def _deserialize(self, zmap_str): catalog = Catalog() for row in zmap_str.split('\n'): if len(row) == 0: continue origin = Origin() event = Event(origins=[origin]) event.preferred_origin_id = origin.resource_id.id # Begin value extraction columns = row.split('\t', 13)[:13] # ignore extra columns values = dict(zip(_STD_ZMAP_COLUMNS + _EXT_ZMAP_COLUMNS, columns)) # Extract origin origin.longitude = self._str2num(values.get('lon')) origin.latitude = self._str2num(values.get('lat')) depth = self._str2num(values.get('depth')) if depth is not None: origin.depth = depth * 1000.0 z_err = self._str2num(values.get('z_err')) if z_err is not None: origin.depth_errors.uncertainty = z_err * 1000.0 h_err = self._str2num(values.get('h_err')) if h_err is not None: ou = OriginUncertainty() ou.horizontal_uncertainty = h_err ou.preferred_description = 'horizontal uncertainty' origin.origin_uncertainty = ou year = self._str2num(values.get('year')) if year is not None: t_fields = ['year', 'month', 'day', 'hour', 'minute', 'second'] comps = [self._str2num(values.get(f)) for f in t_fields] if year % 1 != 0: origin.time = self._decyear2utc(year) elif any(v > 0 for v in comps[1:]): # no seconds involved if len(comps) < 6: utc_args = [int(v) for v in comps if v is not None] # we also have to handle seconds else: utc_args = [ int(v) if v is not None else 0 for v in comps[:-1] ] # just leave float seconds as is utc_args.append(comps[-1]) origin.time = UTCDateTime(*utc_args) mag = self._str2num(values.get('mag')) # Extract magnitude if mag is not None: magnitude = Magnitude(mag=mag) m_err = self._str2num(values.get('m_err')) magnitude.mag_errors.uncertainty = m_err event.magnitudes.append(magnitude) event.preferred_magnitude_id = magnitude.resource_id.id event.scope_resource_ids() catalog.append(event) return catalog
def _deserialize(self, zmap_str): catalog = Catalog() for row in zmap_str.split('\n'): if len(row) == 0: continue origin = Origin() event = Event(origins=[origin]) event.preferred_origin_id = origin.resource_id.id # Begin value extraction columns = row.split('\t', 13)[:13] # ignore extra columns values = dict(zip(_STD_ZMAP_COLUMNS + _EXT_ZMAP_COLUMNS, columns)) # Extract origin origin.longitude = self._str2num(values.get('lon')) origin.latitude = self._str2num(values.get('lat')) depth = self._str2num(values.get('depth')) if depth is not None: origin.depth = depth * 1000.0 z_err = self._str2num(values.get('z_err')) if z_err is not None: origin.depth_errors.uncertainty = z_err * 1000.0 h_err = self._str2num(values.get('h_err')) if h_err is not None: ou = OriginUncertainty() ou.horizontal_uncertainty = h_err ou.preferred_description = 'horizontal uncertainty' origin.origin_uncertainty = ou year = self._str2num(values.get('year')) if year is not None: t_fields = ['year', 'month', 'day', 'hour', 'minute', 'second'] comps = [self._str2num(values.get(f)) for f in t_fields] if year % 1 != 0: origin.time = self._decyear2utc(year) elif any(v > 0 for v in comps[1:]): # no seconds involved if len(comps) < 6: utc_args = [int(v) for v in comps if v is not None] # we also have to handle seconds else: utc_args = [int(v) if v is not None else 0 for v in comps[:-1]] # just leave float seconds as is utc_args.append(comps[-1]) origin.time = UTCDateTime(*utc_args) mag = self._str2num(values.get('mag')) # Extract magnitude if mag is not None: magnitude = Magnitude(mag=mag) m_err = self._str2num(values.get('m_err')) magnitude.mag_errors.uncertainty = m_err event.magnitudes.append(magnitude) event.preferred_magnitude_id = magnitude.resource_id.id event.scope_resource_ids() catalog.append(event) return catalog
