pynwb.file module¶

class pynwb.file.LabMetaData(name)[source]¶

Bases: NWBContainer

Container for storing lab-specific meta-data

The LabMetaData class serves as a base type for defining lab specific meta-data. To define your own lab-specific metadata, create a Neurodata Extension (NDX) for NWB that defines the data to add. Using the LabMetaData container as a base type makes it easy to add your data to an NWBFile without having to modify the NWBFile type itself, since adding of LabMetaData is already implemented. For more details on how to create an extension see the Extending NWB tutorial.

Parameters:: name (str) – name of lab metadata

namespace = 'core'¶

neurodata_type = 'LabMetaData'¶

class pynwb.file.Subject(age=None, age__reference='birth', description=None, genotype=None, sex=None, species=None, subject_id=None, weight=None, date_of_birth=None, strain=None)[source]¶

Bases: NWBContainer

Subject information and metadata.

Parameters:

age (str or timedelta) – The age of the subject. The ISO 8601 Duration format is recommended, e.g., “P90D” for 90 days old.A timedelta will automatically be converted to The ISO 8601 Duration format.
age__reference (str) – Age is with reference to this event. Can be ‘birth’ or ‘gestational’. If reference is omitted, then ‘birth’ is implied. Value can be None when read from an NWB file with schema version 2.0 to 2.5 where age__reference is missing.
description (str) – A description of the subject, e.g., “mouse A10”.
genotype (str) – The genotype of the subject, e.g., “Sst-IRES-Cre/wt;Ai32(RCL-ChR2(H134R)_EYFP)/wt”.
sex (str) – The sex of the subject. Using “F” (female), “M” (male), “U” (unknown), or “O” (other) is recommended.
species (str) – The species of the subject. The formal latin binomal name is recommended, e.g., “Mus musculus”
subject_id (str) – A unique identifier for the subject, e.g., “A10”
weight (float or str) – The weight of the subject, including units. Using kilograms is recommended. e.g., “0.02 kg”. If a float is provided, then the weight will be stored as “[value] kg”.
date_of_birth (datetime) – The datetime of the date of birth. May be supplied instead of age.
strain (str) – The strain of the subject, e.g., “C57BL/6J”

property age¶: The age of the subject. The ISO 8601 Duration format is recommended, e.g., “P90D” for 90 days old.A timedelta will automatically be converted to The ISO 8601 Duration format.

property age__reference¶: Age is with reference to this event. Can be ‘birth’ or ‘gestational’. If reference is omitted, then ‘birth’ is implied. Value can be None when read from an NWB file with schema version 2.0 to 2.5 where age__reference is missing.

property date_of_birth¶: The datetime of the date of birth. May be supplied instead of age.

property description¶: A description of the subject, e.g., “mouse A10”.

property genotype¶: The genotype of the subject, e.g., “Sst-IRES-Cre/wt;Ai32(RCL-ChR2(H134R)_EYFP)/wt”.

namespace = 'core'¶

neurodata_type = 'Subject'¶

property sex¶: The sex of the subject. Using “F” (female), “M” (male), “U” (unknown), or “O” (other) is recommended.

property species¶: The species of the subject. The formal latin binomal name is recommended, e.g., “Mus musculus”

property strain¶: The strain of the subject, e.g., “C57BL/6J”

property subject_id¶: A unique identifier for the subject, e.g., “A10”

property weight¶: The weight of the subject, including units. Using kilograms is recommended. e.g., “0.02 kg”. If a float is provided, then the weight will be stored as “[value] kg”.

class pynwb.file.NWBFile(session_description, identifier, session_start_time, file_create_date=None, timestamps_reference_time=None, experimenter=None, experiment_description=None, session_id=None, institution=None, keywords=None, notes=None, pharmacology=None, protocol=None, related_publications=None, slices=None, source_script=None, source_script_file_name=None, data_collection=None, surgery=None, virus=None, stimulus_notes=None, lab=None, acquisition=None, analysis=None, stimulus=None, stimulus_template=None, epochs=None, epoch_tags=set(), trials=None, invalid_times=None, intervals=None, units=None, processing=None, lab_meta_data=None, electrodes=None, electrode_groups=None, ic_electrodes=None, sweep_table=None, imaging_planes=None, ogen_sites=None, devices=None, subject=None, scratch=None, icephys_electrodes=None, icephys_filtering=None, intracellular_recordings=None, icephys_simultaneous_recordings=None, icephys_sequential_recordings=None, icephys_repetitions=None, icephys_experimental_conditions=None)[source]¶

Bases: MultiContainerInterface, HERDManager

A representation of an NWB file.

