def readX(self,
correlation,
t1=None,
t2=None,
period=24 * 3600,
select=True,
stack=None,
**kwargs):
st = Stream()
if t2 is None:
file_ = self.getX(
correlation, t1, period=period, stack=stack, **kwargs) + '.QHD'
if t1 is None:
st += read(file_)
else:
for file_ in glob(file_):
st += read(file_)
else:
if period == 'day' or period >= 3600 or stack >= 3600:
iterator = yeargen(t1, t2)
else:
iterator = timegen(t1, t2, dt=24 * 3600)
for t in iterator:
file_ = self.getX(
correlation, t, period=period, stack=stack, **
kwargs) + '.QHD'
try:
st += read(file_)
except (ValueError, IOError):
log.warning(
'An error occured when trying to read file %s' % file_)
if select:
st = st.select(expr='%r<st.starttime<%r' %
(t1 - 0.1, t2 + 0.1))
return st
def setUp(self):
# set specific seed value such that random numbers are reproducible
seed(42)
self.Z = random(412) - 0.5
self.N = random(412) - 0.5
self.E = random(412) - 0.5
self.stream = read(os.path.join(os.path.dirname(__file__), 'data', 'PKD_1997_246.mseed'))
def test():
import pylab as plt
from sito.stream import read
from sito.util import cosTaper, get_window
plt.plot(cosTaper(1000, 0.1))
plt.plot(get_window(('gaussian', 100), 1000))
N = 10000
data = np.concatenate((get_window(
('gaussian', 10), N // 4), -2 * get_window(
('gaussian', 10), N // 4), get_window(('gaussian', 100),
N // 4), np.zeros(N // 4)))
src = np.concatenate((get_window(('gaussian', 10),
N // 10), np.zeros(N * 9 // 10)))
#deconvfAnalyse(data, src, 100, water=0.1, gauss=10, tshift=10., pad=0) # try gauss=2, 10, 100
dummy = deconvf(data, src, 100, water=0.01, gauss=2, tshift=10., pad=0)
ms = read('./tests/data_temp/STREAM.QHD')[0:3]
deconvfAnalyse(ms[1].data,
ms[0].data,
100,
water=0.01,
gauss=2,
tshift=10.,
pad=0) # try gauss=2, 10, 100
plt.show()
def main():
ipoc = IPOCStations()
ms = read('/home/richter/Results/IPOC/xcorr/1bit/stack/all_stack_-1.QHD')
setHIDist(ms, ipoc)
# for tr in ms:
# st = tr.stats.station
# if 'PB12' in st or 'PAT' in st or 'HMBC' in st or 'LVC' in st:
# ms.remove(tr)
print (list(set(ms[0].stats.station.split('-'))))[0]
ms = ms.select("(st.station.split('-'))[0][:-1] in 'PB03 PB04 PB07 PB09 PB10 PB14 PATCX'.split()")
ms = ms.select(autocorr=True)
# ms.plot_(-200, 200, relative='middle', absolutescale=10, annotate=True)
# ms.plotXcorrVsDist(-300, 300, absolutescale=200)
# ms.plotXcorrVsDist(-300, relative='starttime', absolutescale=500)
# plt.show()
# ms.filter2(0.05, 0.5)
#ms = ms.select('st.dist<455')
ms.addXcorrSides()
# for tr in ms:
# tr.data = envelope(tr.data)
# ms.normalize()
ms.downsample2(5)
# ms.trim2(100 + np.array(ms.getHI('dist')) / 3., None)
# ms.plotXcorrVsDist(0, 300, relative='starttime')
# ms.plot_(absolutescale=1)
# ms = ms[:1]
# ms = ms[:1]
# ms.plot_()
# plt.show()
# return
print ms
lats = np.linspace(-25, -17, 1500)
lons = np.linspace(-74, -66, 1500)
def setUp(self):
self.path = os.path.dirname(__file__)
file_ = os.path.join(self.path, 'data_temp', 'STREAM.QHD')
try:
self.stream = read(file_)
except Exception as ex:
raise IOError('First start the test for data: ' + str(ex))
self.stream_short = self.stream.copy()
self.stream.trim2(-50, 200)
def setUp(self):
self.path = os.path.dirname(__file__)
file_ = os.path.join(self.path, 'data_temp', 'STREAM.QHD')
try:
self.stream = read(file_)
except Exception as ex:
raise IOError('First start the test for data: ' + str(ex))
self.stream_short = self.stream.copy()
self.stream.trim2(-50, 200)
def test_trace(self):
file_ = os.path.join(self.path, 'data_temp', 'STREAM.QHD')
try:
mt = read(file_)[0]
except IOError:
raise IOError('First start the test for data.')
