def read_cat_ref(cat_file):
"""
Parses a given refrence catalogue (in ascii format,see the header for details)
output is Obspy catalogue object
"""
cat_ref = np.loadtxt(cat_file,delimiter=',',skiprows=1)
cat = Catalog()
for i,e in enumerate(cat_ref):
event = Event(resource_id='smi:local/='+str(i),creation_info='HG')
origin = Origin()
origin.time = UTCDateTime(int(e[2]),int(e[3]),int(e[4]),
int(e[7]),int(e[8]),e[9])
origin.longitude = e[0]
origin.latitude = e[1]
origin.depth = e[6] * 1000. #in meters
event.origins.append(origin)
if ~(np.isnan(e[10])):
mag = Magnitude(creation_info='HER')
mag.mag = e[10]
mag.magnitude_type = 'Mw'
event.magnitudes.append(mag)
if ~(np.isnan(e[11])):
mag = Magnitude(creation_info='MAR')
mag.mag = e[11]
mag.magnitude_type = 'Mw'
event.magnitudes.append(mag)
if ~(np.isnan(e[12])):
mag = Magnitude(creation_info='SIP')
mag.mag = e[12]
mag.magnitude_type = 'Mw'
event.magnitudes.append(mag)
cat.append(event)
return cat
def _parseRecordAE(self, line, event):
"""
Parses the 'additional hypocenter error and magnitude record' AE
"""
orig_time_stderr = self._floatUnused(line[2:7])
latitude_stderr = self._floatUnused(line[8:14])
longitude_stderr = self._floatUnused(line[15:21])
depth_stderr = self._floatUnused(line[22:27])
gap = self._floatUnused(line[28:33])
mag1 = self._float(line[33:36])
mag1_type = line[36:38]
mag2 = self._float(line[43:46])
mag2_type = line[46:48]
evid = event.resource_id.id.split('/')[-1]
#this record is to be associated to the latest origin
origin = event.origins[-1]
self._storeUncertainty(origin.time_errors, orig_time_stderr)
self._storeUncertainty(origin.latitude_errors,
self._latErrToDeg(latitude_stderr))
self._storeUncertainty(
origin.longitude_errors,
self._lonErrToDeg(longitude_stderr, origin.latitude))
self._storeUncertainty(origin.depth_errors, depth_stderr, scale=1000)
origin.quality.azimuthal_gap = gap
if mag1 > 0:
mag = Magnitude()
mag1_id = mag1_type.lower()
res_id = '/'.join((res_id_prefix, 'magnitude', evid, mag1_id))
mag.resource_id = ResourceIdentifier(id=res_id)
mag.creation_info = CreationInfo(
agency_id=origin.creation_info.agency_id)
mag.mag = mag1
mag.magnitude_type = mag1_type
mag.origin_id = origin.resource_id
event.magnitudes.append(mag)
if mag2 > 0:
mag = Magnitude()
mag2_id = mag2_type.lower()
if mag2_id == mag1_id:
mag2_id += '2'
res_id = '/'.join((res_id_prefix, 'magnitude', evid, mag2_id))
mag.resource_id = ResourceIdentifier(id=res_id)
mag.creation_info = CreationInfo(
agency_id=origin.creation_info.agency_id)
mag.mag = mag2
mag.magnitude_type = mag2_type
mag.origin_id = origin.resource_id
event.magnitudes.append(mag)
def plot_some_events():
from obspy.core.event import Catalog, Event, Origin, Magnitude
from obspy.core import UTCDateTime as UTC
eqs = """2008-09-10T16:12:03 6.0 -20.40 -69.40 40
2008-03-24T20:39:06 5.9 -20.10 -69.20 85
2008-03-01T19:51:59 5.7 -20.10 -69.60 15
2008-02-15T16:54:04 5.5 -23.00 -70.20 32
2008-02-04T17:01:30 6.6 -20.20 -70.00 36
2007-12-16T08:09:16 7.1 -22.80 -70.00 14
2007-11-14T15:40:51 7.8 -22.34 -70.06 37""" #GEOFON:-22.30 -69.80
events = []
for eq in eqs.split('\n'):
time, mag, lat, lon, depth = eq.split()
ev = Event(event_type='earthquake', creation_info='GEOFON',
origins=[Origin(time=UTC(time), latitude=float(lat),
longitude=float(lon), depth=float(depth))],
magnitudes=[Magnitude(mag=float(mag), magnitude_type='M')])
events.append(ev)
cat = Catalog(events[::-1])
#print cat
#cat.plot(projection='local')
lons = [ev.origins[0].longitude for ev in cat]
lats = [ev.origins[0].latitude for ev in cat]
dates = [ev.origins[0].time for ev in cat]
mags = [ev.magnitudes[0].mag for ev in cat]
def get_event_object(self):
'''
update events otime,lat,lon and mag with IRIS (or any other clients) catalog
'''
# get parameters from the cataog
if self.use_catalog == 1:
print("WARNING using event data from the IRIS catalog")
cat = self.client.get_events(
starttime=self.otime - self.sec_before_after_event,
endtime=self.otime + self.sec_before_after_event)
self.ev = cat[0]
# use catalog parameters
self.otime = self.ev.origins[0].time
self.elat = self.ev.origins[0].latitude
self.elon = self.ev.origins[0].longitude
self.edep = self.ev.origins[0].depth
self.emag = self.ev.magnitudes[0].mag
# use parameters from the input file
else:
print("WARNING using event data from user-defined catalog")
#self.ev = Event()
org = Origin()
org.latitude = self.elat
org.longitude = self.elon
org.depth = self.edep
org.time = self.otime
mag = Magnitude()
mag.mag = self.emag
mag.magnitude_type = "Mw"
self.ev.origins.append(org)
self.ev.magnitudes.append(mag)
def __toMagnitude(parser, magnitude_el, origin):
"""
Parses a given magnitude etree element.
