def test_deepcopy(self):
"""
Tests deepcopy method of Stats object.
"""
stats = Stats()
stats.network = "BW"
stats["station"] = "ROTZ"
stats["other1"] = {"test1": "1"}
stats["other2"] = AttribDict({"test2": "2"})
stats["other3"] = "test3"
stats2 = copy.deepcopy(stats)
stats.network = "CZ"
stats.station = "RJOB"
self.assertEqual(stats2.__class__, Stats)
self.assertEqual(stats2.network, "BW")
self.assertEqual(stats2.station, "ROTZ")
self.assertEqual(stats2.other1.test1, "1")
self.assertEqual(stats2.other1.__class__, AttribDict)
self.assertEqual(len(stats2.other1), 1)
self.assertEqual(stats2.other2.test2, "2")
self.assertEqual(stats2.other2.__class__, AttribDict)
self.assertEqual(len(stats2.other2), 1)
self.assertEqual(stats2.other3, "test3")
self.assertEqual(stats.network, "CZ")
self.assertEqual(stats.station, "RJOB")
def create_trace(self, channel, stats, data):
"""Utility to create a new trace object.
Parameters
----------
channel : str
channel name.
stats : obspy.core.Stats
channel metadata to clone.
data : numpy.array
channel data.
Returns
-------
obspy.core.Trace
trace containing data and metadata.
"""
stats = Stats(stats)
if self.data_type is None:
stats.data_type = 'adjusted'
else:
stats.data_type = self.data_type
if self.data_type is None:
stats.location = 'A0'
else:
stats.location = self.location
trace = super(AdjustedAlgorithm, self).create_trace(channel, stats,
data)
return trace
def test_deepcopy(self):
"""
Tests deepcopy method of Stats object.
"""
stats = Stats()
stats.network = 'BW'
stats['station'] = 'ROTZ'
stats['other1'] = {'test1': '1'}
stats['other2'] = AttribDict({'test2': '2'})
stats['other3'] = 'test3'
stats2 = copy.deepcopy(stats)
stats.network = 'CZ'
stats.station = 'RJOB'
self.assertEqual(stats2.__class__, Stats)
self.assertEqual(stats2.network, 'BW')
self.assertEqual(stats2.station, 'ROTZ')
self.assertEqual(stats2.other1.test1, '1')
self.assertEqual(stats2.other1.__class__, AttribDict)
self.assertEqual(len(stats2.other1), 1)
self.assertEqual(stats2.other2.test2, '2')
self.assertEqual(stats2.other2.__class__, AttribDict)
self.assertEqual(len(stats2.other2), 1)
self.assertEqual(stats2.other3, 'test3')
self.assertEqual(stats.network, 'CZ')
self.assertEqual(stats.station, 'RJOB')
def test_casted_stats_nscl_writes_to_mseed(self):
"""
Ensure a Stream object that has had its nslc types cast to str can
still be written.
"""
st = Stream(traces=read()[0])
# Get a new stats object with just the basic items in it
stats_items = set(Stats())
new_stats = Stats()
new_stats.__dict__.update({x: st[0].stats[x] for x in stats_items})
with warnings.catch_warnings(record=True):
new_stats.network = 1
new_stats.station = 1.1
new_stats.channel = 'Non'
st[0].stats = new_stats
# try writing stream to bytes buffer
bio = io.BytesIO()
st.write(bio, 'mseed')
bio.seek(0)
# read bytes and compare
stt = read(bio)
# remove _mseed so streams can compare equal
stt[0].stats.pop('mseed')
del stt[0].stats._format # format gets added upon writing
self.assertEqual(st, stt)
def _create_trace(data, channel, starttime, delta=60.):
stats = Stats()
stats.channel = channel
stats.delta = delta
stats.starttime = starttime
stats.npts = len(data)
data = numpy.array(data, dtype=numpy.float64)
return Trace(data, stats)
def test_update(self):
"""
Tests update method of Stats object.
"""
x = Stats({"a": 5})
self.assertTrue("a" in dir(x))
x.update({"b": 5})
self.assertTrue("b" in dir(x))
y = {"a": 5}
y.update({"b": 5})
x = Stats(y)
self.assertTrue("b" in dir(x))
def test_update(self):
"""
Tests update method of Stats object.
"""
x = Stats({'a': 5})
self.assertTrue('a' in dir(x))
x.update({'b': 5})
self.assertTrue('b' in dir(x))
y = {'a': 5}
y.update({'b': 5})
x = Stats(y)
self.assertTrue('b' in dir(x))
def test_nestedStats(self):
"""
Various setter and getter tests.
"""
# 1
stats = Stats()
stats.test = dict()
stats.test['test2'] = 'muh'
self.assertEqual(stats.test.test2, 'muh')
self.assertEqual(stats.test['test2'], 'muh')
self.assertEqual(stats['test'].test2, 'muh')
self.assertEqual(stats['test']['test2'], 'muh')
stats.test['test2'] = 'maeh'
self.assertEqual(stats.test.test2, 'maeh')
self.assertEqual(stats.test['test2'], 'maeh')
self.assertEqual(stats['test'].test2, 'maeh')
self.assertEqual(stats['test']['test2'], 'maeh')
# 2 - multiple initialization
stats = Stats({'muh': 'meah'})
stats2 = Stats(Stats(Stats(stats)))
self.assertEqual(stats2.muh, 'meah')
# 3 - check conversion to AttribDict
stats = Stats()
stats.sub1 = {'muh': 'meah'}
stats.sub2 = AttribDict({'muh2': 'meah2'})
stats2 = Stats(stats)
self.assertTrue(isinstance(stats.sub1, AttribDict))
self.assertTrue(isinstance(stats.sub2, AttribDict))
self.assertEqual(stats2.sub1.muh, 'meah')
self.assertEqual(stats2.sub2.muh2, 'meah2')
def ascii(path, filenames):
""" Reads SPECFEM3D-style ascii data
"""
from numpy import loadtxt
from obspy.core import Stream, Stats, Trace
stream = Stream()
for filename in filenames:
stats = Stats()
data = loadtxt(path +'/'+ filename)
stats.filename = filename
stats.starttime = data[0,0]
stats.sampling_rate = data[0,1] - data[0,0]
stats.npts = len(data[:,0])
try:
parts = filename.split('.')
stats.network = parts[0]
stats.station = parts[1]
stats.channel = temp[2]
except:
pass
stream.append(Trace(data=data[:,1], header=stats))
return stream
def test_nestedStats(self):
"""
Various setter and getter tests.
"""
# 1
stats = Stats()
stats.test = dict()
stats.test["test2"] = "muh"
self.assertEqual(stats.test.test2, "muh")
self.assertEqual(stats.test["test2"], "muh")
self.assertEqual(stats["test"].test2, "muh")
self.assertEqual(stats["test"]["test2"], "muh")
stats.test["test2"] = "maeh"
self.assertEqual(stats.test.test2, "maeh")
self.assertEqual(stats.test["test2"], "maeh")
self.assertEqual(stats["test"].test2, "maeh")
self.assertEqual(stats["test"]["test2"], "maeh")
# 2 - multiple initialization
stats = Stats({"muh": "meah"})
stats2 = Stats(Stats(Stats(stats)))
self.assertEqual(stats2.muh, "meah")
# 3 - check conversion to AttribDict
stats = Stats()
stats.sub1 = {"muh": "meah"}
stats.sub2 = AttribDict({"muh2": "meah2"})
stats2 = Stats(stats)
self.assertTrue(isinstance(stats.sub1, AttribDict))
self.assertTrue(isinstance(stats.sub2, AttribDict))
self.assertEqual(stats2.sub1.muh, "meah")
self.assertEqual(stats2.sub2.muh2, "meah2")
def test_setCalib(self):
"""
Test to prevent setting a calibration factor of 0
"""
x = Stats()
# this should work
x.update({'calib': 1.23})
self.assertTrue(x.calib, 1.23)
# this raises UserWarning
with warnings.catch_warnings(record=True):
warnings.simplefilter('error', UserWarning)
# 1
self.assertRaises(UserWarning, x.__setitem__, 'calib', 0)
# 2
self.assertRaises(UserWarning, x.update, {'calib': 0})
# calib value should nevertheless be set to 0
self.assertTrue(x.calib, 0)
def test_simpleStats(self):
"""
Various setter and getter tests.
