def pick_events(window=(-100, 500), filter=(0.033, 2.), phase='P', new_sampling_rate=20): #@ReservedAssignment
logfile = os.path.dirname(data.rf_events) + '/log_pick_events_%s.txt'
util.checkDir(logfile)
util.setRootLogger(logfile=logfile % '', logdebugfile=logfile % '_debug')
log.info('***** Pick events: %s' % util.parameters())
mod_data.eventPicker(data, component='all', phase=phase, window=window,
filter=filter, new_sampling_rate=new_sampling_rate)
def sort(self, keys='datetime', reverse=False, logit=True):
"""
Sort events after list of keys.
"""
# Check the list and all items.
items = [
'datetime', 'id', 'latidue', 'longitude', 'depth', 'magnitude'
]
msg = "keys must be a list of item strings. Available items to " \
"sort after: \n" + ' '.join(items)
if isinstance(keys, basestring):
keys = [keys]
if not isinstance(keys, list):
raise TypeError(msg)
for _i in keys:
try:
items.index(_i)
except:
raise TypeError(msg)
# Loop over all keys in reversed order.
for _i in keys[::-1]:
super(Events, self).sort(key=lambda x: x[_i], reverse=reverse)
if logit:
log.info('Sort events after %s' %
util.parameters(only=['keys', 'reverse']))
def pick_events(
window=(-100, 500), filter=(0.033, 2.), phase='P',
new_sampling_rate=20): #@ReservedAssignment
logfile = os.path.dirname(data.rf_events) + '/log_pick_events_%s.txt'
util.checkDir(logfile)
util.setRootLogger(logfile=logfile % '', logdebugfile=logfile % '_debug')
log.info('***** Pick events: %s' % util.parameters())
mod_data.eventPicker(data,
component='all',
phase=phase,
window=window,
filter=filter,
new_sampling_rate=new_sampling_rate)
def filter(data, correlations, filters, stack=None, period=24 * 3600): #@ReservedAssignment
log.info('Filter correlations: %s' % util.parameters())
for correlation in correlations:
expr = data.getX(correlation, '????', filter_=None, period=period, stack=stack) + '.QHD'
files = glob(expr)
for file_ in files:
try:
st = read(file_)
except Exception as err:
log.warning('Could not load file, because:/n%s' % str(err))
continue
for filter_ in filters:
st2 = st.copy()
st2.filter2(*filter_)
data.writeX(st2, correlation, st[0].stats.endtime, filter=filter_, period=period, stack=stack)
def stack(data, correlations, dt=-1, filters=None, period=24 * 3600, shift=None, onefile=False, yearfiles=False):
#t1 = t1.__class__(t1.date)
#t2 = t2.__class__(t2.date)
log.info('Stack correlations: %s' % util.parameters())
print 'Stack correlations... '
if filters is None:
filters = (None,)
stack = Stream()
last_year = None
for correlation in ProgressBar()(correlations):
for filter_ in filters:
try:
st = read(data.getX(correlation, '*', filter=filter_, period=period) + '.QHD')
except Exception as err:
log.warning('Could not load file, because:/n%s' % str(err))
else:
print correlation
for some_traces in streamtimegen(st, dt=dt, start=None, shift=shift):
tr = some_traces.calculate('mean')
stack.append(tr)
this_year = (some_traces[0].stats.starttime).year
if last_year is None:
last_year = this_year
#if yearfiles and (some_traces[0].stats.starttime + period).julday == 1 and len(stack) > 0:
if yearfiles and this_year != last_year and len(stack) > 0:
data.writeX(stack, correlation, time=some_traces[0].stats.starttime - 365 * 24 * 3600, filter_=filter_, period=period, stack=(dt, shift))
last_year = this_year
stack = Stream()
if not onefile:
if yearfiles:
time = some_traces[0].stats.starttime
else:
time = None
if len(stack) > 0:
data.writeX(stack, correlation, time=time, filter=filter_, period=period, stack=(dt, shift))
last_year = None
stack = Stream()
if onefile:
data.writeX(stack, ('all', 'all'), time=None, filter=filters[0], period=period, stack=(dt, shift))
def sort(self, keys='datetime', reverse=False, logit=True):
"""
Sort events after list of keys.