:type parser: :class:`~obspy.core.util.xmlwrapper.XMLParser`
:param parser: Open XMLParser object.
:type magnitude_el: etree.element
:param magnitude_el: magnitude element to be parsed.
:return: A ObsPy :class:`~obspy.core.event.Magnitude` object.
"""
global CURRENT_TYPE
mag = Magnitude()
mag.resource_id = ResourceIdentifier(
prefix="/".join([RESOURCE_ROOT, "magnitude"]))
mag.origin_id = origin.resource_id
mag.mag, mag.mag_errors = __toFloatQuantity(parser, magnitude_el, "mag")
# obspyck used to write variance (instead of std) in magnitude error fields
if CURRENT_TYPE == "obspyck":
if mag.mag_errors.uncertainty is not None:
mag.mag_errors.uncertainty = math.sqrt(mag.mag_errors.uncertainty)
mag.mag_errors.confidence_level = 68.3
mag.magnitude_type = parser.xpath2obj("type", magnitude_el)
mag.station_count = parser.xpath2obj("stationCount", magnitude_el, int)
mag.method_id = "%s/magnitude_method/%s/1" % (
RESOURCE_ROOT, parser.xpath2obj('program', magnitude_el))
if str(mag.method_id).lower().endswith("none"):
mag.method_id = None
return mag
def _block2event(block, seed_map, id_default, ph2comp, eventid_map):
"""
Read HypoDD event block
"""
lines = block.strip().splitlines()
yr, mo, dy, hr, mn, sc, la, lo, dp, mg, eh, ez, rms, id_ = lines[0].split()
if eventid_map is not None and id_ in eventid_map:
id_ = eventid_map[id_]
time = UTCDateTime(int(yr),
int(mo),
int(dy),
int(hr),
int(mn),
float(sc),
strict=False)
laterr = None if float(eh) == 0 else float(eh) / DEG2KM
lonerr = (None if laterr is None or float(la) > 89 else laterr /
cos(deg2rad(float(la))))
ez = None if float(ez) == 0 else float(ez) * 1000
rms = None if float(rms) == 0 else float(rms)
picks = []
arrivals = []
for line in lines[1:]:
sta, reltime, weight, phase = line.split()
comp = ph2comp.get(phase, '')
wid = seed_map.get(sta, id_default)
_waveform_id = WaveformStreamID(seed_string=wid.format(sta, comp))
pick = Pick(waveform_id=_waveform_id,
phase_hint=phase,
time=time + float(reltime))
arrival = Arrival(phase=phase,
pick_id=pick.resource_id,
time_weight=float(weight))
picks.append(pick)
arrivals.append(arrival)
qu = OriginQuality(associated_phase_count=len(picks), standard_error=rms)
origin = Origin(arrivals=arrivals,
resource_id="smi:local/origin/" + id_,
quality=qu,
latitude=float(la),
longitude=float(lo),
depth=1000 * float(dp),
latitude_errors=laterr,
longitude_errors=lonerr,
depth_errors=ez,
time=time)
if mg.lower() == 'nan':
magnitudes = []
preferred_magnitude_id = None
else:
magnitude = Magnitude(mag=mg, resource_id="smi:local/magnitude/" + id_)
magnitudes = [magnitude]
preferred_magnitude_id = magnitude.resource_id
event = Event(resource_id="smi:local/event/" + id_,
picks=picks,
origins=[origin],
magnitudes=magnitudes,
preferred_origin_id=origin.resource_id,
preferred_magnitude_id=preferred_magnitude_id)
return event
def setUpClass(cls) -> None:
cls.event = Event(origins=[
Origin(time=UTCDateTime(2019, 1, 1),
latitude=-45.,
longitude=90.0,
depth=10000.)
],
magnitudes=[Magnitude(mag=7.4)])
cls.event.preferred_origin_id = cls.event.origins[0].resource_id
def CUSP_to_SC3_rel_mags(det_cat, temp_cat, selfs):
"""
Take a catalog with relative magnitudes calculated using the Ristau 2009
CUSP equation and correct them using the updated SeisComP3 scale
:param det_cat: Catalog of detections and templates with magnitudes
:param selfs: List of strings for self detection ids
:return:
"""
# Make a dictionary of the CUSP-derived moment, SeisComP M0 for templates
temp_mag_dict = {ev.resource_id.id.split('/')[-1]:
{'Old M0':
local_to_moment(ev.magnitudes[0].mag,
m=0.88, c=0.73),
'New M0':
local_to_moment(ev.magnitudes[0].mag,
m=0.97, c=0.14)}
for ev in temp_cat}
# Now loop the catalog and redo the calculations
for det in det_cat:
# First determine the relative moment (I didn't save these anywhere...)
eid = det.resource_id.id.split('/')[-1]
if eid in selfs:
print('Template event: Adding a Mw magnitude')
det.magnitudes.append(
Magnitude(mag=ML_to_Mw(det.magnitudes[0].mag, m=0.97, c=0.14),
magnitude_type='Mw',
comments=[Comment(text='Ristau et al., 2016 BSSA')]))
continue
tid = det.resource_id.id.split('/')[-1].split('_')[0]
det_mo = Mw_to_M0([m.mag for m in det.magnitudes
if m.magnitude_type == 'Mw'][0])
rel_mo = det_mo / temp_mag_dict[tid]['Old M0']
new_det_mo = rel_mo * temp_mag_dict[tid]['New M0']
new_det_Mw = (2. / 3. * np.log10(new_det_mo)) - 9.
