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 _parseRecordAH(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._floatUnused(line[44:48])
station_number = self._intUnused(line[48:51])
phase_number = self._intUnused(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._coordinateSign(lat_type)
origin.longitude = longitude * self._coordinateSign(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.type = 'hypocenter'
event.origins.append(origin)
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_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 ORNL_events_to_cat(ornl_file):
"""Make Catalog from ORNL locations"""
cat = Catalog()
loc_df = pd.read_csv(ornl_file, infer_datetime_format=True)
loc_df = loc_df.set_index('event_datetime')
eid = 0
for dt, row in loc_df.iterrows():
ot = UTCDateTime(dt)
hmc_east = row['x(m)']
hmc_north = row['y(m)']
hmc_elev = row['z(m)']
errX = row['error_x (m)']
errY = row['error_y (m)']
errZ = row['error_z (m)']
rms = row['rms (millisecond)']
converter = SURF_converter()
lon, lat, elev = converter.to_lonlat((hmc_east, hmc_north,
hmc_elev))
o = Origin(time=ot, latitude=lat, longitude=lon, depth=130 - elev)
o.origin_uncertainty = OriginUncertainty()
o.quality = OriginQuality()
ou = o.origin_uncertainty
oq = o.quality
ou.max_horizontal_uncertainty = np.max([errX, errY])
ou.min_horizontal_uncertainty = np.min([errX, errY])
o.depth_errors.uncertainty = errZ
oq.standard_error = rms * 1e3
extra = AttribDict({
'hmc_east': {
'value': hmc_east,
'namespace': 'smi:local/hmc'
},
'hmc_north': {
'value': hmc_north,
'namespace': 'smi:local/hmc'
},
'hmc_elev': {
'value': hmc_elev,
'namespace': 'smi:local/hmc'
},
'hmc_eid': {
'value': eid,
'namespace': 'smi:local/hmc'
}
})
o.extra = extra
rid = ResourceIdentifier(id=ot.strftime('%Y%m%d%H%M%S%f'))
# Dummy magnitude of 1. for all events until further notice
mag = Magnitude(mag=1., mag_errors=QuantityError(uncertainty=1.))
ev = Event(origins=[o], magnitudes=[mag], resource_id=rid)
ev.preferred_origin_id = o.resource_id.id
cat.events.append(ev)
eid += 1
return cat
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 __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.
"""
origin = Origin()
# I guess setting the program used as the method id is fine.
origin.method_id = parser.xpath2obj('program', origin_el)
# Standard parameters.
origin.time, origin.time_errors = \
__toTimeQuantity(parser, origin_el, "time")
origin.latitude, origin.latitude_errors = \
__toFloatQuantity(parser, origin_el, "latitude")
origin.longitude, origin.longitude_errors = \
__toFloatQuantity(parser, origin_el, "longitude")
origin.depth, origin.depth_errors = \
__toFloatQuantity(parser, origin_el, "depth")
# Figure out the depth type.
depth_type = parser.xpath2obj("depth_type", origin_el, str)
# Map Seishub specific depth type to the QuakeML depth type.
if depth_type == "from location program":
depth_type == "from location"
origin.depth_type = "from location"
# Earth model.
origin.earth_model_id = parser.xpath2obj("earth_mod", origin_el, str)
# Parse th origin uncertainty. Rather verbose but should cover all cases.
pref_desc = parser.xpath2obj("originUncertainty/preferredDescription",
origin_el, str)
hor_uncert = parser.xpath2obj("originUncertainty/horizontalUncertainty",
origin_el, float)
min_hor_uncert = parser.xpath2obj(\
"originUncertainty/minHorizontalUncertainty", origin_el, float)
max_hor_uncert = parser.xpath2obj(\
"originUncertainty/maxHorizontalUncertainty", origin_el, float)
azi_max_hor_uncert = parser.xpath2obj(\
"originUncertainty/azimuthMaxHorizontalUncertainty", origin_el, float)
origin_uncert = {}
if pref_desc:
origin_uncert["preferred_description"] = pref_desc
if hor_uncert:
origin_uncert["horizontal_uncertainty"] = hor_uncert
if min_hor_uncert:
origin_uncert["min_horizontal_uncertainty"] = min_hor_uncert
if max_hor_uncert:
origin_uncert["max_horizontal_uncertainty"] = max_hor_uncert
if azi_max_hor_uncert:
origin_uncert["azimuth_max_horizontal_uncertainty"] = \
azi_max_hor_uncert
if origin_uncert:
origin.origin_uncertainty = origin_uncert
# 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 and s_phase_count:
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)
origin.quality.used_phase_count = phase_count
origin.quality.associated_station_count = \
parser.xpath2obj("associatedStationCount", origin_quality_el, int)
origin.quality.used_station_count = \
parser.xpath2obj("usedStationCount", origin_quality_el, int)
origin.quality.depth_phase_count = \
parser.xpath2obj("depthPhaseCount", origin_quality_el, int)
origin.quality.standard_error = \
parser.xpath2obj("standardError", origin_quality_el, float)
origin.quality.azimuthal_gap = \
parser.xpath2obj("azimuthalGap", origin_quality_el, float)
origin.quality.secondary_azimuthal_gap = \
parser.xpath2obj("secondaryAzimuthalGap", origin_quality_el, float)
origin.quality.ground_truth_level = \
parser.xpath2obj("groundTruthLevel", origin_quality_el, float)
origin.quality.minimum_distance = \
parser.xpath2obj("minimumDistance", origin_quality_el, float)
origin.quality.maximum_distance = \
parser.xpath2obj("maximumDistance", origin_quality_el, float)
origin.quality.median_distance = \
parser.xpath2obj("medianDistance", origin_quality_el, float)
return origin
def _parse_first_line_origin(self, line, event, magnitudes):
"""
Parse the first line of origin data.
:type line: str
:param line: Line to parse.
:type event: :class:`~obspy.core.event.event.Event`
:param event: Event of the origin.
:type magnitudes: list of
:class:`~obspy.core.event.magnitude.Magnitude`
:param magnitudes: Store magnitudes in a list to keep
their positions.
:rtype: :class:`~obspy.core.event.origin.Origin`,
:class:`~obspy.core.event.resourceid.ResourceIdentifier`
:returns: Parsed origin or None, resource identifier of the
origin.
