alphabetical sorting of functions and editing docstring
This commit is contained in:
sebastianp
parent
79829706be
commit
74794061f6
@ -10,165 +10,60 @@ import numpy as np
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from obspy.core import UTCDateTime
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from obspy.core import UTCDateTime
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import obspy.core.event as ope
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import obspy.core.event as ope
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def runProgram(cmd, parameter=None):
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def createAmplitude(pickID, amp, unit, category, cinfo):
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"""
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run an external program specified by cmd with parameters input returning the
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stdout output
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:param cmd: name of the command to run
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:type cmd: str
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:param parameter: filename of parameter file or parameter string
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:type parameter: str
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:return: stdout output
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:rtype: str
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"""
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if parameter:
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cmd.strip()
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cmd += ' %s 2>&1' % parameter
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output = subprocess.check_output('{} | tee /dev/stderr'.format(cmd),
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shell = True)
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def isSorted(iterable):
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return sorted(iterable) == iterable
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def fnConstructor(s):
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if type(s) is str:
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s = s.split(':')[-1]
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else:
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s = getHash(UTCDateTime())
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badchars = re.compile(r'[^A-Za-z0-9_. ]+|^\.|\.$|^ | $|^$')
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badsuffix = re.compile(r'(aux|com[1-9]|con|lpt[1-9]|prn)(\.|$)')
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fn = badchars.sub('_', s)
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if badsuffix.match(fn):
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fn = '_' + fn
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return fn
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def getLogin():
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return pwd.getpwuid(os.getuid())[0]
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def getHash(time):
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'''
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'''
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:param time: time object for which a hash should be calculated
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:type time: :class: `~obspy.core.utcdatetime.UTCDateTime` object
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:param pickID:
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:return: str
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:param amp:
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:param unit:
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:param category:
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:param cinfo:
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:return:
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'''
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'''
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hg = hashlib.sha1()
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amplitude = ope.Amplitude()
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hg.update(time.strftime('%Y-%m-%d %H:%M:%S.%f'))
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amplitude.creation_info = cinfo
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return hg.hexdigest()
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amplitude.generic_amplitude = amp
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amplitude.unit = ope.AmplitudeUnit(unit)
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amplitude.type = ope.AmplitudeCategory(category)
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amplitude.pick_id = pickID
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return amplitude
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def createArrival(pickresID, cinfo, phase, azimuth=None, dist=None):
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'''
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createArrival - function to create an Obspy Arrival
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def getOwner(fn):
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:param pickresID: Resource identifier of the created pick
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return pwd.getpwuid(os.stat(fn).st_uid).pw_name
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:type pickresID: :class: `~obspy.core.event.ResourceIdentifier` object
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:param cinfo: An ObsPy :class: `~obspy.core.event.CreationInfo` object
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def getPatternLine(fn, pattern):
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holding information on the creation of the returned object
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"""
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:type cinfo: :class: `~obspy.core.event.CreationInfo` object
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Takes a file name and a pattern string to search for in the file and
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:param phase: name of the arrivals seismic phase
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returns the first line which contains the pattern string otherwise None.
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:type phase: str
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:param azimuth: azimuth between source and receiver
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:param fn: file name
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:type azimuth: float or int, optional
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:type fn: str
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:param dist: distance between source and receiver
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:param pattern: pattern string to search for
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:type dist: float or int, optional
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:type pattern: str
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:return: An ObsPy :class: `~obspy.core.event.Arrival` object
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:return: the complete line containing pattern or None
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'''
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arrival = ope.Arrival()
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>>> getPatternLine('utils.py', 'python')
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arrival.creation_info = cinfo
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'#!/usr/bin/env python\\n'
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arrival.pick_id = pickresID
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>>> print(getPatternLine('version.py', 'palindrome'))
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arrival.phase = phase
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None
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if azimuth is not None:
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"""
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arrival.azimuth = float(azimuth) if azimuth > -180 else azimuth + 360.
