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-rwxr-xr-xscripts/csv2sto.py105
1 files changed, 72 insertions, 33 deletions
diff --git a/scripts/csv2sto.py b/scripts/csv2sto.py
index 8e5300b..5515e84 100755
--- a/scripts/csv2sto.py
+++ b/scripts/csv2sto.py
@@ -3,19 +3,22 @@
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)
- -h show this help and exit""" % (DEFAULT_NAME, os.path.basename(sys.argv[0]))
+ -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:], "fh")
+ opts, args = getopt.getopt(sys.argv[1:], "fn:hT:")
except getopt.GetoptError, err:
print(str(err))
usage()
@@ -24,61 +27,97 @@ def main():
if len(args) < 2:
usage()
sys.exit(-1)
- elif len(args) > 2:
- print "Merging CSV files currently not supported, only %s considered" % args[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"
- f_csv = args[0]
+ 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 os.path.exists(f_csv):
- print "Error: CSV file %s does not exist" % f_csv
- sys.exit(-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
- fd = open(f_csv, 'r')
- nRows = nColumns = 0
- for line in fd:
- if nRows == 0:
- nCols = len(line.split(','))
- nRows += 1
- fd.close()
+ 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()
fd_sto = open(f_sto, 'w')
fd_sto.write(name + "\n")
- fd_sto.write("nRows=" + str(nRows) + "\n")
- fd_sto.write("nColumns=" + str(nColumns) + "\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")
print "Writing sto file %s with name %s" % (f_sto, name)
-
- colname = os.path.splitext(f_csv)[0]
- print "[+] Adding muscle %s..." % colname
- fd_sto.write("time\t" + colname + "\n")
-
- fd_csv = open(f_csv, 'r')
- cr = csv.reader(fd_csv, delimiter=',')
-
- for i, row in enumerate(cr):
- if i == 0:
- continue # skip header line
- fd_sto.write("\t".join(row) + "\n")
-
- fd_csv.close()
+ if maxtime != DEFAULT_MAXTIME:
+ print "Scaling to maxtime %f" % maxtime
+
+ 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__':