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
163
164
165
166
167
168
169
170
171
|
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# plotsto.py -- Plot all muscle activation signals in a .sto file
#
# Copyright (C) 2013 Tobias Klauser <tklauser@distanz.ch>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License version 2 as
# published by the Free Software Foundation.
import getopt
import os, sys
import numpy as np
import matplotlib.pyplot as plt
def usage():
print("""usage: {} [OPTION...] STO-FILE...
Plot all muscle activation signals in a .sto file.
options:
-m NAMES plot only columns with names from comma-separated list NAMES
-h show this help and exit""".format(os.path.basename(sys.argv[0])))
# .sto header format:
# control
# version=N
# nRows=N
# nColumns=N
# ... (optional header lines)
# endheader
def parse_sto_header(f):
endheader = False
name = ''
nRows = nColumns = 0
name = f.readline()
while True:
line = f.readline().strip()
if line is None:
break
if line == 'endheader':
endheader = True
break
k, v = line.split('=')
if k == 'nRows':
nRows = int(v)
elif k == 'nColumns':
nColumns = int(v)
if not endheader:
print("Error: header not properly terminated by 'endheader' in {}".format(f.name))
return -1, -1
return nRows, nColumns
def read_sto(sto, muscles=None):
f = open(sto, 'r')
nRows, nColumns = parse_sto_header(f)
if nRows <= 0 or nColumns <= 0:
return
print("nRows: " + str(nRows))
print("nColumns: " + str(nColumns))
cols = f.readline().strip().split()
if len(cols) != nColumns:
f.close()
print("Error: nColumns does not match number of columns in file")
return None
i = len(f.readlines())
f.close()
if i != nRows:
print("Error: nRows does not match number of rows in file")
return None
# by default use all columns
idx = list(range(nColumns))
_cols = []
# filter out selected muscles
if not muscles is None:
for i, m in enumerate(cols):
if m in muscles or m == 'time':
_cols.append(m)
else:
idx[i] = None
cols = _cols
act = np.zeros((nRows, len(cols)))
i = 0
endheader = 0
f = open(sto, 'r')
for line in f:
# skip header and column title lines (we know there's an endheader line)
if line.strip() == 'endheader':
endheader = 1
continue
if endheader == 0:
continue
elif endheader == 1:
endheader += 1
continue
data = line.split()
if len(data) != nColumns:
f.close()
print("Error: row {} has less than {} columns".format(i+7, nColumns))
return None
k = 0
for j, val in enumerate(data):
if j in idx:
act[i,k] = float(val.strip())
k += 1
i += 1
f.close()
return act, cols
def main():
try:
opts, args = getopt.getopt(sys.argv[1:], "m:h")
except getopt.GetoptError, err:
print(str(err))
usage()
sys.exit(-1)
if len(args) < 1:
usage()
sys.exit(-1)
muscles = None
for o, a in opts:
if o == '-m':
muscles = [ x.strip() for x in a.split(',') ]
elif o == '-h':
usage()
sys.exit(0)
else:
assert False, "unhandled option"
for sto in args:
if not os.path.exists(sto):
print("Error: File %s not found, skipping".format(sto))
continue
act, cols = read_sto(sto, muscles)
# transpose so we can access it more conveniently
act = act.transpose()
t, ys = act[0], act[1:]
l = []
# see matplotlib.org/examples/pylab_examples/subplots.demo.html
f, ax = plt.subplots(nrows=(len(cols) - 1) / 2, ncols=2, sharex='col', sharey='row')
for i, y in enumerate(ys):
ax[i/2,i%2].plot(t, y)
ax[i/2,i%2].set_title(cols[i+1])
l.append(cols[i+1])
plt.axis([0, t.max(), 0, 1.0], 'equal')
# plt.legend(l, bbox_to_anchor=(1.05, 1.), loc=2, borderaxespad=0.)
plt.show()
if __name__ == '__main__':
main()
|