new_det_ML = (0.97 * new_det_Mw) + 0.14
det.magnitudes.append(
Magnitude(mag=new_det_Mw, magnitude_type='Mw',
comments=[Comment(text='rel_mo={}'.format(rel_mo))]))
det.magnitudes.append(
Magnitude(mag=new_det_ML, magnitude_type='ML',
comments=[Comment(text='rel_mo={}'.format(rel_mo))]))
det.preferred_magnitude_id = det.magnitudes[-2].resource_id.id
return
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 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 setUpClass(cls) -> None:
cls.client = Client("GEONET")
cls.tribe = read_tribe(
os.path.join(
os.path.abspath(os.path.dirname(os.path.dirname(__file__))),
"test_data", "test_tribe.tgz"))
cls.trigger_event = Event(origins=[
Origin(time=UTCDateTime(2019, 1, 1),
latitude=-45.,
longitude=178.0,
depth=10000.)
],
magnitudes=[Magnitude(mag=7.4)])
def _block2event(block, seed_map, id_default, ph2comp):
"""
Read HypoDD event block
"""
lines = block.strip().splitlines()
yr, mo, dy, hr, mn, sc, la, lo, dp, mg, eh, ez, rms, id_ = lines[0].split()
time = UTCDateTime(int(yr),
int(mo),
int(dy),
int(hr),
int(mn),
float(sc),
strict=False)
picks = []
arrivals = []
for line in lines[1:]:
sta, reltime, weight, phase = line.split()
comp = ph2comp.get(phase, '')
wid = seed_map.get(sta, id_default)
_waveform_id = WaveformStreamID(seed_string=wid.format(sta, comp))
pick = Pick(waveform_id=_waveform_id,
phase_hint=phase,
time=time + float(reltime))
arrival = Arrival(phase=phase,
pick_id=pick.resource_id,
time_weight=float(weight))
picks.append(pick)
arrivals.append(arrival)
qu = None if rms == '0.0' else OriginQuality(standard_error=float(rms))
origin = Origin(arrivals=arrivals,
resource_id="smi:local/origin/" + id_,
quality=qu,
latitude=float(la),
longitude=float(lo),
depth=1000 * float(dp),
time=time)
if mg.lower() == 'nan':
magnitudes = []
preferred_magnitude_id = None
else:
magnitude = Magnitude(mag=mg, resource_id="smi:local/magnitude/" + id_)
magnitudes = [magnitude]
preferred_magnitude_id = magnitude.resource_id
event = Event(resource_id="smi:local/event/" + id_,
picks=picks,
origins=[origin],
magnitudes=magnitudes,
preferred_origin_id=origin.resource_id,
preferred_magnitude_id=preferred_magnitude_id)
return event
def _parse_magnitude(self, line):
# 1-5 a5 magnitude type (mb, Ms, ML, mbmle, msmle)
magnitude_type = line[0:5].strip()
# 6 a1 min max indicator (<, >, or blank)
# TODO figure out the meaning of this min max indicator
min_max_indicator = line[5:6].strip()
# 7-10 f4.1 magnitude value
mag = float_or_none(line[6:10])
# 12-14 f3.1 standard magnitude error
mag_errors = float_or_none(line[11:14])
# 16-19 i4 number of stations used to calculate magni-tude
station_count = int_or_none(line[15:19])
# 21-29 a9 author of the origin
author = line[20:29].strip()
# 31-38 a8 origin identification
origin_id = line[30:38].strip()
# process items
if author:
creation_info = CreationInfo(author=author)
else:
creation_info = None
mag_errors = mag_errors and QuantityError(uncertainty=mag_errors)
if origin_id:
origin_id = self._construct_id(['origin', origin_id])
else:
origin_id = None
if not magnitude_type:
magnitude_type = None
# magnitudes have no id field, so construct a unique one at least
resource_id = self._construct_id(['magnitude'], add_hash=True)
if min_max_indicator:
msg = 'Magnitude min/max indicator field not yet implemented'
warnings.warn(msg)
# combine and return
mag = Magnitude(magnitude_type=magnitude_type,
mag=mag,
station_count=station_count,
creation_info=creation_info,
mag_errors=mag_errors,
origin_id=origin_id,
resource_id=resource_id)
# event init always sets an empty QuantityError, even when specifying
# None, which is strange
for key in ['mag_errors']:
setattr(mag, key, None)
return mag
def create_simple_magnitudes(
self,
events: Union[Event, Catalog],
waveforms: Optional[Union[WaveformClient, Stream]] = None,
restrict_to_arrivals: bool = False,
author: Optional[str] = None,
agency_id: Optional[str] = None,
evaluation_mode: EvaluationModeType = "automatic",
evaluation_status: EvaluationStatusType = "preliminary",
) -> Dict[Tuple[str, str], Magnitude]:
"""
Create magnitude objects from calculated source params.
