def write(self, filename, format, **kwargs):
"""
Save stream to file including format specific headers.
See `Stream.write() <obspy.core.stream.Stream.write>` in ObsPy.
"""
if len(self) == 0:
return
for tr in self:
tr._write_format_specific_header(format)
if format.upper() == 'Q':
tr.stats.station = tr.id
if format.upper() == 'H5':
index = self.type
if index is None and 'event_time' in self[0].stats:
index = 'rf'
if index:
import obspyh5
old_index = obspyh5._INDEX
obspyh5.set_index(_H5INDEX[index])
super(RFStream, self).write(filename, format, **kwargs)
if format.upper() == 'H5' and index:
obspyh5.set_index(old_index)
if format.upper() == 'Q':
for tr in self:
tr.stats.station = tr.stats.station.split('.')[1]
def run_xcorr(stream=None,
tw='Scoda',
timenorm=None,
write=False,
write_all=False,
**kw):
if stream is None:
stream = load_stream()
name = f"{YEAR}_mag>{MAG}_q{QU}_{FILTER['freqmin']:02.0f}Hz-{FILTER['freqmax']:02.0f}Hz_{tw}_{timenorm}_dist<{DIST}km_{STACK[0]}{STACK[1]}"
ccs = correlate_stream2(stream,
tw=tw,
timenorm=timenorm,
max_dist=DIST,
tw_len=TW_LEN,
**kw)
add_distbin(ccs, DIST)
if STACK != 'max':
if 'coda' in tw:
ccs_stack1 = tw_stack(ccs.copy(),
'{evid1}-{evid2}',
stack_type=STACK)
else:
ccs_stack1 = copy(ccs).stack('{evid1}-{evid2}', stack_type=STACK)
else:
ccs_stack1 = _select_max(copy(ccs))
if write:
obspyh5.set_index('waveforms/{stack.group}')
ccs_stack1.write(f'{OUT}ccs_stack_{name}.h5', 'H5')
if write_all:
obspyh5.set_index(
'waveforms/{evid1}-{evid2}/{network}.{station}.{location}.{channel}'
)
ccs.write(f'{OUT}ccs_{name}.h5', 'H5', ignore=('processing', ))
return ccs, ccs_stack1
def set_index(index='rf'):
import obspyh5
if index == 'rf':
index = H5INDEX
elif index == 'rf_stack':
index = H5INDEX_STACK
obspyh5.set_index(index)
def write(self, filename, format, **kwargs):
"""
Save stream to file including format specific headers.
See `Stream.write() <obspy.core.stream.Stream.write>` in ObsPy.
"""
if len(self) == 0:
return
for tr in self:
tr._write_format_specific_header(format)
if format.upper() == 'Q':
tr.stats.station = tr.id
if format.upper() == 'H5':
index = self.type
if index is None and 'event_time' in self[0].stats:
index = 'rf'
if index:
import obspyh5
old_index = obspyh5._INDEX
obspyh5.set_index(_H5INDEX[index])
super(RFStream, self).write(filename, format, **kwargs)
if format.upper() == 'H5' and index:
obspyh5.set_index(old_index)
if format.upper() == 'Q':
for tr in self:
tr.stats.station = tr.stats.station.split('.')[1]
def test_stored_index(self):
stream = self.stream
with NamedTemporaryFile(suffix='.h5') as ft:
fname = ft.name
stream.write(fname, 'H5')
set_index('nonesens')
stream.write(fname, 'H5', mode='a', override='ignore')
set_index()
def test_stored_index(self):
stream = self.stream
with NamedTemporaryFile(suffix='.h5') as ft:
fname = ft.name
stream.write(fname, 'H5')
set_index('nonesens')
stream.write(fname, 'H5', mode='a', override='ignore')
set_index()
def test_trc_num(self):
stream = self.stream.copy()
set_index('waveforms/{trc_num:03d}')
with NamedTemporaryFile(suffix='.h5') as ft:
fname = ft.name
stream.write(fname, 'H5')
stream.write(fname, 'H5', mode='a', offset_trc_num=3)
stream2 = read(fname, 'H5')
for tr in stream2:
del tr.stats._format
