Mercurial > repos > stevecassidy > wrassp

annotate cut_timeseries.py @ 3:f188eb0b526d draft

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planemo upload commit 2d22bc12c66a3d1949d4bf4c84e7ce7c4610383c-dirty
author stevecassidy
date Wed, 14 Dec 2016 21:53:57 -0500
parents 6f4db0e89117
children 0026cd452d0e
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1 import csv
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2 import argparse
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6 def parser():
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7 parser = argparse.ArgumentParser(description="Cut data for a segment from a timeseries")
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8 parser.add_argument('--segment_list', required=True, action="store", type=str, help="File containing list of item URLs")
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9 parser.add_argument('--timeseries', required=True, action="store", type=str, help="time series data (comma separated file names)")
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10 parser.add_argument('--identifier', required=True, action="store", type=str, help="Time series dataset identifiers (comma separated)")
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11 parser.add_argument('--cutat', required=True, action="store", type=float, help="cut point 0-1")
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12 parser.add_argument('--output_path', required=True, action="store", type=str, help="Path to output file")
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13 return parser.parse_args()
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14
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16 def read_segment_list(filename):
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17 """Read an segment list from a file
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18 which should be a tabular formatted file
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19 with columns start, end, label, duration, identifier
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20 Return a dictionary with the 'identifier' field as keys
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21 and a dictionary of other values as the values.
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22 """
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23
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24 segments = []
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25 with open(filename) as fd:
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26 csvreader = csv.DictReader(fd, dialect='excel-tab')
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27 if 'identifier' not in csvreader.fieldnames:
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28 return None
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29
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30 for row in csvreader:
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31 segments.append(row)
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32
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33 return segments
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34
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35 def get_tsfile(ident, tsfiles):
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36 """Get the tsfile that matches the identifier """
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37
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38 for tsid, dsname in tsfiles:
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39 if ident in tsid:
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40 return dsname
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41
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42 return ''
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45 def cut(tsfiles, segfile, cutpoint):
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46 """Cut data from tsfile corresponding to the
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47 cutpoint (0-1) for the segment with the id
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48 in segs.
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49 Return... """
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50
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51 segments = read_segment_list(segfile)
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52
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53 headers = ['identifier', 'label']
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54 result = []
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55
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56 for seg in segments:
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57
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58 start = float(seg['start'])
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59 end = float(seg['end'])
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60 label = seg['label']
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61 ident = seg['identifier']
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62 tsfile = get_tsfile(ident, tsfiles)
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63
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64 if tsfile == '':
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65 continue
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66
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67 collect = []
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68 with open(tsfile, 'r') as fd:
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69 reader = csv.reader(fd, dialect=csv.excel_tab)
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70 for row in reader:
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71 if row[0] == 'time':
2
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72 tsheader = row
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73 elif float(row[0]) > start and float(row[0]) < end:
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74 collect.append(row)
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75
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76 # grab the row at the cut point(s)
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77 n = int(cutpoint * len(collect))
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78 row = [ident, label]
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79 row.extend(collect[n])
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80 result.append(row)
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81
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82 headers.extend(tsheader)
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83 return (headers, result)
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84
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85 if __name__=='__main__':
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86
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87 args = parser()
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88
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89 # get the list of timeseries files
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90 tsfiles = args.timeseries.split(',')
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91 tsidents = args.identifier.split(',')
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92
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93
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94 headers,rows = cut(zip(tsidents, tsfiles), args.segment_list, args.cutat)
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95
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96 with open(args.output_path, 'w') as out:
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97 writer = csv.writer(out)
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98 writer.writerow(headers)
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99 for row in rows:
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100 writer.writerow(row)