"""
magnitude_types = []
magnitude_values = []
magnitude_station_counts = []
fields = self.fields['line_1']
time_origin = line[fields['time']].strip()
time_fixed_flag = line[fields['time_fixf']].strip()
latitude = line[fields['lat']].strip()
longitude = line[fields['lon']].strip()
epicenter_fixed_flag = line[fields['epicenter_fixf']].strip()
depth = line[fields['depth']].strip()
depth_fixed_flag = line[fields['depth_fixf']].strip()
phase_count = line[fields['n_def']].strip()
station_count = line[fields['n_sta']].strip()
azimuthal_gap = line[fields['gap']].strip()
magnitude_types.append(line[fields['mag_type_1']].strip())
magnitude_values.append(line[fields['mag_1']].strip())
magnitude_station_counts.append(line[fields['mag_n_sta_1']].strip())
magnitude_types.append(line[fields['mag_type_2']].strip())
magnitude_values.append(line[fields['mag_2']].strip())
magnitude_station_counts.append(line[fields['mag_n_sta_2']].strip())
magnitude_types.append(line[fields['mag_type_3']].strip())
magnitude_values.append(line[fields['mag_3']].strip())
magnitude_station_counts.append(line[fields['mag_n_sta_3']].strip())
author = line[fields['author']].strip()
origin_id = line[fields['id']].strip()
origin = Origin()
origin.quality = OriginQuality()
try:
origin.time = UTCDateTime(time_origin.replace('/', '-'))
origin.latitude = float(latitude)
origin.longitude = float(longitude)
except (TypeError, ValueError):
self._warn('Missing origin data, skipping event')
return None, None
origin.time_fixed = time_fixed_flag.lower() == 'f'
origin.epicenter_fixed = epicenter_fixed_flag.lower() == 'f'
try:
# Convert value from km to m
origin.depth = float(depth) * 1000
except ValueError:
pass
try:
origin.depth_type = DEPTH_TYPES[depth_fixed_flag]
except KeyError:
origin.depth_type = OriginDepthType('from location')
try:
origin.quality.used_phase_count = int(phase_count)
origin.quality.associated_phase_count = int(phase_count)
except ValueError:
pass
try:
origin.quality.used_station_count = int(station_count)
origin.quality.associated_station_count = int(station_count)
except ValueError:
pass
try:
origin.quality.azimuthal_gap = float(azimuthal_gap)
except ValueError:
pass
self.author = author
origin.creation_info = self._get_creation_info()
public_id = "origin/%s" % origin_id
origin_res_id = self._get_res_id(public_id)
for i in range(3):
try:
magnitude = Magnitude()
magnitude.creation_info = self._get_creation_info()
magnitude.magnitude_type = magnitude_types[i]
magnitude.mag = float(magnitude_values[i])
magnitude.station_count = int(magnitude_station_counts[i])
magnitude.origin_id = origin_res_id
magnitudes.append(magnitude)
event.magnitudes.append(magnitude)
except ValueError:
# Magnitude can be empty but we need to keep the
# position between mag1, mag2 or mag3.
magnitudes.append(None)
return origin, origin_res_id
def read_nlloc_hyp(filename, coordinate_converter=None, picks=None, **kwargs):
"""
Reads a NonLinLoc Hypocenter-Phase file to a
:class:`~obspy.core.event.Catalog` object.
.. note::
Coordinate conversion from coordinate frame of NonLinLoc model files /
location run to WGS84 has to be specified explicitly by the user if
necessary.
.. note::
An example can be found on the :mod:`~obspy.nlloc` submodule front
page in the documentation pages.
:param filename: File or file-like object in text mode.
:type coordinate_converter: func
:param coordinate_converter: Function to convert (x, y, z)
coordinates of NonLinLoc output to geographical coordinates and depth
in meters (longitude, latitude, depth in kilometers).
If left `None` NonLinLoc (x, y, z) output is left unchanged (e.g. if
it is in geographical coordinates already like for NonLinLoc in
global mode).
The function should accept three arguments x, y, z and return a
tuple of three values (lon, lat, depth in kilometers).
:type picks: list of :class:`~obspy.core.event.Pick`
:param picks: Original picks used to generate the NonLinLoc location.
If provided, the output event will include the original picks and the
arrivals in the output origin will link to them correctly (with their
`pick_id` attribute). If not provided, the output event will include
(the rather basic) pick information that can be reconstructed from the
NonLinLoc hypocenter-phase file.
:rtype: :class:`~obspy.core.event.Catalog`
"""
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()
lines = data.splitlines()
# remember picks originally used in location, if provided
original_picks = picks
if original_picks is None:
original_picks = []
# determine indices of block start/end of the NLLOC output file
indices_hyp = [None, None]
indices_phases = [None, None]
for i, line in enumerate(lines):
if line.startswith("NLLOC "):
indices_hyp[0] = i
elif line.startswith("END_NLLOC"):
indices_hyp[1] = i
elif line.startswith("PHASE "):
indices_phases[0] = i
elif line.startswith("END_PHASE"):
indices_phases[1] = i
if any([i is None for i in indices_hyp]):
msg = ("NLLOC HYP file seems corrupt,"
" could not detect 'NLLOC' and 'END_NLLOC' lines.")
raise RuntimeError(msg)
# strip any other lines around NLLOC block
lines = lines[indices_hyp[0]:indices_hyp[1]]
# extract PHASES lines (if any)
if any(indices_phases):
if not all(indices_phases):
msg = ("NLLOC HYP file seems corrupt, 'PHASE' block is corrupt.")
raise RuntimeError(msg)
i1, i2 = indices_phases
lines, phases_lines = lines[:i1] + lines[i2 + 1:], lines[i1 + 1:i2]
else:
phases_lines = []
lines = dict([line.split(None, 1) for line in lines])
line = lines["SIGNATURE"]
line = line.rstrip().split('"')[1]
signature, version, date, time = line.rsplit(" ", 3)
creation_time = UTCDateTime().strptime(date + time, str("%d%b%Y%Hh%Mm%S"))
# maximum likelihood origin location info line
line = lines["HYPOCENTER"]
x, y, z = map(float, line.split()[1:7:2])
if coordinate_converter:
x, y, z = coordinate_converter(x, y, z)
# origin time info line
line = lines["GEOGRAPHIC"]
year, month, day, hour, minute = map(int, line.split()[1:6])
seconds = float(line.split()[6])
time = UTCDateTime(year, month, day, hour, minute, seconds)
# distribution statistics line
line = lines["STATISTICS"]
covariance_XX = float(line.split()[7])
covariance_YY = float(line.split()[13])
covariance_ZZ = float(line.split()[17])
stats_info_string = str(
"Note: Depth/Latitude/Longitude errors are calculated from covariance "
"matrix as 1D marginal (Lon/Lat errors as great circle degrees) "
"while OriginUncertainty min/max horizontal errors are calculated "
"from 2D error ellipsoid and are therefore seemingly higher compared "
"to 1D errors. Error estimates can be reconstructed from the "
"following original NonLinLoc error statistics line:\nSTATISTICS " +
lines["STATISTICS"])
# goto location quality info line
line = lines["QML_OriginQuality"].split()
(assoc_phase_count, used_phase_count, assoc_station_count,
used_station_count, depth_phase_count) = map(int, line[1:11:2])
stderr, az_gap, sec_az_gap = map(float, line[11:17:2])
gt_level = line[17]
min_dist, max_dist, med_dist = map(float, line[19:25:2])
# goto location quality info line
line = lines["QML_OriginUncertainty"]
hor_unc, min_hor_unc, max_hor_unc, hor_unc_azim = \
map(float, line.split()[1:9:2])
# assign origin info
event = Event()
cat = Catalog(events=[event])
o = Origin()
event.origins = [o]
o.origin_uncertainty = OriginUncertainty()
o.quality = OriginQuality()
ou = o.origin_uncertainty
oq = o.quality
o.comments.append(Comment(text=stats_info_string))
cat.creation_info.creation_time = UTCDateTime()
cat.creation_info.version = "ObsPy %s" % __version__
event.creation_info = CreationInfo(creation_time=creation_time,
version=version)
event.creation_info.version = version
o.creation_info = CreationInfo(creation_time=creation_time,
version=version)
