def conditionAndTestMultiNoSK(data):
sec_num, sec_loc, Sc0, St0, dSt, start, lag, outpath = data
from getCells import HayCell
cell = HayCell()
stim_seg = cell.apic[sec_num](sec_loc)
soma_seg = cell.soma[0](0.5)
## remove SK_E2 channels
for sec in h.allsec():
try:
sec.uninsert('SK_E2')
except:
pass
print(str(stim_seg))
print('starting lag: ' + str(np.round(lag, 1)))
S, traces = conditionAndTestNoSK(stim_seg, soma_seg, Sc0, St0, dSt, start,
lag)
trace_lists = {}
for key in traces.keys():
trace_lists[key] = traces[key].to_python()
trace_lists['S'] = S
trace_file = outpath + str(stim_seg.sec) + '_lag' + str(np.round(
lag, 1)) + '_w' + str(np.round(S, 3)) + '_traces.json'
with open(trace_file, 'w') as fileObj:
json.dump(trace_lists, fileObj)
print('DONE lag: ' + str(np.round(lag, 1)))
return S
def chirpForMulti(invar):
sec_num, loc, filename = invar
from getCells import HayCell
pt_cell = HayCell()
seg = pt_cell.apic[sec_num](loc)
from neuron import h
for sec in h.allsec():
try:
sec.uninsert('SK_E2')
except:
pass
from chirpUtils import applyChirp, getChirp
amp = 0.0025
f0, f1, t0, Fs, delay = 0.5, 20, 20, 1000, 5 # for looking at bimodal leading phase response in Hay cell
I, t = getChirp(f0, f1, t0, amp, Fs, delay)
print('running chirp on ' + str(seg))
applyChirp(I,
t,
seg,
pt_cell.soma[0](0.5),
t0,
delay,
Fs,
f1,
out_file_name=filename)
def chirpForMulti(invar):
model, sec_num, loc, filename = invar
if model == 'kole':
from getCells import KoleCell
cell, _ = KoleCell()
seg = cell.apic[sec_num](loc)
soma_seg = cell.soma(0.5)
if model == 'kolenoim':
from getCells import KoleCell
cell, _ = KoleCell()
from neuron import h
for sec in h.allsec():
try:
sec.uninsert('Km')
except:
pass
seg = cell.apic[sec_num](loc)
soma_seg = cell.soma(0.5)
elif model == 'neymotinkole':
from getCells import NeymotinKoleCell
cell = NeymotinKoleCell()
seg = cell.apic[sec_num](loc)
soma_seg = cell.soma(0.5)
elif model == 'neymotinharnett':
from getCells import NeymotinHarnettCell
cell = NeymotinHarnettCell()
seg = cell.apic[sec_num](loc)
soma_seg = cell.soma(0.5)
elif model == 'neymotinmigliore':
from getCells import NeymotinMiglioreCell
cell = NeymotinMiglioreCell()
seg = cell.apic[sec_num](loc)
soma_seg = cell.soma(0.5)
elif model == 'hay':
from getCells import HayCell
cell, _ = HayCell()
seg = cell.apic[sec_num](loc)
soma_seg = cell.soma[0](0.5)
elif model == 'ackerantic':
from getCells import AckerAnticCell
cell = AckerAnticCell()
seg = cell.apical[sec_num](loc)
soma_seg = cell.soma[0](0.5)
elif model == 'haymig':
from getCells import HayCellMig
cell, _ = HayCellMig()
seg = cell.apic[sec_num](loc)
soma_seg = cell.soma[0](0.5)
from chirpUtils import applyChirp, getChirp
amp = 0.025
f0, f1, t0, Fs, delay = 0.5, 10, 10, 1000, 5 # for looking at bimodal leading phase response in Hay cell
I, t = getChirp(f0, f1, t0, amp, Fs, delay)
print('running chirp on ' + str(seg))
applyChirp(I, t, seg, soma_seg, t0, delay, Fs, f1, out_file_name=filename)
print(str(sec) + ' ' + str(loc) + ': done')
import multiprocessing
from getCells import HayCell
cell = HayCell()
from synUtils import getLagData, getTp, conditionAndTestMulti, conditionAndTestMultiNoSK
import sys
if sys.argv[-1] == '2':
stim_seg = cell.apic[2](0.5)
soma_seg = cell.soma[0](0.5)
weight = 0.125
start = 200
factor = 4
Sc0 = weight / factor
St0 = weight / (factor*5)
dSt = weight / (factor*10)
Tp, _ = getTp(stim_seg, soma_seg, start, Sc0)
