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#!/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], fontsize=9)
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()
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