# negative values can appear on diagonal of covariance matrix due to a
# precision problem in NLLoc implementation when location coordinates are
# large compared to the covariances.
o.longitude = x
try:
o.longitude_errors.uncertainty = kilometer2degrees(sqrt(covariance_XX))
except ValueError:
if covariance_XX < 0:
msg = ("Negative value in XX value of covariance matrix, not "
"setting longitude error (epicentral uncertainties will "
"still be set in origin uncertainty).")
warnings.warn(msg)
else:
raise
o.latitude = y
try:
o.latitude_errors.uncertainty = kilometer2degrees(sqrt(covariance_YY))
except ValueError:
if covariance_YY < 0:
msg = ("Negative value in YY value of covariance matrix, not "
"setting longitude error (epicentral uncertainties will "
"still be set in origin uncertainty).")
warnings.warn(msg)
else:
raise
o.depth = z * 1e3 # meters!
o.depth_errors.uncertainty = sqrt(covariance_ZZ) * 1e3 # meters!
o.depth_errors.confidence_level = 68
o.depth_type = str("from location")
o.time = time
ou.horizontal_uncertainty = hor_unc
ou.min_horizontal_uncertainty = min_hor_unc
ou.max_horizontal_uncertainty = max_hor_unc
# values of -1 seem to be used for unset values, set to None
for field in ("horizontal_uncertainty", "min_horizontal_uncertainty",
"max_horizontal_uncertainty"):
if ou.get(field, -1) == -1:
ou[field] = None
else:
ou[field] *= 1e3 # meters!
ou.azimuth_max_horizontal_uncertainty = hor_unc_azim
ou.preferred_description = str("uncertainty ellipse")
ou.confidence_level = 68 # NonLinLoc in general uses 1-sigma (68%) level
oq.standard_error = stderr
oq.azimuthal_gap = az_gap
oq.secondary_azimuthal_gap = sec_az_gap
oq.used_phase_count = used_phase_count
oq.used_station_count = used_station_count
oq.associated_phase_count = assoc_phase_count
oq.associated_station_count = assoc_station_count
oq.depth_phase_count = depth_phase_count
oq.ground_truth_level = gt_level
oq.minimum_distance = kilometer2degrees(min_dist)
oq.maximum_distance = kilometer2degrees(max_dist)
oq.median_distance = kilometer2degrees(med_dist)
# go through all phase info lines
for line in phases_lines:
line = line.split()
arrival = Arrival()
o.arrivals.append(arrival)
station = str(line[0])
phase = str(line[4])
arrival.phase = phase
arrival.distance = kilometer2degrees(float(line[21]))
arrival.azimuth = float(line[23])
arrival.takeoff_angle = float(line[24])
arrival.time_residual = float(line[16])
arrival.time_weight = float(line[17])
pick = Pick()
wid = WaveformStreamID(station_code=station)
date, hourmin, sec = map(str, line[6:9])
t = UTCDateTime().strptime(date + hourmin, "%Y%m%d%H%M") + float(sec)
pick.waveform_id = wid
pick.time = t
pick.time_errors.uncertainty = float(line[10])
pick.phase_hint = phase
pick.onset = ONSETS.get(line[3].lower(), None)
pick.polarity = POLARITIES.get(line[5].lower(), None)
# try to determine original pick for each arrival
for pick_ in original_picks:
wid = pick_.waveform_id
if station == wid.station_code and phase == pick_.phase_hint:
pick = pick_
break
else:
# warn if original picks were specified and we could not associate
# the arrival correctly
if original_picks:
msg = ("Could not determine corresponding original pick for "
"arrival. "
"Falling back to pick information in NonLinLoc "
"hypocenter-phase file.")
warnings.warn(msg)
event.picks.append(pick)
arrival.pick_id = pick.resource_id
return cat
def read_nlloc_hyp(filename, coordinate_converter=None, picks=None, **kwargs):
"""
Reads a NonLinLoc Hypocenter-Phase file to a
:class:`~obspy.core.event.Catalog` object.
.. note::
Coordinate conversion from coordinate frame of NonLinLoc model files /
location run to WGS84 has to be specified explicitly by the user if
necessary.
.. note::
An example can be found on the :mod:`~obspy.io.nlloc` submodule front
page in the documentation pages.
:param filename: File or file-like object in text mode.
:type coordinate_converter: func
:param coordinate_converter: Function to convert (x, y, z)
coordinates of NonLinLoc output to geographical coordinates and depth
in meters (longitude, latitude, depth in kilometers).
If left ``None``, NonLinLoc (x, y, z) output is left unchanged (e.g. if
it is in geographical coordinates already like for NonLinLoc in
global mode).
The function should accept three arguments x, y, z (each of type
:class:`numpy.ndarray`) and return a tuple of three
:class:`numpy.ndarray` (lon, lat, depth in kilometers).
:type picks: list of :class:`~obspy.core.event.Pick`
:param picks: Original picks used to generate the NonLinLoc location.
If provided, the output event will include the original picks and the
arrivals in the output origin will link to them correctly (with their
``pick_id`` attribute). If not provided, the output event will include
(the rather basic) pick information that can be reconstructed from the
NonLinLoc hypocenter-phase file.