Returns a dict of {(event_id, magnitude_type): Magnitude}
Parameters
----------
{ew_params}
restrict_to_arrivals
If True, restrict calculations to only include phases associated
with the arrivals on the origin
author
Name of the person generating the magnitudes
agency_id
Name of the agency generating the magnitudes
evaluation_mode
Evaluation mode of the magnitudes
evaluation_status
Evaluation status of the magnitudes
"""
df = self.calc_source_parameters(
events, waveforms, restrict_to_arrivals=restrict_to_arrivals)
eids = set(df.index)
out = {}
for eid in eids:
for col_name, mag_type in self._mag_type_map.items():
log = "log" in mag_type
value = df.loc[eid, col_name]
if not pd.isnull(value):
mag = Magnitude(
magnitude_type=mag_type,
method_id=self._method_uri,
creation_info=self._create_info(author, agency_id),
mag=np.log10(value) if log else value,
evaluation_mode=evaluation_mode,
evaluation_status=evaluation_status,
)
out[(eid, mag_type)] = mag
return out
def read_header_line(string_line):
new_event = Event()
line = string_line
param_event = line.split()[1:]
### check if line as required number of arguments
if len(param_event) != 14:
return new_event
### Get parameters
year, month, day = [int(x) for x in param_event[0:3]]
hour, minu = [int(x) for x in param_event[3:5]]
sec = float(param_event[5])
if sec >= 60:
sec = 59.999
lat, lon, z = [float(x) for x in param_event[6:9]]
mag = float(param_event[9])
errh, errz, rms = [float(x) for x in param_event[10:13]]
_time = UTCDateTime(year, month, day, hour, minu, sec)
_origin_quality = OriginQuality(standard_error=rms)
# change what's next to handle origin with no errors estimates
origin = Origin(time=_time,
longitude=lon,
latitude=lat,
depth=z,
longitude_errors=QuantityError(uncertainty=errh),
latitude_errors=QuantityError(uncertainty=errh),
depth_errors=QuantityError(uncertainty=errz),
quality=_origin_quality)
magnitude = Magnitude(mag=mag, origin_id=origin.resource_id)
### Return
new_event.origins.append(origin)
new_event.magnitudes.append(magnitude)
new_event.preferred_origin_id = origin.resource_id
new_event.preferred_magnitude_id = magnitude.resource_id
return new_event
def _phase_to_event(event_text):
"""
Function to convert the text for one event in hypoDD phase format to \
event object.
:type event_text: dict
:param event_text: dict of two elements, header and picks, header is a \
str, picks is a list of str.
:returns: obspy.core.event.Event
"""
from obspy.core.event import Event, Origin, Magnitude
from obspy.core.event import Pick, WaveformStreamID, Arrival
from obspy import UTCDateTime
ph_event = Event()
# Extract info from header line
# YR, MO, DY, HR, MN, SC, LAT, LON, DEP, MAG, EH, EZ, RMS, ID
header = event_text['header'].split()
ph_event.origins.append(Origin())
ph_event.origins[0].time = UTCDateTime(
year=int(header[1]),
month=int(header[2]),
day=int(header[3]),
hour=int(header[4]),
minute=int(header[5]),
second=int(header[6].split('.')[0]),
microsecond=int(float(('0.' + header[6].split('.')[1])) * 1000000))
ph_event.origins[0].latitude = float(header[7])
ph_event.origins[0].longitude = float(header[8])
ph_event.origins[0].depth = float(header[9]) * 1000
ph_event.origins[0].time_errors['Time_Residual_RMS'] = float(header[13])
ph_event.magnitudes.append(Magnitude())
ph_event.magnitudes[0].mag = float(header[10])
ph_event.magnitudes[0].magnitude_type = 'M'
# Extract arrival info from picks!
for i, pick_line in enumerate(event_text['picks']):
pick = pick_line.split()
_waveform_id = WaveformStreamID(station_code=pick[0])
pick_time = ph_event.origins[0].time + float(pick[1])
ph_event.picks.append(
Pick(waveform_id=_waveform_id, phase_hint=pick[3], time=pick_time))
ph_event.origins[0].arrivals.append(
Arrival(phase=ph_event.picks[i],
pick_id=ph_event.picks[i].resource_id))
ph_event.origins[0].arrivals[i].time_weight = float(pick[2])
return ph_event
def test_reactor_spin_up(self):
reactor = Reactor(client=Client("GEONET"),
listener=self.listener,
trigger_func=self.trigger_func,
template_database=self.template_bank,
config=self.config)
trigger_event = Event(origins=[
Origin(time=UTCDateTime(2019, 1, 1),
latitude=-45.,
longitude=178.0,
depth=10000.)
],
magnitudes=[Magnitude(mag=7.4)])
reactor.spin_up(triggering_event=trigger_event)
time.sleep(10)
with self.assertRaises(SystemExit):
reactor.stop()
def read_regex(event_file, regex=regex_GEOFON, creation_info='GEOFON'):
"""
Read events from event_file with the help of given regular expression.
