def process_traces(config, st):
"""Remove mean, deconvolve and ignore unwanted components."""
out_st = Stream()
for id in sorted(set(tr.id for tr in st)):
# We still use a stream, since the trace can have
# gaps or overlaps
st_sel = st.select(id=id)
network, station, location, channel = id.split('.')
# build a list of all possible ids, from station only
# to full net.sta.loc.chan
ss = [
station,
]
ss.append('.'.join((network, station)))
ss.append('.'.join((network, station, location)))
ss.append('.'.join((network, station, location, channel)))
if config.use_stations is not None:
combined = ("(" + ")|(".join(config.use_stations) + ")").replace(
'.', '\.')
if not any(re.match(combined, s) for s in ss):
logger.warning('%s: ignored from config file' % id)
continue
if config.ignore_stations is not None:
combined = ("(" + ")|(".join(config.ignore_stations) +
")").replace('.', '\.')
if any(re.match(combined, s) for s in ss):
logger.warning('%s: ignored from config file' % id)
continue
try:
_add_hypo_dist_and_arrivals(config, st_sel)
trace = _merge_stream(config, st_sel)
trace.stats.ignore = False
trace_process = _process_trace(config, trace)
out_st.append(trace_process)
except (ValueError, RuntimeError):
continue
if len(out_st) == 0:
logger.error('No traces left! Exiting.')
ssp_exit()
# Rotate traces, if SH or SV is requested
if config.wave_type in ['SH', 'SV']:
for id in sorted(set(tr.id[:-1] for tr in out_st)):
net, sta, loc, chan = id.split('.')
st_sel = out_st.select(network=net,
station=sta,
location=loc,
channel=chan + '?')
t0 = max(tr.stats.starttime for tr in st_sel)
t1 = min(tr.stats.endtime for tr in st_sel)
st_sel.trim(t0, t1)
st_sel.rotate('NE->RT')
return out_st
def _read_pdas(filename, **kwargs):
"""
Reads a PDAS file and returns an ObsPy Stream object.
.. warning::
This function should NOT be called directly, it registers via the
ObsPy :func:`~obspy.core.stream.read` function, call this instead.
:type filename: str
:param filename: PDAS file to be read.
:rtype: :class:`~obspy.core.stream.Stream`
:return: An ObsPy Stream object.
.. rubric:: Example
>>> from obspy import read
>>> st = read("/path/to/p1246001.108")
>>> st # doctest: +ELLIPSIS
<obspy.core.stream.Stream object at 0x...>
>>> print(st) # doctest: +ELLIPSIS
1 Trace(s) in Stream:
... | 1994-04-18T00:00:00.000000Z - ... | 200.0 Hz, 500 samples
"""
extra_headers = {}
with open(filename, "rb") as fh:
items = [fh.readline().split() for i_ in range(11)]
data = fh.read()
for i_ in (0, 1, 2, 3, 7, 8, 9):
extra_headers[items[i_][0].decode()] = items[i_][1].decode()
month, day, year = items[4][1].decode().split("-")
if UTCDateTime().year > 2050:
raise NotImplementedError()
if len(year) == 2:
if int(year) < 50:
year = "20" + year
else:
year = "19" + year
time = items[5][1].decode()
t = UTCDateTime("%s-%s-%sT%s" % (year, month, day, time))
sampling_rate = 1.0 / float(items[6][1].decode())
dtype = items[1][1].decode()
if dtype.upper() == "LONG":
data = from_buffer(data, dtype=np.int16)
elif dtype.upper() == "SHORT":
data = from_buffer(data, dtype=np.int8)
else:
raise NotImplementedError()
tr = Trace(data=data)
tr.stats.starttime = t
tr.stats.sampling_rate = sampling_rate
tr.stats._format = "PDAS"
tr.stats.pdas = extra_headers
