def _create_origins():
ori = ev.Origin(
resource_id=ev.ResourceIdentifier('smi:local/First'),
time=UTCDateTime('2016-05-04T12:00:00'),
time_errors={'uncertainty': .01},
longitude=-111.12525,
longitude_errors={'uncertainty': .020},
latitude=47.48589325,
latitude_errors={'uncertainty': .021},
depth=2.123,
depth_errors={'uncertainty': 1.22},
depth_type='from location',
time_fixed=False,
epicenter_fixed=False,
reference_system_id=ev.ResourceIdentifier(),
method_id=ev.ResourceIdentifier(),
earth_model_id=ev.ResourceIdentifier(),
arrivals=[_get_arrival()],
composite_times=[_get_composite_times()],
quality=_get_origin_quality(),
origin_type='hypocenter',
origin_uncertainty=_get_origin_uncertainty(),
region='US',
evaluation_mode='manual',
evaluation_status='final',
)
state['origin_id'] = ori.resource_id
return ori
def _create_pick():
# setup some of the classes
creation = ev.CreationInfo(
agency='SwanCo',
author='Indago',
creation_time=UTCDateTime(),
version='10.10',
author_url=ev.ResourceIdentifier('smi:local/me.com'),
)
pick = ev.Pick(
time=state['time'],
comments=[ev.Comment(x) for x in 'BOB'],
evaluation_mode='manual',
evaluation_status='final',
creation_info=creation,
phase_hint='P',
polarity='positive',
onset='emergent',
back_azimith_errors={"uncertainty": 10},
slowness_method_id=ev.ResourceIdentifier('smi:local/slow'),
backazimuth=122.1,
horizontal_slowness=12,
method_id=ev.ResourceIdentifier(),
horizontal_slowness_errors={'uncertainty': 12},
filter_id=ev.ResourceIdentifier(),
waveform_id=ev.WaveformStreamID('UU', 'FOO', '--', 'HHZ'),
)
state['pick_id'] = pick.resource_id
return pick
def mag_generator(mag_types):
"""Function to create magnitudes for testing."""
params = {
"origin_id": ev.ResourceIdentifier(),
"method_id": ev.ResourceIdentifier("mag_calculator"),
"station_count": 2,
"azimuthal_gap": 30,
"evaluation_mode": "manual",
"evaluation_status": "reviewed",
}
mags = []
counter = 1
for mt in mag_types:
m = ev.Magnitude(
mag=counter,
magnitude_type=mt,
mag_errors=ev.QuantityError(uncertainty=counter * 0.1,
confidence_level=95),
creation_info=ev.CreationInfo(agency_id="dummy_agency",
author="dummy",
creation_time=UTCDateTime()),
**params,
)
mags.append(m)
return mags
def test_duplicate_station_different_network(self, cat1):
"""
Ensure picks can have duplicated station codes if they have different
network codes. See issue #173.
"""
# Add a copy of first pick, add new resource id and a new network code
new_pick1 = copy.deepcopy(cat1[0].picks[0])
new_pick1.waveform_id.network_code = "NW"
new_pick1.resource_id = ev.ResourceIdentifier()
cat1[0].picks.append(new_pick1)
# Do the same for network codes
new_pick2 = copy.deepcopy(cat1[0].picks[0])
new_pick2.waveform_id.location_code = "04"
new_pick2.resource_id = ev.ResourceIdentifier()
# test passes if this doesnt raise
validate_catalog(cat1)
def make_arrivals(picks):
"""Create arrivals for testing."""
counter = 1
params = {"phase": "P"}
arrivals = []
picks = picks or []
for pick in picks:
a = ev.Arrival(
pick_id=pick.resource_id,
time_correction=counter * 0.05,
azimuth=counter * 5,
distance=counter * 0.1,
takeoff_angle=counter * 2,
time_residual=counter * 0.15,
horizontal_slowness_residual=counter * 0.2,
backazimuth_residual=counter * 0.25,
time_weight=counter * 0.3,
horizontal_slowness_weight=counter * 0.4,
backazimuth_weight=counter * 0.5,
earth_model_id=ev.ResourceIdentifier(),
creation_info=ev.CreationInfo(
agency_id="dummy_agency", author="dummy", creation_time=UTCDateTime()
),
**params,
)
arrivals.append(a)
counter += 1
return arrivals
def make_amplitudes(scnls=None, picks=None):
"""Create amplitudes for testing."""