"""
stats = Stats()
stats.test = 1
self.assertEqual(stats.test, 1)
self.assertEqual(stats['test'], 1)
stats['test2'] = 2
self.assertEqual(stats.test2, 2)
self.assertEqual(stats['test2'], 2)
stats['test'] = 2
self.assertEqual(stats.test, 2)
self.assertEqual(stats['test'], 2)
stats.test2 = 1
self.assertEqual(stats.test2, 1)
self.assertEqual(stats['test2'], 1)
def test_pickleStats(self):
"""
Test pickling Stats objects. Test case for issue #10.
"""
stats = Stats()
stats.muh = 1
stats['maeh'] = 'hallo'
# ASCII
temp = pickle.dumps(stats, protocol=0)
stats2 = pickle.loads(temp)
self.assertEqual(stats, stats2)
# old binary
temp = pickle.dumps(stats, protocol=1)
stats2 = pickle.loads(temp)
self.assertEqual(stats, stats2)
# new binary
temp = pickle.dumps(stats, protocol=2)
stats2 = pickle.loads(temp)
self.assertEqual(stats, stats2)
def get_obspy_trace(self):
"""
Return class contents as obspy.Trace object
"""
stat = Stats()
stat.network = self.net.split(b'\x00')[0].decode()
stat.station = self.sta.split(b'\x00')[0].decode()
location = self.loc.split(b'\x00')[0].decode()
if location == '--':
stat.location = ''
else:
stat.location = location
stat.channel = self.chan.split(b'\x00')[0].decode()
stat.starttime = UTCDateTime(self.start)
stat.sampling_rate = self.rate
stat.npts = len(self.data)
return Trace(data=self.data, header=stat)
def create_empty_trace(trace, channel):
"""
Utility to create an empty trace, similar to another trace.
Parameters
----------
trace: obspy.core.Trace
Trace that is source of most metadata, including array length.
channel: String
Channel name for created Trace.
Returns
-------
obspy.core.Trace
a Trace object, filled with numpy.nan.
"""
stats = Stats(trace.stats)
stats.channel = channel
count = len(trace.data)
numpy_data = numpy.full((count), numpy.nan)
return Trace(numpy_data, stats)
def test_pickle_stats(self):
"""
Test pickling Stats objects. Test case for issue #10.
"""
stats = Stats()
stats.muh = 1
stats['maeh'] = 'hallo'
# ASCII
temp = pickle.dumps(stats, protocol=0)
stats2 = pickle.loads(temp)
self.assertEqual(stats, stats2)
# old binary
temp = pickle.dumps(stats, protocol=1)
stats2 = pickle.loads(temp)
self.assertEqual(stats, stats2)
# new binary
temp = pickle.dumps(stats, protocol=2)
stats2 = pickle.loads(temp)
self.assertEqual(stats, stats2)
# SOH channels sampling_rate & delta == 0. for #1989
stats.sampling_rate = 0
pickle.loads(pickle.dumps(stats, protocol=0))
pickle.loads(pickle.dumps(stats, protocol=1))
pickle.loads(pickle.dumps(stats, protocol=2))
def test_init(self):
"""
Init tests.
"""
stats = Stats({'test': 'muh'})
stats['other1'] = {'test1': '1'}
stats['other2'] = AttribDict({'test2': '2'})
stats['other3'] = 'test3'
self.assertEquals(stats.test, 'muh')
self.assertEquals(stats['test'], 'muh')
self.assertEquals(stats.other1.test1, '1')
self.assertEquals(stats.other1.__class__, AttribDict)
self.assertEquals(len(stats.other1), 1)
self.assertEquals(stats.other2.test2, '2')
self.assertEquals(stats.other2.__class__, AttribDict)
self.assertEquals(len(stats.other2), 1)
self.assertEquals(stats.other3, 'test3')
self.assertTrue('test' in stats)
self.assertTrue('test' in stats.__dict__)
def _make_stats(fi, tr_block_start, standard_orientation, details):
"""
Make Stats object from information contained in the header of the trace.
"""
base_scan_interval = _read(fi, 22, 1, 'binary')
sampling_rate = int(1000 / (base_scan_interval / 16))
# map sampling rate to band code according to seed standard
band_map = {2000: 'G', 1000: 'G', 500: 'D', 250: 'D'}
# geophone instrument code
instrument_code = 'P'
# mapping for "standard_orientation"
standard_component_map = {'2': 'Z', '3': 'N', '4': 'E'}
component = str(_read(fi, tr_block_start + 40, 1, 'binary'))
if standard_orientation:
component = standard_component_map[component]
chan = band_map[sampling_rate] + instrument_code + component
npts = _read(fi, tr_block_start + 27, 3, 'binary')
start_time = _read(fi, tr_block_start + 20 + 2 * 32, 8, 'binary') / 1e6
end_time = start_time + (npts - 1) * (1 / sampling_rate)
network = _read(fi, tr_block_start + 20, 3, 'binary')
station = _read(fi, tr_block_start + 23, 3, 'binary')
location = _read(fi, tr_block_start + 26, 1, 'binary')
statsdict = dict(starttime=UTCDateTime(start_time),
endtime=UTCDateTime(end_time),
sampling_rate=sampling_rate,
npts=npts,
network=str(network),
station=str(station),
location=str(location),
channel=chan)
if details:
statsdict['rg16'] = {}
statsdict['rg16']['initial_headers'] = {}
stats_initial_headers = statsdict['rg16']['initial_headers']
stats_initial_headers.update(_read_initial_headers(fi))
statsdict['rg16']['trace_headers'] = {}
stats_tr_headers = statsdict['rg16']['trace_headers']
stats_tr_headers.update(_read_trace_header(fi, tr_block_start))
nbr_tr_header_block = _read(fi, tr_block_start + 9, 1, 'binary')
if nbr_tr_header_block > 0:
stats_tr_headers.update(
_read_trace_headers(fi, tr_block_start, nbr_tr_header_block))
return Stats(statsdict)
def test_compare_with_dict(self):
"""
Checks if Stats is still comparable to a dict object.
"""
adict = {
'network': '',
'sampling_rate': 1.0,
'test': 1,
'station': '',
'location': '',
'starttime': UTCDateTime(1970, 1, 1, 0, 0),
'delta': 1.0,
'calib': 1.0,
'npts': 0,
'endtime': UTCDateTime(1970, 1, 1, 0, 0),
'channel': ''
}
ad = Stats(adict)
self.assertEqual(ad, adict)
self.assertEqual(adict, ad)
def load_npz(filename, metadata):
"""
Loads previously computed PPSD results (from a
compressed numpy binary in npz format, written with
:meth:`~PPSD.write_npz`).
Metadata have to be specified again during loading because they are not
stored in the npz format.
:type filename: str
:param filename: Name of numpy .npz file with stored PPSD data
:type metadata: :class:`~obspy.core.inventory.inventory.Inventory` or
:class:`~obspy.io.xseed Parser` or str or dict
:param metadata: Response information of instrument. See notes in
:meth:`PPSD.__init__` for details.