:rtype: :class:`~obspy.core.event.Catalog`
"""
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()
lines = data.splitlines()
# remember picks originally used in location, if provided
original_picks = picks
if original_picks is None:
original_picks = []
# determine indices of block start/end of the NLLOC output file
indices_hyp = [None, None]
indices_phases = [None, None]
for i, line in enumerate(lines):
if line.startswith("NLLOC "):
indices_hyp[0] = i
elif line.startswith("END_NLLOC"):
indices_hyp[1] = i
elif line.startswith("PHASE "):
indices_phases[0] = i
elif line.startswith("END_PHASE"):
indices_phases[1] = i
if any([i is None for i in indices_hyp]):
msg = ("NLLOC HYP file seems corrupt,"
" could not detect 'NLLOC' and 'END_NLLOC' lines.")
raise RuntimeError(msg)
# strip any other lines around NLLOC block
lines = lines[indices_hyp[0]:indices_hyp[1]]
# extract PHASES lines (if any)
if any(indices_phases):
if not all(indices_phases):
msg = ("NLLOC HYP file seems corrupt, 'PHASE' block is corrupt.")
raise RuntimeError(msg)
i1, i2 = indices_phases
lines, phases_lines = lines[:i1] + lines[i2 + 1:], lines[i1 + 1:i2]
else:
phases_lines = []
lines = dict([line.split(None, 1) for line in lines])
line = lines["SIGNATURE"]
line = line.rstrip().split('"')[1]
signature, version, date, time = line.rsplit(" ", 3)
creation_time = UTCDateTime().strptime(date + time, str("%d%b%Y%Hh%Mm%S"))
# maximum likelihood origin location info line
line = lines["HYPOCENTER"]
x, y, z = map(float, line.split()[1:7:2])
if coordinate_converter:
x, y, z = coordinate_converter(x, y, z)
# origin time info line
line = lines["GEOGRAPHIC"]
year, month, day, hour, minute = map(int, line.split()[1:6])
seconds = float(line.split()[6])
time = UTCDateTime(year, month, day, hour, minute, seconds)
# distribution statistics line
line = lines["STATISTICS"]
covariance_xx = float(line.split()[7])
covariance_yy = float(line.split()[13])
covariance_zz = float(line.split()[17])
stats_info_string = str(
"Note: Depth/Latitude/Longitude errors are calculated from covariance "
"matrix as 1D marginal (Lon/Lat errors as great circle degrees) "
"while OriginUncertainty min/max horizontal errors are calculated "
"from 2D error ellipsoid and are therefore seemingly higher compared "
"to 1D errors. Error estimates can be reconstructed from the "
"following original NonLinLoc error statistics line:\nSTATISTICS " +
lines["STATISTICS"])
# goto location quality info line
line = lines["QML_OriginQuality"].split()
(assoc_phase_count, used_phase_count, assoc_station_count,
used_station_count, depth_phase_count) = map(int, line[1:11:2])
stderr, az_gap, sec_az_gap = map(float, line[11:17:2])
gt_level = line[17]
min_dist, max_dist, med_dist = map(float, line[19:25:2])
# goto location quality info line
line = lines["QML_OriginUncertainty"]
hor_unc, min_hor_unc, max_hor_unc, hor_unc_azim = \
map(float, line.split()[1:9:2])
# assign origin info
event = Event()
cat = Catalog(events=[event])
o = Origin()
event.origins = [o]
o.origin_uncertainty = OriginUncertainty()
o.quality = OriginQuality()
ou = o.origin_uncertainty
oq = o.quality
o.comments.append(Comment(text=stats_info_string))
cat.creation_info.creation_time = UTCDateTime()
cat.creation_info.version = "ObsPy %s" % __version__
event.creation_info = CreationInfo(creation_time=creation_time,
version=version)
event.creation_info.version = version
o.creation_info = CreationInfo(creation_time=creation_time,
version=version)
# negative values can appear on diagonal of covariance matrix due to a
# precision problem in NLLoc implementation when location coordinates are
# large compared to the covariances.
o.longitude = x
try:
o.longitude_errors.uncertainty = kilometer2degrees(sqrt(covariance_xx))
except ValueError:
if covariance_xx < 0:
msg = ("Negative value in XX value of covariance matrix, not "
"setting longitude error (epicentral uncertainties will "
"still be set in origin uncertainty).")
warnings.warn(msg)
else:
raise
o.latitude = y
try:
o.latitude_errors.uncertainty = kilometer2degrees(sqrt(covariance_yy))
except ValueError:
if covariance_yy < 0:
msg = ("Negative value in YY value of covariance matrix, not "
"setting longitude error (epicentral uncertainties will "
"still be set in origin uncertainty).")
warnings.warn(msg)
else:
raise
o.depth = z * 1e3 # meters!
o.depth_errors.uncertainty = sqrt(covariance_zz) * 1e3 # meters!
o.depth_errors.confidence_level = 68
o.depth_type = str("from location")
o.time = time
ou.horizontal_uncertainty = hor_unc
ou.min_horizontal_uncertainty = min_hor_unc
ou.max_horizontal_uncertainty = max_hor_unc
# values of -1 seem to be used for unset values, set to None
for field in ("horizontal_uncertainty", "min_horizontal_uncertainty",
"max_horizontal_uncertainty"):
if ou.get(field, -1) == -1:
ou[field] = None
else:
ou[field] *= 1e3 # meters!
ou.azimuth_max_horizontal_uncertainty = hor_unc_azim
ou.preferred_description = str("uncertainty ellipse")
ou.confidence_level = 68 # NonLinLoc in general uses 1-sigma (68%) level
oq.standard_error = stderr
oq.azimuthal_gap = az_gap
oq.secondary_azimuthal_gap = sec_az_gap
oq.used_phase_count = used_phase_count
oq.used_station_count = used_station_count
oq.associated_phase_count = assoc_phase_count
oq.associated_station_count = assoc_station_count
oq.depth_phase_count = depth_phase_count
oq.ground_truth_level = gt_level
oq.minimum_distance = kilometer2degrees(min_dist)
oq.maximum_distance = kilometer2degrees(max_dist)
oq.median_distance = kilometer2degrees(med_dist)
# go through all phase info lines
for line in phases_lines:
line = line.split()
arrival = Arrival()
o.arrivals.append(arrival)
station = str(line[0])
phase = str(line[4])
arrival.phase = phase
arrival.distance = kilometer2degrees(float(line[21]))
arrival.azimuth = float(line[23])
arrival.takeoff_angle = float(line[24])
arrival.time_residual = float(line[16])
arrival.time_weight = float(line[17])
pick = Pick()
wid = WaveformStreamID(station_code=station)
date, hourmin, sec = map(str, line[6:9])
t = UTCDateTime().strptime(date + hourmin, "%Y%m%d%H%M") + float(sec)
pick.waveform_id = wid
pick.time = t
pick.time_errors.uncertainty = float(line[10])
pick.phase_hint = phase
pick.onset = ONSETS.get(line[3].lower(), None)
pick.polarity = POLARITIES.get(line[5].lower(), None)
# try to determine original pick for each arrival
for pick_ in original_picks:
wid = pick_.waveform_id
if station == wid.station_code and phase == pick_.phase_hint:
pick = pick_
break
else:
# warn if original picks were specified and we could not associate
# the arrival correctly
if original_picks:
msg = ("Could not determine corresponding original pick for "
"arrival. "
"Falling back to pick information in NonLinLoc "
"hypocenter-phase file.")
warnings.warn(msg)
event.picks.append(pick)
arrival.pick_id = pick.resource_id
return cat
def _read_single_hypocenter(lines, coordinate_converter, original_picks):
"""
Given a list of lines (starting with a 'NLLOC' line and ending with a
'END_NLLOC' line), parse them into an Event.