st = Stream(traces=[tr])
return st
def QC_streams(start, end, st):
# Check start times
if not np.all([tr.stats.starttime == start for tr in st]):
print("* Start times are not all close to true start: ")
[print("* "+tr.stats.channel+" " +
str(tr.stats.starttime)+" " +
str(tr.stats.endtime)) for tr in st]
print("* True start: "+str(start))
print("* -> Shifting traces to true start")
delay = [tr.stats.starttime - start for tr in st]
st_shifted = Stream(
traces=[traceshift(tr, dt) for tr, dt in zip(st, delay)])
st = st_shifted.copy()
# # Check sampling rate
# sr = st[0].stats.sampling_rate
# sr_round = float(floor_decimal(sr, 0))
# if not sr == sr_round:
# print("* Sampling rate is not an integer value: ", sr)
# print("* -> Resampling")
# st.resample(sr_round, no_filter=False)
# Try trimming
dt = st[0].stats.delta
try:
st.trim(start, end-dt, fill_value=0., pad=True)
except:
print("* Unable to trim")
print("* -> Skipping")
print("**************************************************")
return False, None
# Check final lengths - they should all be equal if start times
# and sampling rates are all equal and traces have been trimmed
sr = st[0].stats.sampling_rate
if not np.allclose([tr.stats.npts for tr in st[1:]], st[0].stats.npts):
print("* Lengths are incompatible: ")
[print("* "+str(tr.stats.npts)) for tr in st]
print("* -> Skipping")
print("**************************************************")
return False, None
elif not np.allclose([st[0].stats.npts], int((end - start)*sr), atol=1):
print("* Length is too short: ")
print("* "+str(st[0].stats.npts) +
" ~= "+str(int((end - start)*sr)))
print("* -> Skipping")
print("**************************************************")
return False, None
else:
return True, st
def find_longest_equal(d, p):
"""
Find the longest time and return the new Stream
:param d,p: a Stream object has several time slice
:return d_slice,p_slice: Stream object (For remove response)
:exception pressure date not coherent with displacement
data length too short
"""
d = d.traces
index = 0
tempT = d[0]
for i in range(len(d)):
if len(d[i]) > len(tempT):
index = i
tempT = d[i]
d_slice = d[index]
# the admittance of each day is based on 9 to 30 2000 s long time series
# 9*2000 = 18000
if d_slice.meta.endtime - d_slice.meta.starttime < 18000:
print d_slice.meta.endtime - d_slice.meta.starttime
print "SHORT"
raise AttributeError
p_slice = p.slice(d_slice.meta.starttime, d_slice.meta.endtime)
# Must be a single trace
if len(p_slice.traces) != 1:
print "MUCH"
raise AttributeError
p_slice = p_slice.traces[0]
sta = max(p_slice.meta.starttime, d_slice.meta.starttime)
end = min(p_slice.meta.endtime, d_slice.meta.endtime)
if end - sta < 18000:
print "SHORT"
raise AttributeError
return Stream().append(d_slice).slice(sta, end), Stream().append(p_slice).slice(sta, end)
def test_Porter2011():
import matplotlib
matplotlib.use('Agg')
import numpy as np
from obspy.core import Stream
from telewavesim import utils as ut
from telewavesim import wiggle as wg
modfile = resource_filename('telewavesim',
'examples/models/model_Porter2011.txt')
wvtype = 'P'
npts = 3000 # Number of samples
dt = 0.01 # Sample distance in seconds
slow = 0.06 # Horizontal slowness (or ray parameter) in s/km
baz = np.arange(0., 360., 10.)
