def stack(stream, length=None, move=None):
"""
Stack traces in stream by correlation id
:param stream: |Stream| object with correlations
:param length: time span of one trace in the stack in seconds
(alternatively a string consisting of a number and a unit
-- ``'d'`` for days and ``'h'`` for hours -- can be specified,
i.e. ``'3d'`` stacks together all traces inside a three days time
window, default: None, which stacks together all traces)
:param move: define a moving stack, float or string,
default: None -- no moving stack,
if specified move usually is smaller than length to get an overlap
in the stacked traces
:return: |Stream| object with stacked correlations
"""
stream.sort()
stream_stack = obspy.Stream()
ids = {_corr_id(tr) for tr in stream}
ids.discard(None)
for id_ in ids:
traces = [tr for tr in stream if _corr_id(tr) == id_]
if length is None:
data = np.mean([tr.data for tr in traces], dtype=float, axis=0)
tr_stack = obspy.Trace(data, header=traces[0].stats)
tr_stack.stats.key = tr_stack.stats.key + '_s'
if 'num' in traces[0].stats:
tr_stack.stats.num = sum(tr.stats.num for tr in traces)
else:
tr_stack.stats.num = len(traces)
stream_stack.append(tr_stack)
else:
t1 = traces[0].stats.starttime
lensec = _time2sec(length)
movesec = _time2sec(move) if move else lensec
if (lensec % (24 * 3600) == 0
or isinstance(length, str) and 'd' in length):
t1 = UTC(t1.year, t1.month, t1.day)
elif (lensec % 3600 == 0
or isinstance(length, str) and 'm' in length):
t1 = UTC(t1.year, t1.month, t1.day, t1.hour)
t2 = max(t1, traces[-1].stats.endtime - lensec)
for t in IterTime(t1, t2, dt=movesec):
sel = [
tr for tr in traces
if -0.1 <= tr.stats.starttime - t <= lensec + 0.1
]
if len(sel) == 0:
continue
data = np.mean([tr.data for tr in sel], dtype=float, axis=0)
tr_stack = obspy.Trace(data, header=sel[0].stats)
key_add = '_s%s' % length + (move is not None) * ('m%s' % move)
tr_stack.stats.key = tr_stack.stats.key + key_add
tr_stack.stats.starttime = t
if 'num' in traces[0].stats:
tr_stack.stats.num = sum(tr.stats.num for tr in sel)
else:
tr_stack.stats.num = len(sel)
stream_stack.append(tr_stack)
return stream_stack
def correlate(io,
day,
outkey,
edge=60,
length=3600,
overlap=1800,
demean_window=True,
discard=None,
only_auto_correlation=False,
station_combinations=None,
component_combinations=('ZZ', ),
max_lag=100,
keep_correlations=False,
stack='1d',
njobs=0,
**preprocessing_kwargs):
"""
Correlate data of one day
:param io: io config dictionary
:param day: |UTC| object with day
:param outkey: the output key for the HDF5 index
:param edge: additional time span requested from day before and after
in seconds
:param length: length of correlation in seconds (string possible)
:param overlap: length of overlap in seconds (string possible)
:param demean_window: demean each window individually before correlating
:param discard: discard correlations with less data coverage
(float from interval [0, 1])
:param only_auto_correlations: Only correlate stations with itself
(different components possible)
:param station_combinations: specify station combinations
(e.g. ``'CX.PATCX-CX.PB01``, network code can be
omitted, e.g. ``'PATCX-PB01'``, default: all)
:param component_combinations: component combinations to calculate,
tuple of strings with length two, e.g. ``('ZZ', 'ZN', 'RR')``,
if ``'R'`` or ``'T'`` is specified, components will be rotated after
preprocessing, default: only ZZ components
:param max_lag: max time lag in correlations in seconds
:param keep_correlatons: write correlations into HDF5 file (dafault: False)
:param stack: stack correlations and write stacks into HDF5 file
(default: ``'1d'``, must be smaller than one day or one day)
.. note::
If you want to stack larger time spans
use the separate stack command on correlations or stacked
correlations.