dummy = 'repr(mt) = ' + str(repr(mt)) + '\nstr(mt) = ' + str(mt)
dummy += '\nmt.stats = ' + str(mt.stats) + '\nmt.data = ' + str(mt.data)
dummy += '\nmt.print_(mod=0) = ' + mt.print_(mod=0)
dummy += '\nmt.print_(mod=1) = ' + mt.print_(mod=1)
def test_trace(self):
file_ = os.path.join(self.path, 'data_temp', 'STREAM.QHD')
try:
mt = read(file_)[0]
except IOError:
raise IOError('First start the test for data.')
dummy = 'repr(mt) = ' + str(repr(mt)) + '\nstr(mt) = ' + str(mt)
dummy += '\nmt.stats = ' + str(mt.stats) + '\nmt.data = ' + str(
mt.data)
dummy += '\nmt.print_(mod=0) = ' + mt.print_(mod=0)
dummy += '\nmt.print_(mod=1) = ' + mt.print_(mod=1)
def readX(self, correlation, t1=None, t2=None, period=24 * 3600, select=True, stack=None, **kwargs):
st = Stream()
if t2 is None:
file_ = self.getX(correlation, t1, period=period, stack=stack, **kwargs) + ".QHD"
if t1 is None:
st += read(file_)
else:
for file_ in glob(file_):
st += read(file_)
else:
if period == "day" or period >= 3600 or stack >= 3600:
iterator = yeargen(t1, t2)
else:
iterator = timegen(t1, t2, dt=24 * 3600)
for t in iterator:
file_ = self.getX(correlation, t, period=period, stack=stack, **kwargs) + ".QHD"
try:
st += read(file_)
except (ValueError, IOError):
log.warning("An error occured when trying to read file %s" % file_)
if select:
st = st.select(expr="%r<st.starttime<%r" % (t1 - 0.1, t2 + 0.1))
return st
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 test():
import pylab as plt
from sito.stream import read
from sito.util import cosTaper, get_window
plt.plot(cosTaper(1000, 0.1))
plt.plot(get_window(('gaussian', 100), 1000))
N = 10000
data = np.concatenate((get_window(('gaussian', 10), N // 4), -2 * get_window(('gaussian', 10), N // 4), get_window(('gaussian', 100), N // 4), np.zeros(N // 4)))
src = np.concatenate((get_window(('gaussian', 10), N // 10), np.zeros(N * 9 // 10)))
#deconvfAnalyse(data, src, 100, water=0.1, gauss=10, tshift=10., pad=0) # try gauss=2, 10, 100
dummy = deconvf(data, src, 100, water=0.01, gauss=2, tshift=10., pad=0)
ms = read('./tests/data_temp/STREAM.QHD')[0:3]
deconvfAnalyse(ms[1].data, ms[0].data, 100, water=0.01, gauss=2, tshift=10., pad=0) # try gauss=2, 10, 100
plt.show()
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 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 main():
ipoc = IPOCStations()
ms = read('/home/richter/Results/IPOC/xcorr/1bit/stack/all_stack_-1.QHD')
setHIDist(ms, ipoc)
# for tr in ms:
# st = tr.stats.station
# if 'PB12' in st or 'PAT' in st or 'HMBC' in st or 'LVC' in st:
# ms.remove(tr)
print(list(set(ms[0].stats.station.split('-'))))[0]
ms = ms.select(
"(st.station.split('-'))[0][:-1] in 'PB03 PB04 PB07 PB09 PB10 PB14 PATCX'.split()"
)
ms = ms.select(autocorr=True)
# ms.plot_(-200, 200, relative='middle', absolutescale=10, annotate=True)
# ms.plotXcorrVsDist(-300, 300, absolutescale=200)
# ms.plotXcorrVsDist(-300, relative='starttime', absolutescale=500)
# plt.show()
# ms.filter2(0.05, 0.5)
#ms = ms.select('st.dist<455')
ms.addXcorrSides()
# for tr in ms:
# tr.data = envelope(tr.data)
# ms.normalize()
ms.downsample2(5)
# ms.trim2(100 + np.array(ms.getHI('dist')) / 3., None)
# ms.plotXcorrVsDist(0, 300, relative='starttime')
# ms.plot_(absolutescale=1)
# ms = ms[:1]
# ms = ms[:1]
# ms.plot_()
# plt.show()
# return
print ms
lats = np.linspace(-25, -17, 1500)
lons = np.linspace(-74, -66, 1500)
def getRawStream(self,
date,
station,
component='Z',
endtime=False,
checkfile=False):
if component == 'all':
component = 'ZNE'
NC = len(component)
if NC > 1:
stream = Stream()
if checkfile:
stream = []
