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genrn.py
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genrn.py
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'''
generic neuron modelling class
calling from python calls genrn with t-junction electrophysiology and morphology--
peripheral fiber, drg with soma, central fiber
properties taken from Waxman
'''
from neuron import h
import logging as lgg
import re
class gesec():
def __init__(self, name='sec', ions={'na': 58, 'k': -92, 'ca': -129, 'cl': -89}):
self.name = name
self.sec = h.Section(name=name)
self.mechs = []
self.pps = []
self.ions = {}
for ion in ions:
self.ions[ion] = {'e': ions[ion], 'mechs': []}
self.insert = self.im = self.insert_mech
self.ims = self.insert_mechs
self.gm = self.get_mechs
self.gs = self.get_sec
def insert_mechs(self, mechs, *mmechs):
if isinstance(mechs, str):
self.insert_mech(mechs)
for mech in mmechs:
self.insert_mech(mech)
else:
for mech in mechs:
if 'ions' not in mech and 'params' not in mech:
self.insert_mech(mech, params = mechs[mech])
else:
mech = mechs[mech]
if 'ions' not in mech: mech['ions'] = {}
if 'params' not in mech: mech['params'] = {}
self.insert_mech(mech, mechs[mech]['ions'], mechs[mech]['params'])
def insert_mech(self, mech, ions = {}, params = {}):
# TODO ->DONE does sec.insert(mech) insert mech if the mechanism already exists in section?
# answer from NEURON: it shouldn't
# if not self.sec.has_membrane(mech):
# self.sec.insert(mech)
self.sec.insert(mech)
self.mechs.append(mech)
islst = isinstance(ions, (list, set, tuple))
# use list, set, tuple or dictionary.
for ion in ions:
if ion not in self.ions:
if islst: self.ions[ion] = {'e': False, 'mechs': []}
else: self.ions[ion] = {'e': ions[ion], 'mechs': []}
if islst: pass
else:
# post is the Nernst potential.
post = ions[ion]
if hasattr(self.sec, 'e%s' %(ion)) & post:
pre = getattr(self.sec, 'e%s' %(ion))
if (pre != post):
lgg.info("Note: replacing Nernst potential %s mV -> %s mV" %(pre, post))
setattr(self.sec, 'e%s' %(ion), post)
for param in params:
# if there is a function for the parameter, call it
if not callable(params[param]): setattr(self.sec, '%s_%s' %(param, mech), params[param])
else: self.fset_mech(mech, param, params[param])
# add mech to any ionlist
for ion in self.ions.keys():
if hasattr(self.sec, "i%s_%s" %(ion, mech)):
self.ions[ion]['mechs'].append(mech)
def fset_mech(self, mech, param, func):
for seg in self.sec:
val = func(seg.x)
setattr(seg, '%s_%s' %(param, mech), val)
def set_props(self, props):
for prop in props:
if callable(props[prop]):
self.fset_prop(self.sec, prop, props[prop])
else:
setattr(self.sec, '%s' %(prop), props[prop])
def fset_prop(self, prop, func):
#set properties of the segment, diam
for seg in self.sec:
val = func(seg.x)
setattr(seg, prop, val)
def get_mechs(self):
return self.mechs
def set_nernsts(self):
# set Nernst for all ions
for ion in self.ions:
post = self.ions[ion]['e']
if post and hasattr(self.sec, "e%s" %(ion)):
pre = getattr(self.sec, 'e%s' % (ion))
if (pre != post):
lgg.info("Note: replacing Nernst potential %s mV -> %s mV" % (pre, post))
setattr(self.sec, 'e%s' % (ion), post)
def get_sec(self):
return self.sec
def __lt__(self, mechs):
self.insert_mechs(mechs)
def __call__(self, item):
return self.sec(item)
# def __iter__(self):
# def __next__(self):
# def __getitem__(self, item):
class genrn():
