-
Notifications
You must be signed in to change notification settings - Fork 4
/
Copy pathconf.py
162 lines (152 loc) · 6.08 KB
/
conf.py
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
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
import ConfigParser
import io
import sys
# default config as string
def_config = """
[set]
boost_every = 0.0
boost_halfw = 5.0
er_scale = 1.0
ca_stim = 0.0
ca_stimT = 2000.0
ip3rtau = 400
ip3_notorigin = 120400.0
ip3_origin = 120400.0
gserca = 1.9565
gleak = 18.06
stim_minx = 498
stim_maxx = 502
ip3_stim = 1.25
ip3_stimT = 2000
IP3ForceInit = 0
ip3_init = 0.1
cacyt_init = 0.0001
caAvg_init = 0.0017
cadiff = 0.080
ip3diff = 1.415
gCaChannels = 1.e-6
spaceum = 1.0
synLoclist = [0.5]
nstimStart = 1000
nstimInterval = 1
nstimNumber = 40
nconnThreshold = 0
nconnDelay = 0
nconnWeight = 20
nconnActive = 1
electrical = 0
[run]
recdt = 5
tstop = 30000
dt = 1
cvodeactive = 1
runit = 0
simstr = '14aug5_A'
saveout = 0
dodraw = 0
loadState = 0
ipydebug = 0
statestr = 'mystate'
savestate = 0
useInitDict = 0
loadRXDStateOnly = 1
"""
# write config file starting with defaults and new entries
# specified in section (sec) , option (opt), and value (val)
# saves to output filepath fn
def writeconf (fn,sec,opt,val):
conf = ConfigParser.ConfigParser()
conf.readfp(io.BytesIO(def_config)) # start with defaults
# then change entries by user-specs
for i in xrange(len(sec)): conf.set(sec[i],opt[i],val[i])
# write config file
with open(fn, 'wb') as cfile: conf.write(cfile)
# read config file
def readconf (fn="cawave.cfg"):
config = ConfigParser.ConfigParser()
config.read(fn)
def conffloat (base,var,defa): # defa is default value
val = defa
try: val=config.getfloat(base,var)
except: pass
return val
def confint (base,var,defa):
val = defa
try: val=config.getint(base,var)
except: pass
return val
def confstr (base,var,defa):
val = defa
try: val = config.get(base,var)
except: pass
return val
def conflist (base, var, defa):
val = defa
try: val = config.get(base, var)
except: pass
return eval(val) # eval will convert the string to a list
er_scale = conffloat("set","er_scale", 1.0)
ip3_notorigin = conffloat("set","ip3_notorigin", 120400.0)
ip3_origin = conffloat("set","ip3_origin", 120400.0)
gserca0 = conffloat("set","gserca", 1.9565)
boost_every = conffloat("set","boost_every", 0.0)
boost_halfw = conffloat("set","boost_halfw", 5.0)
gleak0 = conffloat("set","gleak", 18.06)
ip3rtau = conffloat("set","ip3rtau", 400.0)
recdt = conffloat("run","recdt", 5.0)
tstop = conffloat("run","tstop", 30000.0)
cvodeactive = confint("run","cvodeactive", 1)
dt = conffloat("run","dt", 50.0)
runit = conffloat("run","runit", 0.0)
simstr = confstr("run","simstr","13nov18_")
saveout = conffloat("run","saveout",0.0)
stim_minx = conffloat("set","stim_minx",123)#498.0)
stim_maxx = conffloat("set","stim_maxx",127)#502.0)
dodraw = conffloat("run","dodraw",0.0)
loadState = confint('run', 'loadState', 0)
loadRXDStateOnly = confint('run','loadRXDStateOnly',1)
ipydebug = confint('run','ipydebug',0)
savestate = confint("run","savestate",0)