model = ut.read_model(modfile)
trR = Stream()
trT = Stream()
# Loop over range of data
for bb in baz:
# Calculate the plane waves seismograms
trxyz = ut.run_plane(model, slow, npts, dt, bb, wvtype=wvtype,
obs=False)
# Then the transfer functions in Z-R-T coordinate system
tfs = ut.tf_from_xyz(trxyz, pvh=False)
# Append to streams
trR.append(tfs[0])
trT.append(tfs[1])
# Set frequency corners in Hz
f1 = 0.01
f2 = 1.0
# Filter to get wave-like traces
trR.filter('bandpass', freqmin=f1, freqmax=f2, corners=2, zerophase=True)
trT.filter('bandpass', freqmin=f1, freqmax=f2, corners=2, zerophase=True)
# Stack over all traces
trR_stack, trT_stack = ut.stack_all(trR, trT, pws=True)
# Plot as wiggles
with tempfile.TemporaryDirectory() as tempdir:
wg.rf_wiggles_baz(trR, trT, trR_stack, trT_stack, 'test', btyp='baz',
scale=1.e3, tmin=-5., tmax=8., save=True,
ftitle=join(tempdir, 'porter2011.png'),
wvtype='P')
def get_waveforms(self,
network,
station,
location,
channel,
starttime,
endtime,
automerge=False,
trace_count_threshold=200):
starttime = UTCDateTime(starttime).timestamp
endtime = UTCDateTime(endtime).timestamp
query = "select * from wdb where net='%s' and sta='%s' and loc='%s' and cha='%s' " \
%(network, station, location, channel) + \
"and et>=%f and st<=%f" \
% (starttime, endtime)
rows = self.conn.execute(query).fetchall()
s = Stream()
if (len(rows) > trace_count_threshold): return s
#print 'rank: %d net: %s sta: %s loc:%s cha:%s ntraces: %d'%(self.rank,
# network, station,
# location, channel, len(rows))
#return s
for row in rows:
ds_id, net, sta, loc, cha, st, et, tag = row
station_data = self.asdf_datasets[ds_id].waveforms['%s.%s' %
(net, sta)]
try:
s += station_data[tag]
except:
pass
# end try
# end for
if (automerge):
try:
s.merge(method=-1)
except:
pass
# end try
# end if
# Trim traces
for t in s:
t.trim(starttime=UTCDateTime(starttime),
endtime=UTCDateTime(endtime))
# end for
return s
def test_setVersion(self):
"""
Tests if SAC version is set when writing
"""
tempfile = NamedTemporaryFile().name
np.random.seed(815)
st = Stream([Trace(data=np.random.randn(1000))])
st.write(tempfile, format="SAC")
st2 = read(tempfile, format="SAC")
os.remove(tempfile)
self.assertEqual(st2[0].stats['sac'].nvhdr, 6)
def test__set_metadata():
"""edge_test.EdgeFactory_test.test__set_metadata()
"""
# Call _set_metadata with 2 traces, and make certain the stats get
# set for both traces.
trace1 = Trace()
trace2 = Trace()
stream = Stream(traces=[trace1, trace2])
EdgeFactory()._set_metadata(stream, "BOU", "H", "variation", "minute")
assert_equal(stream[0].stats["channel"], "H")
assert_equal(stream[1].stats["channel"], "H")
def test__set_metadata():
"""edge_test.EdgeFactory_test.test__set_metadata()
"""
# Call _set_metadata with 2 traces, and make certain the stats get
# set for both traces.
trace1 = Trace()
trace2 = Trace()
stream = Stream(traces=[trace1, trace2])
EdgeFactory()._set_metadata(stream, 'BOU', 'H', 'variation', 'minute')
assert_equals(stream[0].stats['channel'], 'H')
assert_equals(stream[1].stats['channel'], 'H')
def tracebufs2obspyStream(tbuflist):
"""
Returns obspy.Stream object from input list of tracebuf2 objects
"""
if not tbuflist:
return None
tlist = []
for tb in tbuflist:
tlist.append(tb.getObspyTrace())
strm = Stream(tlist)
return strm
def plot_stack(trace,
times,
description,
offset_before=0.5,
offset_after=1.5,
plot_span=False,
filebase=None,
show=True):
"""
Plot a stack of time series from one trace
trace is an obspy Trace object
title is the title to put on the graph
outfile is the filename to write the plot out to (None = print to screen)
times is a list of UTCDateTimes
plot_span: whether to plot a time series spanning the first to last time
"""
title = description + f', orientation_code="{trace.stats.channel[-1]}"'
assert offset_before >= 0,\
f'plot_stack "{description}": offset_before < 0 ({offset_before:g})'
assert offset_after > 0,\
f'plot_stack "{description}": offset_after <= 0 ({offset_after:g})'
if plot_span:
_plot_span(times, Stream(traces=[trace]))