"""
try:
# some paranoid checks..
assert lines[0].startswith("NLLOC ")
assert lines[-1].startswith("END_NLLOC")
for line in lines[1:-1]:
assert not line.startswith("NLLOC ")
assert not line.startswith("END_NLLOC")
except Exception:
msg = ("This should not have happened, please report this as a bug at "
"https://github.com/obspy/obspy/issues.")
raise Exception(msg)
indices_phases = [None, None]
for i, line in enumerate(lines):
if line.startswith("PHASE "):
indices_phases[0] = i
elif line.startswith("END_PHASE"):
indices_phases[1] = i
# extract PHASES lines (if any)
if any(indices_phases):
if not all(indices_phases):
msg = ("NLLOC HYP file seems corrupt, 'PHASE' block is corrupt.")
raise RuntimeError(msg)
i1, i2 = indices_phases
lines, phases_lines = lines[:i1] + lines[i2 + 1:], lines[i1 + 1:i2]
else:
phases_lines = []
lines = dict([line.split(None, 1) for line in lines[:-1]])
line = lines["SIGNATURE"]
line = line.rstrip().split('"')[1]
signature, version, date, time = line.rsplit(" ", 3)
# new NLLoc > 6.0 seems to add prefix 'run:' before date
if date.startswith('run:'):
date = date[4:]
signature = signature.strip()
creation_time = UTCDateTime.strptime(date + time, str("%d%b%Y%Hh%Mm%S"))
if coordinate_converter:
# maximum likelihood origin location in km info line
line = lines["HYPOCENTER"]
x, y, z = coordinate_converter(*map(float, line.split()[1:7:2]))
else:
# maximum likelihood origin location lon lat info line
line = lines["GEOGRAPHIC"]
y, x, z = map(float, line.split()[8:13:2])
# maximum likelihood origin time info line
line = lines["GEOGRAPHIC"]
year, mon, day, hour, min = map(int, line.split()[1:6])
seconds = float(line.split()[6])
time = UTCDateTime(year, mon, day, hour, min, seconds, strict=False)
# distribution statistics line
line = lines["STATISTICS"]
covariance_xx = float(line.split()[7])
covariance_yy = float(line.split()[13])
covariance_zz = float(line.split()[17])
stats_info_string = str(
"Note: Depth/Latitude/Longitude errors are calculated from covariance "
"matrix as 1D marginal (Lon/Lat errors as great circle degrees) "
"while OriginUncertainty min/max horizontal errors are calculated "
"from 2D error ellipsoid and are therefore seemingly higher compared "
"to 1D errors. Error estimates can be reconstructed from the "
"following original NonLinLoc error statistics line:\nSTATISTICS " +
lines["STATISTICS"])
# goto location quality info line
line = lines["QML_OriginQuality"].split()
(assoc_phase_count, used_phase_count, assoc_station_count,
used_station_count, depth_phase_count) = map(int, line[1:11:2])
stderr, az_gap, sec_az_gap = map(float, line[11:17:2])
gt_level = line[17]
min_dist, max_dist, med_dist = map(float, line[19:25:2])
# goto location quality info line
line = lines["QML_OriginUncertainty"]
if "COMMENT" in lines:
comment = lines["COMMENT"].strip()
comment = comment.strip('\'"')
comment = comment.strip()
hor_unc, min_hor_unc, max_hor_unc, hor_unc_azim = \
map(float, line.split()[1:9:2])
# assign origin info
event = Event()
o = Origin()
event.origins = [o]
event.preferred_origin_id = o.resource_id
o.origin_uncertainty = OriginUncertainty()
o.quality = OriginQuality()
ou = o.origin_uncertainty
oq = o.quality
o.comments.append(Comment(text=stats_info_string, force_resource_id=False))
event.comments.append(Comment(text=comment, force_resource_id=False))
# SIGNATURE field's first item is LOCSIG, which is supposed to be
# 'Identification of an individual, institiution or other entity'
# according to
# http://alomax.free.fr/nlloc/soft6.00/control.html#_NLLoc_locsig_
# so use it as author in creation info
event.creation_info = CreationInfo(creation_time=creation_time,
version=version,
author=signature)
o.creation_info = CreationInfo(creation_time=creation_time,
version=version,
author=signature)
# negative values can appear on diagonal of covariance matrix due to a
# precision problem in NLLoc implementation when location coordinates are
# large compared to the covariances.
o.longitude = x
try:
o.longitude_errors.uncertainty = kilometer2degrees(sqrt(covariance_xx))
except ValueError:
if covariance_xx < 0:
msg = ("Negative value in XX value of covariance matrix, not "
"setting longitude error (epicentral uncertainties will "
"still be set in origin uncertainty).")
warnings.warn(msg)
else:
raise
o.latitude = y
try:
o.latitude_errors.uncertainty = kilometer2degrees(sqrt(covariance_yy))
except ValueError:
if covariance_yy < 0:
msg = ("Negative value in YY value of covariance matrix, not "
"setting longitude error (epicentral uncertainties will "
"still be set in origin uncertainty).")
warnings.warn(msg)
else:
raise
o.depth = z * 1e3 # meters!
o.depth_errors.uncertainty = sqrt(covariance_zz) * 1e3 # meters!
o.depth_errors.confidence_level = 68
o.depth_type = str("from location")
o.time = time
ou.horizontal_uncertainty = hor_unc
ou.min_horizontal_uncertainty = min_hor_unc
ou.max_horizontal_uncertainty = max_hor_unc
# values of -1 seem to be used for unset values, set to None
for field in ("horizontal_uncertainty", "min_horizontal_uncertainty",
"max_horizontal_uncertainty"):
if ou.get(field, -1) == -1:
ou[field] = None
else:
ou[field] *= 1e3 # meters!
