def get_event_filename(event, prefix): """ Helper function generating a descriptive event filename. :param event: The event object. :param prefix: A prefix for the file, denoting e.g. the event catalog. >>> from obspy import read_events >>> event = read_events()[0] >>> print get_event_filename(event, "GCMT") GCMT_event_KYRGYZSTAN-XINJIANG_BORDER_REG._Mag_4.4_2012-4-4-14.xml """ from obspy.geodetics import FlinnEngdahl mag = event.preferred_magnitude() or event.magnitudes[0] org = event.preferred_origin() or event.origins[0] # Get the flinn_engdahl region for a nice name. fe = FlinnEngdahl() region_name = fe.get_region(org.longitude, org.latitude) region_name = region_name.replace(" ", "_") # Replace commas, as some file systems cannot deal with them. region_name = region_name.replace(",", "") return "%s_event_%s_Mag_%.1f_%s-%s-%s-%s.xml" % \ (prefix, region_name, mag.mag, org.time.year, org.time.month, org.time.day, org.time.hour)
def main(argv=None): parser = ArgumentParser(prog='obspy-flinn-engdahl', description=__doc__.strip()) parser.add_argument('-V', '--version', action='version', version='%(prog)s ' + __version__) parser.add_argument('longitude', type=float, help='Longitude (in degrees) of point. Positive for ' 'East, negative for West.') parser.add_argument('latitude', type=float, help='Latitude (in degrees) of point. Positive for ' 'North, negative for South.') args = parser.parse_args(argv) flinn_engdahl = FlinnEngdahl() print(flinn_engdahl.get_region(args.longitude, args.latitude))
def setUp(self): self.flinnengdahl = FlinnEngdahl() self.samples_file = os.path.join( os.path.dirname(__file__), 'data', 'flinnengdahl.csv' )
class UtilFlinnEngdahlTestCase(unittest.TestCase): def setUp(self): self.flinnengdahl = FlinnEngdahl() self.samples_file = os.path.join( os.path.dirname(__file__), 'data', 'flinnengdahl.csv' ) def test_coordinates(self): with open(self.samples_file, 'r') as fh: for line in fh: longitude, latitude, checked_region = line.strip().split('\t') longitude = float(longitude) latitude = float(latitude) region = self.flinnengdahl.get_region(longitude, latitude) self.assertEqual( region, checked_region, msg="(%f, %f) got %s instead of %s" % ( longitude, latitude, region, checked_region ) ) def test_script(self): with open(self.samples_file, 'r') as fh: # Testing once is sufficient. line = fh.readline() longitude, latitude, checked_region = line.strip().split('\t') with CatchOutput() as out: obspy_flinnengdahl([longitude, latitude]) region = out.stdout.strip() self.assertEqual( region, checked_region.encode('utf-8'), msg='(%s, %s) got %s instead of %s' % ( longitude, latitude, region, checked_region ) )
def _read_ndk(filename, *args, **kwargs): # @UnusedVariable """ Reads an NDK file to a :class:`~obspy.core.event.Catalog` object. :param filename: File or file-like object in text mode. """ # Read the whole file at once. While an iterator would be more efficient # the largest NDK file out in the wild is 13.7 MB so it does not matter # much. if not hasattr(filename, "read"): # Check if it exists, otherwise assume its a string. try: with open(filename, "rt") as fh: data = fh.read() except: try: data = filename.decode() except: data = str(filename) data = data.strip() else: data = filename.read() if hasattr(data, "decode"): data = data.decode() # Create iterator that yields lines. def lines_iter(): prev_line = -1 while True: next_line = data.find("\n", prev_line + 1) if next_line < 0: break yield data[prev_line + 1: next_line] prev_line = next_line if len(data) > prev_line + 1: yield data[prev_line + 1:] # Use one Flinn Engdahl object for all region determinations. fe = FlinnEngdahl() cat = Catalog(resource_id=_get_resource_id("catalog", str(uuid.uuid4()))) # Loop over 5 lines at once. for _i, lines in enumerate(itertools.zip_longest(*[lines_iter()] * 5)): if None in lines: msg = "Skipped last %i lines. Not a multiple of 5 lines." % ( lines.count(None)) warnings.warn(msg, ObsPyNDKWarning) continue # Parse the lines to a human readable dictionary. try: record = _read_lines(*lines) except (ValueError, ObsPyNDKException): exc = traceback.format_exc() msg = ( "Could not parse event %i (faulty file?). Will be " "skipped. Lines of the event:\n" "\t%s\n" "%s") % (_i + 1, "\n\t".join(lines), exc) warnings.warn(msg, ObsPyNDKWarning) continue # Use one creation info for essentially every item. creation_info = CreationInfo( agency_id="GCMT", version=record["version_code"] ) # Use the ObsPy Flinn Engdahl region determiner as the region in the # NDK files is oftentimes trimmed. region = fe.get_region(record["centroid_longitude"], record["centroid_latitude"]) # Create an event object. event = Event( force_resource_id=False, event_type="earthquake", event_type_certainty="known", event_descriptions=[ EventDescription(text=region, type="Flinn-Engdahl region"), EventDescription(text=record["cmt_event_name"], type="earthquake name") ] ) # Assemble the time for the reference origin. try: time = _parse_date_time(record["date"], record["time"]) except ObsPyNDKException: msg = ("Invalid time in event %i. '%s' and '%s' cannot be " "assembled to a valid time. Event will be skipped.") % \ (_i + 1, record["date"], record["time"]) warnings.warn(msg, ObsPyNDKWarning) continue # Create two origins, one with the reference latitude/longitude and # one with the centroidal values. ref_origin = Origin( force_resource_id=False, time=time, longitude=record["hypo_lng"], latitude=record["hypo_lat"], # Convert to m. depth=record["hypo_depth_in_km"] * 1000.0, origin_type="hypocenter", comments=[Comment(text="Hypocenter catalog: %s" % record["hypocenter_reference_catalog"], force_resource_id=False)] ) ref_origin.comments[0].resource_id = _get_resource_id( record["cmt_event_name"], "comment", tag="ref_origin") ref_origin.resource_id = _get_resource_id(record["cmt_event_name"], "origin", tag="reforigin") cmt_origin = Origin( force_resource_id=False, longitude=record["centroid_longitude"], longitude_errors={ "uncertainty": record["centroid_longitude_error"]}, latitude=record["centroid_latitude"], latitude_errors={ "uncertainty": record["centroid_latitude_error"]}, # Convert to m. depth=record["centroid_depth_in_km"] * 1000.0, depth_errors={ "uncertainty": record["centroid_depth_in_km_error"] * 1000}, time=ref_origin["time"] + record["centroid_time"], time_errors={"uncertainty": record["centroid_time_error"]}, depth_type=record["type_of_centroid_depth"], origin_type="centroid", time_fixed=False, epicenter_fixed=False, creation_info=creation_info.copy() ) cmt_origin.resource_id = _get_resource_id(record["cmt_event_name"], "origin", tag="cmtorigin") event.origins = [ref_origin, cmt_origin] event.preferred_origin_id = cmt_origin.resource_id.id # Create the magnitude object. mag = Magnitude( force_resource_id=False, mag=round(record["Mw"], 2), magnitude_type="Mwc", origin_id=cmt_origin.resource_id, creation_info=creation_info.copy() ) mag.resource_id = _get_resource_id(record["cmt_event_name"], "magnitude", tag="moment_mag") event.magnitudes = [mag] event.preferred_magnitude_id = mag.resource_id.id # Add the reported mb, MS magnitudes as additional magnitude objects. event.magnitudes.append(Magnitude( force_resource_id=False, mag=record["mb"], magnitude_type="mb", comments=[Comment( force_resource_id=False, text="Reported magnitude in NDK file. Most likely 'mb'." )] )) event.magnitudes[-1].comments[-1].resource_id = _get_resource_id( record["cmt_event_name"], "comment", tag="mb_magnitude") event.magnitudes[-1].resource_id = _get_resource_id( record["cmt_event_name"], "magnitude", tag="mb") event.magnitudes.append(Magnitude( force_resource_id=False, mag=record["MS"], magnitude_type="MS", comments=[Comment( force_resource_id=False, text="Reported magnitude in NDK file. Most likely 'MS'." )] )) event.magnitudes[-1].comments[-1].resource_id = _get_resource_id( record["cmt_event_name"], "comment", tag="MS_magnitude") event.magnitudes[-1].resource_id = _get_resource_id( record["cmt_event_name"], "magnitude", tag="MS") # Take care of the moment tensor. tensor = Tensor( m_rr=record["m_rr"], m_rr_errors={"uncertainty": record["m_rr_error"]}, m_pp=record["m_pp"], m_pp_errors={"uncertainty": record["m_pp_error"]}, m_tt=record["m_tt"], m_tt_errors={"uncertainty": record["m_tt_error"]}, m_rt=record["m_rt"], m_rt_errors={"uncertainty": record["m_rt_error"]}, m_rp=record["m_rp"], m_rp_errors={"uncertainty": record["m_rp_error"]}, m_tp=record["m_tp"], m_tp_errors={"uncertainty": record["m_tp_error"]}, creation_info=creation_info.copy() ) mt = MomentTensor( force_resource_id=False, scalar_moment=record["scalar_moment"], tensor=tensor, data_used=[DataUsed(**i) for i in record["data_used"]], inversion_type=record["source_type"], source_time_function=SourceTimeFunction( type=record["moment_rate_type"], duration=record["moment_rate_duration"] ), derived_origin_id=cmt_origin.resource_id, creation_info=creation_info.copy() ) mt.resource_id = _get_resource_id(record["cmt_event_name"], "momenttensor") axis = [Axis(**i) for i in record["principal_axis"]] focmec = FocalMechanism( force_resource_id=False, moment_tensor=mt, principal_axes=PrincipalAxes( # The ordering is the same as for the IRIS SPUD service and # from a website of the Saint Louis University Earthquake # center so it should be correct. t_axis=axis[0], p_axis=axis[2], n_axis=axis[1] ), nodal_planes=NodalPlanes( nodal_plane_1=NodalPlane(**record["nodal_plane_1"]), nodal_plane_2=NodalPlane(**record["nodal_plane_2"]) ), comments=[ Comment(force_resource_id=False, text="CMT Analysis Type: %s" % record["cmt_type"].capitalize()), Comment(force_resource_id=False, text="CMT Timestamp: %s" % record["cmt_timestamp"])], creation_info=creation_info.copy() ) focmec.comments[0].resource_id = _get_resource_id( record["cmt_event_name"], "comment", tag="cmt_type") focmec.comments[1].resource_id = _get_resource_id( record["cmt_event_name"], "comment", tag="cmt_timestamp") focmec.resource_id = _get_resource_id(record["cmt_event_name"], "focal_mechanism") event.focal_mechanisms = [focmec] event.preferred_focal_mechanism_id = focmec.resource_id.id # Set at end to avoid duplicate resource id warning. event.resource_id = _get_resource_id(record["cmt_event_name"], "event") cat.append(event) if len(cat) == 0: msg = "No valid events found in NDK file." raise ObsPyNDKException(msg) return cat
def __init__(self): self.flinn_engdahl = FlinnEngdahl()
