From d4bb265c37526aa0b5dacca745e70636f68d78cc Mon Sep 17 00:00:00 2001 From: sebastianp Date: Tue, 1 Dec 2015 11:12:45 +0100 Subject: [PATCH 1/2] first time commiting, please rectify and tell me what is wrong. --- pylot/core/util/utils.py | 496 +++++++++++++++++++++------------------ 1 file changed, 266 insertions(+), 230 deletions(-) diff --git a/pylot/core/util/utils.py b/pylot/core/util/utils.py index 2d3b0e8b..fca9d48e 100644 --- a/pylot/core/util/utils.py +++ b/pylot/core/util/utils.py @@ -11,140 +11,70 @@ import numpy as np from obspy.core import UTCDateTime import obspy.core.event as ope -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) - - - -def fnConstructor(s): - 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 getLogin(): - return pwd.getpwuid(os.getuid())[0] - - -def getHash(time): +def createArrival(pickresID, cinfo, phase, azimuth=None, dist=None): ''' - :param time: time object for which a hash should be calculated - :type time: :class: `~obspy.core.utcdatetime.UTCDateTime` object - :return: str + createArrival - function to create an Obspy Arrival + :param pickresID: Resource identifier of the created pick + :type pickresID: :class: `~obspy.core.event.ResourceIdentifier` object + + # eventnum is no input for this function + :param eventnum: human-readable event identifier + :type eventnum: str + + :param cinfo: An ObsPy :class: `~obspy.core.event.CreationInfo` object + holding information on the creation of the returned object + :type cinfo: :class: `~obspy.core.event.CreationInfo` object + :param phase: name of the arrivals seismic phase + :type phase: str + + # also no input for this function + :param station: name of the station at which the seismic phase has been + picked + :type station: str + :param authority_id: name of the institution carrying out the processing + :type authority_id: str + + :param azimuth: azimuth between source and receiver + :type azimuth: float or int, optional + :param dist: distance between source and receiver + :type dist: float or int, optional + :return: An ObsPy :class: `~obspy.core.event.Arrival` object ''' - hg = hashlib.sha1() - hg.update(time.strftime('%Y-%m-%d %H:%M:%S.%f')) - return hg.hexdigest() - - -def getOwner(fn): - return pwd.getpwuid(os.stat(fn).st_uid).pw_name - - -def prepTimeAxis(stime, trace): - 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 + arrival = ope.Arrival() + arrival.creation_info = cinfo + arrival.pick_id = pickresID + arrival.phase = phase + if azimuth is not None: + arrival.azimuth = float(azimuth) if azimuth > -180 else azimuth + 360. #what about azimuth > 180? 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 demeanTrace(trace, window): - """ - returns the DATA where each trace is demean by the average value within - WINDOW - :param trace: waveform trace object - :type trace: `~obspy.core.stream.Trace` - :param inoise: range of indices of DATA within the WINDOW - :type window: tuple - :return: trace - :rtype: `~obspy.core.stream.Trace` - """ - trace.data -= trace.data[window].mean() - return trace - - -def getGlobalTimes(stream): - 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 + arrival.azimuth = azimuth + arrival.distance = dist + return arrival +def createAmplitude(pickID, amp, unit, category, cinfo): + ''' + :param pickID: + :param amp: + :param unit: + :param category: + :param cinfo: + :return: + ''' + amplitude = ope.Amplitude() + amplitude.creation_info = cinfo + amplitude.generic_amplitude = amp + amplitude.unit = ope.AmplitudeUnit(unit) + amplitude.type = ope.AmplitudeCategory(category) + amplitude.pick_id = pickID + return amplitude def createCreationInfo(agency_id=None, creation_time=None, author=None): + ''' + :param agency_id: + :param creation_time: + :param author: + :return: + ''' if author is None: author = getLogin() if creation_time is None: @@ -153,56 +83,6 @@ def createCreationInfo(agency_id=None, creation_time=None, author=None): creation_time=creation_time) -def createResourceID(timetohash, restype, authority_id=None, hrstr=None): - ''' - - :param timetohash: - :param restype: type of the resource, e.g. 'orig', 'earthquake' ... - :type restype: str - :param authority_id: name of the institution carrying out the processing - :type authority_id: str, optional - :return: - ''' - assert isinstance(timetohash, UTCDateTime), "'timetohash' is not an ObsPy" \ - "UTCDateTime object" - hid = getHash(timetohash) - 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 createOrigin(origintime, cinfo, latitude, longitude, depth): - ''' - createOrigin - function to create an ObsPy Origin - :param origintime: the origins time of occurence - :type origintime: :class: `~obspy.core.utcdatetime.UTCDateTime` object - :param latitude: latitude in decimal degree of the origins location - :type latitude: float - :param longitude: longitude in decimal degree of the origins location - :type longitude: float - :param depth: hypocentral depth of the origin - :type depth: float - :return: An ObsPy :class: `~obspy.core.event.Origin` object - ''' - - assert isinstance(origintime, UTCDateTime), "origintime has to be " \ - "a UTCDateTime object, but " \ - "actually is of type " \ - "'%s'" % type(origintime) - - origin = ope.Origin() - origin.time = origintime - origin.creation_info = cinfo - origin.latitude = latitude - origin.longitude = longitude - origin.depth = depth - return origin - - def createEvent(origintime, cinfo, originloc=None, etype=None, resID=None, authority_id=None): ''' @@ -247,14 +127,56 @@ def createEvent(origintime, cinfo, originloc=None, etype=None, resID=None, event.origins = [o] return event +def createMagnitude(originID, cinfo): + ''' + createMagnitude - function to create an ObsPy Magnitude object + :param originID: + :param