print(f'Plotting stack "{title}"')
colors = plt.cm.rainbow(np.linspace(0, 1, len(times)))
offset_vertical = 0
# time_zero = UTCDateTime(times[0])
ax = plt.axes()
max_val = 0
# Set up y axis range
for time in times:
temp = trace.slice(time - offset_before, time + offset_after)
if abs(temp.max()) > max_val:
max_val = abs(temp.max())
# Plot the subtraces
for time, c in zip(times, colors):
offset_vertical += max_val
t = trace.slice(time - offset_before, time + offset_after)
ax.plot(t.times("utcdatetime") - time,
t.data - offset_vertical,
color=c,
label=time.strftime('%H:%M:%S') +
'.{:02d}'.format(int(time.microsecond / 1e4)))
offset_vertical += max_val
ax.set_title(title)
ax.grid()
ax.legend()
if filebase:
plt.savefig(filebase + '_' + get_valid_filename(description) +
'_stack.png')
if show:
plt.show()
def create_random_trace(sampling_rate=40.0, duration=5.0, **header_kwargs):
header = {
'sampling_rate': sampling_rate,
'starttime': UTCDateTime(0),
'channel': 'Z',
'station': 'test'
}
header = {**header, **header_kwargs}
data = np.random.uniform(-1, 1, (int(duration * sampling_rate)))
trace = Trace(data=data, header=header)
trace.stats.data_type = 'test'
return Stream(traces=[trace])
def _writeData(self, traceData, stats, timeObj):
streamObj = Stream([Trace(data=traceData, header=stats)])
filename = self._prepareFilename(timeObj)
offset = int(np.mean(streamObj.traces[0].data))
streamObj.traces[0].data = np.array(
[x - offset for x in streamObj.traces[0].data])
self.logger.debug("[" + strftime('%X') +
"] Saving %d samples (corrected by %d) to %s..." %
(len(traceData), offset, filename))
streamObj.write(filename, format='MSEED')
def read_sds(event,
sds_root,
phase="P",
component="Z",
trace_length=30,
sample_rate=100,
random_time=0):
stream = Stream()
client = Client(sds_root=sds_root)
for pick in event.picks:
if not pick.phase_hint == phase:
print("Skip " + pick.phase_hint + " phase pick")
continue
if not pick.waveform_id.channel_code[-1] == component:
print(pick.waveform_id.channel_code)
continue
t = event.origins[0].time
if pick.time > t + trace_length:
t = pick.time - trace_length + 5
print("origin: " + t.isoformat() + " pick: " +
pick.time.isoformat())
if random_time:
t = t - random_time + np.random.random_sample() * random_time * 2
net = "*"
sta = pick.waveform_id.station_code
loc = "*"
chan = "??" + component
st = client.get_waveforms(net, sta, loc, chan, t, t + trace_length + 1)
if st.traces:
trace = st.traces[0]
trace = signal_preprocessing(trace)
points = trace_length * sample_rate + 1
try:
trim_trace(trace, points)
except Exception as err:
print(err)
continue
stream += st.traces[0]
else:
print("No trace in ", t.isoformat(), net, sta, loc, chan)
return stream
def _read_SES3D(fh, headonly=False):
"""
Internal SES3D parsing routine.
"""
# Import here to avoid circular imports.
from obspy.core import AttribDict, Trace, Stream
# Read the header.
component = fh.readline().split()[0].lower()
npts = int(fh.readline().split()[-1])
delta = float(fh.readline().split()[-1])
# Skip receiver location line.
fh.readline()
rec_loc = fh.readline().split()
rec_x, rec_y, rec_z = list(map(float,
[rec_loc[1], rec_loc[3], rec_loc[5]]))
# Skip the source location line.
fh.readline()
src_loc = fh.readline().split()
src_x, src_y, src_z = list(map(float,
[src_loc[1], src_loc[3], src_loc[5]]))
# Read the data.
if headonly is False:
data = np.array(list(map(float, fh.readlines())), dtype="float32")
else:
data = np.array([])
ses3d = AttribDict()
ses3d.receiver_latitude = rotations.colat2lat(rec_x)
ses3d.receiver_longitude = rec_y
ses3d.receiver_depth_in_m = rec_z
ses3d.source_latitude = rotations.colat2lat(src_x)
ses3d.source_longitude = src_y
ses3d.source_depth_in_m = src_z
header = {
"delta": delta,
"channel": COMPONENT_MAP[component],
"ses3d": ses3d,
"npts": npts
}
# Setup Obspy Stream/Trace structure.
tr = Trace(data=data, header=header)
# Small check.
if headonly is False and npts != tr.stats.npts:
msg = "The sample count specified in the header does not match " + \
"the actual data count."