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fobj = open(fn, 'r')
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for line in fobj.readlines():
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if pattern in line:
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fobj.close()
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return line
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return None
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def prepTimeAxis(stime, trace):
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nsamp = trace.stats.npts
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srate = trace.stats.sampling_rate
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tincr = trace.stats.delta
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etime = stime + nsamp / srate
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time_ax = np.arange(stime, etime, tincr)
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if len(time_ax) < nsamp:
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print 'elongate time axes by one datum'
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time_ax = np.arange(stime, etime + tincr, tincr)
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elif len(time_ax) > nsamp:
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print 'shorten time axes by one datum'
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time_ax = np.arange(stime, etime - tincr, tincr)
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if len(time_ax) != nsamp:
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raise ValueError('{0} samples of data \n '
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'{1} length of time vector \n'
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'delta: {2}'.format(nsamp, len(time_ax), tincr))
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return time_ax
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def scaleWFData(data, factor=None, components='all'):
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"""
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produce scaled waveforms from given waveform data and a scaling factor,
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waveform may be selected by their components name
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:param data: waveform data to be scaled
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:type data: `~obspy.core.stream.Stream` object
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:param factor: scaling factor
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:type factor: float
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:param components: components labels for the traces in data to be scaled by
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the scaling factor (optional, default: 'all')
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:type components: tuple
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:return: scaled waveform data
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:rtype: `~obspy.core.stream.Stream` object
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"""
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if components is not 'all':
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for comp in components:
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if factor is None:
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max_val = np.max(np.abs(data.select(component=comp)[0].data))
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data.select(component=comp)[0].data /= 2 * max_val
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else:
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data.select(component=comp)[0].data /= 2 * factor
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else:
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else:
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for tr in data:
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arrival.azimuth = azimuth
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if factor is None:
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arrival.distance = dist
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max_val = float(np.max(np.abs(tr.data)))
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return arrival
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tr.data /= 2 * max_val
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else:
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tr.data /= 2 * factor
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return data
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def demeanTrace(trace, window):
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"""
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returns the DATA where each trace is demean by the average value within
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WINDOW
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:param trace: waveform trace object
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:type trace: `~obspy.core.stream.Trace`
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:param inoise: range of indices of DATA within the WINDOW
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:type window: tuple
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:return: trace
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:rtype: `~obspy.core.stream.Trace`
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"""
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trace.data -= trace.data[window].mean()
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return trace
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def getGlobalTimes(stream):
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min_start = UTCDateTime()
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max_end = None
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for trace in stream:
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if trace.stats.starttime < min_start:
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min_start = trace.stats.starttime
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if max_end is None or trace.stats.endtime > max_end:
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max_end = trace.stats.endtime
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return min_start, max_end
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def createCreationInfo(agency_id=None, creation_time=None, author=None):
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def createCreationInfo(agency_id=None, creation_time=None, author=None):
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'''
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:param agency_id:
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:param creation_time:
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:param author:
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:return:
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'''
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if author is None:
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if author is None:
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author = getLogin()
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author = getLogin()
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if creation_time is None:
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if creation_time is None:
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@ -176,57 +71,6 @@ def createCreationInfo(agency_id=None, creation_time=None, author=None):
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return ope.CreationInfo(agency_id=agency_id, author=author,
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return ope.CreationInfo(agency_id=agency_id, author=author,
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creation_time=creation_time)
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creation_time=creation_time)
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def createResourceID(timetohash, restype, authority_id=None, hrstr=None):
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'''
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:param timetohash:
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:param restype: type of the resource, e.g. 'orig', 'earthquake' ...
