# import ipdb
from neuron import h,gui
import struct_tools as st
import numpy as np
class cell(object):
def __init__(self, Vrest, Rm, Ra, Cm, records=[], check = False, use_channels = True):
self.Name = 'pyr2005'
# Load the neuron structure from .swc converted to .hoc geometry
if use_channels:
h.load_file('bdnf.hoc')
else:
h.load_file('bdnf_passive.hoc')
models = st.get_cell_list()
# select the brach apic[93] and insert it in a new sectionlist
self.soma_sl = h.SectionList()
self.branch_sl = h.SectionList()
self.branch37_sl = h.SectionList()
self.branch8_sl = h.SectionList()
self.branch16_sl = h.SectionList()
self.apical_sl = h.SectionList()
self.basal_sl = h.SectionList()
self.user5_sl = h.SectionList()
self.axon_sl = h.SectionList()
for m in models:
cell = st.get_section_list(m)
for sec in cell:
sec.push()
if 'apical_dendrite[38]' in sec.name():
self.branch_sl.subtree()
self.branch_base = sec
if 'apical_dendrite[37]' in sec.name():
self.branch37_sl.subtree()
self.branch37_base = sec
if 'apical_dendrite[8]' in sec.name():
self.branch8_sl.subtree()
self.branch8_base = sec
if 'apical_dendrite[16]' in sec.name():
self.branch16_sl.subtree()
self.branch16_base = sec
if 'soma' in sec.name():
self.soma = sec
self.soma_sl.append()
if 'apical_dendrite' in sec.name():
self.apical_sl.append()
if 'dendrite' in sec.name():
self.basal_sl.append()
if 'user5' in sec.name():
self.user5_sl.append()
h.pop_section()
if check:
print('List of kept sections:')
print((cell.printnames()))
print(('Apical',apical_sl.printnames()))
print(('Basal',basal_sl.printnames()))
print(('Axon',axon_sl.printnames()))
print(('User',user5_sl.printnames()))
special_sections = {
'soma':self.soma,
'branch_base':self.branch_base}
if check:
print((self.branch_sl.printnames()))
# Put sections into a dictionary
self.branch38 = {}
for sec in self.branch_sl:
self.branch38[sec.name()] = sec
self.branch37 = {}
for sec in self.branch37_sl:
self.branch37[sec.name()] = sec
self.branch8 = {}
for sec in self.branch8_sl:
self.branch8[sec.name()] = sec
self.branch16 = {}
for sec in self.branch16_sl:
self.branch16[sec.name()] = sec
# # print self.branch93['apic[95]'].diam
# # access main branch
# self.soma.push()
# self.branch_base = self.branch93['apic[93]']
# # set origin for distance
# h.distance(0,0.5)
# # Adjust the nseg
# st.geom_nseg(self.branch_sl, check = check)
# Increase the number of segments to at least 10 per section
# in the branch to have enough segments for the spines
for br in [self.branch_sl,self.branch37_sl,self.branch8_sl,self.branch16_sl]:
for sec in br:
sec.nseg = max(30,sec.nseg)
# # Set biophysical properties
# Rm = 26000 # Ohm/cm2
# print "Imput resistance Rm = ", Rm," Ohm/cm2"
# Cm = 1.41
# Ra = 150
# RaAx = 50
# self.segments = [['%s_%g'%(sec.name(),seg.x),seg] for sec in self.branch_sl for seg in sec]
# # The "apic" rad Sectionlists
# # should insert the following channels
# apic_channels = ['pas','hd','na3','kdr','kad','kap','cacum','cal','can','cat','cagk']
# basal_channels = ['hd','na3','kdr','kap','cacum','cal','can','cat','cagk']
# soma_channels = ['hd','na3','kdr','kap','km','kd','cacum','cal','can','cat','cagk']
# axon_channels = ['na3','kdr','kap','km']
# gna = 0.07
# gkdr = 0.06
# gkap = 0.0015
# gkad = 0.001
# ghd=5.5e-7
# gkm=0.0001
# gkd = 0.0001
# sh = 5
# nash = 8
# kash = 12
# kdrsh = sh
# kmsh = 12
# kdsh = 0
# hdsh = 0
# gc = 1.e-5
# gcal=gc
# gcan=gc
# gcat=gc
# gKc = 3e-05
# for sec in self.apical_sl:
# for ch in channels:
# sec.insert(ch)
# # sec.tau_cacum = 200
# # sec.depth_cacum = sec.diam/2
# sec.e_pas = Vrest
# sec.g_pas = 1.0/Rm
# sec.Ra = Ra
# sec.cm = Cm
# sec.ghdbar_hd = ghd
# sec.vhalfl_hd = -73
# sec.sh_hd = hdsh
# sec.ehd_hd=-30
# sec.gbar_na3=gna
# sec.sh_na3=nash
# sec.gkdrbar_kdr=gkdr
# sec.sh_kdr=kdrsh
# sec.gkabar_kap=0
# sec.sh_kap=kash
# sec.gkabar_kad=0
# sec.sh_kad=kash
# sec.gcalbar_cal=gc
# sec.gcanbar_can=gc
# sec.gcatbar_cat=gc
# sec.gbar_cagk= gKc
# Store data
self.records = {}
# Time
self.records['time'] = {'val':h.Vector(),'unit':'ms'}
