def iter_event_processed_data(events,
inventory,
pin,
format,
yield_traces=False,
pbar=None):
"""Iterator yielding streams or traces which are read from disc."""
for meta in iter_event_metadata(events, inventory, pbar=pbar):
meta['channel'] = '???'
if 'event_time' not in meta and format != 'H5':
meta['event_time'] = _DummyUTC()
fname = FNAMES[format].format(root=pin, **meta)
kwargs = {}
if format == 'H5':
meta.pop('channel')
kwargs['readonly'] = meta
try:
stream = read_rf(fname, format, **kwargs)
except:
pass
else:
if yield_traces:
for tr in stream:
yield tr
else:
yield stream
def _read(stats, path, root, format):
fname = os.path.join(path, FNAMES[format])
if format == 'H5':
stats.pop('channel')
if isinstance(stats['event_time'], _DummyUTC):
stats.pop('event_time')
fname = fname.format(root=root, **stats)
kwargs = {}
if format == 'H5':
set_index()
kwargs['readonly'] = stats
try:
return read_rf(fname, format, **kwargs)
except:
pass
def _read(stats, path, root, format):
fname = os.path.join(path, FNAMES[format])
if format == 'H5':
stats.pop('channel')
if isinstance(stats['event_time'], _DummyUTC):
stats.pop('event_time')
fname = fname.format(root=root, **stats)
kwargs = {}
if format == 'H5':
set_index()
kwargs['readonly'] = stats
try:
return read_rf(fname, format, **kwargs)
except:
pass
def test_deconvolution_of_stream_Qpeak_position(self):
# S receiver deconvolution
from pkg_resources import resource_filename
fname = resource_filename('rf', 'example/minimal_example_S.tar.gz')
stream = read_rf(fname)[:3]
rfstats(stream, phase='S')
stream.filter('bandpass', freqmin=0.2, freqmax=0.5)
stream.trim2(10, 120, reftime='starttime')
stream.rotate('ZNE->LQT')
# check that maximum in Q component is at 0s (at S onset)
test_deconvolve_Qpeak(self, stream, 'time')
test_deconvolve_Qpeak(self, stream, 'freq')
test_deconvolve_Qpeak(self, stream, 'time', winsrc=(-5, 18, 5))
test_deconvolve_Qpeak(self, stream, 'freq', winsrc=(-5, 18, 5))
test_deconvolve_Qpeak(self, stream, 'time', winsrc=(-20, 40, 5))
test_deconvolve_Qpeak(self, stream, 'freq', winsrc=(-20, 40, 5))
def test_deconvolution_of_stream_Qpeak_position(self):
# S receiver deconvolution
from pkg_resources import resource_filename
fname = resource_filename('rf', 'example/minimal_example_S.tar.gz')
stream = read_rf(fname)[:3]
rfstats(stream, phase='S')
stream.filter('bandpass', freqmin=0.2, freqmax=0.5)
stream.trim2(10, 120, reftime='starttime')
stream.rotate('ZNE->LQT')
# check that maximum in Q component is at 0s (at S onset)
test_deconvolve_Qpeak(self, stream, 'time')
test_deconvolve_Qpeak(self, stream, 'freq')
test_deconvolve_Qpeak(self, stream, 'time', winsrc=(-5, 18, 5))
test_deconvolve_Qpeak(self, stream, 'freq', winsrc=(-5, 18, 5))
test_deconvolve_Qpeak(self, stream, 'time', winsrc=(-20, 40, 5))
test_deconvolve_Qpeak(self, stream, 'freq', winsrc=(-20, 40, 5))
def test_deconvolution_of_stream_Lpeak_position(self):
stream = read_rf()[:3]
rfstats(stream)
stream.filter('bandpass', freqmin=0.4, freqmax=1)
stream.trim2(5, 95, reftime='starttime')
stream.rotate('ZNE->LQT')
# check that maximum in L component is at 0s (at P onset)
test_deconvolve_Lpeak(self, stream, 'time')
test_deconvolve_Lpeak(self, stream, 'freq')
test_deconvolve_Lpeak(self, stream, 'time', winsrc=(-20, 40, 5))
test_deconvolve_Lpeak(self, stream, 'freq', winsrc=(-20, 40, 5))
stream.trim2(5, 70, reftime='starttime')
test_deconvolve_Lpeak(self, stream, 'time')
test_deconvolve_Lpeak(self, stream, 'freq')
test_deconvolve_Lpeak(self, stream, 'time', winsrc=(-20, 40, 5))
test_deconvolve_Lpeak(self, stream, 'freq', winsrc=(-20, 40, 5))
test_deconvolve_Lpeak(self, stream, 'time', winsrc=(-5, 18, 5))
test_deconvolve_Lpeak(self, stream, 'freq', winsrc=(-5, 18, 5))
def minimal_example_Srf():
"""
Return S receiver functions calculated from example data.
