def test_add_stimulus_presentations(nwbfile, stimulus_presentations_behavior,
stimulus_timestamps, roundtrip,
roundtripper,
stimulus_templates: StimulusTemplate):
nwb.add_stimulus_timestamps(nwbfile, stimulus_timestamps)
nwb.add_stimulus_presentations(nwbfile, stimulus_presentations_behavior)
nwb.add_stimulus_template(nwbfile=nwbfile,
stimulus_template=stimulus_templates)
# Add index for this template to NWB in-memory object:
nwb_template = nwbfile.stimulus_template[stimulus_templates.image_set_name]
compare = (stimulus_presentations_behavior['image_set'] ==
nwb_template.name)
curr_stimulus_index = stimulus_presentations_behavior[compare]
nwb.add_stimulus_index(nwbfile, curr_stimulus_index, nwb_template)
if roundtrip:
obt = roundtripper(nwbfile, BehaviorNwbApi)
else:
obt = BehaviorNwbApi.from_nwbfile(nwbfile)
expected = stimulus_presentations_behavior.copy()
expected['is_change'] = [False, True, True, True, True]
obtained = obt.get_stimulus_presentations()
pd.testing.assert_frame_equal(expected[sorted(expected.columns)],
obtained[sorted(obtained.columns)],
check_dtype=False)
def test_add_stimulus_presentations(nwbfile, stimulus_presentations_behavior, stimulus_timestamps, roundtrip, roundtripper, stimulus_templates):
nwb.add_stimulus_timestamps(nwbfile, stimulus_timestamps)
nwb.add_stimulus_presentations(nwbfile, stimulus_presentations_behavior)
for key, val in stimulus_templates.items():
nwb.add_stimulus_template(nwbfile, val, key)
# Add index for this template to NWB in-memory object:
nwb_template = nwbfile.stimulus_template[key]
curr_stimulus_index = stimulus_presentations_behavior[stimulus_presentations_behavior['image_set'] == nwb_template.name]
nwb.add_stimulus_index(nwbfile, curr_stimulus_index, nwb_template)
if roundtrip:
obt = roundtripper(nwbfile, BehaviorOphysNwbApi)
else:
obt = BehaviorOphysNwbApi.from_nwbfile(nwbfile)
pd.testing.assert_frame_equal(stimulus_presentations_behavior, obt.get_stimulus_presentations(), check_dtype=False)
def save(self, session_object):
nwbfile = NWBFile(
session_description=str(session_object.metadata['session_type']),
identifier=str(session_object.ophys_experiment_id),
session_start_time=session_object.metadata['experiment_datetime'],
file_create_date=pytz.utc.localize(datetime.datetime.now()))
# Add stimulus_timestamps to NWB in-memory object:
nwb.add_stimulus_timestamps(nwbfile,
session_object.stimulus_timestamps)
# Add running data to NWB in-memory object:
unit_dict = {
'v_sig': 'V',
'v_in': 'V',
'speed': 'cm/s',
'timestamps': 's',
'dx': 'cm'
}
nwb.add_running_data_df_to_nwbfile(nwbfile,
session_object.running_data_df,
unit_dict)
# Add stimulus template data to NWB in-memory object:
for name, image_data in session_object.stimulus_templates.items():
nwb.add_stimulus_template(nwbfile, image_data, name)
# Add index for this template to NWB in-memory object:
nwb_template = nwbfile.stimulus_template[name]
stimulus_index = session_object.stimulus_presentations[
session_object.stimulus_presentations['image_set'] ==
nwb_template.name]
nwb.add_stimulus_index(nwbfile, stimulus_index, nwb_template)
# Add stimulus presentations data to NWB in-memory object:
nwb.add_stimulus_presentations(nwbfile,
session_object.stimulus_presentations)
# Add trials data to NWB in-memory object:
nwb.add_trials(nwbfile, session_object.trials,
TRIAL_COLUMN_DESCRIPTION_DICT)
# Add licks data to NWB in-memory object:
if len(session_object.licks) > 0:
nwb.add_licks(nwbfile, session_object.licks)
# Add rewards data to NWB in-memory object:
if len(session_object.rewards) > 0:
nwb.add_rewards(nwbfile, session_object.rewards)
# Add max_projection image data to NWB in-memory object:
nwb.add_max_projection(nwbfile, session_object.max_projection)
# Add average_image image data to NWB in-memory object:
nwb.add_average_image(nwbfile, session_object.average_projection)
# Add segmentation_mask_image image data to NWB in-memory object:
nwb.add_segmentation_mask_image(nwbfile,
session_object.segmentation_mask_image)
# Add metadata to NWB in-memory object:
nwb.add_metadata(nwbfile, session_object.metadata)
# Add task parameters to NWB in-memory object:
nwb.add_task_parameters(nwbfile, session_object.task_parameters)