self.records['time']['val'].record(h._ref_t, sec = self.branch_base)
# Spikes
self.record_spikes()
# Records set from paramenters.py
for r in records:
section = special_sections[r['section']]
self.records['%s'%r['section']] = {
'%s_%g'%(r['variable'],r['location']):{
'unit':r['unit']}}
print((self.records))
local_rec = self.records['%s'%r['section']]['%s_%g'%(r['variable'],r['location'])]
# self.records['%s_%g'%(r['variable'],r['location'])]
if 'point_process' in list(r.keys()):
local_rec['val'] = self.record_variable(section,
r['variable'],
location=r['location'],
point_process = r['point_process'])
else:
local_rec['val'] = self.record_variable(section,
r['variable'],
location=r['location'])
def balance_currents(self, Vrest, check = False):
# Arguments: $1 Vrest
h.v_init = Vrest
h.init()
if check:
print(("Balancing all currents to %g mV "%Vrest))
h.finitialize(Vrest)
for sec in self.branch_sl:
for seg in sec:
if check:
e_pas = seg.e_pas
seg.e_pas = Vrest
if h.ismembrane("na_ion"):
seg.e_pas = seg.e_pas + (seg.ina + seg.ik) / seg.g_pas
if h.ismembrane("hd"):
seg.e_pas = seg.e_pas + seg.i_hd/seg.g_pas
if h.ismembrane("ca_ion"):
seg.e_pas = seg.e_pas + seg.ica/seg.g_pas
if check:
print((e_pas, seg.e_pas))
# print (seg.ina+seg.ik+seg.ica+seg.i_hd)/seg.g_pas + Vrest
def record(self, to_record):
self.records = {}
if 'vm' in to_record:
self.records['vms'] = {}
for sec in self.branch_sl:
secs = self.records['vms'][sec.name] = {}
for seg in sec:
secs[seg.x] = h.Vector()
secs[seg.x].record(seg._ref_v)
if 'spikes' in to_record:
self.records['spikes'] = h.Vector()
self.nc_spike = h.NetCon(self.branch93['apic[93]'](0.5)._ref_v, None,-20,0,1, sec = self.branch93['apic[93]'])
self.nc_spike.record(self.records['spikes'])
def record_spikes(self, threshold=-30):
self.spiketimes = h.Vector()
self.spikecount = h.APCount(0.5, sec=self.branch_base)
self.spikecount.thresh = threshold
self.spikecount.record(self.spiketimes)
def record_variable(self, section, variable, location=0.5, point_process=None):
v = h.Vector()
if point_process is not None:
eval('v.record(getattr(section,"%s")._ref_%s, sec = section)'%(point_process,variable))
else:
eval('v.record(section(%g)._ref_%s, sec = section)'%(location,variable))
return v
def save_records(self, store, index = None, write_datasets = True):
if index is not None:
g = store.create_group('%s_%g'%(self.Name, index))
else:
g = store.create_group(self.Name)
# Loop over sections
for r_n,r in list(self.records.items()):
print((r_n,list(r.keys())))
r_g = g.create_group(r_n)
# Write section time
if r_n is 'time':
r_u = r_g.create_dataset('Unit', data = np.string_(r['unit']))
if write_datasets:
data = np.array(r['val'])
data_length = data.shape[0]
r_v = r_g.create_dataset('Data',
data = data,
compression="gzip",
compression_opts=9,
chunks=(min(100,data_length),)
)
else:
r_v = r_g.create_dataset('Data',
(1e5,),
dtype = 'float',
compression="gzip")#,
#compression_opts=9)
#chunks=(100,))
else:
# Loop over variables in sections
for v_n,v in list(r.items()):
v_g = r_g.create_group(v_n)
v_u = v_g.create_dataset('Unit', data = np.string_(v['unit']))
if write_datasets:
data = np.array(v['val'])
data_length = data.shape[0]
v_v = v_g.create_dataset('Data',
data = data,
compression="gzip",
compression_opts=9,
chunks=(min(100,data_length),)
)
else:
v_v = v_g.create_dataset('Data',
(1e5,),
dtype = 'float',
compression="gzip")#,
#compression_opts=9)
#chunks=(100,))
# def store_records(self, section_group, index = None):
# # dset = section_group['%s_%g'%(self.Name, index)]['Data']
# if index is not None:
# dgroup = section_group['%s_%g'%(self.Name, index)]
# else:
# dgroup = section_group[self.Name]
# print dgroup.keys()
# for r_n,r in self.records.iteritems():
# print dgroup[r_n]['Data']
# data = np.array(r['val'])
# print data.shape
# # dgroup[r_n]['Data'][:] =
# # dgroup[r_n]['Data'].resize((500,))
# # print dgroup[r_n]['Data']
if __name__ == '__main__':
Vrest = -70 # mV
Rm = 26000
RmDend = Rm
RaAll= 150
CmDend = 1.4
b = cell(Vrest, RmDend, RaAll, CmDend)
