-
Notifications
You must be signed in to change notification settings - Fork 20
/
test.sh
executable file
·154 lines (110 loc) · 4.48 KB
/
test.sh
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
set -ex
## Test readers
python -m c302.SpreadsheetDataReader
python -m c302.UpdatedSpreadsheetDataReader
python -m c302.UpdatedSpreadsheetDataReader2
python -m c302.OpenWormReader
## (Re)generate NeuroML 2 & LEMS files from the python scripts
python -m c302.c302_IClamp A
python -m c302.c302_Syns A
python -m c302.c302_Social A
python -m c302.c302_Pharyngeal A
python -m c302.c302_Full A
python -m c302.c302_Muscles A
python -m c302.c302_Oscillator A
python -m c302.c302_IClamp B
python -m c302.c302_Syns B
python -m c302.c302_Social B
python -m c302.c302_Pharyngeal B
python -m c302.c302_Full B
python -m c302.c302_Muscles B
python -m c302.c302_Oscillator B
python -m c302.c302_IClamp C
python -m c302.c302_Syns C
python -m c302.c302_Social C
python -m c302.c302_Pharyngeal C
python -m c302.c302_Full C
python -m c302.c302_Muscles C
python -m c302.c302_Oscillator C
python -m c302.c302_IClamp C0
python -m c302.c302_Syns C0
python -m c302.c302_Social C0
python -m c302.c302_Pharyngeal C0
python -m c302.c302_Full C0
python -m c302.c302_Muscles C0
python -m c302.c302_Oscillator C0
python -m c302.c302_IClamp C1
python -m c302.c302_Syns C1
python -m c302.c302_Social C1
python -m c302.c302_Pharyngeal C1
python -m c302.c302_Full C1
python -m c302.c302_Muscles C1
python -m c302.c302_Oscillator C1
python -m c302.c302_IClamp C2
python -m c302.c302_Syns C2
python -m c302.c302_Social C2
python -m c302.c302_Pharyngeal C2
python -m c302.c302_Full C2
python -m c302.c302_Muscles C2
python -m c302.c302_Oscillator C2
python -m c302.c302_FW C2
python -m c302.c302_IClamp D
python -m c302.c302_Syns D
python -m c302.c302_Social D
python -m c302.c302_Pharyngeal D
python -m c302.c302_Full D
python -m c302.c302_Muscles D
python -m c302.c302_Oscillator D
python -m c302.c302_IClamp D1
python -m c302.c302_Syns D1
python -m c302.c302_Social D1
python -m c302.c302_Pharyngeal D1
python -m c302.c302_Full D1
python -m c302.c302_Muscles D1
python -m c302.c302_Oscillator D1
cd examples
## Validate generated NeuroML 2
pynml -validate c302_A_Full.net.nml
pynml -validate c302_A_Pharyngeal.net.nml
pynml -validate c302_A_Syns.net.nml
pynml -validate c302_A_Social.net.nml
pynml -validate c302_A_Muscles.net.nml
# Not validating B files as they use non NeuroML 2 compliant IaFCell model with activity...
pynml -validate c302_C_Full.net.nml
pynml -validate c302_C_Pharyngeal.net.nml
pynml -validate c302_C1_Full.net.nml
pynml -validate c302_C1_Pharyngeal.net.nml
pynml -validate c302_D_Full.net.nml
pynml -validate c302_D_Pharyngeal.net.nml
#pynml -validate c302_D1_Full.net.nml
#pynml -validate c302_D1_Pharyngeal.net.nml
## Try running these in jNeuroML with no GUI
#pynml LEMS_c302_A_Full.xml -nogui # Takes 2 mins to run!
pynml LEMS_c302_A_Pharyngeal.xml -nogui
pynml LEMS_c302_A_Syns.xml -nogui
pynml LEMS_c302_A_Social.xml -nogui
#pynml LEMS_c302_B_Full.xml -nogui # Takes 2 mins to run!
pynml LEMS_c302_B_Pharyngeal.xml -nogui
pynml LEMS_c302_B_Syns.xml -nogui
pynml LEMS_c302_B_Social.xml -nogui
## Try regenerating using command line options
cd ..
c302 MyNetwork parameters_C -cells ["AVBR","VD3"] -cellstostimulate ["AVBR"] -paramoverride {"unphysiological_offset_current":"2.9pA"} -duration 300
c302 c302_A_Syns2 parameters_A -cells ["ADAL","AIBL","RIVR","RMEV"] -cellstostimulate ["ADAL","RIVR"] -duration 500 -dt 0.1 -vmin -72 -vmax -48
c302 c302_A_Weights parameters_A -cells ["ADAL","AIBL","I1L","I3","DB5","PVCR"] -cellstostimulate ["ADAL","I1L","PVCR"] -connnumberoverride=["I1L-I3":2.5] -connnumberscaling=["PVCR-DB5":5] -duration 500 -dt 0.1 -vmin -72 -vmax -48
c302 c302_C1_Test parameters_C1 -cellstostimulate AFDL -connnumberscaling {"I1L-I3":2}
mkdir -p cells
c302 c302_D1_Weights parameters_D1 -cells ["ADAL","AIBL","I1L","I3","DB5","PVCR"] -cellstostimulate ["ADAL","I1L","PVCR"] -connnumberoverride=["I1L-I3":2.5] -connnumberscaling=["PVCR-DB5":5] -duration 500 -dt 0.1
cd examples
## Try converting some to NEURON
pynml LEMS_c302_A_Full.xml -neuron
pynml LEMS_c302_B_Pharyngeal.xml -neuron
pynml LEMS_c302_C_Syns.xml -neuron
nrnivmodl
cd -
## Try helper scripts
python -m c302.runAndPlot -test
python -m c302.c302_utils -nogui
echo
echo " Successfully completed all c302 tests!"
echo