# Add roi metrics to NWB in-memory object:
nwb.add_cell_specimen_table(nwbfile,
session_object.cell_specimen_table)
# Add dff to NWB in-memory object:
nwb.add_dff_traces(nwbfile, session_object.dff_traces,
session_object.ophys_timestamps)
# Add corrected_fluorescence to NWB in-memory object:
nwb.add_corrected_fluorescence_traces(
nwbfile, session_object.corrected_fluorescence_traces)
# Add motion correction to NWB in-memory object:
nwb.add_motion_correction(nwbfile, session_object.motion_correction)
# Write the file:
with NWBHDF5IO(self.path, 'w') as nwb_file_writer:
nwb_file_writer.write(nwbfile)
return nwbfile
def save(self, session_object):
# Cannot type session_object due to a circular dependency
# TODO fix circular dependency and add type
session_metadata: BehaviorOphysMetadata = \
session_object.api.get_metadata()
session_type = session_metadata.session_type
nwbfile = NWBFile(
session_description=session_type,
identifier=str(session_object.ophys_experiment_id),
session_start_time=session_metadata.date_of_acquisition,
file_create_date=pytz.utc.localize(datetime.datetime.now()),
institution="Allen Institute for Brain Science",
keywords=[
"2-photon", "calcium imaging", "visual cortex", "behavior",
"task"
],
experiment_description=get_expt_description(session_type))
# Add stimulus_timestamps to NWB in-memory object:
nwb.add_stimulus_timestamps(nwbfile,
session_object.stimulus_timestamps)
# Add running acquisition ('dx', 'v_sig', 'v_in') data to NWB
# This data should be saved to NWB but not accessible directly from
# Sessions
nwb.add_running_acquisition_to_nwbfile(
nwbfile, session_object.api.get_running_acquisition_df())
# Add running data to NWB in-memory object:
nwb.add_running_speed_to_nwbfile(nwbfile,
session_object.running_speed,
name="speed",
from_dataframe=True)
nwb.add_running_speed_to_nwbfile(nwbfile,
session_object.raw_running_speed,
name="speed_unfiltered",
from_dataframe=True)
# Add stimulus template data to NWB in-memory object:
# Use the semi-private _stimulus_templates attribute because it is
# a StimulusTemplate object. The public stimulus_templates property
# of the session_object returns a DataFrame.
session_stimulus_templates = session_object._stimulus_templates
self._add_stimulus_templates(
nwbfile=nwbfile,
stimulus_templates=session_stimulus_templates,
stimulus_presentations=session_object.stimulus_presentations)
# search for omitted rows and add stop_time before writing to NWB file
set_omitted_stop_time(
stimulus_table=session_object.stimulus_presentations)
# Add stimulus presentations data to NWB in-memory object:
nwb.add_stimulus_presentations(nwbfile,
session_object.stimulus_presentations)
# Add trials data to NWB in-memory object:
nwb.add_trials(nwbfile, session_object.trials,
TRIAL_COLUMN_DESCRIPTION_DICT)
# Add licks data to NWB in-memory object:
if len(session_object.licks) > 0:
nwb.add_licks(nwbfile, session_object.licks)
# Add rewards data to NWB in-memory object:
if len(session_object.rewards) > 0:
nwb.add_rewards(nwbfile, session_object.rewards)
# Add max_projection image data to NWB in-memory object:
nwb.add_max_projection(nwbfile, session_object.max_projection)
# Add average_image image data to NWB in-memory object:
nwb.add_average_image(nwbfile, session_object.average_projection)
# Add segmentation_mask_image image data to NWB in-memory object:
nwb.add_segmentation_mask_image(nwbfile,
session_object.segmentation_mask_image)
# Add metadata to NWB in-memory object:
nwb.add_metadata(nwbfile, session_object.metadata, behavior_only=False)
# Add task parameters to NWB in-memory object:
nwb.add_task_parameters(nwbfile, session_object.task_parameters)
# Add roi metrics to NWB in-memory object:
nwb.add_cell_specimen_table(nwbfile,
session_object.cell_specimen_table,
session_object.metadata)
# Add dff to NWB in-memory object:
nwb.add_dff_traces(nwbfile, session_object.dff_traces,
session_object.ophys_timestamps)
# Add corrected_fluorescence to NWB in-memory object:
nwb.add_corrected_fluorescence_traces(
nwbfile, session_object.corrected_fluorescence_traces)
# Add motion correction to NWB in-memory object:
nwb.add_motion_correction(nwbfile, session_object.motion_correction)