for comp in component:
stream.extend(self.getRawStream(date, station, comp, endtime))
if checkfile:
import numpy as np
return np.all(stream)
#if None in stream:
# raise ValueError('One or more component is None')
Ns = [stream[i].stats.npts for i in range(NC)]
#N1, N2, N3 = len(st_list[0]), len(st_list[1]), len(st_list[2])
#Ns = (N1, N2, N3)
if max(Ns) - min(Ns) > 1:
raise ValueError('Components have different length')
elif max(Ns) - min(Ns) == 1:
for i in range(NC):
if Ns[i] > min(Ns):
stream[i].data = stream[i].data[:-1]
stream[i].stats.ntps -= 1
#return st_list[0] + st_list[1] + st_list[2]
return stream
if station == 'LVC':
log.warning('Using BH channel for LVC')
file_ = self.lookForMseed(date, station, 'BH' + component)
else:
file_ = self.lookForMseed(date, station, 'HH' + component)
if file_ == None:
raise ValueError('No IPOC file for %s %s %s' %
(station, component, date.date))
elif checkfile:
return True
merge_later = False
try:
if endtime and date.julday == endtime.julday:
ms = read(file_,
format='MSEED',
starttime=date,
endtime=endtime)
elif endtime and date.julday != endtime.julday:
border = date.__class__(date.date) + 24 * 3600
ms1 = read(file_, starttime=date) #, endtime=border)
ms2 = self.getRawStream(border, station, component, endtime)
ms = ms1 + ms2
ms.merge()
merge_later = True
else:
ms = read(file_)
except (ValueError, TypeError) as ex:
raise ValueError('Error reading IPOC file %s because:\n%s' %
(file_, str(ex)))
if len(ms) == 0:
raise ValueError('No traces in IPOC stream!')
if station == 'LVC':
for tr in ms:
if tr.stats.channel[-1] == '1':
tr.stats.channel = tr.stats.channel[:-1] + 'N'
elif tr.stats.channel[-1] == '2':
tr.stats.channel = tr.stats.channel[:-1] + 'E'
if any([network == 'NC' for network in ms.getHI('network')]):
# change network code to CX
ms.setHI('network', 'CX')
if merge_later:
ms.merge()
return ms
def getRawStream(self, date, station, component="Z", endtime=False, checkfile=False):
if component == "all":
component = "ZNE"
NC = len(component)
if NC > 1:
stream = Stream()
if checkfile:
stream = []
for comp in component:
stream.extend(self.getRawStream(date, station, comp, endtime))
if checkfile:
import numpy as np
return np.all(stream)
# if None in stream:
# raise ValueError('One or more component is None')
Ns = [stream[i].stats.npts for i in range(NC)]
# N1, N2, N3 = len(st_list[0]), len(st_list[1]), len(st_list[2])
# Ns = (N1, N2, N3)
if max(Ns) - min(Ns) > 1:
raise ValueError("Components have different length")
elif max(Ns) - min(Ns) == 1:
for i in range(NC):
if Ns[i] > min(Ns):
stream[i].data = stream[i].data[:-1]
stream[i].stats.ntps -= 1
# return st_list[0] + st_list[1] + st_list[2]
return stream
if station == "LVC":
log.warning("Using BH channel for LVC")
file_ = self.lookForMseed(date, station, "BH" + component)
else:
file_ = self.lookForMseed(date, station, "HH" + component)
if file_ == None:
raise ValueError("No IPOC file for %s %s %s" % (station, component, date.date))
elif checkfile:
return True
merge_later = False
try:
if endtime and date.julday == endtime.julday:
ms = read(file_, format="MSEED", starttime=date, endtime=endtime)
elif endtime and date.julday != endtime.julday:
border = date.__class__(date.date) + 24 * 3600
ms1 = read(file_, starttime=date) # , endtime=border)
ms2 = self.getRawStream(border, station, component, endtime)
ms = ms1 + ms2
ms.merge()
merge_later = True
else:
ms = read(file_)
except (ValueError, TypeError) as ex:
raise ValueError("Error reading IPOC file %s because:\n%s" % (file_, str(ex)))
if len(ms) == 0:
raise ValueError("No traces in IPOC stream!")