ou.azimuth_max_horizontal_uncertainty = hor_unc_azim
ou.preferred_description = str("uncertainty ellipse")
ou.confidence_level = 68 # NonLinLoc in general uses 1-sigma (68%) level
oq.standard_error = stderr
oq.azimuthal_gap = az_gap
oq.secondary_azimuthal_gap = sec_az_gap
oq.used_phase_count = used_phase_count
oq.used_station_count = used_station_count
oq.associated_phase_count = assoc_phase_count
oq.associated_station_count = assoc_station_count
oq.depth_phase_count = depth_phase_count
oq.ground_truth_level = gt_level
oq.minimum_distance = kilometer2degrees(min_dist)
oq.maximum_distance = kilometer2degrees(max_dist)
oq.median_distance = kilometer2degrees(med_dist)
# go through all phase info lines
for line in phases_lines:
line = line.split()
arrival = Arrival()
o.arrivals.append(arrival)
station = str(line[0])
phase = str(line[4])
arrival.phase = phase
arrival.distance = kilometer2degrees(float(line[21]))
arrival.azimuth = float(line[23])
arrival.takeoff_angle = float(line[24])
arrival.time_residual = float(line[16])
arrival.time_weight = float(line[17])
pick = Pick()
# network codes are not used by NonLinLoc, so they can not be known
# when reading the .hyp file.. to conform with QuakeML standard set an
# empty network code
wid = WaveformStreamID(network_code="", station_code=station)
# have to split this into ints for overflow to work correctly
date, hourmin, sec = map(str, line[6:9])
ymd = [int(date[:4]), int(date[4:6]), int(date[6:8])]
hm = [int(hourmin[:2]), int(hourmin[2:4])]
t = UTCDateTime(*(ymd + hm), strict=False) + float(sec)
pick.waveform_id = wid
pick.time = t
pick.time_errors.uncertainty = float(line[10])
pick.phase_hint = phase
pick.onset = ONSETS.get(line[3].lower(), None)
pick.polarity = POLARITIES.get(line[5].lower(), None)
# try to determine original pick for each arrival
for pick_ in original_picks:
wid = pick_.waveform_id
if station == wid.station_code and phase == pick_.phase_hint:
pick = pick_
break
else:
# warn if original picks were specified and we could not associate
# the arrival correctly
if original_picks:
msg = ("Could not determine corresponding original pick for "
"arrival. "
"Falling back to pick information in NonLinLoc "
"hypocenter-phase file.")
warnings.warn(msg)
event.picks.append(pick)
arrival.pick_id = pick.resource_id
event.scope_resource_ids()
return event
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 _parseRecordDp(self, line, event):
"""
Parses the 'source parameter data - primary' record Dp
"""
source_contributor = line[2:6].strip()
computation_type = line[6]
exponent = self._intZero(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._floatWithFormat(orig_time_stderr, "2.1", scale)
centroid_latitude = self._floatWithFormat(line[17:21], "4.2")
lat_type = line[21]
if centroid_latitude is not None:
centroid_latitude *= self._coordinateSign(lat_type)
lat_stderr = line[22:25]
if lat_stderr == "FX":
lat_stderr = "Fixed"
else:
lat_stderr = self._floatWithFormat(lat_stderr, "3.2", scale)
centroid_longitude = self._floatWithFormat(line[25:30], "5.2")
lon_type = line[30]
if centroid_longitude is not None:
centroid_longitude *= self._coordinateSign(lon_type)
lon_stderr = line[31:34]
if lon_stderr == "FX":
lon_stderr = "Fixed"
else:
lon_stderr = self._floatWithFormat(lon_stderr, "3.2", scale)
centroid_depth = self._floatWithFormat(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._floatWithFormat(depth_stderr, "2.1", scale)
station_number = self._intZero(line[40:43])
component_number = self._intZero(line[43:46])
station_number2 = self._intZero(line[46:48])
component_number2 = self._intZero(line[48:51])
# unused: half_duration = self._floatWithFormat(line[51:54], '3.1')
moment = self._floatWithFormat(line[54:56], "2.1")
moment_stderr = self._floatWithFormat(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._storeUncertainty(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._storeUncertainty(origin.latitude_errors, self._latErrToDeg(lat_stderr))
self._storeUncertainty(origin.longitude_errors, self._lonErrToDeg(lon_stderr, origin.latitude))
if depth_stderr == "Fixed":
origin.depth_type = "operator assigned"
else:
origin.depth_type = "from location"
self._storeUncertainty(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.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._storeUncertainty(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 _parseRecordDp(self, line, event):
"""
Parses the 'source parameter data - primary' record Dp
"""
source_contributor = line[2:6].strip()
computation_type = line[6]
exponent = self._intZero(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._floatWithFormat(orig_time_stderr, '2.1', scale)
centroid_latitude = self._floatWithFormat(line[17:21], '4.2')
lat_type = line[21]
if centroid_latitude is not None:
centroid_latitude *= self._coordinateSign(lat_type)
lat_stderr = line[22:25]
if lat_stderr == 'FX':
lat_stderr = 'Fixed'
else:
lat_stderr = self._floatWithFormat(lat_stderr, '3.2', scale)
centroid_longitude = self._floatWithFormat(line[25:30], '5.2')
lon_type = line[30]
if centroid_longitude is not None:
centroid_longitude *= self._coordinateSign(lon_type)
lon_stderr = line[31:34]
if lon_stderr == 'FX':
lon_stderr = 'Fixed'
else:
lon_stderr = self._floatWithFormat(lon_stderr, '3.2', scale)
centroid_depth = self._floatWithFormat(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._floatWithFormat(depth_stderr, '2.1', scale)
station_number = self._intZero(line[40:43])
component_number = self._intZero(line[43:46])
station_number2 = self._intZero(line[46:48])
component_number2 = self._intZero(line[48:51])
#unused: half_duration = self._floatWithFormat(line[51:54], '3.1')
moment = self._floatWithFormat(line[54:56], '2.1')
moment_stderr = self._floatWithFormat(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._storeUncertainty(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._storeUncertainty(origin.latitude_errors,
self._latErrToDeg(lat_stderr))
self._storeUncertainty(
origin.longitude_errors,
self._lonErrToDeg(lon_stderr, origin.latitude))
if depth_stderr == 'Fixed':
origin.depth_type = 'operator assigned'
else:
origin.depth_type = 'from location'
self._storeUncertainty(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.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._storeUncertainty(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 _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
def surf_events_to_cat(loc_file, pick_file):
"""
Take location files (hypoinverse formatted) and picks (format TBD)
and creates a single obspy catalog for later use and dissemination.