# Add eye tracking and rig geometry to NWB in-memory object
# if eye_tracking data exists.
if session_object.eye_tracking is not None:
self.add_eye_tracking_data_to_nwb(
nwbfile, session_object.eye_tracking,
session_object.eye_tracking_rig_geometry)
# Add events
self.add_events(nwbfile=nwbfile, events=session_object.events)
# Write the file:
with NWBHDF5IO(self.path, 'w') as nwb_file_writer:
nwb_file_writer.write(nwbfile)
return nwbfile
def save(self, session_object):
session_metadata: BehaviorMetadata = \
session_object.api.get_metadata()
session_type = str(session_metadata.session_type)
nwbfile = NWBFile(
session_description=session_type,
identifier=str(session_object.behavior_session_id),
session_start_time=session_metadata.date_of_acquisition,
file_create_date=pytz.utc.localize(datetime.datetime.now()),
institution="Allen Institute for Brain Science",
keywords=["visual", "behavior", "task"],
experiment_description=get_expt_description(session_type))
# Add stimulus_timestamps to NWB in-memory object:
nwb.add_stimulus_timestamps(nwbfile,
session_object.stimulus_timestamps)
# Add running acquisition ('dx', 'v_sig', 'v_in') data to NWB
# This data should be saved to NWB but not accessible directly from
# Sessions
nwb.add_running_acquisition_to_nwbfile(
nwbfile, session_object.api.get_running_acquisition_df())
# Add running data to NWB in-memory object:
nwb.add_running_speed_to_nwbfile(nwbfile,
session_object.running_speed,
name="speed",
from_dataframe=True)
nwb.add_running_speed_to_nwbfile(nwbfile,
session_object.raw_running_speed,
name="speed_unfiltered",
from_dataframe=True)
# Add stimulus template data to NWB in-memory object:
# Use the semi-private _stimulus_templates attribute because it is
# a StimulusTemplate object. The public stimulus_templates property
# of the session_object returns a DataFrame.
session_stimulus_templates = session_object._stimulus_templates
self._add_stimulus_templates(
nwbfile=nwbfile,
stimulus_templates=session_stimulus_templates,
stimulus_presentations=session_object.stimulus_presentations)
# search for omitted rows and add stop_time before writing to NWB file
set_omitted_stop_time(
stimulus_table=session_object.stimulus_presentations)
# Add stimulus presentations data to NWB in-memory object:
nwb.add_stimulus_presentations(nwbfile,
session_object.stimulus_presentations)
# Add trials data to NWB in-memory object:
nwb.add_trials(nwbfile, session_object.trials,
TRIAL_COLUMN_DESCRIPTION_DICT)
# Add licks data to NWB in-memory object:
if len(session_object.licks) > 0:
nwb.add_licks(nwbfile, session_object.licks)
# Add rewards data to NWB in-memory object:
if len(session_object.rewards) > 0:
nwb.add_rewards(nwbfile, session_object.rewards)
# Add metadata to NWB in-memory object:
nwb.add_metadata(nwbfile, session_object.metadata, behavior_only=True)
# Add task parameters to NWB in-memory object:
nwb.add_task_parameters(nwbfile, session_object.task_parameters)
# Write the file:
with NWBHDF5IO(self.path, 'w') as nwb_file_writer:
nwb_file_writer.write(nwbfile)
return nwbfile
def create_nwb_file(session, nwb_file_path):
logging.info('Staring session {}'.format(session.session_id))
nwbfile = pynwb.NWBFile(
session_description=session.description,
session_id=str(session.session_id),
identifier=str(session.experiment_metadata['experiment_id']),
session_start_time=session.start_time,
# experiment_description=str(session.experiment_metadata['experiment_id'])
)
### Build the stimulus table ###
stim_table_df = session.stimulus_table