counter = 1
amps = []
scnls = scnls or []
params = {
"type": "A",
"unit": "dimensionless",
"method_id": "mag_calculator",
"filter_id": ev.ResourceIdentifier("Wood-Anderson"),
"magnitude_hint": "M",
"category": "point",
"evaluation_mode": "manual",
"evaluation_status": "confirmed",
}
for scnl in scnls:
a = ev.Amplitude(
generic_amplitude=counter,
generic_amplitude_errors=ev.QuantityError(
uncertainty=counter * 0.1, confidence_level=95
),
period=counter * 2,
snr=counter * 5,
time_window=ev.TimeWindow(0, 0.1, UTCDateTime()),
waveform_id=ev.WaveformStreamID(seed_string=scnl),
scaling_time=UTCDateTime(),
scaling_time_errors=ev.QuantityError(
uncertainty=counter * 0.001, confidence_level=95
),
creation_info=ev.CreationInfo(
agency_id="dummy_agency", author="dummy", creation_time=UTCDateTime()
),
**params,
)
amps.append(a)
counter += 1
picks = picks or []
for pick in picks:
a = ev.Amplitude(
generic_amplitude=counter,
generic_amplitude_errors=ev.QuantityError(
uncertainty=counter * 0.1, confidence_level=95
),
period=counter * 2,
snr=counter * 5,
time_window=ev.TimeWindow(0, 0.1, UTCDateTime()),
pick_id=pick.resource_id,
scaling_time=UTCDateTime(),
scaling_time_errors=ev.QuantityError(
uncertainty=counter * 0.001, confidence_level=95
),
creation_info=ev.CreationInfo(
agency_id="dummy_agency", author="dummy", creation_time=UTCDateTime()
),
**params,
)
amps.append(a)
counter += 1
return amps
def test_put_event_no_reference_time(self, ebank):
"""Test that putting an event with no reference time raises."""
# get an event with no reference time and no id
event = obspy.read_events()[0]
event.origins.clear()
event.preferred_origin_id = None
event.resource_id = ev.ResourceIdentifier()
with pytest.raises(ValueError):
ebank.put_events(event)
def _get_arrival():
return ev.Arrival(
resource_id=ev.ResourceIdentifier('smi:local/Ar1'),
pick_id=state['pick_id'],
phase='P',
time_correction=.2,
azimuth=12,
distance=10,
takeoff_angle=15,
takeoff_angle_errors={'uncertainty': 10.2},
time_residual=.02,
horizontal_slowness_residual=12.2,
backazimuth_residual=12.2,
time_weight=.23,
horizontal_slowness_weight=12,
backazimuth_weight=12,
earth_model_id=ev.ResourceIdentifier(),
commens=[ev.Comment(x) for x in 'Nothing'],
)
def _create_magnitudes():
return ev.Magnitude(
resource_id=ev.ResourceIdentifier(),
mag=5.5,
mag_errors={'uncertainty': .01},
magnitude_type='Mw',
origin_id=state['origin_id'],
station_count=1,
station_magnitude_contributions=[_get_station_mag_contrib()],
)
def _construct_object(ser: pd.Series,
df_dict: Dict[str, pd.DataFrame],
cls,
recursive=True):
"""
Construct the object represented by a series.
