def main():
"""
define main function
:return:
"""
rffile = '/g/data/ha3/am7399/shared/OA-ZRT-R-cleaned.h5'
output_folder = '/g/data/ha3/am7399/shared/OA_piercing'
s = read_rf(rffile, 'H5')
g = Geometry(start_lat_lon=(-17.4, 132.9),
azimuth=80,
lengthkm=1000,
nx=100,
widthkm=450,
ny=45,
depthkm=75,
nz=375,
debug=False)
#g = Geometry(start_lat_lon=(-18.35, 138.45), azimuth=90,
# lengthkm=450, nx=45, widthkm=350, ny=35, depthkm=100, nz=500, debug=False)
m = Migrate(geometry=g, stream=s, debug=False, output_folder=output_folder)
m.execute()
return
def test_slice2(self):
stream = read_rf()
endtimes = [tr.stats.endtime for tr in stream]
stream = stream.slice2(-50, -20, 'endtime')
for t0, tr in zip(endtimes, stream):
self.assertEqual(tr.stats.starttime - t0, -50)
self.assertEqual(tr.stats.endtime - t0, -20)
def test_trim2(self):
stream = read_rf()
starttimes = [tr.stats.starttime for tr in stream]
stream.trim2(50, 100, 'starttime')
for t0, tr in zip(starttimes, stream):
self.assertEqual(tr.stats.starttime - t0, 50)
self.assertEqual(tr.stats.endtime - t0, 100)
def test_io_header(testcase, stream, ignore=()):
for format in FORMATS:
stream1 = stream.copy()
suffix = '.' + format.upper()
if format == 'sh':
format = 'q'
suffix = '.QHD'
elif format == 'h5':
for tr in stream1:
tr.stats.pop('sac', None)
with NamedTemporaryFile(suffix=suffix) as ft:
fname = ft.name
stream1.write(fname, format.upper())
stream2 = read_rf(fname)
st1 = stream1[0].stats
st2 = stream2[0].stats
for head in _HEADERS:
if head in st1 and head not in ignore:
testcase.assertIn(head, st2)
msg = ("AssertionError for header '%s' with format '%s': "
"%s and %s not equal within 2 places")
testcase.assertAlmostEqual(
st1[head],
st2[head],
2,
msg=msg % (head, format, st1[head], st2[head]))
if len(ignore) == 0 or format != 'q':
testcase.assertEqual(stream1[0].id, stream2[0].id)
def read_h5_rf(src_file, network=None, station=None, loc='', root='/waveforms'):
"""Helper function to load data from hdf5 file generated by rf library or script `rf_quality_filter.py`.
For faster loading time, a particular network and station may be specified.
:param src_file: File from which to load data
:type src_file: str or Path
:param network: Specific network to load, defaults to None
:type network: str, optional
:param station: Specific station to load, defaults to None
:type station: str, optional
:param root: Root path in hdf5 file where to start looking for data, defaults to '/waveforms'
:type root: str, optional
:return: All the loaded data in a rf.RFStream container.
:rtype: rf.RFStream
"""
logger = logging.getLogger(__name__)
if (network is None and station is not None) or (network is not None and station is None):
logger.warning("network and station should both be specified - IGNORING incomplete specification")
group = root
elif network and station:
group = root + '/{}.{}.{}'.format(network.upper(), station.upper(), loc.upper())
else:
group = root
# end if
rf_data = rf.read_rf(src_file, format='h5', group=group)
return rf_data
def test_slice2(self):
stream = read_rf()
endtimes = [tr.stats.endtime for tr in stream]
stream = stream.slice2(-50, -20, 'endtime')
for t0, tr in zip(endtimes, stream):
self.assertEqual(tr.stats.starttime - t0, -50)
self.assertEqual(tr.stats.endtime - t0, -20)
def test_io_header(testcase, stream, ignore=()):
for format in FORMATS:
stream1 = stream.copy()
suffix = '.' + format.upper()
if format == 'sh':
format = 'q'
suffix = '.QHD'
elif format == 'h5':
for tr in stream1:
tr.stats.pop('sac', None)
with NamedTemporaryFile(suffix=suffix) as ft:
fname = ft.name
stream1.write(fname, format.upper())
stream2 = read_rf(fname)
st1 = stream1[0].stats
st2 = stream2[0].stats
for head in _HEADERS:
if head in st1 and head not in ignore:
testcase.assertIn(head, st2)
msg = ("AssertionError for header '%s' with format '%s': "
"%s and %s not equal within 2 places")
testcase.assertAlmostEqual(
st1[head], st2[head], 2,
msg=msg % (head, format, st1[head], st2[head])
)
if len(ignore) == 0 or format != 'q':
testcase.assertEqual(stream1[0].id, stream2[0].id)
def test_trim2(self):
stream = read_rf()
starttimes = [tr.stats.starttime for tr in stream]
stream.trim2(50, 100, 'starttime')
for t0, tr in zip(starttimes, stream):
self.assertEqual(tr.stats.starttime - t0, 50)
self.assertEqual(tr.stats.endtime - t0, 100)
def main(rf_h5_file, output_folder, start_lat_lon, azimuth, dimensions,
num_cells, debug):
"""Perform 3D migration of RFs to volumetric space, stacking RF amplitudes in each cell.
Example usage:
python rf_3dmigrate.py --start-lat-lon -17.4 132.9 --azimuth 80 --dimensions 1000 450 75 \
--num-cells 100 45 375 /g/data/ha3/am7399/shared/OA-ZRT-R-cleaned.h5 /g/data/ha3/am7399/shared/OA_piercing
The script produces text data files which are converted to visualization using experimental
ipython notebook `sandbox/plot_3dmigrate.ipynb`.
