Andrew Tritt ajtritt

Bioinformatician turned data engineer

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

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 / 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 / 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 / iso_time_benchmark.py

Created August 30, 2017 16:24

Benchamark ISO time arithmetic

	from datetime import datetime
	from timeit import timeit

	iso_setup = '''
	from datetime import datetime
	iso_start = "2017-08-30T16:01:18Z"
	iso_end = "2017-08-30T16:01:20Z"
	fmt = "%Y-%m-%dT%H:%M:%SZ"
	'''

ajtritt / io_scenarios.py

Last active September 22, 2017 04:27

Examples of how to use PyNWB in certain I/O scenarios

	import pynwb

	foo_ext_path = 'foo.namespace.yaml' # custom extension
	foo_nwb_path = 'foo.nwb' # file using custom extension
	bar_ext_path = 'bar.namespace.yaml' # another custom extension
	bar_nwb_path = 'bar.nwb' # file using this other custom extension
	baz_nwb_path = 'baz.nwb' # file with no extensions

	############ READ #############

ajtritt / simple_parallelize.py

Created October 6, 2017 19:39

A script to demonstrate how parallelize embarassingly parallel problems using core Python functionality

	import filterframework
	import pynwb
	import multiprocessing # this is a core Python package

	def my_analysis_func(...):
	# user writes this
	...

	nwb_file = pynwb.NWBFile(...)
	query_string = 'a toy query string'

ajtritt / nwb_backward.py

Last active October 12, 2017 21:06

get_builder_dt and get_builder_ns for nwb 1.x


	def get_builder_ns(self, builder):
	return 'core'

	def get_builder_dt(self, builder):
	attrs = builder.attributes
	ndt = attrs.get('neurodata_type')
	if ndt == 'Module':
	return 'ProcessingModule'
	elif ndt == 'TimeSeries':

ajtritt / jongbloets_icephys.py

Created December 7, 2017 19:19

Writing Intracellular Ephys data (for Bart Jongbloets)

	""" import the pynwb packages"""
	from pynwb import NWBFile, TimeSeries, get_manager
	from pynwb.form.backends.hdf5 import HDF5IO
	from pynwb.icephys import CurrentClampSeries
	from pynwb.icephys import VoltageClampSeries
	import datetime
	import numpy as np
	import os

	experimentID = 'BJ5523'#folderPath.split('/')[-1]

ajtritt / mschacter_example.py

Created January 13, 2018 01:20

Some code that exposed a bug

	"""
	This code was breaking at write. See https://github.com/NeurodataWithoutBorders/pynwb/issues/317

	mschachter hacked PyNWB and then had problems reading. See https://github.com/NeurodataWithoutBorders/pynwb/issues/318

	This commit should fix both of these issues: https://github.com/NeurodataWithoutBorders/pynwb/commit/72fafa686748de25571d0abd6aa43cd3ab889bb9
	"""
	import json
	from datetime import datetime
	import numpy as np