class Unpickler(object): """ De-serializes a mchedr string into an ObsPy Catalog object. """ def __init__(self): self.flinn_engdahl = FlinnEngdahl() def load(self, filename): """ Reads mchedr file into ObsPy catalog object. :type file: str :param file: File name to read. :rtype: :class:`~obspy.core.event.Catalog` :returns: ObsPy Catalog object. """ if not isinstance(filename, (str, native_str)): raise TypeError('File name must be a string.') self.filename = filename self.fh = open(filename, 'rb') return self._deserialize() def loads(self, string): """ Parses mchedr string into ObsPy catalog object. :type string: str :param string: QuakeML string to parse. :rtype: :class:`~obspy.core.event.Catalog` :returns: ObsPy Catalog object. """ self.fh = io.BytesIO(string) self.filename = None return self._deserialize() def _int(self, string): try: return int(string) except ValueError: return None def _int_unused(self, string): val = self._int(string) if val < 0: val = None return val def _int_zero(self, string): val = self._int(string) if val is None: val = 0 return val def _float(self, string): try: return float(string) except ValueError: return None def _float_unused(self, string): val = self._float(string) if val < 0: val = None return val def _float_with_format(self, string, format_string, scale=1): ndigits, ndec = map(int, format_string.split('.')) nint = ndigits - ndec val = self._float(string[0:nint] + '.' + string[nint:nint + ndec]) if val is not None: val *= scale return val def _store_uncertainty(self, error, value, scale=1): if not isinstance(error, QuantityError): raise TypeError("'error' is not a 'QuantityError'") if value is not None: error['uncertainty'] = value * scale def _coordinate_sign(self, type): if type == 'S' or type == 'W': return -1 else: return 1 def _tensor_code_sign(self, code): """ Converts tensor from 'x,y,z' system to 'r,t,p' and translates 'f' code to 'p' """ system = {'xx': ('tt', 1), 'yy': ('pp', 1), 'zz': ('rr', 1), 'xy': ('tp', -1), 'xz': ('rt', 1), 'yz': ('rp', -1), 'ff': ('pp', 1), 'rf': ('rp', 1), 'tf': ('tp', 1)} return system.get(code, (code, 1)) def _tensor_store(self, tensor, code, value, error): code, sign = self._tensor_code_sign(code) if code in ('rr', 'tt', 'pp', 'rt', 'rp', 'tp'): setattr(tensor, "m_%s" % code, value * sign) self._store_uncertainty(getattr(tensor, "m_%s_errors" % code), error) def _decode_fe_region_number(self, number): """ Converts Flinn-Engdahl region number to string. """ if not isinstance(number, int): number = int(number) return self.flinn_engdahl.get_region_by_number(number) def _to_rad(self, degrees): radians = np.pi * degrees / 180 return radians def _to_deg(self, radians): degrees = 180 * radians / np.pi return degrees def _spherical_to_cartesian(self, spherical_coords): length, azimuth, plunge = spherical_coords plunge_rad = self._to_rad(plunge) azimuth_rad = self._to_rad(azimuth) x = length * np.sin(plunge_rad) * np.cos(azimuth_rad) y = length * np.sin(plunge_rad) * np.sin(azimuth_rad) z = length * np.cos(plunge_rad) return (x, y, z) def _angle_between(self, u1, u2): """ Returns the angle in degrees between unit vectors 'u1' and 'u2': Source: https://stackoverflow.com/q/2827393 """ angle = np.arccos(np.dot(u1, u2)) if np.isnan(angle): if (u1 == u2).all(): angle = 0.0 else: angle = np.pi return round(self._to_deg(angle), 1) def _lat_err_to_deg(self, latitude_stderr): """ Convert latitude error from km to degrees using a simple formula """ if latitude_stderr is not None: return round(latitude_stderr / 111.1949, 4) else: return None def _lon_err_to_deg(self, longitude_stderr, latitude): """ Convert longitude error from km to degrees using a simple formula """ if longitude_stderr is not None and latitude is not None: return round(longitude_stderr / (111.1949 * math.cos(self._to_rad(latitude))), 4) else: return None def _parse_record_hy(self, line): """ Parses the 'hypocenter' record HY """ date = line[2:10] time = line[11:20] # unused: location_quality = line[20] latitude = self._float(line[21:27]) lat_type = line[27] longitude = self._float(line[29:36]) lon_type = line[36] depth = self._float(line[38:43]) # unused: depth_quality = line[43] standard_dev = self._float(line[44:48]) station_number = self._int(line[48:51]) # unused: version_flag = line[51] fe_region_number = line[52:55] fe_region_name = self._decode_fe_region_number(fe_region_number) source_code = line[55:60].strip() event = Event() # FIXME: a smarter way to define evid? evid = date + time res_id = '/'.join((res_id_prefix, 'event', evid)) event.resource_id = ResourceIdentifier(id=res_id) description = EventDescription( type='region name', text=fe_region_name) event.event_descriptions.append(description) description = EventDescription( type='Flinn-Engdahl region', text=fe_region_number) event.event_descriptions.append(description) origin = Origin() res_id = '/'.join((res_id_prefix, 'origin', evid)) origin.resource_id = ResourceIdentifier(id=res_id) origin.creation_info = CreationInfo() if source_code: origin.creation_info.agency_id = source_code else: origin.creation_info.agency_id = 'USGS-NEIC' res_id = '/'.join((res_id_prefix, 'earthmodel/ak135')) origin.earth_model_id = ResourceIdentifier(id=res_id) origin.time = UTCDateTime(date + time) origin.latitude = latitude * self._coordinate_sign(lat_type) origin.longitude = longitude * self._coordinate_sign(lon_type) origin.depth = depth * 1000 origin.depth_type = 'from location' origin.quality = OriginQuality() origin.quality.associated_station_count = station_number origin.quality.standard_error = standard_dev # associated_phase_count can be incremented in records 'P ' and 'S ' origin.quality.associated_phase_count = 0 # depth_phase_count can be incremented in record 'S ' origin.quality.depth_phase_count = 0 origin.origin_type = 'hypocenter' origin.region = fe_region_name event.origins.append(origin) return event def _parse_record_e(self, line, event): """ Parses the 'error and magnitude' record E """ orig_time_stderr = self._float(line[2:7]) latitude_stderr = self._float(line[8:14]) longitude_stderr = self._float(line[15:21]) depth_stderr = self._float(line[22:27]) mb_mag = self._float(line[28:31]) mb_nsta = self._int(line[32:35]) ms_mag = self._float(line[36:39]) ms_nsta = self._int(line[39:42]) mag1 = self._float(line[42:45]) mag1_type = line[45:47] mag1_source_code = line[47:51].strip() mag2 = self._float(line[51:54]) mag2_type = line[54:56] mag2_source_code = line[56:60].strip() evid = event.resource_id.id.split('/')[-1] origin = event.origins[0] self._store_uncertainty(origin.time_errors, orig_time_stderr) self._store_uncertainty(origin.latitude_errors, self._lat_err_to_deg(latitude_stderr)) self._store_uncertainty(origin.longitude_errors, self._lon_err_to_deg(longitude_stderr, origin.latitude)) self._store_uncertainty(origin.depth_errors, depth_stderr, scale=1000) if mb_mag is not None: mag = Magnitude() res_id = '/'.join((res_id_prefix, 'magnitude', evid, 'mb')) mag.resource_id = ResourceIdentifier(id=res_id) mag.creation_info = CreationInfo(agency_id='USGS-NEIC') mag.mag = mb_mag mag.magnitude_type = 'Mb' mag.station_count = mb_nsta mag.origin_id = origin.resource_id event.magnitudes.append(mag) if ms_mag is not None: mag = Magnitude() res_id = '/'.join((res_id_prefix, 'magnitude', evid, 'ms')) mag.resource_id = ResourceIdentifier(id=res_id) mag.creation_info = CreationInfo(agency_id='USGS-NEIC') mag.mag = ms_mag mag.magnitude_type = 'Ms' mag.station_count = ms_nsta mag.origin_id = origin.resource_id event.magnitudes.append(mag) if mag1 is not None: mag = Magnitude() mag1_id = mag1_type.lower() res_id = '/'.join((res_id_prefix, 'magnitude', evid, mag1_id)) mag.resource_id = ResourceIdentifier(id=res_id) mag.creation_info = CreationInfo(agency_id=mag1_source_code) mag.mag = mag1 mag.magnitude_type = mag1_type mag.origin_id = origin.resource_id event.magnitudes.append(mag) if mag2 is not None: mag = Magnitude() mag2_id = mag2_type.lower() if mag2_id == mag1_id: mag2_id += '2' res_id = '/'.join((res_id_prefix, 'magnitude', evid, mag2_id)) mag.resource_id = ResourceIdentifier(id=res_id) mag.creation_info = CreationInfo(agency_id=mag2_source_code) mag.mag = mag2 mag.magnitude_type = mag2_type mag.origin_id = origin.resource_id event.magnitudes.append(mag) def _parse_record_l(self, line, event): """ Parses the '90 percent error ellipse' record L """ origin = event.origins[0] semi_major_axis_azimuth = self._float(line[2:8]) if semi_major_axis_azimuth is None: return semi_major_axis_plunge = self._float(line[8:13]) semi_major_axis_length = self._float(line[13:21]) intermediate_axis_azimuth = self._float(line[21:27]) intermediate_axis_plunge = self._float(line[27:32]) # This is called "intermediate_axis_length", # but it is definitively a "semi_intermediate_axis_length", # since in most cases: # (intermediate_axis_length / 2) < semi_minor_axis_length intermediate_axis_length = self._float(line[32:40]) semi_minor_axis_azimuth = self._float(line[40:46]) semi_minor_axis_plunge = self._float(line[46:51]) semi_minor_axis_length = self._float(line[51:59]) if (semi_minor_axis_azimuth == semi_minor_axis_plunge == semi_minor_axis_length == 0): semi_minor_axis_azimuth = intermediate_axis_azimuth semi_minor_axis_plunge = intermediate_axis_plunge semi_minor_axis_length = intermediate_axis_length origin.depth_type = 'operator assigned' # FIXME: The following code needs to be double-checked! semi_major_axis_unit_vect = \ self._spherical_to_cartesian((1, semi_major_axis_azimuth, semi_major_axis_plunge)) semi_minor_axis_unit_vect = \ self._spherical_to_cartesian((1, semi_minor_axis_azimuth, semi_minor_axis_plunge)) major_axis_rotation = \ self._angle_between(semi_major_axis_unit_vect, semi_minor_axis_unit_vect) origin.origin_uncertainty = OriginUncertainty() origin.origin_uncertainty.preferred_description = \ 'confidence ellipsoid' origin.origin_uncertainty.confidence_level = 90 confidence_ellipsoid = ConfidenceEllipsoid() confidence_ellipsoid.semi_major_axis_length = \ semi_major_axis_length * 1000 confidence_ellipsoid.semi_minor_axis_length = \ semi_minor_axis_length * 1000 confidence_ellipsoid.semi_intermediate_axis_length = \ intermediate_axis_length * 1000 confidence_ellipsoid.major_axis_plunge = semi_major_axis_plunge confidence_ellipsoid.major_axis_azimuth = semi_major_axis_azimuth # We need to add 90 to match NEIC QuakeML format, # but I don't understand why... confidence_ellipsoid.major_axis_rotation = \ major_axis_rotation + 90 origin.origin_uncertainty.confidence_ellipsoid = confidence_ellipsoid def _parse_record_a(self, line, event): """ Parses the 'additional parameters' record A """ origin = event.origins[0] phase_number = self._int(line[2:6]) station_number = self._int(line[7:10]) gap = self._float(line[10:15]) # unused: official_mag = line[16:19] # unused: official_mag_type = line[19:21] # unused: official_mag_source_code = line[21:26] # unused: deaths_field_descriptor = line[27] # unused: dead_people = line[28:35] # unused: injuries_field_descriptor = line[35] # unused: injured_people = line[36:43] # unused: damaged_buildings_descriptor = line[43] # unused: damaged_buildings = line[44:51] # unused: event_quality_flag = line[51] origin.quality.used_phase_count = phase_number origin.quality.used_station_count = station_number origin.quality.azimuthal_gap = gap def _parse_record_c(self, line, event): """ Parses the 'general comment' record C """ try: comment = event.comments[0] comment.text += line[2:60] except IndexError: comment = Comment() comment.resource_id = ResourceIdentifier(prefix=res_id_prefix) event.comments.append(comment) comment.text = line[2:60] # strip non printable-characters comment.text = \ "".join(x for x in comment.text if x in s.printable) def _parse_record_ah(self, line, event): """ Parses the 'additional hypocenter' record AH """ date = line[2:10] time = line[11:20] # unused: hypocenter_quality = line[20] latitude = self._float(line[21:27]) lat_type = line[27] longitude = self._float(line[29:36]) lon_type = line[36] # unused: preliminary_flag = line[37] depth = self._float(line[38:43]) # unused: depth_quality = line[43] standard_dev = self._float_unused(line[44:48]) station_number = self._int_unused(line[48:51]) phase_number = self._int_unused(line[51:55]) source_code = line[56:60].strip() evid = event.resource_id.id.split('/')[-1] origin = Origin() res_id = '/'.join((res_id_prefix, 'origin', evid, source_code.lower())) origin.resource_id = ResourceIdentifier(id=res_id) origin.creation_info = CreationInfo(agency_id=source_code) origin.time = UTCDateTime(date + time) origin.latitude = latitude * self._coordinate_sign(lat_type) origin.longitude = longitude * self._coordinate_sign(lon_type) origin.depth = depth * 1000 origin.depth_type = 'from location' origin.quality = OriginQuality() origin.quality.standard_error = standard_dev origin.quality.used_station_count = station_number origin.quality.used_phase_count = phase_number origin.origin_type = 'hypocenter' event.origins.append(origin) def _parse_record_ae(self, line, event): """ Parses the 'additional hypocenter error and magnitude record' AE """ orig_time_stderr = self._float_unused(line[2:7]) latitude_stderr = self._float_unused(line[8:14]) longitude_stderr = self._float_unused(line[15:21]) depth_stderr = self._float_unused(line[22:27]) gap = self._float_unused(line[28:33]) mag1 = self._float(line[33:36]) mag1_type = line[36:38] mag2 = self._float(line[43:46]) mag2_type = line[46:48] evid = event.resource_id.id.split('/')[-1] # this record is to be associated to the latest origin origin = event.origins[-1] self._store_uncertainty(origin.time_errors, orig_time_stderr) self._store_uncertainty(origin.latitude_errors, self._lat_err_to_deg(latitude_stderr)) self._store_uncertainty(origin.longitude_errors, self._lon_err_to_deg(longitude_stderr, origin.latitude)) self._store_uncertainty(origin.depth_errors, depth_stderr, scale=1000) origin.quality.azimuthal_gap = gap if mag1 > 0: mag = Magnitude() mag1_id = mag1_type.lower() res_id = '/'.join((res_id_prefix, 'magnitude', evid, mag1_id)) mag.resource_id = ResourceIdentifier(id=res_id) mag.creation_info = CreationInfo( agency_id=origin.creation_info.agency_id) mag.mag = mag1 mag.magnitude_type = mag1_type mag.origin_id = origin.resource_id event.magnitudes.append(mag) if mag2 > 0: mag = Magnitude() mag2_id = mag2_type.lower() if mag2_id == mag1_id: mag2_id += '2' res_id = '/'.join((res_id_prefix, 'magnitude', evid, mag2_id)) mag.resource_id = ResourceIdentifier(id=res_id) mag.creation_info = CreationInfo( agency_id=origin.creation_info.agency_id) mag.mag = mag2 mag.magnitude_type = mag2_type mag.origin_id = origin.resource_id event.magnitudes.append(mag) def _parse_record_dp(self, line, event): """ Parses the 'source parameter data - primary' record Dp """ source_contributor = line[2:6].strip() computation_type = line[6] exponent = self._int_zero(line[7]) scale = math.pow(10, exponent) centroid_origin_time = line[8:14] + '.' + line[14] orig_time_stderr = line[15:17] if orig_time_stderr == 'FX': orig_time_stderr = 'Fixed' else: orig_time_stderr = \ self._float_with_format(orig_time_stderr, '2.1', scale) centroid_latitude = self._float_with_format(line[17:21], '4.2') lat_type = line[21] if centroid_latitude is not None: centroid_latitude *= self._coordinate_sign(lat_type) lat_stderr = line[22:25] if lat_stderr == 'FX': lat_stderr = 'Fixed' else: lat_stderr = self._float_with_format(lat_stderr, '3.2', scale) centroid_longitude = self._float_with_format(line[25:30], '5.2') lon_type = line[30] if centroid_longitude is not None: centroid_longitude *= self._coordinate_sign(lon_type) lon_stderr = line[31:34] if lon_stderr == 'FX': lon_stderr = 'Fixed' else: lon_stderr = self._float_with_format(lon_stderr, '3.2', scale) centroid_depth = self._float_with_format(line[34:38], '4.1') depth_stderr = line[38:40] if depth_stderr == 'FX' or depth_stderr == 'BD': depth_stderr = 'Fixed' else: depth_stderr = self._float_with_format(depth_stderr, '2.1', scale) station_number = self._int_zero(line[40:43]) component_number = self._int_zero(line[43:46]) station_number2 = self._int_zero(line[46:48]) component_number2 = self._int_zero(line[48:51]) # unused: half_duration = self._float_with_format(line[51:54], '3.1') moment = self._float_with_format(line[54:56], '2.1') moment_stderr = self._float_with_format(line[56:58], '2.1') moment_exponent = self._int(line[58:60]) if (moment is not None) and (moment_exponent is not None): moment *= math.pow(10, moment_exponent) if (moment_stderr is not None) and (moment_exponent is not None): moment_stderr *= math.pow(10, moment_exponent) evid = event.resource_id.id.split('/')[-1] # Create a new origin only if centroid time is defined: origin = None if centroid_origin_time.strip() != '.': origin = Origin() res_id = '/'.join((res_id_prefix, 'origin', evid, source_contributor.lower(), 'mw' + computation_type.lower())) origin.resource_id = ResourceIdentifier(id=res_id) origin.creation_info = \ CreationInfo(agency_id=source_contributor) date = event.origins[0].time.strftime('%Y%m%d') origin.time = UTCDateTime(date + centroid_origin_time) # Check if centroid time is on the next day: if origin.time < event.origins[0].time: origin.time += timedelta(days=1) self._store_uncertainty(origin.time_errors, orig_time_stderr) origin.latitude = centroid_latitude origin.longitude = centroid_longitude origin.depth = centroid_depth * 1000 if lat_stderr == 'Fixed' and lon_stderr == 'Fixed': origin.epicenter_fixed = True else: self._store_uncertainty(origin.latitude_errors, self._lat_err_to_deg(lat_stderr)) self._store_uncertainty(origin.longitude_errors, self._lon_err_to_deg(lon_stderr, origin.latitude)) if depth_stderr == 'Fixed': origin.depth_type = 'operator assigned' else: origin.depth_type = 'from location' self._store_uncertainty(origin.depth_errors, depth_stderr, scale=1000) quality = OriginQuality() quality.used_station_count = \ station_number + station_number2 quality.used_phase_count = \ component_number + component_number2 origin.quality = quality origin.origin_type = 'centroid' event.origins.append(origin) focal_mechanism = FocalMechanism() res_id = '/'.join((res_id_prefix, 'focalmechanism', evid, source_contributor.lower(), 'mw' + computation_type.lower())) focal_mechanism.resource_id = ResourceIdentifier(id=res_id) focal_mechanism.creation_info = \ CreationInfo(agency_id=source_contributor) moment_tensor = MomentTensor() if origin is not None: moment_tensor.derived_origin_id = origin.resource_id else: # this is required for QuakeML validation: res_id = '/'.join((res_id_prefix, 'no-origin')) moment_tensor.derived_origin_id = \ ResourceIdentifier(id=res_id) for mag in event.magnitudes: if mag.creation_info.agency_id == source_contributor: moment_tensor.moment_magnitude_id = mag.resource_id res_id = '/'.join((res_id_prefix, 'momenttensor', evid, source_contributor.lower(), 'mw' + computation_type.lower())) moment_tensor.resource_id = ResourceIdentifier(id=res_id) moment_tensor.scalar_moment = moment self._store_uncertainty(moment_tensor.scalar_moment_errors, moment_stderr) data_used = DataUsed() data_used.station_count = station_number + station_number2 data_used.component_count = component_number + component_number2 if computation_type == 'C': res_id = '/'.join((res_id_prefix, 'methodID=CMT')) focal_mechanism.method_id = ResourceIdentifier(id=res_id) # CMT algorithm uses long-period body waves, # very-long-period surface waves and # intermediate period surface waves (since 2004 # for shallow and intermediate-depth earthquakes # --Ekstrom et al., 2012) data_used.wave_type = 'combined' if computation_type == 'M': res_id = '/'.join((res_id_prefix, 'methodID=moment_tensor')) focal_mechanism.method_id = ResourceIdentifier(id=res_id) # FIXME: not sure which kind of data is used by # "moment tensor" algorithm. data_used.wave_type = 'unknown' elif computation_type == 'B': res_id = '/'.join((res_id_prefix, 'methodID=broadband_data')) focal_mechanism.method_id = ResourceIdentifier(id=res_id) # FIXME: is 'combined' correct here? data_used.wave_type = 'combined' elif computation_type == 'F': res_id = '/'.join((res_id_prefix, 'methodID=P-wave_first_motion')) focal_mechanism.method_id = ResourceIdentifier(id=res_id) data_used.wave_type = 'P waves' elif computation_type == 'S': res_id = '/'.join((res_id_prefix, 'methodID=scalar_moment')) focal_mechanism.method_id = ResourceIdentifier(id=res_id) # FIXME: not sure which kind of data is used # for scalar moment determination. data_used.wave_type = 'unknown' moment_tensor.data_used = [data_used] focal_mechanism.moment_tensor = moment_tensor event.focal_mechanisms.append(focal_mechanism) return focal_mechanism def _parse_record_dt(self, line, focal_mechanism): """ Parses the 'source parameter data - tensor' record Dt """ tensor = Tensor() exponent = self._int_zero(line[3:5]) scale = math.pow(10, exponent) for i in range(6, 51 + 1, 9): code = line[i:i + 2] value = self._float_with_format(line[i + 2:i + 6], '4.2', scale) error = self._float_with_format(line[i + 6:i + 9], '3.2', scale) self._tensor_store(tensor, code, value, error) focal_mechanism.moment_tensor.tensor = tensor def _parse_record_da(self, line, focal_mechanism): """ Parses the 'source parameter data - principal axes and nodal planes' record Da """ exponent = self._int_zero(line[3:5]) scale = math.pow(10, exponent) t_axis_len = self._float_with_format(line[5:9], '4.2', scale) t_axis_stderr = self._float_with_format(line[9:12], '3.2', scale) t_axis_plunge = self._int(line[12:14]) t_axis_azimuth = self._int(line[14:17]) n_axis_len = self._float_with_format(line[17:21], '4.2', scale) n_axis_stderr = self._float_with_format(line[21:24], '3.2', scale) n_axis_plunge = self._int(line[24:26]) n_axis_azimuth = self._int(line[26:29]) p_axis_len = self._float_with_format(line[29:33], '4.2', scale) p_axis_stderr = self._float_with_format(line[33:36], '3.2', scale) p_axis_plunge = self._int(line[36:38]) p_axis_azimuth = self._int(line[38:41]) np1_strike = self._int(line[42:45]) np1_dip = self._int(line[45:47]) np1_slip = self._int(line[47:51]) np2_strike = self._int(line[51:54]) np2_dip = self._int(line[54:56]) np2_slip = self._int(line[56:60]) t_axis = Axis() t_axis.length = t_axis_len self._store_uncertainty(t_axis.length_errors, t_axis_stderr) t_axis.plunge = t_axis_plunge t_axis.azimuth = t_axis_azimuth n_axis = Axis() n_axis.length = n_axis_len self._store_uncertainty(n_axis.length_errors, n_axis_stderr) n_axis.plunge = n_axis_plunge n_axis.azimuth = n_axis_azimuth p_axis = Axis() p_axis.length = p_axis_len self._store_uncertainty(p_axis.length_errors, p_axis_stderr) p_axis.plunge = p_axis_plunge p_axis.azimuth = p_axis_azimuth principal_axes = PrincipalAxes() principal_axes.t_axis = t_axis principal_axes.n_axis = n_axis principal_axes.p_axis = p_axis focal_mechanism.principal_axes = principal_axes nodal_plane_1 = NodalPlane() nodal_plane_1.strike = np1_strike nodal_plane_1.dip = np1_dip nodal_plane_1.rake = np1_slip nodal_plane_2 = NodalPlane() nodal_plane_2.strike = np2_strike nodal_plane_2.dip = np2_dip nodal_plane_2.rake = np2_slip nodal_planes = NodalPlanes() nodal_planes.nodal_plane_1 = nodal_plane_1 nodal_planes.nodal_plane_2 = nodal_plane_2 focal_mechanism.nodal_planes = nodal_planes def _parse_record_dc(self, line, focal_mechanism): """ Parses the 'source parameter data - comment' record Dc """ try: comment = focal_mechanism.comments[0] comment.text += line[2:60] except IndexError: comment = Comment() comment.resource_id = ResourceIdentifier(prefix=res_id_prefix) focal_mechanism.comments.append(comment) comment.text = line[2:60] def _parse_record_p(self, line, event): """ Parses the 'primary phase record' P The primary phase is the first phase of the reading, regardless its type. """ station = line[2:7].strip() phase = line[7:15] arrival_time = line[15:24] residual = self._float(line[25:30]) # unused: residual_flag = line[30] distance = self._float(line[32:38]) # degrees azimuth = self._float(line[39:44]) backazimuth = round(azimuth % -360 + 180, 1) mb_period = self._float(line[44:48]) mb_amplitude = self._float(line[48:55]) # nanometers mb_magnitude = self._float(line[56:59]) # unused: mb_usage_flag = line[59] origin = event.origins[0] evid = event.resource_id.id.split('/')[-1] waveform_id = WaveformStreamID() waveform_id.station_code = station # network_code is required for QuakeML validation waveform_id.network_code = ' ' station_string = \ waveform_id.get_seed_string()\ .replace(' ', '-').replace('.', '_').lower() prefix = '/'.join((res_id_prefix, 'waveformstream', evid, station_string)) waveform_id.resource_uri = ResourceIdentifier(prefix=prefix) pick = Pick() prefix = '/'.join((res_id_prefix, 'pick', evid, station_string)) pick.resource_id = ResourceIdentifier(prefix=prefix) date = origin.time.strftime('%Y%m%d') pick.time = UTCDateTime(date + arrival_time) # Check if pick is on the next day: if pick.time < origin.time: pick.time += timedelta(days=1) pick.waveform_id = waveform_id pick.backazimuth = backazimuth onset = phase[0] if onset == 'e': pick.onset = 'emergent' phase = phase[1:] elif onset == 'i': pick.onset = 'impulsive' phase = phase[1:] elif onset == 'q': pick.onset = 'questionable' phase = phase[1:] pick.phase_hint = phase.strip() event.picks.append(pick) if mb_amplitude is not None: amplitude = Amplitude() prefix = '/'.join((res_id_prefix, 'amp', evid, station_string)) amplitude.resource_id = ResourceIdentifier(prefix=prefix) amplitude.generic_amplitude = mb_amplitude * 1E-9 amplitude.unit = 'm' amplitude.period = mb_period amplitude.type = 'AB' amplitude.magnitude_hint = 'Mb' amplitude.pick_id = pick.resource_id amplitude.waveform_id = pick.waveform_id event.amplitudes.append(amplitude) station_magnitude = StationMagnitude() prefix = '/'.join((res_id_prefix, 'stationmagntiude', evid, station_string)) station_magnitude.resource_id = ResourceIdentifier(prefix=prefix) station_magnitude.origin_id = origin.resource_id station_magnitude.mag = mb_magnitude # station_magnitude.mag_errors['uncertainty'] = 0.0 station_magnitude.station_magnitude_type = 'Mb' station_magnitude.amplitude_id = amplitude.resource_id station_magnitude.waveform_id = pick.waveform_id res_id = '/'.join( (res_id_prefix, 'magnitude/generic/body_wave_magnitude')) station_magnitude.method_id = \ ResourceIdentifier(id=res_id) event.station_magnitudes.append(station_magnitude) arrival = Arrival() prefix = '/'.join((res_id_prefix, 'arrival', evid, station_string)) arrival.resource_id = ResourceIdentifier(prefix=prefix) arrival.pick_id = pick.resource_id arrival.phase = pick.phase_hint arrival.azimuth = azimuth arrival.distance = distance arrival.time_residual = residual res_id = '/'.join((res_id_prefix, 'earthmodel/ak135')) arrival.earth_model_id = ResourceIdentifier(id=res_id) origin.arrivals.append(arrival) origin.quality.minimum_distance = min( d for d in (arrival.distance, origin.quality.minimum_distance) if d is not None) origin.quality.maximum_distance = \ max(arrival.distance, origin.quality.minimum_distance) origin.quality.associated_phase_count += 1 return pick, arrival def _parse_record_m(self, line, event, pick): """ Parses the 'surface wave record' M """ # unused: Z_comp = line[7] z_period = self._float(line[9:13]) # note: according to the format documentation, # column 20 should be blank. However, it seems that # z_amplitude includes that column z_amplitude = self._float(line[13:21]) # micrometers # TODO: N_comp and E_comp seems to be never there msz_mag = line[49:52] ms_mag = self._float(line[53:56]) # unused: Ms_usage_flag = line[56] evid = event.resource_id.id.split('/')[-1] station_string = \ pick.waveform_id.get_seed_string()\ .replace(' ', '-').replace('.', '_').lower() amplitude = None if z_amplitude is not None: amplitude = Amplitude() prefix = '/'.join((res_id_prefix, 'amp', evid, station_string)) amplitude.resource_id = ResourceIdentifier(prefix=prefix) amplitude.generic_amplitude = z_amplitude * 1E-6 amplitude.unit = 'm' amplitude.period = z_period amplitude.type = 'AS' amplitude.magnitude_hint = 'Ms' amplitude.pick_id = pick.resource_id event.amplitudes.append(amplitude) if msz_mag is not None: station_magnitude = StationMagnitude() prefix = '/'.join((res_id_prefix, 'stationmagntiude', evid, station_string)) station_magnitude.resource_id = ResourceIdentifier(prefix=prefix) station_magnitude.origin_id = event.origins[0].resource_id station_magnitude.mag = ms_mag station_magnitude.station_magnitude_type = 'Ms' if amplitude is not None: station_magnitude.amplitude_id = amplitude.resource_id event.station_magnitudes.append(station_magnitude) def _parse_record_s(self, line, event, p_pick, p_arrival): """ Parses the 'secondary phases' record S Secondary phases are following phases of the reading, and can be P-type or S-type. """ arrivals = [] phase = line[7:15].strip() arrival_time = line[15:24] if phase: arrivals.append((phase, arrival_time)) phase = line[25:33].strip() arrival_time = line[33:42] if phase: arrivals.append((phase, arrival_time)) phase = line[43:51].strip() arrival_time = line[51:60] if phase: arrivals.append((phase, arrival_time)) evid = event.resource_id.id.split('/')[-1] station_string = \ p_pick.waveform_id.get_seed_string()\ .replace(' ', '-').replace('.', '_').lower() origin = event.origins[0] for phase, arrival_time in arrivals: if phase[0:2] == 'D=': # unused: depth = self._float(phase[2:7]) try: depth_usage_flag = phase[7] except IndexError: # usage flag is not defined depth_usage_flag = None # FIXME: I'm not sure that 'X' actually # means 'used' if depth_usage_flag == 'X': # FIXME: is this enough to say that # the event is constrained by depth phases? origin.depth_type = 'constrained by depth phases' origin.quality.depth_phase_count += 1 else: pick = Pick() prefix = '/'.join((res_id_prefix, 'pick', evid, station_string)) pick.resource_id = ResourceIdentifier(prefix=prefix) date = origin.time.strftime('%Y%m%d') pick.time = UTCDateTime(date + arrival_time) # Check if pick is on the next day: if pick.time < origin.time: pick.time += timedelta(days=1) pick.waveform_id = p_pick.waveform_id pick.backazimuth = p_pick.backazimuth onset = phase[0] if onset == 'e': pick.onset = 'emergent' phase = phase[1:] elif onset == 'i': pick.onset = 'impulsive' phase = phase[1:] elif onset == 'q': pick.onset = 'questionable' phase = phase[1:] pick.phase_hint = phase.strip() event.picks.append(pick) arrival = Arrival() prefix = '/'.join((res_id_prefix, 'arrival', evid, station_string)) arrival.resource_id = ResourceIdentifier(prefix=prefix) arrival.pick_id = pick.resource_id arrival.phase = pick.phase_hint arrival.azimuth = p_arrival.azimuth arrival.distance = p_arrival.distance origin.quality.associated_phase_count += 1 origin.arrivals.append(arrival) def _deserialize(self): catalog = Catalog() res_id = '/'.join((res_id_prefix, self.filename.replace(':', '/')))\ .replace('\\', '/').replace('//', '/') catalog.resource_id = ResourceIdentifier(id=res_id) catalog.description = 'Created from NEIC PDE mchedr format' catalog.comments = '' catalog.creation_info = CreationInfo(creation_time=UTCDateTime()) for line in self.fh.readlines(): # XXX: ugly, probably we should do everything in byte strings # here? Is the pde / mchedr format unicode aware? line = line.decode() record_id = line[0:2] if record_id == 'HY': event = self._parse_record_hy(line) catalog.append(event) elif record_id == 'P ': pick, arrival = self._parse_record_p(line, event) elif record_id == 'E ': self._parse_record_e(line, event) elif record_id == 'L ': self._parse_record_l(line, event) elif record_id == 'A ': self._parse_record_a(line, event) elif record_id == 'C ': self._parse_record_c(line, event) elif record_id == 'AH': self._parse_record_ah(line, event) elif record_id == 'AE': self._parse_record_ae(line, event) elif record_id == 'Dp': focal_mechanism = self._parse_record_dp(line, event) elif record_id == 'Dt': self._parse_record_dt(line, focal_mechanism) elif record_id == 'Da': self._parse_record_da(line, focal_mechanism) elif record_id == 'Dc': self._parse_record_dc(line, focal_mechanism) elif record_id == 'M ': self._parse_record_m(line, event, pick) elif record_id == 'S ': self._parse_record_s(line, event, pick, arrival) self.fh.close() # strip extra whitespaces from event comments for event in catalog: for comment in event.comments: comment.text = comment.text.strip() return catalog