Parameters:

session_description (str) – a description of the session where this data was generated
identifier (str) – a unique text identifier for the file
session_start_time (datetime) – the start date and time of the recording session
file_create_date (ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator or datetime) – the date and time the file was created and subsequent modifications made
timestamps_reference_time (datetime) – date and time corresponding to time zero of all timestamps; defaults to value of session_start_time
experimenter (tuple or list or str) – name of person who performed experiment
experiment_description (str) – general description of the experiment
session_id (str) – lab-specific ID for the session
institution (str) – institution(s) where experiment is performed
keywords (ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator) – Terms to search over
notes (str) – Notes about the experiment.
pharmacology (str) – Description of drugs used, including how and when they were administered. Anesthesia(s), painkiller(s), etc., plus dosage, concentration, etc.
protocol (str) – Experimental protocol, if applicable. E.g., include IACUC protocol
related_publications (tuple or list or str) – Publication information.PMID, DOI, URL, etc. If multiple, concatenate together and describe which is which. such as PMID, DOI, URL, etc
slices (str) – Description of slices, including information about preparation thickness, orientation, temperature and bath solution
source_script (str) – Script file used to create this NWB file.
source_script_file_name (str) – Name of the source_script file
data_collection (str) – Notes about data collection and analysis.
surgery (str) – Narrative description about surgery/surgeries, including date(s) and who performed surgery.
virus (str) – Information about virus(es) used in experiments, including virus ID, source, date made, injection location, volume, etc.
stimulus_notes (str) – Notes about stimuli, such as how and where presented.
lab (str) – lab where experiment was performed
acquisition (list or tuple) – Raw TimeSeries objects belonging to this NWBFile
analysis (list or tuple) – result of analysis
stimulus (list or tuple) – Stimulus TimeSeries objects belonging to this NWBFile
stimulus_template (list or tuple) – Stimulus template TimeSeries objects belonging to this NWBFile
epochs (TimeIntervals) – Epoch objects belonging to this NWBFile
epoch_tags (tuple or list or set) – A sorted list of tags used across all epochs
trials (TimeIntervals) – A table containing trial data
invalid_times (TimeIntervals) – A table containing times to be omitted from analysis
intervals (list or tuple) – any TimeIntervals tables storing time intervals
units (Units) – A table containing unit metadata
processing (list or tuple) – ProcessingModule objects belonging to this NWBFile
lab_meta_data (list or tuple) – an extension that contains lab-specific meta-data
electrodes (DynamicTable) – the ElectrodeTable that belongs to this NWBFile
electrode_groups (Iterable) – the ElectrodeGroups that belong to this NWBFile
ic_electrodes (list or tuple) – DEPRECATED use icephys_electrodes parameter instead. IntracellularElectrodes that belong to this NWBFile
sweep_table (SweepTable) – the SweepTable that belong to this NWBFile
imaging_planes (list or tuple) – ImagingPlanes that belong to this NWBFile
ogen_sites (list or tuple) – OptogeneticStimulusSites that belong to this NWBFile
devices (list or tuple) – Device objects belonging to this NWBFile
subject (Subject) – subject metadata
scratch (list or tuple) – scratch data
icephys_electrodes (list or tuple) – IntracellularElectrodes that belong to this NWBFile.
icephys_filtering (str) – [DEPRECATED] Use IntracellularElectrode.filtering instead. Description of filtering used.
intracellular_recordings (IntracellularRecordingsTable) – the IntracellularRecordingsTable table that belongs to this NWBFile
icephys_simultaneous_recordings (SimultaneousRecordingsTable) – the SimultaneousRecordingsTable table that belongs to this NWBFile
icephys_sequential_recordings (SequentialRecordingsTable) – the SequentialRecordingsTable table that belongs to this NWBFile
icephys_repetitions (RepetitionsTable) – the RepetitionsTable table that belongs to this NWBFile
icephys_experimental_conditions (ExperimentalConditionsTable) – the ExperimentalConditionsTable table that belongs to this NWBFile

all_children()[source]¶

Get a list of all child objects and their child objects recursively.

If the object has an object_id, the object will be added to “ret” to be returned. If that object has children, they will be added to the “stack” in order to be: 1) Checked to see if has an object_id, if so then add to “ret” 2) Have children that will also be checked

property objects¶

property modules¶

property ec_electrode_groups¶

property ec_electrodes¶

property ic_electrodes¶

property icephys_filtering¶

add_ic_electrode(*args, **kwargs)[source]¶: This method is deprecated and will be removed in future versions. Please use add_icephys_electrode instead

create_ic_electrode(*args, **kwargs)[source]¶: This method is deprecated and will be removed in future versions. Please use create_icephys_electrode instead

get_ic_electrode(*args, **kwargs)[source]¶: This method is deprecated and will be removed in future versions. Please use get_icephys_electrode instead

add_epoch_column(name, description, data=[], table=False, index=False, enum=False, term_set=None, col_cls=<class 'hdmf.common.table.VectorData'>)[source]¶

Add a column to the epoch table.: See add_column for more details

Parameters:

name (str) – the name of this VectorData
description (str) – a description for this column
data (ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator or DataIO) – a dataset where the first dimension is a concatenation of multiple vectors
table (bool or DynamicTable) – whether or not this is a table region or the table the region applies to
index (bool or VectorIndex or ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator or int) –
- False (default): do not generate a VectorIndex
- True: generate one empty VectorIndex
- VectorIndex: Use the supplied VectorIndex
- array-like of ints: Create a VectorIndex and use these values as the data
- int: Recursively create n VectorIndex objects for a multi-ragged array
enum (bool or ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator) – whether or not this column contains data from a fixed set of elements
term_set (TermSet) – the set of terms used to validate data on add
col_cls (type) – class to use to represent the column data. If table=True, this field is ignored and a DynamicTableRegion object is used. If enum=True, this field is ignored and a EnumData object is used.