warnings.warn(msg)
return Stream(traces=[tr])
def stream_seishub_read(host="localhost", port=8080, timeout=100,
start_time="2010-01-01 00:20:03", time_interval=30,
network_id="PF", station_id="", location_id="",
channel_id="HLE", get_paz=False, remove_mean=False,
remove_trend=False):
""" Seishub server client.
For a detailed description of how it works refer to ObsPy website
(obspy.org)
"""
client = Client_seis(base_url="http://" + host + ':' + str(port),
timeout=timeout)
t = UTCDateTime(start_time)
st = Stream()
if station_id == "":
st = client.waveform.getWaveform(network_id, str(station_id),
location_id,
channel_id, t, t + time_interval)
else:
for station in station_id:
try:
st += client.waveform.getWaveform(network_id, str(station),
location_id,
channel_id,
t,
t + time_interval)
except:
pass
if len(st) > 0:
if remove_trend:
st = stream_detrend(st)
if remove_mean:
st = stream_demean(st)
st.merge(method=1, fill_value=0, interpolation_samples=1)
n_trace = len(st)
else:
n_trace = 0
if get_paz:
paz = client.station.getPAZ(network_id, station_id, t)
return st, paz, n_trace
else:
return st, n_trace
return st, n_trace
def __init__(self, filename=None, headonly=False, dummy=False):
if dummy:
self.stream = self.set_dummy()
else:
if not os.path.isfile(filename):
raise Vol12Error("Can't find file %s." % filename)
self.fn = filename
self.f = open(self.fn, 'r')
self.stream = Stream()
self.headonly = headonly
for i in xrange(3):
self.stream += self.read_comp(self.f)
self.f.close()
def test_bugfix_setStats(self):
"""
Test related to issue #4.
"""
st = Stream([Trace()])
st += st
# change stats attributes
st[0].stats.station = 'AAA'
st[1].stats['station'] = 'BBB'
self.assertEquals(st[0].stats.station, 'BBB')
self.assertEquals(st[0].stats['station'], 'BBB')
self.assertEquals(st[1].stats['station'], 'BBB')
self.assertEquals(st[1].stats.station, 'BBB')
def _build_weight_st(config, spec_st, specnoise_st):
"""Build the weight spectrum."""
weight_st = Stream()
spec_ids = set(sp.id[:-1] for sp in spec_st if not sp.stats.ignore)
for specid in spec_ids:
try:
spec_h = _select_spectra(spec_st, specid + 'H')[0]
specnoise_h = _select_spectra(specnoise_st, specid + 'H')[0]
except Exception:
continue
weight = _build_weight(config, spec_h, specnoise_h)
weight_st.append(weight)
return weight_st
def linear_ramp_trend(sampling_rate=40.0, duration=5.0, height=1.0, mean=0.5):
header = {
'sampling_rate': sampling_rate,
'starttime': UTCDateTime(0),
'channel': 'Z',
'station': 'test'
}
data = np.random.uniform(-1, 1, (int(duration * sampling_rate)))
data += np.linspace(0, height, num=int(duration * sampling_rate))
data += mean * np.ones(int(duration * sampling_rate))
trace = Trace(data=data, header=header)
trace.stats.data_type = 'test'
return Stream(traces=[trace])
def create_triangle_trace(sampling_rate=40.0, duration=5.0, **header_kwargs):
header = {
'sampling_rate': sampling_rate,
'starttime': UTCDateTime(0),
'channel': 'Z',
'station': 'test'
}
header = {**header, **header_kwargs}
x = np.linspace(0, duration, num=int(duration * sampling_rate))
data = signal.triang(int(duration * sampling_rate))
trace = Trace(data=data, header=header)
trace.stats.data_type = 'test'
return Stream(traces=[trace])
def create_impulse_stream(sampling_rate=40.0, duration=5.0, **header_kwargs):
header = {
'sampling_rate': sampling_rate,
'starttime': UTCDateTime(0),
'channel': 'Z',
'station': 'test'
}
header = {**header, **header_kwargs}
data = np.zeros(int(duration * sampling_rate))
