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#!/usr/bin/env python
import os, sys
import getopt
import csv
import numpy as np
DEFAULT_NAME = 'control'
DEFAULT_MAXTIME = 100.0
def usage():
print """usage: %s [OPTION...] CSV-FILE STO-FILE
-f force overwrite of existing files
-n name of the sto file (default: %s)
-T N scale time such that it goes from 0.0 to N
-h show this help and exit""" % (DEFAULT_NAME, os.path.basename(sys.argv[0]))
def main():
try:
opts, args = getopt.getopt(sys.argv[1:], "fn:hT:")
except getopt.GetoptError, err:
print(str(err))
usage()
sys.exit(-1)
if len(args) < 2:
usage()
sys.exit(-1)
overwrite = False
name = DEFAULT_NAME
maxtime = DEFAULT_MAXTIME
for o, a in opts:
if o == '-f':
overwrite = True
elif o == '-n':
name = a
elif o == '-T':
maxtime = float(a)
elif o == '-h':
usage()
sys.exit(0)
else:
assert False, "unhandled option"
fs_csv = args[0:-1]
for f_csv in fs_csv:
if not os.path.exists(f_csv):
print "Error: CSV file %s does not exist" % f_csv
sys.exit(-1)
f_sto = args[-1]
if not overwrite and os.path.exists(f_sto):
print "Error: STO file %s already exists" % f_sto
sys.exit(-1)
# determine number of columns and rows
tot_nRows = tot_nCols = 0
for f_csv in fs_csv:
fd = open(f_csv, 'r')
nRows = nColumns = 0
for line in fd:
if nRows == 0:
nCols = len(line.split(','))
nRows += 1
if tot_nRows == 0:
tot_nRows = nRows
elif tot_nRows != nRows:
print "Error: Number of rows in CSV files does not match"
sys.exit(-1)
if tot_nCols == 0:
tot_nCols = nCols
elif tot_nCols != nCols:
print "Error: Number of columns in CSV files does not match"
sys.exit(-1)
fd.close()
print "Writing sto file %s with name %s" % (f_sto, name)
if maxtime != DEFAULT_MAXTIME:
print "Scaling to maxtime %f" % maxtime
fd_sto = open(f_sto, 'w')
fd_sto.write(name + "\n")
fd_sto.write("version=1\n")
fd_sto.write("nRows=" + str(tot_nRows) + "\n")
fd_sto.write("nColumns=" + str(tot_nCols) + "\n")
fd_sto.write("endheader\n")
fd_sto.write("time")
for f_csv in fs_csv:
colname = os.path.splitext(os.path.basename(f_csv))[0]
print "[+] Adding muscle %s..." % colname
fd_sto.write("\t" + colname)
fd_sto.write("\n")
fds_csv = [ open(f_csv, 'r') for f_csv in fs_csv ]
crs = [ csv.reader(fd_csv, delimiter=',') for fd_csv in fds_csv ]
times = np.zeros((tot_nRows - 1, len(fds_csv)))
vals = np.zeros((tot_nRows - 1, len(fds_csv)))
for i, cr in enumerate(crs):
cr.next() # skip header line
for j, row in enumerate(cr):
t,y = map(float, row)
if maxtime != DEFAULT_MAXTIME:
# Assume default 0-100 time in all input files for now
t = (t / 100.0) * maxtime
times[j,i] = t
vals[j,i] = y
# XXX: For now assume same time spacing in all CSV files
for i, row in enumerate(times):
fd_sto.write(str(row[0]))
for val in vals[i]:
fd_sto.write("\t" + str(val))
fd_sto.write("\n");
for fd_csv in fds_csv:
fd_csv.close()
fd_sto.close()
if __name__ == '__main__':
main()
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