def _deserialize(self, zmap_str): catalog = Catalog() for row in zmap_str.split("\n"): if len(row) == 0: continue origin = Origin() event = Event(origins=[origin]) event.preferred_origin_id = origin.resource_id.id # Begin value extraction columns = row.split("\t", 13)[:13] # ignore extra columns values = dict(zip(_STD_ZMAP_COLUMNS + _EXT_ZMAP_COLUMNS, columns)) # Extract origin origin.longitude = self._str2num(values.get("lon")) origin.latitude = self._str2num(values.get("lat")) depth = self._str2num(values.get("depth")) if depth is not None: origin.depth = depth * 1000.0 z_err = self._str2num(values.get("z_err")) if z_err is not None: origin.depth_errors.uncertainty = z_err * 1000.0 h_err = self._str2num(values.get("h_err")) if h_err is not None: ou = OriginUncertainty() ou.horizontal_uncertainty = h_err ou.preferred_description = "horizontal uncertainty" origin.origin_uncertainty = ou year = self._str2num(values.get("year")) if year is not None: t_fields = ["year", "month", "day", "hour", "minute", "second"] comps = [self._str2num(values.get(f)) for f in t_fields] if year % 1 != 0: origin.time = self._decyear2utc(year) elif any(v > 0 for v in comps[1:]): utc_args = [int(v) for v in comps if v is not None] origin.time = UTCDateTime(*utc_args) mag = self._str2num(values.get("mag")) # Extract magnitude if mag is not None: magnitude = Magnitude(mag=mag) m_err = self._str2num(values.get("m_err")) magnitude.mag_errors.uncertainty = m_err event.magnitudes.append(magnitude) event.preferred_magnitude_id = magnitude.resource_id.id catalog.append(event) return catalog
def __toOrigin(parser, origin_el): """ Parses a given origin etree element. :type parser: :class:`~obspy.core.util.xmlwrapper.XMLParser` :param parser: Open XMLParser object. :type origin_el: etree.element :param origin_el: origin element to be parsed. :return: A ObsPy :class:`~obspy.core.event.Origin` object. """ global CURRENT_TYPE origin = Origin() origin.resource_id = ResourceIdentifier(prefix="/".join([RESOURCE_ROOT, "origin"])) # I guess setting the program used as the method id is fine. origin.method_id = "%s/location_method/%s/1" % (RESOURCE_ROOT, parser.xpath2obj('program', origin_el)) if str(origin.method_id).lower().endswith("none"): origin.method_id = None # Standard parameters. origin.time, origin.time_errors = \ __toTimeQuantity(parser, origin_el, "time") origin.latitude, origin_latitude_error = \ __toFloatQuantity(parser, origin_el, "latitude") origin.longitude, origin_longitude_error = \ __toFloatQuantity(parser, origin_el, "longitude") origin.depth, origin.depth_errors = \ __toFloatQuantity(parser, origin_el, "depth") if origin_longitude_error: origin_longitude_error = origin_longitude_error["uncertainty"] if origin_latitude_error: origin_latitude_error = origin_latitude_error["uncertainty"] # Figure out the depth type. depth_type = parser.xpath2obj("depth_type", origin_el) # Map Seishub specific depth type to the QuakeML depth type. if depth_type == "from location program": depth_type = "from location" if depth_type is not None: origin.depth_type = depth_type # XXX: CHECK DEPTH ORIENTATION!! if CURRENT_TYPE == "seiscomp3": origin.depth *= 1000 if origin.depth_errors.uncertainty: origin.depth_errors.uncertainty *= 1000 else: # Convert to m. origin.depth *= -1000 if origin.depth_errors.uncertainty: origin.depth_errors.uncertainty *= 1000 # Earth model. earth_mod = parser.xpath2obj('earth_mod', origin_el, str) if earth_mod: earth_mod = earth_mod.split() earth_mod = ",".join(earth_mod) origin.earth_model_id = "%s/earth_model/%s/1" % (RESOURCE_ROOT, earth_mod) if (origin_latitude_error is None or origin_longitude_error is None) and \ CURRENT_TYPE not in ["seiscomp3", "toni"]: print "AAAAAAAAAAAAA" raise Exception if origin_latitude_error and origin_latitude_error: if CURRENT_TYPE in ["baynet", "obspyck"]: uncert = OriginUncertainty() if origin_latitude_error > origin_longitude_error: uncert.azimuth_max_horizontal_uncertainty = 0 else: uncert.azimuth_max_horizontal_uncertainty = 90 uncert.min_horizontal_uncertainty, \ uncert.max_horizontal_uncertainty = \ sorted([origin_longitude_error, origin_latitude_error]) uncert.min_horizontal_uncertainty *= 1000.0 uncert.max_horizontal_uncertainty *= 1000.0 uncert.preferred_description = "uncertainty ellipse" origin.origin_uncertainty = uncert elif CURRENT_TYPE == "earthworm": uncert = OriginUncertainty() uncert.horizontal_uncertainty = origin_latitude_error uncert.horizontal_uncertainty *= 1000.0 uncert.preferred_description = "horizontal uncertainty" origin.origin_uncertainty = uncert elif CURRENT_TYPE in ["seiscomp3", "toni"]: pass else: raise Exception # Parse the OriginQuality if