def chirpForMulti(invar):
model, sec_num, loc, filename = invar
cell = HayCellSWC('../suter_shepherd/' + model)
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(seg) + ': done')
def chirpForMulti(invar):
sec_num, loc, morph_file, filename = invar
from getCells import HayCellSWC
pt_cell = HayCellSWC(morphology_file=morph_file)
seg = pt_cell.apic[sec_num](loc)
from chirpUtils import applyChirp, getChirp
amp = 0.0025
f0, f1, t0, Fs, delay = 0.5, 30, 30, 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:
ZinSynchFreq.append(freqs[-1])
else:
ZinSynchFreq.append(nan)
freqs = out['Freq'][np.argwhere(out['ZcPhase'] > 0)]
if len(freqs) > 0:
freqs = freqs[freqs < 10]
ZcSynchFreq.append(freqs[-1])
else:
ZcSynchFreq.append(nan)
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,
'ZinSynchFreq': ZinSynchFreq,
'ZcSynchFreq': ZcSynchFreq
}
savemat(filename + '.mat', output)
savemat(filename + '.mat', output)
moprh_path = '/u/craig/L5PYR_Resonance/suter_shepherd/'
morph_files = listdir(moprh_path)
for morph_file in morph_files:
cellID = morph_file.split('.')[0]
try:
mkdir('/u/craig/L5PYR_Resonance/SuterChirpData/' + cellID)
except:
pass
data = []
from getCells import HayCellSWC
pt_cell = HayCellSWC(morphology_file=moprh_path + morph_file)
for ind, sec in enumerate(pt_cell.apic):
nseg = sec.nseg
if nseg == 1:
data.append([
ind, 0.5, moprh_path + morph_file,
'/u/craig/L5PYR_Resonance/SuterChirpData/' + cellID + '/apic' +
str(ind) + '_0.5'
])
else:
for loc in np.linspace(1 / (nseg + 1), nseg / (nseg + 1), nseg):
data.append([
ind, loc, moprh_path + morph_file,
'/u/craig/L5PYR_Resonance/SuterChirpData/' + cellID +
'/apic' + str(ind) + '_' + str(loc)
])
with open('suter_shepherd_trunk_data.json', 'rb') as fileObj:
models = json.load(fileObj)
## handle each model accordingly
# for model in models:
# model = sys.argv[-1]
for model in models.keys():
if len(models[model]) > 0:
cellID = model.split('.')[0]
try:
os.mkdir('/u/craig/L5PYR_Resonance/Hay/mig_suter_trunk_data/' +
cellID + '/')
except:
pass
from getCells import HayCellSWC
cell = HayCellSWC('../suter_shepherd/' + model)
for sec_num in models[model]:
nseg = cell.apic[sec_num].nseg
if nseg == 1:
data.append([
model, sec_num, 0.5,
'/u/craig/L5PYR_Resonance/Hay/mig_suter_trunk_data/' +
cellID + '/' + 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/mig_suter_trunk_data/' +
cellID + '/' + str(cell.apic[sec_num](loc))