def __init__(self, allen_id=None):
self = self
if allen_id == None:
self.allen_id = 566302806
glif_api = GlifApi()
self.nc = glif_api.get_neuron_configs([self.allen_id
])[self.allen_id]
self.glif = GlifNeuron.from_dict(self.nc)
self.metad = glif_api.get_neuronal_models_by_id([self.allen_id])[0]
else:
glif_api = GlifApi()
self.allen_id = allen_id
self.glif = glif_api.get_neuronal_models_by_id([allen_id])[0]
self.nc = glif_api.get_neuron_configs([allen_id])[allen_id]
self.glif = GlifNeuron.from_dict(self.nc)
self.metad = glif_api.get_neuronal_models_by_id([self.allen_id])[0]
def sim_Brian2_AllenSDK(neuron_config, data):
stim = data['stimulus']
dt = 1.0 / data['sampling_rate']
stim_unit = data['stimulus_unit']
if stim_unit == 'pA':
stim = stim * 1E12 # convert pA to Amps
# Brian2 simulation
shift_stim = np.pad(stim[1:],(0,1),mode='edge') # shift stimulus left once
param_dict = load_AllenSDK_parameters(neuron_config, dt)
init_values = load_AllenSDK_initial_values(neuron_config)
# With method = 'euler' the error w.r.t. AllenSDK traces is smaller in some cases
# AllenSDK solves exponentials analytically, which results in small discrepancies
output_Brian2 = glif_model.run_brian_sim(shift_stim * b2.amp, dt * b2.second, init_values, param_dict, 'exact')
t, V, I_0, I_1, = output_Brian2
print("info: Brian2 simulation DONE")
# AllenSDK simulation
glif = GlifNeuron.from_dict(neuron_config)
glif.dt = dt
output_AllenSDK = glif.run(stim)
V_0 = output_AllenSDK['voltage']
I_0_0 = output_AllenSDK['AScurrents'][:,0]
I_1_0 = output_AllenSDK['AScurrents'][:,1]
print("info: AllenSDK simulation DONE")
return (t, V, V_0, I_0, I_0_0, I_1, I_1_0, )
def set_attrs(self, **attrs):
self.model.attrs.update(attrs)
#self.nc.update(attrs)
for k, v in attrs.items():
self.nc[k] = v
self.glif = GlifNeuron.from_dict(self.nc)
return self.glif
def get_voltage(self, neuron_config, stim_name):
ephys_sweeps = self.cfg.ephys_sweeps
ephys_sweep = next(s for s in ephys_sweeps
if s['stimulus_name'] == stim_name)
ds = NwbDataSet(self.ephys_file_name)
data = ds.get_sweep(ephys_sweep['sweep_number'])
stimulus = data['stimulus']
stimulus = stimulus[stimulus != 0]
stimulus = stimulus[:self.cfg.stimulus_allow]
# initialize the neuron
neuron = GlifNeuron.from_dict(neuron_config)
# Set dt
neuron.dt = 1.0 / data['sampling_rate']
# simulate the neuron
output = neuron.run(stimulus)
voltage = output['voltage'] * 1e3
voltage = voltage[~np.isnan(voltage)]
voltage = voltage[:self.cfg.signal_allow]
return output, voltage, neuron, stimulus
def set_attrs(self):#, **attrs):
nc = glif_api.get_neuron_configs([neuronal_model_id])[neuronal_model_id]
neuron_config = glif_api.get_neuron_configs([neuronal_model_id])
#nc = glif_api.get_neuron_configs([neuronal_model_id])[neuronal_model_id]
#neuron_config = glif_api.get_neuron_configs([neuronal_model_id])
neuron_config = neuron_config['566302806']
self.nm = GlifNeuron.from_dict(neuron_config)
return self.nm
def init_backend(self,
attrs=None,
cell_name='alice',
current_src_name='hannah',
DTC=None):
backend = 'GLIF'
super(GLIFBackend, self).init_backend()
self.model._backend.use_memory_cache = False
self.current_src_name = current_src_name
self.cell_name = cell_name
self.vM = None
self.allen_id = None
self.attrs = attrs
self.nc = None
self.temp_attrs = None
if self.allen_id == None:
try:
self.nc = pickle.load(open(str('allen_id.p'), 'rb'))
except:
self.allen_id = 566302806
glif_api = GlifApi()
self.nc = glif_api.get_neuron_configs([self.allen_id
])[self.allen_id]
pickle.dump(copy.copy(self.nc), open(str('allen_id.p'), 'wb'))
else:
try:
self.nc = pickle.load(open(str('allen_id.p'), 'rb'))
except:
glif_api = GlifApi()
self.allen_id = allen_id
self.glif = glif_api.get_neuronal_models_by_id([allen_id])[0]
self.nc = glif_api.get_neuron_configs([self.allen_id
])[self.allen_id]
pickle.dump(self.nc, open(str('allen_id.p'), 'wb'))
self.glif = GlifNeuron.from_dict(self.nc)
if type(attrs) is not type(None):
self.set_attrs(**attrs)
self.sim_attrs = attrs
if type(DTC) is not type(None):
if type(DTC.attrs) is not type(None):
self.set_attrs(**DTC.attrs)
if hasattr(DTC, 'current_src_name'):
self._current_src_name = DTC.current_src_name
if hasattr(DTC, 'cell_name'):
self.cell_name = DTC.cell_name
def run_one_cell(glif_dir, curr_pA, dt=5e-7, show_plot=True):
# initialize the neuron
neuron_config = json_utilities.read('%s/neuron_config.json'%glif_dir)
neuron = GlifNeuron.from_dict(neuron_config)