"""
# Check the list and all items.
items = ['datetime', 'id', 'latidue', 'longitude', 'depth', 'magnitude']
msg = "keys must be a list of item strings. Available items to " \
"sort after: \n" + ' '.join(items)
if isinstance(keys, basestring):
keys = [keys]
if not isinstance(keys, list):
raise TypeError(msg)
for _i in keys:
try:
items.index(_i)
except:
raise TypeError(msg)
# Loop over all keys in reversed order.
for _i in keys[::-1]:
super(Events, self).sort(key=lambda x: x[_i], reverse=reverse)
if logit:
log.info('Sort events after %s' % util.parameters(only=['keys', 'reverse']))
def stack_day(data, correlations, dt=-1, start=None, onefile=False):
#t1 = t1.__class__(t1.date)
#t2 = t2.__class__(t2.date)
log.info('Stack day correlations: %s' % util.parameters())
if start is not None:
dt_log = '%s-%s' % (dt, start)
else:
dt_log = dt
stack = Stream()
for correlation in correlations:
try:
days = read(data.getXDay(correlation, '*') + '.QHD')
except Exception as err:
log.warning('Could not load file, because:/n%s' % str(err))
else:
for somedays in streamdaygen(days, dt=dt, start=start):
tr = somedays.calculate('mean')
stack.append(tr)
if not onefile:
data.writeXDayStack(stack, correlation, dt_log)
stack = Stream()
if onefile:
data.writeXDayStack(stack, ('all', 'all'), dt_log)
def noisexcorrf(data, correlations, t1, t2, shift_sec, period=24 * 3600,
pool=None, max_preload=5, overlap=0):
"""
Freqeuency domain noise cross correlation
Expects day files prepared with prepare()
"""
if period == 'day':
period = 24 * 3600
elif period == 'hour':
period = 3600
log.info('Noise cross correlation: %s' % util.parameters())
print 'Noise cross correlation...'
# if period != 24 * 3600:
# raise ValueError('function at the moment only '
# 'working with period=24*3600.')
if 24 * 3600 % period != 0:
raise ValueError('period has to be factor of a day')
for correlation in ProgressBar()(correlations):
autocorr = correlation[0] == correlation[1]
station1 = correlation[0][:-1]
station2 = correlation[1][:-1]
comp1 = correlation[0][-1]
comp2 = correlation[1][-1]
# data1 = FloatingStream(data, t1, station1, shift_sec, component=comp1, period=period)
# if not autocorr:
# data2 = FloatingStream(data, t1, station2, 0, component=comp2, period=period)
xcorr = [] if pool else Stream()
stream1 = None
for t in timegen(t1, t2, 24 * 3600):
if len(xcorr) > 0 and (t - period).date != t.date and (
(period >= 3600 and t.julday == 1) or period < 3600):
data.writeX(_get_async_resutls(xcorr) if pool else xcorr,
correlation, t - period, period=period)
xcorr = [] if pool else Stream()
if (not (data.getStream(t, station1, component=comp1, check=True) and
(autocorr or data.getStream(t, station2, component=comp2, check=True)))):
log.debug('No data for %s %s' % (str(correlation), t))
continue
try:
if overlap == 0 or stream1 is None:
stream1 = data.getStream(t, station1, component=comp1)
else:
stream1 = stream1 + data.getStream(t, station1, component=comp1)
stream1.merge()
stream1.trim(t - overlap, None)
if autocorr:
stream2 = stream1
else:
if overlap == 0:
stream2 = data.getStream(t, station2, component=comp2)
else:
raise NotImplementedError()
except ValueError:
log.warning('Could not load data for %s %s' % (str(correlation), t))
continue
if not (len(stream1) == len(stream2) == 1):
log.debug('Stream is not compatible (%d,%d traces)' % (len(stream1), len(stream2)))
continue
tr1 = stream1[0]
tr2 = stream2[0]
if tr1.stats.sampling_rate != tr2.stats.sampling_rate:
raise ValueError('Sampling rate is different.')
if period == 24 * 3600:
# check data
if tr1.stats.npts != tr2.stats.npts:
log.info('Discard data because of different npts %d vs %d' % (tr1.stats.npts, tr2.stats.npts))
continue
log.debug ('Calculating xcorr for %s' % t)
# original implementation only ok for period == 'day'
args = (tr1, tr2, shift_sec, correlation)
if pool:
if len(xcorr) >= max_preload:
xcorr[-max_preload].wait()
xcorr.append(pool.apply_async(_noisexcorr_traces, args))
else:
xcorr.append(_noisexcorr_traces(*args))
# new implementation for all other periods
else:
if tr1.stats.is_fft:
tr1.ifft()
if tr2.stats.is_fft:
tr2.ifft()
t1_ = tr1.stats.starttime
while t1_ + period <= tr1.stats.endtime + 1:
t2_ = t1_ + period
tr1_ = tr1.slice(t1_, t2_)
tr2_ = tr2.slice(t1_, t2_)
args = (tr1_, tr2_, shift_sec, correlation)
if pool:
if len(xcorr) >= max_preload:
xcorr[-max_preload].wait()
xcorr.append(pool.apply_async(_noisexcorr_traces, args))
else:
xcorr.append(_noisexcorr_traces(*args))
t1_ = t1_ + period - overlap
if len(xcorr) > 0:
data.writeX(_get_async_resutls(xcorr) if pool else xcorr,
correlation, t, period=period)
def prepare(data, stations, t1, t2, component='all', use_floating_stream=True,
use_client=True, #arclink_client_for_LVC=None,
pool=None, max_preload=5, **kwargs):
"""
Prepare data for cross correlation.
