[seiscomp, scanloc] Install, add .gitignore
This commit is contained in:
764
bin/dump_picks
Executable file
764
bin/dump_picks
Executable file
@ -0,0 +1,764 @@
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#!/usr/bin/env seiscomp-python
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############################################################################
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# Copyright (C) 2016 by gempa GmbH #
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# #
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# All Rights Reserved. #
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# #
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# NOTICE: All information contained herein is, and remains #
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# the property of gempa GmbH and its suppliers, if any. The intellectual #
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# and technical concepts contained herein are proprietary to gempa GmbH #
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# and its suppliers. #
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# Dissemination of this information or reproduction of this material #
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# is strictly forbidden unless prior written permission is obtained #
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# from gempa GmbH. #
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# #
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# Author: Enrico Ellguth, Dirk Roessler #
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# Email: enrico.ellguth@gempa.de, roessler@gempa.de #
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############################################################################
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import datetime
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import os
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import sys
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from seiscomp import core, datamodel, io
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from seiscomp.client import Application
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from seiscomp import geo
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def str2time(timestring):
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"""
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Liberally accept many time string formats and convert them to a
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seiscomp.core.Time
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"""
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timestring = timestring.strip()
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for c in ["-", "/", ":", "T", "Z"]:
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timestring = timestring.replace(c, " ")
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timestring = timestring.split()
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assert 3 <= len(timestring) <= 6
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timestring.extend((6 - len(timestring)) * ["0"])
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timestring = " ".join(timestring)
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fmt = "%Y %m %d %H %M %S"
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if timestring.find(".") != -1:
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fmt += ".%f"
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t = core.Time()
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t.fromString(timestring, fmt)
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return t
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def utc():
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return datetime.datetime.now(datetime.timezone.utc).replace(tzinfo=None)
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class DumpPicks(Application):
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def __init__(self, argc, argv):
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Application.__init__(self, argc, argv)
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self.output = "-"
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self.type = "0"
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self.margin = [300]
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self.originID = None
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self.bbox = None
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self.noamp = False
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self.automatic = False
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self.manual = False
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self.checkInventory = False
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self.author = None
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self.hours = None
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self.minutes = None
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self.start = None
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self.end = None
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self.network = None
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self.station = None
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self.tmin = str2time("1970-01-01 00:00:00")
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self.tmax = str2time(str(utc()))
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self.delay = None
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self.setMessagingEnabled(False)
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self.setDatabaseEnabled(True, True)
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def createCommandLineDescription(self):
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self.commandline().addGroup("Dump")
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self.commandline().addStringOption(
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"Dump",
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"hours",
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"Start search hours before now considering object time, not creation time. "
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"If --minutes is given as well they will be added. "
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"If set, --time-window, --start, --end are ignored.",
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)
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self.commandline().addStringOption(
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"Dump",
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"minutes",
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"Start search minutes before now considering object time, not creation time. "
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"If --hours is given as well they will be added. "
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"If set, --time-window, --start, --end are ignored.",
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)
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self.commandline().addStringOption(
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"Dump",
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"start",
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"Start time of search until now considering object time, not creation time."
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" If set, --time-window is ignored.",
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)
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self.commandline().addStringOption(
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"Dump",
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"end",
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"End time of search considering object time, not creation time. If set, "
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"--time-window is ignored.",
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)
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self.commandline().addStringOption(
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"Dump",
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"time-window,t",
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"Specify time window to search picks and amplitudes by their time. Use one "
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"single string which must be enclosed by quotes in case of spaces in the "
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"time string. Times are of course in UTC and separated by a tilde '~'. "
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"Uses: 1970-01-01 00:00:00 to now if not set.",
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)
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self.commandline().addStringOption(
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"Dump",
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"maximum-delay",
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"Maximum allowed delay of picks or amplitudes, hence the difference between"
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" creation time and actual time value. Allows identifcation of picks found "
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"in real time.",
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)
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self.commandline().addStringOption(
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"Dump",
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"region,r",
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"Dump picks only from sensors in given region. Implies loading an "
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"inventory.\n"
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"Format: minLat,minLon,maxLat,maxLon \n"
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"Default: -90,-180,90,180 if not set.",
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)
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self.commandline().addOption(
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"Dump",
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"check-inventory,c",
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"Dump picks only when corresponding streams are found in inventory.",
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)
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self.commandline().addStringOption(
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"Dump",
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"origin,O",
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"Origin ID. Dump all "
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"picks associated with the origin that has the given origin ID.",
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)
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self.commandline().addOption("Dump", "manual,m", "Dump only manual picks.")