# important! set the neuron's dt value for your stimulus in seconds
neuron.dt = dt
# make a short square pulse. stimulus units should be in Amps.
stimulus = [ 0.0 ] * int(0.1/neuron.dt) + [ curr_pA * 1e-12 ] * int(1/neuron.dt) + [ 0.0 ] * int(0.1/neuron.dt)
times = [ i*neuron.dt for i in range(len(stimulus)) ]
# simulate the neuron
output = neuron.run(stimulus)
print "run.."
voltage = output['voltage']
threshold = output['threshold']
spike_times = output['interpolated_spike_times']
info = "Model %s; %spA stimulation; dt=%ss; %i spikes"%(glif_dir,curr_pA,dt,len(spike_times))
print(info)
v_file = open('%s/original.v.dat'%glif_dir,'w')
th_file = open('%s/original.thresh.dat'%glif_dir,'w')
for i in range(len(times)):
t = times[i]
v = voltage[i]
th = threshold[i]
v_file.write('%s\t%s\n'%(t,v))
th_file.write('%s\t%s\n'%(t,th))
v_file.close()
th_file.close()
pynml.generate_plot([times],
[voltage],
"Membrane potential; %s"%info,
colors = ['k'],
xaxis = "Time (s)",
yaxis = "Voltage (V)",
grid = True,
show_plot_already=False,
save_figure_to='%s/MembranePotential_%ipA.png'%(glif_dir,curr_pA))
pynml.generate_plot([times],
[threshold],
"Threshold; %s"%info,
colors = ['r'],
xaxis = "Time (s)",
yaxis = "Voltage (V)",
grid = True,
show_plot_already=show_plot,
save_figure_to='%s/Threshold_%ipA.png'%(glif_dir,curr_pA))
def test_simulate():
logging.getLogger().setLevel(logging.DEBUG)
neuron_config = json_utilities.read(os.path.join(OUTPUT_DIR, '%d_neuron_config.json' % NEURONAL_MODEL_ID))
ephys_sweeps = json_utilities.read(os.path.join(OUTPUT_DIR, 'ephys_sweeps.json'))
ephys_file_name = os.path.join(OUTPUT_DIR, '%d.nwb' % NEURONAL_MODEL_ID)
neuron = GlifNeuron.from_dict(neuron_config)
sweep_numbers = [ s['sweep_number'] for s in ephys_sweeps ]
simulate_neuron(neuron, sweep_numbers, ephys_file_name, ephys_file_name, 0.05)
def main():
args = parse_arguments()
logging.getLogger().setLevel(args.log_level)
glif_api = None
if (args.neuron_config_file is None or args.sweeps_file is None
or args.ephys_file is None):
assert args.neuronal_model_id is not None, Exception(
"A neuronal model id is required if no neuron config file, sweeps file, or ephys data file is provided."
)
glif_api = GlifApi()
glif_api.get_neuronal_model(args.neuronal_model_id)
if args.neuron_config_file:
neuron_config = json_utilities.read(args.neuron_config_file)
else:
neuron_config = glif_api.get_neuron_config()
if args.sweeps_file:
sweeps = json_utilities.read(args.sweeps_file)
else:
sweeps = glif_api.get_ephys_sweeps()
if args.ephys_file:
ephys_file = args.ephys_file
else:
ephys_file = 'stimulus_%d.nwb' % args.neuronal_model_id
if not os.path.exists(ephys_file):
logging.info("Downloading stimulus to %s." % ephys_file)
glif_api.cache_stimulus_file(ephys_file)
else:
logging.warning("Reusing %s because it already exists." %
ephys_file)
if args.output_ephys_file:
output_ephys_file = args.output_ephys_file
else:
logging.warning(
"Overwriting input file data with simulated data in place.")