useInitDict = confint("run","useInitDict",0) # whether to use sstvars init dict
statestr = confstr('run', 'statestr', 'mystate')
ip3_stim = conffloat("set","ip3_stim", 1.25)
ip3_stimT = conffloat("set","ip3_stimT",2000.0)
IP3ForceInit = confint("set","IP3ForceInit",0)
ip3_init = conffloat("set","ip3_init",0.1)
caCYT_init = conffloat("set","caCYT_init",0.0001)
caAvg_init = conffloat("set","caAvg_init",0.0017)
caDiff = conffloat("set","caDiff",0.080) # calcium diffusion coefficient
ip3Diff = conffloat("set","ip3Diff",1.415) # ip3 diffusion coefficient
gCaChannels = conffloat('set', 'gCaChannels', 1.e-6)
spaceum = conffloat("set","spaceum",1.0) # spatial resolution for each segment, in um (nseg=L/spaceum)
ca_stim = conffloat("set","ca_stim",0.0)
ca_stimT = conffloat("set","ca_stimT",2000.0)
synLoclist = conflist('set', 'synLoclist', []) # list of locations to insert depolarizing synapses
nstimStart = conffloat('set', 'nstimStart', 1000)
nstimInterval = conffloat('set', 'nstimInterval', 1)
nstimNumber = conffloat('set', 'nstimNumber', 40)
nconnThreshold = conffloat('set', 'nconnThreshold', 0)
nconnDelay = conffloat('set', 'nconnDelay', 0)
nconnWeight = conffloat('set', 'nconnWeight', 20)
nconnActive = confint('set', 'nconnActive', 1)
electrical = confint('set', 'electrical', 0) # whether to include ion channels and synapses
sys.stdout = open("./simconfloaded.log", "w") # will direct the print output to simconfloaded.log file
print "er_scale:",er_scale,",ip3_notorigin:",ip3_notorigin,",ip3_origin:",ip3_origin,\
",gserca:",gserca0,",boost_every:",boost_every,",ip3_stim:",ip3_stim, ",ip3rtau:",ip3rtau,\
"cvodeactive:",cvodeactive," ,dt:",dt," ,runit:",runit," ,simstr:",simstr," ,saveout:",saveout,\
"stim_minx:",stim_minx," ,stim_maxx:",stim_maxx," ,dodraw:",dodraw, ', loadState:',loadState, ", ip3_stimT:",ip3_stimT,\
" ,ip3_init:",ip3_init, " ,caCYT_init:",caCYT_init, " ,caAvg_init:",caAvg_init,\
" ,caDiff:",caDiff, " ,ip3Diff:",ip3Diff, " ,gCaChannels:",gCaChannels, " ,spaceum:",spaceum,\
" ,ca_stim:",ca_stim, " ,ca_stimT:",ca_stimT," ,recdt:",recdt,\
" ,boost_halfw:",boost_halfw," ,gleak0:",gleak0, ' ,synLoclist:', synLoclist, ' ,nstimStart:', nstimStart,\
' ,nstimInterval:', nstimInterval, ' ,nstimNumber:', nstimNumber, ' ,nconnThreshold:', nconnThreshold,\
' ,nconnDelay:', nconnDelay, ' ,nconnWeight:', nconnWeight, ' ,nconnActive:', nconnActive, \
' ,ipydebug:', ipydebug, ' ,statestr:', statestr, ' ,savestate:', savestate, ' ,useInitDict:', useInitDict, \
' ,IP3ForceInit:', IP3ForceInit, ' ,loadRXDStateOnly:', loadRXDStateOnly, ' ,electrical:', electrical
sys.stdout = sys.__stdout__
return er_scale,ip3_notorigin,ip3_origin,gserca0,boost_every,ip3_stim,\
gleak0,ip3rtau,recdt,tstop,cvodeactive,dt,runit,simstr,saveout,\
stim_minx,stim_maxx,dodraw,loadState,ip3_stimT,ip3_init,caCYT_init,caAvg_init,\
caDiff,ip3Diff,gCaChannels,spaceum,ca_stim,ca_stimT,boost_halfw,synLoclist,\
nstimStart, nstimInterval, nstimNumber, nconnThreshold, nconnDelay, nconnWeight, nconnActive, \
ipydebug, statestr, savestate, useInitDict, IP3ForceInit, loadRXDStateOnly, electrical