pynn_brainscales.brainscales2.populations.NixIO

class pynn_brainscales.brainscales2.populations.NixIO(filename, mode='rw')

Bases: neo.io.baseio.BaseIO

Class for reading and writing NIX files.

__init__(filename, mode='rw')

Initialise IO instance and NIX file.

Parameters

filename – Full path to the file

Methods

__init__(filename[, mode])

Initialise IO instance and NIX file.

close()

Closes the open nix file and resets maps.

iter_blocks()

Returns an iterator which can be used to consecutively load and convert all Blocks from the NIX File.

read_all_blocks([lazy])

read_block([index, nixname, neoname, lazy])

Loads a Block from the NIX file along with all contained child objects and returns the equivalent Neo Block.

write_all_blocks(neo_blocks[, use_obj_names])

Convert all neo_blocks to the NIX equivalent and write them to the file.

write_block(block[, use_obj_names])

Convert the provided Neo Block to a NIX Block and write it to the NIX file.

Attributes

extensions

is_readable

is_writable

mode

name

readable_objects

supported_objects

writeable_objects

close()

Closes the open nix file and resets maps.

extensions = ['h5', 'nix']
is_readable = True
is_writable = True
iter_blocks()

Returns an iterator which can be used to consecutively load and convert all Blocks from the NIX File.

mode = 'file'
name = 'NIX'
read_all_blocks(lazy=False)
read_block(index=None, nixname=None, neoname=None, lazy=False)

Loads a Block from the NIX file along with all contained child objects and returns the equivalent Neo Block.

The Block to read can be specified in one of three ways: - Index (position) in the file - Name of the NIX Block (see […] for details on the naming) - Name of the original Neo Block

If no arguments are specified, the first Block is returned and consecutive calls to the function return the next Block in the file. After all Blocks have been loaded this way, the function returns None.

If more than one argument is specified, the precedence order is: index, nixname, neoname

Note that Neo objects can be anonymous or have non-unique names, so specifying a Neo name may be ambiguous.

See also NixIO.iter_blocks().

Parameters

  • index – The position of the Block to be loaded (creation order)

  • nixname – The name of the Block in NIX

  • neoname – The name of the original Neo Block

readable_objects = [<class 'neo.core.block.Block'>]
supported_objects = [<class 'neo.core.block.Block'>, <class 'neo.core.segment.Segment'>, <class 'neo.core.group.Group'>, <class 'neo.core.view.ChannelView'>, <class 'neo.core.analogsignal.AnalogSignal'>, <class 'neo.core.irregularlysampledsignal.IrregularlySampledSignal'>, <class 'neo.core.epoch.Epoch'>, <class 'neo.core.event.Event'>, <class 'neo.core.spiketrain.SpikeTrain'>]
write_all_blocks(neo_blocks, use_obj_names=False)

Convert all neo_blocks to the NIX equivalent and write them to the file.

Parameters

  • neo_blocks – List (or iterable) containing Neo blocks

  • use_obj_names – If True, will not generate unique object names

but will instead try to use the name of each Neo object. If these are not unique, an exception will be raised.

write_block(block, use_obj_names=False)

Convert the provided Neo Block to a NIX Block and write it to the NIX file.

Parameters

  • block – Neo Block to be written

  • use_obj_names – If True, will not generate unique object names

but will instead try to use the name of each Neo object. If these are not unique, an exception will be raised.

writeable_objects = [<class 'neo.core.block.Block'>]