nwbfile = add_stimulus_timestamps(nwbfile,
stim_table_df['start_time'].values)
nwbfile = add_stimulus_presentations(nwbfile, stim_table_df)
### Image Segmentation ###
optical_channel = pynwb.ophys.OpticalChannel(
name='optical_channel',
description='description',
emission_lambda=session.emission_wavelength)
# device = pynwb.device.Device(name='Allen Institute two-photon pipeline: {}'.format(session.session_metadata['rig']))
device = pynwb.device.Device(
name='{}'.format(session.session_metadata['rig']))
nwbfile.add_device(device)
imaging_plane = nwbfile.create_imaging_plane(
name=session.imaging_plane_name,
optical_channel=optical_channel,
description=session.imaging_plane_name,
device=device,
excitation_lambda=session.excitation_lambda,
imaging_rate=session.imaging_rate,
indicator=session.calcium_indicator,
location='area: {},depth: {}'.format(
session.experiment_metadata["area"],
str(session.experiment_metadata["depth"])),
unit="Fluorescence (au)",
reference_frame="Intrinsic imaging home",
)
ophys_module = nwbfile.create_processing_module(
session.ophys_module_name,
'contains optical physiology processed data')
max_projection = pynwb.ophys.TwoPhotonSeries(
name='max_project',
data=[session.max_projection],
imaging_plane=imaging_plane,
dimension=[session.image_width, session.image_height],
rate=30.0)
# nwbfile.add_acquisition(max_projection)
ophys_module.add_data_interface(max_projection)
img_seg = pynwb.ophys.ImageSegmentation(
name=session.image_segmentation_name)
ophys_module.add_data_interface(img_seg)
ps = img_seg.create_plane_segmentation(
name=session.plane_segmentation_name,
description=
"Segmentation for imaging plane (de Vries et al., 2019, Nat Neurosci)",
imaging_plane=imaging_plane,
)
for cell_id, roi_mask in session.roi_masks.items():
ps.add_roi(id=cell_id, image_mask=roi_mask)
rt_region = ps.create_roi_table_region(
description="segmented cells with cell_specimen_ids")
### Fluorescence traces ###
fluorescence = pynwb.ophys.Fluorescence()
ophys_module.add_data_interface(fluorescence)
timestamps = session.twop_timestamps
raw_traces = session.raw_traces
assert (raw_traces.shape[1] <= timestamps.shape[0])
fluorescence.create_roi_response_series(
name='raw_traces',
data=raw_traces,
rois=rt_region,
unit='lumens',
timestamps=timestamps[:raw_traces.shape[1]])
neuropil_traces = session.neuropil_traces
assert (neuropil_traces.shape[1] <= timestamps.shape[0])
fluorescence.create_roi_response_series(
name='neuropil_traces',
data=neuropil_traces,
rois=rt_region,
unit='lumens',
timestamps=timestamps[:neuropil_traces.shape[1]])
demixed_traces = session.demixed_traces
assert (demixed_traces.shape[1] <= timestamps.shape[0])
fluorescence.create_roi_response_series(
name='demixed_traces',
data=demixed_traces,
rois=rt_region,
unit='lumens',
timestamps=timestamps[:demixed_traces.shape[1]])
dff_traces = session.dff_traces
assert (dff_traces.shape[1] <= timestamps.shape[0])
fluorescence.create_roi_response_series(
name='DfOverF',
data=session.dff_traces,
rois=rt_region,
unit='lumens',
timestamps=timestamps[:dff_traces.shape[1]])
### Running Speed ###
running_velocity = pynwb.base.TimeSeries(
name="running_speed",
data=session.running_velocity[:len(session.stimulus_timestamps)],
timestamps=session.stimulus_timestamps,
unit="cm/s",
description="Speed of the mouse on a rotating wheel",
)
behavior_module = pynwb.behavior.BehavioralTimeSeries()
behavior_module.add_timeseries(running_velocity)
ophys_module.add_data_interface(behavior_module)