output_ephys_file = ephys_file
neuron = GlifNeuron.from_dict(neuron_config)
# filter out test sweeps
sweep_numbers = [
s['sweep_number'] for s in sweeps if s['stimulus_name'] != 'Test'
]
simulate_neuron(neuron, sweep_numbers, ephys_file, output_ephys_file,
args.spike_cut_value)
def test_3():
neuron_config = json_utilities.read('neuron_config.json')
ephys_sweeps = json_utilities.read('ephys_sweeps.json')
ephys_file_name = 'stimulus.nwb'
neuron = GlifNeuron.from_dict(neuron_config)
# sweep_numbers = [ s['sweep_number'] for s in ephys_sweeps
# if s['stimulus_units'] == 'Amps' ]
sweep_numbers = [7]
simulate_neuron(neuron, sweep_numbers,
ephys_file_name, ephys_file_name, 0.05)
def test_3(configured_glif_api, neuron_config_file, ephys_sweeps_file):
neuron_config = json_utilities.read(neuron_config_file)
ephys_sweeps = json_utilities.read(ephys_sweeps_file)
ephys_file_name = 'stimulus.nwb'
neuron = GlifNeuron.from_dict(neuron_config)
# sweep_numbers = [ s['sweep_number'] for s in ephys_sweeps
# if s['stimulus_units'] == 'Amps' ]
sweep_numbers = [7]
simulate_neuron(neuron, sweep_numbers,
ephys_file_name, ephys_file_name, 0.05)
def generate_train_from_model_id(model_id,
stimulus_amplitude=1e-8,
duration=1e6,
noise_exponent=0):
glif_api = GlifApi()
neuron_config = glif_api.get_neuron_configs([model_id])
neuron = GlifNeuron.from_dict(neuron_config[model_id])
stimulus = stimulus_amplitude * colorednoise(exponent=noise_exponent,
size=int(duration))
neuron.dt = 5e-6
output = neuron.run(stimulus)
spike_times = output['interpolated_spike_times']
return spike_times
def main():
args = parse_arguments()
logging.getLogger().setLevel(args.log_level)
glif_api = None
if (args.neuron_config_file is None or
args.sweeps_file is None or
args.ephys_file is None):
assert args.neuronal_model_id is not None, Exception("A neuronal model id is required if no neuron config file, sweeps file, or ephys data file is provided.")
glif_api = GlifApi()
glif_api.get_neuronal_model(args.neuronal_model_id)
if args.neuron_config_file:
neuron_config = json_utilities.read(args.neuron_config_file)
else:
neuron_config = glif_api.get_neuron_config()
if args.sweeps_file:
sweeps = json_utilities.read(args.sweeps_file)
else:
sweeps = glif_api.get_ephys_sweeps()
if args.ephys_file:
ephys_file = args.ephys_file
else:
ephys_file = 'stimulus_%d.nwb' % args.neuronal_model_id
if not os.path.exists(ephys_file):
logging.info("Downloading stimulus to %s." % ephys_file)
glif_api.cache_stimulus_file(ephys_file)
else:
logging.warning("Reusing %s because it already exists." % ephys_file)
if args.output_ephys_file:
output_ephys_file = args.output_ephys_file
else:
logging.warning("Overwriting input file data with simulated data in place.")
output_ephys_file = ephys_file
neuron = GlifNeuron.from_dict(neuron_config)
# filter out test sweeps
sweep_numbers = [ s['sweep_number'] for s in sweeps if s['stimulus_name'] != 'Test' ]
simulate_neuron(neuron, sweep_numbers, ephys_file, output_ephys_file, args.spike_cut_value)
def runGlifNeuron(neuron_config, I, dt_ms):
"""Run a allensdk GlifNeuron and return voltages and spike-times"""
# Get the neuron configuration
neuron = GlifNeuron.from_dict(neuron_config)
neuron.dt = dt_ms * 1.0e-03 # convert from miliseconds to seconds
# Run the simulation
output = neuron.run(I)
# Return run-time, voltage trace and spike times
voltages = output['voltage'] * 1.0e03 # convert to mV
times = [t * dt_ms for t in xrange(len(I))]
spike_times = output[
'interpolated_spike_times'] * 1.0e03 # return interpolated spike-times in miliseconds
#spike_times = output['grid_spike_times'] * 1.0e03 # return grid spike-times in miliseconds
return times, voltages, spike_times
def test_run_glifneuron(configured_glif_api, neuron_config_file):
# initialize the neuron
neuron_config = json_utilities.read(neuron_config_file)
neuron = GlifNeuron.from_dict(neuron_config)
# make a short square pulse. stimulus units should be in Amps.
stimulus = [0.0] * 100 + [10e-9] * 100 + [0.0] * 100
# important! set the neuron's dt value for your stimulus in seconds
neuron.dt = 5e-6
# simulate the neuron
output = neuron.run(stimulus)
voltage = output['voltage']
threshold = output['threshold']
spike_times = output['interpolated_spike_times']
def test_2():
# initialize the neuron
neuron_config = json_utilities.read('neuron_config.json')
neuron = GlifNeuron.from_dict(neuron_config)
