def test_mseed_float32(_data, inv_output):
mseed = _data['mseed']
# inv_obj = _data['inventory']
mseed2 = _data['mseed_'+inv_output]
sio = StringIO()
# so, apparently mseed2 has still the eoncoding of the original mseed,
# which is "STEIM2" for the current mseed (mapped to np.int32, see
# obspy.io.mseed.headers.ENCODINGS
# if we set a custom encoding, IT MUST MATCH the dtype of the trace data
# THIS RAISES WARNING (commented out):
# mseed2.write(sio, format="MSEED")
# THIS IS FINE:
mseed2.write(sio, format="MSEED", encoding=5)
# NOW LET"'s CONVERT:
mseed2_32 = Stream([Trace(trace.data.astype(np.float32), trace.stats)
for trace in mseed2])
sio32 = StringIO()
mseed2_32.write(sio32, format='MSEED', encoding=4)
# sio32 HAS APPROX HALF THE LENGTH OF sio64 (uncomment below and debug breakpoint or print):
# size32 = len(sio32.getvalue())
# size64 = len(sio64.getvalue())
# let's see how this affects data. What is the relative error?
mseed64 = obspy_read(sio)
mseed32 = obspy_read(sio32)
print ""
print inv_output
for t64, t32, i in zip(mseed64, mseed32, count()):
min = np.nanmin(t64.data)
max = np.nanmax(t64.data)
range = np.abs(max-min)
diff = np.abs(t64.data - t32.data) / range
meanerr = np.nanmean(diff)
maxerr = np.nanmax(diff)
minerr = np.nanmin(diff)
print "Trace#%d" % (i+1)
print "min %.2E" % min
print "max %.2E" % max
print "min err ([0,1]): %.2E" % minerr
print "mean err ([0,1]): %.2E" % meanerr
print "max err ([0,1]): %.2E" % maxerr
g = 9
print ""
h = 9
def test_pick_amplitude_assocs(miniseed_conf, algorithm, mseed):
picker = pickermaps[algorithm]()
st = obspy_read(mseed)
st2 = Stream(st[0:1])
event = picker.event(st2, config=miniseed_conf)
assert len(event.picks) == len(event.amplitudes)
for p, a in zip(event.picks, event.amplitudes):
assert a.pick_id == p.resource_id
def _read_waveforms(self, database_filename, format='NORDIC'):
if format == 'NORDIC':
full_wavefile = self._get_nordic_wavefile_name(database_filename)
else:
raise NameError(f'type {type} not implemented')
stream = obspy_read(full_wavefile, 'MSEED')
# get rid of bad last sample in some streams, and detrend
for tr in stream:
tr.data = tr.data[:-10]
tr.detrend(type='demean')
return stream, full_wavefile
def _data():
"""returns a dict with fields 'mseed', 'mseed_ACC', 'mseed_VEL', 'mseed_DISP' (all Streams.
The latter three after removing the response)
'inventory' (an inventory object) and two strings: 'mseed_path' and 'inventory_path'"""
folder = os.path.join(os.path.dirname(os.path.abspath(__file__)), '..', 'data')
mseed_path = os.path.join(folder, 'trace_GE.APE.mseed')
mseed = obspy_read(mseed_path)
inv_path = os.path.join(folder, 'inventory_GE.APE.xml')
s = StringIO()
with open(inv_path) as _opn:
s.write(_opn.read())
s.seek(0)
inv_obj = read_inventory(s)
ret = {'mseed': mseed, 'inventory': inv_obj, 'mseed_path': mseed_path,
'data_path': folder,
'inventory_path': inv_path}
for inv_output in ['ACC', 'VEL', 'DISP']:
mseed2 = remove_response(mseed, inv_obj, output=inv_output)
ret['mseed_'+inv_output] = mseed2
return ret
def pick(config_file):
"""
:param config_file: user supplied config file for picking
:return: tba
"""
log.info('Reading config file...')