Parameters
----------
ser
df_dict
cls
recursive
Returns
-------
"""
# using pandas string methods to classify type of each index member
istr = ser.index.str
flattened_attrs = istr.startswith("__")
nested_atts = istr.startswith("_") & (~istr.endswith("_")) & (
~flattened_attrs)
special = istr.startswith("_") & istr.endswith("_")
basic = (~flattened_attrs) & (~nested_atts) & (~special)
# ensure each index falls into exactly one category
attr_sum = flattened_attrs.astype(int) + nested_atts + special + basic
assert np.all(np.equal(attr_sum, 1))
# put basic types into dict
basics = ser[basic][ser[basic].astype(bool)] # collect NonNull basic type
out = {
x: TO_CLASS_FUNCS[x](ser[x]) if x in TO_CLASS_FUNCS else v
for x, v in basics.items()
}
# add resource id
obj_id = ser.name
out["resource_id"] = ev.ResourceIdentifier(obj_id)
# inflate flattened objects
flat = ser[flattened_attrs]
out.update(_inflate_flattened(flat[flat.astype(bool)]))
# add nested objects
if recursive:
for attr_name, table_name in ser[nested_atts].items():
klass = ATTR_TO_CLASS[attr_name[1:]]
# get dataframe, filter on parent id
dff = df_dict.get(table_name, None)
if dff is None or dff.empty:
continue # none of this type are defined in tables
df = dff[dff["_parent_id_"] == obj_id]
if df.empty:
continue
# recurse, creating nested objects
func = partial(_construct_object, df_dict=df_dict, cls=klass)
out[attr_name[1:]] = df.apply(func, axis=1).values.tolist()
return cls(**out)
def simple_catalog_to_merge(self, bingham_catalog):
"""
Create a simple catalog to merge into bingham_cat using only one event.
"""
cat = obspy.Catalog(events=bingham_catalog[:2]).copy()
# drop first pick
cat[0].picks = cat[0].picks[1:]
# modify the picks to whole seconds, reset pick IDS
for pick, _, _ in yield_obj_parent_attr(cat, ev.Pick):
pick.time -= (pick.time.timestamp) % 1
pick.id = ev.ResourceIdentifier(referred_object=pick)
return cat
def picks_from_picksdict(picks, creation_info=None):
picks_list = list()
for station, onsets in picks.items():
for label, phase in onsets.items():
if not isinstance(phase, dict) and not isinstance(
phase, AttribDict):
continue
onset = phase['mpp']
try:
ccode = phase['channel']
ncode = phase['network']
except:
continue
pick = ope.Pick()
if creation_info:
pick.creation_info = creation_info
pick.time = onset
error = phase['spe']
pick.time_errors.uncertainty = error
try:
epp = phase['epp']
lpp = phase['lpp']
pick.time_errors.lower_uncertainty = onset - epp
pick.time_errors.upper_uncertainty = lpp - onset
except (KeyError, TypeError) as e:
warnings.warn(str(e), RuntimeWarning)
try:
picker = phase['picker']
except KeyError as e:
warnings.warn(e.message, RuntimeWarning)
picker = 'Unknown'
pick.phase_hint = label
pick.method_id = ope.ResourceIdentifier(id=picker)
pick.waveform_id = ope.WaveformStreamID(station_code=station,
channel_code=ccode,
network_code=ncode)
try:
polarity = phase['fm']
if polarity == 'U' or '+':
pick.polarity = 'positive'
elif polarity == 'D' or '-':
pick.polarity = 'negative'
else:
pick.polarity = 'undecidable'
except KeyError as e:
if 'fm' in str(
e): # no polarity information found for this phase
pass
else:
raise e
picks_list.append(pick)
return picks_list
def _get_moment_tensor():
return ev.MomentTensor(
scalar_moment=12213,
tensor=_get_tensor(),
variance=12.23,
variance_reduction=98,
double_couple=.22,
clvd=.55,
iso=.33,
source_time_function=_get_source_time_function(),
data_used=[_get_data_used()],
method_id=ev.ResourceIdentifier(),
inversion_type='general',
)
def create_resourceID(timetohash, restype, authority_id=None, hrstr=None):
'''
:param timetohash:
:type timetohash
:param restype: type of the resource, e.g. 'orig', 'earthquake' ...