:param rf_h5_file: Source file containing receiver functions
:type rf_h5_file: str or Path
:param output_folder: Folder in which to output results
:type output_folder: str or Path
"""
s = read_rf(rf_h5_file, 'H5')
g = Geometry(start_lat_lon=start_lat_lon,
azimuth=azimuth,
lengthkm=dimensions[0],
nx=num_cells[0],
widthkm=dimensions[1],
ny=num_cells[1],
depthkm=dimensions[2],
nz=num_cells[2],
debug=debug)
m = Migrate(geometry=g, stream=s, debug=False, output_folder=output_folder)
m.execute()
def plot_RF_profile(
profilefileloc,
destination="./",
trimrange=(int(inpRFdict['rf_display_settings']['trim_min']),
int(inpRFdict['rf_display_settings']['trim_max']))):
logger = logging.getLogger(__name__)
logger.info("--> Plotting the RF profile")
# plt.style.use('classic')
for azimuth in [0, 90]:
inpfiles = glob.glob(
profilefileloc +
f"{str(inpRFdict['filenames']['rfprofile_compute_result_prefix'])}{azimuth}_*.h5"
)
if len(inpfiles):
for inpfile in inpfiles:
logger.info(f"----> RF profile {inpfile}")
pstream = read_rf(inpfile)
divparam = inpfile.split("_")[-4:-1]
divsuffix = inpfile.split("_")[-1].split(".")[0]
pstream.trim2(trimrange[0], trimrange[1], 'onset')
for chn in ['L', 'Q']:
outputimage = destination + f"{chn}_{azimuth}_{divsuffix}_profile.png"
if not os.path.exists(outputimage):
plt.figure()
pstream.select(channel='??' +
chn).normalize().plot_profile(
scale=1.5,
top='hist',
fillcolors=('r', 'b'))
plt.gcf().set_size_inches(15, 10)
plt.title(f'Channel: {chn} Azimuth {azimuth}')
plt.savefig(outputimage, dpi=200, bbox_inches='tight')
logger.info(f"------> Output image: {outputimage}")
plt.close('all')
def test_moveout_vs_XY(self):
stream = read_rf()[:1]
stream._write_test_header()
stream.decimate(10)
N = len(stream[0])
t = np.linspace(0, 20 * np.pi, N)
stream[0].data = np.sin(t) * np.exp(-0.04 * t)
stream[0].stats.slowness = 4.0
stream1 = stream.copy()
stream2 = stream.copy()
stream3 = stream.copy()
stream3[0].stats.slowness = 9.0
stream4 = stream3.copy()
stream5 = stream.copy()
stream6 = stream.copy()
stream7 = stream.copy()
stream8 = stream.copy()
stream9 = stream.copy()
stream10 = stream.copy()
stream1.moveout()
stream3.moveout()
stream5.moveout(phase='Ppps')
stream7.moveout(phase='Ppss')
stream9.moveout(phase='Psss')
# stream2._moveout_xy()
# print(repr(stream2[0].data))
# stream4._moveout_xy()
# print(repr(stream6[0].data))
# stream6._moveout_xy(phase='Ppps')
# print(repr(stream6[0].data))
# stream8._moveout_xy(phase='Ppss')
# print(repr(stream8[0].data))
# stream10._moveout_xy(phase='Psss')
# print(repr(stream10[0].data))
stream2[0].data = XY_PSMOUT_REF4
stream4[0].data = XY_PSMOUT_REF9
stream6[0].data = XY_PPPSMOUT_REF4
stream8[0].data = XY_PPSSMOUT_REF4
stream8[0].data = XY_PSSSMOUT_REF4
np.testing.assert_array_almost_equal(stream1[0].data,
stream2[0].data,
decimal=2)
np.testing.assert_array_almost_equal(stream3[0].data,
stream4[0].data,
decimal=2)
np.testing.assert_array_almost_equal(stream5[0].data,
stream6[0].data,
decimal=2)
np.testing.assert_array_almost_equal(stream7[0].data,
stream8[0].data,
decimal=2)
np.testing.assert_array_almost_equal(stream9[0].data,
stream10[0].data,
decimal=2)
def plot_RF(dataRFfileloc, destImg, fig_frmt="png"):
logger = logging.getLogger(__name__)
logger.info("--> Plotting the receiver functions")
rffiles = glob.glob(
dataRFfileloc +
f"*-{str(inpRFdict['filenames']['rf_compute_data_suffix'])}.h5")
for i, rffile in enumerate(rffiles):
stream = read_rf(rffile, 'H5')
outfigname1 = destImg + f"{stream[0].stats.station}" + '_L.' + fig_frmt
outfigname2 = destImg + f"{stream[0].stats.station}" + '_Q.' + fig_frmt
if not os.path.exists(outfigname1) and not os.path.exists(outfigname2):
kw = {
'trim': (int(inpRFdict['rf_display_settings']['trim_min']),
int(inpRFdict['rf_display_settings']['trim_max'])),
'fillcolors': ('black', 'gray'),
'trace_height':
float(inpRFdict['rf_display_settings']['trace_height'])
}
if str(inpRFdict['rf_display_settings']['rf_info']) == "default":
kw['info'] = (('back_azimuth', u'baz (°)', 'C0'),
('distance', u'dist (°)', 'C3'))
else:
kw['info'] = None
num_trace = len(
stream.select(component='L',
station=stream[0].stats.station).sort(
['back_azimuth']))
if num_trace > 0:
try:
stream.select(component='L',
station=stream[0].stats.station).sort(
['back_azimuth']).plot_rf(**kw)
plt.savefig(destImg + f"{stream[0].stats.station}" +
'_L.' + fig_frmt)
plt.close('all')
stream.select(component='Q',
station=stream[0].stats.station).sort(
['back_azimuth']).plot_rf(**kw)
plt.savefig(destImg + f"{stream[0].stats.station}" +
'_Q.' + fig_frmt)
plt.close('all')
logger.info(
"----> Plotting RF {}/{}, {}-{} Traces: {}".format(
i + 1, len(rffiles), stream[0].stats.network,
stream[0].stats.station, num_trace))
except Exception as e:
logger.error("Unexpected error", exc_info=True)
else:
logger.info("----> {} traces for {}-{}".format(
num_trace, stream[0].stats.network,
stream[0].stats.station))
def test_io_format(format):
stream1 = stream.copy()
suffix = '.' + format.upper()
if format == 'sh':
format = 'q'
suffix = '.QHD'
with NamedTemporaryFile(suffix=suffix) as ft:
fname = ft.name
stream1.write(fname, format.upper())
stream2 = read_rf(fname)
st2 = stream2[0].stats
self.assertNotIn('event_time', st2)
def test_polarity_R_component(self):
"""issue #4"""
stream = read_rf()
rfstats(stream)
stream.filter('bandpass', freqmin=0.5, freqmax=2)
stream.trim2(10, 110, reftime='starttime')
stream.rf(rotate='NE->RT')
for tr in stream.select(component='R'):
onset = tr.stats.onset - tr.stats.starttime
dt = tr.stats.delta
self.assertAlmostEqual(tr.data.argmax() * dt - onset, 0,
delta=0.01)
def test_polarity_R_component(self):
"""issue #4"""
stream = read_rf()
rfstats(stream)
stream.filter('bandpass', freqmin=0.5, freqmax=2)
stream.trim2(10, 110, reftime='starttime')
stream.rf(rotate='NE->RT')
for tr in stream.select(component='R'):
onset = tr.stats.onset - tr.stats.starttime
dt = tr.stats.delta
self.assertAlmostEqual(tr.data.argmax() * dt - onset, 0,
delta=0.01)
def main(rf_file,
output_file,
start_latlon,
end_latlon,
width,
spacing,
max_depth,
stacked_scale,
channels,
title=None):
# rf_file is the clean H5 file of ZRT receiver functions, generated by rf_quality_filter.py
channels = channels.split(',')
# Range of stacked amplitude for imshow to get best contrast
vmin, vmax = (-stacked_scale, stacked_scale)
output_file_base, ext = os.path.splitext(output_file)
if ext != ".png":
output_file += ".png"
print("Reading HDF5 file...")