# make a short square pulse. stimulus units should be in Amps.
stimulus = [0.0] * 100 + [10e-9] * 100 + [0.0] * 100
# important! set the neuron's dt value for your stimulus in seconds
neuron.dt = 5e-6
# simulate the neuron
output = neuron.run(stimulus)
voltage = output['voltage']
threshold = output['threshold']
spike_times = output['interpolated_spike_times']
def test_6(stimulus):
# define your own custom voltage reset rule
# this one linearly scales the input voltage
def custom_voltage_reset_rule(neuron, voltage_t0, custom_param_a, custom_param_b):
return custom_param_a * voltage_t0 + custom_param_b
# initialize a neuron from a neuron config file
neuron_config = json_utilities.read('neuron_config.json')
neuron = GlifNeuron.from_dict(neuron_config)
# configure a new method and overwrite the neuron's old method
method = neuron.configure_method('custom', custom_voltage_reset_rule,
{'custom_param_a': 0.1, 'custom_param_b': 0.0})
neuron.voltage_reset_method = method
truncate = 56041
output = neuron.run(stimulus[0:truncate])
def test_6(configured_glif_api, neuron_config_file, stimulus):
# define your own custom voltage reset rule
# this one linearly scales the input voltage
def custom_voltage_reset_rule(neuron, voltage_t0, custom_param_a, custom_param_b):
return custom_param_a * voltage_t0 + custom_param_b
# initialize a neuron from a neuron config file
neuron_config = json_utilities.read(neuron_config_file)
neuron = GlifNeuron.from_dict(neuron_config)
# configure a new method and overwrite the neuron's old method
method = neuron.configure_method('custom', custom_voltage_reset_rule,
{'custom_param_a': 0.1, 'custom_param_b': 0.0})
neuron.voltage_reset_method = method
truncate = 56041
output = neuron.run(stimulus[0:truncate])
def output():
neuron_config = json_utilities.read('neuron_config.json')
ephys_sweeps = json_utilities.read('ephys_sweeps.json')
ephys_file_name = 'stimulus.nwb'
# pull out the stimulus for the first sweep
ephys_sweep = ephys_sweeps[0]
ds = NwbDataSet(ephys_file_name)
data = ds.get_sweep(ephys_sweep['sweep_number'])
stimulus = data['stimulus']
# initialize the neuron
# important! update the neuron's dt for your stimulus
neuron = GlifNeuron.from_dict(neuron_config)
neuron.dt = 1.0 / data['sampling_rate']
# simulate the neuron
truncate = 56041
output = neuron.run(stimulus[0:truncate])
return output
def test_run_glifneuron(configured_glif_api, neuron_config_file):
# initialize the neuron
neuron_config = json_utilities.read(neuron_config_file)
neuron = GlifNeuron.from_dict(neuron_config)
# make a short square pulse. stimulus units should be in Amps.
stimulus = [0.0] * 100 + [10e-9] * 100 + [0.0] * 100
# important! set the neuron's dt value for your stimulus in seconds
neuron.dt = 5e-6
# simulate the neuron
output = neuron.run(stimulus)
expected_fields = {"AScurrents", "grid_spike_times",
"interpolated_spike_threshold",
"interpolated_spike_times",
"interpolated_spike_voltage",
"spike_time_steps", "threshold", "voltage"}
assert expected_fields.difference(output.keys()) == set()
def test_run():
# initialize the neuron
neuron_config = json_utilities.read(
os.path.join(OUTPUT_DIR, '%d_neuron_config.json' % NEURONAL_MODEL_ID))
neuron = GlifNeuron.from_dict(neuron_config)
# make a short square pulse. stimulus units should be in Amps.
stimulus = [0.0] * 100 + [10e-9] * 100 + [0.0] * 100
# important! set the neuron's dt value for your stimulus in seconds
neuron.dt = 5e-6
# simulate the neuron
output = neuron.run(stimulus)
voltage = output['voltage']
threshold = output['threshold']
plt.plot(voltage)
plt.plot(threshold)
plt.savefig(os.path.join(OUTPUT_DIR, 'plot.png'))
def output(neuron_config_file, ephys_sweeps_file):
neuron_config = json_utilities.read(neuron_config_file)
ephys_sweeps = json_utilities.read(ephys_sweeps_file)
ephys_file_name = 'stimulus.nwb'
# pull out the stimulus for the first sweep
ephys_sweep = ephys_sweeps[0]
ds = NwbDataSet(ephys_file_name)
data = ds.get_sweep(ephys_sweep['sweep_number'])
stimulus = data['stimulus']
# initialize the neuron
# important! update the neuron's dt for your stimulus
neuron = GlifNeuron.from_dict(neuron_config)
neuron.dt = 1.0 / data['sampling_rate']
# simulate the neuron
truncate = 56041
output = neuron.run(stimulus[0:truncate])
return output
def test_run():
# initialize the neuron
neuron_config = json_utilities.read(os.path.join(
OUTPUT_DIR, '%d_neuron_config.json' % NEURONAL_MODEL_ID))
neuron = GlifNeuron.from_dict(neuron_config)
