ajtritt

import argparse
import os
import socket
import torch
from torch import nn
import torch.nn.functional as F
from torchvision import transforms
from torchvision.datasets import MNIST
from torch.utils.data import DataLoader, random_split
import pytorch_lightning as pl

ajtritt

import argparse
import sys
import h5py
import numpy as np

desc = '''
Concatenate one or more .npy files into a dataset into an HDF5 file
'''
parser = argparse.ArgumentParser(description=desc)
parser.add_argument('output_h5', help='the .h5 file to write converted data to')

ajtritt

BLACK = 0
RED = 1

class Interval(object):

    def __init__(self, start, end):
        self.__start = start
        self.__end = end
        self.__max = end
        self.__left = None

ajtritt

class MyClass(object):

    def __init__(self, p):
        self.__x = p

    @property
    def x(self):
        return self.__x

ajtritt

"""
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

ajtritt

""" 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

    
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

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

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

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"
'''