add_epoch_metadata_column(*args, **kwargs)[source]¶: This method is deprecated and will be removed in future versions. Please use add_epoch_column instead

add_epoch(start_time, stop_time, tags=None, timeseries=None)[source]¶

Creates a new Epoch object. Epochs are used to track intervals: in an experiment, such as exposure to a certain type of stimuli (an interval where orientation gratings are shown, or of sparse noise) or a different paradigm (a rat exploring an enclosure versus sleeping between explorations)

Parameters:

start_time (float) – Start time of epoch, in seconds
stop_time (float) – Stop time of epoch, in seconds
tags (str or list or tuple) – user-defined tags used throughout time intervals
timeseries (list or tuple or TimeSeries) – the TimeSeries this epoch applies to

add_electrode_column(name, description, data=[], table=False, index=False, enum=False, term_set=None, col_cls=<class 'hdmf.common.table.VectorData'>)[source]¶

Add a column to the electrode table.: See add_column for more details

Parameters:

name (str) – the name of this VectorData
description (str) – a description for this column
data (ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator or DataIO) – a dataset where the first dimension is a concatenation of multiple vectors
table (bool or DynamicTable) – whether or not this is a table region or the table the region applies to
index (bool or VectorIndex or ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator or int) –
- False (default): do not generate a VectorIndex
- True: generate one empty VectorIndex
- VectorIndex: Use the supplied VectorIndex
- array-like of ints: Create a VectorIndex and use these values as the data
- int: Recursively create n VectorIndex objects for a multi-ragged array
enum (bool or ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator) – whether or not this column contains data from a fixed set of elements
term_set (TermSet) – the set of terms used to validate data on add
col_cls (type) – class to use to represent the column data. If table=True, this field is ignored and a DynamicTableRegion object is used. If enum=True, this field is ignored and a EnumData object is used.

add_electrode(x=None, y=None, z=None, imp=None, location=None, filtering=None, group=None, id=None, rel_x=None, rel_y=None, rel_z=None, reference=None, enforce_unique_id=True)[source]¶

Add an electrode to the electrodes table.

See add_row for more details.

Required fields are location and group and any columns that have been added (through calls to add_electrode_columns).

Parameters:

x (float) – the x coordinate of the position (+x is posterior)
y (float) – the y coordinate of the position (+y is inferior)
z (float) – the z coordinate of the position (+z is right)
imp (float) – the impedance of the electrode, in ohms
location (str) – the location of electrode within the subject e.g. brain region. Required.
filtering (str) – description of hardware filtering, including the filter name and frequency cutoffs
group (ElectrodeGroup) – the ElectrodeGroup object to add to this NWBFile. Required.
id (int) – a unique identifier for the electrode
rel_x (float) – the x coordinate within the electrode group
rel_y (float) – the y coordinate within the electrode group
rel_z (float) – the z coordinate within the electrode group
reference (str) – Description of the reference electrode and/or reference scheme used for this electrode, e.g.,”stainless steel skull screw” or “online common average referencing”.
enforce_unique_id (bool) – enforce that the id in the table must be unique

create_electrode_table_region(region, description, name='electrodes')[source]¶

Parameters:

region (slice or list or tuple) – the indices of the table
description (str) – a brief description of what this electrode is
name (str) – the name of this container

add_unit_column(name, description, data=[], table=False, index=False, enum=False, term_set=None, col_cls=<class 'hdmf.common.table.VectorData'>)[source]¶

Add a column to the unit table.: See add_column for more details

Parameters:

name (str) – the name of this VectorData
description (str) – a description for this column
data (ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator or DataIO) – a dataset where the first dimension is a concatenation of multiple vectors
table (bool or DynamicTable) – whether or not this is a table region or the table the region applies to
index (bool or VectorIndex or ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator or int) –
- False (default): do not generate a VectorIndex
- True: generate one empty VectorIndex
- VectorIndex: Use the supplied VectorIndex
- array-like of ints: Create a VectorIndex and use these values as the data
- int: Recursively create n VectorIndex objects for a multi-ragged array
enum (bool or ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator) – whether or not this column contains data from a fixed set of elements
term_set (TermSet) – the set of terms used to validate data on add
col_cls (type) – class to use to represent the column data. If table=True, this field is ignored and a DynamicTableRegion object is used. If enum=True, this field is ignored and a EnumData object is used.

add_unit(spike_times=None, obs_intervals=None, electrodes=None, electrode_group=None, waveform_mean=None, waveform_sd=None, waveforms=None, id=None)[source]¶

Add a unit to the unit table.: See add_row for more details.