stream = rf.read_rf(rf_file, 'H5')
matrix_norm, sample_density, length, stn_params = \
ccp_generate(stream, start_latlon, end_latlon, width=width, spacing=spacing, max_depth=max_depth,
channels=channels, station_map_file=output_file_base + '_MAP.png')
if matrix_norm is not None:
plot_ccp(matrix_norm,
length,
max_depth,
spacing,
ofile=output_file,
vlims=(vmin, vmax),
metadata=stn_params,
title=title)
if sample_density is not None:
sample_density_file = output_file_base + '_SAMPLE_DENSITY.png'
# Use median of number of events per station to set the scale range.
sc = sorted([
s['event_count'] for s in stn_params.values() if s is not None
])
median_samples = sc[len(sc) // 2]
plot_ccp(sample_density,
length,
max_depth,
spacing,
ofile=sample_density_file,
vlims=(0, median_samples),
metadata=stn_params,
title=title + ' [sample density]' if title else None)
def test_io_format(format):
stream1 = stream.copy()
suffix = '.' + format.upper()
if format == 'sh':
format = 'q'
suffix = '.QHD'
with NamedTemporaryFile(suffix=suffix) as ft:
fname = ft.name
stream1.write(fname, format.upper())
stream2 = read_rf(fname)
st1 = stream1[0].stats
st2 = stream2[0].stats
for head in HEADERS:
self.assertAlmostEqual(st1[head], st2[head], 4, msg=head)
self.assertEqual(stream1[0].id, stream2[0].id)
def test_moveout_vs_XY(self):
stream = read_rf()[:1]
stream._write_test_header()
stream.decimate(10)
N = len(stream[0])
t = np.linspace(0, 20 * np.pi, N)
stream[0].data = np.sin(t) * np.exp(-0.04 * t)
stream[0].stats.slowness = 4.0
stream1 = stream.copy()
stream2 = stream.copy()
stream3 = stream.copy()
stream3[0].stats.slowness = 9.0
stream4 = stream3.copy()
stream5 = stream.copy()
stream6 = stream.copy()
stream7 = stream.copy()
stream8 = stream.copy()
stream9 = stream.copy()
stream10 = stream.copy()
stream1.moveout()
stream3.moveout()
stream5.moveout(phase="Ppps")
stream7.moveout(phase="Ppss")
stream9.moveout(phase="Psss")
# stream2._moveout_xy()
# print(repr(stream2[0].data))
# stream4._moveout_xy()
# print(repr(stream6[0].data))
# stream6._moveout_xy(phase='Ppps')
# print(repr(stream6[0].data))
# stream8._moveout_xy(phase='Ppss')
# print(repr(stream8[0].data))
# stream10._moveout_xy(phase='Psss')
# print(repr(stream10[0].data))
stream2[0].data = XY_PSMOUT_REF4
stream4[0].data = XY_PSMOUT_REF9
stream6[0].data = XY_PPPSMOUT_REF4
stream8[0].data = XY_PPSSMOUT_REF4
stream8[0].data = XY_PSSSMOUT_REF4
np.testing.assert_array_almost_equal(stream1[0].data, stream2[0].data, decimal=2)
np.testing.assert_array_almost_equal(stream3[0].data, stream4[0].data, decimal=2)
np.testing.assert_array_almost_equal(stream5[0].data, stream6[0].data, decimal=2)
np.testing.assert_array_almost_equal(stream7[0].data, stream8[0].data, decimal=2)
np.testing.assert_array_almost_equal(stream9[0].data, stream10[0].data, decimal=2)
def main():
"""
define main function
:return:
"""
#rffile = '/home/rakib/work/pst/rf/notebooks/rf_pt15_to5Hz.h5'
rffile = '/media/data/work/GA/rf/rf_pt15_to5Hz.h5'
s = read_rf(rffile, 'H5')
g = Geometry(start_lat_lon=(-18.75, 138.15), azimuth=80,
lengthkm=450, nx=45, widthkm=350, ny=35, depthkm=100, nz=500, debug=False)
#g = Geometry(start_lat_lon=(-18.35, 138.45), azimuth=90,
# lengthkm=450, nx=45, widthkm=350, ny=35, depthkm=100, nz=500, debug=False)
m = Migrate(geometry=g, stream=s, debug=False)
m.execute()
return
def test_io_header(self):
def test_io_format(format):
stream1 = stream.copy()
suffix = '.' + format.upper()
if format == 'sh':
format = 'q'
suffix = '.QHD'
with NamedTemporaryFile(suffix=suffix) as ft:
fname = ft.name
stream1.write(fname, format.upper())
stream2 = read_rf(fname)
st1 = stream1[0].stats
st2 = stream2[0].stats
for head in HEADERS:
self.assertAlmostEqual(st1[head], st2[head], 4, msg=head)
self.assertEqual(stream1[0].id, stream2[0].id)
stream = read_rf()[:1]
for tr in stream:
tr.stats.location = '11'
stream._write_test_header()
for format in FORMATHEADERS:
test_io_format(format)
def test_deconvolution(self):
ms = rf.read_rf()
ms.decimate(10)
for i in range(len(ms)):
ms[i].stats.channel = ms[i].stats.channel[:2] + 'LQT'[i]
t = np.linspace(0, 30, len(ms[0]))
hann1 = get_window('hann', 10)
hann2 = get_window('hann', 50)
ms[0].data[:] = 0
ms[0].data[40:50] = hann1
ms[0].data[50:60] = -hann1
ms[1].data[:] = 0
ms[1].data[100:150] = hann2
ms[1].data[240:290] = hann2
ms_orig = ms.copy()
data3 = convolve(ms[1].data, ms[0].data, 'full')[50:350]/np.sum(np.abs(ms[0].data))
ms[1].data = data3
ms[2].data = -ms[1].data
for tr in ms:
tr.stats.sampling_rate = 1
tr.stats.onset = tr.stats.starttime + 40
ms.deconvolve(deconvolve_method='time')
def main(rf_file, output_file, start_latlon, end_latlon, width, spacing, max_depth, channels,
background_model, stacked_scale=None, title=None):
# rf_file is the clean H5 file of ZRT receiver functions, generated by rf_quality_filter.py
print("Reading HDF5 file...")
