pynwb.core module

pynwb.core.prepend_string(string, prepend=' ')

class pynwb.core.NWBMixin(name)

Bases: hdmf.container.AbstractContainer

Parameters:name (str) – the name of this container

get_ancestor(neurodata_type=None)

Traverse parent hierarchy and return first instance of the specified data_type

Parameters:neurodata_type (str) – the data_type to search for

class pynwb.core.NWBContainer(name)

Bases: pynwb.core.NWBMixin, hdmf.container.Container

Parameters:name (str) – the name of this container

namespace = 'core'

neurodata_type = 'NWBContainer'

class pynwb.core.NWBDataInterface(name)

Bases: pynwb.core.NWBContainer

Parameters:name (str) – the name of this container

namespace = 'core'

neurodata_type = 'NWBDataInterface'

class pynwb.core.NWBData(name, data)

Bases: pynwb.core.NWBMixin, hdmf.container.Data

Parameters:

• name (str) – the name of this container
• data (ndarray or list or tuple or Dataset or HDMFDataset or AbstractDataChunkIterator or DataIO or Data) – the source of the data

data

__getitem__(args)

append(arg)

extend(arg)

namespace = 'core'

neurodata_type = 'NWBData'

class pynwb.core.ScratchData(name, data, notes='')

Bases: pynwb.core.NWBData

Parameters:

• name (str) – the name of this container
• data (ndarray or list or tuple or Dataset or HDMFDataset or AbstractDataChunkIterator or DataIO or Data) – the source of the data
• notes (str) – notes about the data

namespace = 'core'

neurodata_type = 'ScratchData'

class pynwb.core.NWBTable(columns, name, data=[])

Bases: pynwb.core.NWBData

Subclasses should specify the class attribute __columns__.

This should be a list of dictionaries with the following keys:

• name the column name
• type the type of data in this column
• doc a brief description of what gets stored in this column

For reference, this list of dictionaries will be used with docval to autogenerate the add_row method for adding data to this table.

If __columns__ is not specified, no custom add_row method will be added.

The class attribute __defaultname__ can also be set to specify a default name for the table class. If __defaultname__ is not specified, then name will need to be specified when the class is instantiated.

Parameters:

• columns (list or tuple) – a list of the columns in this table
• name (str) – the name of this container
• data (ndarray or list or tuple or Dataset or HDMFDataset or AbstractDataChunkIterator or DataIO) – the source of the data

columns

add_row(values)

Parameters:values (dict) – the values for each column

which(**kwargs)

Query a table

__getitem__(args)

to_dataframe()

Produce a pandas DataFrame containing this table’s data.

classmethod from_dataframe(df, name=None, extra_ok=False)

Construct an instance of NWBTable (or a subclass) from a pandas DataFrame. The columns of the dataframe

should match the columns defined on the NWBTable subclass.

Parameters:

• df (DataFrame) – input data
• name (str) – the name of this container
• extra_ok (bool) – accept (and ignore) unexpected columns on the input dataframe

class pynwb.core.NWBTableRegion(name, table, region)

Bases: pynwb.core.NWBData, hdmf.container.DataRegion

A class for representing regions i.e. slices or indices into an NWBTable

Parameters:

• name (str) – the name of this container
• table (NWBTable) – the ElectrodeTable this region applies to
• region (slice or list or tuple or RegionReference) – the indices of the table

table

The ElectrodeTable this region applies to

region

The indices into table

__getitem__(idx)

class pynwb.core.MultiContainerInterface(name)

Bases: pynwb.core.NWBDataInterface, hdmf.container.MultiContainerInterface

Defined in PyNWB for API backward compatibility. See HDMF MultiContainterInterface for details.

Parameters:name (str) – the name of this container