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:type restype: str
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:param authority_id: name of the institution carrying out the processing
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:type authority_id: str, optional
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:return:
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'''
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assert isinstance(timetohash, UTCDateTime), "'timetohash' is not an ObsPy" \
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"UTCDateTime object"
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hid = getHash(timetohash)
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if hrstr is None:
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resID = ope.ResourceIdentifier(restype + '/' + hid[0:6])
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else:
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resID = ope.ResourceIdentifier(restype + '/' + hrstr + '_' + hid[0:6])
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if authority_id is not None:
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resID.convertIDToQuakeMLURI(authority_id=authority_id)
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return resID
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def createOrigin(origintime, cinfo, latitude, longitude, depth):
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'''
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createOrigin - function to create an ObsPy Origin
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:param origintime: the origins time of occurence
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:type origintime: :class: `~obspy.core.utcdatetime.UTCDateTime` object
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:param latitude: latitude in decimal degree of the origins location
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:type latitude: float
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:param longitude: longitude in decimal degree of the origins location
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:type longitude: float
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:param depth: hypocentral depth of the origin
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:type depth: float
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:return: An ObsPy :class: `~obspy.core.event.Origin` object
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'''
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assert isinstance(origintime, UTCDateTime), "origintime has to be " \
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"a UTCDateTime object, but " \
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"actually is of type " \
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"'%s'" % type(origintime)
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origin = ope.Origin()
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origin.time = origintime
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origin.creation_info = cinfo
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origin.latitude = latitude
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origin.longitude = longitude
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origin.depth = depth
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return origin
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def createEvent(origintime, cinfo, originloc=None, etype=None, resID=None,
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def createEvent(origintime, cinfo, originloc=None, etype=None, resID=None,
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authority_id=None):
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authority_id=None):
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'''
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'''
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@ -271,14 +115,60 @@ def createEvent(origintime, cinfo, originloc=None, etype=None, resID=None,
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event.origins = [o]
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event.origins = [o]
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return event
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return event
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def createMagnitude(originID, cinfo):
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'''
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createMagnitude - function to create an ObsPy Magnitude object
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:param originID:
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:type originID:
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:param cinfo:
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:type cinfo:
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:return:
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'''
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magnitude = ope.Magnitude()
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magnitude.creation_info = cinfo
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magnitude.origin_id = originID
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return magnitude
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def createOrigin(origintime, cinfo, latitude, longitude, depth):
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'''
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createOrigin - function to create an ObsPy Origin
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:param origintime: the origins time of occurence
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:type origintime: :class: `~obspy.core.utcdatetime.UTCDateTime` object
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:param cinfo:
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:type cinfo:
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:param latitude: latitude in decimal degree of the origins location
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:type latitude: float
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:param longitude: longitude in decimal degree of the origins location
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:type longitude: float
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:param depth: hypocentral depth of the origin
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:type depth: float
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:return: An ObsPy :class: `~obspy.core.event.Origin` object
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'''
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assert isinstance(origintime, UTCDateTime), "origintime has to be " \
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"a UTCDateTime object, but " \
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"actually is of type " \
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"'%s'" % type(origintime)
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origin = ope.Origin()
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origin.time = origintime
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origin.creation_info = cinfo
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origin.latitude = latitude
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origin.longitude = longitude
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origin.depth = depth
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return origin
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def createPick(origintime, picknum, picktime, eventnum, cinfo, phase, station,
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def createPick(origintime, picknum, picktime, eventnum, cinfo, phase, station,
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wfseedstr, authority_id):
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wfseedstr, authority_id):
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'''
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'''
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createPick - function to create an ObsPy Pick
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createPick - function to create an ObsPy Pick
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:param origintime:
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:type origintime:
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:param picknum: number of the created pick
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:param picknum: number of the created pick
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:type picknum: int
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:type picknum: int
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:param picktime:
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:type picktime:
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:param eventnum: human-readable event identifier
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:param eventnum: human-readable event identifier
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:type eventnum: str
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:type eventnum: str
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:param cinfo: An ObsPy :class: `~obspy.core.event.CreationInfo` object
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:param cinfo: An ObsPy :class: `~obspy.core.event.CreationInfo` object
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@ -306,64 +196,43 @@ def createPick(origintime, picknum, picktime, eventnum, cinfo, phase, station,
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pick.waveform_id = ope.ResourceIdentifier(id=wfseedstr, prefix='file:/')
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pick.waveform_id = ope.ResourceIdentifier(id=wfseedstr, prefix='file:/')
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return pick
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return pick
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def createResourceID(timetohash, restype, authority_id=None, hrstr=None):
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def createArrival(pickresID, cinfo, phase, azimuth=None, dist=None):
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'''
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'''
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createArrival - function to create an Obspy Arrival
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:param pickresID: Resource identifier of the created pick
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:param timetohash:
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:type pickresID: :class: `~obspy.core.event.ResourceIdentifier` object
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:type timetohash
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:param eventnum: human-readable event identifier
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:param restype: type of the resource, e.g. 'orig', 'earthquake' ...