stream = rf.read_rf(rf_file, 'H5')
output_file_base, ext = os.path.splitext(output_file)
if ext != ".png":
output_file += ".png"
# endif
colormap = 'jet'
fig, fig_map, _ = run(stream, start_latlon, end_latlon, width, spacing, max_depth, channels, background_model,
stacked_scale, title, colormap=colormap)
if fig is not None:
fig.savefig(output_file, dpi=300)
plt.close(fig)
# endif
if fig_map is not None:
station_map_file = output_file_base + '_MAP.png'
fig_map.savefig(station_map_file, dpi=300)
plt.close(fig_map)
def test_deconvolution(self):
ms = rf.read_rf()
ms.decimate(10)
for i in range(len(ms)):
ms[i].stats.channel = ms[i].stats.channel[:2] + 'LQT'[i]
t = np.linspace(0, 30, len(ms[0]))
hann1 = get_window('hann', 10)
hann2 = get_window('hann', 50)
ms[0].data[:] = 0
ms[0].data[40:50] = hann1
ms[0].data[50:60] = -hann1
ms[1].data[:] = 0
ms[1].data[100:150] = hann2
ms[1].data[240:290] = hann2
ms_orig = ms.copy()
data3 = convolve(ms[1].data, ms[0].data, 'full')[50:350] / np.sum(
np.abs(ms[0].data))
ms[1].data = data3
ms[2].data = -ms[1].data
for tr in ms:
tr.stats.sampling_rate = 1
tr.stats.onset = tr.stats.starttime + 40
ms.deconvolve(deconvolve_method='time')
#-------------Main---------------------------------
if __name__ == '__main__':
''' This program composes vespagrams to identify RF converted phases and their multiples
please refer to Tian et al. GRL 2005 VOL. 32, L08301, doi:10.1029/2004GL021885 for good examples
input - H5 file with receiver functions
output - PDF files to print
Dependencies - rf and obspy packages beside other standard python packages
The image is composed using triangulation. It gives good results but block median or mean must be implemented at some stage to reduce size of PDF.
'''
stream = rf.read_rf('/g/data/ha3/am7399/shared/OA-ZRT-R-cleaned.h5', 'H5')
rf_type = 'LQT-Q '
filter_type = 'bandpass'
freqmin = 0.03
freqmax = 0.5
#we use a zero-phase-shift band-pass filter using 2 corners. This is done in two runs forward and backward,
# so we end up with 4 corners de facto.
# Lets assume we have LQT orientation
selected_stream=stream.select(component='Q').filter(filter_type, freqmin=freqmin, freqmax=freqmax,
corners=2,zerophase=True).interpolate(10)
# if none lets try ZRT
if len(selected_stream)<=0:
selected_stream=stream.select(component='R').filter(filter_type, freqmin=freqmin, freqmax=freqmax,
# AG
import os.path
# import matplotlib.pyplot as plt
# import numpy as np
from rf import read_rf, RFStream
from rf import IterMultipleComponents
# from rf.imaging import plot_profile_map
# from rf.profile import profile
from tqdm import tqdm
data = read_rf('DATA/7X-event_waveforms_for_rf.h5', 'H5')
# exclude bad stations
inc_set = list(set([tr.stats.inclination for tr in data]))
data_filtered = RFStream([
tr for tr in data if tr.stats.inclination in inc_set
and tr.stats.station not in ['MIJ2', 'MIL2']
])
stream = RFStream()
for stream3c in tqdm(IterMultipleComponents(data, 'onset', 3)):
stream3c.detrend('linear').resample(100)
stream3c.taper(0.01)
stream3c.filter('bandpass', freqmin=0.01, freqmax=15)
if len(stream3c) != 3:
continue
a1 = stream3c[0].stats['asdf']
a2 = stream3c[1].stats['asdf']
a3 = stream3c[2].stats['asdf']
stream3c[0].stats['asdf'] = []
stations = []
for station in stream:
stations.append([
station.stats.station.encode('utf-8'),
station.stats.station_longitude, station.stats.station_latitude
])
return np.unique(np.array(stations), axis=0)
#-------------Main---------------------------------
if __name__ == '__main__':
""" It is an example of how to plot nice maps """
import rf
streams = rf.read_rf('DATA/7X-LQT-Q-cleaned.h5', 'H5')
# Lets see intersection of rays at 50km depth
ppoints = streams.ppoints(50.)
# initialization of map
m = plot_map(ppoints)
# RF package uses lat,lon meanwhile others use lon,lat notion
lon, lat = m(ppoints[:, 1], ppoints[:, 0])
plt.plot(lon, lat, 'bx', markersize=5, markeredgewidth=0.1)
# Now lets plot stations
coordinates = get_stations(streams)
if coordinates.ndim == 1:
import rf
import geopy
from geopy.distance import VincentyDistance, distance
from shapely.geometry import LineString, Point
from rf_tools import *
from latexify import latexify
# IMPORT PASSIVE SEISMIC DATA
#eqdir='/Users/brookkeats/Dropbox/Documents/Oxford_DPhil/Misc_data_files/RF_data/'
eqdir = '/Users/brookkeats/Documents/DPhil/Data/RF_data/'
#eqfile='PI_netw_M5.5+v2_raw_data.h5'
#eqfile='PI_netw_M5.5+v2_instr_corr_data.h5'
eqfile = 'NCMS_ASU_M5.5+instr_corr_data.h5'
eq_st = rf.read_rf(eqdir + eqfile)
# PRE PROCESS DATA
eq_st.filter('bandpass',
freqmin=1. / 20,
freqmax=4.,
corners=2,
zerophase=True)
#eq_st.filter('lowpass', freq=4., corners=2, zerophase=True)
# FILTER EVENTS BY SNR
SNR_llim = 2
snr_eq_st = SNR_st_filter(eq_st, SNR_llim=SNR_llim)
# CALCULATE RECEIVER FUNCTIONS
fmax = 1
def test_read_rf(self):
self.assertIsInstance(read_rf(), RFStream)
# stream3c[1].data=stream3c[0].data*(amax['amax']/np.amax(stream3c[0].data))
amax = {'amax': np.amax(stream3c[2].data)}
stream3c[2].stats['asdf'] = a3
stream3c[2].stats.update(amax)
# stream3c[2].filter('bandpass', freqmin=0.03, freqmax=1.00, corners=2, zerophase=True)
# stream3c[2].data=stream3c[0].data*(amax['amax']/np.amax(stream3c[0].data))
stream3c.trim2(-25, 75, 'onset')
# print np.max(stream3c[0].data),np.max(stream3c[1].data),np.max(stream3c[2].data)
return stream3c
print "Lets start the show..."