data = getLagData(2, 0.5, Sc0, St0, dSt, start, Tp, 1, '/u/craig/L5PYR_Resonance/timeDomainOutput/HayApic2/')
data = tuple(data)
elif sys.argv[-1] == '36':
stim_seg = cell.apic[36](0.8)
soma_seg = cell.soma[0](0.5)
weight = 0.065
start = 200
factor = 4
Sc0 = weight / factor
St0 = weight / (factor*5)
dSt = weight / (factor*10)
Tp, _ = getTp(stim_seg, soma_seg, start, Sc0)
# load in packages
import sys
import os
# Handle command line arguments
## load cell
if sys.argv[-1] == 'Hay':
from getCells import HayCell
pt_cell = HayCell()
elif sys.argv[-1] == 'Neymotin':
from getCells import NeymotinCell
pt_cell = NeymotinCell()
elif sys.argv[-1] == 'AckerAntic':
from getCells import AckerAnticCell
pt_cell = AckerAnticCell()
elif sys.argv[-1] == 'Kole':
from getCells import KoleCell
pt_cell = KoleCell()
else:
from getCells import AllenCell
try:
pt_cell = AllenCell(sys.argv[-1])
except:
print('Error: invalid cell type')
## create output directories
out_path = '/home/craig_kelley_downstate_edu/L5PYR_Resonance/' + sys.argv[
-1] + '/'
try:
os.mkdir(out_path + 'impedance_measures')
except:
else:
for loc in np.linspace(1/(nseg+1), nseg/(nseg+1), nseg):
data.append([model, sec_num, loc, '/u/craig/L5PYR_Resonance/Neymotin/harnett_trunk_data/'+str(cell.apic[sec_num](loc))])
if model == 'neymotinmigliore':
from getCells import NeymotinMiglioreCell
cell = NeymotinMiglioreCell()
for sec_num, sec in enumerate(cell.apical_maintrunk):
nseg = sec.nseg
if nseg == 1:
data.append([model, sec_num, 0.5, '/u/craig/L5PYR_Resonance/Neymotin/migliore_trunk_data/'+str(cell.apic[sec_num](0.5))])
else:
for loc in np.linspace(1/(nseg+1), nseg/(nseg+1), nseg):
data.append([model, sec_num, loc, '/u/craig/L5PYR_Resonance/Neymotin/migliore_trunk_data/'+str(cell.apic[sec_num](loc))])
if model == 'hay':
from getCells import HayCell
cell, trunk = HayCell()
for sec_num in trunk:
nseg = cell.apic[sec_num].nseg
if nseg == 1:
data.append([model, sec_num, 0.5, '/u/craig/L5PYR_Resonance/Hay/trunk_data/'+str(cell.apic[sec_num](0.5))])
else:
for loc in np.linspace(1/(nseg+1), nseg/(nseg+1), nseg):
data.append([model, sec_num, loc, '/u/craig/L5PYR_Resonance/Hay/trunk_data/'+str(cell.apic[sec_num](loc))])
if model == 'haymig':
from getCells import HayCellMig
cell, trunk = HayCellMig()
for sec_num in trunk:
nseg = cell.apic[sec_num].nseg
if nseg == 1:
data.append([model, sec_num, 0.5, '/u/craig/L5PYR_Resonance/Hay/mig_trunk_data/'+str(cell.apic[sec_num](0.5))])
else:
# Load in the goods
import numpy as np
import sys
from scipy.io import savemat
from math import nan
# parse cmd line inputs, load PT cell template
## load cell
from getCells import HayCell
morph_file = sys.argv[-2]
pt_cell = HayCell(morphology_file=morph_file)
## specify stimulated section and soma segment
section = sys.argv[-1]
if section.split('.')[1][:4] == 'apic':
sec = pt_cell.apic[int(section.split('.')[1].split('[')[1].split(']')[0])]
else:
sec = pt_cell.dend[int(section.split('.')[1].split('[')[1].split(']')[0])]
soma_seg = pt_cell.soma[0](0.5)
# define current stimulus
from chirpUtils import applyChirp
from chirpUtils import getChirp
amp = 0.0025
f0, f1, t0, Fs, delay = 0.5, 50, 50, 1000, 12
I, t = getChirp(f0, f1, t0, amp, Fs, delay)
# define output variables
ZinResAmp = []
ZinResFreq = []
def chirpForMulti(invar):
sec_num, loc, filename = invar
from getCells import HayCell
pt_cell = HayCell()
seg = pt_cell.apic[sec_num](loc)