### Motion Correction ###
# NOTE: Older versions of pynwb had a schema bug in ophys.CorrectedImageStack class that prevents it from being
# acccessed. Unfortunately currently allensdk has frozen pynwb at version 1.0.2. To fix we need to add the
# x/y corrections as a time series rather than using CorrectImageStack.
# add_motion_correction_cis(session, ophys_module, nwbfile)
add_motion_correction_pm(session, ophys_module, nwbfile)
### Subject and lab metadata ###
sex_lu = {'F': 'female', 'M': 'male'}
subject_metadata = pynwb.file.Subject(
age=session.session_metadata['age'][1:],
genotype=session.session_metadata['full_genotype'],
sex=sex_lu.get(session.session_metadata['sex'], 'unknown'),
species='Mus musculus',
subject_id=str(session.session_metadata['specimen_id']),
description=session.session_metadata['name'])
nwbfile.subject = subject_metadata
### Events ###
# add_events_discrete(session=session, ophys_module=ophys_module, nwbfile=nwbfile)
add_events_contiguous(session=session,
ophys_module=ophys_module,
nwbfile=nwbfile,
roi_table=rt_region)
# pd.set_option('display.max_columns', None)
# nwbfile.units = pynwb.misc.Units.from_dataframe(session.units, name='units')
# # events_indices = session.event_indices
# nwbfile.units.add_column(
# name='event_times',
# data=session.event_times,
# index=session.event_indices,
# description='times (s) of detected L0 events'
# )
#
# nwbfile.units.add_column(
# name='event_amplitudes',
# data=session.event_amps,
# index=session.event_indices,
# description='amplitudes (s) of detected L0 events'
# )
### Eye Tracking ###
eye_dlc_path = session.eye_dlc_screen_mapping
if eye_dlc_path is not None:
eye_gazing_data = read_eye_gaze_mappings(eye_dlc_path)
add_eye_gaze_mapping_data_to_nwbfile(nwbfile, eye_gazing_data)
with pynwb.NWBHDF5IO(str(nwb_file_path), mode="w") as io:
io.write(nwbfile)
def write_ecephys_nwb(output_path,
session_id,
session_start_time,
stimulus_table_path,
invalid_epochs,
probes,
running_speed_path,
session_sync_path,
eye_tracking_rig_geometry,
eye_dlc_ellipses_path,
eye_gaze_mapping_path,
pool_size,
optotagging_table_path=None,
session_metadata=None,
**kwargs):
nwbfile = pynwb.NWBFile(
session_description='Data and metadata for an Ecephys session',
identifier=f"{session_id}",
session_id=f"{session_id}",
session_start_time=session_start_time,
institution="Allen Institute for Brain Science")
if session_metadata is not None:
nwbfile = add_metadata_to_nwbfile(nwbfile, session_metadata)
stimulus_columns_to_drop = [
"colorSpace", "depth", "interpolate", "pos", "rgbPedestal", "tex",
"texRes", "flipHoriz", "flipVert", "rgb", "signalDots"
]
stimulus_table = read_stimulus_table(
stimulus_table_path, columns_to_drop=stimulus_columns_to_drop)
nwbfile = add_stimulus_timestamps(
nwbfile, stimulus_table['start_time'].values
) # TODO: patch until full timestamps are output by stim table module
nwbfile = add_stimulus_presentations(nwbfile, stimulus_table)
nwbfile = add_invalid_times(nwbfile, invalid_epochs)
if optotagging_table_path is not None:
optotagging_table = pd.read_csv(optotagging_table_path)
nwbfile = add_optotagging_table_to_nwbfile(nwbfile, optotagging_table)
nwbfile = add_probewise_data_to_nwbfile(nwbfile, probes)
running_speed, raw_running_data = read_running_speed(running_speed_path)
add_running_speed_to_nwbfile(nwbfile, running_speed)
add_raw_running_data_to_nwbfile(nwbfile, raw_running_data)
add_eye_tracking_rig_geometry_data_to_nwbfile(nwbfile,
eye_tracking_rig_geometry)