"""
data = np.load(filename)
ppsd = PPSD(Stats(), metadata=metadata)
for key in NPZ_STORE_KEYS:
setattr(ppsd, key, data[key])
return ppsd
def process_step(self, step, stream):
"""Filters stream for one step.
Filters all traces in stream.
Parameters
----------
step : array element
step holding variables for one filtering operation
stream : obspy.core.Stream
stream of data to filter
Returns
-------
out : obspy.core.Stream
stream containing 1 trace per original trace.
"""
# gather variables from step
input_sample_period = step["input_sample_period"]
output_sample_period = step["output_sample_period"]
window = np.array(step["window"])
decimation = int(output_sample_period / input_sample_period)
numtaps = len(window)
window = window / sum(window)
out = Stream()
for trace in stream:
starttime, data = self.align_trace(step, trace)
# check that there is still enough data to filter
if len(data) < numtaps:
continue
filtered = self.firfilter(data, window, decimation)
stats = Stats(trace.stats)
stats.delta = output_sample_period
stats.data_interval = step["data_interval"]
stats.data_interval_type = step["data_interval_type"]
stats.filter_comments = step["filter_comments"]
stats.starttime = starttime
stats.npts = len(filtered)
trace_out = self.create_trace(stats.channel, stats, filtered)
out += trace_out
return out
def test_exception_reading_newer_npz(self):
"""
Checks that an exception is properly raised when trying to read a npz
that was written on a more recent ObsPy version (specifically that has
a higher 'ppsd_version' number which is used to keep track of changes
in PPSD and the npz file used for serialization).
"""
msg = ("Trying to read/add a PPSD npz with 'ppsd_version=100'. This "
"file was written on a more recent ObsPy version that very "
"likely has incompatible changes in PPSD internal structure "
"and npz serialization. It can not safely be read with this "
"ObsPy version (current 'ppsd_version' is {!s}). Please "
"consider updating your ObsPy installation.".format(
PPSD(stats=Stats(), metadata=None).ppsd_version))
# 1 - loading a npz
data = np.load(self.example_ppsd_npz)
# we have to load, modify 'ppsd_version' and save the npz file for the
# test..
items = {key: data[key] for key in data.files}
# deliberately set a higher ppsd_version number
items['ppsd_version'] = items['ppsd_version'].copy()
items['ppsd_version'].fill(100)
with NamedTemporaryFile() as tf:
filename = tf.name
with open(filename, 'wb') as fh:
np.savez(fh, **items)
with self.assertRaises(ObsPyException) as e:
PPSD.load_npz(filename)
self.assertEqual(str(e.exception), msg)
# 2 - adding a npz
ppsd = PPSD.load_npz(self.example_ppsd_npz)
for method in (ppsd.add_npz, ppsd._add_npz):
with NamedTemporaryFile() as tf:
filename = tf.name
with open(filename, 'wb') as fh:
np.savez(fh, **items)
with self.assertRaises(ObsPyException) as e:
method(filename)
self.assertEqual(str(e.exception), msg)
def _make_stats(theader, gheader, standard_orientation):
"""
Make Stats object from information from several blocks.
"""
sampling_rate = int(1000. / (gheader['base_scan'] / 16.))
# get channel code
component = str(theader['channel_code'])
if standard_orientation:
component = STANDARD_COMPONENT_MAP[component]
chan = BAND_MAP[sampling_rate] + INSTRUMENT_CODE + component
statsdict = dict(
starttime=UTCDateTime(theader['time'] / 1000000.),
sampling_rate=sampling_rate,
npts=theader['samples'],
network=str(theader['line_number']),
station=str(theader['point']),
location=str(theader['index']),
channel=chan,
)
return Stats(statsdict)
def map_blocks_header(whole_list_reformat, data_block_headers):
network = "CWBSN"
station_id = str(data_block_headers["stationid"])
event_time = data_block_headers["starttime"]
channel = data_block_headers["channel"]
sampling_rate = data_block_headers["sampling_rate"]
starttime = data_block_headers["starttime"]
instrument_type = data_block_headers["instrument_type"]
list_of_single_station = list(filter(lambda staid: staid['stationid'] == station_id, whole_list_reformat))
list_lt_evt_time = [element for element in list_of_single_station if
element['stet'] > event_time and element['stbt'] <= event_time ]
if len(list_lt_evt_time) != 1:
raise AttributeError("station operational date ambiguity")
else:
station = list_lt_evt_time[0]["station"]
stla = list_lt_evt_time[0]["stla"]
stlo = list_lt_evt_time[0]["stlo"]
stel = list_lt_evt_time[0]["stel"]
trace_stats = Stats(header={"station": station, "sampling_rate": sampling_rate,
"starttime": starttime, "channel": channel, "network": network,
"stla": stla, "stlo": stlo, "stel": stel, "instrument_type": instrument_type})
return trace_stats
def read_specfem_seismogram(output_files, network, station, band):
st = Stream()
for component in 'ZNE':
channel = '%sX%s' % (band, component)
filename = os.path.join(output_files,
'%s.%s.%s.sem.ascii' % (network, station,
channel))
tmp = np.genfromtxt(filename)
stats = Stats()
stats.network = network
stats.station = station
stats.channel = channel
stats.delta = tmp[1, 0] - tmp[0, 0]
stats.npts = tmp.shape[0]
stats.starttime = tmp[0, 0]
tr = Trace(tmp[:, 1], stats)
st += tr
return st
def test_raw_input_client():
"""edge_test.RawInputClient_test.test_raw_input_client()
"""
network = "NT"
station = "BOU"
channel = "MVH"
location = "R0"
data = [0, 1, 2, 3, 4, 5]
starttime = UTCDateTime("2019-12-01")
trace = Trace(
numpy.array(data, dtype=numpy.float64),
Stats({
"channel": channel,
"delta": 60.0,
"location": location,
"network": network,
"npts": len(data),
"starttime": starttime,
"station": station,
}),
)
client = MockRawInputClient(
tag="tag",
host="host",
port="port",
station=station,
channel=channel,
location=location,
network=network,
)
trace_send = EdgeFactory()._convert_trace_to_int(trace.copy())
client.send_trace("minute", trace_send)
# verify data was sent
assert_equal(len(client.last_send), 1)
def test_nestedStats(self):
"""
Various setter and getter tests.
"""
#1
stats = Stats()
stats.test = dict()
stats.test['test2'] = 'muh'
self.assertEqual(stats.test.test2, 'muh')
self.assertEqual(stats.test['test2'], 'muh')
self.assertEqual(stats['test'].test2, 'muh')
self.assertEqual(stats['test']['test2'], 'muh')
stats.test['test2'] = 'maeh'
self.assertEqual(stats.test.test2, 'maeh')
self.assertEqual(stats.test['test2'], 'maeh')
self.assertEqual(stats['test'].test2, 'maeh')
self.assertEqual(stats['test']['test2'], 'maeh')
#2 - multiple initialization
stats = Stats({'muh': 'meah'})
stats2 = Stats(Stats(Stats(stats)))
self.assertEqual(stats2.muh, 'meah')
#3 - check conversion to AttribDict
stats = Stats()
stats.sub1 = {'muh': 'meah'}
stats.sub2 = AttribDict({'muh2': 'meah2'})
stats2 = Stats(stats)
self.assertTrue(isinstance(stats.sub1, AttribDict))
self.assertTrue(isinstance(stats.sub2, AttribDict))
self.assertEqual(stats2.sub1.muh, 'meah')
self.assertEqual(stats2.sub2.muh2, 'meah2')
def readSEISAN(filename, headonly=False, **kwargs): # @UnusedVariable
"""
Reads a SEISAN file and returns an ObsPy Stream object.