cf = config.Config(config_file)
log.info('Preparing time series')
st = Stream()
if cf.seeds:
for f in cf.miniseeds:
st += obspy_read(f)
log.info('Miniseeds accumulated')
else:
raise NotImplementedError
log.info('Applying picking algorithm')
picker = pickermaps[cf.picker['algorithm']](**cf.picker['params'])
event = picker.event(st, config=cf)
event.write(filename='test.xml', format='SC3ML')
def test_1dassociater(random_filename):
db_assoc = random_filename(ext='.db')
db_tt_test = random_filename(ext='.db')
# Our SQLite databases are:
db_assoc = 'sqlite:///' + db_assoc
shutil.copy(db_tt, db_tt_test)
db_tt_test = 'sqlite:///' + db_tt_test
# Traveltime database
# Connect to our databases
engine_assoc = create_engine(db_assoc, echo=False)
# # Create the tables required to run the 1D associator
tables1D.Base.metadata.create_all(engine_assoc)
Session = sessionmaker(bind=engine_assoc)
session = Session()
# Find all waveform data in the data directory
file_list = glob.glob(os.path.join(EX_DATA, '*.msd'))
# Define our picker instance
picker = fbpicker.FBPicker(t_long=5,
freqmin=0.5,
mode='rms',
t_ma=20,
nsigma=3,
t_up=0.78,
nr_len=2,
nr_coeff=2,
pol_len=10,
pol_coeff=10,
uncert_coeff=3)
st = Stream()
for f in file_list:
st += obspy_read(f)
# Pick the waveforms
for s in st:
# st.merge() # merge will cause issues if there is a data gap
s.detrend('linear')
scnl, picks, polarity, snr, uncert = picker.picks(s)
t_create = datetime.utcnow() # Record the time we made the picks
# Add each pick to the database
for i in range(len(picks)):
log.debug('st = {} Pick = {} {} {} scnl = {}'.format(
s, i, picks[i], picks[i].datetime, scnl))
new_pick = tables1D.Pick(scnl, picks[i].datetime, polarity[i],
snr[i], uncert[i], t_create)
session.add(new_pick) # Add pick i to the database
session.commit() # Commit the pick to the database
log.debug('Wrote picks')
# Define the associator
assocOK = assoc1D.LocalAssociator(db_assoc,
db_tt_test,
max_km=350,
aggregation=1,
aggr_norm='L2',
cutoff_outlier=30,
assoc_ot_uncert=7,
nsta_declare=3,
loc_uncert_thresh=0.2)
# Identify candidate events (Pick Aggregation)
assocOK.id_candidate_events()
# Associate events
assocOK.associate_candidates()
print("Unit Testing for 1Dassociator ...............")
# +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
# Function Testing rms sort list
# +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
radius = [
('SIO', -137.26, 68.992, 83.5, 0.7514, 0),
('U32A', -137.26, 68.992, 203.0, 1.8268, 1),
('W35A', -137.26, 68.992, 42.5, 0.3825, 2),
('OKCFA', -137.26, 68.992, 33.0, 0.297, 3),
('X34A', -137.26, 68.992, 122.0, 1.0979, 4),
('FNO', -137.26, 68.992, 36.5, 0.3285, 5),
]
lon = -137.26
lat = 68.992
st_declare = 3 # number of station requires to monitor earth quake
rms_sort = []
rms_sort, cb = assocOK._LocalAssociator__accumulate_rms_sort(
radius, lon, lat, st_declare)
print("")
print('rms = {}'.format(rms_sort))
print('Combinations Stations = {}'.format(cb))
print("")
assert len(rms_sort) > 0
# +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
# Function Testing for radius paremeters
# +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
# candis_arr = [Candidate Event <2013-06-16T15:38:50.150000 U32A 203.00 1.83 18 19>]
# radius=[]
# radius, lon, lat = assocOK.accumulate_radius(candis_arr)
# print ("")
# print ("Radius = {}".format(radius))
# print ("Lon = {}".format(lon))
# print ("Lat = {}".format(lat))
# Add singles stations to events
assocOK.single_phase()
events = assocOK.assoc_db.query(Associated).all()
assert len(events) == 1
event = events[0]
assert event.nsta == 3
print(event.longitude)
print(event.latitude)
print('event.longitude = ', event.longitude)
print('event.latitude = ', event.latitude)
def get_stream_with_gaps(_data):
mseed_dir = _data['data_path']
return obspy_read(os.path.join(mseed_dir, "IA.BAKI..BHZ.D.2016.004.head"))