set_index()
self.assertEqual(len(stream2), 6)
self.assertEqual(stream2[::2], stream)
self.assertEqual(stream2[1::2], stream)
def test_read_files_saved_prior_version_0_3(self):
stream = self.stream
index_v_0_2 = ('{network}.{station}/{location}.{channel}/'
'{starttime.datetime:%Y-%m-%dT%H:%M:%S}_'
'{endtime.datetime:%Y-%m-%dT%H:%M:%S}')
set_index(index_v_0_2)
with NamedTemporaryFile(suffix='.h5') as ft:
fname = ft.name
stream.write(fname, 'H5', group='waveforms')
stream2 = read(fname, 'H5', group='waveforms')
stream3 = read(fname, 'H5')
set_index()
for tr in stream2:
del tr.stats._format
for tr in stream3:
del tr.stats._format
self.assertEqual(stream, stream2)
self.assertEqual(stream, stream3)
def test_read_files_saved_prior_version_0_3(self):
stream = self.stream
index_v_0_2 = ('{network}.{station}/{location}.{channel}/'
'{starttime.datetime:%Y-%m-%dT%H:%M:%S}_'
'{endtime.datetime:%Y-%m-%dT%H:%M:%S}')
with NamedTemporaryFile(suffix='.h5') as ft:
fname = ft.name
set_index(index_v_0_2)
stream.write(fname, 'H5', group='waveforms')
stream2 = read(fname, 'H5', group='waveforms')
stream3 = read(fname, 'H5')
for tr in stream2:
del tr.stats._format
for tr in stream3:
del tr.stats._format
self.assertEqual(stream, stream2)
self.assertEqual(stream, stream3)
set_index()
def write_h5_event_stream(dest_h5_file, stream, mode='a', ignore=()):
"""
Write stream to HDF5 file in event indexed format using obspy.
:param dest_h5_file: File in which to write the stream.
:type dest_h5_file: str or pathlib.Path
:param stream: The stream to write
:type stream: obspy.Stream
:param mode: Write mode, such as 'w' or 'a'. Use 'a' to iteratively write multiple streams to one file.
:type mode: str
:param ignore: List of headers to ignore when writing attributes to group. Passed on directly to obspyh5.writeh5
:type ignore: Any iterable of str
"""
# Lock down format of obspyh5 node layout in HDF5 to ensure compatibility with
# custom iterators.
assert mode.lower() != 'r', 'Write mode cannot be \'r\''
prior_index = obspyh5._INDEX
obspyh5.set_index(EVENTIO_H5INDEX)
stream.write(dest_h5_file, 'H5', mode=mode, ignore=ignore)
obspyh5.set_index(prior_index)
def test_hdf5_plugin_and_xcorr_index(self):
set_index('xcorr')
stream = self.stream.copy()
for i, tr in enumerate(stream): # manipulate stats object
station1, station2 = 'ST1', 'ST%d' % i
channel1, channel2 = 'HHZ', u'HHN'
s = tr.stats
# we manipulate seed id so that important information gets
# printed by obspy
s.network, s.station = s.station1, s.channel1 = station1, channel1
s.location, s.channel = s.station2, s.channel2 = station2, channel2
s.network1 = s.network2 = 'BW'
s.location1 = s.location2 = ''
stream.sort()
with NamedTemporaryFile(suffix='.h5') as ft:
fname = ft.name
stream.write(fname, 'H5')
stream2 = read(fname).sort()
for tr in stream2:
del tr.stats._format
set_index()
self.assertEqual(stream, stream2)
def test_hdf5_plugin_and_xcorr_index(self):
set_index('xcorr')
stream = self.stream.copy()
for i, tr in enumerate(stream): # manipulate stats object
station1, station2 = 'ST1', 'ST%d' % i
channel1, channel2 = 'HHZ', u'HHN'
s = tr.stats
# we manipulate seed id so that important information gets
# printed by obspy
s.network, s.station = s.station1, s.channel1 = station1, channel1