cinfo: + :param authority_id: # is no input + :return: + ''' + magnitude = ope.Magnitude() + magnitude.creation_info = cinfo + magnitude.origin_id = originID + return magnitude + +def createOrigin(origintime, cinfo, latitude, longitude, depth): + ''' + createOrigin - function to create an ObsPy Origin + :param origintime: the origins time of occurence + :type origintime: :class: `~obspy.core.utcdatetime.UTCDateTime` object + # cinfo missing + :param latitude: latitude in decimal degree of the origins location + :type latitude: float + :param longitude: longitude in decimal degree of the origins location + :type longitude: float + :param depth: hypocentral depth of the origin + :type depth: float + :return: An ObsPy :class: `~obspy.core.event.Origin` object + ''' + + assert isinstance(origintime, UTCDateTime), "origintime has to be " \ + "a UTCDateTime object, but " \ + "actually is of type " \ + "'%s'" % type(origintime) + + origin = ope.Origin() + origin.time = origintime + origin.creation_info = cinfo + origin.latitude = latitude + origin.longitude = longitude + origin.depth = depth + return origin def createPick(origintime, picknum, picktime, eventnum, cinfo, phase, station, wfseedstr, authority_id): ''' createPick - function to create an ObsPy Pick + # origintime missing :param picknum: number of the created pick :type picknum: int + # picktime missing :param eventnum: human-readable event identifier :type eventnum: str :param cinfo: An ObsPy :class: `~obspy.core.event.CreationInfo` object @@ -282,61 +204,175 @@ def createPick(origintime, picknum, picktime, eventnum, cinfo, phase, station, pick.waveform_id = ope.ResourceIdentifier(id=wfseedstr, prefix='file:/') return pick - -def createArrival(pickresID, cinfo, phase, azimuth=None, dist=None): +def createResourceID(timetohash, restype, authority_id=None, hrstr=None): ''' - createArrival - function to create an Obspy Arrival - :param pickresID: Resource identifier of the created pick - :type pickresID: :class: `~obspy.core.event.ResourceIdentifier` object - :param eventnum: human-readable event identifier - :type eventnum: str - :param cinfo: An ObsPy :class: `~obspy.core.event.CreationInfo` object - holding information on the creation of the returned object - :type cinfo: :class: `~obspy.core.event.CreationInfo` object - :param phase: name of the arrivals seismic phase - :type phase: str - :param station: name of the station at which the seismic phase has been - picked - :type station: str + + :param timetohash: + # type (timetohas) missing + :param restype: type of the resource, e.g. 'orig', 'earthquake' ... + :type restype: str :param authority_id: name of the institution carrying out the processing - :type authority_id: str - :param azimuth: azimuth between source and receiver - :type azimuth: float or int, optional - :param dist: distance between source and receiver - :type dist: float or int, optional - :return: An ObsPy :class: `~obspy.core.event.Arrival` object - ''' - arrival = ope.Arrival() - arrival.creation_info = cinfo - arrival.pick_id = pickresID - arrival.phase = phase - if azimuth is not None: - arrival.azimuth = float(azimuth) if azimuth > -180 else azimuth + 360. - else: - arrival.azimuth = azimuth - arrival.distance = dist - return arrival - - -def createMagnitude(originID, cinfo): - ''' - createMagnitude - function to create an ObsPy Magnitude object - :param originID: - :param cinfo: - :param authority_id: + :type authority_id: str, optional + # hrstr missing :return: ''' - magnitude = ope.Magnitude() - magnitude.creation_info = cinfo - magnitude.origin_id = originID - return magnitude + assert isinstance(timetohash, UTCDateTime), "'timetohash' is not an ObsPy" \ + "UTCDateTime object" + hid = getHash(timetohash) + 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): + """ + returns the DATA where each trace is demean by the average value within + WINDOW + :param trace: waveform trace object + :type trace: `~obspy.core.stream.Trace` + :param inoise: range of indices of DATA within the WINDOW # not used + # param (window) mising + :type window: tuple + :return: trace + :rtype: `~obspy.core.stream.Trace` + """ + trace.data -= trace.data[window].mean() + return trace -def createAmplitude(pickID, amp, unit, category, cinfo): - amplitude = ope.Amplitude() - amplitude.creation_info = cinfo - amplitude.generic_amplitude = amp - amplitude.unit = ope.AmplitudeUnit(unit) - amplitude.type = ope.AmplitudeCategory(category) - amplitude.pick_id = pickID - return amplitude +def fnConstructor(s): + ''' + + :param 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: + :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: + :return: + ''' + return pwd.getpwuid(os.stat(fn).st_uid).pw_name + +def prepTimeAxis(stime, trace): + ''' + + :param stime: + :param 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 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) + # no return command? + +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 \ No newline at end of file From a9d5f74a032bfa63ac167f5cc4c1d8772126a3ff Mon Sep 17 00:00:00 2001 From: sebastianp Date: Tue, 1 Dec 2015 12:30:24 +0100 Subject: [PATCH 2/2] minor change at createResourceID --- pylot/core/util/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pylot/core/util/utils.py b/pylot/core/util/utils.py index fca9d48e..6cfb86d7 100644 --- a/pylot/core/util/utils.py +++ b/pylot/core/util/utils.py @@ -213,7 +213,7 @@ def createResourceID(timetohash, restype, authority_id=None, hrstr=None): :type restype: str :param authority_id: name of the institution carrying out the processing :type authority_id: str, optional - # hrstr missing + :param hrstr: :return: ''' assert isinstance(timetohash, UTCDateTime), "'timetohash' is not an ObsPy" \