README.md

ndx-structured-behavior Extension for NWB

The extension ndx_structured_behavior defines a collection of interlinked table data structures for storing behavioral tasks and data. While the extension has been designed with BEADL in mind, the data structures are general and are intended to be useful even without BEADL. For additional information about BEADL, please visit https://beadl.org/.

The ndx-structured-behavior data model:

Installation

git clone https://github.com/rly/ndx-structured-behavior.git
cd ndx-structured-behavior
pip install -e .

Usage

ndx-structured-behavior/src/pynwb/tests/example.py

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	from ndx_beadl import (Task, BEADLTaskProgram, BEADLTaskSchema, EventTypesTable, EventsTable,
	StateTypesTable, StatesTable, TrialsTable, ActionTypesTable, ActionsTable, TaskArgumentsTable)
	from ndx_beadl.beadl_xml_parser import BeadlXMLParser
	from pynwb import NWBHDF5IO
	from pynwb.file import NWBFile, Subject
	import datetime
	import os
	# Input file paths with the example BEADL data
	base_dir = os.path.dirname(os.path.abspath(__file__))
	beadl_task_schema_file = os.path.join(base_dir, "BEADL.xsd")
	beadl_task_program_file = os.path.join(base_dir, "LightChasingTask.xml")
	beadl_data_file = os.path.join(base_dir, "BeadlDataSample.mat")
	# Output file paths
	nwb_filepath = os.path.join(base_dir, "beadl_light_chasing_task.nwb")
	# Import the BEADL task schema and task program
	with open(beadl_task_schema_file, "r") as test_xsd_file:
	test_xsd = test_xsd_file.read()
	with open(beadl_task_program_file, "r") as test_xml_file:
	test_xml = test_xml_file.read()
	beadl_task_schema = BEADLTaskSchema(
	name='task_schema',
	data=test_xsd,
	version="0.1.0",
	language="XSD"
	)
	beadl_task_program = BEADLTaskProgram(
	name='task_program',
	data=test_xml,
	schema=beadl_task_schema,
	language="XML"
	)
	# Create a new Tasks object and add the BEADL task metadata
	task_arg_table = TaskArgumentsTable(beadl_task_program=beadl_task_program, populate_from_program=True)
	event_types = EventTypesTable(description="description", beadl_task_program=beadl_task_program,
	populate_from_program=True)
	action_types = ActionTypesTable(description="description", beadl_task_program=beadl_task_program,
	populate_from_program=True)
	state_types = StateTypesTable(description="description", beadl_task_program=beadl_task_program,
	populate_from_program=True)
	task = Task(
	task_program=beadl_task_program,
	task_schema=beadl_task_schema,
	event_types=event_types,
	state_types=state_types,
	action_types=action_types,
	task_arguments=task_arg_table
	)
	# Create Events, Actions, and States
	events = EventsTable(description="description", event_types_table=event_types)
	_ = events.populate_from_matlab(data_path=beadl_data_file)
	actions = ActionsTable(description="description", action_types_table=action_types)
	_ = actions.populate_from_matlab(data_path=beadl_data_file)
	states = StatesTable(description="description", state_types_table=state_types)
	_ = states.populate_from_matlab(data_path=beadl_data_file)
	trials = TrialsTable(description="description", states_table=states, events_table=events, actions_table=actions)
	_ = trials.populate_from_matlab(data_path=beadl_data_file)
	# Create NWBFile
	nwbfile = NWBFile(
	session_description="session_description",
	identifier="LightChasingTask",
	session_start_time=datetime.datetime.now(datetime.timezone.utc),
	subject=Subject(subject_id="SP_W2_RH")
	)
	# Add Beadl Data
	nwbfile.add_lab_meta_data(task)
	nwbfile.add_acquisition(states)
	nwbfile.add_acquisition(events)
	nwbfile.add_acquisition(actions)
	nwbfile.trials = trials
	# Write the NWBFile
	with NWBHDF5IO(nwb_filepath, mode="w") as io:
	io.write(nwbfile)
	# Read the NWBFile
	io = NWBHDF5IO(nwb_filepath, mode="r")
	read_nwbfile = io.read()

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This extension was created using ndx-template.