"""
with open(event_file, 'r') as f:
filedata = f.read()
event_matches = re.finditer(regex, filedata, re.VERBOSE + re.MULTILINE)
list_ = [i.groupdict() for i in event_matches]
events = []
for event in list_:
# convert numbers to float and int types
for key, item in event.iteritems():
if util.isint(item):
event[key] = int(item)
elif util.isfloat(item):
event[key] = float(item)
else:
event[key] = item.strip()
if 'latitude_sign' in event and event['latitude_sign'] == 'S':
event['latitude'] = -event['latitude']
if 'longitude_sign' in event and event['longitude_sign'] == 'W':
event['longitude'] = -event['longitude']
if 'AM' in event:
ci = creation_info + (' automatic'
if event['AM'] == 'A' else ' manual')
else:
ci = creation_info
ev = Event(
event_type='earthquake',
creation_info=ci,
origins=[
Origin(time=UTC(event['time']),
latitude=event['latitude'],
longitude=event['longitude'],
depth=event['depth'])
],
magnitudes=[Magnitude(mag=event['magnitude'], magnitude_type='M')],
event_descriptions=[
EventDescription(event['flinn'], 'flinn-engdahl region')
] if 'flinn' in event else None)
events.append(ev)
events.sort(key=lambda x: x.origins[0].time)
return Catalog(events)
def ncedc_dd_to_cat(path):
"""
Read csv of ncedc dd locations to catalog
:param path:
:return:
"""
cat = Catalog()
with open(path, 'r') as f:
next(f)
for ln in f:
ot, lat, lon, dp, mag, mt, _, _, _, _, _, eid = ln.split(',')
ot = UTCDateTime('T'.join(ot.split()))
o = Origin(latitude=lat, longitude=lon,
depth=float(dp) * 1000, time=ot)
m = Magnitude(mag=mag, magnitude_type=mt)
ev = Event(origins=[o], magnitudes=[m],
resource_id=ResourceIdentifier(id=eid))
cat.events.append(ev)
return cat
def parse_eq_Canada(file_path):
"""
Parse eqcanada text file to an obspy Catalog
:param file_path: Path to downloaded file
:return:
"""
cat = Catalog()
with open(file_path, 'r') as f:
next(f)
for ln in f:
line = ln.split('|')
rid = ResourceIdentifier(id='smi:local/{}'.format(line[0]))
o = Origin(time=UTCDateTime(line[1]), latitude=float(line[2]),
longitude=float(line[3]), depth=float(line[4]))
m = Magnitude(magnitude_type=line[5], mag=float(line[6]))
e = Event(resource_id=rid, force_resource_id=False,
origins=[o], magnitudes=[m])
cat.events.append(e)
return cat
def _mags(obj, evid, stamag=False, wid=None):
mags = []
pm = None
for magtype1, magtype2 in MAG_MAP.items():
magkey = 'mean ' * (not stamag) + 'magnitude ' + magtype1
if magkey in obj:
magv = obj[magkey]
if 'inf' in magv:
warn('invalid value for magnitude: %s (event id %s)'
% (magv, evid))
else:
magv = float(magv)
mag = (StationMagnitude(station_magnitude_type=magtype2,
mag=magv, waveform_id=wid)
if stamag else
Magnitude(magnitude_type=magtype2, mag=magv))
mags.append(mag)
if len(mags) == 1:
pm = mags[0].resource_id
return mags, pm
def test_more_than_three_mags(self):
cat = Catalog()
cat += full_test_event()
cat[0].magnitudes.append(
Magnitude(mag=0.9,
magnitude_type='MS',
creation_info=CreationInfo('TES'),
origin_id=cat[0].origins[0].resource_id))
with NamedTemporaryFile(suffix='.out') as tf:
# raises UserWarning: mb is not convertible
with warnings.catch_warnings():
warnings.simplefilter('ignore', UserWarning)
cat.write(tf.name, format='nordic')
# raises "UserWarning: AIN in header, currently unsupported"
with warnings.catch_warnings():
warnings.simplefilter('ignore', UserWarning)
cat_back = read_events(tf.name)
for event_1, event_2 in zip(cat, cat_back):
self.assertTrue(
len(event_1.magnitudes) == len(event_2.magnitudes))
_assert_similarity(event_1, event_2)
def read_origin(event_str):
"""
Read the origin information from the REST file string
:param event_str: Contents of file as list of str
:type event_str: list
:returns: :class:`obspy.core.event.Event`
"""
event = Event()
head = event_str[0].split()
try:
gap = float(head[17])
except IndexError:
gap = None
origin = Origin(
time=UTCDateTime(
year=int(head[0]), julday=int(head[1]), hour=int(head[2]),
minute=int(head[3])) + float(head[4]),
latitude=float(head[5]), longitude=float(head[6]),
depth=float(head[7]) * 1000, origin_quality=OriginQuality(
standard_error=float(head[9]),
azimuthal_gap=gap,
used_phase_count=int(head[17])),
longitude_errors=QuantityError(
uncertainty=kilometer2degrees(float(head[12]))),
latitude_errors=QuantityError(
uncertainty=kilometer2degrees(float(head[11]))),
depth_errors=QuantityError(uncertainty=float(head[13]) * 1000),
method_id=ResourceIdentifier("smi:local/REST"),
evaluation_mode="automatic")
event.origins.append(origin)
try:
event.magnitudes.append(Magnitude(
mag=float(head[19]), magnitude_type="M"))
except IndexError:
pass
return event
def event_to_quakeml(event, filename):
"""
Write one of those events to QuakeML.
"""
# Create all objects.
cat = Catalog()
ev = Event()
org = Origin()
mag = Magnitude()
fm = FocalMechanism()
mt = MomentTensor()
t = Tensor()
# Link them together.
cat.append(ev)
ev.origins.append(org)
ev.magnitudes.append(mag)
ev.focal_mechanisms.append(fm)
fm.moment_tensor = mt
mt.tensor = t
# Fill values
ev.resource_id = "smi:inversion/%s" % str(event["identifier"])
org.time = event["time"]
org.longitude = event["longitude"]
org.latitude = event["latitude"]
org.depth = event["depth_in_km"] * 1000
mag.mag = event["Mw"]
mag.magnitude_type = "Mw"
t.m_rr = event["Mrr"]
t.m_tt = event["Mpp"]
t.m_pp = event["Mtt"]
t.m_rt = event["Mrt"]
t.m_rp = event["Mrp"]
t.m_tp = event["Mtp"]
cat.write(filename, format="quakeml")
def test_reactor_spin_up(self):
rt_client = RealTimeClient(server_url="link.geonet.org.nz")
reactor = Reactor(client=Client("GEONET"),
rt_client=rt_client,
listener=self.listener,
trigger_func=self.trigger_func,
template_database=self.template_bank,
template_lookup_kwargs=dict(),
real_time_tribe_kwargs=dict(threshold=8,
threshold_type="MAD",
trig_int=2),
plot_kwargs=dict(),
listener_kwargs=dict(make_templates=False))
trigger_event = Event(origins=[
Origin(time=UTCDateTime(2019, 1, 1),
latitude=-45.,
longitude=178.0,
depth=10000.)