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:type eventnum: str
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:type restype: str
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:param cinfo: An ObsPy :class: `~obspy.core.event.CreationInfo` object
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holding information on the creation of the returned object
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:type cinfo: :class: `~obspy.core.event.CreationInfo` object
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:param phase: name of the arrivals seismic phase
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:type phase: str
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:param station: name of the station at which the seismic phase has been
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picked
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:type station: str
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:param authority_id: name of the institution carrying out the processing
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:param authority_id: name of the institution carrying out the processing
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:type authority_id: str
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:type authority_id: str, optional
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:param azimuth: azimuth between source and receiver
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:param hrstr:
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:type azimuth: float or int, optional
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:type hrstr:
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:param dist: distance between source and receiver
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:type dist: float or int, optional
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:return: An ObsPy :class: `~obspy.core.event.Arrival` object
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'''
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arrival = ope.Arrival()
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arrival.creation_info = cinfo
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arrival.pick_id = pickresID
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arrival.phase = phase
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if azimuth is not None:
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arrival.azimuth = float(azimuth) if azimuth > -180 else azimuth + 360.
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else:
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arrival.azimuth = azimuth
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arrival.distance = dist
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return arrival
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def createMagnitude(originID, cinfo):
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'''
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createMagnitude - function to create an ObsPy Magnitude object
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:param originID:
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:param cinfo:
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:param authority_id:
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:return:
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:return:
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'''
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'''
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magnitude = ope.Magnitude()
|
assert isinstance(timetohash, UTCDateTime), "'timetohash' is not an ObsPy" \
|
||||||
magnitude.creation_info = cinfo
|
"UTCDateTime object"
|
||||||
magnitude.origin_id = originID
|
hid = getHash(timetohash)
|
||||||
return magnitude
|
if hrstr is None:
|
||||||
|
resID = ope.ResourceIdentifier(restype + '/' + hid[0:6])
|
||||||
|
else:
|
||||||
|
resID = ope.ResourceIdentifier(restype + '/' + hrstr + '_' + hid[0:6])
|
||||||
|
if authority_id is not None:
|
||||||
|
resID.convertIDToQuakeMLURI(authority_id=authority_id)
|
||||||
|
return resID
|
||||||
|
|
||||||
|
def demeanTrace(trace, window):
|
||||||
def createAmplitude(pickID, amp, unit, category, cinfo):
|
"""
|
||||||
amplitude = ope.Amplitude()
|
returns the DATA where each trace is demean by the average value within
|
||||||
amplitude.creation_info = cinfo
|
WINDOW
|
||||||
amplitude.generic_amplitude = amp
|
:param trace: waveform trace object
|
||||||
amplitude.unit = ope.AmplitudeUnit(unit)
|
:type trace: `~obspy.core.stream.Trace`
|
||||||
amplitude.type = ope.AmplitudeCategory(category)
|
:param window:
|
||||||
amplitude.pick_id = pickID
|
:type window: tuple
|
||||||
return amplitude
|
:return: trace
|
||||||
|
:rtype: `~obspy.core.stream.Trace`
|
||||||
|
"""
|
||||||
|
trace.data -= trace.data[window].mean()
|
||||||
|
return trace
|
||||||
|
|
||||||
def findComboBoxIndex(combo_box, val):
|
def findComboBoxIndex(combo_box, val):
|
||||||
"""
|
"""
|
||||||
@ -372,11 +241,184 @@ def findComboBoxIndex(combo_box, val):
|
|||||||
:param combo_box: Combo box object.
|
:param combo_box: Combo box object.
|
||||||
:type combo_box: QComboBox
|
:type combo_box: QComboBox
|
||||||
:param val: Name of a combo box to search for.
|
:param val: Name of a combo box to search for.