Day files of raw data are loaded (from files data.raw), and the prepared
data is again written to day files (to files data.raw).
@param data: sito.data object with attributes (raw, x_prep) set
@param stations: tuple of stations
@param t1: UTC object with date of first day
@param t2: UTC object with date of last day
@param filter_: tuple of min and max frequencies (or None) for filtering
@param downsample: downsample to this sampling rate (or None)
@param component: string out of ('Z', 'N', 'E', 'all')
@param normalize: method for normalizing the data in time domain (or None)
see xcorr.timeNorm
@param param_norm: parameter passed to xcorr.timeNorm()
@param whitening: bool, apply spectral whitening, default: False
@type use_floating_stream: bool
@param use_floating_stream: You should set this to True, if you have day
files which do not start/end exactly at midnight
default: False
@param reserve: parameter passed to FloatingStream()
should be the time between the end/beginning of your data and
midnight
Her is the documentation string of xcorr.timeNorm
"""
# filter=(None, None), downsample=None, #@ReservedAssignment
# eventremoval=None, param_removal=None,
# normalize=None, param_norm=None,
# whitening=None, filter_before_whitening=True, use_this_filter_after_whitening=None,
# freq_domain=False, discard=0.5):
# kwargs = dict(filter=filter, downsample=downsample, #@ReservedAssignment
# eventremoval=eventremoval, param_removal=param_removal,
# normalize=normalize, param_norm=param_norm,
# whitening=whitening, filter_before_whitening=filter_before_whitening,
# use_this_filter_after_whitening=use_this_filter_after_whitening,
# freq_domain=freq_domain, discard=discard)
log.info('Prepare data for noise correlation: %s' % util.parameters())
print 'Prepare data for noise correlation...'
if pool:
async_results = []
if use_client:
if 'trim' not in kwargs:
kwargs['trim'] = 'day'
for station in ProgressBar()(stations):
for t_day in daygen(t1, t2):
#for (station, t_day) in ProgressBar()(itertools.product(stations, daygen(t1, t2))):
try:
stream = data.getRawStreamFromClient(t_day - 60, t_day + 24 * 3600 + 60, station, component=component)
except Exception as ex:
log.info('Error loading station %s day %s: %s' % (str(station), t_day.date, ex))
continue
# if station != 'LVC' or not arclink_client_for_LVC:
# continue
# try:
# stream = arclink_client_for_LVC.getWaveform('GE', 'LVC', '10', 'BH' + component,
# t_day - 60, t_day + 24 * 3600 + 60)
# except:
# continue
# else:
# log.info('Found data on GEOFON.')
if len(stream) == 0:
log.info('Stream length 0 station %s day %s' % (str(station), t_day.date))
continue
## one day
def _callback(msg):
if msg:
log.info(msg % ((stream[0].stats.npts / stream[0].stats.sampling_rate / 24 / 3600),
str(station), t_day.date))
args = (stream, data.getDay(station, t_day, data.x_prep))
if pool:
if len(async_results) >= max_preload:
async_results[-max_preload].wait()
async_results.append(
pool.apply_async(_prepare_stream, args, kwargs, callback=_callback))
else:
_callback(_prepare_stream(*args, **kwargs))
else:
if not use_floating_stream:
data2 = data
for station in stations:
if use_floating_stream:
data2 = FloatingStream(data, t1, station, 0, component=component, use_get_raw=True)
for t_day in daygen(t1, t2):
try:
stream = data2.getRawStream(t_day, station, component=component)
except ValueError:
log.info('Error loading station %s day %s' % (str(station), t_day.date))
continue
if len(stream) == 0:
log.info('Stream length 0 station %s day %s' % (str(station), t_day.date))
continue
## one day
def _callback(msg):
if msg:
log.info(msg % ((stream[0].stats.npts / stream[0].stats.sampling_rate / 24 / 3600),
str(station), t_day.date))
args = (stream, data.getDay(station, t_day, data.x_prep))
if pool:
if len(async_results) >= max_preload:
async_results[-max_preload].wait()
async_results.append(
pool.apply_async(_prepare_stream, args, kwargs, callback=_callback))
else:
_callback(_prepare_stream(*args, **kwargs))
if pool:
for res in async_results:
res.wait()