:param njobs: number of jobs used. Some tasks will run parallel
(preprocessing and correlation).
:param \*\*preprocessing_kwargs: all other kwargs are passed to
`preprocess`
"""
inventory = io['inventory']
length = _time2sec(length)
overlap = _time2sec(overlap)
if not keep_correlations and stack is None:
msg = ('keep_correlation is False and stack is None -> correlations '
' would not be saved')
raise ValueError(msg)
components = set(''.join(component_combinations))
if 'R' in components or 'T' in components:
load_components = components - {'R', 'T'} | {'N', 'E'}
else:
load_components = components
if station_combinations is not None:
load_stations = set(sta for comb in station_combinations
for sta in comb.split('-'))
else:
load_stations = None
# load data
stream = obspy.Stream()
for smeta in _iter_station_meta(inventory, load_components):
if (load_stations is not None and smeta['station'] not in load_stations
and '.'.join((smeta['network'], smeta['station']))
not in load_stations):
continue
stream2 = get_data(smeta,
io['data'],
io['data_format'],
day,
overlap=overlap,
edge=edge)
if stream2:
stream += stream2
if len(stream) == 0:
log.warning('empty stream for day %s', str(day)[:10])
return
preprocess(stream,
day,
inventory,
overlap=overlap,
njobs=njobs,
**preprocessing_kwargs)
# collect trace pairs for correlation
next_day = day + 24 * 3600
stations = sorted({tr.id[:-1] for tr in stream})
tasks = []
for station1, station2 in itertools.combinations_with_replacement(
stations, 2):
if only_auto_correlation and station1 != station2:
continue
if station_combinations and not any(
set(station_comb.split('-')) ==
({station1.rsplit('.', 2)[0],
station2.rsplit('.', 2)[0]} if '.' in (station_comb) else
{station1.
split('.')[1], station2.split('.')[1]})
for station_comb in station_combinations):
continue
stream1 = Stream([tr for tr in stream if tr.id[:-1] == station1])
stream2 = Stream([tr for tr in stream if tr.id[:-1] == station2])
datetime1 = _midtime(stream1[0].stats)
datetime2 = _midtime(stream2[0].stats)
msg = 'Cannot get coordinates for channel %s datetime %s'
try:
c1 = inventory.get_coordinates(stream1[0].id, datetime=datetime1)
except Exception as ex:
raise RuntimeError(msg % (stream1[0].id, datetime1)) from ex
try:
c2 = inventory.get_coordinates(stream2[0].id, datetime=datetime2)
except Exception as ex:
raise RuntimeError(msg % (stream2[0].id, datetime2)) from ex
args = (c1['latitude'], c1['longitude'], c2['latitude'],
c2['longitude'])
dist, azi, baz = gps2dist_azimuth(*args)
if ('R' in components or 'T' in components) and station1 != station2:
stream1 = stream1.copy()
stream1b = stream1.copy().rotate('NE->RT', azi)
stream1.extend(stream1b.select(component='R'))
stream1.extend(stream1b.select(component='T'))
stream2 = stream2.copy()
stream2b = stream2.copy().rotate('NE->RT', azi)
stream2.extend(stream2b.select(component='R'))
stream2.extend(stream2b.select(component='T'))
it_ = (itertools.product(stream1, stream2) if station1 != station2 else
itertools.combinations_with_replacement(stream1, 2))
for tr1, tr2 in it_:
comps = tr1.stats.channel[-1] + tr2.stats.channel[-1]
if component_combinations and (comps not in component_combinations
and comps[::-1]
not in component_combinations):
continue
tasks.append((tr1, tr2, dist, azi, baz))
# start correlation
do_work = partial(_slide_and_correlate_traces, day, next_day, length,
overlap, discard, max_lag, outkey, demean_window)
streams = start_parallel_jobs_inner_loop(tasks, do_work, njobs)
xstream = Stream()
xstream.traces = [tr for s_ in streams for tr in s_]
if len(xstream) > 0:
res = {}
if keep_correlations:
res['corr'] = xstream
if stack:
res['stack'] = yam.stack.stack(xstream, stack)
return res