def _read_ndk(filename, *args, **kwargs): # @UnusedVariable """ Reads an NDK file to a :class:`~obspy.core.event.Catalog` object. :param filename: File or file-like object in text mode. """ # Read the whole file at once. While an iterator would be more efficient # the largest NDK file out in the wild is 13.7 MB so it does not matter # much. if not hasattr(filename, "read"): # Check if it exists, otherwise assume its a string. try: with open(filename, "rt") as fh: data = fh.read() except Exception: try: data = filename.decode() except Exception: data = str(filename) data = data.strip() else: data = filename.read() if hasattr(data, "decode"): data = data.decode() # Create iterator that yields lines. def lines_iter(): prev_line = -1 while True: next_line = data.find("\n", prev_line + 1) if next_line < 0: break yield data[prev_line + 1:next_line] prev_line = next_line if len(data) > prev_line + 1: yield data[prev_line + 1:] # Use one Flinn Engdahl object for all region determinations. fe = FlinnEngdahl() cat = Catalog(resource_id=_get_resource_id("catalog", str(uuid.uuid4()))) # Loop over 5 lines at once. for _i, lines in enumerate(zip_longest(*[lines_iter()] * 5)): if None in lines: msg = "Skipped last %i lines. Not a multiple of 5 lines." % ( lines.count(None)) warnings.warn(msg, ObsPyNDKWarning) continue # Parse the lines to a human readable dictionary. try: record = _read_lines(*lines) except (ValueError, ObsPyNDKException): exc = traceback.format_exc() msg = ("Could not parse event %i (faulty file?). Will be " "skipped. Lines of the event:\n" "\t%s\n" "%s") % (_i + 1, "\n\t".join(lines), exc) warnings.warn(msg, ObsPyNDKWarning) continue # Use one creation info for essentially every item. creation_info = CreationInfo(agency_id="GCMT", version=record["version_code"]) # Use the ObsPy Flinn Engdahl region determiner as the region in the # NDK files is oftentimes trimmed. region = fe.get_region(record["centroid_longitude"], record["centroid_latitude"]) # Create an event object. event = Event(force_resource_id=False, event_type="earthquake", event_type_certainty="known", event_descriptions=[ EventDescription(text=region, type="Flinn-Engdahl region"), EventDescription(text=record["cmt_event_name"], type="earthquake name") ]) # Assemble the time for the reference origin. try: time = _parse_date_time(record["date"], record["time"]) except ObsPyNDKException: msg = ("Invalid time in event %i. '%s' and '%s' cannot be " "assembled to a valid time. Event will be skipped.") % \ (_i + 1, record["date"], record["time"]) warnings.warn(msg, ObsPyNDKWarning) continue # Create two origins, one with the reference latitude/longitude and # one with the centroidal values. ref_origin = Origin( force_resource_id=False, time=time, longitude=record["hypo_lng"], latitude=record["hypo_lat"], # Convert to m. depth=record["hypo_depth_in_km"] * 1000.0, origin_type="hypocenter", comments=[ Comment(text="Hypocenter catalog: %s" % record["hypocenter_reference_catalog"], force_resource_id=False) ]) ref_origin.comments[0].resource_id = _get_resource_id( record["cmt_event_name"], "comment", tag="ref_origin") ref_origin.resource_id = _get_resource_id(record["cmt_event_name"], "origin", tag="reforigin") cmt_origin = Origin( force_resource_id=False, longitude=record["centroid_longitude"], longitude_errors={ "uncertainty": record["centroid_longitude_error"] }, latitude=record["centroid_latitude"], latitude_errors={"uncertainty": record["centroid_latitude_error"]}, # Convert to m. depth=record["centroid_depth_in_km"] * 1000.0, depth_errors={ "uncertainty": record["centroid_depth_in_km_error"] * 1000 }, time=ref_origin["time"] + record["centroid_time"], time_errors={"uncertainty": record["centroid_time_error"]}, depth_type=record["type_of_centroid_depth"], origin_type="centroid", time_fixed=False, epicenter_fixed=False, creation_info=creation_info.copy()) cmt_origin.resource_id = _get_resource_id(record["cmt_event_name"], "origin", tag="cmtorigin") event.origins = [ref_origin, cmt_origin] event.preferred_origin_id = cmt_origin.resource_id.id # Create the magnitude object. mag = Magnitude(force_resource_id=False, mag=round(record["Mw"], 2), magnitude_type="Mwc", origin_id=cmt_origin.resource_id, creation_info=creation_info.copy()) mag.resource_id = _get_resource_id(record["cmt_event_name"], "magnitude", tag="moment_mag") event.magnitudes = [mag] event.preferred_magnitude_id = mag.resource_id.id # Add the reported mb, MS magnitudes as additional magnitude objects. event.magnitudes.append( Magnitude( force_resource_id=False, mag=record["mb"], magnitude_type="mb", comments=[ Comment( force_resource_id=False, text="Reported magnitude in NDK file. Most likely 'mb'." ) ])) event.magnitudes[-1].comments[-1].resource_id = _get_resource_id( record["cmt_event_name"], "comment", tag="mb_magnitude") event.magnitudes[-1].resource_id = _get_resource_id( record["cmt_event_name"], "magnitude", tag="mb") event.magnitudes.append( Magnitude( force_resource_id=False, mag=record["MS"], magnitude_type="MS", comments=[ Comment( force_resource_id=False, text="Reported magnitude in NDK file. Most likely 'MS'." ) ])) event.magnitudes[-1].comments[-1].resource_id = _get_resource_id( record["cmt_event_name"], "comment", tag="MS_magnitude") event.magnitudes[-1].resource_id = _get_resource_id( record["cmt_event_name"], "magnitude", tag="MS") # Take care of the moment tensor. tensor = Tensor(m_rr=record["m_rr"], m_rr_errors={"uncertainty": record["m_rr_error"]}, m_pp=record["m_pp"], m_pp_errors={"uncertainty": record["m_pp_error"]}, m_tt=record["m_tt"], m_tt_errors={"uncertainty": record["m_tt_error"]}, m_rt=record["m_rt"], m_rt_errors={"uncertainty": record["m_rt_error"]}, m_rp=record["m_rp"], m_rp_errors={"uncertainty": record["m_rp_error"]}, m_tp=record["m_tp"], m_tp_errors={"uncertainty": record["m_tp_error"]}, creation_info=creation_info.copy()) mt = MomentTensor( force_resource_id=False, scalar_moment=record["scalar_moment"], tensor=tensor, data_used=[DataUsed(**i) for i in record["data_used"]], inversion_type=record["source_type"], source_time_function=SourceTimeFunction( type=record["moment_rate_type"], duration=record["moment_rate_duration"]), derived_origin_id=cmt_origin.resource_id, creation_info=creation_info.copy()) mt.resource_id = _get_resource_id(record["cmt_event_name"], "momenttensor") axis = [Axis(**i) for i in record["principal_axis"]] focmec = FocalMechanism( force_resource_id=False, moment_tensor=mt, principal_axes=PrincipalAxes( # The ordering is the same as for the IRIS SPUD service and # from a website of the Saint Louis University Earthquake # center so it should be correct. t_axis=axis[0], p_axis=axis[2], n_axis=axis[1]), nodal_planes=NodalPlanes( nodal_plane_1=NodalPlane(**record["nodal_plane_1"]), nodal_plane_2=NodalPlane(**record["nodal_plane_2"])), comments=[ Comment(force_resource_id=False, text="CMT Analysis Type: %s" % record["cmt_type"].capitalize()), Comment(force_resource_id=False, text="CMT Timestamp: %s" % record["cmt_timestamp"]) ], creation_info=creation_info.copy()) focmec.comments[0].resource_id = _get_resource_id( record["cmt_event_name"], "comment", tag="cmt_type") focmec.comments[1].resource_id = _get_resource_id( record["cmt_event_name"], "comment", tag="cmt_timestamp") focmec.resource_id = _get_resource_id(record["cmt_event_name"], "focal_mechanism") event.focal_mechanisms = [focmec] event.preferred_focal_mechanism_id = focmec.resource_id.id # Set at end to avoid duplicate resource id warning. event.resource_id = _get_resource_id(record["cmt_event_name"], "event") cat.append(event) if len(cat) == 0: msg = "No valid events found in NDK file." raise ObsPyNDKException(msg) return cat
class Unpickler(object): """ De-serializes a mchedr string into an ObsPy Catalog object. """ def __init__(self): self.flinn_engdahl = FlinnEngdahl() def load(self, filename): """ Reads mchedr file into ObsPy catalog object. :type file: str :param file: File name to read. :rtype: :class:`~obspy.core.event.Catalog` :returns: ObsPy Catalog object. """ if not isinstance(filename, (str, native_str)): raise TypeError('File name must be a string.') self.filename = filename self.fh = open(filename, 'rb') return self._deserialize() def loads(self, string): """ Parses mchedr string into ObsPy catalog object. :type string: str :param string: QuakeML string to parse. :rtype: :class:`~obspy.core.event.Catalog` :returns: ObsPy Catalog object. """ self.fh = io.BytesIO(string) self.filename = None return self._deserialize() def _int(self, string): try: return int(string) except ValueError: return None def _int_unused(self, string): val = self._int(string) if val < 0: val = None return val def _int_zero(self, string): val = self._int(string) if val is None: val = 0 return val def _float(self, string): try: return float(string) except ValueError: return None def _float_unused(self, string): val = self._float(string) if val < 0: val = None return val def _float_with_format(self, string, format_string, scale=1): ndigits, ndec = map(int, format_string.split('.')) nint = ndigits - ndec val = self._float(string[0:nint] + '.' + string[nint:nint + ndec]) if val is not None: val *= scale return val def _store_uncertainty(self, error, value, scale=1): if not isinstance(error, QuantityError): raise TypeError("'error' is not a 'QuantityError'") if value is not None: error['uncertainty'] = value * scale def _coordinate_sign(self, type): if type == 'S' or type == 'W': return -1 else: return 1 def _tensor_code_sign(self, code): """ Converts tensor from 'x,y,z' system to 'r,t,p' and translates 