if station == "LVC":
for tr in ms:
if tr.stats.channel[-1] == "1":
tr.stats.channel = tr.stats.channel[:-1] + "N"
elif tr.stats.channel[-1] == "2":
tr.stats.channel = tr.stats.channel[:-1] + "E"
if any([network == "NC" for network in ms.getHI("network")]):
# change network code to CX
ms.setHI("network", "CX")
if merge_later:
ms.merge()
return ms
def get_vel(stream):
ms = stream.copy()
ms.addXcorrSides()
for tr in ms:
tr.data = np.abs(envelope(tr.data))
dists = ms.getHI('dist')
maxi = ms.getMaxima()
v, _ = curve_fit(lambda x, a: x * a, maxi, dists, p0=1)
return v[0]
#ms = read('/home/richter/Results/IPOC/xcorr/FINAL_filter0.01-0.5_1bit_whitening/stack/day_PB0[12345]Z-PB0[12345]Z_stack_all.QHD')
path = '/home/richter/Results/IPOC/xcorr/FINAL_filter0.01-0.5_1bit_whitening'
ms = read(path + '/stack/day_*_stack_all.QHD')
output = path + '/xcorr_vs_dist.pdf'
ipoc = IPOCStations()
setHIDist(ms, ipoc)
print 'no correlation for pairs:', no_corr_pairs(ms, ipoc)
v = get_vel(ms)
#v = 3.03093386
print 'velocity:', v
fig = plt.figure(figsize=(10, 12))
plot = ms.plotXcorrVsDist(-300,
300,
scale=10,
fig=fig,
figtitle='%d cross-correlations' % len(ms))
def getStream(self,
date,
station,
component='Z',
endtime=False,
filename=None,
check=False):
"""
Return a stream from local day files.
:param date: if endtime==False: The whole day is returned
if endtime!=False: starttime for stream
:param component: 'Z', 'N', 'E' or 'all'
:param endtime: read from filename only till endtime (if != False)
:param filename: use this expression as filename (None= use self.raw)
:return: one-component or 3-component stream
"""
if filename == None:
filename = self.getstr + '.QHD'
filename = filename % (station, date.year, date.julday)
if check:
return os.path.isfile(filename)
if not os.path.isfile(filename):
raise ValueError('No filename for %s %s %s at %s' %
(station, component, date.date, filename))
try:
if endtime and date.julday == (endtime - 0.001).julday:
ms = read(filename, starttime=date, endtime=endtime)
elif endtime and date.julday != endtime.julday:
border = date.__class__(date.date) + 24 * 3600
ms1 = read(filename, starttime=date) #, endtime=border)
ms2 = self.getStream(border, station, component, endtime)
ms = ms1 + ms2
ms.merge()
else:
ms = read(filename)
except:
raise ValueError('Error reading filename %s' % filename)
#if component == 'all':
# component = 'ZNE'
NC = len(component)
if NC == 1:
ms = ms.select(component=component)
ms.merge()
if len(ms) > 1:
raise ValueError('Gaps in data')
else:
if NC == 2:
ms = (ms.select(component=component[0]) +
ms.select(component=component[1]))
if len(ms) > NC:
raise ValueError('Gaps in data')
elif len(ms) < NC:
raise ValueError('Not enough components')
Ns = [ms[i].stats.npts for i in range(NC)]
#N1, N2, N3 = len(ms[0]), len(ms[1]), len(ms[2])
#Ns = (N1, N2, N3)
if max(Ns) - min(Ns) > 1:
raise ValueError('Components have different length')
elif max(Ns) - min(Ns) == 1:
for i in range(NC):
if Ns[i] > min(Ns):
ms[i].data = ms[i].data[:-1]
ms[i].stats.ntps -= 1
if len(ms) == 0:
raise ValueError('No traces in stream!')