def __init__(self,x=0,y=0,z=0,ID=0,v_init=None,
secs = {'genrn': {}},
mechs = {},
ions = {},
cons = ()):
self.tags = {'all': []}
# secs -> pointer
self.secs = {}
self.gesecs = self.tags['all']
# self.useions = re.compile("USEION ([A-Za-z0-9]+)")
self.init_cell(secs, ions)
self.initialize_mechs('all', mechs, ions)
self.connect_secs(cons)
self.v_init = v_init
def return_sec(self, sec):
if isinstance(sec, type(h.Section())): return sec
elif isinstance(sec, str): return self.secs[sec].sec
elif isinstance(sec, type(gesec())): return sec.sec
raise TypeError
def return_gesec(self, sec):
if isinstance(self, type(h.Section())): return self.secs[sec.name]
elif isinstance(sec, str): return self.secs[sec]
elif isinstance(sec, type(gesec())): return sec
raise TypeError
def init_cell(self, secs, ions):
for sec in secs:
self.add_comp(sec, ions, sec[0:3])
self.set_props(sec = sec, props = secs[sec])
def add_comp(self, sec, ions, *tags):
sec_ = gesec(sec, ions)
# sec_ -> pointer
self.secs[sec] = (sec_)
self.tags['all'].append(sec_)
self.__dict__[sec] = sec_.sec
for tag in tags:
try: self.tags[tag].append(sec_)
except: self.tags[tag] = [sec_]
def set_props(self, sec, props):
sec = self.return_gesec(sec)
sec.set_props(props)
def tag_set_props(self, tag, props):
for sec in self.tags[tag]:
for prop in props:
setattr(sec.sec, '%s' %(prop), props[prop])
def fset_prop(self, sec, prop, func):
sec = self.return_gesec(sec)
#set properties of the segment, diam
sec.fset_prop(prop, func)
def insert_mech(self, sec, mech, ions={}, params={}):
sec = self.return_gesec(sec)
sec.insert_mech(mech, ions, params)
def initialize_mechs(self, tag, mechs, ions):
for sec in self.tags[tag]:
for mech in mechs:
sec.insert(mech)
for param in mechs[mech]:
setattr(sec.sec, '%s_%s' %(param, mech), mechs[mech][param])
for ion in ions:
try: setattr(sec.sec, 'e%s' %(ion), ions[ion])
except: pass
def fset_mech(self, sec, mech, param, func):
sec = self.return_gesec(sec)
sec.fset_mech(mech, param, func)
def connect_secs(self, cons):
for con in cons:
try:
exestr = 'self.%s.connect(self.%s)' %(con[0], con[1])
exec(exestr)
lgg.info('%s[1] -> %s[0]' %(con[1], con[0]))
except:
lgg.info('failed to connect: %s[1] -> %s[0]' %(con[1], con[0]))
def edit_mechs(self, tag, mech, param, value):
for sec in self.tags[tag]:
setattr(sec.sec, '%s_%s' %(param, mech), value)
def tag_fedit_mechs(self, tag, mech, param, func):
for sec in self.tags[tag]:
for seg in sec.sec:
val = func(seg.x)
setattr(seg, '%s_%s' %(param, mech), val)
def get_dict(self, tag = 'all'):
rpr = {}
for sec in self.tags[tag]:
rpr[sec.sec] = sec.sec.psection()
return rpr
# additional not called init functions
def init_nernsts(self):
for sec in self.secs:
self.secs[sec].set_nernsts()
def init_pas(self, v_init, set_pas = False):
e = {}
h.finitialize(v_init)
h.fcurrent()
i_net = 0
lgg.info("fcurrent() values (%s mV)" %(v_init))
for sec in self.secs:
for mech in sec.mechs:
for ion in sec.ions:
try:
i = getattr(sec.sec, 'i%s_%s' %(ion, mech))
lgg.info("(%s)->%s:->%s=%s mA/cm2" %(sec.name, mech, ion, i))
i_net += i
except: pass
lgg.info("(%s)->i_net = %s" %(sec.name, i_net))
try:
e_pas = sec.sec.v + i_net / sec.g_pas
lgg.info("(%s)->e_pas calculated at %s mV" %(e_pas))
if set_pas:
sec.sec.e_pas = e_pas
except: pass
## OoOP: indexing>function>unary>power>mul>add>bitshift>and>xor>or>gt
def __truediv__(self, item):
return self.secs[item]
def __gt__(self, item):