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self.commandline().addOption(
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"Dump", "automatic,a", "Dump only automatic picks."
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)
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self.commandline().addOption(
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"Dump",
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"no-amp,n",
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"Do not dump amplitudes from picks. "
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"Amplitudes are not required by scanloc.",
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)
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self.commandline().addStringOption(
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"Dump", "author", "Filter picks by the given author."
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)
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self.commandline().addStringOption(
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"Dump",
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"net-sta",
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"Filter picks and amplitudes by given network code or "
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"network and station code. Format: NET or NET.STA.",
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)
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self.commandline().addGroup("Output")
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self.commandline().addStringOption(
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"Output",
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"output,o",
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"Name of output file. If not given, all data is written to stdout.",
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)
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self.commandline().addStringOption(
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"Output",
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"type",
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f"Type of output format. Default: {self.type}.\n"
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"0 / scml: SCML containing all objects (default if option is not used)\n"
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"1 / streams: Time windows and streams for all picks like in scevtstreams\n"
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"2 / caps: Time windows and streams in capstool format\n"
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"3 / fdsnws: Time windows and streams in FDSN dataselect webservice POST \
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format\n"
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"Except for type 0, only picks are considered ignoring all other objects.",
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)
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self.commandline().addOption(
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"Output",
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"formatted,f",
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"Output formatted XML. Default is unformatted. Applies only for type 0.",
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)
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self.commandline().addStringOption(
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"Output",
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"margin",
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"Time margin applied around pick times along with --type = [1:]. Use 2 "
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"comma-separted values (before,after) for asymmetric margins, e.g. "
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f"--margin 120,300. Default: {self.margin[0]} s.",
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)
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def printUsage(self):
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print(
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f"""Usage:
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{os.path.basename(__file__)} [options]
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Read picks and amplitudes from database and dump them to a file or to standard output.\
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"""
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)
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Application.printUsage(self)
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print(
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f"""Examples:
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Dump all picks within a region and a period of time
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{os.path.basename(__file__)} -d localhost -t 2023-01-20T13:52:00~2023-01-20T13:57:00\
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-r "-10,-90,10,120"
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Search 24 hours before now for automatic picks from author "scautopick" with low delay \
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ignoring amplitudes
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{os.path.basename(__file__)} -d localhost --hours 24 -a -n --author "scautopick" \
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--maximum-delay 60
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Dump the streams of picks with time windows fetching the corresponding data from a \
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local CAPS server
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{os.path.basename(__file__)} -d localhost --type 2 --margin 60 | capstool \