# make a short square pulse. stimulus units should be in Amps.
stimulus = [0.0] * 100 + [10e-9] * 100 + [0.0] * 100
# important! set the neuron's dt value for your stimulus in seconds
neuron.dt = 5e-6
# simulate the neuron
output = neuron.run(stimulus)
voltage = output['voltage']
threshold = output['threshold']
plt.plot(voltage)
plt.plot(threshold)
plt.savefig(os.path.join(OUTPUT_DIR, 'plot.png'))
def get_model(path, EW):
'''Runs the model for a specified neuron and model
inputs:
path: string
folder path with files for the neuron
EW: string
end of file searching for: options '_GLIF1_neuron_config.json',_GLIF2_neuron_config.json' etc.
returns:
run_data: dictionary
contains data from the model run
'''
specimen_id=int(os.path.basename(path)[:9])
file=get_file_path_endswith(path, EW)
# load data
dir_name=os.path.join(relative_path, 'mouse_nwb/specimen_'+ str(specimen_id))
all_sweeps=ctc.get_ephys_sweeps(specimen_id, os.path.join(dir_name, 'ephys_sweeps.json'))
#all_sweeps=ctc.get_ephys_sweeps(specimen_id)
sweeps=get_sweep_num_by_name(all_sweeps, 'Noise 2')
noise2_sweeps = get_sweep_num_by_name(all_sweeps, 'Noise 2')
# noise2_data=ctc.get_ephys_data(specimen_id).get_sweep(noise2_sweeps[0])
noise2_data=ctc.get_ephys_data(specimen_id, os.path.join(dir_name, 'ephys.nwb')).get_sweep(noise2_sweeps[0])
# run model with current
stimulus2=noise2_data['stimulus']
neuron_config=ju.read(file)
neuron_config['dt']=1./noise2_data['sampling_rate'] #reset dt to the stimulus dt not the optimization dt
neuron = GlifNeuron.from_dict(neuron_config)
1/noise2_data['sampling_rate']
run_data = neuron.run(stimulus2)
run_data['time']=np.arange(0, len(run_data['voltage']))*neuron_config['dt']
run_data['El_reference']=neuron_config['El_reference']
run_data['stimulus']=noise2_data['stimulus']
return run_data
def __init__(self):
self = self
import allensdk.core.json_utilities as json_utilities
from allensdk.model.glif.glif_neuron import GlifNeuron
try:
from allensdk.api.queries.glif_api import GlifApi
from allensdk.core.cell_types_cache import CellTypesCache
import allensdk.core.json_utilities as json_utilities
import sciunit
except:
import os
os.system('pip install allensdk')
from allensdk.api.queries.glif_api import GlifApi
from allensdk.core.cell_types_cache import CellTypesCache
import allensdk.core.json_utilities as json_utilities
os.system('pip install git+https://github.com/scidash/sciunit@dev')
neuronal_model_id = 566302806
glif_api = GlifApi()
nc = glif_api.get_neuron_configs([neuronal_model_id])[neuronal_model_id]
self.nm = GlifNeuron.from_dict(nc)
import allensdk.core.json_utilities as json_utilities
from allensdk.model.glif.glif_neuron import GlifNeuron
# initialize the neuron
neuron_config = json_utilities.read('neuron_config.json')
neuron = GlifNeuron.from_dict(neuron_config)
# make a short square pulse. stimulus units should be in Amps.
stimulus = [ 0.0 ] * 100 + [ 10e-9 ] * 100 + [ 0.0 ] * 100
# important! set the neuron's dt value for your stimulus in seconds
neuron.dt = 5e-6
# simulate the neuron
output = neuron.run(stimulus)
voltage = output['voltage']
threshold = output['threshold']
spike_times = output['interpolated_spike_times']
def cycle(specimen_id_directory, ends_with, model_string, data_dict):
'''Calculates the explained variance ratio for the specified specimen_id_directory and model.
This function is here for the repetitive nature of the code.
inputs:
specimen_id_directory: string
path to structured data directory containing neuron_config, preprocessor, etc., files.
ends_with: string
end of file searching for: options "_GLIF1_neuron_config.json","_GLIF2_neuron_config.json" etc.
model_string: string
string searching for in model name: options '(LIF)', '(LIF-R)', '(LIF-ASC)', '(LIF-R_ASC)', '(LIF-R_ASC_A')
data_dict: dictionary
contains data returned by extract_data
output:
writes explained variance ratios into file ending with 'exp_var_ratio_10ms.json' in specimen_id_directory
'''
# see if specified model configuration file exist in the data folders
try:
file = get_file_path_endswith(specimen_id_directory, ends_with)
except:
return
specimen_id = int(os.path.basename(specimen_id_directory)[:9])
cre = os.path.basename(specimen_id_directory)[10:]
#confirming the dt of noise 1 and noise 2 are the same in the file
if data_dict['n1_dt'] != data_dict['n2_dt']:
raise Exception('The dt in noise 1 and noise 2 is not the same.')
