From ad8331cb1acd2bb29d282914a6f042af63e43a04 Mon Sep 17 00:00:00 2001 From: Tobias Klauser Date: Fri, 21 Dec 2012 17:31:10 +0100 Subject: csv2sto: update to merge multiple CSV files Still same time spacing is needed... --- scripts/csv2sto.py | 105 ++++++++++++++++++++++++++++++++++++----------------- 1 file 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__': -- cgit v1.2.3-54-g00ecf