Parameters:

spike_times (ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator) – the spike times for each unit
obs_intervals (ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator) – the observation intervals (valid times) for each unit. All spike_times for a given unit should fall within these intervals. [[start1, end1], [start2, end2], …]
electrodes (ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator) – the electrodes that each unit came from
electrode_group (ElectrodeGroup) – the electrode group that each unit came from
waveform_mean (ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator) – the spike waveform mean for each unit. Shape is (time,) or (time, electrodes)
waveform_sd (ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator) – the spike waveform standard deviation for each unit. Shape is (time,) or (time, electrodes)
waveforms (ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator) – Individual waveforms for each spike. If the dataset is three-dimensional, the third dimension shows the response from different electrodes that all observe this unit simultaneously. In this case, the electrodes column of this Units table should be used to indicate which electrodes are associated with this unit, and the electrodes dimension here should be in the same order as the electrodes referenced in the electrodes column of this table.
id (int) – the id for each unit

add_trial_column(name, description, data=[], table=False, index=False, enum=False, term_set=None, col_cls=<class 'hdmf.common.table.VectorData'>)[source]¶

Add a column to the trial table.: See add_column for more details

Parameters:

name (str) – the name of this VectorData
description (str) – a description for this column
data (ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator or DataIO) – a dataset where the first dimension is a concatenation of multiple vectors
table (bool or DynamicTable) – whether or not this is a table region or the table the region applies to
index (bool or VectorIndex or ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator or int) –
- False (default): do not generate a VectorIndex
- True: generate one empty VectorIndex
- VectorIndex: Use the supplied VectorIndex
- array-like of ints: Create a VectorIndex and use these values as the data
- int: Recursively create n VectorIndex objects for a multi-ragged array
enum (bool or ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator) – whether or not this column contains data from a fixed set of elements
term_set (TermSet) – the set of terms used to validate data on add
col_cls (type) – class to use to represent the column data. If table=True, this field is ignored and a DynamicTableRegion object is used. If enum=True, this field is ignored and a EnumData object is used.

add_trial(start_time, stop_time, tags=None, timeseries=None)[source]¶

Add a trial to the trial table.

See add_interval for more details.

Required fields are start_time, stop_time, and any columns that have been added (through calls to add_trial_columns).

Parameters:

start_time (float) – Start time of epoch, in seconds
stop_time (float) – Stop time of epoch, in seconds
tags (str or list or tuple) – user-defined tags used throughout time intervals
timeseries (list or tuple or TimeSeries) – the TimeSeries this epoch applies to

add_invalid_times_column(name, description, data=[], table=False, index=False, enum=False, term_set=None, col_cls=<class 'hdmf.common.table.VectorData'>)[source]¶

Add a column to the invalid times table.: See add_column for more details

Parameters:

name (str) – the name of this VectorData
description (str) – a description for this column
data (ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator or DataIO) – a dataset where the first dimension is a concatenation of multiple vectors
table (bool or DynamicTable) – whether or not this is a table region or the table the region applies to
index (bool or VectorIndex or ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator or int) –
- False (default): do not generate a VectorIndex
- True: generate one empty VectorIndex
- VectorIndex: Use the supplied VectorIndex
- array-like of ints: Create a VectorIndex and use these values as the data
- int: Recursively create n VectorIndex objects for a multi-ragged array
enum (bool or ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator) – whether or not this column contains data from a fixed set of elements
term_set (TermSet) – the set of terms used to validate data on add
col_cls (type) – class to use to represent the column data. If table=True, this field is ignored and a DynamicTableRegion object is used. If enum=True, this field is ignored and a EnumData object is used.

add_invalid_time_interval(start_time, stop_time, tags=None, timeseries=None)[source]¶

Add a time interval to the invalid times table.

See add_row for more details.

Required fields are start_time, stop_time, and any columns that have been added (through calls to add_invalid_times_columns).

Parameters:

start_time (float) – Start time of epoch, in seconds
stop_time (float) – Stop time of epoch, in seconds
tags (str or list or tuple) – user-defined tags used throughout time intervals
timeseries (list or tuple or TimeSeries) – the TimeSeries this epoch applies to

set_electrode_table(electrode_table)[source]¶

Set the electrode table of this NWBFile to an existing ElectrodeTable

Parameters:: electrode_table (DynamicTable) – the ElectrodeTable for this file

add_acquisition(nwbdata, use_sweep_table=False)[source]¶

Parameters:

nwbdata (NWBDataInterface or DynamicTable) – None
use_sweep_table (bool) – Use the deprecated SweepTable

add_stimulus(timeseries, use_sweep_table=False)[source]¶

Parameters:

timeseries (TimeSeries) – None
use_sweep_table (bool) – Use the deprecated SweepTable

add_stimulus_template(timeseries, use_sweep_table=False)[source]¶

Parameters:

timeseries (TimeSeries or Images) – None
use_sweep_table (bool) – Use the deprecated SweepTable

get_intracellular_recordings()[source]¶

Get the NWBFile.intracellular_recordings table.

In contrast to NWBFile.intracellular_recordings, this function will create the IntracellularRecordingsTable table if not yet done, whereas NWBFile.intracellular_recordings will return None if the table is currently not being used.

Returns:: The NWBFile.intracellular_recordings table
Return type:: IntracellularRecordingsTable

add_intracellular_recording(electrode=None, stimulus_start_index=None, stimulus_index_count=None, stimulus=None, response_start_index=None, response_index_count=None, response=None, electrode_metadata=None, stimulus_metadata=None, response_metadata=None)[source]¶

Add a intracellular recording to the intracellular_recordings table. If the

electrode, stimulus, and/or response do not exist yet in the NWBFile, then they will be added to this NWBFile before adding them to the table.