# initializing data structures for explained variance calculations
ev = {}
ev['after_opt'] = {}
ev['before_opt'] = {}
ev['model_spike_times_same_across_sweeps'] = {}
ev['run_model_spike_times_match_database'] = {}
# get the spike indicies of the model from the .nwb file in the database
if specimen_id == 580895033:
if ends_with == '_GLIF1_neuron_config.json':
ev['model_spike_times_same_across_sweeps']['n1'] = 1
ev['model_spike_times_same_across_sweeps']['n2'] = 1
ev['run_model_spike_times_match_database']['n2'] = True
ev["n2_after_opt_sanitycheck"] = 0.9838105341820447
ev["after_opt"]["noise_1"] = 0.9793973377573459
ev["after_opt"]["noise_2"] = 0.983810807305087
ev["before_opt"]["noise_1"] = 0.8454442315760935
ev["before_opt"]["noise_2"] = 0.8493365092125525
if ends_with == '_GLIF2_neuron_config.json':
ev['model_spike_times_same_across_sweeps']['n1'] = 1
ev['model_spike_times_same_across_sweeps']['n2'] = 1
ev['run_model_spike_times_match_database']['n2'] = True
ev["n2_after_opt_sanitycheck"] = 0.9889582213030378
ev["after_opt"]["noise_1"] = 0.9885054832008723
ev["after_opt"]["noise_2"] = 0.988952726396574
ev["before_opt"]["noise_1"] = 0.8852614534451949
ev["before_opt"]["noise_2"] = 0.8882540368687765
if ends_with == '_GLIF3_neuron_config.json':
ev['model_spike_times_same_across_sweeps']['n1'] = 1
ev['model_spike_times_same_across_sweeps']['n2'] = 1
ev['run_model_spike_times_match_database']['n2'] = True
ev["n2_after_opt_sanitycheck"] = 0.972059377795663
ev["after_opt"]["noise_1"] = 0.964542013582842
ev["after_opt"]["noise_2"] = 0.972065677218419
ev["before_opt"]["noise_1"] = 0.9175506860780771
ev["before_opt"]["noise_2"] = 0.9192162154035345
if ends_with == '_GLIF4_neuron_config.json':
ev['model_spike_times_same_across_sweeps']['n1'] = 1
ev['model_spike_times_same_across_sweeps']['n2'] = 1
ev['run_model_spike_times_match_database']['n2'] = True
ev["n2_after_opt_sanitycheck"] = 0.9838078849900366
ev["after_opt"]["noise_1"] = 0.9774371918205483
ev["after_opt"]["noise_2"] = 0.983816449506429
ev["before_opt"]["noise_1"] = 0.9481063969607645
ev["before_opt"]["noise_2"] = 0.952096857211585
if ends_with == '_GLIF5_neuron_config.json':
ev['model_spike_times_same_across_sweeps']['n1'] = 1
ev['model_spike_times_same_across_sweeps']['n2'] = 1
ev['run_model_spike_times_match_database']['n2'] = True
ev["n2_after_opt_sanitycheck"] = 0.9836467816928267
ev["after_opt"]["noise_1"] = 0.9784782997497251
ev["after_opt"]["noise_2"] = 0.983643486774882
ev["before_opt"]["noise_1"] = 0.8846618004335125
ev["before_opt"]["noise_2"] = 0.8904106067655934
json_utilities.write(
os.path.join(
specimen_id_directory,
str(specimen_id) + '_' + cre + ends_with[:7] +
'exp_var_ratio_10ms.json'), ev)
print '\twrote output to ', os.path.join(
specimen_id_directory,
str(specimen_id) + '_' + cre + ends_with[:7] +
'exp_var_ratio_10ms.json')
return
model_n1_nwb_ind = get_model_spike_ind_from_nwb(
ends_with, specimen_id_directory, model_string,
data_dict['noise1_sweeps'], data_dict['n1_dt'], where_running)[0]
# get explained variances
ev['after_opt']['noise_1'] = exVar(data_dict['noise1_spike_ind'],
[model_n1_nwb_ind], [.01],
data_dict['n1_dt'],
len(data_dict['noise1_stim']))[0]
ev['after_opt']['noise_2'] = get_ev_from_folder(
ends_with, specimen_id_directory,
model_string) # get explained varience ratio from glif api
#----------------------------------------------------------------------------------------------
#---------grabbing data along with performing a series of sanity checks for later use-----------
#----------------------------------------------------------------------------------------------
neuron_config = json_utilities.read(file)
neuron_config['dt'] = data_dict['n2_dt']
neuron = GlifNeuron.from_dict(neuron_config) #set up model for running
print '\trunning', specimen_id, 'noise 2 after optimization as a sanity check to compare with what is in database'
model_n2_after = neuron.run(data_dict['noise2_stim']) #running model
print '\tfinished', specimen_id, 'running model on noise 2 after optimization as a sanity check to compare with what is in database'
# before calculating explained variance this is a sanity check to make sure spike times and steps match with the dt within the same file
assert model_n2_after['grid_spike_times'] / data_dict[
'n2_dt'] == model_n2_after['spike_time_steps']
# calculate the explained variance from the the model run
ev_GLIF1_n2_after = exVar(data_dict['noise2_spike_ind'],
[model_n2_after['spike_time_steps']],
[.01], data_dict['n2_dt'],
len(data_dict['noise2_stim']))