:type restype: str
:param authority_id: name of the institution carrying out the processing
:type authority_id: str, optional
:param hrstr:
:type hrstr:
:return:
'''
assert isinstance(timetohash, UTCDateTime), "'timetohash' is not an ObsPy" \
"UTCDateTime object"
hid = getHash(timetohash)
if hrstr is None:
resID = ope.ResourceIdentifier(restype + '/' + hid[0:6])
else:
resID = ope.ResourceIdentifier(restype + '/' + hrstr)
if authority_id is not None:
resID.convertIDToQuakeMLURI(authority_id=authority_id)
return resID
def test_preferred_no_origins(self):
""" when the preferred id is set but origin is empty None should be
returned. """
event = obspy.read_events()[0]
# clear origins and ensure resource_id is not holding a reference
event.origins.clear()
rid = str(ev.ResourceIdentifier())
event.preferred_origin_id = rid
# It should now return None
with pytest.warns(UserWarning):
assert get_preferred(event, "origin") is None
# but if init_empty it should return an empty origin
with pytest.warns(UserWarning):
ori = get_preferred(event, "origin", init_empty=True)
assert isinstance(ori, ev.Origin)
def test_object_with_slots(self):
"""Ensure it still works with slots objects."""
class Slot:
__slots__ = ("hey", "bob")
def __init__(self, hey, bob):
self.hey = hey
self.bob = bob
slot = Slot(hey=ev.ResourceIdentifier("bob"), bob="ugh")
rids = [
x[0] for x in yield_obj_parent_attr(slot, ev.ResourceIdentifier)
]
assert len(rids) == 1
assert str(rids[0]) == "bob"
def sm_generator(scnls=None, amplitudes=None):
"""Function to create station magntiudes for testing."""
counter = 1
sms = []
scnls = scnls or []
params = {
"origin_id": ev.ResourceIdentifier(),
"station_magnitude_type": "M",
"method_id": "mag_calculator",
}
for scnl in scnls:
sm = ev.StationMagnitude(
mag=counter,
mag_errors=ev.QuantityError(uncertainty=counter * 0.1,
confidence_level=95),
waveform_id=ev.WaveformStreamID(seed_string=scnl),
creation_info=ev.CreationInfo(agency_id="dummy_agency",
author="dummy",
creation_time=UTCDateTime()),
**params,
)
sms.append(sm)
counter += 1
amplitudes = amplitudes or []
for amp in amplitudes:
sm = ev.StationMagnitude(
mag=counter,
mag_errors=ev.QuantityError(uncertainty=counter * 0.1,
confidence_level=95),
amplitude_id=amp.resource_id,
creation_info=ev.CreationInfo(agency_id="dummy_agency",
author="dummy",
creation_time=UTCDateTime()),
**params,
)
sms.append(sm)
counter += 1
return sms
def create_pick(origintime, picknum, picktime, eventnum, cinfo, phase, station,
wfseedstr, authority_id):
'''
create_pick - function to create an ObsPy Pick
:param origintime:
:type origintime:
:param picknum: number of the created pick
:type picknum: int
:param picktime:
:type picktime:
:param eventnum: human-readable event identifier
:type eventnum: str
:param cinfo: An ObsPy :class: `~obspy.core.event.CreationInfo` object
holding information on the creation of the returned object
:type cinfo: :class: `~obspy.core.event.CreationInfo` object
:param phase: name of the arrivals seismic phase
:type phase: str
:param station: name of the station at which the seismic phase has been
picked
:type station: str
:param wfseedstr: A SEED formatted string of the form
network.station.location.channel in order to set a referenced waveform
:type wfseedstr: str, SEED formatted
:param authority_id: name of the institution carrying out the processing
:type authority_id: str
:return: An ObsPy :class: `~obspy.core.event.Pick` object
'''
pickID = eventnum + '_' + station.strip() + '/{0:03d}'.format(picknum)
pickresID = create_resourceID(origintime, 'pick', authority_id, pickID)
pick = ope.Pick()
pick.resource_id = pickresID
pick.time = picktime
pick.creation_info = cinfo
pick.phase_hint = phase
pick.waveform_id = ope.ResourceIdentifier(id=wfseedstr, prefix='file:/')
return pick
def new_catalog(self):
"""Change the resource ids of events in the default catalog, return."""
cat = obspy.read_events()
for event in cat:
event.resource_id = ev.ResourceIdentifier()
return cat
def rid(some_id):
if some_id not in RID_CACHE:
RID_CACHE[some_id] = oe.ResourceIdentifier(some_id)
return RID_CACHE[some_id]
def test_defined_resource_id(self):
"""Ensure the defined resource_id sticks."""
rid = str(ev.ResourceIdentifier())
out = esc.ResourceIdentifier(id=rid)
assert out.id == rid