# Collect eye tracking/gaze mapping data from files
eye_tracking_frame_times = su.get_synchronized_frame_times(
session_sync_file=session_sync_path,
sync_line_label_keys=Dataset.EYE_TRACKING_KEYS)
eye_dlc_tracking_data = read_eye_dlc_tracking_ellipses(
Path(eye_dlc_ellipses_path))
if eye_gaze_mapping_path:
eye_gaze_data = read_eye_gaze_mappings(Path(eye_gaze_mapping_path))
else:
eye_gaze_data = None
add_eye_tracking_data_to_nwbfile(nwbfile, eye_tracking_frame_times,
eye_dlc_tracking_data, eye_gaze_data)
Manifest.safe_make_parent_dirs(output_path)
with pynwb.NWBHDF5IO(output_path, mode='w') as io:
logging.info(f"writing session nwb file to {output_path}")
io.write(nwbfile, cache_spec=True)
probes_with_lfp = [p for p in probes if p["lfp"] is not None]
probe_outputs = write_probewise_lfp_files(probes_with_lfp,
session_id,
session_metadata,
session_start_time,
pool_size=pool_size)
return {'nwb_path': output_path, "probe_outputs": probe_outputs}
def write_ecephys_nwb(output_path,
session_id,
session_start_time,
stimulus_table_path,
invalid_epochs,
probes,
running_speed_path,
session_sync_path,
eye_tracking_rig_geometry,
eye_dlc_ellipses_path,
eye_gaze_mapping_path,
pool_size,
optotagging_table_path=None,
session_metadata=None,
**kwargs):
nwbfile = pynwb.NWBFile(session_description='EcephysSession',
identifier='{}'.format(session_id),
session_start_time=session_start_time)
if session_metadata is not None:
nwbfile = add_metadata_to_nwbfile(nwbfile, session_metadata)
stimulus_table = read_stimulus_table(stimulus_table_path)
nwbfile = add_stimulus_timestamps(
nwbfile, stimulus_table['start_time'].values
) # TODO: patch until full timestamps are output by stim table module
nwbfile = add_stimulus_presentations(nwbfile, stimulus_table)
nwbfile = add_invalid_times(nwbfile, invalid_epochs)
if optotagging_table_path is not None:
optotagging_table = pd.read_csv(optotagging_table_path)
nwbfile = add_optotagging_table_to_nwbfile(nwbfile, optotagging_table)
nwbfile = add_probewise_data_to_nwbfile(nwbfile, probes)
running_speed, raw_running_data = read_running_speed(running_speed_path)
add_running_speed_to_nwbfile(nwbfile, running_speed)
add_raw_running_data_to_nwbfile(nwbfile, raw_running_data)
# --- Add eye tracking ellipse fits to nwb file ---
eye_tracking_frame_times = su.get_synchronized_frame_times(
session_sync_file=session_sync_path,
sync_line_label_keys=Dataset.EYE_TRACKING_KEYS)
eye_dlc_tracking_data = read_eye_dlc_tracking_ellipses(
Path(eye_dlc_ellipses_path))
if eye_tracking_data_is_valid(eye_dlc_tracking_data=eye_dlc_tracking_data,
synced_timestamps=eye_tracking_frame_times):
add_eye_tracking_ellipse_fit_data_to_nwbfile(
nwbfile,
eye_dlc_tracking_data=eye_dlc_tracking_data,
synced_timestamps=eye_tracking_frame_times)
# --- Append eye tracking rig geometry info to nwb file (with eye tracking) ---
append_eye_tracking_rig_geometry_data_to_nwbfile(
nwbfile, eye_tracking_rig_geometry=eye_tracking_rig_geometry)
# --- Add gaze mapped positions to nwb file ---
if eye_gaze_mapping_path:
eye_gaze_data = read_eye_gaze_mappings(Path(eye_gaze_mapping_path))
add_eye_gaze_mapping_data_to_nwbfile(nwbfile,
eye_gaze_data=eye_gaze_data)
Manifest.safe_make_parent_dirs(output_path)
io = pynwb.NWBHDF5IO(output_path, mode='w')
logging.info(f"writing session nwb file to {output_path}")
io.write(nwbfile)
io.close()
probes_with_lfp = [p for p in probes if p["lfp"] is not None]
probe_outputs = write_probewise_lfp_files(probes_with_lfp,
session_start_time,
pool_size=pool_size)
return {'nwb_path': output_path, "probe_outputs": probe_outputs}