.. warning::
This function should NOT be called directly, it registers via the
ObsPy :func:`~obspy.core.stream.read` function, call this instead.
:type filename: str
:param filename: SEISAN file to be read.
:rtype: :class:`~obspy.core.stream.Stream`
:return: A ObsPy Stream object.
.. rubric:: Example
>>> from obspy import read
>>> st = read("/path/to/2001-01-13-1742-24S.KONO__004")
>>> st # doctest: +ELLIPSIS
<obspy.core.stream.Stream object at 0x...>
>>> print(st) # doctest: +ELLIPSIS
4 Trace(s) in Stream:
.KONO.0.B0Z | 2001-01-13T17:45:01.999000Z - ... | 20.0 Hz, 6000 samples
.KONO.0.L0Z | 2001-01-13T17:42:24.924000Z - ... | 1.0 Hz, 3542 samples
.KONO.0.L0N | 2001-01-13T17:42:24.924000Z - ... | 1.0 Hz, 3542 samples
.KONO.0.L0E | 2001-01-13T17:42:24.924000Z - ... | 1.0 Hz, 3542 samples
"""
def _readline(fh, length=80):
data = fh.read(length + 8)
end = length + 4
start = 4
return data[start:end]
# read data chunk from given file
fh = open(filename, 'rb')
data = fh.read(80 * 12)
# get version info from file
(byteorder, arch, _version) = _getVersion(data)
# fetch lines
fh.seek(0)
# start with event file header
# line 1
data = _readline(fh)
number_of_channels = int(data[30:33])
# calculate number of lines with channels
number_of_lines = number_of_channels // 3 + (number_of_channels % 3 and 1)
if number_of_lines < 10:
number_of_lines = 10
# line 2
data = _readline(fh)
# line 3
for _i in xrange(0, number_of_lines):
data = _readline(fh)
# now parse each event file channel header + data
stream = Stream()
dlen = arch / 8
dtype = byteorder + 'i' + str(dlen)
stype = '=i' + str(dlen)
for _i in xrange(number_of_channels):
# get channel header
temp = _readline(fh, 1040)
# create Stats
header = Stats()
header['network'] = (temp[16] + temp[19]).strip()
header['station'] = temp[0:5].strip()
header['location'] = (temp[7] + temp[12]).strip()
header['channel'] = (temp[5:7] + temp[8]).strip()
header['sampling_rate'] = float(temp[36:43])
header['npts'] = int(temp[43:50])
# create start and end times
year = int(temp[9:12]) + 1900
month = int(temp[17:19])
day = int(temp[20:22])
hour = int(temp[23:25])
mins = int(temp[26:28])
secs = float(temp[29:35])
header['starttime'] = UTCDateTime(year, month, day, hour, mins) + secs
if headonly:
# skip data
fh.seek(dlen * (header['npts'] + 2), 1)
stream.append(Trace(header=header))
else:
# fetch data
data = np.fromfile(fh, dtype=dtype, count=header['npts'] + 2)
# convert to system byte order
data = np.require(data, stype)
stream.append(Trace(data=data[2:], header=header))
return stream
def moveout_test(PSS_file, q, phase):
"""
Creates synthetic PRFs and stacks them after depth migration.
Parameters
----------
PSS_file : str
Filename of raysum file containing P-Sv-Sh traces.
q : float
Slowness [s/m].
phase : str
Either "P" for Ps or "S" for Sp.
Returns
-------
z : np.array
Depth vector.
stack : np.array
Receiver function stack.
RF_mo : np.array
Matrix containing all depth migrated RFs.
RF : np.array
Matrix containing all RFs.
dt : float
Sampling interval.
PSS : np.array
Matrix containing all traces in P-Sv-Sh.
"""
rayp = q * 1.111949e5
PSS, dt, M, N, shift = read_raysum(phase, PSS_file=PSS_file)
# Create receiver functions
RF = []
RF_mo = []
stats = Stats()
stats.npts = N
stats.delta = dt
stats.starttime = UTCDateTime(0)
for i in range(M):
if phase == "P":
data, _, IR = it(PSS[i, 0, :],
PSS[i, 1, :],
dt,
shift=shift,
width=4)
elif phase == "S":
data, _, _ = it(PSS[i, 1, :],
PSS[i, 0, :],
dt,
shift=shift,
width=4)
RF.append(data)
z, rfc = moveout(data,
stats,
UTCDateTime(shift),
rayp[i],
phase,
fname="raysum.dat")
RF_mo.append(rfc)
stack = np.average(RF_mo, axis=0)
plt.close('all')
plt.figure()
for mo in RF_mo:
plt.plot(z, mo)
return z, stack, RF_mo, RF, dt, PSS
def rf_test(phase,
dip,
rfloc='output/waveforms/RF',
geom_file='3D.geom',
decon_meth='it'):
"""
Creates synthetic PRFs from Raysum data.
Parameters
----------
phase : string
"P" or "S".
dip : int
Dip of the LAB in deg, determines, which files to use
rfloc : The parental directory, in which the RFs are saved.
geom_file : str, optional
Filename of the geometry file
Returns
-------
rfs: list
List of RFTrace objects. Will in addition be saved in SAC format.
"""
# Determine filenames
PSS_file = []
for i in range(16):
PSS_file.append('3D_' + str(dip) + '_' + str(i) + '.tr')
# Read geometry
baz, q, dN, dE = read_geom(geom_file, phase)
# statlat = dN/(DEG2KM*1000)
d = np.sqrt(np.square(dN) + np.square(dE))
az = np.rad2deg(np.arccos(dN / d))
i = np.where(dE < 0)
az[i] = az[i] + 180
statlat = []
statlon = []
for azimuth, delta in zip(az, d):
if delta == 0:
statlat.append(0)
statlon.append(0)
continue
coords = Geodesic.WGS84.Direct(0, 0, azimuth, delta)
statlat.append(coords["lat2"])
statlon.append(coords["lon2"])
# for n, longitude in enumerate(lon):
# y, _, _ = gps2dist_azimuth(latitude, 0, latitude, longitude)
# statlon = dE/(DEG2KM*1000)
rayp = q * DEG2KM * 1000
# Read traces
stream = []
for f in PSS_file:
PSS, dt, _, N, shift = read_raysum(phase, PSS_file=f)
stream.append(PSS)
streams = np.vstack(stream)
del stream
M = len(baz)
if M != streams.shape[0]:
raise ValueError([
"Number of traces", streams.shape[0], """does not
equal the number of backazimuths in the geom file""", M
])
rfs = []
odir = os.path.join(rfloc, phase, 'raysum', str(dip))
ch = ['BHP', 'BHV', 'BHH'] # Channel names
os.makedirs(odir, exist_ok=True)
# Create RF objects
for i, st in enumerate(streams):
s = Stream()
for j, tr in enumerate(st):
stats = Stats()
stats.npts = N
stats.delta = dt
stats.st # if old:
stats.channel = ch[j]
stats.network = 'RS'
stats.station = str(dip)
s.append(Trace(data=tr, header=stats))
# Create info dictionary for rf creation
info = {
'onset': [UTCDateTime(0) + shift],
'starttime': [UTCDateTime(0)],
'statlat': statlat[i],
'statlon': statlon[i],
'statel': 0,
'rayp_s_deg': [rayp[i]],
'rbaz': [baz[i]],
'rdelta': [np.nan],
'ot_ret': [0],
'magnitude': [np.nan],
'evt_depth': [np.nan],
'evtlon': [np.nan],
'evtlat': [np.nan]
}
rf = createRF(s, phase=phase, method=decon_meth, info=info)
# Write RF
rf.write(os.path.join(odir, str(i) + '.sac'), format='SAC')
rfs.append(rf)
return rfs, statlat, statlon
def test_ppsd_restricted_stacks(self, state, image_path):
"""
Test PPSD.calculate_histogram() with restrictions to what data should
be stacked. Also includes image tests.