Note: For more complex organization of intracellular recordings you may also be interested in the related SimultaneousRecordingsTable, SequentialRecordingsTable, RepetitionsTable, and ExperimentalConditionsTable tables and the related functions of NWBFile: add_icephys_simultaneous_recording, add_icephys_sequential_recording, add_icephys_repetition, and add_icephys_experimental_condition.

Parameters:

electrode (IntracellularElectrode) – The intracellular electrode used
stimulus_start_index (int) – Start index of the stimulus
stimulus_index_count (int) – Stop index of the stimulus
stimulus (TimeSeries) – The TimeSeries (usually a PatchClampSeries) with the stimulus
response_start_index (int) – Start index of the response
response_index_count (int) – Stop index of the response
response (TimeSeries) – The TimeSeries (usually a PatchClampSeries) with the response
electrode_metadata (dict) – Additional electrode metadata to be stored in the electrodes table
stimulus_metadata (dict) – Additional stimulus metadata to be stored in the stimuli table
response_metadata (dict) – Additional resposnse metadata to be stored in the responses table

Returns:

Integer index of the row that was added to IntracellularRecordingsTable

Return type:

int

get_icephys_simultaneous_recordings()[source]¶

Get the NWBFile.icephys_simultaneous_recordings table.

In contrast to NWBFile.icephys_simultaneous_recordings, this function will create the SimultaneousRecordingsTable table if not yet done, whereas NWBFile.icephys_simultaneous_recordings will return None if the table is currently not being used.

Returns:: The NWBFile.icephys_simultaneous_recordings table
Return type:: SimultaneousRecordingsTable

add_icephys_simultaneous_recording(recordings)[source]¶

Add a new simultaneous recording to the icephys_simultaneous_recordings table

Parameters:: recordings (ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator) – the indices of the recordings belonging to this simultaneous recording
Returns:: Integer index of the row that was added to SimultaneousRecordingsTable
Return type:: int

get_icephys_sequential_recordings()[source]¶

Get the NWBFile.icephys_sequential_recordings table.

In contrast to NWBFile.icephys_sequential_recordings, this function will create the IntracellularRecordingsTable table if not yet done, whereas NWBFile.icephys_sequential_recordings will return None if the table is currently not being used.

Returns:: The NWBFile.icephys_sequential_recordings table
Return type:: SequentialRecordingsTable

add_icephys_sequential_recording(stimulus_type, simultaneous_recordings)[source]¶

Add a new sequential recording to the icephys_sequential_recordings table

Parameters:

stimulus_type (str) – the type of stimulus used for the sequential recording
simultaneous_recordings (ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator) – the indices of the simultaneous_recordings belonging to this sequential recording

Returns:

Integer index of the row that was added to SequentialRecordingsTable

Return type:

int

get_icephys_repetitions()[source]¶

Get the NWBFile.icephys_repetitions table.

In contrast to NWBFile.icephys_repetitions, this function will create the RepetitionsTable table if not yet done, whereas NWBFile.icephys_repetitions will return None if the table is currently not being used.

Returns:: The NWBFile.icephys_repetitions table
Return type:: RepetitionsTable

add_icephys_repetition(sequential_recordings=None)[source]¶

Add a new repetition to the RepetitionsTable table

Parameters:: sequential_recordings (ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator) – the indices of the sequential recordings belonging to this repetition
Returns:: Integer index of the row that was added to RepetitionsTable
Return type:: int

get_icephys_experimental_conditions()[source]¶

Get the NWBFile.icephys_experimental_conditions table.

In contrast to NWBFile.icephys_experimental_conditions, this function will create the RepetitionsTable table if not yet done, whereas NWBFile.icephys_experimental_conditions will return None if the table is currently not being used.

Returns:: The NWBFile.icephys_experimental_conditions table
Return type:: ExperimentalConditionsTable

add_icephys_experimental_condition(repetitions=None)[source]¶

Add a new condition to the ExperimentalConditionsTable table

Parameters:: repetitions (ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator) – the indices of the repetitions belonging to this condition
Returns:: Integer index of the row that was added to ExperimentalConditionsTable
Return type:: int

get_icephys_meta_parent_table()[source]¶

Get the top-most table in the intracellular ephys metadata table hierarchy that exists in this NWBFile.

The intracellular ephys metadata consists of a hierarchy of DynamicTables, i.e., experimental_conditions –> repetitions –> sequential_recordings –> simultaneous_recordings –> intracellular_recordings etc. In a given NWBFile not all tables may exist. This convenience functions returns the top-most table that exists in this file. E.g., if the file contains only the simultaneous_recordings and intracellular_recordings tables then the function would return the simultaneous_recordings table. Similarly, if the file contains all tables then it will return the experimental_conditions table.