"""
cache_key = 'minimal_example_Srf'
if cache_key in __CACHE:
return __CACHE[cache_key].copy()
from rf.rfstream import read_rf, rfstats
fname = resource_filename('rf', 'example/minimal_example_S.tar.gz')
stream = read_rf(fname)
rfstats(stream, phase='S')
stream.filter('bandpass', freqmin=0.2, freqmax=0.5)
stream.trim2(10, 120, reftime='starttime')
stream.rf(method='S', winsrc=(-5, 15, 5))
stream.moveout(phase='Sp')
stream.ppoints(50, pp_phase='P')
__CACHE[cache_key] = stream
return stream.copy()
def minimal_example_rf():
"""
Return receiver functions calculated from the data returned by read_rf().
"""
cache_key = 'minimal_example_rf'
if cache_key in __CACHE:
return __CACHE[cache_key].copy()
from rf.rfstream import read_rf, rfstats
stream = read_rf()
rfstats(stream)
stream.filter('bandpass', freqmin=0.5, freqmax=2)
stream.trim2(10, 110, reftime='starttime')
stream.rf(winsrc=(-5, 25, 5))
stream.moveout()
stream.trim2(-10, 80, reftime='onset')
stream.ppoints(50)
__CACHE[cache_key] = stream
return stream.copy()
def test_deconvolution_of_stream_Lpeak_position(self):
stream = read_rf()[:3]
rfstats(stream)
stream.filter('bandpass', freqmin=0.4, freqmax=1)
stream.trim2(5, 95, reftime='starttime')
stream.rotate('ZNE->LQT')
# check that maximum in L component is at 0s (at P onset)
test_deconvolve_Lpeak(self, stream, 'time')
test_deconvolve_Lpeak(self, stream, 'freq')
test_deconvolve_Lpeak(self, stream, 'time', winsrc=(-20, 40, 5))
test_deconvolve_Lpeak(self, stream, 'freq', winsrc=(-20, 40, 5))
stream.trim2(5, 70, reftime='starttime')
test_deconvolve_Lpeak(self, stream, 'time')
test_deconvolve_Lpeak(self, stream, 'freq')
test_deconvolve_Lpeak(self, stream, 'time', winsrc=(-20, 40, 5))
test_deconvolve_Lpeak(self, stream, 'freq', winsrc=(-20, 40, 5))
test_deconvolve_Lpeak(self, stream, 'time', winsrc=(-5, 18, 5))
test_deconvolve_Lpeak(self, stream, 'freq', winsrc=(-5, 18, 5))
def test_deconvolve_custom_function(self):
def test_func_stream(rsp, src, **kw):
for r_ in rsp:
r_.data[:] = 1
r_.stats.custom = 'X'
src.data
return rsp
stream = read_rf()[:3]
rfstats(stream)
stream1 = stream.copy()
stream1.rf(deconvolve='func', func=test_func_stream)
for tr in stream1:
np.testing.assert_equal(tr.data, 1)
self.assertIn('custom', tr.stats)
stream1 = stream
stream1.deconvolve(method='func', func=test_func_stream)
for tr in stream1:
np.testing.assert_equal(tr.data, 1)
self.assertIn('custom', tr.stats)
def iter_event_processed_data(events, inventory, pin, format,
yield_traces=False, pbar=None):
"""Iterator yielding streams or traces which are read from disc."""
for meta in iter_event_metadata(events, inventory, pbar=pbar):
meta['channel'] = '???'
if 'event_time' not in meta and format != 'H5':
meta['event_time'] = _DummyUTC()
fname = FNAMES[format].format(root=pin, **meta)
kwargs = {}
if format == 'H5':
meta.pop('channel')
kwargs['readonly'] = meta
try:
stream = read_rf(fname, format, **kwargs)
except Exception:
pass
else:
if yield_traces:
for tr in stream:
yield tr
else:
yield stream
def run_commands(command,
commands=(),
events=None,
inventory=None,
objects=None,
get_waveforms=None,
data=None,
plugin=None,
phase=None,
moveout_phase=None,
path_in=None,
path_out=None,
format='Q',
newformat=None,
**kw):
"""Load files, apply commands and write result files."""