],
magnitudes=[Magnitude(mag=7.4)])
reactor.background_spin_up(triggering_event=trigger_event)
time.sleep(10)
reactor.stop()
def _on_file_save(self):
"""
Creates a new obspy.core.event.Magnitude object and writes the moment
magnitude to it.
"""
# Get the save filename.
filename = QtGui.QFileDialog.getSaveFileName(caption="Save as...")
filename = os.path.abspath(str(filename))
mag = Magnitude()
mag.mag = self.final_result["moment_magnitude"]
mag.magnitude_type = "Mw"
mag.station_count = self.final_result["station_count"]
mag.evaluation_mode = "manual"
# Link to the used origin.
mag.origin_id = self.current_state["event"].origins[0].resource_id
mag.method_id = "Magnitude picker Krischer"
# XXX: Potentially change once this program gets more stable.
mag.evaluation_status = "preliminary"
# Write the other results as Comments.
mag.comments.append( \
Comment("Seismic moment in Nm: %g" % \
self.final_result["seismic_moment"]))
mag.comments.append( \
Comment("Circular source radius in m: %.2f" % \
self.final_result["source_radius"]))
mag.comments.append( \
Comment("Stress drop in Pa: %.2f" % \
self.final_result["stress_drop"]))
mag.comments.append( \
Comment("Very rough Q estimation: %.1f" % \
self.final_result["quality_factor"]))
event = copy.deepcopy(self.current_state["event"])
event.magnitudes.append(mag)
cat = Catalog()
cat.events.append(event)
cat.write(filename, format="quakeml")
def test_creating_minimal_quakeml_with_mt(self):
"""
Tests the creation of a minimal QuakeML containing origin, magnitude
and moment tensor.
"""
# Rotate into physical domain
lat, lon, depth, org_time = 10.0, -20.0, 12000, UTCDateTime(2012, 1, 1)
mrr, mtt, mpp, mtr, mpr, mtp = 1E18, 2E18, 3E18, 3E18, 2E18, 1E18
scalar_moment = math.sqrt(
mrr ** 2 + mtt ** 2 + mpp ** 2 + mtr ** 2 + mpr ** 2 + mtp ** 2)
moment_magnitude = 0.667 * (math.log10(scalar_moment) - 9.1)
# Initialise event
ev = Event(event_type="earthquake")
ev_origin = Origin(time=org_time, latitude=lat, longitude=lon,
depth=depth, resource_id=ResourceIdentifier())
ev.origins.append(ev_origin)
# populate event moment tensor
ev_tensor = Tensor(m_rr=mrr, m_tt=mtt, m_pp=mpp, m_rt=mtr, m_rp=mpr,
m_tp=mtp)
ev_momenttensor = MomentTensor(tensor=ev_tensor)
ev_momenttensor.scalar_moment = scalar_moment
ev_momenttensor.derived_origin_id = ev_origin.resource_id
ev_focalmechanism = FocalMechanism(moment_tensor=ev_momenttensor)
ev.focal_mechanisms.append(ev_focalmechanism)
# populate event magnitude
ev_magnitude = Magnitude()
ev_magnitude.mag = moment_magnitude
ev_magnitude.magnitude_type = 'Mw'
ev_magnitude.evaluation_mode = 'automatic'
ev.magnitudes.append(ev_magnitude)
# write QuakeML file
cat = Catalog(events=[ev])
memfile = io.BytesIO()
cat.write(memfile, format="quakeml", validate=IS_RECENT_LXML)
memfile.seek(0, 0)
new_cat = _read_quakeml(memfile)
self.assertEqual(len(new_cat), 1)
event = new_cat[0]
self.assertEqual(len(event.origins), 1)
self.assertEqual(len(event.magnitudes), 1)
self.assertEqual(len(event.focal_mechanisms), 1)
org = event.origins[0]
mag = event.magnitudes[0]
fm = event.focal_mechanisms[0]
self.assertEqual(org.latitude, lat)
self.assertEqual(org.longitude, lon)
self.assertEqual(org.depth, depth)
self.assertEqual(org.time, org_time)
