def test_spike_times(self):
expected = [
2.937305, 3.16453 , 3.24271 , 4.1622 , 4.24182 ,
10.0898 , 10.132545, 10.176095, 10.2361 , 10.660655,
10.762125, 10.863465, 10.93833 , 11.140815, 11.19246 ,
11.24553 , 11.696305, 11.812655, 11.90469 , 12.056755,
12.15794 , 12.233905, 12.47577 , 12.741295, 12.82861 ,
12.923175, 18.05068 , 18.139875, 18.17693 , 18.221485,
18.24337 , 18.39981 , 18.470705, 18.759675, 18.82183 ,
18.877475, 18.91033 , 18.941195, 19.050515, 19.12557 ,
19.15963 , 19.188655, 19.226205, 19.29813 , 19.420665,
19.47627 , 19.763365, 19.824225, 19.897995, 19.93155 ,
20.04916 , 20.11832 , 20.148755, 20.18004 , 20.22173 ,
20.2433 , 20.40018 , 20.470915, 20.759715, 20.82156 ,
20.866465, 20.90807 , 20.939175]
bp = BiophysicalPerisomaticApi('http://api.brain-map.org')
bp.cache_stimulus = True # change to False to not download the large stimulus NWB file
neuronal_model_id = 472451419 # get this from the web site as above
bp.cache_data(neuronal_model_id, working_directory='neuronal_model')
cwd = os.path.realpath(os.curdir)
print(cwd)
os.chdir(os.path.join(cwd, 'neuronal_model'))
manifest = ju.read('manifest.json')
manifest['biophys'][0]['model_file'][0] = 'manifest_51.json'
manifest['runs'][0]['sweeps'] = [51]
ju.write('manifest_51.json', manifest)
subprocess.call(['nrnivmodl', './modfiles'])
run(Config().load('manifest_51.json'))
#os.chdir(cwd)
nwb_out = NwbDataSet('work/386049444.nwb')
spikes = nwb_out.get_spike_times(51)
numpy.testing.assert_array_almost_equal(spikes, expected)
# open up a list of all of the experiments
all_experiments = mcc.get_experiments(dataframe=True)
from allensdk.api.queries.biophysical_perisomatic_api import \
BiophysicalPerisomaticApi
from allensdk.api.queries.cell_types_api import CellTypesApi
import allensdk.core.swc as swc
import os
from allensdk.core.nwb_data_set import NwbDataSet
from IPython import __main__
bp = BiophysicalPerisomaticApi('http://api.brain-map.org')
ct = CellTypesApi()
cells = ct.list_cells()
#Below is one way, I can create URL, queries and get the result in a local python dictionary.
import allensdk
import mpi4py as MPI
import numpy as np
import csv
import pickle
import sys
#import glob
def __main__():
from allensdk.api.queries.biophysical_perisomatic_api import \
BiophysicalPerisomaticApi
bp = BiophysicalPerisomaticApi('http://api.brain-map.org')
bp.cache_stimulus = True # change to False to not download the large stimulus NWB file
neuronal_model_id = 472451419 # get this from the web site as above
bp.cache_data(neuronal_model_id, working_directory='neuronal_model')
from allensdk.api.queries.biophysical_perisomatic_api import BiophysicalPerisomaticApi
neuronal_model_ids = [472300877, 472363762, 472442377, 473561660, 473863035, 473561729, 472421285, 472301074, \
473872986, 472306616, 329321704, 472912107, 472352327, 471085845, 472912177, 472304676, \
473860269, 472447460, 472427533, 472304539, 473465774, 472430904, 473862845, 472450023, \
473862496, 473863578, 473871773, 329322394, 472299363, 472455509, 472349114, 471081668, \
472451419, 471087975, 472424854, 473863510, 473871592, 472299294, 473835796, 473871429, \
473465456, 472306460, 472440759, 472434498, 472915634, 472306544, 473862421, 471086533, \
473834758]
#neuronal_model_ids = [472451419]
print("---- Downloading %i cell models..." % len(neuronal_model_ids))
for neuronal_model_id in neuronal_model_ids:
print("---- Downloading cell model: %s..." % neuronal_model_id)
try:
bp = BiophysicalPerisomaticApi('http://api.brain-map.org')
bp.cache_stimulus = False # change to False to not download the large stimulus NWB file
bp.cache_data(neuronal_model_id,
working_directory='%i' % neuronal_model_id)
except IndexError:
print("Problem!")