for opt in kw:
if opt not in DICT_OPTIONS:
raise ParseError('Unknown config option: %s' % opt)
for opt in DICT_OPTIONS:
default = None if opt == 'boxbins' else {}
d = kw.setdefault(opt, default)
if isinstance(d, basestring):
kw[opt] = json.loads(d)
if phase is not None:
kw['options']['phase'] = phase
if moveout_phase is not None:
kw['moveout']['phase'] = moveout_phase
if kw['boxbins'] is not None:
kw['boxes']['bins'] = np.linspace(*kw['boxbins'])
try:
if command == 'calc':
assert len(commands) < 3
if len(commands) == 2:
assert commands[0] != commands[1]
elif command == 'calc':
assert len(commands) < 2
except:
raise ParseError('calc or moveout command given more than once')
# Read events and inventory
try:
if command in ('stack', 'plot'):
events = None
elif command != 'print' or objects[0] == 'events':
if (not isinstance(events, obspy.Catalog)
or not isinstance(events, list) or
(len(events) == 2 and isinstance(events[0], basestring))):
if isinstance(events, basestring):
format_ = None
else:
events, format_ = events
events = obspy.read_events(events, format_)
if command != 'print' or objects[0] == 'stations':
if not isinstance(inventory, obspy.Inventory):
if isinstance(inventory, basestring):
format_ = None
else:
inventory, format_ = inventory
inventory = obspy.read_inventory(inventory, format_)
except (KeyboardInterrupt, SystemExit):
raise
except:
print('cannot read events or stations')
return
# Initialize get_waveforms
if command == 'data':
try:
# Initialize get_waveforms
if get_waveforms is None:
get_waveforms = init_data(data,
client_options=kw['client_options'],
plugin=plugin)
except (KeyboardInterrupt, SystemExit):
raise
except:
print('cannot initalize data')
return
# Print command
if command == 'print':
if objects[0] == 'events':
print(events.__str__(True))
elif objects[0] == 'stations':
print(inventory)
else:
from rf.rfstream import RFStream
stream = sum((read_rf(fname) for fname in objects), RFStream())
print(stream.__str__(True))
return
# Select appropriate iterator
if command == 'data':
iter_ = iter_event_data(events,
inventory,
get_waveforms,
pbar=tqdm(),
**kw['options'])
elif command == 'plot-profile':
iter_ = _iter_profile(path_in, format)
else:
yt = command == 'profile'
iter_ = iter_event_processed_data(events,
inventory,
path_in,
format,
pbar=tqdm(),
yield_traces=yt)
# Run all commands
if command == 'convert':
for stream in iter_:
write(stream, path_out, newformat)
elif command == 'plot':
for stream in iter_:
channels = set(tr.stats.channel for tr in stream)
for ch in channels:
st2 = stream.select(channel=ch)
fname = PLOT_FNAMES.format(root=path_out, **st2[0].stats)
_create_dir(fname)
st2.sort(['back_azimuth'])
st2.plot_rf(fname, **kw['plot'])
elif command == 'plot-profile':
for stream in iter_:
channels = set(tr.stats.channel for tr in stream)
for ch in channels:
st2 = stream.select(channel=ch)
fname = PLOT_PROFILE_FNAMES.format(root=path_out,
**st2[0].stats)
_create_dir(fname)
st2.plot_profile(fname, **kw['plot_profile'])
elif command == 'stack':
for stream in iter_:
stack = stream.stack()
write(stack, path_out, format, type='stack')
elif command == 'profile':
from rf.profile import get_profile_boxes, profile
boxx = get_profile_boxes(**kw['boxes'])
prof = profile(iter_, boxx, **kw['profile'])
write(prof, path_out, format, type='profile')
else:
commands = [command] + list(commands)
for stream in iter_:
for command in commands:
if command == 'data':
pass
elif command == 'calc':
stream.rf(**kw['rf'])
elif command == 'moveout':
stream.moveout(**kw['moveout'])
else:
raise NotImplementedError
write(stream, path_out, format)
def _iter_profile(pin, format):
fname = PROFILE_FNAMES[format].format(root=pin, box_pos='*', channel='???')