Returns:: DynamicTable object or None

add_scratch(data, name=None, notes=None, table_description='', description=None)[source]¶

Add data to the scratch space

Parameters:

data (str or int or float or bytes or bool or ndarray or list or tuple or DataFrame or DynamicTable or NWBContainer or ScratchData) – The data to add to the scratch space.
name (str) – The name of the data. Required only when passing in a scalar, numpy.ndarray, list, or tuple
notes (str) – Notes to add to the data. Only used when passing in numpy.ndarray, list, or tuple. This argument is not recommended. Use the description argument instead.
table_description (str) – Description for the internal DynamicTable used to store a pandas.DataFrame. This argument is not recommended. Use the description argument instead.
description (str) – Description of the data. Required only when passing in a scalar, numpy.ndarray, list, tuple, or pandas.DataFrame. Ignored when passing in an NWBContainer, DynamicTable, or ScratchData object.

get_scratch(name, convert=True)[source]¶

Get data from the scratch space

Parameters:

name (str) – the name of the object to get
convert (bool) – return the original data, not the NWB object

copy()[source]¶: Shallow copy of an NWB file. Useful for linking across files.

property acquisition¶: a dictionary containing the NWBDataInterface or DynamicTable in this NWBFile

add_analysis(analysis)¶

Add one or multiple NWBContainer or DynamicTable objects to this NWBFile

Parameters:: analysis (list or tuple or dict or NWBContainer or DynamicTable) – one or multiple NWBContainer or DynamicTable objects to add to this NWBFile

add_device(devices)¶

Add one or multiple Device objects to this NWBFile

Parameters:: devices (list or tuple or dict or Device) – one or multiple Device objects to add to this NWBFile

add_electrode_group(electrode_groups)¶

Add one or multiple ElectrodeGroup objects to this NWBFile

Parameters:: electrode_groups (list or tuple or dict or ElectrodeGroup) – one or multiple ElectrodeGroup objects to add to this NWBFile

add_icephys_electrode(icephys_electrodes)¶

Add one or multiple IntracellularElectrode objects to this NWBFile

Parameters:: icephys_electrodes (list or tuple or dict or IntracellularElectrode) – one or multiple IntracellularElectrode objects to add to this NWBFile

add_imaging_plane(imaging_planes)¶

Add one or multiple ImagingPlane objects to this NWBFile

Parameters:: imaging_planes (list or tuple or dict or ImagingPlane) – one or multiple ImagingPlane objects to add to this NWBFile

add_lab_meta_data(lab_meta_data)¶

Add one or multiple LabMetaData objects to this NWBFile

Parameters:: lab_meta_data (list or tuple or dict or LabMetaData) – one or multiple LabMetaData objects to add to this NWBFile

add_ogen_site(ogen_sites)¶

Add one or multiple OptogeneticStimulusSite objects to this NWBFile

Parameters:: ogen_sites (list or tuple or dict or OptogeneticStimulusSite) – one or multiple OptogeneticStimulusSite objects to add to this NWBFile

add_processing_module(processing)¶

Add one or multiple ProcessingModule objects to this NWBFile

Parameters:: processing (list or tuple or dict or ProcessingModule) – one or multiple ProcessingModule objects to add to this NWBFile

add_time_intervals(intervals)¶

Add one or multiple TimeIntervals objects to this NWBFile

Parameters:: intervals (list or tuple or dict or TimeIntervals) – one or multiple TimeIntervals objects to add to this NWBFile

property analysis¶: a dictionary containing the NWBContainer or DynamicTable in this NWBFile

create_device(name, description=None, manufacturer=None)¶

Create a Device object and add it to this NWBFile

Parameters:

name (str) – the name of this device
description (str) – Description of the device (e.g., model, firmware version, processing software version, etc.)
manufacturer (str) – the name of the manufacturer of this device

Returns:

the Device object that was created

Return type:

Device

create_electrode_group(name, description, location, device, position=None)¶

Create an ElectrodeGroup object and add it to this NWBFile

Parameters:

name (str) – the name of this electrode group
description (str) – description of this electrode group
location (str) – description of location of this electrode group
device (Device) – the device that was used to record from this electrode group
position (ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator) – stereotaxic position of this electrode group (x, y, z)

Returns:

the ElectrodeGroup object that was created

Return type:

ElectrodeGroup

create_icephys_electrode(name, device, description, slice=None, seal=None, location=None, resistance=None, filtering=None, initial_access_resistance=None, cell_id=None)¶

Create an IntracellularElectrode object and add it to this NWBFile

Parameters:

name (str) – the name of this electrode
device (Device) – the device that was used to record from this electrode
description (str) – Recording description, description of electrode (e.g., whole-cell, sharp, etc).
slice (str) – Information about slice used for recording.
seal (str) – Information about seal used for recording.
location (str) – Area, layer, comments on estimation, stereotaxis coordinates (if in vivo, etc).
resistance (str) – Electrode resistance, unit: Ohm.
filtering (str) – Electrode specific filtering.
initial_access_resistance (str) – Initial access resistance.
cell_id (str) – Unique ID of cell.

