epilepsy/sd.py at master · research-team/epilepsy · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
from neuron import h, gui
import matplotlib
matplotlib.use('TkAgg')
import matplotlib.pyplot as pyplot
import math
#neuron.load_mechanisms("./mod")
from fiber import fiber

def set_recording_vectors(compartment):
    ''' recording voltage
    Parameters
    ----------
    compartment: NEURON section
        compartment for recording
    Returns
    -------
    v_vec: h.Vector()
        recorded voltage
    t_vec: h.Vector()

        recorded time
    '''
    v_vec = h.Vector()   # Membrane potential vector at compartment
    t_vec = h.Vector()        # Time stamp vector
    v_vec.record(compartment(0.5)._ref_v)
    t_vec.record(h._ref_t)
    return v_vec, t_vec

def addpointers(cell, glia):
    for sec in cell.accums:
        for sec_g in glia.diffs:
            print(sec_g.ina)
            h.setpointer(sec_g._ref_ina, 'inag', sec)
    # for sec in cell.all:
    #     for sec_g in glia.all:
    #         print(sec_g.ina_nakpump)
    #         h.setpointer(sec_g._ref_ina_nakpump, 'inag_accum', sec)
    #         h.setpointer(sec._ref_icag_accum, 'ica', sec_g)
    #         h.setpointer(sec._ref_iclg_accum, 'icl', sec_g)
    #         h.setpointer(sec._ref_iag_accum, 'ia', sec_g)
    #         h.setpointer(sec._ref_diamg_accum, 'diam', sec_g)
    #         h.setpointer(sec_g._ref_ko, 'kog_getconc', sec)
    #         h.setpointer(sec_g._ref_naog_getconc, 'nao', sec)
    #         h.setpointer(sec_g._ref_caog_getconc, 'cao', sec)
    #         h.setpointer(sec_g._ref_clog_getconc, 'clo', sec)
    #         h.setpointer(sec_g._ref_aog_getconc, 'ao', sec)
    #         h.setpointer(sec_g._ref_kig_getconc, 'kg_accum', sec)
    #         h.setpointer(sec_g._ref_naig_getconc, 'nag_accum', sec)
    #         h.setpointer(sec_g._ref_caig_getconc, 'cag_accum', sec)
    #         h.setpointer(sec_g._ref_clig_getconc, 'clg_accum', sec)
    #         h.setpointer(sec_g._ref_aig_getconc, 'ag_accum', sec)

def balance(cell, vinit=-55):
    ''' voltage balance
    Parameters
    ----------
    cell: NEURON cell
        cell for balance
    vinit: int (mV)
        initialized voltage
    '''
    for sec in cell.all:
        if ((-(sec.ina_nattxs + sec.ina_navv1p8 + sec.ina_Nav1_3 + sec.ina_nakpump) / (vinit - sec.ena)) < 0):
            sec.pumpina_extrapump = -(sec.ina_nattxs + sec.ina_navv1p8 + sec.ina_Nav1_3 + sec.ina_nakpump)
        else:
            sec.gnaleak_leak = -(sec.ina_nattxs + sec.ina_navv1p8 + sec.ina_Nav1_3 + sec.ina_nakpump) / (vinit - sec.ena)

        if ((-(sec.ik_kdr + sec.ik_nakpump + sec.ik_kap + sec.ik_kad) / (vinit - sec.ek)) < 0):
            sec.pumpik_extrapump = -(sec.ik_kdr + sec.ik_nakpump + sec.ik_kap + sec.ik_kad)
        else:
            sec.gkleak_leak = -(sec.ik_kdr + sec.ik_nakpump + sec.ik_kap + sec.ik_kad) / (vinit - sec.ek)

def init(cell, glia, vinit=-70, vglia=-88):
    ''' simulation control
    Parameters
    ----------
    cell: NEURON cell
        cell for simulation
    tstop: int (ms)
        simulation time
    vinit: int (mV)
        initialized voltage
    '''
    h.finitialize()
    for sec in cell.all:
        sec.v = vinit
    for sec in glia.all:
      sec.v = vglia
      sec.nai = setnag_accum
      sec.ki = setkg_accum
      sec.cli = setclg_accum
      sec.ai = setag_accum

    h.fcurrent()


def simulate():
    h.frecord_init()
    h.tstop = tstop
    h.run()

def show_output(v_vec, t_vec):
    ''' show graphs
    Parameters
    ----------
    v_vec: h.Vector()
        recorded voltage
    t_vec: h.Vector()
        recorded time
    '''
    dend_plot = pyplot.plot(t_vec, v_vec)
    pyplot.xlabel('time (ms)')
    pyplot.ylabel('mV')

if __name__ == '__main__':
    cell = fiber(False)
    glia = fiber(True)
    for sec in h.allsec():
        h.psection(sec=sec) #show parameters of each section
    # addpointers(cell,glia)
    # branch_vec, t_vec = set_recording_vectors(cell.branch)
    # simulate(cell, glia)
    # show_output(branch_vec, t_vec)
    # pyplot.show()