# from neuron import h
# for sec in h.allsec():
# try: sec.uninsert('SK_E2')
# except: pass
from chirpUtils import applyChirp, getChirp
amp = 0.0025
f0, f1, t0, Fs, delay = 0.5, 20, 20, 1000, 5 # for looking at bimodal leading phase response in Hay cell
I, t = getChirp(f0, f1, t0, amp, Fs, delay)
print('running chirp on ' + str(seg))
out = applyChirp(I, t, seg, pt_cell.soma[0](0.5), t0, delay, Fs, f1)
ZinResAmp = []
ZinResFreq = []
ZcResAmp = []
ZcResFreq = []
dist = []
QfactorIn = []
QfactorTrans = []
fVarIn = []
fVarTrans = []
ZinPeakPhaseFreq = []
ZinLeadPhaseBW = []
ZinLeadPhaseMinFreq = []
ZinSynchFreq = []
ZinLeadPhaseBool = []
ZcPeakPhaseFreq = []
ZcLeadPhaseBW = []
ZcLeadPhaseMinFreq = []
ZcSynchFreq = []
ZcLeadPhaseBool = []
ZinResAmp.append(out['ZinResAmp'])
ZinResFreq.append(out['ZinResFreq'])
ZcResAmp.append(out['ZcResAmp'])
ZcResFreq.append(out['ZcResFreq'])
dist.append(out['dist'])
QfactorIn.append(out['QfactorIn'])
QfactorTrans.append(out['QfactorTrans'])
fVarIn.append(out['fVarIn'])
fVarTrans.append(out['fVarTrans'])
freqs = out['Freq'][np.argwhere(out['ZinPhase'] > 0)]
if len(freqs) > 0:
ZinPeakPhaseFreq.append(out['Freq'][np.argwhere(
out['ZinPhase'] == np.max(out['ZinPhase']))])
ZinLeadPhaseBW.append(freqs[-1] - freqs[0])
ZinLeadPhaseMinFreq.append(freqs[0])
ZinSynchFreq.append(freqs[-1])
ZinLeadPhaseBool.append(out['ZinPhase'] > 0)
else:
ZinPeakPhaseFreq.append(nan)
ZinLeadPhaseBW.append(0)
ZinLeadPhaseMinFreq.append(nan)
ZinSynchFreq.append(nan)
ZinLeadPhaseBool.append(out['ZinPhase'] > 0)
freqs = out['Freq'][np.argwhere(out['ZcPhase'] > 0)]
if len(freqs) > 0:
ZcPeakPhaseFreq.append(
out['Freq'][np.argwhere(out['ZcPhase'] == np.max(out['ZcPhase']))])
ZcLeadPhaseBW.append(freqs[-1] - freqs[0])
ZcLeadPhaseMinFreq.append(freqs[0])
ZcSynchFreq.append(freqs[-1])
ZcLeadPhaseBool.append(out['ZcPhase'])
else:
ZcPeakPhaseFreq.append(nan)
ZcLeadPhaseBW.append(0)
ZcLeadPhaseMinFreq.append(nan)
ZcSynchFreq.append(nan)
ZcLeadPhaseBool.append(out['ZcPhase'])
print(str(sec) + ' ' + str(loc) + ': done')
output = {
'ZinResAmp': ZinResAmp,
'ZinResFreq': ZinResFreq,
'ZcResAmp': ZcResAmp,
'ZcResFreq': ZcResFreq,
'dist': dist,
'QfactorIn': QfactorIn,
'QfactorTrans': QfactorTrans,
'fVarIn': fVarIn,
'fVarTrans': fVarTrans,
'ZinPeakPhaseFreq': ZinPeakPhaseFreq,
'ZinLeadPhaseBW': ZinLeadPhaseBW,
'ZinLeadPhaseMinFreq': ZinLeadPhaseMinFreq,
'ZinSynchFreq': ZinSynchFreq,
'ZinLeadPhaseBool': ZinLeadPhaseBool,
'ZcPeakPhaseFreq': ZcPeakPhaseFreq,
'ZcLeadPhaseBW': ZcLeadPhaseBW,
'ZcLeadPhaseMinFreq': ZcLeadPhaseMinFreq,
'ZcSynchFreq': ZcSynchFreq,
'ZcLeadPhaseBool': ZcLeadPhaseBool
}
savemat(filename + '.mat', output)
# Load in the goods
import numpy as np
import sys
from scipy.io import savemat
from math import nan
# parse cmd line inputs, load PT cell template
## load cell
if sys.argv[-2] == 'Hay':
from getCells import HayCell
pt_cell = HayCell()
elif sys.argv[-2] == 'Neymotin':
from getCells import NeymotinCell
pt_cell = NeymotinCell(slope=100)
elif sys.argv[-2] == 'AckerAntic':
from getCells import AckerAnticCell
pt_cell = AckerAnticCell()
elif sys.argv[-2] == 'Kole':
from getCells import KoleCell
pt_cell = KoleCell()
else:
from getCells import AllenCell
# try:
pt_cell = AllenCell(sys.argv[-2])
# except:
# print('Error: invalid cell type')
## specify stimulated section and soma segment
section = sys.argv[-1]
if sys.argv[-2] == 'Neymotin' or sys.argv[-2] == 'Hay' or sys.argv[
-2] == 'Kole':