'f' code to 'p' """ system = { 'xx': ('tt', 1), 'yy': ('pp', 1), 'zz': ('rr', 1), 'xy': ('tp', -1), 'xz': ('rt', 1), 'yz': ('rp', -1), 'ff': ('pp', 1), 'rf': ('rp', 1), 'tf': ('tp', 1) } return system.get(code, (code, 1)) def _tensor_store(self, tensor, code, value, error): code, sign = self._tensor_code_sign(code) if code in ('rr', 'tt', 'pp', 'rt', 'rp', 'tp'): setattr(tensor, "m_%s" % code, value * sign) self._store_uncertainty(getattr(tensor, "m_%s_errors" % code), error) def _decode_fe_region_number(self, number): """ Converts Flinn-Engdahl region number to string. """ if not isinstance(number, int): number = int(number) return self.flinn_engdahl.get_region_by_number(number) def _to_rad(self, degrees): radians = np.pi * degrees / 180 return radians def _to_deg(self, radians): degrees = 180 * radians / np.pi return degrees def _spherical_to_cartesian(self, spherical_coords): length, azimuth, plunge = spherical_coords plunge_rad = self._to_rad(plunge) azimuth_rad = self._to_rad(azimuth) x = length * np.sin(plunge_rad) * np.cos(azimuth_rad) y = length * np.sin(plunge_rad) * np.sin(azimuth_rad) z = length * np.cos(plunge_rad) return (x, y, z) def _angle_between(self, u1, u2): """ Returns the angle in degrees between unit vectors 'u1' and 'u2': Source: https://stackoverflow.com/q/2827393 """ angle = np.arccos(np.dot(u1, u2)) if np.isnan(angle): if (u1 == u2).all(): angle = 0.0 else: angle = np.pi return round(self._to_deg(angle), 1) def _lat_err_to_deg(self, latitude_stderr): """ Convert latitude error from km to degrees using a simple formula """ if latitude_stderr is not None: return round(latitude_stderr / 111.1949, 4) else: return None def _lon_err_to_deg(self, longitude_stderr, latitude): """ Convert longitude error from km to degrees using a simple formula """ if longitude_stderr is not None and latitude is not None: return round( longitude_stderr / (111.1949 * math.cos(self._to_rad(latitude))), 4) else: return None def _parse_record_hy(self, line): """ Parses the 'hypocenter' record HY """ date = line[2:10] time = line[11:20] # unused: location_quality = line[20] latitude = self._float(line[21:27]) lat_type = line[27] longitude = self._float(line[29:36]) lon_type = line[36] depth = self._float(line[38:43]) # unused: depth_quality = line[43] standard_dev = self._float(line[44:48]) station_number = self._int(line[48:51]) # unused: version_flag = line[51] fe_region_number = line[52:55] fe_region_name = self._decode_fe_region_number(fe_region_number) source_code = line[55:60].strip() event = Event() # FIXME: a smarter way to define evid? evid = date + time res_id = '/'.join((res_id_prefix, 'event', evid)) event.resource_id = ResourceIdentifier(id=res_id) description = EventDescription(type='region name', text=fe_region_name) event.event_descriptions.append(description) description = EventDescription(type='Flinn-Engdahl region', text=fe_region_number) event.event_descriptions.append(description) origin = Origin() res_id = '/'.join((res_id_prefix, 'origin', evid)) origin.resource_id = ResourceIdentifier(id=res_id) origin.creation_info = CreationInfo() if source_code: origin.creation_info.agency_id = source_code else: origin.creation_info.agency_id = 'USGS-NEIC' res_id = '/'.join((res_id_prefix, 'earthmodel/ak135')) origin.earth_model_id = ResourceIdentifier(id=res_id) origin.time = UTCDateTime(date + time) origin.latitude = latitude * self._coordinate_sign(lat_type) origin.longitude = longitude * self._coordinate_sign(lon_type) origin.depth = depth * 1000 origin.depth_type = 'from location' origin.quality = OriginQuality() origin.quality.associated_station_count = station_number origin.quality.standard_error = standard_dev # associated_phase_count can be incremented in records 'P ' and 'S ' origin.quality.associated_phase_count = 0 # depth_phase_count can be incremented in record 'S ' origin.quality.depth_phase_count = 0 origin.origin_type = 'hypocenter' origin.region = fe_region_name event.origins.append(origin) return event def _parse_record_e(self, line, event): """ Parses the 'error and magnitude' record E """ orig_time_stderr = self._float(line[2:7]) latitude_stderr = self._float(line[8:14]) longitude_stderr = self._float(line[15:21]) depth_stderr = self._float(line[22:27]) mb_mag = self._float(line[28:31]) mb_nsta = self._int(line[32:35]) ms_mag = self._float(line[36:39]) ms_nsta = self._int(line[39:42]) mag1 = self._float(line[42:45]) mag1_type = line[45:47] mag1_source_code = line[47:51].strip() mag2 = self._float(line[51:54]) mag2_type = line[54:56] mag2_source_code = line[56:60].strip() evid = event.resource_id.id.split('/')[-1] origin = event.origins[0] self._store_uncertainty(origin.time_errors, orig_time_stderr) self._store_uncertainty(origin.latitude_errors, self._lat_err_to_deg(latitude_stderr)) self._store_uncertainty( origin.longitude_errors, self._lon_err_to_deg(longitude_stderr, origin.latitude)) self._store_uncertainty(origin.depth_errors, depth_stderr, scale=1000) if mb_mag is not None: mag = Magnitude() res_id = '/'.join((res_id_prefix, 'magnitude', evid, 'mb')) mag.resource_id = ResourceIdentifier(id=res_id) mag.creation_info = CreationInfo(agency_id='USGS-NEIC') mag.mag = mb_mag mag.magnitude_type = 'Mb' mag.station_count = mb_nsta mag.origin_id = origin.resource_id event.magnitudes.append(mag) if ms_mag is not None: mag = Magnitude() res_id = '/'.join((res_id_prefix, 'magnitude', evid, 'ms')) mag.resource_id = ResourceIdentifier(id=res_id) mag.creation_info = CreationInfo(agency_id='USGS-NEIC') mag.mag = ms_mag mag.magnitude_type = 'Ms' mag.station_count = ms_nsta mag.origin_id = origin.resource_id event.magnitudes.append(mag) if mag1 is not None: mag = Magnitude() mag1_id = mag1_type.lower() res_id = '/'.join((res_id_prefix, 'magnitude', evid, mag1_id)) mag.resource_id = ResourceIdentifier(id=res_id) mag.creation_info = CreationInfo(agency_id=mag1_source_code) mag.mag = mag1 mag.magnitude_type = mag1_type mag.origin_id = origin.resource_id event.magnitudes.append(mag) if mag2 is not None: mag = Magnitude() mag2_id = mag2_type.lower() if mag2_id == mag1_id: mag2_id += '2' res_id = '/'.join((res_id_prefix, 'magnitude', evid, mag2_id)) mag.resource_id = ResourceIdentifier(id=res_id) mag.creation_info = CreationInfo(agency_id=mag2_source_code) mag.mag = mag2 mag.magnitude_type = mag2_type mag.origin_id = origin.resource_id event.magnitudes.append(mag) def _parse_record_l(self, line, event): """ Parses the '90 percent error ellipse' record L """ origin = event.origins[0] semi_major_axis_azimuth = self._float(line[2:8]) if semi_major_axis_azimuth is None: return semi_major_axis_plunge = self._float(line[8:13]) semi_major_axis_length = self._float(line[13:21]) intermediate_axis_azimuth = self._float(line[21:27]) intermediate_axis_plunge = self._float(line[27:32]) # This is called "intermediate_axis_length", # but it is definitively a "semi_intermediate_axis_length", # since in most cases: # (intermediate_axis_length / 2) < semi_minor_axis_length intermediate_axis_length = self._float(line[32:40]) semi_minor_axis_azimuth = self._float(line[40:46]) semi_minor_axis_plunge = self._float(line[46:51]) semi_minor_axis_length = self._float(line[51:59]) if (semi_minor_axis_azimuth == semi_minor_axis_plunge == semi_minor_axis_length == 0): semi_minor_axis_azimuth = intermediate_axis_azimuth semi_minor_axis_plunge = intermediate_axis_plunge semi_minor_axis_length = intermediate_axis_length origin.depth_type = 'operator assigned' # FIXME: The following code needs to be double-checked! semi_major_axis_unit_vect = \ self._spherical_to_cartesian((1, semi_major_axis_azimuth, semi_major_axis_plunge)) semi_minor_axis_unit_vect = \ self._spherical_to_cartesian((1, semi_minor_axis_azimuth, semi_minor_axis_plunge)) major_axis_rotation = \ self._angle_between(semi_major_axis_unit_vect, semi_minor_axis_unit_vect) origin.origin_uncertainty = OriginUncertainty() origin.origin_uncertainty.preferred_description = \ 'confidence ellipsoid' origin.origin_uncertainty.confidence_level = 90 confidence_ellipsoid = ConfidenceEllipsoid() confidence_ellipsoid.semi_major_axis_length = \ semi_major_axis_length * 1000 confidence_ellipsoid.semi_minor_axis_length = \ semi_minor_axis_length * 1000 confidence_ellipsoid.semi_intermediate_axis_length = \ intermediate_axis_length * 1000 confidence_ellipsoid.major_axis_plunge = semi_major_axis_plunge confidence_ellipsoid.major_axis_azimuth = semi_major_axis_azimuth # We need to add 90 to match NEIC QuakeML format, # but I don't understand why... confidence_ellipsoid.major_axis_rotation = \ major_axis_rotation + 90 origin.origin_uncertainty.confidence_ellipsoid = confidence_ellipsoid def _parse_record_a(self, line, event): """ Parses the 'additional parameters' record A """ origin = event.origins[0] phase_number = self._int(line[2:6]) station_number = self._int(line[7:10]) gap = self._float(line[10:15]) # unused: official_mag = line[16:19] # unused: official_mag_type = line[19:21] # unused: official_mag_source_code = line[21:26] # unused: deaths_field_descriptor = line[27] # unused: dead_people = line[28:35] # unused: injuries_field_descriptor = line[35] # unused: injured_people = line[36:43] # unused: damaged_buildings_descriptor = line[43] # unused: damaged_buildings = line[44:51] # unused: event_quality_flag = line[51] origin.quality.used_phase_count = phase_number origin.quality.used_station_count = station_number origin.quality.azimuthal_gap = gap def _parse_record_c(self, line, event): """ Parses the 'general comment' record C """ try: comment = event.comments[0] comment.text += line[2:60] except IndexError: comment = Comment() comment.resource_id = ResourceIdentifier(prefix=res_id_prefix) event.comments.append(comment) comment.text = line[2:60] # strip non printable-characters comment.text = \ "".join(x for x in comment.text if x in s.printable) def _parse_record_ah(self, line, event): """ Parses the 'additional hypocenter' record AH """ date = line[2:10] time = line[11:20] # unused: hypocenter_quality = line[20] latitude = self._float(line[21:27]) lat_type = line[27] longitude = self._float(line[29:36]) lon_type = line[36] # unused: preliminary_flag = line[37] depth = self._float(line[38:43]) # unused: depth_quality = line[43] standard_dev = self._float_unused(line[44:48]) station_number = self._int_unused(line[48:51]) phase_number = self._int_unused(line[51:55]) source_code = line[56:60].strip() evid = event.resource_id.id.split('/')[-1] origin = Origin() res_id = '/'.join((res_id_prefix, 'origin', evid, source_code.lower())) origin.resource_id = ResourceIdentifier(id=res_id) origin.creation_info = CreationInfo(agency_id=source_code) origin.time = UTCDateTime(date + time) origin.latitude = latitude * self._coordinate_sign(lat_type) origin.longitude = longitude * self._coordinate_sign(lon_type) origin.depth = depth * 1000 origin.depth_type = 'from location' origin.quality = OriginQuality() origin.quality.standard_error = standard_dev origin.quality.used_station_count = station_number origin.quality.used_phase_count = phase_number origin.origin_type = 'hypocenter' event.origins.append(origin) def _parse_record_ae(self, line, event): """ Parses the 'additional hypocenter error and magnitude record' AE """ orig_time_stderr = self._float_unused(line[2:7]) latitude_stderr = self._float_unused(line[8:14]) longitude_stderr = self._float_unused(line[15:21]) depth_stderr = self._float_unused(line[22:27]) gap = self._float_unused(line[28:33]) mag1 = self._float(line[33:36]) mag1_type = line[36:38] mag2 = self._float(line[43:46]) mag2_type = line[46:48] evid = event.resource_id.id.split('/')[-1] # this record is to be associated to the latest origin origin = event.origins[-1] self._store_uncertainty(origin.time_errors, orig_time_stderr) self._store_uncertainty(origin.latitude_errors, self._lat_err_to_deg(latitude_stderr)) self._store_uncertainty( origin.longitude_errors, self._lon_err_to_deg(longitude_stderr, origin.latitude)) self._store_uncertainty(origin.depth_errors, depth_stderr, scale=1000) origin.quality.azimuthal_gap = gap if mag1 > 0: mag = Magnitude() mag1_id = mag1_type.lower() res_id = '/'.join((res_id_prefix, 'magnitude', evid, mag1_id)) mag.resource_id = ResourceIdentifier(id=res_id) mag.creation_info = CreationInfo( agency_id=origin.creation_info.agency_id) mag.mag = mag1 mag.magnitude_type = mag1_type mag.origin_id = origin.resource_id event.magnitudes.append(mag) if mag2 > 0: mag = Magnitude() mag2_id = mag2_type.lower() if mag2_id == mag1_id: mag2_id += '2' res_id = '/'.join((res_id_prefix, 'magnitude', evid, mag2_id)) mag.resource_id = ResourceIdentifier(id=res_id) mag.creation_info = CreationInfo( agency_id=origin.creation_info.agency_id) mag.mag = mag2 mag.magnitude_type = mag2_type mag.origin_id = origin.resource_id event.magnitudes.append(mag) def _parse_record_dp(self, line, event): """ Parses the 'source parameter data - primary' record Dp """ source_contributor = line[2:6].strip() computation_type = line[6] exponent = self._int_zero(line[7]) scale = math.pow(10, exponent) centroid_origin_time = line[8:14] + '.' + line[14] orig_time_stderr = line[15:17] if orig_time_stderr == 'FX': orig_time_stderr = 'Fixed' else: orig_time_stderr = \ self._float_with_format(orig_time_stderr, '2.1', scale) centroid_latitude = self._float_with_format(line[17:21], '4.2') lat_type = line[21] if centroid_latitude is not None: centroid_latitude *= self._coordinate_sign(lat_type) lat_stderr = line[22:25] if lat_stderr == 'FX': lat_stderr = 'Fixed' else: lat_stderr = self._float_with_format(lat_stderr, '3.2', scale) centroid_longitude = self._float_with_format(line[25:30], '5.2') lon_type = line[30] if centroid_longitude is not None: centroid_longitude *= self._coordinate_sign(lon_type) lon_stderr = line[31:34] if lon_stderr == 'FX': lon_stderr = 'Fixed' else: lon_stderr = self._float_with_format(lon_stderr, '3.2', scale) centroid_depth = self._float_with_format(line[34:38], '4.1') depth_stderr = line[38:40] if depth_stderr == 'FX' or depth_stderr == 'BD': depth_stderr = 'Fixed' else: depth_stderr = self._float_with_format(depth_stderr, '2.1', scale) station_number = self._int_zero(line[40:43]) component_number = self._int_zero(line[43:46]) station_number2 = self._int_zero(line[46:48]) component_number2 = self._int_zero(line[48:51]) # unused: half_duration = self._float_with_format(line[51:54], '3.1') moment = self._float_with_format(line[54:56], '2.1') moment_stderr = self._float_with_format(line[56:58], '2.1') moment_exponent = self._int(line[58:60]) if (moment is not None) and (moment_exponent is not None): moment *= math.pow(10, moment_exponent) if (moment_stderr is not None) and (moment_exponent is not None): moment_stderr *= math.pow(10, moment_exponent) evid = event.resource_id.id.split('/')[-1] # Create a new origin only if centroid time is defined: origin = None if centroid_origin_time.strip() != '.': origin = Origin() res_id = '/'.join( (res_id_prefix, 'origin', evid, source_contributor.lower(), 'mw' + computation_type.lower())) origin.resource_id = ResourceIdentifier(id=res_id) origin.creation_info = \ CreationInfo(agency_id=source_contributor) date = event.origins[0].time.strftime('%Y%m%d') origin.time = UTCDateTime(date + centroid_origin_time) # Check if centroid time is on the next day: if origin.time < event.origins[0].time: origin.time += timedelta(days=1) self._store_uncertainty(origin.time_errors, orig_time_stderr) origin.latitude = centroid_latitude origin.longitude = centroid_longitude origin.depth = centroid_depth * 1000 if lat_stderr == 'Fixed' and lon_stderr == 'Fixed': origin.epicenter_fixed = True else: self._store_uncertainty(origin.latitude_errors, self._lat_err_to_deg(lat_stderr)) self._store_uncertainty( origin.longitude_errors, self._lon_err_to_deg(lon_stderr, origin.latitude)) if depth_stderr == 'Fixed': origin.depth_type = 'operator assigned' else: origin.depth_type = 'from location' self._store_uncertainty(origin.depth_errors, depth_stderr, scale=1000) quality = OriginQuality() quality.used_station_count = \ station_number + station_number2 quality.used_phase_count = \ component_number + component_number2 origin.quality = quality origin.origin_type = 'centroid' event.origins.append(origin) focal_mechanism = FocalMechanism() res_id = '/'.join( (res_id_prefix, 'focalmechanism', evid, source_contributor.lower(), 'mw' + computation_type.lower())) focal_mechanism.resource_id = ResourceIdentifier(id=res_id) focal_mechanism.creation_info = \ CreationInfo(agency_id=source_contributor) moment_tensor = MomentTensor() if origin is not None: moment_tensor.derived_origin_id = origin.resource_id else: # this is required for QuakeML validation: res_id = '/'.join((res_id_prefix, 'no-origin')) moment_tensor.derived_origin_id = \ ResourceIdentifier(id=res_id) for mag in event.magnitudes: if mag.creation_info.agency_id == source_contributor: moment_tensor.moment_magnitude_id = mag.resource_id res_id = '/'.join( (res_id_prefix, 'momenttensor', evid, source_contributor.lower(), 'mw' + computation_type.lower())) moment_tensor.resource_id = ResourceIdentifier(id=res_id) moment_tensor.scalar_moment = moment self._store_uncertainty(moment_tensor.scalar_moment_errors, moment_stderr) data_used = DataUsed() data_used.station_count = station_number + station_number2 data_used.component_count = component_number + component_number2 if computation_type == 'C': res_id = '/'.join((res_id_prefix, 'methodID=CMT')) focal_mechanism.method_id = ResourceIdentifier(id=res_id) # CMT algorithm uses long-period body waves, # very-long-period surface waves and # intermediate period surface waves (since 2004 # for shallow and intermediate-depth earthquakes # --Ekstrom et al., 2012) data_used.wave_type = 'combined' if computation_type == 'M': res_id = '/'.join((res_id_prefix, 'methodID=moment_tensor')) focal_mechanism.method_id = ResourceIdentifier(id=res_id) # FIXME: not sure which kind of data is used by # "moment tensor" algorithm. data_used.wave_type = 'unknown' elif computation_type == 'B': res_id = '/'.join((res_id_prefix, 'methodID=broadband_data')) focal_mechanism.method_id = ResourceIdentifier(id=res_id) # FIXME: is 'combined' correct here? data_used.wave_type = 'combined' elif computation_type == 'F': res_id = '/'.join((res_id_prefix, 'methodID=P-wave_first_motion')) focal_mechanism.method_id = ResourceIdentifier(id=res_id) data_used.wave_type = 'P waves' elif computation_type == 'S': res_id = '/'.join((res_id_prefix, 'methodID=scalar_moment')) focal_mechanism.method_id = ResourceIdentifier(id=res_id) # FIXME: not sure which kind of data is used # for scalar moment determination. data_used.wave_type = 'unknown' moment_tensor.data_used = [data_used] focal_mechanism.moment_tensor = moment_tensor event.focal_mechanisms.append(focal_mechanism) return focal_mechanism def _parse_record_dt(self, line, focal_mechanism): """ Parses the 'source parameter data - tensor' record Dt """ tensor = Tensor() exponent = self._int_zero(line[3:5]) scale = math.pow(10, exponent) for i in range(6, 51 + 1, 9): code = line[i:i + 2] value = self._float_with_format(line[i + 2:i + 6], '4.2', scale) error = self._float_with_format(line[i + 6:i + 9], '3.2', scale) self._tensor_store(tensor, code, value, error) focal_mechanism.moment_tensor.tensor = tensor def _parse_record_da(self, line, focal_mechanism): """ Parses the 'source parameter data - principal axes and nodal planes' record Da """ exponent = self._int_zero(line[3:5]) scale = math.pow(10, exponent) t_axis_len = self._float_with_format(line[5:9], '4.2', scale) t_axis_stderr = self._float_with_format(line[9:12], '3.2', scale) t_axis_plunge = self._int(line[12:14]) t_axis_azimuth = self._int(line[14:17]) n_axis_len = self._float_with_format(line[17:21], '4.2', scale) n_axis_stderr = self._float_with_format(line[21:24], '3.2', scale) n_axis_plunge = self._int(line[24:26]) n_axis_azimuth = self._int(line[26:29]) p_axis_len = self._float_with_format(line[29:33], '4.2', scale) p_axis_stderr = self._float_with_format(line[33:36], '3.2', scale) p_axis_plunge = self._int(line[36:38]) p_axis_azimuth = self._int(line[38:41]) np1_strike = self._int(line[42:45]) np1_dip = self._int(line[45:47]) np1_slip = self._int(line[47:51]) np2_strike = self._int(line[51:54]) np2_dip = self._int(line[54:56]) np2_slip = self._int(line[56:60]) t_axis = Axis() t_axis.length = t_axis_len self._store_uncertainty(t_axis.length_errors, t_axis_stderr) t_axis.plunge = t_axis_plunge t_axis.azimuth = t_axis_azimuth n_axis = Axis() n_axis.length = n_axis_len self._store_uncertainty(n_axis.length_errors, n_axis_stderr) n_axis.plunge = n_axis_plunge n_axis.azimuth = n_axis_azimuth p_axis = Axis() p_axis.length = p_axis_len self._store_uncertainty(p_axis.length_errors, p_axis_stderr) p_axis.plunge = p_axis_plunge p_axis.azimuth = p_axis_azimuth principal_axes = PrincipalAxes() principal_axes.t_axis = t_axis principal_axes.n_axis = n_axis principal_axes.p_axis = p_axis