# Moment tensor.
mt = fm.moment_tensor.tensor
self.assertTrue((fm.moment_tensor.scalar_moment - scalar_moment) /
scalar_moment < scalar_moment * 1E-10)
self.assertEqual(mt.m_rr, mrr)
self.assertEqual(mt.m_pp, mpp)
self.assertEqual(mt.m_tt, mtt)
self.assertEqual(mt.m_rt, mtr)
self.assertEqual(mt.m_rp, mpr)
self.assertEqual(mt.m_tp, mtp)
# Mag
self.assertAlmostEqual(mag.mag, moment_magnitude)
self.assertEqual(mag.magnitude_type, "Mw")
self.assertEqual(mag.evaluation_mode, "automatic")
for line in lines:
line_elements = line.split()
eid = line_elements[-1]
otime = uh.eid2otime(eid)
elon = line_elements[6]
elat = line_elements[7]
edep = float(line_elements[8]) * 1000.0 # meters
emag = line_elements[16]
# create event object
orig = Origin()
orig.longitude = elon
orig.latitude = elat
orig.depth = edep
orig.time = otime
mag = Magnitude()
mag.mag = emag
mag.magnitude_type = "Mw"
ev = Event()
ev.origins.append(orig)
ev.magnitudes.append(mag)
if send_request:
# get waveforms
client = Client("IRIS")
getwaveform_iris.run_get_waveform(c=client,
event=ev,
min_dist=min_dist,
max_dist=max_dist,
before=tbefore_sec,
after=tafter_sec,
lat = out_3[i][6::33]
lon = out_3[i][7::33]
orid=out_3[i][8::33]
dep = out_3[i][9::33]
ml=out_3[i][10::33]
for x, times in enumerate(pick_time):
event.resource_id=str(out_3[i][0]) #assign evid
rd = str(out_3[i][0])
picks = Pick(resource_id=rd, time=UTCDateTime(pick_time[x]),
waveform_id = WaveformStreamID(network_code="CI", station_code=str(sta[x]), channel_code=str(cha[x])), phase_hint=str(phase[x]))
origin = Origin(resource_id=(str(orid[x])),
time = UTCDateTime(e_time[x]),
longitude= str(lon[x]),
latitude=str(lat[x]),
depth=str(dep[x]))
magnitude = Magnitude(mag = ml[x], magnitude_type = "M", origin_id = (str(orid[x])))
arrival = Arrival(pick_id = rd, phase = str(phase[x]))
event.picks.append(picks)
event.origins.append(origin)
origin.arrivals.append(arrival)
event.magnitudes.append(magnitude)
db_catalog.append(event)
#Only include picks for stations used
all_picks=[]
for event in db_catalog:
stations = ['KCT', 'KMPB', 'KCR', 'KHMB', 'KCS', 'KCO', 'KMR', 'KPP']
event.picks = [pick for pick in event.picks if pick.waveform_id.station_code in stations]
all_picks+= [(pick.waveform_id.station_code, pick.waveform_id.channel_code) for pick in event.picks]
def _read_ndk(filename, *args, **kwargs): # @UnusedVariable
"""
Reads an NDK file to a :class:`~obspy.core.event.Catalog` object.
:param filename: File or file-like object in text mode.
"""
# Read the whole file at once. While an iterator would be more efficient
# the largest NDK file out in the wild is 13.7 MB so it does not matter
# much.
if not hasattr(filename, "read"):
# Check if it exists, otherwise assume its a string.
try:
with open(filename, "rt") as fh:
data = fh.read()
except Exception:
try:
data = filename.decode()
except Exception:
data = str(filename)
data = data.strip()
else:
data = filename.read()
if hasattr(data, "decode"):
data = data.decode()
# Create iterator that yields lines.
def lines_iter():
prev_line = -1
while True:
next_line = data.find("\n", prev_line + 1)
if next_line < 0:
break
yield data[prev_line + 1:next_line]
prev_line = next_line
if len(data) > prev_line + 1:
yield data[prev_line + 1:]
# Use one Flinn Engdahl object for all region determinations.
fe = FlinnEngdahl()
cat = Catalog(resource_id=_get_resource_id("catalog", str(uuid.uuid4())))
# Loop over 5 lines at once.
for _i, lines in enumerate(zip_longest(*[lines_iter()] * 5)):
if None in lines:
msg = "Skipped last %i lines. Not a multiple of 5 lines." % (
lines.count(None))
warnings.warn(msg, ObsPyNDKWarning)
continue
# Parse the lines to a human readable dictionary.
try:
record = _read_lines(*lines)
except (ValueError, ObsPyNDKException):
exc = traceback.format_exc()
msg = ("Could not parse event %i (faulty file?). Will be "
"skipped. Lines of the event:\n"
"\t%s\n"
"%s") % (_i + 1, "\n\t".join(lines), exc)
warnings.warn(msg, ObsPyNDKWarning)
continue
# Use one creation info for essentially every item.
creation_info = CreationInfo(agency_id="GCMT",
version=record["version_code"])
# Use the ObsPy Flinn Engdahl region determiner as the region in the
# NDK files is oftentimes trimmed.
region = fe.get_region(record["centroid_longitude"],
record["centroid_latitude"])
# Create an event object.
event = Event(force_resource_id=False,
event_type="earthquake",
event_type_certainty="known",
event_descriptions=[
EventDescription(text=region,
type="Flinn-Engdahl region"),
EventDescription(text=record["cmt_event_name"],
type="earthquake name")
])
# Assemble the time for the reference origin.
try:
time = _parse_date_time(record["date"], record["time"])
except ObsPyNDKException:
msg = ("Invalid time in event %i. '%s' and '%s' cannot be "
"assembled to a valid time. Event will be skipped.") % \
(_i + 1, record["date"], record["time"])
warnings.warn(msg, ObsPyNDKWarning)