:param loc_file: File path
:param pick_file: File path
:return: obspy.core.Catalog
"""
# Read/parse location file and create Events for each
surf_cat = Catalog()
# Parse the pick file to a dictionary
pick_dict = parse_picks(pick_file)
with open(loc_file, 'r') as f:
next(f)
for ln in f:
ln = ln.strip('\n')
line = ln.split(',')
eid = line[0]
if eid not in pick_dict:
print('No picks for this location, skipping for now.')
continue
ot = UTCDateTime(line[1])
hmc_east = float(line[2])
hmc_north = float(line[3])
hmc_elev = float(line[4])
gap = float(line[-5])
rms = float(line[-3])
errXY = float(line[-2])
errZ = float(line[-1])
converter = SURF_converter()
lon, lat, elev = converter.to_lonlat((hmc_east, hmc_north,
hmc_elev))
o = Origin(time=ot, longitude=lon, latitude=lat, depth=130 - elev)
o.origin_uncertainty = OriginUncertainty()
o.quality = OriginQuality()
ou = o.origin_uncertainty
oq = o.quality
ou.horizontal_uncertainty = errXY * 1e3
ou.preferred_description = "horizontal uncertainty"
o.depth_errors.uncertainty = errZ * 1e3
oq.standard_error = rms
oq.azimuthal_gap = gap
extra = AttribDict({
'hmc_east': {
'value': hmc_east,
'namespace': 'smi:local/hmc'
},
'hmc_north': {
'value': hmc_north,
'namespace': 'smi:local/hmc'
},
'hmc_elev': {
'value': hmc_elev,
'namespace': 'smi:local/hmc'
},
'hmc_eid': {
'value': eid,
'namespace': 'smi:local/hmc'
}
})
o.extra = extra
rid = ResourceIdentifier(id=ot.strftime('%Y%m%d%H%M%S%f'))
# Dummy magnitude of 1. for all events until further notice
mag = Magnitude(mag=1., mag_errors=QuantityError(uncertainty=1.))
ev = Event(origins=[o], magnitudes=[mag],
picks=pick_dict[eid], resource_id=rid)
surf_cat.append(ev)
return surf_cat
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 _read_single_hypocenter(lines, coordinate_converter, original_picks):
"""
Given a list of lines (starting with a 'NLLOC' line and ending with a
'END_NLLOC' line), parse them into an Event.
"""
try:
# some paranoid checks..
assert lines[0].startswith("NLLOC ")
assert lines[-1].startswith("END_NLLOC")
for line in lines[1:-1]:
assert not line.startswith("NLLOC ")
assert not line.startswith("END_NLLOC")
except Exception:
msg = ("This should not have happened, please report this as a bug at "
"https://github.com/obspy/obspy/issues.")
raise Exception(msg)
indices_phases = [None, None]
for i, line in enumerate(lines):
if line.startswith("PHASE "):
indices_phases[0] = i
elif line.startswith("END_PHASE"):
indices_phases[1] = i
# extract PHASES lines (if any)
if any(indices_phases):
if not all(indices_phases):
msg = ("NLLOC HYP file seems corrupt, 'PHASE' block is corrupt.")
raise RuntimeError(msg)
i1, i2 = indices_phases
lines, phases_lines = lines[:i1] + lines[i2 + 1:], lines[i1 + 1:i2]
else:
phases_lines = []
lines = dict([line.split(None, 1) for line in lines[:-1]])
line = lines["SIGNATURE"]
line = line.rstrip().split('"')[1]
signature, version, date, time = line.rsplit(" ", 3)
# new NLLoc > 6.0 seems to add prefix 'run:' before date
if date.startswith('run:'):
date = date[4:]
signature = signature.strip()
creation_time = UTCDateTime.strptime(date + time, str("%d%b%Y%Hh%Mm%S"))
if coordinate_converter:
# maximum likelihood origin location in km info line
line = lines["HYPOCENTER"]
x, y, z = coordinate_converter(*map(float, line.split()[1:7:2]))
else:
# maximum likelihood origin location lon lat info line
line = lines["GEOGRAPHIC"]
y, x, z = map(float, line.split()[8:13:2])
# maximum likelihood origin time info line
line = lines["GEOGRAPHIC"]
year, mon, day, hour, min = map(int, line.split()[1:6])
seconds = float(line.split()[6])
time = UTCDateTime(year, mon, day, hour, min, seconds, strict=False)
# distribution statistics line
line = lines["STATISTICS"]
covariance_xx = float(line.split()[7])
covariance_yy = float(line.split()[13])
covariance_zz = float(line.split()[17])
stats_info_string = str(
"Note: Depth/Latitude/Longitude errors are calculated from covariance "
"matrix as 1D marginal (Lon/Lat errors as great circle degrees) "
"while OriginUncertainty min/max horizontal errors are calculated "
"from 2D error ellipsoid and are therefore seemingly higher compared "
"to 1D errors. Error estimates can be reconstructed from the "
"following original NonLinLoc error statistics line:\nSTATISTICS " +
lines["STATISTICS"])
# goto location quality info line
line = lines["QML_OriginQuality"].split()
(assoc_phase_count, used_phase_count, assoc_station_count,
used_station_count, depth_phase_count) = map(int, line[1:11:2])
stderr, az_gap, sec_az_gap = map(float, line[11:17:2])
gt_level = line[17]
min_dist, max_dist, med_dist = map(float, line[19:25:2])
# goto location quality info line
line = lines["QML_OriginUncertainty"]
if "COMMENT" in lines:
comment = lines["COMMENT"].strip()
comment = comment.strip('\'"')
comment = comment.strip()
hor_unc, min_hor_unc, max_hor_unc, hor_unc_azim = \
map(float, line.split()[1:9:2])
# assign origin info
event = Event()
o = Origin()
event.origins = [o]
event.preferred_origin_id = o.resource_id
o.origin_uncertainty = OriginUncertainty()
o.quality = OriginQuality()
ou = o.origin_uncertainty
oq = o.quality
o.comments.append(Comment(text=stats_info_string, force_resource_id=False))
event.comments.append(Comment(text=comment, force_resource_id=False))
# SIGNATURE field's first item is LOCSIG, which is supposed to be
# 'Identification of an individual, institiution or other entity'
# according to
# http://alomax.free.fr/nlloc/soft6.00/control.html#_NLLoc_locsig_
# so use it as author in creation info
event.creation_info = CreationInfo(creation_time=creation_time,
version=version,
author=signature)
o.creation_info = CreationInfo(creation_time=creation_time,
version=version,
author=signature)
# negative values can appear on diagonal of covariance matrix due to a
# precision problem in NLLoc implementation when location coordinates are
# large compared to the covariances.
o.longitude = x
try:
o.longitude_errors.uncertainty = kilometer2degrees(sqrt(covariance_xx))
except ValueError:
if covariance_xx < 0:
msg = ("Negative value in XX value of covariance matrix, not "
"setting longitude error (epicentral uncertainties will "
"still be set in origin uncertainty).")
warnings.warn(msg)
else:
raise
o.latitude = y
try:
o.latitude_errors.uncertainty = kilometer2degrees(sqrt(covariance_yy))
except ValueError:
if covariance_yy < 0:
msg = ("Negative value in YY value of covariance matrix, not "
"setting longitude error (epicentral uncertainties will "
"still be set in origin uncertainty).")
warnings.warn(msg)
else:
raise
o.depth = z * 1e3 # meters!
o.depth_errors.uncertainty = sqrt(covariance_zz) * 1e3 # meters!