data[0] = 1
trace = Trace(data=data, header=header)
trace.stats.data_type = 'test'
return Stream(traces=[trace])
def _read_data(self):
# Read data
data = [None for _ in self.station.name]
for i in range(self.station.nsta):
st = Stream()
for c in self.header.component:
st.append(
read('%s/%s.%c.dat' %
(self.header.datadir, self.station.name[i], c),
format='SAC')[0])
data[i] = st
return data
def add_arrival_to_obspy_trace(obspy_trace, reformat_p_file):
from obspy.core import Stream
station = obspy_trace.stats.station
arrival = list(filter(lambda sta: sta['station'] == station, reformat_p_file))
obspy_trace.stats.o = reformat_p_file[0]["o"]
obspy_trace.stats.evla = reformat_p_file[0]["evla"]
obspy_trace.stats.evlo = reformat_p_file[0]["evlo"]
obspy_trace.stats.evdp = reformat_p_file[0]["evdp"]
obspy_trace.stats.mag = reformat_p_file[0]["mag"]
if arrival:
obspy_trace.stats.t1 = arrival[0]["t1"]
obspy_trace.stats.t2 = arrival[0]["t2"]
return Stream(traces=obspy_trace)
def axisem2mseed(path):
"""
change .dat files into MSEED format
"""
global test_param
if not os.path.isdir(os.path.join(path, 'MSEED')):
os.mkdir(os.path.join(path, 'MSEED'))
else:
print 'Following directory already exists:'
print os.path.join(path, 'MSEED')
sys.exit()
t = UTCDateTime(0)
traces = []
for file in glob.iglob(os.path.join(path, '*.dat')):
stationID = file.split('/')[-1].split('_')[0]
networkID = file.split('/')[-1].split('_')[1]
chan = file.split('/')[-1].split('_')[-1].split('.')[0]
if chan == 'E': chan = 'BHE'
elif chan == 'N': chan = 'BHN'
elif chan == 'Z': chan = 'BHZ'
try:
dat = np.loadtxt(file)
npts = len(dat[:,0])
stats = {'network': networkID,
'station': stationID,
'location': '',
'channel': chan,
'npts': npts,
'sampling_rate': (npts - 1.)/(dat[-1,0] - dat[0,0]),
'starttime': t + dat[0,0],
'mseed' : {'dataquality': 'D'}}
st = Stream(Trace(data=dat[:,1], header=stats))
if test_param['convSTF'] == 'Y':
sigma = test_param['halfduration'] / np.sqrt(2.) / 3.5
convSTF(st, sigma=sigma)
if test_param['filter'] == 'Y':
st.filter('lowpass', freq=test_param['fmax'], corners=2)
st.filter('lowpass', freq=test_param['fmax'], corners=2)
st.filter('lowpass', freq=test_param['fmax'], corners=2)
st.filter('lowpass', freq=test_param['fmax'], corners=2)
st.filter('highpass', freq=test_param['fmin'], corners=2)
st.filter('highpass', freq=test_param['fmin'], corners=2)
fname = os.path.join(path, 'MSEED', 'dis.' + stationID + '..' + chan)
st.write(fname, format='MSEED')
except Exception, e:
print e
print networkID + '.' + stationID + '.' + chan + '.mseed'
print '-------------------------------------------------'
def write_seisan(filename, args):
""" writes seisan file from baikal one """
bf = BaikalFile(filename)
if not bf.valid:
print("Invalid file {}".format(filename))
return
header = bf.MainHeader
# datetime
date = datetime.datetime(header["year"], header["month"], header["day"])
delta = datetime.timedelta(seconds=header["to"])
dt = date + delta
_time = dt.time() # time
# make utc datetime
utcdatetime = UTCDateTime(date.year,
date.month,
date.day,
_time.hour,
_time.minute,
_time.second,
_time.microsecond,
precision=3)
bf.traces = bf.traces.astype(np.int32)
bf.traces = bf.traces[:3]
traces = []
for channel, data in zip(CHANNELS, bf.traces):
stats = DEFAULT_STATS.copy()
stats.update({
"station": header['station'].upper()[:3],
'channel': channel,
'sampling_rate': int(1. / header["dt"]),
"delta": header["dt"],
"npts": data.size, #shape[0]
'starttime': utcdatetime,
})