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-H localhost -o data.mseed
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Dump the streams of picks with time windows fetching the corresponding data from a \
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local SDS archive
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{os.path.basename(__file__)} -d localhost --type 1 --margin 60 | scart -dsE -l - \
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/archive -o data.mseed
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"""
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)
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def init(self):
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if not Application.init(self):
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return False
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try:
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self.output = self.commandline().optionString("output")
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except RuntimeError:
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pass
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try:
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self.type = self.commandline().optionString("type")
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except RuntimeError:
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pass
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if self.type == "scml":
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self.type = "0"
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elif self.type == "streams":
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self.type = "1"
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elif self.type == "caps":
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self.type = "2"
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elif self.type == "fdsnws":
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self.type = "3"
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try:
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self.margin = self.commandline().optionString("margin").split(",")
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except RuntimeError:
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pass
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try:
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self.originID = self.commandline().optionString("origin")
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except RuntimeError:
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pass
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if not self.originID:
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try:
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boundingBox = self.commandline().optionString("region")
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self.bbox = boundingBox.split(",")
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if len(self.bbox) != 4:
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print(
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"Invalid region given, expected lat0,lon0,lat1,lon1",
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file=sys.stderr,
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)
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return False
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self.bbox[0] = str(geo.GeoCoordinate.normalizeLat(float(self.bbox[0])))
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self.bbox[1] = str(geo.GeoCoordinate.normalizeLon(float(self.bbox[1])))
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self.bbox[2] = str(geo.GeoCoordinate.normalizeLat(float(self.bbox[2])))
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self.bbox[3] = str(geo.GeoCoordinate.normalizeLon(float(self.bbox[3])))
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self.checkInventory = True
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except RuntimeError:
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boundingBox = "-90,-180,90,180"
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self.bbox = boundingBox.split(",")
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print("Settings", file=sys.stderr)
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print(
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f" + considered region: {self.bbox[0]} - {self.bbox[2]} deg North, "
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f"{self.bbox[1]} - {self.bbox[3]} deg East",
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file=sys.stderr,
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)
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try:
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self.hours = float(self.commandline().optionString("hours"))
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except RuntimeError:
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pass
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try:
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self.minutes = float(self.commandline().optionString("minutes"))
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except RuntimeError:
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pass
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try:
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self.start = self.commandline().optionString("start")
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except RuntimeError:
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pass
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try:
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self.end = self.commandline().optionString("end")
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except RuntimeError:
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pass
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delta = 0.0
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if self.hours:
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delta = self.hours * 60
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if self.minutes:
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delta += self.minutes
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if self.hours or self.minutes:
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print(
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" + time window set by hours and/or minutes option: ignoring all "
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"other time parameters",
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file=sys.stderr,
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)
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dt = datetime.timedelta(minutes=delta)
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self.tmin = str2time(str(utc() - dt))
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self.tmax = str2time(str(utc()))
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self.start = None
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self.end = None
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else:
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if self.start:
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print(
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" + time window set by start option: ignoring --time-window",
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file=sys.stderr,
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)
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self.tmin = str2time(self.start)
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if self.end:
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print(
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" + time window set by end option: ignoring --time-window",
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file=sys.stderr,
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)
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self.tmax = str2time(self.end)
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if not self.start and not self.end:
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try:
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self.tmin, self.tmax = map(
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str2time,
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self.commandline().optionString("time-window").split("~"),
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)
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print(
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" + time window set by time-window option", file=sys.stderr
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)
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except RuntimeError:
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print(
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" + no time window given exlicitly: Assuming defaults",
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file=sys.stderr,
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)
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print(
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f" + considered time window: {str(self.tmin)} - {str(self.tmax)}",
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file=sys.stderr,
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)
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else:
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print(
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" + searching for picks is based on originID, ignoring "
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"region and time window",
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file=sys.stderr,
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)
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try:
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self.delay = float(self.commandline().optionString("maximum-delay"))
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except RuntimeError:
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pass
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if not self.checkInventory:
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self.checkInventory = self.commandline().hasOption("check-inventory")
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if self.checkInventory:
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print(
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" + dumping only picks for streams found in inventory", file=sys.stderr
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)
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else:
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print(
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" + do not consider inventory information for dumping picks",
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file=sys.stderr,
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)
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if self.commandline().hasOption("no-amp"):
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self.noamp = True
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else:
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self.noamp = False
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if self.type != "0":
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self.noamp = True