Returns:

the IntracellularElectrode object that was created

Return type:

IntracellularElectrode

create_imaging_plane(name, optical_channel, description, device, excitation_lambda, indicator, location, imaging_rate=None, manifold=None, conversion=1.0, unit='meters', reference_frame=None, origin_coords=None, origin_coords_unit='meters', grid_spacing=None, grid_spacing_unit='meters')¶

Create an ImagingPlane object and add it to this NWBFile

Parameters:

name (str) – the name of this container
optical_channel (list or OpticalChannel) – One of possibly many groups storing channel-specific data.
description (str) – Description of this ImagingPlane.
device (Device) – the device that was used to record
excitation_lambda (float) – Excitation wavelength in nm.
indicator (str) – Calcium indicator
location (str) – Location of image plane.
imaging_rate (float) – Rate images are acquired, in Hz. If the corresponding TimeSeries is present, the rate should be stored there instead.
manifold (ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator) – DEPRECATED: Physical position of each pixel. size=(“height”, “width”, “xyz”). Deprecated in favor of origin_coords and grid_spacing.
conversion (float) – DEPRECATED: Multiplier to get from stored values to specified unit (e.g., 1e-3 for millimeters) Deprecated in favor of origin_coords and grid_spacing.
unit (str) – DEPRECATED: Base unit that coordinates are stored in (e.g., Meters). Deprecated in favor of origin_coords_unit and grid_spacing_unit.
reference_frame (str) – Describes position and reference frame of manifold based on position of first element in manifold.
origin_coords (ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator) – Physical location of the first element of the imaging plane (0, 0) for 2-D data or (0, 0, 0) for 3-D data. See also reference_frame for what the physical location is relative to (e.g., bregma).
origin_coords_unit (str) – Measurement units for origin_coords. The default value is ‘meters’.
grid_spacing (ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator) – Space between pixels in (x, y) or voxels in (x, y, z) directions, in the specified unit. Assumes imaging plane is a regular grid. See also reference_frame to interpret the grid.
grid_spacing_unit (str) – Measurement units for grid_spacing. The default value is ‘meters’.

Returns:

the ImagingPlane object that was created

Return type:

ImagingPlane

create_lab_meta_data(name)¶

Create a LabMetaData object and add it to this NWBFile

Parameters:: name (str) – name of lab metadata
Returns:: the LabMetaData object that was created
Return type:: LabMetaData

create_ogen_site(name, device, description, excitation_lambda, location)¶

Create an OptogeneticStimulusSite object and add it to this NWBFile

Parameters:

name (str) – The name of this stimulus site.
device (Device) – The device that was used.
description (str) – Description of site.
excitation_lambda (float) – Excitation wavelength in nm.
location (str) – Location of stimulation site.

Returns:

the OptogeneticStimulusSite object that was created

Return type:

OptogeneticStimulusSite

create_processing_module(name, description, data_interfaces=None)¶

Create a ProcessingModule object and add it to this NWBFile

Parameters:

name (str) – The name of this processing module
description (str) – Description of this processing module
data_interfaces (list or tuple or dict) – NWBDataInterfaces that belong to this ProcessingModule

Returns:

the ProcessingModule object that was created

Return type:

ProcessingModule

create_time_intervals(name, description='experimental intervals', id=None, columns=None, colnames=None)¶

Create a TimeIntervals object and add it to this NWBFile

Parameters:

name (str) – name of this TimeIntervals
description (str) – Description of this TimeIntervals
id (ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator or DataIO or ElementIdentifiers) – the identifiers for this table
columns (tuple or list) – the columns in this table
colnames (ndarray or list or tuple or Dataset or Array or StrDataset or HDMFDataset or AbstractDataChunkIterator) – the ordered names of the columns in this table. columns must also be provided.

Returns:

the TimeIntervals object that was created

Return type:

TimeIntervals

property data_collection¶: Notes about data collection and analysis.

property devices¶: a dictionary containing the Device in this NWBFile

property electrode_groups¶: a dictionary containing the ElectrodeGroup in this NWBFile

property electrodes¶: the ElectrodeTable that belongs to this NWBFile

property epoch_tags¶: A sorted list of tags used across all epochs

property epochs¶: Epoch objects belonging to this NWBFile

property experiment_description¶: general description of the experiment

property experimenter¶: name of person who performed experiment

property file_create_date¶: the date and time the file was created and subsequent modifications made

get_acquisition(name=None)¶

Get a NWBDataInterface from this NWBFile

Parameters:: name (str) – the name of the NWBDataInterface or DynamicTable
Returns:: the NWBDataInterface or DynamicTable with the given name
Return type:: (<class ‘pynwb.core.NWBDataInterface’>, <class ‘hdmf.common.table.DynamicTable’>)

get_analysis(name=None)¶

Get a NWBContainer from this NWBFile

Parameters:: name (str) – the name of the NWBContainer or DynamicTable
Returns:: the NWBContainer or DynamicTable with the given name
Return type:: (<class ‘pynwb.core.NWBContainer’>, <class ‘hdmf.common.table.DynamicTable’>)

get_device(name=None)¶

Get a Device from this NWBFile

Parameters:: name (str) – the name of the Device
Returns:: the Device with the given name
Return type:: Device

get_electrode_group(name=None)¶

Get an ElectrodeGroup from this NWBFile

Parameters:: name (str) – the name of the ElectrodeGroup
Returns:: the ElectrodeGroup with the given name
Return type:: ElectrodeGroup

get_icephys_electrode(name=None)¶

Get an IntracellularElectrode from this NWBFile

Parameters:: name (str) – the name of the IntracellularElectrode
Returns:: the IntracellularElectrode with the given name
Return type:: IntracellularElectrode