continue
# Create two origins, one with the reference latitude/longitude and
# one with the centroidal values.
ref_origin = Origin(
force_resource_id=False,
time=time,
longitude=record["hypo_lng"],
latitude=record["hypo_lat"],
# Convert to m.
depth=record["hypo_depth_in_km"] * 1000.0,
origin_type="hypocenter",
comments=[
Comment(text="Hypocenter catalog: %s" %
record["hypocenter_reference_catalog"],
force_resource_id=False)
])
ref_origin.comments[0].resource_id = _get_resource_id(
record["cmt_event_name"], "comment", tag="ref_origin")
ref_origin.resource_id = _get_resource_id(record["cmt_event_name"],
"origin",
tag="reforigin")
cmt_origin = Origin(
force_resource_id=False,
longitude=record["centroid_longitude"],
longitude_errors={
"uncertainty": record["centroid_longitude_error"]
},
latitude=record["centroid_latitude"],
latitude_errors={"uncertainty": record["centroid_latitude_error"]},
# Convert to m.
depth=record["centroid_depth_in_km"] * 1000.0,
depth_errors={
"uncertainty": record["centroid_depth_in_km_error"] * 1000
},
time=ref_origin["time"] + record["centroid_time"],
time_errors={"uncertainty": record["centroid_time_error"]},
depth_type=record["type_of_centroid_depth"],
origin_type="centroid",
time_fixed=False,
epicenter_fixed=False,
creation_info=creation_info.copy())
cmt_origin.resource_id = _get_resource_id(record["cmt_event_name"],
"origin",
tag="cmtorigin")
event.origins = [ref_origin, cmt_origin]
event.preferred_origin_id = cmt_origin.resource_id.id
# Create the magnitude object.
mag = Magnitude(force_resource_id=False,
mag=round(record["Mw"], 2),
magnitude_type="Mwc",
origin_id=cmt_origin.resource_id,
creation_info=creation_info.copy())
mag.resource_id = _get_resource_id(record["cmt_event_name"],
"magnitude",
tag="moment_mag")
event.magnitudes = [mag]
event.preferred_magnitude_id = mag.resource_id.id
# Add the reported mb, MS magnitudes as additional magnitude objects.
event.magnitudes.append(
Magnitude(
force_resource_id=False,
mag=record["mb"],
magnitude_type="mb",
comments=[
Comment(
force_resource_id=False,
text="Reported magnitude in NDK file. Most likely 'mb'."
)
]))
event.magnitudes[-1].comments[-1].resource_id = _get_resource_id(
record["cmt_event_name"], "comment", tag="mb_magnitude")
event.magnitudes[-1].resource_id = _get_resource_id(
record["cmt_event_name"], "magnitude", tag="mb")
event.magnitudes.append(
Magnitude(
force_resource_id=False,
mag=record["MS"],
magnitude_type="MS",
comments=[
Comment(
force_resource_id=False,
text="Reported magnitude in NDK file. Most likely 'MS'."
)
]))
event.magnitudes[-1].comments[-1].resource_id = _get_resource_id(
record["cmt_event_name"], "comment", tag="MS_magnitude")
event.magnitudes[-1].resource_id = _get_resource_id(
record["cmt_event_name"], "magnitude", tag="MS")
# Take care of the moment tensor.
tensor = Tensor(m_rr=record["m_rr"],
m_rr_errors={"uncertainty": record["m_rr_error"]},
m_pp=record["m_pp"],
m_pp_errors={"uncertainty": record["m_pp_error"]},
m_tt=record["m_tt"],
m_tt_errors={"uncertainty": record["m_tt_error"]},
m_rt=record["m_rt"],
m_rt_errors={"uncertainty": record["m_rt_error"]},
m_rp=record["m_rp"],
m_rp_errors={"uncertainty": record["m_rp_error"]},
m_tp=record["m_tp"],
m_tp_errors={"uncertainty": record["m_tp_error"]},
creation_info=creation_info.copy())
mt = MomentTensor(
force_resource_id=False,
scalar_moment=record["scalar_moment"],
tensor=tensor,
data_used=[DataUsed(**i) for i in record["data_used"]],
inversion_type=record["source_type"],
source_time_function=SourceTimeFunction(
type=record["moment_rate_type"],
duration=record["moment_rate_duration"]),
derived_origin_id=cmt_origin.resource_id,
creation_info=creation_info.copy())
mt.resource_id = _get_resource_id(record["cmt_event_name"],
"momenttensor")
axis = [Axis(**i) for i in record["principal_axis"]]
focmec = FocalMechanism(
force_resource_id=False,
moment_tensor=mt,
principal_axes=PrincipalAxes(
# The ordering is the same as for the IRIS SPUD service and
# from a website of the Saint Louis University Earthquake
# center so it should be correct.
t_axis=axis[0],
p_axis=axis[2],
n_axis=axis[1]),
nodal_planes=NodalPlanes(
nodal_plane_1=NodalPlane(**record["nodal_plane_1"]),
nodal_plane_2=NodalPlane(**record["nodal_plane_2"])),
comments=[
Comment(force_resource_id=False,
text="CMT Analysis Type: %s" %
record["cmt_type"].capitalize()),
Comment(force_resource_id=False,
text="CMT Timestamp: %s" % record["cmt_timestamp"])
],
creation_info=creation_info.copy())
focmec.comments[0].resource_id = _get_resource_id(
record["cmt_event_name"], "comment", tag="cmt_type")
focmec.comments[1].resource_id = _get_resource_id(
record["cmt_event_name"], "comment", tag="cmt_timestamp")
focmec.resource_id = _get_resource_id(record["cmt_event_name"],
"focal_mechanism")
event.focal_mechanisms = [focmec]
event.preferred_focal_mechanism_id = focmec.resource_id.id
# Set at end to avoid duplicate resource id warning.
event.resource_id = _get_resource_id(record["cmt_event_name"], "event")
cat.append(event)
if len(cat) == 0:
msg = "No valid events found in NDK file."
raise ObsPyNDKException(msg)
return cat