#data = read_rf('DATA/7X-event_waveforms_for_rf.h5', 'H5')
data = read_rf('DATA/7X-MA12.h5', 'H5')
print "Data in..."
'''
# we can exclude bad stations
inc_set = list(set([tr.stats.inclination for tr in data]))
data_filtered = RFStream([tr for tr in data if tr.stats.inclination in inc_set and tr.stats.station not in ['MIJ2', 'MIL2']])
'''
stream = RFStream()
rf_streams = Parallel(n_jobs=-1,
verbose=1)(map(delayed(do_rf),
IterMultipleComponents(data, 'onset', 3)))
for i, rf in enumerate(rf_streams):
event_id = {'event_id': 0}
def test_read_rf(self):
self.assertIsInstance(read_rf(), RFStream)
def calc_h_kappa(vp=6.3,
p=0.06,
w1=0.75,
w2=0.25,
outfile="h-kappa-values.txt",
data_dir_loc="../results/dataRF",
outloc="./"):
f = open(outloc + outfile, 'w')
data_files = glob.glob(data_dir_loc + "/*-rf_profile_rfs.h5")
for data in data_files:
network = ntpath.basename(data).split('-')[0]
station = ntpath.basename(data).split('-')[1]
st = read_rf(data)
st = st.select(component="L")
len_trace_list = []
for tr in st:
lentr = tr.stats.npts
len_trace_list.append(lentr)
if len(set(len_trace_list)) > 1:
continue
st = st.stack()
for index, trace in enumerate(st):
errorphase = False
nbphase = 0
[xpeaks, ypeaks] = [], []
trace.filter('bandpass', freqmin=0.005, freqmax=2)
t = trace.stats.starttime
pps = trace.stats.sampling_rate
trace.trim(t + 24, t + 44)
xpeaks, ypeaks = find_peaks(trace, height=0.02, distance=50)
if len(xpeaks) > 2:
if len(xpeaks) < 5:
# print('nb of peaks =',len(xpeaks))
plt.plot(trace)
plt.plot(xpeaks, trace[xpeaks], "x")
plt.plot(np.zeros_like(trace), "--", color="gray")
t0 = xpeaks[0] / pps
t1 = xpeaks[1] / pps
t2 = xpeaks[2] / pps
if len(xpeaks) > 3:
t3 = xpeaks[3] / pps
if t0 < 2.5 and t0 > 0:
t0 = t0
else:
t0 = np.NaN
errorphase = True
if t1 < 7.0 and t1 > 2.6:
t1 = t1
else:
t1 = np.NaN
errorphase = True
if t2 < 14.0 and t2 > 7.5:
t2 = t2
else:
if t3 and t3 < 14.0 and t2 > 7.5:
t2 = t3
else:
t2 = np.NaN
errorphase = True
try:
if w1 + w2 != 1:
raise ValueError(
'Weights are not properly defined')
except ValueError as e:
exit(str(e))
# Measure the difference between theory and data:
if not errorphase:
numpoints = 1000
hs = np.linspace(20, 40, numpoints)
Kappas = np.linspace(1.5, 2.5, numpoints)
H, K = np.meshgrid(hs, Kappas)
depth1 = (t1 - t0) / (np.sqrt((K / vp)**2 - (p)**2) -
np.sqrt((1 / vp)**2 - (p)**2))
depth2 = (t2 - t0) / (np.sqrt((K / vp)**2 - (p)**2) +
np.sqrt((1 / vp)**2 - (p)**2))
deltas = np.absolute((w1 * depth1 + w2 * depth2) - H)
## VISUALIZATION
# fig, ax = plt.subplots(2,2,figsize=(8,6),gridspec_kw={"width_ratios":[1, 0.05]})
fig = plt.figure()
delta_lvs = np.linspace(np.amin(deltas),
np.amax(deltas), 30)
fig, axes = plt.subplots(nrows=2, ncols=1)
cmap = plt.get_cmap('rainbow_r')
CS = axes[0].contourf(H,
K,
deltas,
levels=delta_lvs,
cmap=cmap)
result = np.where(deltas == np.amin(deltas))
axes[0].plot(H[result], K[result], 'ko')
f.write(
f"{network},{station},{trace.stats.station_latitude:.4f},{trace.stats.station_longitude:.4f},{H[result][0]:.2f},{K[result][0]:.2f}\n"
)
# axes[0].clabel(CS, inline=1, fontsize=10, fmt='%2.1f', colors='w')
axes[0].set_title(r'$H$-$\kappa$ grid search')
axes[0].set_xlabel('H')
axes[0].set_ylabel(r'$\kappa$')
times_data = np.arange(0, len(trace.data)) / pps
axes[1].plot(times_data, trace.data)
axes[1].plot(xpeaks / pps, trace[xpeaks], "x")
axes[1].annotate(
'P',
(t0 + 0.2, trace.data[np.where(times_data == t0)]),
textcoords='data',
size=10)
axes[1].annotate(
'PS', (t1, trace.data[np.where(times_data == t1)]),
textcoords='data',
size=10)
axes[1].annotate(
'PpPs',
(t2, trace.data[np.where(times_data == t2)]),
textcoords='data',
size=10)
plt.tight_layout()
fig.subplots_adjust(right=0.82)
cbar_ax = fig.add_axes([0.85, 0.56, 0.03, 0.36])
fig.colorbar(CS, cax=cbar_ax)
plt.savefig(
outloc +
f'H-K_{network}-{station}-h-k_outfile-{index}.png')
# else:
# print('bad peaks')
f.close()
def main(input_h5_file, output_pdf_file):
''' This program composes vespagrams to identify RF converted phases and their multiples
please refer to Tian et al. GRL 2005 VOL. 32, L08301, doi:10.1029/2004GL021885 for good examples
input - H5 file with receiver functions
output - PDF files to print
Dependencies - rf and obspy packages beside other standard python packages
The image is composed using triangulation. It gives good results but block median or mean must
be implemented at some stage to reduce size of PDF.