get_imaging_plane(name=None)¶

Get an ImagingPlane from this NWBFile

Parameters:: name (str) – the name of the ImagingPlane
Returns:: the ImagingPlane with the given name
Return type:: ImagingPlane

get_lab_meta_data(name=None)¶

Get a LabMetaData from this NWBFile

Parameters:: name (str) – the name of the LabMetaData
Returns:: the LabMetaData with the given name
Return type:: LabMetaData

get_ogen_site(name=None)¶

Get an OptogeneticStimulusSite from this NWBFile

Parameters:: name (str) – the name of the OptogeneticStimulusSite
Returns:: the OptogeneticStimulusSite with the given name
Return type:: OptogeneticStimulusSite

get_processing_module(name=None)¶

Get a ProcessingModule from this NWBFile

Parameters:: name (str) – the name of the ProcessingModule
Returns:: the ProcessingModule with the given name
Return type:: ProcessingModule

get_stimulus(name=None)¶

Get a TimeSeries from this NWBFile

Parameters:: name (str) – the name of the TimeSeries
Returns:: the TimeSeries with the given name
Return type:: TimeSeries

get_stimulus_template(name=None)¶

Get a TimeSeries from this NWBFile

Parameters:: name (str) – the name of the TimeSeries or Images
Returns:: the TimeSeries or Images with the given name
Return type:: (<class ‘pynwb.base.TimeSeries’>, <class ‘pynwb.base.Images’>)

get_time_intervals(name=None)¶

Get a TimeIntervals from this NWBFile

Parameters:: name (str) – the name of the TimeIntervals
Returns:: the TimeIntervals with the given name
Return type:: TimeIntervals

property icephys_electrodes¶: a dictionary containing the IntracellularElectrode in this NWBFile

property icephys_experimental_conditions¶: A table for grouping different intracellular recording repetitions together that belong to the same experimental experimental_conditions.

property icephys_repetitions¶: A table for grouping different intracellular recording sequential recordings together.With each SweepSequence typically representing a particular type of stimulus, the RepetitionsTable table is typically used to group sets of stimuli applied in sequence.

property icephys_sequential_recordings¶: A table for grouping different simultaneous intracellular recording from the SimultaneousRecordingsTable table together. This is typically used to group together simultaneous recordings where the a sequence of stimuli of the same type with varying parameters have been presented in a sequence.

property icephys_simultaneous_recordings¶: SimultaneousRecordingsTable table for grouping different intracellular recordings fromthe IntracellularRecordingsTable table together that were recorded simultaneously from different electrodes

property identifier¶: a unique text identifier for the file

property imaging_planes¶: a dictionary containing the ImagingPlane in this NWBFile

property institution¶: institution(s) where experiment is performed

property intervals¶: a dictionary containing the TimeIntervals in this NWBFile

property intracellular_recordings¶: IntracellularRecordingsTable table to group together a stimulus and response from a single intracellular electrode and a single simultaneous recording.

property invalid_times¶: A table containing times to be omitted from analysis

property keywords¶: Terms to search over

property lab¶: lab where experiment was performed

property lab_meta_data¶: a dictionary containing the LabMetaData in this NWBFile

namespace = 'core'¶

neurodata_type = 'NWBFile'¶

property notes¶: Notes about the experiment.

property ogen_sites¶: a dictionary containing the OptogeneticStimulusSite in this NWBFile

property pharmacology¶: Description of drugs used, including how and when they were administered. Anesthesia(s), painkiller(s), etc., plus dosage, concentration, etc.

property processing¶: a dictionary containing the ProcessingModule in this NWBFile

property protocol¶: Experimental protocol, if applicable. E.g., include IACUC protocol

property related_publications¶: Publication information.PMID, DOI, URL, etc. If multiple, concatenate together and describe which is which. such as PMID, DOI, URL, etc

property scratch¶: a dictionary containing the DynamicTable, NWBContainer, or ScratchData in this NWBFile

property session_description¶: a description of the session where this data was generated

property session_id¶: lab-specific ID for the session

property session_start_time¶: the start date and time of the recording session

property slices¶: Description of slices, including information about preparation thickness, orientation, temperature and bath solution

property source_script¶: Script file used to create this NWB file.

property source_script_file_name¶: Name of the source_script file

property stimulus¶: a dictionary containing the TimeSeries in this NWBFile

property stimulus_notes¶: Notes about stimuli, such as how and where presented.

property stimulus_template¶: a dictionary containing the TimeSeries or Images in this NWBFile

property subject¶: subject metadata

property surgery¶: Narrative description about surgery/surgeries, including date(s) and who performed surgery.

property sweep_table¶: the SweepTable that belong to this NWBFile

property timestamps_reference_time¶: date and time corresponding to time zero of all timestamps; defaults to value of session_start_time

property trials¶: A table containing trial data

property units¶: A table containing unit metadata

property virus¶: Information about virus(es) used in experiments, including virus ID, source, date made, injection location, volume, etc.

pynwb.file.ElectrodeTable(name='electrodes', description='metadata about extracellular electrodes')[source]¶

pynwb.file.TrialTable(name='trials', description='metadata about experimental trials')[source]¶

pynwb.file.InvalidTimesTable(name='invalid_times', description='time intervals to be removed from analysis')[source]¶