applicable. if not origin_el.xpath("originQuality"): return origin origin_quality_el = origin_el.xpath("originQuality")[0] origin.quality = OriginQuality() origin.quality.associated_phase_count = \ parser.xpath2obj("associatedPhaseCount", origin_quality_el, int) # QuakeML does apparently not distinguish between P and S wave phase # count. Some Seishub event files do. p_phase_count = parser.xpath2obj("P_usedPhaseCount", origin_quality_el, int) s_phase_count = parser.xpath2obj("S_usedPhaseCount", origin_quality_el, int) # Use both in case they are set. if p_phase_count is not None and s_phase_count is not None: phase_count = p_phase_count + s_phase_count # Also add two Seishub element file specific elements. origin.quality.p_used_phase_count = p_phase_count origin.quality.s_used_phase_count = s_phase_count # Otherwise the total usedPhaseCount should be specified. else: phase_count = parser.xpath2obj("usedPhaseCount", origin_quality_el, int) if p_phase_count is not None: origin.quality.setdefault("extra", AttribDict()) origin.quality.extra.usedPhaseCountP = {'value': p_phase_count, 'namespace': NAMESPACE} if s_phase_count is not None: origin.quality.setdefault("extra", AttribDict()) origin.quality.extra.usedPhaseCountS = {'value': s_phase_count, 'namespace': NAMESPACE} origin.quality.used_phase_count = phase_count associated_station_count = \ parser.xpath2obj("associatedStationCount", origin_quality_el, int) used_station_count = parser.xpath2obj("usedStationCount", origin_quality_el, int) depth_phase_count = parser.xpath2obj("depthPhaseCount", origin_quality_el, int) standard_error = parser.xpath2obj("standardError", origin_quality_el, float) azimuthal_gap = parser.xpath2obj("azimuthalGap", origin_quality_el, float) secondary_azimuthal_gap = \ parser.xpath2obj("secondaryAzimuthalGap", origin_quality_el, float) ground_truth_level = parser.xpath2obj("groundTruthLevel", origin_quality_el, str) minimum_distance = parser.xpath2obj("minimumDistance", origin_quality_el, float) maximum_distance = parser.xpath2obj("maximumDistance", origin_quality_el, float) median_distance = parser.xpath2obj("medianDistance", origin_quality_el, float) if minimum_distance is not None: minimum_distance = kilometer2degrees(minimum_distance) if maximum_distance is not None: maximum_distance = kilometer2degrees(maximum_distance) if median_distance is not None: median_distance = kilometer2degrees(median_distance) if associated_station_count is not None: origin.quality.associated_station_count = associated_station_count if used_station_count is not None: origin.quality.used_station_count = used_station_count if depth_phase_count is not None: origin.quality.depth_phase_count = depth_phase_count if standard_error is not None and not math.isnan(standard_error): origin.quality.standard_error = standard_error if azimuthal_gap is not None: origin.quality.azimuthal_gap = azimuthal_gap if secondary_azimuthal_gap is not None: origin.quality.secondary_azimuthal_gap = secondary_azimuthal_gap if ground_truth_level is not None: origin.quality.ground_truth_level = ground_truth_level if minimum_distance is not None: origin.quality.minimum_distance = minimum_distance if maximum_distance is not None: origin.quality.maximum_distance = maximum_distance if median_distance is not None and not math.isnan(median_distance): origin.quality.median_distance = median_distance return origin
def __toOrigin(parser, origin_el): """ Parses a given origin etree element. :type parser: :class:`~obspy.core.util.xmlwrapper.XMLParser` :param parser: Open XMLParser object. :type origin_el: etree.element :param origin_el: origin element to be parsed. :return: A ObsPy :class:`~obspy.core.event.Origin` object. """ global CURRENT_TYPE origin = Origin() origin.resource_id = ResourceIdentifier( prefix="/".join([RESOURCE_ROOT, "origin"])) # I guess setting the program used as the method id is fine. origin.method_id = "%s/location_method/%s/1" % ( RESOURCE_ROOT, parser.xpath2obj('program', origin_el)) if str(origin.method_id).lower().endswith("none"): origin.method_id = None # Standard parameters. origin.time, origin.time_errors = \ __toTimeQuantity(parser, origin_el, "time") origin.latitude, origin_latitude_error = \ __toFloatQuantity(parser, origin_el, "latitude") origin.longitude, origin_longitude_error = \ __toFloatQuantity(parser, origin_el, "longitude") origin.depth, origin.depth_errors = \ __toFloatQuantity(parser, origin_el, "depth") if origin_longitude_error: origin_longitude_error = origin_longitude_error["uncertainty"] if origin_latitude_error: origin_latitude_error = origin_latitude_error["uncertainty"] # Figure out the depth type. depth_type = parser.xpath2obj("depth_type", origin_el) # Map Seishub specific depth type to the QuakeML depth type. if depth_type == "from location program": depth_type = "from location" if depth_type is not None: origin.depth_type = depth_type # XXX: CHECK DEPTH ORIENTATION!! if CURRENT_TYPE == "seiscomp3": origin.depth *= 1000 if origin.depth_errors.uncertainty: origin.depth_errors.uncertainty *= 1000 else: # Convert to m. origin.depth *= -1000 if origin.depth_errors.uncertainty: origin.depth_errors.uncertainty *= 1000 # Earth model. earth_mod = parser.xpath2obj('earth_mod', origin_el, str) if earth_mod: earth_mod = earth_mod.split() earth_mod = ",".join(earth_mod) origin.earth_model_id = "%s/earth_model/%s/1" % (RESOURCE_ROOT, earth_mod) if (origin_latitude_error is None or origin_longitude_error is None) and \ CURRENT_TYPE not in ["seiscomp3", "toni"]: print "AAAAAAAAAAAAA" raise Exception if origin_latitude_error and origin_latitude_error: if CURRENT_TYPE in ["baynet", "obspyck"]: uncert = OriginUncertainty() if origin_latitude_error > origin_longitude_error: uncert.azimuth_max_horizontal_uncertainty = 0 else: uncert.azimuth_max_horizontal_uncertainty = 90 uncert.min_horizontal_uncertainty, \ uncert.max_horizontal_uncertainty = \ sorted([origin_longitude_error, origin_latitude_error]) uncert.min_horizontal_uncertainty *= 1000.0 uncert.max_horizontal_uncertainty *= 1000.0 uncert.preferred_description = "uncertainty ellipse" origin.origin_uncertainty = uncert elif CURRENT_TYPE == "earthworm": uncert = OriginUncertainty() uncert.horizontal_uncertainty = origin_latitude_error uncert.horizontal_uncertainty *= 1000.0 uncert.preferred_description = "horizontal uncertainty" origin.origin_uncertainty = uncert elif CURRENT_TYPE in ["seiscomp3", "toni"]: pass else: raise Exception # Parse the OriginQuality if applicable. if not origin_el.xpath("originQuality"): return origin origin_quality_el = origin_el.xpath("originQuality")[0] origin.quality = OriginQuality() origin.quality.associated_phase_count = \ parser.xpath2obj("associatedPhaseCount", origin_quality_el, int) # QuakeML does apparently not distinguish between P and S wave phase # count. Some Seishub event files do. p_phase_count = parser.xpath2obj("P_usedPhaseCount", origin_quality_el, int) s_phase_count = parser.xpath2obj("S_usedPhaseCount", origin_quality_el, int) # Use both in case they are set. if p_phase_count is not None and s_phase_count is not None: phase_count = p_phase_count + s_phase_count # Also add two Seishub element file specific elements. origin.quality.p_used_phase_count = p_phase_count origin.quality.s_used_phase_count = s_phase_count # Otherwise the total usedPhaseCount should be specified. else: phase_count = parser.xpath2obj("usedPhaseCount", origin_quality_el, int) if p_phase_count is not None: origin.quality.setdefault("extra", AttribDict()) origin.quality.extra.usedPhaseCountP = { 'value': p_phase_count, 'namespace': NAMESPACE } if s_phase_count is not None: origin.quality.setdefault("extra", AttribDict()) origin.quality.extra.usedPhaseCountS = { 'value': s_phase_count, 'namespace': NAMESPACE } origin.quality.used_phase_count = phase_count associated_station_count = \ parser.xpath2obj("associatedStationCount", origin_quality_el, int) used_station_count = parser.xpath2obj("usedStationCount", origin_quality_el, int) depth_phase_count = parser.xpath2obj("depthPhaseCount", origin_quality_el, int) standard_error = parser.xpath2obj("standardError", origin_quality_el, float) azimuthal_gap = parser.xpath2obj("azimuthalGap", origin_quality_el, float) secondary_azimuthal_gap = \ parser.xpath2obj("secondaryAzimuthalGap", origin_quality_el, float) ground_truth_level = parser.xpath2obj("groundTruthLevel", origin_quality_el, str) minimum_distance = parser.xpath2obj("minimumDistance", origin_quality_el, float) maximum_distance = parser.xpath2obj("maximumDistance", origin_quality_el, float) median_distance = parser.xpath2obj("medianDistance", origin_quality_el, float) if minimum_distance is not None: minimum_distance = kilometer2degrees(minimum_distance) if maximum_distance is not None: maximum_distance = kilometer2degrees(maximum_distance) if median_distance is not None: median_distance = kilometer2degrees(median_distance) if associated_station_count is not None: origin.quality.associated_station_count = associated_station_count if used_station_count is not None: origin.quality.used_station_count = used_station_count if depth_phase_count is not None: origin.quality.depth_phase_count = depth_phase_count if standard_error is not None and not math.isnan(standard_error): origin.quality.standard_error = standard_error if azimuthal_gap is not None: origin.quality.azimuthal_gap = azimuthal_gap if secondary_azimuthal_gap is not None: origin.quality.secondary_azimuthal_gap = secondary_azimuthal_gap if ground_truth_level is not None: origin.quality.ground_truth_level = ground_truth_level if minimum_distance is not None: origin.quality.minimum_distance = minimum_distance if maximum_distance is not None: origin.quality.maximum_distance = maximum_distance if median_distance is not None and not math.isnan(median_distance): origin.quality.median_distance = median_distance return origin
def _map_join2origin(self, db): """ Return an Origin instance from an dict of CSS key/values Inputs ====== db : dict of key/values of CSS fields related to the origin (see Join) Returns ======= obspy.core.event.Origin Notes ===== Any object that supports the dict 'get' method can be passed as input, e.g. OrderedDict, custom classes, etc. Join ---- origin <- origerr (outer) """ #-- Basic location ------------------------------------------ origin = Origin() origin.latitude = db.get('lat') origin.longitude = db.get('lon') origin.depth = _km2m(db.get('depth')) origin.time = _utc(db.get('time')) origin.extra = {} #-- Quality ------------------------------------------------- quality = OriginQuality( associated_phase_count = db.get('nass'), used_phase_count = db.get('ndef'), standard_error = db.get('sdobs'), ) origin.quality = quality #-- Solution Uncertainties ---------------------------------- # in CSS the ellipse is projected onto the horizontal plane # using the covariance matrix uncertainty = OriginUncertainty() a = _km2m(db.get('smajax')) b = _km2m(db.get('sminax')) s = db.get('strike') dep_u = _km2m(db.get('sdepth')) time_u = db.get('stime') uncertainty.max_horizontal_uncertainty = a uncertainty.min_horizontal_uncertainty = b uncertainty.azimuth_max_horizontal_uncertainty = s uncertainty.horizontal_uncertainty = a uncertainty.preferred_description = "horizontal uncertainty" if db.get('conf') is not None: uncertainty.confidence_level = db.get('conf') * 100. if uncertainty.horizontal_uncertainty is not None: origin.origin_uncertainty = uncertainty #-- Parameter Uncertainties --------------------------------- if all([a, b, s]): n, e = _get_NE_on_ellipse(a, b, s) lat_u = _m2deg_lat(n) lon_u = _m2deg_lon(e, lat=origin.latitude) origin.latitude_errors = {'uncertainty': lat_u} origin.longitude_errors = {'uncertainty': lon_u} if dep_u: origin.depth_errors = {'uncertainty': dep_u} if time_u: origin.time_errors = {'uncertainty': time_u} #-- Analyst-determined Status ------------------------------- posted_author = _str(db.get('auth')) mode, status = self.get_event_status(posted_author) origin.evaluation_mode = mode origin.evaluation_status = status # Save etype per origin due to schema differences... css_etype = _str(db.get('etype')) # Compatible with future patch rename "_namespace" -> "namespace" origin.extra['etype'] = { 'value': css_etype, 'namespace': CSS_NAMESPACE } origin.creation_info = CreationInfo( creation_time = _utc(db.get('lddate')), agency_id = self.agency, version = db.get('orid'), author = posted_author, ) origin.resource_id = self._rid(origin) return origin