#retrieve gesec objects in a tag using '>' operator, by tag or section name (i.e. self>'all')
try: return self.tags[item]
except KeyError: return self.secs[item]
def __rshift__(self, tag):
#retrieve section objects in a tag using '>>' operator (i.e. self>>'all)
return [sec.sec for sec in self.tags[tag]]
def __call__(self, item):
#returns the gesec items of a specific tag
try: return self.tags[item]
except KeyError: return self.secs[item]
def __getitem__(self, item):
#indices for sections (sections stored in order of creation)
return self.tags['all'][item].sec
def __repr__(self):
#printing a shows consolidated information about class
rpr = ''
for sec in self.tags['all']:
r = sec.sec.psection()
rpr += '%s\n' %(sec.sec.name())
rpr += 'parent:\t%s\n' %(r['morphology']['parent'])
rpr += 'morphology:\tL:%f\tdiam:%f\n' %(r['morphology']['L'], max(r['morphology']['diam']))
rpr += 'mechs:\t%s\n\n' %(list(r['density_mechs'].keys()))
return rpr
def cal_nseg( sec, freq, d_lambda ):
#neuron+python of https://www.neuron.yale.edu/neuron/static/docs/d_lambda/d_lambda.html
nseq = lambda fc_: int((sec.L / (d_lambda * fc_) + 0.9) / 2) * 2 + 1
fpfrc = 4 * h.PI * freq * sec.Ra * sec.cm
h.define_shape()
fc = 0
n3d = sec.n3d()
if n3d < 2:
fc = 1e5 * h.sqrt(sec.diam / (fpfrc))
return nseq(fc)
x1 = sec.arc3d(0)
d1 = sec.diam3d(0)
for i in range(n3d):
x2 = sec.arc3d(i)
d2 = sec.diam3d(i)
fc += (x2 - x1) / h.sqrt(d1 + d2)
x2 = x1
d2 = d1
fc *= h.sqrt(2) * 1e-5 * h.sqrt(fpfrc)
return nseq(sec.L/fc)
# for debugging
if __name__ == '__main__':# section morphologies
# sec dimensions
# from tjunction paper
#secs = {'axnperi': {'nseg':100, 'L':5000, 'diam': 0.8, 'cm': 1.2, 'Ra': 123 },
# 'drgperi': {'nseg':100, 'L':100, 'diam': 0.8, 'cm': 1.2, 'Ra': 123 },
# 'drgstem': {'nseg':100, 'L':75, 'diam': 1.4, 'cm': 1.2, 'Ra': 123 },
# 'drgsoma': {'nseg':1, 'L':25, 'diam': 25 , 'cm': 1.2, 'Ra': 123 },
# 'drgcntr': {'nseg':100, 'L':100, 'diam': 0.4, 'cm': 1.2, 'Ra': 123 },
# 'axncntr': {'nseg':100, 'L':5000, 'diam': 0.4, 'cm': 1.2, 'Ra': 123 }}
# our values:
# nseg with frequency<50, d_lambda 0.1
# use cal_nseg(sec, 50, 0.1) for values
# props for the sections
secs = {'drgperi': {'nseg':257, 'L':5000, 'diam': 0.8, 'cm': 1.2, 'Ra': 123 },
'drgstem': {'nseg':3 , 'L':75 , 'diam': 1.4, 'cm': 1.2, 'Ra': 123 },
'drgsoma': {'nseg':1 , 'L':30 , 'diam': 23 , 'cm': 1.2, 'Ra': 123 },
'drgcntr': {'nseg':363, 'L':5000, 'diam': 0.4, 'cm': 1.2, 'Ra': 123 }}
# section mechanisms
mechs = {'nav17m' : {'gnabar': 0.018 },
'nav18m' : {'gnabar': 0.026 },
'kdr' : {'gkbar' : 0.0035},
'ka' : {'gkbar' : 0.0055},
'pas' : {'g': 5.75e-5, 'e': -58.91}}
# ion reversal potentials
ions = {'na': 67.1,
'k' : -84.7 }
# connection list
#------------------------------------------------------------#
# #
# What the morphology looks like (paper) #
# [1] #
# drgsoma #
# [0] #
# [1] #
# drgstem #
# [0] #
# [0]anxperi[1]-[0]drgperi[1]-^-[0]drgscntr[1]-[0]axncntr[1] #
# #
# ^ ^ #
# | axon initial segment | #
# #
#------------------------------------------------------------#
# 0 -> 1
#cons = (('drgperi', 'axnperi'),
# ('axncntr', 'drgcntr'),
# ('drgstem', 'drgperi'),
# ('drgsoma', 'drgstem'),
# ('drgcntr', 'drgperi'))
# simplified connection list
cons = (('drgstem', 'drgperi'),
('drgsoma', 'drgstem'),
('drgcntr', 'drgperi'))
args = {'secs': secs, 'mechs': mechs, 'ions': ions, 'cons': cons}
test = genrn(**args)
print(test.get_dict())