|
||||||
|
:type val:
|
||||||
:return: index value of item with name val or 0
|
:return: index value of item with name val or 0
|
||||||
"""
|
"""
|
||||||
|
|
||||||
return combo_box.findText(val) if combo_box.findText(val) is not -1 else 0
|
return combo_box.findText(val) if combo_box.findText(val) is not -1 else 0
|
||||||
|
|
||||||
|
def fnConstructor(s):
|
||||||
|
'''
|
||||||
|
|
||||||
|
:param s:
|
||||||
|
:type s:
|
||||||
|
:return:
|
||||||
|
'''
|
||||||
|
if type(s) is str:
|
||||||
|
s = s.split(':')[-1]
|
||||||
|
else:
|
||||||
|
s = getHash(UTCDateTime())
|
||||||
|
|
||||||
|
badchars = re.compile(r'[^A-Za-z0-9_. ]+|^\.|\.$|^ | $|^$')
|
||||||
|
badsuffix = re.compile(r'(aux|com[1-9]|con|lpt[1-9]|prn)(\.|$)')
|
||||||
|
|
||||||
|
fn = badchars.sub('_', s)
|
||||||
|
|
||||||
|
if badsuffix.match(fn):
|
||||||
|
fn = '_' + fn
|
||||||
|
return fn
|
||||||
|
|
||||||
|
def getGlobalTimes(stream):
|
||||||
|
'''
|
||||||
|
|
||||||
|
:param stream:
|
||||||
|
:type stream
|
||||||
|
:return:
|
||||||
|
'''
|
||||||
|
min_start = UTCDateTime()
|
||||||
|
max_end = None
|
||||||
|
for trace in stream:
|
||||||
|
if trace.stats.starttime < min_start:
|
||||||
|
min_start = trace.stats.starttime
|
||||||
|
if max_end is None or trace.stats.endtime > max_end:
|
||||||
|
max_end = trace.stats.endtime
|
||||||
|
return min_start, max_end
|
||||||
|
|
||||||
|
def getHash(time):
|
||||||
|
'''
|
||||||
|
:param time: time object for which a hash should be calculated
|
||||||
|
:type time: :class: `~obspy.core.utcdatetime.UTCDateTime` object
|
||||||
|
:return: str
|
||||||
|
'''
|
||||||
|
hg = hashlib.sha1()
|
||||||
|
hg.update(time.strftime('%Y-%m-%d %H:%M:%S.%f'))
|
||||||
|
return hg.hexdigest()
|
||||||
|
|
||||||
|
def getLogin():
|
||||||
|
'''
|
||||||
|
|
||||||
|
:return:
|
||||||
|
'''
|
||||||
|
return pwd.getpwuid(os.getuid())[0]
|
||||||
|
|
||||||
|
def getOwner(fn):
|
||||||
|
'''
|
||||||
|
|
||||||
|
:param fn:
|
||||||
|
:type fn:
|
||||||
|
:return:
|
||||||
|
'''
|
||||||
|
return pwd.getpwuid(os.stat(fn).st_uid).pw_name
|
||||||
|
|
||||||
|
def getPatternLine(fn, pattern):
|
||||||
|
"""
|
||||||
|
Takes a file name and a pattern string to search for in the file and
|
||||||
|
returns the first line which contains the pattern string otherwise None.