'''
stream = rf.read_rf(input_h5_file, 'H5')
rf_type = 'LQT-Q '
filter_type = 'bandpass'
freqmin = 0.03
freqmax = 0.5
# we use a zero-phase-shift band-pass filter using 2 corners. This is done in two runs forward and backward,
# so we end up with 4 corners de facto.
# Lets assume we have LQT orientation
selected_stream = stream.select(component='Q').filter(
filter_type,
freqmin=freqmin,
freqmax=freqmax,
corners=2,
zerophase=True).interpolate(10)
# if none lets try ZRT
if not selected_stream:
selected_stream = stream.select(component='R').filter(
filter_type,
freqmin=freqmin,
freqmax=freqmax,
corners=2,
zerophase=True).interpolate(10)
rf_type = 'ZRT-R '
# end if
if not selected_stream:
print("Tried Q and R components but neither found, quitting...")
exit(-1)
# end if
station_list = []
# here we collect station names but maybe ID is more appropriate in case of having the same station names
# in different deployments
for tr in selected_stream:
station_list.append(tr.stats.station)
net = tr.stats.network
# end for
pdf = PdfPages(output_pdf_file)
case_description = rf_type + filter_type + ' ' + str(freqmin) + '-' + str(
freqmax) + ' Hz'
pdf.attach_note(case_description)
d = pdf.infodict()
d['Title'] = rf_type + 'RF vespagrams of ' + net + ' network'
d['Keywords'] = case_description
station_list = np.unique(np.array(station_list))
print("Gathered ", len(station_list), " stations")
# Define layout of the page outer_grid
columns = 3
rows = 2
frame = 0
figure = 1
# ------------------------------------------
# Main loop here over all stations
for i, station in enumerate(station_list):
if frame == 0:
printed = False
fig = plt.figure(figsize=(11.69, 8.27))
outer_grid = gridspec.GridSpec(columns,
rows,
wspace=0.2,
hspace=0.2)
# end if
print("Station ", station, i + 1, " of ", station_list.shape[0])
traces = selected_stream.select(station=station)
print('Contains: ', len(traces), ' events')
# we choose short RF to simplify and speed up the processing
# from -5 to 20 seconds and slowness range from 5 to 9 s/deg
# its enough to see multiples and possible LAB conversion at ~19 sec (~160km)
traces = traces.trim2(-5, 20, 'onset')
moved = []
slow = []
for tr in traces:
tr.normalize()
# This 'if' block is designed to check correct data placement on vespagram to
# trace the logic (debugging purposes)
DEBUG_PLACEMENT = False
if DEBUG_PLACEMENT and (tr.stats.slowness >
6.) and (tr.stats.slowness < 7.):
print('altered')
data = tr.data.copy()
print(data.shape, tr.stats.delta)
# 500 below corresponds to 0 with sampling rate of 100Hz
# TODO: !Change these array indices to be computed, not magic numbers!
data[500:800] = 1.
moved.append(data)
else:
moved.append(tr.data.copy() / np.max(np.abs(tr.data)))
slow.append(tr.stats.slowness)
# end if
# end for
print("Slowness min and max: ", np.min(slow), np.max(slow))
slow.append(np.min(slow) - 0.1)
moved.append(np.zeros(traces[0].data.shape))
slow.append(np.max(slow) + 0.1)
moved.append(np.zeros(traces[0].data.shape))
slow = np.array(slow)
idx = np.argsort(slow)
moved = np.nan_to_num(np.array(moved))
# moved = np.array(moved)
slow = slow[idx]
moved = moved[idx, :]
z = moved.copy()
# Some simple stacking to reduce data size on the image, this block can be safely commented out
idx = []
idx.append(True) # first row with zeroes
slo_cum = 0.
elements = 1
for j in xrange(1, slow.shape[0] - 2):
if np.abs(slow[j + 1] - slow[j]) < 0.1 and slo_cum < 0.2:
slow[j + 1] = (slow[j] + slow[j + 1]) / 2.
moved[j, :] = moved[j, :] * elements
moved[j + 1, :] = np.sum(moved[j:j + 2, :],
axis=0) / (elements + 1)
elements = elements + 1
idx.append(False)
slo_cum = slo_cum + np.abs(slow[j + 1] - slow[j])
else:
idx.append(True)
slo_cum = 0
elements = 1
# end if
# end for
idx.append(True) # before last
idx.append(True) # last row with zeroes
idx = np.array(idx)
print(idx.shape, slow.shape, moved.shape)
slow = slow[idx]
moved = moved[idx, :]
z = moved.copy()
# ------------------------------ end of stacking ------------------------
# print('minmax',np.min(z),np.max(z))
x = np.array(list(range(moved.shape[1]))) * traces[0].stats.delta - 5.
x = np.repeat([x], moved.shape[0], axis=0)
y = np.ones((moved.shape[0], moved.shape[1]))
phase_Ps = []
phase_Pms = []
phase_PpPmS = []
phase_PpSmS = []
phase_slow = []
# basin part
phase_Pbs = []
phase_PpPbs = []
for j in xrange(slow.shape[0]):
y[j, :] = y[j, :] * slow[j]
phase_Ps.append(
simple_model.calculate_delay_times(slow[j], phase='PS'))
phase_Pms.append(
simple_model.calculate_delay_times(slow[j], phase='PmS'))
phase_PpPmS.append(
simple_model.calculate_delay_times(slow[j], phase='PpPmS'))
phase_PpSmS.append(
simple_model.calculate_delay_times(slow[j], phase='PpSmS'))
phase_slow.append(np.ones(phase_Ps[-1].shape[0]) * slow[j])
# basin, we will use reflection at the top layer only
if zb.size > 0:
phase_Pbs.append(
basin_model.calculate_delay_times(slow[j], phase='PS'))
phase_PpPbs.append(
basin_model.calculate_delay_times(slow[j], phase='PpPmS'))
# end if
# end for
xi = np.linspace(-5, 20, 200)
yi = np.linspace(0, 9, 400)
# Gridding the data using triangulation. standard gridding doesn't work well here
triang = tri.Triangulation(x.flatten(), y.flatten())
interpolator = tri.LinearTriInterpolator(triang, z.flatten())
xi, yi = np.meshgrid(xi, yi)
zi = interpolator(xi, yi)
# Define two plots as inner_grid to place them inside one cell of outer_grid
inner_grid = gridspec.GridSpecFromSubplotSpec(
2, 1, subplot_spec=outer_grid[frame], wspace=0.5, hspace=0.)