s.location, s.channel = s.station2, s.channel2 = station2, channel2
s.network1 = s.network2 = 'BW'
s.location1 = s.location2 = ''
stream.sort()
with NamedTemporaryFile(suffix='.h5') as ft:
fname = ft.name
stream.write(fname, 'H5')
stream2 = read(fname).sort()
for tr in stream2:
del tr.stats._format
set_index()
self.assertEqual(stream, stream2)
def load(io, key, seedid=None, day=None, do='return', prep_kw={},
fname=None, format=None):
"""
Load object and do something with it
:param io: io
:param key: key of object to load
(key inside HDF5 file, or one of data, prepdata, stations)
:param seedid: seed id of a channel (for data or prepdata)
:param day: |UTC| object with day (for data or prepdata)
:param do: specifies what to do with the object, default is ``'return'``
which simply returns the object, other possible values are
``'print'`` -- print object (used by print command),
``'load'`` -- load object in IPython session (used by load command),
``'export'`` -- export correlations to different file format
(used by export command)
:param dict prep_kw: options passed to preprocess (for prepdata only)
:param fname: file name (for export command)
:param format: target format (for export command)
"""
if key == 'stations':
obj = io['inventory']
elif key in ('data', 'prepdata'):
if seedid is None or day is None:
msg = 'seedid and day must be given for data or prepdata'
raise ParseError(msg)
if key == 'prepdata':
prep_keys = ('remove_response', 'remove_response_options',
'demean', 'filter', 'normalization',
'time_norm_options', 'spectral_whitening_options',
'tolerance_shift',
'downsample')
prep_kw = {k: prep_kw.get(k) for k in prep_keys}
obj = _load_data(seedid, day, io['data'], io.get('data_format'),
key, inventory=io['inventory'], **prep_kw)
else:
is_stretch = 't' in _analyze_key(key)
fname_in = _get_fname(io, key)
if is_stretch:
obj = read_dicts(fname_in, key)
if do == 'print':
obj = '\n\n'.join(str(o) for o in obj)
else:
obj = obspy.read(fname_in, 'H5', group=key, headonly=do == 'print')
if do == 'print':
obj = obj.__str__(extended=True)
if do == 'print':
print(obj)
elif do == 'load':
_start_ipy(obj)
elif do == 'return':
return obj
elif do == 'export':
print('export', obj)
if format == 'H5':
obspyh5.set_index()
obj.write(fname, format)
if format == 'H5':
from yam.io import INDEX
obspyh5.set_index(INDEX)
else:
raise
import h5py
import obspyh5
import yam
import os.path
import obspy
from yam.util import _analyze_key, _get_fname
INDEX = ('{key}/{network1}.{station1}-{network2}.{station2}/'
'{location1}.{channel1}-{location2}.{channel2}/'
'{starttime.datetime:%Y-%m-%dT%H:%M}')
INDEX_STRETCH = ('{key}/{network1}.{station1}-{network2}.{station2}/'
'{location1}.{channel1}-{location2}.{channel2}')
obspyh5.set_index(INDEX)
def write_dict(dict_, fname, mode='a', libver='latest', dtype='float16'):
"""
Write similarity matrix into HDF5 file
:param dict_: Dictionary with stretching results
(output from `~yam.stretch.stretch()`)
:param fname: file name
:param mode: file mode (default ``'a'`` -- write into file)
:param libver: use latest version of HDF5 file format
:param dtype: type for similarity matrix
"""
with h5py.File(fname, mode=mode, libver=libver) as f:
f.attrs['file_format_stretch'] = 'yam'