"""
# set up a bogus PPSD, with fixed random psds but with real start times
# of psd pieces, to facilitate testing the stack selection.
ppsd = PPSD(stats=Stats(dict(sampling_rate=150)),
metadata=None,
db_bins=(-200, -50, 20.),
period_step_octaves=1.4)
# change data to nowadays used nanoseconds POSIX timestamp
ppsd._times_processed = [
UTCDateTime(t)._ns for t in np.load(
os.path.join(state.path, "ppsd_times_processed.npy")).tolist()
]
np.random.seed(1234)
ppsd._binned_psds = [
arr for arr in np.random.uniform(-200, -50, (
len(ppsd._times_processed), len(ppsd.period_bin_centers)))
]
# Test callback function that selects a fixed random set of the
# timestamps. Also checks that we get passed the type we expect,
# which is 1D numpy ndarray of int type.
def callback(t_array):
assert isinstance(t_array, np.ndarray)
assert t_array.shape == (len(ppsd._times_processed), )
assert np.issubdtype(t_array.dtype, np.integer)
np.random.seed(1234)
res = np.random.randint(0, 2, len(t_array)).astype(bool)
return res
# test several different sets of stack criteria, should cover
# everything, even with lots of combined criteria
stack_criteria_list = [
dict(starttime=UTCDateTime(2015, 3, 8), month=[2, 3, 5, 7, 8]),
dict(endtime=UTCDateTime(2015, 6, 7),
year=[2015],
time_of_weekday=[(1, 0, 24), (2, 0, 24), (-1, 0, 11)]),
dict(year=[2013, 2014, 2016, 2017], month=[2, 3, 4]),
dict(month=[1, 2, 5, 6, 8], year=2015),
dict(isoweek=[4, 5, 6, 13, 22, 23, 24, 44, 45]),
dict(time_of_weekday=[(5, 22, 24), (6, 0, 2), (6, 22, 24)]),
dict(callback=callback, month=[1, 3, 5, 7]),
dict(callback=callback)
]
expected_selections = np.load(
os.path.join(state.path, "ppsd_stack_selections.npy"))
# test every set of criteria
for stack_criteria, expected_selection in zip(stack_criteria_list,
expected_selections):
selection_got = ppsd._stack_selection(**stack_criteria)
np.testing.assert_array_equal(selection_got, expected_selection)
plot_kwargs = dict(max_percentage=15,
xaxis_frequency=True,
period_lim=(0.01, 50))
ppsd.calculate_histogram(**stack_criteria_list[1])
fig = ppsd.plot(show=False, **plot_kwargs)
fig.axes[1].set_xlim(left=fig.axes[1].get_xlim()[0] - 2)
image_path_1 = image_path.parent / 'test_ppsd_restricted_stacks_1.png'
with np.errstate(under='ignore'):
fig.savefig(image_path_1)
# test it again, checking that updating an existing plot with different
# stack selection works..
# a) we start with the stack for the expected image and test that it
# matches (like above):
ppsd.calculate_histogram(**stack_criteria_list[1])
image_path_2 = image_path.parent / 'test_ppsd_restricted_stacks_2.png'
with np.errstate(under='ignore'):
fig.savefig(image_path_2)
ppsd.calculate_histogram(**stack_criteria_list[1])
image_path_3 = image_path.parent / 'test_ppsd_restricted_stacks_3.png'
ppsd._plot_histogram(fig=fig, draw=True)
with np.errstate(under='ignore'):
fig.savefig(image_path_3)
def test_component(self):
"""
Test setting and getting of component.
"""
stats = Stats()
# Channel with 3 characters
stats.channel = 'HHZ'
self.assertEqual(stats.component, 'Z')
stats.component = 'L'
self.assertEqual(stats.component, 'L')
self.assertEqual(stats.channel, 'HHL')
stats['component'] = 'Q'
self.assertEqual(stats['component'], 'Q')
self.assertEqual(stats.channel, 'HHQ')
# Channel with 1 character as component
stats.channel = 'N'
stats.component = 'E'
self.assertEqual(stats.channel, 'E')
self.assertEqual(stats.component, 'E')
# Channel with 0 characters
stats.channel = ''
self.assertEqual(stats.component, '')
stats.component = 'Z'
self.assertEqual(stats.channel, 'Z')
# Components must be single character
stats.channel = 'HHZ'
with self.assertRaises(ValueError):
stats.component = ''
self.assertEqual(stats.channel, 'HHZ')
with self.assertRaises(ValueError):
stats.component = 'ZZ'
self.assertEqual(stats.channel, 'HHZ')
def _read_asc(filename,
headonly=False,
skip=0,
delta=None,
length=None,
**kwargs): # @UnusedVariable
"""
Reads a Seismic Handler ASCII file and returns an ObsPy Stream object.
.. warning::
This function should NOT be called directly, it registers via the
ObsPy :func:`~obspy.core.stream.read` function, call this instead.
:type filename: str
:param filename: ASCII file to be read.
:type headonly: bool, optional
:param headonly: If set to True, read only the head. This is most useful
for scanning available data in huge (temporary) data sets.
:type skip: int, optional
:param skip: Number of lines to be skipped from top of file. If defined
only one trace is read from file.
:type delta: float, optional
:param delta: If ``skip`` is used, ``delta`` defines sample offset in
seconds.
:type length: int, optional
:param length: If ``skip`` is used, ``length`` defines the number of values
to be read.
:rtype: :class:`~obspy.core.stream.Stream`
:return: A ObsPy Stream object.
.. rubric:: Example
>>> from obspy import read
>>> st = read("/path/to/QFILE-TEST-ASC.ASC")
>>> st # doctest: +ELLIPSIS
<obspy.core.stream.Stream object at 0x...>
>>> print(st) # doctest: +ELLIPSIS
3 Trace(s) in Stream:
.TEST..BHN | 2009-10-01T12:46:01.000000Z - ... | 20.0 Hz, 801 samples
.TEST..BHE | 2009-10-01T12:46:01.000000Z - ... | 20.0 Hz, 801 samples
.WET..HHZ | 2010-01-01T01:01:05.999000Z - ... | 100.0 Hz, 4001 samples
"""
fh = open(filename, 'rt')
# read file and split text into channels
channels = []
headers = {}
data = io.StringIO()
for line in fh.readlines()[skip:]:
if line.isspace():
# blank line
# check if any data fetched yet
if len(headers) == 0 and data.tell() == 0:
continue
# append current channel
data.seek(0)
channels.append((headers, data))
# create new channel
headers = {}
data = io.StringIO()
if skip:
# if skip is set only one trace is read, everything else makes
# no sense.
break
continue
elif line[0].isalpha():
# header entry
key, value = line.split(':', 1)
key = key.strip()
value = value.strip()
headers[key] = value
elif not headonly:
# data entry - may be written in multiple columns
data.write(line.strip() + ' ')
fh.close()
# create ObsPy stream object
stream = Stream()
# custom header
custom_header = {}
if delta:
custom_header["delta"] = delta
if length:
custom_header["npts"] = length
for headers, data in channels:
# create Stats
header = Stats(custom_header)
header['sh'] = {}
channel = [' ', ' ', ' ']
# generate headers
for key, value in headers.items():
if key == 'DELTA':
header['delta'] = float(value)
elif key == 'LENGTH':
header['npts'] = int(value)
elif key == 'CALIB':
header['calib'] = float(value)
elif key == 'STATION':
header['station'] = value
elif key == 'COMP':
channel[2] = value[0]
elif key == 'CHAN1':
channel[0] = value[0]
elif key == 'CHAN2':
channel[1] = value[0]
elif key == 'START':
# 01-JAN-2009_01:01:01.0
# 1-OCT-2009_12:46:01.000
header['starttime'] = to_utcdatetime(value)
else:
# everything else gets stored into sh entry
if key in SH_KEYS_INT:
header['sh'][key] = int(value)
elif key in SH_KEYS_FLOAT:
header['sh'][key] = float(value)
else:
header['sh'][key] = value
# set channel code
header['channel'] = ''.join(channel)
if headonly:
# skip data
stream.append(Trace(header=header))
else:
# read data
data = loadtxt(data, dtype=np.float32, ndmin=1)
# cut data if requested
if skip and length:
data = data[:length]
# use correct value in any case
header["npts"] = len(data)
stream.append(Trace(data=data, header=header))
return stream
def append(self, trace, gap_overlap_check=False, verbose=False):
"""
Appends a Trace object to this RtTrace.