# save coordinates
stats['gse2']["lat"] = header['latitude']
stats['gse2']["lon"] = header["longitude"]
trace = Trace(data=data, header=stats)
traces.append(trace)
# create Stream
stream = Stream(traces)
#== write seisan
# date
name = "{year:04}-{month:02}-{day:02}".format(**header)
# time
name += "-{t.hour:02}-{t.minute:02}".format(t=stats['starttime'])
# + station name + Day_of_Year
name += "{0}__{1:03}".format(stats["station"],
stats['starttime'].timetuple().tm_yday)
print('Writing GSE2 file %s.' % name)
writeGSE2(stream, os.path.join(args.outdir, name))
def get_waveforms(self, **kwargs):
stream = self.bank.get_waveforms(**kwargs)
traces = []
for trace in stream:
data = trace.data[:-1]
header = {
'delta': trace.stats.delta,
'station': trace.stats.station,
'starttime': trace.stats.starttime,
'channel': trace.stats.channel,
'network': trace.stats.network
}
traces.append(Trace(data, header=header))
return Stream(traces=traces)
def custom_get_waveforms(network, station, location, channel, starttime,
endtime, quality=None, minimumlength=None,
longestonly=None, filename=None, attach_response=False,
**kwargs):
with pyasdf.ASDFDataSet('/g/data/ha3/Passive/_ANU/7X(2009-2011)/ASDF/7X(2009-2011).h5', mode='r') as asdfDataSet:
st = Stream()
# ignoring channel for now as all the 7D network waveforms have only BH? channels
filteredList = [i for i in asdfDataSet.waveforms[network + '.' + station].list() if
'raw_recording' in i and
UTC(i.split("__")[1]) < starttime and
UTC(i.split("__")[2]) > endtime]
for t in filteredList:
st += asdfDataSet.waveforms[network + '.' + station][t]
return st
def add(self, stream, verbose=True):
"""
Process all traces with compatible information and add their spectral
estimates to the histogram containg the probabilistic psd.
Also ensures that no piece of data is inserted twice.
"""
# return later if any changes were applied to the ppsd statistics
changed = False
# prepare the list of traces to go through
if isinstance(stream, Trace):
stream = Stream([stream])
# select appropriate traces
stream = stream.select(id=self.id,
sampling_rate=self.sampling_rate)
# save information on available data and gaps
self.__insert_data_times(stream)
self.__insert_gap_times(stream)
# merge depending on skip_on_gaps set during __init__
stream.merge(self.merge_method, fill_value=0)
for tr in stream:
# the following check should not be necessary due to the select()..
if not self.__sanity_check(tr):
msg = "Skipping incompatible trace."
warnings.warn(msg)
continue
t1 = tr.stats.starttime
t2 = tr.stats.endtime
while t1 + PPSD_LENGTH <= t2:
if self.__check_time_present(t1):
msg = "Already computed time spans detected (e.g. %s), " + \
"skipping these slices."
msg = msg % t1
print msg
else:
# throw warnings if trace length is different than one
# hour..!?!
slice = tr.slice(t1, t1 + PPSD_LENGTH)
success = self.__process(slice)
if success:
self.__insert_used_time(t1)
if verbose:
stdout.write("\r adding %s" % t1)
stdout.flush()
changed = True
t1 += PPSD_STRIDE # advance half an hour
if verbose:
stdout.write("\r")
stdout.flush()
return changed
def query_sql_db(self, query, sql_filename, sta):
# Open a new st object
st = Stream()
# Initialize (open/create) the sqlalchemy sqlite engine
engine = create_engine('sqlite:///' + sql_filename)
Session = sessionmaker()
Session.configure(bind=engine)
session = Session()
for matched_waveform in session.query(Waveforms).filter(query):
st += self.ds.waveforms[sta][matched_waveform.full_id]
return(st)