ev['n2_after_opt_sanitycheck'] = ev_GLIF1_n2_after[
0] #this is from the rerun done here
# Sanity check to make sure model spike times from the database are all the same..
# Note that all of these should have been eliminated via the "check_sweeps_and_rm_folders.py" script
glif_spike_times_n1 = get_model_spike_times_from_nwb(
ends_with, specimen_id_directory, model_string,
data_dict['noise1_sweeps'], where_running)
ev['model_spike_times_same_across_sweeps'][
'n1'] = check_spike_times_identical(glif_spike_times_n1)
glif_spike_times_n2 = get_model_spike_times_from_nwb(
ends_with, specimen_id_directory, model_string,
data_dict['noise2_sweeps'], where_running)
ev['model_spike_times_same_across_sweeps'][
'n2'] = check_spike_times_identical(glif_spike_times_n2)
# sanity check to make sure calculated model spike times run here match what is in the Allen Institute Cell Types Database.
# just checking against first sweep since they sweeps should all be identical
ev['run_model_spike_times_match_database']['n2'] = np.allclose(
model_n2_after['grid_spike_times'],
glif_spike_times_n2[0],
atol=.0001,
rtol=0,
equal_nan=True)
#--------------------------------------------------------
#--------------------------------------------------------
#--------------------------------------------------------
# running and calculating exp var for data before optimization
neuron_config['dt'] = data_dict['n1_dt']
neuron_config['coeffs']['th_inf'] = 1.0
neuron = GlifNeuron.from_dict(neuron_config)
print '\trunning noise 1', specimen_id, 'before optimization'
model_n1_before = neuron.run(data_dict['noise1_stim'])
ev_GLIF1_n1_before = exVar(data_dict['noise1_spike_ind'],
[model_n1_before['spike_time_steps']],
[.01], data_dict['n1_dt'],
len(data_dict['noise1_stim']))
print '\tfinished noise 1', specimen_id, 'before optimization'
print '\trunning noise 2', specimen_id, 'before optimization'
model_n2_before = neuron.run(data_dict['noise2_stim'])
ev_GLIF1_n2_before = exVar(data_dict['noise2_spike_ind'],
[model_n2_before['spike_time_steps']],
[.01], data_dict['n2_dt'],
len(data_dict['noise2_stim']))
print '\tfinished noise 2', specimen_id, 'before optimization'
ev['before_opt']['noise_1'] = ev_GLIF1_n1_before[0]
ev['before_opt']['noise_2'] = ev_GLIF1_n2_before[0]
# save the file to the local structured data directory
json_utilities.write(
os.path.join(
specimen_id_directory,
str(specimen_id) + '_' + cre + ends_with[:7] +
'exp_var_ratio_10ms.json'), ev)
print '\twrote output to ', os.path.join(
specimen_id_directory,
str(specimen_id) + '_' + cre + ends_with[:7] +
'exp_var_ratio_10ms.json')
def set_attrs(self, **attrs):
self.model.attrs.update(attrs)
self.glif = GlifNeuron.from_dict(attrs)
return self.glif
import allensdk.core.json_utilities as json_utilities
from allensdk.model.glif.glif_neuron import GlifNeuron
from allensdk.model.glif.simulate_neuron import simulate_neuron
neuron_config = json_utilities.read('neuron_config.json')
ephys_sweeps = json_utilities.read('ephys_sweeps.json')
ephys_file_name = 'stimulus.nwb'
neuron = GlifNeuron.from_dict(neuron_config)
sweep_numbers = [ s['sweep_number'] for s in ephys_sweeps
if s['stimulus_units'] == 'Amps' ]
simulate_neuron(neuron, sweep_numbers, ephys_file_name, ephys_file_name, 0.05)
class glifBackend(Backend):
backend = 'glif'
try:
from allensdk.api.queries.glif_api import GlifApi
from allensdk.core.cell_types_cache import CellTypesCache
import allensdk.core.json_utilities as json_utilities
except:
import os
os.system('pip install allensdk')
from allensdk.api.queries.glif_api import GlifApi
from allensdk.core.cell_types_cache import CellTypesCache
import allensdk.core.json_utilities as json_utilities
neuronal_model_id = 566302806
# download model metadata
glif_api = GlifApi()
nm = glif_api.get_neuronal_models_by_id([neuronal_model_id])[0]
# download the model configuration file
nc = glif_api.get_neuron_configs([neuronal_model_id])[neuronal_model_id]