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if self.noamp:
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print(" + dumping picks without amplitudes", file=sys.stderr)
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else:
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print(" + dumping picks with amplitudes", file=sys.stderr)
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if self.commandline().hasOption("manual"):
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self.manual = True
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print(" + dumping only manual objects", file=sys.stderr)
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else:
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self.manual = False
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print(" + considering also manual objects", file=sys.stderr)
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||||
if self.commandline().hasOption("automatic"):
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if not self.manual:
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self.automatic = True
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print(" + dumping only automatic picks", file=sys.stderr)
|
||||
else:
|
||||
print(
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||||
"EXIT - Script was started with competing options -a and -m",
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||||
file=sys.stderr,
|
||||
)
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||||
return False
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else:
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||||
self.automatic = False
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print(" + considering also automatic objects", file=sys.stderr)
|
||||
|
||||
try:
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||||
self.author = self.commandline().optionString("author")
|
||||
except RuntimeError:
|
||||
pass
|
||||
|
||||
networkStation = None
|
||||
try:
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||||
networkStation = self.commandline().optionString("net-sta")
|
||||
print(
|
||||
f" + filter objects by network / station code: {networkStation}",
|
||||
file=sys.stderr,
|
||||
)
|
||||
except RuntimeError:
|
||||
pass
|
||||
|
||||
if networkStation:
|
||||
try:
|
||||
self.network = networkStation.split(".")[0]
|
||||
except IndexError:
|
||||
print(
|
||||
f"Error in network code '{networkStation}': Use '--net-sta' with "
|
||||
"format NET or NET.STA",
|
||||
file=sys.stderr,
|
||||
)
|
||||
return False
|
||||
|
||||
try:
|
||||
self.station = networkStation.split(".")[1]
|
||||
except IndexError:
|
||||
print(
|
||||
f" + no station code given in '--net-sta {networkStation}' - "
|
||||
"using all stations from network",
|
||||
file=sys.stderr,
|
||||
)
|
||||
|
||||
return True
|
||||
|
||||
def run(self):
|
||||
db = self.database()
|
||||
|
||||
def _T(name):
|
||||
return db.convertColumnName(name)
|
||||
|
||||
def _time(time):
|
||||
return db.timeToString(time)
|
||||
|
||||
colLat, colLon = _T("latitude"), _T("longitude")
|
||||
|
||||
dbq = self.query()
|
||||
ep = datamodel.EventParameters()
|
||||
picks = []
|
||||
noAmps = 0
|
||||
|
||||
if self.originID:
|
||||
for p in dbq.getPicks(self.originID):
|
||||
picks.append(datamodel.Pick.Cast(p))
|
||||
|
||||
for p in picks:
|
||||
dbq.loadComments(p)
|
||||
ep.add(p)
|
||||
|
||||
if not self.noamp:
|
||||
for a in dbq.getAmplitudesForOrigin(self.originID):
|
||||
amp = datamodel.Amplitude.Cast(a)
|
||||
ep.add(amp)
|
||||
|
||||
else:
|
||||
fmt = "%Y-%m-%d %H:%M:%S"
|
||||
if self.checkInventory:
|
||||
q = (
|
||||
"select distinct(PPick.%s), Pick.* "
|
||||
"from PublicObject as PPick, Pick, Network, Station, SensorLocation "
|
||||
"where PPick._oid=Pick._oid and Network._oid=Station._parent_oid and "
|
||||
"Station._oid=SensorLocation._parent_oid and Station.%s >= %s and "
|
||||
"Station.%s <= %s and Station.%s >= %s and Station.%s <= %s and "
|
||||
"SensorLocation.%s=Pick.%s and SensorLocation.%s <= Pick.%s and "
|
||||
"(SensorLocation.%s is null or SensorLocation.%s > Pick.%s) and "
|
||||
"Station.%s=Pick.%s and Network.%s=Pick.%s and "
|
||||
"Pick.%s >= '%s' and Pick.%s < '%s'"
|
||||
""
|
||||
% (
|
||||
_T("publicID"),
|
||||
colLat,
|
||||
self.bbox[0],
|
||||
colLat,
|
||||
self.bbox[2],
|
||||
colLon,
|
||||
self.bbox[1],
|
||||
colLon,
|
||||
self.bbox[3],
|
||||
_T("code"),
|
||||
_T("waveformID_locationCode"),
|
||||
_T("start"),
|
||||
_T("time_value"),
|
||||
_T("end"),
|
||||
_T("end"),
|
||||
_T("time_value"),
|
||||
_T("code"),
|
||||
_T("waveformID_stationCode"),
|
||||
_T("code"),
|
||||
_T("waveformID_networkCode"),
|
||||
_T("time_value"),
|
||||
self.tmin.toString(fmt),
|
||||
_T("time_value"),
|
||||
self.tmax.toString(fmt),
|
||||
)
|
||||
)
|
||||
else:
|
||||
q = (
|
||||
"select distinct(PPick.%s), Pick.* "
|
||||
"from PublicObject as PPick, Pick "
|
||||
"where PPick._oid=Pick._oid and "
|
||||
"Pick.%s >= '%s' and Pick.%s < '%s'"
|
||||
""
|
||||
% (
|
||||
_T("publicID"),
|
||||
_T("time_value"),
|
||||
self.tmin.toString(fmt),
|
||||
_T("time_value"),
|
||||
self.tmax.toString(fmt),
|
||||
)
|
||||
)
|
||||
|
||||
if self.manual:
|
||||
q = q + f" and Pick.{_T('evaluationMode')} = 'manual' "
|
||||
|
||||
if self.automatic:
|
||||
q = q + f" and Pick.{_T('evaluationMode')} = 'automatic' "
|
||||
|
||||
if self.author:
|
||||
q = q + f" and Pick.{_T('creationInfo_author')} = '{self.author}' "
|
||||
|
||||
if self.network:
|
||||
q = q + f" and Pick.{_T('waveformID_networkCode')} = '{self.network}' "
|
||||
|
||||
if self.station:
|
||||
q = q + f" and Pick.{_T('waveformID_stationCode')} = '{self.station}' "