yield read_rf(fname)
def run_commands(command, commands=(), events=None, inventory=None,
objects=None, get_waveforms=None, data=None, plugin=None,
phase=None, moveout_phase=None,
path_in=None, path_out=None, format='Q',
newformat=None, **kw):
"""Load files, apply commands and write result files."""
for opt in kw:
if opt not in DICT_OPTIONS:
raise ParseError('Unknown config option: %s' % opt)
for opt in DICT_OPTIONS:
default = None if opt == 'boxbins' else {}
d = kw.setdefault(opt, default)
if isinstance(d, basestring):
kw[opt] = json.loads(d)
if phase is not None:
kw['options']['phase'] = phase
if moveout_phase is not None:
kw['moveout']['phase'] = moveout_phase
if kw['boxbins'] is not None:
kw['boxes']['bins'] = np.linspace(*kw['boxbins'])
try:
if command == 'calc':
assert len(commands) < 3
if len(commands) == 2:
assert commands[0] != commands[1]
elif command == 'calc':
assert len(commands) < 2
except Exception:
raise ParseError('calc or moveout command given more than once')
# Read events and inventory
try:
if command in ('stack', 'plot'):
events = None
elif command != 'print' or objects[0] == 'events':
if (not isinstance(events, obspy.Catalog) or
not isinstance(events, list) or
(len(events) == 2 and isinstance(events[0], basestring))):
if isinstance(events, basestring):
format_ = None
else:
events, format_ = events
events = obspy.read_events(events, format_)
if command != 'print' or objects[0] == 'stations':
if not isinstance(inventory, obspy.Inventory):
if isinstance(inventory, basestring):
format_ = None
else:
inventory, format_ = inventory
inventory = obspy.read_inventory(inventory, format_)
except Exception:
print('cannot read events or stations')
return
# Initialize get_waveforms
if command == 'data':
try:
# Initialize get_waveforms
if get_waveforms is None:
get_waveforms = init_data(
data, client_options=kw['client_options'], plugin=plugin)
except Exception:
print('cannot initalize data')
return
# Print command
if command == 'print':
if objects[0] == 'events':
print(events.__str__(True))
elif objects[0] == 'stations':
print(inventory)
else:
from rf.rfstream import RFStream
stream = sum((read_rf(fname) for fname in objects), RFStream())
print(stream.__str__(True))
return
# Select appropriate iterator
if command == 'data':
iter_ = iter_event_data(events, inventory, get_waveforms, pbar=tqdm(),
**kw['options'])
elif command == 'plot-profile':
iter_ = _iter_profile(path_in, format)
else:
yt = command == 'profile'
iter_ = iter_event_processed_data(
events, inventory, path_in, format, pbar=tqdm(), yield_traces=yt)
# Run all commands
if command == 'convert':
for stream in iter_:
write(stream, path_out, newformat)
elif command == 'plot':
for stream in iter_:
channels = set(tr.stats.channel for tr in stream)
for ch in channels:
st2 = stream.select(channel=ch)
fname = PLOT_FNAMES.format(root=path_out, **st2[0].stats)
_create_dir(fname)
st2.sort(['back_azimuth'])
st2.plot_rf(fname, **kw['plot'])
elif command == 'plot-profile':
for stream in iter_:
channels = set(tr.stats.channel for tr in stream)
for ch in channels:
st2 = stream.select(channel=ch)
fname = PLOT_PROFILE_FNAMES.format(root=path_out,
**st2[0].stats)
_create_dir(fname)
st2.plot_profile(fname, **kw['plot_profile'])
elif command == 'stack':
for stream in iter_:
stack = stream.stack()
write(stack, path_out, format, type='stack')
elif command == 'profile':
from rf.profile import get_profile_boxes, profile
boxx = get_profile_boxes(**kw['boxes'])
prof = profile(iter_, boxx, **kw['profile'])
write(prof, path_out, format, type='profile')
else:
commands = [command] + list(commands)
for stream in iter_:
for command in commands:
if command == 'data':
pass
elif command == 'calc':
stream.rf(**kw['rf'])
elif command == 'moveout':
stream.moveout(**kw['moveout'])
else:
raise NotImplementedError
write(stream, path_out, format)
def _iter_profile(pin, format):
fname = PROFILE_FNAMES[format].format(root=pin, box_pos='*', channel='???')
yield read_rf(fname)