Registered real-time processing will be applied to copy of appended
Trace object before it is appended. This RtTrace will be truncated
from the beginning to RtTrace.max_length, if specified.
Sampling rate, data type and trace.id of both traces must match.
:type trace: :class:`~obspy.core.trace.Trace`
:param trace: :class:`~obspy.core.trace.Trace` object to append to
this RtTrace
:type gap_overlap_check: bool, optional
:param gap_overlap_check: Action to take when there is a gap or overlap
between the end of this RtTrace and start of appended Trace:
If True, raise TypeError.
If False, all trace processing memory will be re-initialized to
prevent false signal in processed trace.
(default is ``True``).
:type verbose: bool, optional
:param verbose: Print additional information to stdout
:return: NumPy :class:`np.ndarray` object containing processed trace
data from appended Trace object.
"""
if not isinstance(trace, Trace):
# only add Trace objects
raise TypeError("Only obspy.core.trace.Trace objects are allowed")
# sanity checks
if self.have_appended_data:
# check id
if self.getId() != trace.getId():
raise TypeError("Trace ID differs:", self.getId(),
trace.getId())
# check sample rate
if self.stats.sampling_rate != trace.stats.sampling_rate:
raise TypeError("Sampling rate differs:",
self.stats.sampling_rate,
trace.stats.sampling_rate)
# check calibration factor
if self.stats.calib != trace.stats.calib:
raise TypeError("Calibration factor differs:",
self.stats.calib, trace.stats.calib)
# check data type
if self.data.dtype != trace.data.dtype:
raise TypeError("Data type differs:", self.data.dtype,
trace.data.dtype)
# TODO: IMPORTANT? Should improve check for gaps and overlaps
# and handle more elegantly
# check times
gap_or_overlap = False
if self.have_appended_data:
#delta = int(math.floor(\
# round((rt.stats.starttime - lt.stats.endtime) * sr, 5) )) - 1
diff = trace.stats.starttime - self.stats.endtime
delta = diff * self.stats.sampling_rate - 1.0
if verbose:
msg = "%s: Overlap/gap of (%g) samples in data: (%s) (%s) " + \
"diff=%gs dt=%gs"
print msg % (self.__class__.__name__, delta,
self.stats.endtime, trace.stats.starttime, diff,
self.stats.delta)
if delta < -0.1:
msg = "Overlap of (%g) samples in data: (%s) (%s) diff=%gs" + \
" dt=%gs"
msg = msg % (-delta, self.stats.endtime, trace.stats.starttime,
diff, self.stats.delta)
if gap_overlap_check:
raise TypeError(msg)
gap_or_overlap = True
if delta > 0.1:
msg = "Gap of (%g) samples in data: (%s) (%s) diff=%gs" + \
" dt=%gs"
msg = msg % (delta, self.stats.endtime, trace.stats.starttime,
diff, self.stats.delta)
if gap_overlap_check:
raise TypeError(msg)
gap_or_overlap = True
if gap_or_overlap:
msg += " - Trace processing memory will be re-initialized."
warnings.warn(msg, UserWarning)
else:
# correct start time to pin absolute trace timing to start of
# appended trace, this prevents slow drift of nominal trace
# timing from absolute time when nominal sample rate differs
# from true sample rate
self.stats.starttime = \
self.stats.starttime + diff - self.stats.delta
if verbose:
print "%s: self.stats.starttime adjusted by: %gs" \
% (self.__class__.__name__, diff - self.stats.delta)
# first apply all registered processing to Trace
for proc in self.processing:
process_name, options, rtmemory_list = proc
# if gap or overlap, clear memory
if gap_or_overlap and rtmemory_list != None:
for n in range(len(rtmemory_list)):
rtmemory_list[n] = RtMemory()
# apply processing
trace = trace.copy()
dtype = trace.data.dtype
if hasattr(process_name, '__call__'):
# check if direct function call
trace.data = process_name(trace.data, **options)
else:
# got predefined function
func = REALTIME_PROCESS_FUNCTIONS[process_name.lower()][0]
options['rtmemory_list'] = rtmemory_list
trace.data = func(trace, **options)
# assure dtype is not changed
trace.data = np.require(trace.data, dtype=dtype)
# if first data, set stats
if not self.have_appended_data:
self.data = np.array(trace.data)
self.stats = Stats(header=trace.stats)
self.have_appended_data = True
return trace
# handle all following data sets
# fix Trace.__add__ parameters
# TODO: IMPORTANT? Should check for gaps and overlaps and handle
# more elegantly
sum_trace = Trace.__add__(self,
trace,
method=0,
interpolation_samples=0,
fill_value='latest',
sanity_checks=True)
# Trace.__add__ returns new Trace, so update to this RtTrace
self.data = sum_trace.data
# left trim if data length exceeds max_length
if self.max_length != None:
max_samples = int(self.max_length * self.stats.sampling_rate + 0.5)
if np.size(self.data) > max_samples:
starttime = self.stats.starttime + (np.size(self.data) - \
max_samples) / self.stats.sampling_rate
self._ltrim(starttime,
pad=False,
nearest_sample=True,
fill_value=None)
return trace
def raw_import(gzip_filename):
"""
Makes a 'raw' stream file from the gzipped csv file.
The csv file has been downloaded from the JAXA website.
The method makes a raw stream which does not yet have the frames
reconstructed.
:type gzip_filename: str
:param gzip_filename: gzipped filename of the CSV file to be read.
:rtype: :class:`~obspy.core.stream.Stream`
:return: A ObsPy Stream object.