|
||||
|
||||
for p in dbq.getObjectIterator(q, datamodel.Pick.TypeInfo()):
|
||||
pick = datamodel.Pick.Cast(p)
|
||||
if (
|
||||
self.delay
|
||||
and float(pick.creationInfo().creationTime() - pick.time().value())
|
||||
> self.delay
|
||||
):
|
||||
continue
|
||||
picks.append(pick)
|
||||
|
||||
for p in picks:
|
||||
dbq.loadComments(p)
|
||||
ep.add(p)
|
||||
|
||||
if not self.noamp:
|
||||
if self.checkInventory:
|
||||
q = (
|
||||
"select distinct(PAmplitude.%s), Amplitude.* "
|
||||
"from PublicObject as PAmplitude, Amplitude, PublicObject \
|
||||
as PPick, Pick, Network, Station, SensorLocation "
|
||||
"where PAmplitude._oid=Amplitude._oid and "
|
||||
"PPick._oid=Pick._oid and Network._oid=Station._parent_oid and "
|
||||
"Station._oid=SensorLocation._parent_oid and Station.%s >= %s and "
|
||||
"Station.%s <= %s and Station.%s >= %s and Station.%s <= %s and "
|
||||
"SensorLocation.%s=Pick.%s and SensorLocation.%s <= Pick.%s and "
|
||||
"(SensorLocation.%s is null or SensorLocation.%s > Pick.%s) and "
|
||||
"Station.%s=Pick.%s and Network.%s=Pick.%s and "
|
||||
"Pick.%s >= '%s' and Pick.%s < '%s' and PPick.%s=Amplitude.%s"
|
||||
""
|
||||
% (
|
||||
_T("publicID"),
|
||||
colLat,
|
||||
self.bbox[0],
|
||||
colLat,
|
||||
self.bbox[2],
|
||||
colLon,
|
||||
self.bbox[1],
|
||||
colLon,
|
||||
self.bbox[3],
|
||||
_T("code"),
|
||||
_T("waveformID_locationCode"),
|
||||
_T("start"),
|
||||
_T("time_value"),
|
||||
_T("end"),
|
||||
_T("end"),
|
||||
_T("time_value"),
|
||||
_T("code"),
|
||||
_T("waveformID_stationCode"),
|
||||
_T("code"),
|
||||
_T("waveformID_networkCode"),
|
||||
_T("time_value"),
|
||||
self.tmin.toString(fmt),
|
||||
_T("time_value"),
|
||||
self.tmax.toString(fmt),
|
||||
_T("publicID"),
|
||||
_T("pickID"),
|
||||
)
|
||||
)
|
||||
else:
|
||||
q = (
|
||||
"select distinct(PAmplitude.%s), Amplitude.* "
|
||||
"from PublicObject as PAmplitude, Amplitude, PublicObject as PPick, Pick "
|
||||
"where PAmplitude._oid=Amplitude._oid and PPick._oid=Pick._oid and "
|
||||
"Pick.%s >= '%s' and Pick.%s < '%s' and PPick.%s=Amplitude.%s"
|
||||
""
|
||||
% (
|
||||
_T("publicID"),
|
||||
_T("time_value"),
|
||||
self.tmin.toString(fmt),
|
||||
_T("time_value"),
|
||||
self.tmax.toString(fmt),
|
||||
_T("publicID"),
|
||||
_T("pickID"),
|
||||
)
|
||||
)
|
||||
|
||||
if self.manual:
|
||||
q = q + f" and Pick.{_T('evaluationMode')} = 'manual' "
|
||||
if self.automatic:
|
||||
q = q + f" and Pick.{_T('evaluationMode')} = 'automatic' "
|
||||
|
||||
if self.author:
|
||||
q = q + f" and Pick.{_T('creationInfo_author')} = '{self.author}' "
|
||||
|
||||
if self.network:
|
||||
q = q + " and Pick.%s = '%s' " % (
|
||||
_T("waveformID_networkCode"),
|
||||
self.network,
|
||||
)
|
||||
|
||||
if self.station:
|
||||
q = q + " and Pick.%s = '%s' " % (
|
||||
_T("waveformID_stationCode"),
|
||||
self.station,
|
||||
)
|
||||
|
||||
for a in dbq.getObjectIterator(q, datamodel.Amplitude.TypeInfo()):
|
||||
amp = datamodel.Amplitude.Cast(a)
|
||||
if (
|
||||
self.delay
|
||||
and float(
|
||||
amp.creationInfo().creationTime()
|
||||
- amp.timeWindow().reference()
|
||||
)
|
||||
> self.delay
|
||||
):
|
||||
continue
|
||||
ep.add(amp)
|
||||
noAmps += 1
|
||||
|
||||
if self.type == "0":
|
||||
ar = io.XMLArchive()
|
||||
ar.create(self.output)
|
||||
ar.setFormattedOutput(self.commandline().hasOption("formatted"))
|
||||
ar.writeObject(ep)
|
||||
ar.close()
|
||||
elif self.type in ["1", "2", "3"]:
|
||||
if len(picks) == 0:
|
||||
print(
|
||||
"No picks are found and written",
|
||||
file=sys.stderr,
|
||||
)
|
||||
return False
|
||||
|
||||
# convert times to string depending on requested output format
|
||||
# time and line format
|
||||
if self.type == "2":
|
||||
timeFMT = "%Y,%m,%d,%H,%M,%S"
|
||||
lineFMT = "{0} {1} {2} {3} {4} {5}"
|
||||
elif self.type == "3":
|
||||
timeFMT = "%FT%T"
|
||||
lineFMT = "{2} {3} {4} {5} {0} {1}"
|
||||
else:
|
||||
timeFMT = "%F %T"
|
||||
lineFMT = "{0};{1};{2}.{3}.{4}.{5}"
|
||||
|
||||
lines = set()
|
||||
for pick in picks:
|
||||
net = pick.waveformID().networkCode()
|
||||
station = pick.waveformID().stationCode()
|
||||
loc = pick.waveformID().locationCode()
|
||||
channelGroup = f"{pick.waveformID().channelCode()[:2]}*"
|
||||
|
||||
# FDSNWS requires empty location to be encoded by 2 dashes
|
||||
if not loc and self.type == "3":
|
||||
loc = "--"
|
||||
|
||||
# add some marging to picks times
|
||||
minTime = pick.time().value() - core.TimeSpan(float(self.margin[0]))
|
||||
maxTime = pick.time().value() + core.TimeSpan(float(self.margin[-1]))
|
||||
minTime = minTime.toString(timeFMT)
|
||||
maxTime = maxTime.toString(timeFMT)
|
||||
lines.add(
|
||||
lineFMT.format(minTime, maxTime, net, station, loc, channelGroup)
|
||||
)
|
||||
|
||||
if self.output == "-":
|
||||
out = sys.stdout
|
||||
else:
|
||||
print(f"Output data to file: {self.output}", file=sys.stderr)
|
||||
try:
|
||||
out = open(self.output, "w", encoding="utf8")
|
||||
except Exception:
|
||||
print("Cannot create output file '{self.output}'", file=sys.stderr)
|
||||
return False
|
||||
|
||||
for line in sorted(lines):
|
||||
print(line, file=out)
|
||||
|
||||
if self.output != "-":
|
||||
out.close()
|
||||
else:
|
||||
print(
|
||||
f"Unspupported output format '{self.type}': No objects are written",
|
||||
file=sys.stderr,
|
||||
)
|
||||
return False
|
||||
|
||||
print(
|
||||
f"Saved: {len(picks):d} picks, {noAmps:d} amplitudes",
|
||||
file=sys.stderr,
|
||||
)
|
||||
return True
|
||||
|
||||
|
||||
def main(argv):
|
||||
app = DumpPicks(len(argv), argv)
|
||||
return app()
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
sys.exit(main(sys.argv))
|
||||
Reference in New Issue
Block a user