neuron_config = glif_api.get_neuron_configs([neuronal_model_id])
json_utilities.write('neuron_config.json', neuron_config)
# download information about the cell
ctc = CellTypesCache()
ctc.get_ephys_data(nm['specimen_id'], file_name='stimulus.nwb')
ctc.get_ephys_sweeps(nm['specimen_id'], file_name='ephys_sweeps.json')
import allensdk.core.json_utilities as json_utilities
from allensdk.model.glif.glif_neuron import GlifNeuron
# initialize the neuron
neuron_config = json_utilities.read('neuron_config.json')
neuron_config = neuron_config['566302806']
neuron = GlifNeuron.from_dict(neuron_config)
def init_backend(self, attrs=None, simulator='neuron', DTC=None):
from pyNN import neuron
self.neuron = neuron
from pyNN.neuron import simulator as sim
from pyNN.neuron import setup as setup
from pyNN.neuron import Izhikevich
from pyNN.neuron import Population
from pyNN.neuron import DCSource
self.Izhikevich = Izhikevich
self.Population = Population
self.DCSource = DCSource
self.setup = setup
self.model_path = None
self.related_data = {}
self.lookup = {}
self.attrs = {}
super(pyNNBackend, self).init_backend() #*args, **kwargs)
if DTC is not None:
self.set_attrs(**DTC.attrs)
backend = 'pyNN'
def get_membrane_potential(self):
"""Must return a neo.core.AnalogSignal.
And must destroy the hoc vectors that comprise it.
"""
dt = float(copy.copy(self.neuron.dt))
data = self.population.get_data().segments[0]
return data.filter(name="v")[0]
def _local_run(self):
'''
pyNN lazy array demands a minimum population size of 3. Why is that.
'''
import numpy as np
results = {}
#self.population.record('v')
#self.population.record('spikes')
# For ome reason you need to record from all three neurons in a population
# In order to get the membrane potential from only the stimulated neuron.
self.population[0:2].record(('v', 'spikes', 'u'))
'''
self.Iz.record('v')
self.Iz.record('spikes')
# For ome reason you need to record from all three neurons in a population
# In order to get the membrane potential from only the stimulated neuron.
self.Iz.record(('v', 'spikes','u'))
'''
#self.neuron.run(650.0)
DURATION = 1000.0
self.neuron.run(DURATION)
data = self.population.get_data().segments[0]
vm = data.filter(name="v")[0] #/10.0
results['vm'] = vm
#print(vm)
sample_freq = DURATION / len(vm)
results['t'] = np.arange(0, len(vm), DURATION / len(vm))
results['run_number'] = results.get('run_number', 0) + 1
return results
def load_model(self):
self.Iz = None
self.population = None
self.setup(timestep=0.01, min_delay=1.0)
import pyNN
#i_offset=[0.014, 0.0, 0.0]
pop = self.neuron.Population(
3,
pyNN.neuron.Izhikevich(a=0.02,
b=0.2,
c=-65,
d=6,
i_offset=[0.014, -65.0, 0.0])) #,v=-65))
self.population = pop
def set_attrs(self, **attrs):
#attrs = copy.copy(self.model.attrs)
self.init_backend()
#self.set_attrs(**attrs)
self.model.attrs.update(attrs)
assert type(self.model.attrs) is not type(None)
attrs['i_offset'] = None
attrs_ = {x: attrs[x] for x in ['a', 'b', 'c', 'd', 'i_offset']}
attrs_['i_offset'] = 0.014 #[0.014,-attrs_['v0'],0.0]
#self.population[0].initialize()
self.population[0].set_parameters(**attrs_)
print(self.population[0].get_parameters())
self.neuron.h.psection()
return self
def inject_square_current(self, current):
import copy
attrs = copy.copy(self.model.attrs)
self.init_backend()
self.set_attrs(**attrs)
c = copy.copy(current)
if 'injected_square_current' in c.keys():
c = current['injected_square_current']
c['delay'] = re.sub('\ ms$', '', str(c['delay'])) # take delay
c['duration'] = re.sub('\ ms$', '', str(c['duration']))
c['amplitude'] = re.sub('\ pA$', '', str(c['amplitude']))
stop = float(c['delay']) + float(c['duration'])
start = float(c['delay'])
amplitude = float(c['amplitude']) / 1000.0
#print('amplitude',amplitude)
electrode = self.neuron.DCSource(start=start,
stop=stop,
amplitude=amplitude)
print(self.population[0])
print(type(self.population[0]))
print(self.population[0].get_parameters())
electrode.inject_into(self.population[0:1])