return ms
return s2 - s1
def get_vel(stream):
ms = stream.copy()
ms.addXcorrSides()
for tr in ms:
tr.data = np.abs(envelope(tr.data))
dists = ms.getHI('dist')
maxi = ms.getMaxima()
v, _ = curve_fit(lambda x, a: x * a, maxi, dists, p0=1)
return v[0]
#ms = read('/home/richter/Results/IPOC/xcorr/FINAL_filter0.01-0.5_1bit_whitening/stack/day_PB0[12345]Z-PB0[12345]Z_stack_all.QHD')
path = '/home/richter/Results/IPOC/xcorr/FINAL_filter0.01-0.5_1bit_whitening'
ms = read(path + '/stack/day_*_stack_all.QHD')
output = path + '/xcorr_vs_dist.pdf'
ipoc = IPOCStations()
setHIDist(ms, ipoc)
print 'no correlation for pairs:', no_corr_pairs(ms, ipoc)
v = get_vel(ms)
#v = 3.03093386
print 'velocity:', v
fig = plt.figure(figsize=(10, 12))
plot = ms.plotXcorrVsDist(-300, 300, scale=10, fig=fig,
figtitle='%d cross-correlations' % len(ms))
plot.ax.plot((-300, 0, 300), (300 * v, 0, 300 * v), 'r')
d = 30
def getStream(self, date, station, component="Z", endtime=False, filename=None, check=False):
"""
Return a stream from local day files.
:param date: if endtime==False: The whole day is returned
if endtime!=False: starttime for stream
:param component: 'Z', 'N', 'E' or 'all'
:param endtime: read from filename only till endtime (if != False)
:param filename: use this expression as filename (None= use self.raw)
:return: one-component or 3-component stream
"""
if filename == None:
filename = self.getstr + ".QHD"
filename = filename % (station, date.year, date.julday)
if check:
return os.path.isfile(filename)
if not os.path.isfile(filename):
raise ValueError("No filename for %s %s %s at %s" % (station, component, date.date, filename))
try:
if endtime and date.julday == (endtime - 0.001).julday:
ms = read(filename, starttime=date, endtime=endtime)
elif endtime and date.julday != endtime.julday:
border = date.__class__(date.date) + 24 * 3600
ms1 = read(filename, starttime=date) # , endtime=border)
ms2 = self.getStream(border, station, component, endtime)
ms = ms1 + ms2
ms.merge()
else:
ms = read(filename)
except:
raise ValueError("Error reading filename %s" % filename)
# if component == 'all':
# component = 'ZNE'
NC = len(component)
if NC == 1:
ms = ms.select(component=component)
ms.merge()
if len(ms) > 1:
raise ValueError("Gaps in data")
else:
if NC == 2:
ms = ms.select(component=component[0]) + ms.select(component=component[1])
if len(ms) > NC:
raise ValueError("Gaps in data")
elif len(ms) < NC:
raise ValueError("Not enough components")
Ns = [ms[i].stats.npts for i in range(NC)]
# N1, N2, N3 = len(ms[0]), len(ms[1]), len(ms[2])
# Ns = (N1, N2, N3)
if max(Ns) - min(Ns) > 1:
raise ValueError("Components have different length")
elif max(Ns) - min(Ns) == 1:
for i in range(NC):
if Ns[i] > min(Ns):
ms[i].data = ms[i].data[:-1]
ms[i].stats.ntps -= 1
if len(ms) == 0:
raise ValueError("No traces in stream!")
return ms
