Andrew Tritt ajtritt

Bioinformatician turned data engineer

ajtritt / example_table_no_group.py

Created August 16, 2017 04:13

An example of how to create and use a table by itself

	import numpy as np
	from pynwb import get_class, load_namespaces
	from datetime import datetime
	from pynwb import NWBFile
	import pandas as pd
	from form.backends.hdf5 import HDF5IO
	from pynwb import get_build_manager

	ns_path = "alleninstitute.namespace.yaml"
	ext_source = "alleninstitute.extensions.yaml"

ajtritt / example_table.py

Created August 16, 2017 04:09

An example of how to use NWBDatasetSpec to create a table

	import numpy as np
	from pynwb import get_class, load_namespaces
	from datetime import datetime
	from pynwb import NWBFile
	import pandas as pd
	from form.backends.hdf5 import HDF5IO
	from pynwb import get_build_manager

	ns_path = "alleninstitute.namespace.yaml"
	ext_source = "alleninstitute.extensions.yaml"

ajtritt / regref_dim_scales.py

Last active August 2, 2017 18:26

Using a slice to label a dimension with HDF5

	import os
	import h5py
	import numpy as np

	# Create compound data type
	# a table with columns channel ID, xyz-coordinates, and impedence
	coord_dt = np.dtype([('x', np.float), ('y', np.float), ('z', np.float)])
	ch_dt = np.dtype([("id", np.int), ("coord", coord_dt), ("imp", np.float)])

	# Make a fake channel table

ajtritt / firing_rate_extension.py

Created July 29, 2017 05:04

fix of example extension and dynamic class

	#fix of https://gist.github.com/nicain/be598d5b7be5f2ffe1fd7e8d27c87ec3
	#
	from pynwb.spec import NWBNamespaceBuilder, NWBGroupSpec, NWBAttributeSpec
	import numpy as np
	from pynwb import get_class, load_namespaces

	mylab = 'alleninstitute'
	ns_path = "%s.namespace.yaml" % mylab
	ext_source = "%s.extensions.yaml" % mylab