o.depth_errors.confidence_level = 68
o.depth_type = str("from location")
o.time = time
ou.horizontal_uncertainty = hor_unc
ou.min_horizontal_uncertainty = min_hor_unc
ou.max_horizontal_uncertainty = max_hor_unc
# values of -1 seem to be used for unset values, set to None
for field in ("horizontal_uncertainty", "min_horizontal_uncertainty",
"max_horizontal_uncertainty"):
if ou.get(field, -1) == -1:
ou[field] = None
else:
ou[field] *= 1e3 # meters!
ou.azimuth_max_horizontal_uncertainty = hor_unc_azim
ou.preferred_description = str("uncertainty ellipse")
ou.confidence_level = 68 # NonLinLoc in general uses 1-sigma (68%) level
oq.standard_error = stderr
oq.azimuthal_gap = az_gap
oq.secondary_azimuthal_gap = sec_az_gap
oq.used_phase_count = used_phase_count
oq.used_station_count = used_station_count
oq.associated_phase_count = assoc_phase_count
oq.associated_station_count = assoc_station_count
oq.depth_phase_count = depth_phase_count
oq.ground_truth_level = gt_level
oq.minimum_distance = kilometer2degrees(min_dist)
oq.maximum_distance = kilometer2degrees(max_dist)
oq.median_distance = kilometer2degrees(med_dist)
# go through all phase info lines
for line in phases_lines:
line = line.split()
arrival = Arrival()
o.arrivals.append(arrival)
station = str(line[0])
phase = str(line[4])
arrival.phase = phase
arrival.distance = kilometer2degrees(float(line[21]))
arrival.azimuth = float(line[23])
arrival.takeoff_angle = float(line[24])
arrival.time_residual = float(line[16])
arrival.time_weight = float(line[17])
pick = Pick()
# network codes are not used by NonLinLoc, so they can not be known
# when reading the .hyp file.. to conform with QuakeML standard set an
# empty network code
wid = WaveformStreamID(network_code="", station_code=station)
# have to split this into ints for overflow to work correctly
date, hourmin, sec = map(str, line[6:9])
ymd = [int(date[:4]), int(date[4:6]), int(date[6:8])]
hm = [int(hourmin[:2]), int(hourmin[2:4])]
t = UTCDateTime(*(ymd + hm), strict=False) + float(sec)
pick.waveform_id = wid
pick.time = t
pick.time_errors.uncertainty = float(line[10])
pick.phase_hint = phase
pick.onset = ONSETS.get(line[3].lower(), None)
pick.polarity = POLARITIES.get(line[5].lower(), None)
# try to determine original pick for each arrival
for pick_ in original_picks:
wid = pick_.waveform_id
if station == wid.station_code and phase == pick_.phase_hint:
pick = pick_
break
else:
# warn if original picks were specified and we could not associate
# the arrival correctly
if original_picks:
msg = ("Could not determine corresponding original pick for "
"arrival. "
"Falling back to pick information in NonLinLoc "
"hypocenter-phase file.")
warnings.warn(msg)
event.picks.append(pick)
arrival.pick_id = pick.resource_id
event.scope_resource_ids()
return event
def _parse_first_line_origin(self, line, event, magnitudes):
"""
Parse the first line of origin data.
:type line: str
:param line: Line to parse.
:type event: :class:`~obspy.core.event.event.Event`
:param event: Event of the origin.
:type magnitudes: list of
:class:`~obspy.core.event.magnitude.Magnitude`
:param magnitudes: Store magnitudes in a list to keep
their positions.
:rtype: :class:`~obspy.core.event.origin.Origin`,
:class:`~obspy.core.event.resourceid.ResourceIdentifier`
:returns: Parsed origin or None, resource identifier of the
origin.
"""
magnitude_types = []
magnitude_values = []
magnitude_station_counts = []
fields = self.fields['line_1']
time_origin = line[fields['time']].strip()
time_fixed_flag = line[fields['time_fixf']].strip()
latitude = line[fields['lat']].strip()
longitude = line[fields['lon']].strip()
epicenter_fixed_flag = line[fields['epicenter_fixf']].strip()
depth = line[fields['depth']].strip()
depth_fixed_flag = line[fields['depth_fixf']].strip()
phase_count = line[fields['n_def']].strip()
station_count = line[fields['n_sta']].strip()
azimuthal_gap = line[fields['gap']].strip()
magnitude_types.append(line[fields['mag_type_1']].strip())
magnitude_values.append(line[fields['mag_1']].strip())
magnitude_station_counts.append(line[fields['mag_n_sta_1']].strip())
magnitude_types.append(line[fields['mag_type_2']].strip())
magnitude_values.append(line[fields['mag_2']].strip())
magnitude_station_counts.append(line[fields['mag_n_sta_2']].strip())
magnitude_types.append(line[fields['mag_type_3']].strip())
magnitude_values.append(line[fields['mag_3']].strip())
magnitude_station_counts.append(line[fields['mag_n_sta_3']].strip())
author = line[fields['author']].strip()
origin_id = line[fields['id']].strip()
origin = Origin()
origin.quality = OriginQuality()
try:
origin.time = UTCDateTime(time_origin.replace('/', '-'))
origin.latitude = float(latitude)
origin.longitude = float(longitude)
except (TypeError, ValueError):
self._warn('Missing origin data, skipping event')
return None, None
origin.time_fixed = time_fixed_flag.lower() == 'f'
origin.epicenter_fixed = epicenter_fixed_flag.lower() == 'f'
try:
# Convert value from km to m
origin.depth = float(depth) * 1000
except ValueError:
pass
try:
origin.depth_type = DEPTH_TYPES[depth_fixed_flag]
except KeyError:
origin.depth_type = OriginDepthType('from location')
try:
origin.quality.used_phase_count = int(phase_count)
origin.quality.associated_phase_count = int(phase_count)
except ValueError:
pass
try:
origin.quality.used_station_count = int(station_count)
origin.quality.associated_station_count = int(station_count)
except ValueError:
pass
try:
origin.quality.azimuthal_gap = float(azimuthal_gap)
except ValueError:
pass
self.author = author
origin.creation_info = self._get_creation_info()
public_id = "origin/%s" % origin_id
origin_res_id = self._get_res_id(public_id)
for i in range(3):
try:
magnitude = Magnitude()
magnitude.creation_info = self._get_creation_info()
magnitude.magnitude_type = magnitude_types[i]
magnitude.mag = float(magnitude_values[i])
magnitude.station_count = int(magnitude_station_counts[i])
magnitude.origin_id = origin_res_id
magnitudes.append(magnitude)
event.magnitudes.append(magnitude)
except ValueError:
# Magnitude can be empty but we need to keep the
# position between mag1, mag2 or mag3.
magnitudes.append(None)
return origin, origin_res_id
