj_old.description)
nInt = len(obj_old['start_time'])
for ind in np.arange(nInt):
obj.add_interval(start_time=obj_old['start_time'][ind],
stop_time=obj_old['stop_time'][ind])
# Add to file
nwb_new.add_time_intervals(obj)
# Stimulus --------------------------------------------------------
if 'stimulus' in cp_objs:
all_objs_names = list(nwb_old.stimulus.keys())
for obj_name in all_objs_names:
obj_old = nwb_old.stimulus[obj_name]
obj = TimeSeries(name=obj_old.name,
description=obj_old.description,
data=obj_old.data[:],
rate=obj_old.rate,
resolution=obj_old.resolution,
conversion=obj_old.conversion,
starting_time=obj_old.starting_time,
unit=obj_old.unit)
nwb_new.add_stimulus(obj)
# Processing modules ----------------------------------------------
if 'ecephys' in cp_objs:
interfaces = [
nwb_old.processing['ecephys'].data_interfaces[key]
for key in cp_objs['ecephys']
]
# Add ecephys module to NWB file
ecephys_module = ProcessingModule(
name='ecephys',
description='Extracellular electrophysiology data.')
nwb_new.add_processing_module(ecephys_module)
for interface_old in interfaces:
obj = copy_obj(interface_old, nwb_old, nwb_new)
if obj is not None:
ecephys_module.add_data_interface(obj)
if 'behavior' in cp_objs:
interfaces = [
nwb_old.processing['behavior'].data_interfaces[key]
for key in cp_objs['behavior']
]
if 'behavior' not in nwb_new.processing:
# Add behavior module to NWB file
behavior_module = ProcessingModule(
name='behavior', description='behavioral data.')
nwb_new.add_processing_module(behavior_module)
for interface_old in interfaces:
obj = copy_obj(interface_old, nwb_old, nwb_new)
if obj is not None:
behavior_module.add_data_interface(obj)
# Acquisition -----------------------------------------------------
# Can get raw ElecetricalSeries and Mic recording
if 'acquisition' in cp_objs:
for acq_name in cp_objs['acquisition']:
obj_old = nwb_old.acquisition[acq_name]
acq = copy_obj(obj_old, nwb_old, nwb_new)
nwb_new.add_acquisition(acq)
# Surveys ---------------------------------------------------------
if 'surveys' in cp_objs and 'behavior' in nwb_old.processing:
surveys_list = [
v for v in
nwb_old.processing['behavior'].data_interfaces.values()
if v.neurodata_type == 'SurveyTable'
]
if cp_objs['surveys'] and len(surveys_list) > 0:
if 'behavior' not in nwb_new.processing:
# Add behavior module to NWB file
behavior_module = ProcessingModule(
name='behavior', description='behavioral data.')
nwb_new.add_processing_module(behavior_module)
for obj_old in surveys_list:
srv = copy_obj(obj_old, nwb_old, nwb_new)
behavior_module.add_data_interface(srv)
# Subject ---------------------------------------------------------
if nwb_old.subject is not None:
if 'subject' in cp_objs:
try:
cortical_surfaces = CorticalSurfaces()
surfaces = nwb_old.subject.cortical_surfaces.surfaces
for sfc in list(surfaces.keys()):
cortical_surfaces.create_surface(
name=surfaces[sfc].name,
faces=surfaces[sfc].faces,
vertices=surfaces[sfc].vertices)
nwb_new.subject = ECoGSubject(
cortical_surfaces=cortical_surfaces,
subject_id=nwb_old.subject.subject_id,
age=nwb_old.subject.age,
description=nwb_old.subject.description,
genotype=nwb_old.subject.genotype,
sex=nwb_old.subject.sex,
species=nwb_old.subject.species,
weight=nwb_old.subject.weight,
date_of_birth=nwb_old.subject.date_of_birth)
except:
nwb_new.subject = Subject(**nwb_old.subject.fields)
# Write new file with copied fields
if save_to_file:
io2.write(nwb_new, link_data=False)
# Close old file and return new nwbfile object
if io1:
io1.close()
return nwb_new