ax1 = plt.Subplot(fig, inner_grid[0])
ax2 = plt.Subplot(fig, inner_grid[1], sharex=ax1)
lim = np.max(np.abs(zi[zi < 0]) * 0.5)
levels = np.linspace(-lim, lim, 15)
# print("Levels ",-lim,lim)
cmap = plt.cm.jet
cs = ax1.contourf(xi, yi, zi, levels=levels, extend='both', cmap=cmap)
cs.cmap.set_under('k')
cs.cmap.set_over('k')
ax1.set_ylim(5, 9)
ax1.set_xlim(-5, 20)
ax1.plot(phase_Ps, slow,
color='black') # direct conversion, positive amplitude
ax1.plot(phase_PpPmS, slow,
color='crimson') # multiples, positive amplitude
ax1.plot(phase_PpSmS, slow,
color='purple') # multiples, negative amplitude
ax1.annotate('Pms',
xy=(phase_Ps[-1][0], 9.1),
xycoords='data',
ha='center',
va='bottom',
rotation=0.,
annotation_clip=False,
fontsize=7)
ax1.annotate('Ps LAB',
xy=(phase_Ps[-1][-1], 9.1),
xycoords='data',
ha='center',
va='bottom',
rotation=0.,
annotation_clip=False,
fontsize=7)
if phase_Pbs:
ax1.annotate('Pbs',
xy=(phase_Pbs[-1][0], 9.1),
xycoords='data',
ha='center',
va='bottom',
rotation=0.,
annotation_clip=False,
fontsize=7)
ax1.plot(phase_Pbs, slow, color='black')
ax1.plot(phase_PpPbs, slow, color='crimson')
# end if
ax1.spines['bottom'].set_visible(False)
ax1.tick_params(labelbottom='off')
ax1.spines['bottom'].set_visible(False)
ax1.yaxis.tick_right()
ax1.yaxis.set_label_position("right")
xlabels = ax1.get_xticklabels()
ylabels = ax1.get_yticklabels()
for label in xlabels:
label.set_rotation(90)
label.set_fontsize(7)
# end for
for label in ylabels:
label.set_rotation(90)
label.set_fontsize(7)
# end for
ax1.annotate(station,
xy=(-0.08, 0),
ha='left',
va='center',
xycoords='axes fraction',
textcoords='offset points',
rotation=90.)
start, end = ax1.get_ylim()
ax1.yaxis.set_ticks(np.arange(start + 1, end + 1, 1))
cs = ax2.contourf(xi,
-1. * yi,
zi,
levels=levels,
extend='both',
cmap=cmap)
cs.cmap.set_under('k')
cs.cmap.set_over('k')
ax2.spines['top'].set_visible(False)
ax2.set_ylim(-9, -5)
ax2.set_xlim(-5, 20)
ax2.yaxis.tick_right()
ax2.yaxis.set_label_position("right")
ylabels = ax2.get_yticklabels()
ax2.plot(phase_Ps, -slow, color='black')
ax2.plot(phase_PpPmS, -slow, color='crimson')
ax2.plot(phase_PpSmS, -slow, color='purple')
ax2.annotate('+PpPms',
xy=(phase_PpPmS[-1][0], -9.1),
xycoords='data',
ha='center',
va='top',
rotation=0.,
annotation_clip=False,
fontsize=7,
color='crimson')
ax2.annotate('-PpSms',
xy=(phase_PpSmS[-1][0], -9.1),
xycoords='data',
ha='center',
va='top',
rotation=0.,
annotation_clip=False,
fontsize=7,
color='purple')
if phase_PpPbs:
ax2.annotate('+PpPbs',
xy=(phase_PpPbs[-1][0], -9.1),
xycoords='data',
ha='center',
va='top',
rotation=0.,
annotation_clip=False,
fontsize=7,
color='crimson')
ax2.plot(phase_PpPbs, -slow, color='crimson')
ax2.plot(phase_Pbs, -slow, color='black')
# end if
for label in ylabels:
label.set_rotation(90)
label.set_fontsize(7)
# end for
if frame > 3:
xlabels = ax2.get_xticklabels()
for label in xlabels:
label.set_rotation(90)
label.set_fontsize(7)
ax2.set_xlabel('Time (sec.)')
else:
ax2.set_xticklabels([])
# end if
if (frame % 2) != 0:
ax2.annotate('Slowness s/deg',
xy=(1.2, 1),
ha='left',
va='center',
xycoords='axes fraction',
textcoords='offset points',
rotation=90.)
# end if
start, end = ax2.get_ylim()
ax2.yaxis.set_ticks(np.arange(start, end, 1))
traces.moveout()
x = np.array(list(range(
traces[0].data.shape[0]))) * traces[0].stats.delta - 5.
y = traces.stack()
# Some amplitude scaling to have nice plot
y = y[0].data / 1.5 - 5.
ax2.plot(x, y, clip_on=False, linewidth=3, color='white')
ax2.plot(x, y, clip_on=False, linewidth=1)
fig.add_subplot(ax1)
fig.add_subplot(ax2)
frame = frame + 1
print('frame', frame)
if frame >= rows * columns:
cb_ax = fig.add_axes([0.25, 0.98, 0.5, 0.02])
labels = fig.colorbar(cs,
cax=cb_ax,
ticks=[np.min(zi), 0,
np.max(zi)],
orientation='horizontal',
extend='neither',
extendfrac=0.00001,
extendrect=True,
drawedges=False)
# labels.set_ticks([np.min(zi), 0, np.max(zi)])
# labels.set_ticklabels(['-', '0', '+'])
cb_ax.set_xticks([np.min(zi), 0, np.max(zi)])
cb_ax.set_xticklabels(['-', '0', '+'])
# labels.ax.set_yticklabels(['-', '0', '+'])
pdf.savefig()
figure += 1
frame = 0
printed = True
# plt.show()
plt.close()
# end if
# end for
if not printed:
cb_ax = fig.add_axes([0.25, 0.95, 0.5, 0.02])
labels = fig.colorbar(cs,
cax=cb_ax,
ticks=[-1, 0, 1],
orientation='horizontal',
extend='neither',
extendfrac=0.00001,
extendrect=True,
drawedges=False)
labels.ax.set_xticklabels(['-', '0', '+', ''])
pdf.savefig()
plt.close()
# end if
pdf.close()
trig[2] >= best_trig_margin and trig[4] >= best_upper:
mintrigdiff = abs(trace.stats.event_time + mean_parrival -
trace.stats.starttime - trig[0][0])
besttrig = trig[0][0]
best_trig_margin = trig[2]
best_band = trig[3]
best_upper = trig[4]
return (best_band, best_trig_margin, best_upper)
else:
print('Something went wrong ... ')
return None, None, None
in_streamfile = 'data/7X-rf_profile_data-15deg.h5'
out_streamfile = 'data/7X-rf_profile_data-15deg-out.h5'
st = read_rf(in_streamfile, 'H5')
stz = [tr for tr in st if tr.stats.channel.endswith('Z')]
stn = [tr for tr in st if tr.stats.channel.endswith('N')]
ste = [tr for tr in st if tr.stats.channel.endswith('E')]
output_from_z = []
for trz, trn, tre in zip(stz, stn, ste):
band, margin, upper = extract_filter_params(trz)
if band and margin and upper:
for tr in [trz, trn, tre]:
clean_trace(tr,
tr.stats.starttime,
tr.stats.endtime,
freqmin=band[0],
freqmax=band[1])
print('Plot the cleaned trace here')
#simple_model=rf.simple_model.load_model(fname='iasp91')
#-------------Main---------------------------------
if __name__ == '__main__':
''' This program composes vespagrams to identify RF converted phases and their multiples
please refer to Tian et al. GRL 2005 VOL. 32, L08301, doi:10.1029/2004GL021885 for good examples
input - H5 file with receiver functions
output - PDF files to print
Dependencies - rf and obspy packages beside other standard python packages
The image is composed using triangulation. It gives good results but block median or mean must be implemented at some stage to reduce size of PDF.