"""
# read the gzipped csv file
with gzip.open(gzip_filename, 'rt') as fh:
# read file
buf = []
header = next(fh).split(',')
# read the header
# it should contain either 1 channel or 3
if len(header) == 8:
# the RESP files use either 'MH1', 'MH2', 'MHZ'
# the JAXA files use 'LPX', 'LPY', 'LPZ'
# X should point north, Y east, but this is not always the case
# so we rename LPX to MH1, and LPY to MH2
channels = ['MH1', 'MH2', 'MHZ']
raw_channels = ['_M1', '_M2', '_MZ']
for line in fh:
temp = line.split(',')
try:
temp[4] = UTCDateTime(temp[4])
except ValueError as e:
# this is a specific error which is found in the csv file
if temp[4] == '1975-49-11 19:13:04.232000':
temp[4] = UTCDateTime('1975-09-11 19:13:04.232000')
else:
raise
try:
temp[0] = int(temp[0])
except ValueError as e:
# this is a specific error which is found in the csv file
if temp[4] == UTCDateTime(
'1975-09-15 12:53:36.849000') and temp[0] == '<3':
temp[0] = 83
else:
raise
buf.append(
(temp[1], temp[2], temp[4], int(temp[0]), int(temp[3]),
int(temp[5]), int(temp[6]), int(temp[7])))
elif len(header) == 6:
channels = ['SPZ']
raw_channels = ['_SZ']
for line in fh:
# check the manual list of points which have been removed
if line in remove_manually:
continue
temp = line.split(',')
# the original order:
# frame_count, ap_station, ground_station, nc, time, spz
# make a tuple (in a new order so that it can be sorted):
# ap_station, ground_station, time, frame_count, nc, spz
buf.append(
(temp[1], temp[2], UTCDateTime(temp[4]), int(temp[0]),
int(temp[3]), int(temp[5])))
# sort by ap_station, ground_station and time (and also everything else,
# but that won't matter)
buf.sort()
stream = Stream()
data_x = []
data_y = []
data_z = []
data_sz = []
abs_times = []
frame_count_ncs = []
corr_frame_count_ncs = []
stats = Stats()
stats.delta = DELTA
network = 'XA'
last_id = None
for data in buf:
# read in the data from the buffer
station = data[0].rjust(3, 'S')
ground_station = data[1].rjust(2, '0')
time = data[2]
frame_count = data[3]
nc = data[4]
# create a combination of frame count and nc - from 0.0 to 89.75
frame_count_nc = float(frame_count) + (float(nc) - 1.) * 0.25
id = "{0:s}.{1:s}.{2:s}.{3:s}".format(network, station, ground_station,
channels[0])
# check whether we are adding to an existing one, or creating a new one
if (last_id is None or last_id != id):
# before creating the new one, add previous trace(s) to the stream
if len(abs_times) > 0:
_make_traces(stream=stream,
stats=stats,
header=header,
channels=raw_channels,
data_x=data_x,
data_y=data_y,
data_z=data_z,
data_sz=data_sz,
abs_times=abs_times,
frame_count_ncs=frame_count_ncs)
data_x = []
data_y = []
data_z = []
data_sz = []
abs_times = []
frame_count_ncs = []
stats = Stats()
stats.delta = DELTA
stats.starttime = time
stats.network = network
stats.station = station
stats.location = ground_station
# add the data) from any line
if len(header) == 8:
data_x.append(data[5])
data_y.append(data[6])
data_z.append(data[7])
else:
data_sz.append(data[5])
abs_times.append(time.timestamp)
frame_count_ncs.append(frame_count_nc)
last_id = id
# add the last one
if len(abs_times) > 0:
_make_traces(stream=stream,
stats=stats,
header=header,
channels=raw_channels,
data_x=data_x,
data_y=data_y,
data_z=data_z,
data_sz=data_sz,
abs_times=abs_times,
frame_count_ncs=frame_count_ncs)
return stream
year=2009,
month=4,
day=7,
hour=20,
minute=12,
second=55,
)
station = Stats({
'longitude': -149.8174,
'latitude': 61.5919,
'starttime': origin_time - 100.,
'endtime': origin_time - 100.,
'npts': 19999,
'delta': 0.02,
'station': 'BIGB',
'location': '',
'id': 'YV.BIGB',
'catalog_origin_time': origin_time,
'catalog_depth': 33033.5998535,
'catalog_distance': 15.8500907298,
'catalog_azimuth': 345.527768889,
})
origin = Origin(
time=origin_time,
latitude=61.4542007446,
longitude=-149.742797852,
depth=33033.5998535,
)
return None
return x
headers = {}
data = StringIO()
# read file
fh = open(filename_in, 'rt')
for i in xrange(64):
key, value = fh.readline().strip().split(':', 1)
headers[key.strip()] = value.strip()
# create ObsPy stream object
stream = Stream()
header = Stats()
header['dyna'] = {}
header['network'] = headers['NETWORK']
header['station'] = headers['STATION_CODE']
header['location'] = headers['LOCATION']
header['channel'] = headers['STREAM']
try:
header['starttime'] = toUTCDateTime(
headers['DATE_TIME_FIRST_SAMPLE_YYYYMMDD_HHMMSS']
) # use toUTCDateTime to convert from DYNA format
except:
header['starttime'] = toUTCDateTime('19700101_000000')
header['sampling_rate'] = 1 / float(headers['SAMPLING_INTERVAL_S'])
header['delta'] = float(headers['SAMPLING_INTERVAL_S'])
header['npts'] = int(headers['NDATA'])
def xcorr2(tr1,
tr2,
sta1_inv=None,
sta2_inv=None,
instrument_response_output='vel',
water_level=50.,
window_seconds=3600,
window_overlap=0.1,
window_buffer_length=0,
interval_seconds=86400,
taper_length=0.05,
resample_rate=None,
flo=None,
fhi=None,
clip_to_2std=False,
whitening=False,
whitening_window_frequency=0,
one_bit_normalize=False,
envelope_normalize=False,
verbose=1,
logger=None):
# Length of window_buffer in seconds
window_buffer_seconds = window_buffer_length * window_seconds
adjusted_taper_length = taper_length
if (window_buffer_seconds):
# adjust taper length
adjusted_taper_length = taper_length / (1. + window_buffer_length * 2.)
# end if
sr1 = tr1.stats.sampling_rate
sr2 = tr2.stats.sampling_rate
sr1_orig = sr1
sr2_orig = sr2
tr1_d_all = tr1.data # refstn
tr2_d_all = tr2.data
lentr1_all = tr1_d_all.shape[0]
lentr2_all = tr2_d_all.shape[0]
window_samples_1 = (window_seconds + 2 * window_buffer_seconds) * sr1
window_samples_2 = (window_seconds + 2 * window_buffer_seconds) * sr2
interval_samples_1 = interval_seconds * sr1
interval_samples_2 = interval_seconds * sr2
sr = 0
resll = []
# set day-aligned start-indices
maxStartTime = max(tr1.stats.starttime, tr2.stats.starttime)
dayAlignedStartTime = UTCDateTime(year=maxStartTime.year,
month=maxStartTime.month,
day=maxStartTime.day)
itr1s = (dayAlignedStartTime - tr1.stats.starttime) * sr1
itr2s = (dayAlignedStartTime - tr2.stats.starttime) * sr2
if (resample_rate):
sr1 = resample_rate
sr2 = resample_rate
# end if
sr = max(sr1, sr2)
xcorlen = int(2 * window_seconds * sr - 1)
fftlen = 2**(int(np.log2(xcorlen)) + 1)
intervalCount = 0
windowsPerInterval = [
] # Stores the number of windows processed per interval
intervalStartSeconds = []
intervalEndSeconds = []
while itr1s < lentr1_all and itr2s < lentr2_all:
itr1e = min(lentr1_all, itr1s + interval_samples_1)
itr2e = min(lentr2_all, itr2s + interval_samples_2)
while ((itr1s < 0) or (itr2s < 0)):
itr1s += (window_samples_1 - 2*window_buffer_seconds*sr1_orig) - \
(window_samples_1 - 2*window_buffer_seconds*sr1_orig) * window_overlap
itr2s += (window_samples_2 - 2*window_buffer_seconds*sr2_orig) - \
(window_samples_2 - 2*window_buffer_seconds*sr2_orig) * window_overlap
# end while
if (np.fabs(itr1e - itr1s) < sr1_orig
or np.fabs(itr2e - itr2s) < sr2_orig):
itr1s = itr1e
itr2s = itr2e
continue
# end if
if (tr1.stats.starttime + itr1s / sr1_orig !=
tr2.stats.starttime + itr2s / sr2_orig):
if (logger): logger.warning('Detected misaligned traces..')
