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Added removeSmallFamily.py, redpy.table.removeSmallFamilies(), and additional verbosity option in redpy.table.removeFamily()
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| # REDPy - Repeating Earthquake Detector in Python | ||
| # Copyright (C) 2016-2020 Alicia Hotovec-Ellis ([email protected]) | ||
| # Licensed under GNU GPLv3 (see LICENSE.txt) | ||
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| import redpy.config | ||
| import redpy.table | ||
| import argparse | ||
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| """ | ||
| Run this script to remove small families/clusters (i.e., families that have less than M members and are more than D days | ||
| old). Reclusters and remakes images when done. This module works by determining the families that need to be removed, | ||
| and then it passes those families to removeFamily.py. Note: Removing families from datasets with manny families and | ||
| repeaters may take a significant amount of time. | ||
| usage: removeSmallFamily.py [-h] [-v] [-c CONFIGFILE] [-m MINMEMBERS] [-d MAXDAYS] [-t SEEDTIME] | ||
| optional arguments: | ||
| -h, --help show this help message and exit | ||
| -v, --verbose increase written print statements | ||
| -m, --MINMEMBERS minimum family size to keep (default: 5) | ||
| -d, --MAXDAYS maximum age of a family (days) to keep; measured from first member in family | ||
| in other words: keep families less than or equal to d days old | ||
| (default: 0; i.e., removes all small families) | ||
| -t --SEEDTIME Time from which to compute families' ages (default: last trigger time UTC) | ||
| If a family started after the seedtime, it will be kept | ||
| -l --LIST Lists families to keep and remove, but does not actually modify anything. Automatically uses | ||
| verbose mode. | ||
| -c CONFIGFILE, --configfile CONFIGFILE | ||
| use configuration file named CONFIGFILE instead of | ||
| default settings.cfg | ||
| """ | ||
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| parser = argparse.ArgumentParser(description= | ||
| "Run this script to manually remove small families/clusters") | ||
| parser.add_argument("-v", "--verbose", action="count", default=0, | ||
| help="increase written print statements") | ||
| parser.add_argument("-c", "--configfile", | ||
| help="use configuration file named CONFIGFILE instead of default settings.cfg") | ||
| parser.add_argument("-m", "--minmembers", type=int, default=5, | ||
| help="minimum family size to keep") | ||
| parser.add_argument("-d", "--maxdays", type=int, default=0, | ||
| help="maximum age of a family to be saved (default: 0, i.e., removes every small family regardless of age") | ||
| parser.add_argument("-t", "--seedtime", default=False, | ||
| help="time from which to compute families' repose times (YYYY-MM-DDTHH:MM:SS) (deafult: last trigger time UTC)") | ||
| parser.add_argument("-l", "--list", action="store_true", default=False, | ||
| help="list families to keep and remove, but do not execute") | ||
| args = parser.parse_args() | ||
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| def main(args): | ||
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| if args.configfile: | ||
| opt = redpy.config.Options(args.configfile) | ||
| if args.verbose: print("Using config file: {0}".format(args.configfile)) | ||
| else: | ||
| opt = redpy.config.Options("settings.cfg") | ||
| if args.verbose: print("Using config file: settings.cfg") | ||
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| if args.verbose: print("Opening hdf5 table: {0}".format(opt.filename)) | ||
| h5file, rtable, otable, ttable, ctable, jtable, dtable, ftable = redpy.table.openTable(opt) | ||
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| # Check for MPL version mismatch | ||
| redpy.table.checkMPL(rtable, ftable, ttable, otable, dtable, opt) | ||
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| oldnClust = ftable.attrs.nClust | ||
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| # Determines which families to remove, sends to table.removeFamilies(), outputs number of families removed | ||
| cnums = redpy.table.removeSmallFamilies(rtable, ctable, dtable, ftable, ttable, args.minmembers, args.maxdays, | ||
| args.seedtime, opt, list_only=args.list, verbose=args.verbose) | ||
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| if len(cnums) > 0: | ||
| # Only update plots if there are families removed | ||
| if args.verbose: print("Creating plots...") | ||
| redpy.plotting.createPlots(rtable, ftable, ttable, ctable, otable, opt) | ||
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| if args.verbose: print("Cleaning up old .html & .png files...") | ||
| redpy.plotting.cleanHTML(oldnClust, ftable.attrs.nClust, opt) | ||
| else: | ||
| if args.verbose: print("No families removed. No plots to update...") | ||
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| if args.verbose: print("Closing table...") | ||
| h5file.close() | ||
| if args.verbose: print("Done") | ||
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| if __name__ == "__main__": | ||
| main(args) |