'''
stream = rf.read_rf('DATA/7X-rf_zrt.h5', 'H5')
rf_type = 'LQT-Q '
filter_type = 'bandpass'
freqmin = 0.03
freqmax = 0.5
#we use a zero-phase-shift band-pass filter using 2 corners. This is done in two runs forward and backward, so we end up with 4 corners de facto.
# Lets assume we have LQT orientation
selected_stream = stream.select(component='Q').filter(
filter_type,
freqmin=freqmin,
freqmax=freqmax,
corners=2,
zerophase=True).interpolate(10)
# if none lets try ZRT
'station_latlon': (-25, 140),
'layerprops': [upper_crust, lower_crust, mantle]
}
raw_file = 'synth_events_2L.h5'
synthesize_dataset('propmatrix', raw_file, 'SY', 'AAA', src_latlon, fs,
time_window, **generator_args)
# Generate receiver function
rf_file = 'synth_rf_2L.h5'
resample_rate = 6.25 # Hz
event_waveforms_to_rf(raw_file,
rf_file,
resample_rate,
taper_limit=0.05,
filter_band=(0.02, 1.0),
trim_start_time=-5.0 - 275 * resample_rate,
trim_end_time=150,
rotation_type='ZRT',
deconv_domain='iter')
# Read in RF and convert to text format
rf_dat_file = os.path.splitext(rf_file)[0] + '.dat'
rf_data = rf.read_rf(rf_file, format='h5')
rf_data.trim2(-5.0, 25.0, reftime='onset', nearest_sample=True)
rf_data = rf_data.select(component='R')[0]
times = rf_data.times() - (rf_data.stats.onset - rf_data.stats.starttime)
with open(rf_dat_file, 'w') as f:
for t, d in zip(times, rf_data.data):
f.write('{:2.2f}, {:.8f}\n'.format(t, d))
# end with
import os
import sys
from obspy import read_inventory, Stream
from rf import read_rf
from eqcorrscan.utils.clustering import cluster
from eqcorrscan.utils.stacking import linstack, PWS_stack
import pandas as pd
stream = read_rf('data/7X-rf_profile_rfs-cleaned.h5', 'H5')
inv = read_inventory('data/7X-inventory.xml')
def convert_ms_to_ascii(msfile_path, outfile_folder):
msf = read(msfile_path)
convert_ms_to_ascii(msf, outfile_folder)
def convert_stream_to_ascii(stream, outfile_folder, group_len):
df = pd.DataFrame(columns=['offset_from_onset', 'value'])
offset = -5.0
for i in range(len(stream[0].data)):
df.loc[i] = [offset, stream[0].data[i]]
offset += stream[0].stats.delta
df.to_csv(outfile_folder + '/' + stream[0].stats.network + '.' +
stream[0].stats.station + '..' + stream[0].stats.channel + '.' +
str(group_len) + '.dat',
sep=' ',
index=False,
header=False)
def compute_rf(dataRFfileloc):
logger = logging.getLogger(__name__)
all_rfdatafile = glob.glob(
dataRFfileloc +
f"*-{str(inpRFdict['filenames']['data_rf_suffix'])}.h5")
for jj, rfdatafile in enumerate(all_rfdatafile):
network = rfdatafile.split("-")[0]
station = rfdatafile.split("-")[1]
rffile = f"{network}-{station}-{str(inpRFdict['filenames']['rf_compute_data_suffix'])}.h5"
datatmp = read_rf(rfdatafile, 'H5')
if not os.path.exists(rffile):
logger.info(
f"--> Computing RF for {rfdatafile}, {jj+1}/{len(all_rfdatafile)}"
)
data = read_rf(rfdatafile, 'H5')
stream = RFStream()
for stream3c in tqdm.tqdm(IterMultipleComponents(data, 'onset',
3)):
if len(stream3c) != 3:
continue
## check if the length of all three traces are equal
lenphase = 100
for tr in stream3c:
lentr = tr.stats.npts
lengt = tr.stats.sampling_rate * lenphase
if lentr != lengt:
if tr.stats.sampling_rate < 20:
logger.warning(
f"Sampling rate too low: {tr.stats.sampling_rate}, required >= 20Hz"
)
stream3c.remove(tr)
continue
elif tr.stats.sampling_rate >= 20:
if tr.stats.sampling_rate % 20 == 0:
factor = int(tr.stats.sampling_rate / 20)
tr.decimate(factor,
strict_length=False,
no_filter=True)
if tr.stats.npts > tr.stats.sampling_rate * lenphase:
t = tr.stats.starttime
tr.trim(
t, t + lenphase -
(1 / tr.stats.sampling_rate))
continue
else:
tr.resample(20.0)
if tr.stats.npts > tr.stats.sampling_rate * lenphase:
t = tr.stats.starttime
tr.trim(
t, t + lenphase -
(1 / tr.stats.sampling_rate))
continue
else:
pass
test_npts = []
for tr in stream3c:
lentr = tr.stats.npts
test_npts.append(lentr)
if len(set(test_npts)) > 1:
continue
stream3c.filter(
'bandpass',
freqmin=float(inpRFdict['rf_filter_settings']['minfreq']),
freqmax=float(inpRFdict['rf_filter_settings']['maxfreq']))
try:
stream3c.rf()
except Exception as e:
logger.warning("Problem applying rf method", exc_info=True)
stream3c.moveout()
stream.extend(stream3c)
stream.write(rffile, 'H5')
else:
# logger.info(f"--> {rffile} already exists!, {jj}/{len(all_rfdatafile)}")
logger.info(
f"--> Verifying RF computation {jj+1}/{len(all_rfdatafile)}")