|
||||||
|
|
||||||
|
:param fn: file name
|
||||||
|
:type fn: str
|
||||||
|
:param pattern: pattern string to search for
|
||||||
|
:type pattern: str
|
||||||
|
:return: the complete line containing pattern or None
|
||||||
|
|
||||||
|
>>> getPatternLine('utils.py', 'python')
|
||||||
|
'#!/usr/bin/env python\\n'
|
||||||
|
>>> print(getPatternLine('version.py', 'palindrome'))
|
||||||
|
None
|
||||||
|
"""
|
||||||
|
fobj = open(fn, 'r')
|
||||||
|
for line in fobj.readlines():
|
||||||
|
if pattern in line:
|
||||||
|
fobj.close()
|
||||||
|
return line
|
||||||
|
|
||||||
|
return None
|
||||||
|
|
||||||
|
def isSorted(iterable):
|
||||||
|
'''
|
||||||
|
|
||||||
|
:param iterable:
|
||||||
|
:type iterable:
|
||||||
|
:return:
|
||||||
|
'''
|
||||||
|
return sorted(iterable) == iterable
|
||||||
|
|
||||||
|
def prepTimeAxis(stime, trace):
|
||||||
|
'''
|
||||||
|
|
||||||
|
:param stime:
|
||||||
|
:type stime:
|
||||||
|
:param trace:
|
||||||
|
:type trace:
|
||||||
|
:return:
|
||||||
|
'''
|
||||||
|
nsamp = trace.stats.npts
|
||||||
|
srate = trace.stats.sampling_rate
|
||||||
|
tincr = trace.stats.delta
|
||||||
|
etime = stime + nsamp / srate
|
||||||
|
time_ax = np.arange(stime, etime, tincr)
|
||||||
|
if len(time_ax) < nsamp:
|
||||||
|
print 'elongate time axes by one datum'
|
||||||
|
time_ax = np.arange(stime, etime + tincr, tincr)
|
||||||
|
elif len(time_ax) > nsamp:
|
||||||
|
print 'shorten time axes by one datum'
|
||||||
|
time_ax = np.arange(stime, etime - tincr, tincr)
|
||||||
|
if len(time_ax) != nsamp:
|
||||||
|
raise ValueError('{0} samples of data \n '
|
||||||
|
'{1} length of time vector \n'
|
||||||
|
'delta: {2}'.format(nsamp, len(time_ax), tincr))
|
||||||
|
return time_ax
|
||||||
|
|
||||||
|
def scaleWFData(data, factor=None, components='all'):
|
||||||
|
"""
|
||||||
|
produce scaled waveforms from given waveform data and a scaling factor,
|
||||||
|
waveform may be selected by their components name
|
||||||
|
:param data: waveform data to be scaled
|
||||||
|
:type data: `~obspy.core.stream.Stream` object
|
||||||
|
:param factor: scaling factor
|
||||||
|
:type factor: float
|
||||||
|
:param components: components labels for the traces in data to be scaled by
|
||||||
|
the scaling factor (optional, default: 'all')
|
||||||
|
:type components: tuple
|
||||||
|
:return: scaled waveform data
|
||||||
|
:rtype: `~obspy.core.stream.Stream` object
|
||||||
|
"""
|
||||||
|
if components is not 'all':
|
||||||
|
for comp in components:
|
||||||
|
if factor is None:
|
||||||
|
max_val = np.max(np.abs(data.select(component=comp)[0].data))
|
||||||
|
data.select(component=comp)[0].data /= 2 * max_val
|
||||||
|
else:
|
||||||
|
data.select(component=comp)[0].data /= 2 * factor
|
||||||
|
else:
|
||||||
|
for tr in data:
|
||||||
|
if factor is None:
|
||||||
|
max_val = float(np.max(np.abs(tr.data)))
|
||||||
|
tr.data /= 2 * max_val
|
||||||
|
else:
|
||||||
|
tr.data /= 2 * factor
|
||||||
|
|
||||||
|
return data
|
||||||
|
|
||||||
|
def runProgram(cmd, parameter=None):
|
||||||
|
"""
|
||||||
|
run an external program specified by cmd with parameters input returning the
|
||||||
|
stdout output
|
||||||
|
|
||||||
|
:param cmd: name of the command to run
|
||||||
|
:type cmd: str
|
||||||
|
:param parameter: filename of parameter file or parameter string
|
||||||
|
:type parameter: str
|
||||||
|
:return: stdout output
|
||||||
|
:rtype: str
|
||||||
|
"""
|
||||||
|
|
||||||
|
if parameter:
|
||||||
|
cmd.strip()
|
||||||
|
cmd += ' %s 2>&1' % parameter
|
||||||
|
|
||||||
|
output = subprocess.check_output('{} | tee /dev/stderr'.format(cmd),
|
||||||
|
shell = True)
|
||||||
|
|
||||||
if __name__ == "__main__":
|
if __name__ == "__main__":
|
||||||
import doctest
|
import doctest
|
||||||
doctest.testmod()
|
doctest.testmod()
|
||||||
|
|||||||
Loading…
Reference in New Issue
Block a user