allensdk.brain_observatory.nwb package

Submodules

• allensdk.brain_observatory.nwb.metadata module
• allensdk.brain_observatory.nwb.nwb_api module
• allensdk.brain_observatory.nwb.schemas module

Module contents

allensdk.brain_observatory.nwb.add_average_image(nwbfile, average_image, image_api=None)

allensdk.brain_observatory.nwb.add_cell_specimen_table(nwbfile, cell_specimen_table)

allensdk.brain_observatory.nwb.add_corrected_fluorescence_traces(nwbfile, corrected_fluorescence_traces)

allensdk.brain_observatory.nwb.add_dff_traces(nwbfile, dff_traces, ophys_timestamps)

allensdk.brain_observatory.nwb.add_eye_gaze_data_interfaces(pynwb_container: pynwb.core.NWBContainer, pupil_areas: pandas.core.series.Series, eye_areas: pandas.core.series.Series, screen_coordinates: pandas.core.frame.DataFrame, screen_coordinates_spherical: pandas.core.frame.DataFrame, synced_timestamps: pandas.core.series.Series) → pynwb.core.NWBContainer

allensdk.brain_observatory.nwb.add_eye_gaze_mapping_data_to_nwbfile(nwbfile: pynwb.file.NWBFile, eye_gaze_data: dict) → pynwb.file.NWBFile

allensdk.brain_observatory.nwb.add_eye_tracking_ellipse_fit_data_to_nwbfile(nwbfile: pynwb.file.NWBFile, eye_dlc_tracking_data: dict, synced_timestamps: pandas.core.series.Series) → pynwb.file.NWBFile

allensdk.brain_observatory.nwb.add_image(nwbfile, image_data, image_name, module_name, module_description, image_api=None)

allensdk.brain_observatory.nwb.add_invalid_times(nwbfile, epochs)

Write invalid times to nwbfile if epochs are not empty Parameters ———- nwbfile: pynwb.NWBFile epochs: list of dicts

records of invalid epochs

Returns:

pynwb.NWBFile

allensdk.brain_observatory.nwb.add_licks(nwbfile, licks)

allensdk.brain_observatory.nwb.add_max_projection(nwbfile, max_projection, image_api=None)

allensdk.brain_observatory.nwb.add_metadata(nwbfile, metadata)

allensdk.brain_observatory.nwb.add_motion_correction(nwbfile, motion_correction)

allensdk.brain_observatory.nwb.add_rewards(nwbfile, rewards_df)

allensdk.brain_observatory.nwb.add_running_data_df_to_nwbfile(nwbfile, running_data_df, unit_dict, index_key='timestamps')

Adds running speed data to an NWBFile as timeseries in acquisition and processing

Parameters:

nwbfile : pynwb.NWBFile

File to which runnign speeds will be written

running_speed : pandas.DataFrame

Contains ‘speed’ and ‘times’, ‘v_in’, ‘vsig’, ‘dx’

unit : str, optional

SI units of running speed values

Returns:

nwbfile : pynwb.NWBFile

allensdk.brain_observatory.nwb.add_running_speed_to_nwbfile(nwbfile, running_speed, name='speed', unit='cm/s')

Adds running speed data to an NWBFile as a timeseries in acquisition

Parameters:

nwbfile : pynwb.NWBFile

File to which runnign speeds will be written

running_speed : RunningSpeed

Contains attributes ‘values’ and ‘timestamps’

name : str, optional

used as name of timeseries object

unit : str, optional

SI units of running speed values

Returns:

nwbfile : pynwb.NWBFile

allensdk.brain_observatory.nwb.add_segmentation_mask_image(nwbfile, segmentation_mask_image, image_api=None)

allensdk.brain_observatory.nwb.add_stimulus_index(nwbfile, stimulus_index, nwb_template)

allensdk.brain_observatory.nwb.add_stimulus_presentations(nwbfile, stimulus_table, tag='stimulus_epoch')

Adds a stimulus table (defining stimulus characteristics for each time point in a session) to an nwbfile as epochs.

Parameters:

nwbfile : pynwb.NWBFile

stimulus_table: pd.DataFrame

Each row corresponds to an epoch of time. Columns define the epoch (start and stop time) and its characteristics. Nans will be replaced with the empty string. Required columns are:

start_time :: the time at which this epoch started stop_time :: the time at which this epoch ended

tag : str, optional

Each epoch in an nwb file has one or more tags. This string will be applied as a tag to all epochs created here

Returns:

nwbfile : pynwb.NWBFile

allensdk.brain_observatory.nwb.add_stimulus_template(nwbfile, image_data, name)

allensdk.brain_observatory.nwb.add_stimulus_timestamps(nwbfile, stimulus_timestamps, module_name='stimulus')

allensdk.brain_observatory.nwb.add_task_parameters(nwbfile, task_parameters)

allensdk.brain_observatory.nwb.add_trials(nwbfile, trials, description_dict={})

allensdk.brain_observatory.nwb.create_eye_gaze_mapping_dataframe(eye_gaze_data: dict) → pandas.core.frame.DataFrame

allensdk.brain_observatory.nwb.create_eye_tracking_nwb_processing_module(eye_dlc_tracking_data: dict, synced_timestamps: pandas.core.series.Series) → pynwb.base.ProcessingModule

allensdk.brain_observatory.nwb.create_gaze_mapping_nwb_processing_modules(eye_gaze_data: dict)

allensdk.brain_observatory.nwb.eye_tracking_data_is_valid(eye_dlc_tracking_data: dict, synced_timestamps: pandas.core.series.Series) → bool

allensdk.brain_observatory.nwb.read_eye_dlc_tracking_ellipses(input_path: pathlib.Path) → dict

Reads eye tracking ellipse fit data from an h5 file.

Args:

input_path (Path): Path to eye tracking ellipse fit h5 file

Returns:

dict: Loaded h5 data. Each ‘params’ field contains dataframes with]

ellipse fit parameters. Dataframes contain 5 columns each consisting of: “center_x”, “center_y”, “height”, “phi”, “width”

allensdk.brain_observatory.nwb.read_eye_gaze_mappings(input_path: pathlib.Path) → dict

Reads eye gaze mapping data from an h5 file.

Args:

input_path (Path): Path to eye gaze mapping h5 data file produced by

‘allensdk.brain_observatory.gaze_mapping’ module.

Returns:

dict: Loaded h5 data.

*_eye_areas: Area of eye (in pixels^2) over time *_pupil_areas: Area of pupil (in pixels^2) over time *_screen_coordinates: y, x screen coordinates (in cm) over time *_screen_coordinates_spherical: y, x screen coordinates (in deg) over time synced_frame_timestamps: synced timestamps for video frames (in sec)

allensdk.brain_observatory.nwb.setup_table_for_epochs(table, timeseries, tag)

allensdk.brain_observatory.nwb.setup_table_for_invalid_times(invalid_epochs)

Create table with invalid times if invalid_epochs are present

Parameters:

invalid_epochs: list of dicts

of invalid epoch records

Returns:

pd.DataFrame of invalid times if epochs are not empty, otherwise return None