focal_mechanism.principal_axes = principal_axes nodal_plane_1 = NodalPlane() nodal_plane_1.strike = np1_strike nodal_plane_1.dip = np1_dip nodal_plane_1.rake = np1_slip nodal_plane_2 = NodalPlane() nodal_plane_2.strike = np2_strike nodal_plane_2.dip = np2_dip nodal_plane_2.rake = np2_slip nodal_planes = NodalPlanes() nodal_planes.nodal_plane_1 = nodal_plane_1 nodal_planes.nodal_plane_2 = nodal_plane_2 focal_mechanism.nodal_planes = nodal_planes def _parse_record_dc(self, line, focal_mechanism): """ Parses the 'source parameter data - comment' record Dc """ try: comment = focal_mechanism.comments[0] comment.text += line[2:60] except IndexError: comment = Comment() comment.resource_id = ResourceIdentifier(prefix=res_id_prefix) focal_mechanism.comments.append(comment) comment.text = line[2:60] def _parse_record_p(self, line, event): """ Parses the 'primary phase record' P The primary phase is the first phase of the reading, regardless its type. """ station = line[2:7].strip() phase = line[7:15] arrival_time = line[15:24] residual = self._float(line[25:30]) # unused: residual_flag = line[30] distance = self._float(line[32:38]) # degrees azimuth = self._float(line[39:44]) backazimuth = round(azimuth % -360 + 180, 1) mb_period = self._float(line[44:48]) mb_amplitude = self._float(line[48:55]) # nanometers mb_magnitude = self._float(line[56:59]) # unused: mb_usage_flag = line[59] origin = event.origins[0] evid = event.resource_id.id.split('/')[-1] waveform_id = WaveformStreamID() waveform_id.station_code = station # network_code is required for QuakeML validation waveform_id.network_code = ' ' station_string = \ waveform_id.get_seed_string()\ .replace(' ', '-').replace('.', '_').lower() prefix = '/'.join( (res_id_prefix, 'waveformstream', evid, station_string)) waveform_id.resource_uri = ResourceIdentifier(prefix=prefix) pick = Pick() prefix = '/'.join((res_id_prefix, 'pick', evid, station_string)) pick.resource_id = ResourceIdentifier(prefix=prefix) date = origin.time.strftime('%Y%m%d') pick.time = UTCDateTime(date + arrival_time) # Check if pick is on the next day: if pick.time < origin.time: pick.time += timedelta(days=1) pick.waveform_id = waveform_id pick.backazimuth = backazimuth onset = phase[0] if onset == 'e': pick.onset = 'emergent' phase = phase[1:] elif onset == 'i': pick.onset = 'impulsive' phase = phase[1:] elif onset == 'q': pick.onset = 'questionable' phase = phase[1:] pick.phase_hint = phase.strip() event.picks.append(pick) if mb_amplitude is not None: amplitude = Amplitude() prefix = '/'.join((res_id_prefix, 'amp', evid, station_string)) amplitude.resource_id = ResourceIdentifier(prefix=prefix) amplitude.generic_amplitude = mb_amplitude * 1E-9 amplitude.unit = 'm' amplitude.period = mb_period amplitude.type = 'AB' amplitude.magnitude_hint = 'Mb' amplitude.pick_id = pick.resource_id amplitude.waveform_id = pick.waveform_id event.amplitudes.append(amplitude) station_magnitude = StationMagnitude() prefix = '/'.join( (res_id_prefix, 'stationmagntiude', evid, station_string)) station_magnitude.resource_id = ResourceIdentifier(prefix=prefix) station_magnitude.origin_id = origin.resource_id station_magnitude.mag = mb_magnitude # station_magnitude.mag_errors['uncertainty'] = 0.0 station_magnitude.station_magnitude_type = 'Mb' station_magnitude.amplitude_id = amplitude.resource_id station_magnitude.waveform_id = pick.waveform_id res_id = '/'.join( (res_id_prefix, 'magnitude/generic/body_wave_magnitude')) station_magnitude.method_id = \ ResourceIdentifier(id=res_id) event.station_magnitudes.append(station_magnitude) arrival = Arrival() prefix = '/'.join((res_id_prefix, 'arrival', evid, station_string)) arrival.resource_id = ResourceIdentifier(prefix=prefix) arrival.pick_id = pick.resource_id arrival.phase = pick.phase_hint arrival.azimuth = azimuth arrival.distance = distance arrival.time_residual = residual res_id = '/'.join((res_id_prefix, 'earthmodel/ak135')) arrival.earth_model_id = ResourceIdentifier(id=res_id) origin.arrivals.append(arrival) origin.quality.minimum_distance = min( d for d in (arrival.distance, origin.quality.minimum_distance) if d is not None) origin.quality.maximum_distance = \ max(arrival.distance, origin.quality.minimum_distance) origin.quality.associated_phase_count += 1 return pick, arrival def _parse_record_m(self, line, event, pick): """ Parses the 'surface wave record' M """ # unused: Z_comp = line[7] z_period = self._float(line[9:13]) # note: according to the format documentation, # column 20 should be blank. However, it seems that # z_amplitude includes that column z_amplitude = self._float(line[13:21]) # micrometers # TODO: N_comp and E_comp seems to be never there msz_mag = line[49:52] ms_mag = self._float(line[53:56]) # unused: Ms_usage_flag = line[56] evid = event.resource_id.id.split('/')[-1] station_string = \ pick.waveform_id.get_seed_string()\ .replace(' ', '-').replace('.', '_').lower() amplitude = None if z_amplitude is not None: amplitude = Amplitude() prefix = '/'.join((res_id_prefix, 'amp', evid, station_string)) amplitude.resource_id = ResourceIdentifier(prefix=prefix) amplitude.generic_amplitude = z_amplitude * 1E-6 amplitude.unit = 'm' amplitude.period = z_period amplitude.type = 'AS' amplitude.magnitude_hint = 'Ms' amplitude.pick_id = pick.resource_id event.amplitudes.append(amplitude) if msz_mag is not None: station_magnitude = StationMagnitude() prefix = '/'.join( (res_id_prefix, 'stationmagntiude', evid, station_string)) station_magnitude.resource_id = ResourceIdentifier(prefix=prefix) station_magnitude.origin_id = event.origins[0].resource_id station_magnitude.mag = ms_mag station_magnitude.station_magnitude_type = 'Ms' if amplitude is not None: station_magnitude.amplitude_id = amplitude.resource_id event.station_magnitudes.append(station_magnitude) def _parse_record_s(self, line, event, p_pick, p_arrival): """ Parses the 'secondary phases' record S Secondary phases are following phases of the reading, and can be P-type or S-type. """ arrivals = [] phase = line[7:15].strip() arrival_time = line[15:24] if phase: arrivals.append((phase, arrival_time)) phase = line[25:33].strip() arrival_time = line[33:42] if phase: arrivals.append((phase, arrival_time)) phase = line[43:51].strip() arrival_time = line[51:60] if phase: arrivals.append((phase, arrival_time)) evid = event.resource_id.id.split('/')[-1] station_string = \ p_pick.waveform_id.get_seed_string()\ .replace(' ', '-').replace('.', '_').lower() origin = event.origins[0] for phase, arrival_time in arrivals: if phase[0:2] == 'D=': # unused: depth = self._float(phase[2:7]) try: depth_usage_flag = phase[7] except IndexError: # usage flag is not defined depth_usage_flag = None # FIXME: I'm not sure that 'X' actually # means 'used' if depth_usage_flag == 'X': # FIXME: is this enough to say that # the event is constrained by depth phases? origin.depth_type = 'constrained by depth phases' origin.quality.depth_phase_count += 1 else: pick = Pick() prefix = '/'.join( (res_id_prefix, 'pick', evid, station_string)) pick.resource_id = ResourceIdentifier(prefix=prefix) date = origin.time.strftime('%Y%m%d') pick.time = UTCDateTime(date + arrival_time) # Check if pick is on the next day: if pick.time < origin.time: pick.time += timedelta(days=1) pick.waveform_id = p_pick.waveform_id pick.backazimuth = p_pick.backazimuth onset = phase[0] if onset == 'e': pick.onset = 'emergent' phase = phase[1:] elif onset == 'i': pick.onset = 'impulsive' phase = phase[1:] elif onset == 'q': pick.onset = 'questionable' phase = phase[1:] pick.phase_hint = phase.strip() event.picks.append(pick) arrival = Arrival() prefix = '/'.join( (res_id_prefix, 'arrival', evid, station_string)) arrival.resource_id = ResourceIdentifier(prefix=prefix) arrival.pick_id = pick.resource_id arrival.phase = pick.phase_hint arrival.azimuth = p_arrival.azimuth arrival.distance = p_arrival.distance origin.quality.associated_phase_count += 1 origin.arrivals.append(arrival) def _deserialize(self): catalog = Catalog() res_id = '/'.join((res_id_prefix, self.filename.replace(':', '/')))\ .replace('\\', '/').replace('//', '/') catalog.resource_id = ResourceIdentifier(id=res_id) catalog.description = 'Created from NEIC PDE mchedr format' catalog.comments = '' catalog.creation_info = CreationInfo(creation_time=UTCDateTime()) for line in self.fh.readlines(): # XXX: ugly, probably we should do everything in byte strings # here? Is the pde / mchedr format unicode aware? line = line.decode() record_id = line[0:2] if record_id == 'HY': event = self._parse_record_hy(line) catalog.append(event) elif record_id == 'P ': pick, arrival = self._parse_record_p(line, event) elif record_id == 'E ': self._parse_record_e(line, event) elif record_id == 'L ': self._parse_record_l(line, event) elif record_id == 'A ': self._parse_record_a(line, event) elif record_id == 'C ': self._parse_record_c(line, event) elif record_id == 'AH': self._parse_record_ah(line, event) elif record_id == 'AE': self._parse_record_ae(line, event) elif record_id == 'Dp': focal_mechanism = self._parse_record_dp(line, event) elif record_id == 'Dt': self._parse_record_dt(line, focal_mechanism) elif record_id == 'Da': self._parse_record_da(line, focal_mechanism) elif record_id == 'Dc': self._parse_record_dc(line, focal_mechanism) elif record_id == 'M ': self._parse_record_m(line, event, pick) elif record_id == 'S ': self._parse_record_s(line, event, pick, arrival) self.fh.close() # strip extra whitespaces from event comments for event in catalog: for comment in event.comments: comment.text = comment.text.strip() event.scope_resource_ids() return catalog
from __future__ import (absolute_import, division, print_function, unicode_literals) from future.builtins import * # NOQA @UnusedWildImport import math import uuid import warnings from obspy import UTCDateTime from obspy.core.event import (Catalog, Comment, Event, EventDescription, Origin, Magnitude, FocalMechanism, MomentTensor, Tensor, SourceTimeFunction) from obspy.geodetics import FlinnEngdahl _fe = FlinnEngdahl() def _get_resource_id(cmtname, res_type, tag=None): """ Helper function to create consistent resource ids. """ res_id = "smi:local/cmtsolution/%s/%s" % (cmtname, res_type) if tag is not None: res_id += "#" + tag return res_id def _buffer_proxy(filename_or_buf, function, reset_fp=True, file_mode="rb", *args, **kwargs): """
def setUp(self): self.flinnengdahl = FlinnEngdahl() self.samples_file = os.path.join(os.path.dirname(__file__), 'data', 'flinnengdahl.csv')