Ryan Ly rly

Neuroscience research software engineer. Technical lead of the NWB data standard and software for neurophysiology.

rly / print_namespaces.ipynb

Last active July 6, 2022 06:51

Notebook demonstrating the loading of NWB namespaces in different contexts

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rly / print_namespaces.py

Created July 1, 2022 16:11

Demonstration of the loading of NWB namespaces in different contexts

	import pynwb
	from pynwb.spec import NWBDatasetSpec, NWBGroupSpec, NWBNamespace

	from hdmf.spec import NamespaceCatalog
	from hdmf.build import TypeMap


	def print_namespace_versions(type_map):
	"""Print the namespace name and version of all namespaces in the given type map."""
	for ns_name in type_map.namespace_catalog.namespaces:

rly / example_iterator.py

Created June 20, 2022 16:36

Demonstration of how to trim and repack (change compression, chunking, etc.) of a very large HDF5 dataset in an NWB file

	from pynwb import NWBHDF5IO
	import pynwb
	from hdmf.data_utils import GenericDataChunkIterator
	from hdmf.backends.hdf5.h5_utils import H5DataIO

	filepath = r"D:\GiocomoData_dandiset53\000053\sub-npI1\sub-npI1_ses-20190413_behavior+ecephys.nwb"


	class H5DatasetDataChunkIterator(GenericDataChunkIterator):
	"""A data chunk iterator that reads chunks over the 0th dimension of an HDF5 dataset up to a max length.

rly / demo_insert_labmemberinfo.ipynb

Last active January 25, 2022 01:21

Demonstration of how to insert a row into the LabMemberInfo table in nwb_datajoint

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rly / export_move_container.py

Last active January 21, 2022 17:23

Demonstration of how to move a container from one location to another after it has been written to disk.

	from pynwb import NWBFile, NWBHDF5IO
	from pynwb.ecephys import LFP, ElectricalSeries
	import numpy as np
	import datetime


	# Create a test file
	nwb = NWBFile(
	session_description='session_description',
	identifier='identifier',

rly / write_unit_marks.py

Last active May 13, 2021 15:05

Script to add marks per electrode per spike time per unit (doubly indexed column) to Units table

	import datetime
	import numpy as np
	from pynwb import NWBFile, NWBHDF5IO, validate


	nwbfile = NWBFile(
	session_description='session_description',
	identifier='identifier',
	session_start_time=datetime.datetime.now(datetime.timezone.utc),
	)

rly / trim_beans.py

Last active May 10, 2021 21:31

Script to trim the Frank Lab beans20190718.nwb file to 2 GB

	import pynwb
	import ndx_franklab_novela

	with pynwb.NWBHDF5IO('beans20190718.nwb', 'r') as io:
	nwbfile = io.read()
	orig_eseries = nwbfile.acquisition['e-series']
	n_timestamps = 4000000 # / 20000 Hz sampling rate = 200 seconds
	data = orig_eseries.data[0:n_timestamps, :]
	ts = orig_eseries.timestamps[0:n_timestamps]
	electrodes = nwbfile.create_electrode_table_region(