windowCount = 0
wtr1s = int(itr1s)
wtr2s = int(itr2s)
resl = []
while wtr1s < itr1e and wtr2s < itr2e:
wtr1e = int(min(itr1e, wtr1s + window_samples_1))
wtr2e = int(min(itr2e, wtr2s + window_samples_2))
# Discard small windows
if ((wtr1e - wtr1s < window_samples_1)
or (wtr2e - wtr2s < window_samples_2)
or (wtr1e - wtr1s < sr1_orig)
or (wtr2e - wtr2s < sr2_orig)):
wtr1s = int(np.ceil(itr1e))
wtr2s = int(np.ceil(itr2e))
continue
# end if
# Discard windows with masked regions, i.e. with gaps or windows that are all zeros
if (not (np.ma.is_masked(tr1_d_all[wtr1s:wtr1e])
or np.ma.is_masked(tr2_d_all[wtr2s:wtr2e])
or np.sum(tr1_d_all[wtr1s:wtr1e]) == 0
or np.sum(tr2_d_all[wtr2s:wtr2e]) == 0)):
#logger.info('%s, %s' % (tr1.stats.starttime + wtr1s / 200., tr1.stats.starttime + wtr1e / sr1_orig))
#logger.info('%s, %s' % (tr2.stats.starttime + wtr2s / 200., tr2.stats.starttime + wtr2e / sr2_orig))
tr1_d = np.array(tr1_d_all[wtr1s:wtr1e], dtype=np.float32)
tr2_d = np.array(tr2_d_all[wtr2s:wtr2e], dtype=np.float32)
# STEP 1: detrend
tr1_d = signal.detrend(tr1_d)
tr2_d = signal.detrend(tr2_d)
# STEP 2: demean
tr1_d -= np.mean(tr1_d)
tr2_d -= np.mean(tr2_d)
# STEP 3: remove response
if (sta1_inv):
resp_tr1 = Trace(
data=tr1_d,
header=Stats(
header={
'sampling_rate':
sr1_orig,
'npts':
len(tr1_d),
'network':
tr1.stats.network,
'station':
tr1.stats.station,
'location':
tr1.stats.location,
'channel':
tr1.stats.channel,
'starttime':
tr1.stats.starttime + float(wtr1s) / sr1_orig,
'endtime':
tr1.stats.starttime + float(wtr1e) / sr1_orig
}))
try:
resp_tr1.remove_response(
inventory=sta1_inv,
output=instrument_response_output.upper(),
water_level=water_level)
except Exception as e:
print(e)
# end try
tr1_d = resp_tr1.data
# end if
# remove response
if (sta2_inv):
resp_tr2 = Trace(
data=tr2_d,
header=Stats(
header={
'sampling_rate':
sr2_orig,
'npts':
len(tr2_d),
'network':
tr2.stats.network,
'station':
tr2.stats.station,
'location':
tr2.stats.location,
'channel':
tr2.stats.channel,
'starttime':
tr2.stats.starttime + float(wtr2s) / sr2_orig,
'endtime':
tr2.stats.starttime + float(wtr2e) / sr2_orig
}))
try:
resp_tr2.remove_response(
inventory=sta2_inv,
output=instrument_response_output.upper(),
water_level=water_level)
except Exception as e:
print(e)
# end try
tr2_d = resp_tr2.data
# end if
# STEPS 4, 5: resample after lowpass @ resample_rate/2 Hz
if (resample_rate):
tr1_d = lowpass(tr1_d,
resample_rate / 2.,
sr1_orig,
corners=2,
zerophase=True)
tr2_d = lowpass(tr2_d,
resample_rate / 2.,
sr2_orig,
corners=2,
zerophase=True)
tr1_d = Trace(
data=tr1_d,
header=Stats(header={
'sampling_rate': sr1_orig,
'npts': window_samples_1
})).resample(resample_rate, no_filter=True).data
tr2_d = Trace(
data=tr2_d,
header=Stats(header={
'sampling_rate': sr2_orig,
'npts': window_samples_2
})).resample(resample_rate, no_filter=True).data
# end if
# STEP 6: Bandpass
if (flo and fhi):
tr1_d = bandpass(tr1_d,
flo,
fhi,
sr1,
corners=2,
zerophase=True)
tr2_d = bandpass(tr2_d,
flo,
fhi,
sr2,
corners=2,
zerophase=True)
# end if
# STEP 7: time-domain normalization
# clip to +/- 2*std
if (clip_to_2std):
std_tr1 = np.std(tr1_d)
std_tr2 = np.std(tr2_d)
clip_indices_tr1 = np.fabs(tr1_d) > 2 * std_tr1
clip_indices_tr2 = np.fabs(tr2_d) > 2 * std_tr2
tr1_d[clip_indices_tr1] = 2 * std_tr1 * np.sign(
tr1_d[clip_indices_tr1])
tr2_d[clip_indices_tr2] = 2 * std_tr2 * np.sign(
tr2_d[clip_indices_tr2])
# end if
# 1-bit normalization
if (one_bit_normalize):
tr1_d = np.sign(tr1_d)
tr2_d = np.sign(tr2_d)
# end if
# Apply Rhys Hawkins-style default time domain normalization
if (clip_to_2std == 0 and one_bit_normalize == 0):
# 0-mean
tr1_d -= np.mean(tr1_d)
tr2_d -= np.mean(tr2_d)
# unit-std
tr1_d /= np.std(tr1_d)
tr2_d /= np.std(tr2_d)
# end if
# STEP 8: taper
if (adjusted_taper_length > 0):
tr1_d = taper(
tr1_d,
int(np.round(adjusted_taper_length * tr1_d.shape[0])))
tr2_d = taper(
tr2_d,
int(np.round(adjusted_taper_length * tr2_d.shape[0])))
# end if
# STEP 9: spectral whitening
if (whitening):
tr1_d = whiten(tr1_d,
sr1,
window_freq=whitening_window_frequency)
tr2_d = whiten(tr2_d,
sr2,
window_freq=whitening_window_frequency)
# STEP 10: taper
if (adjusted_taper_length > 0):
tr1_d = taper(
tr1_d,
int(
np.round(adjusted_taper_length *
tr1_d.shape[0])))
tr2_d = taper(
tr2_d,
int(
np.round(adjusted_taper_length *
tr2_d.shape[0])))
# end if
# end if
# STEP 11: Final bandpass
# apply zero-phase bandpass
if (flo and fhi):
tr1_d = bandpass(tr1_d,
flo,
fhi,
sr1,
corners=2,
zerophase=True)
tr2_d = bandpass(tr2_d,
flo,
fhi,
sr2,
corners=2,
zerophase=True)
# end if
if (window_buffer_seconds):
# extract window of interest from buffered window
tr1_d = tr1_d[int(window_buffer_seconds *
sr1):-int(window_buffer_seconds * sr1)]
tr2_d = tr2_d[int(window_buffer_seconds *
sr2):-int(window_buffer_seconds * sr2)]
# end if
# cross-correlate waveforms
if (sr1 < sr2):
fftlen2 = fftlen
fftlen1 = int((fftlen2 * 1.0 * sr1) / sr)
rf = zeropad_ba(
fftn(zeropad(tr1_d, fftlen1), shape=[fftlen1]),
fftlen2) * fftn(zeropad(ndflip(tr2_d), fftlen2),
shape=[fftlen2])
elif (sr1 > sr2):
fftlen1 = fftlen
fftlen2 = int((fftlen1 * 1.0 * sr2) / sr)
rf = fftn(zeropad(tr1_d, fftlen1),
shape=[fftlen1]) * zeropad_ba(
fftn(zeropad(ndflip(tr2_d), fftlen2),
shape=[fftlen2]), fftlen1)
else:
rf = fftn(zeropad(tr1_d, fftlen), shape=[fftlen]) * fftn(
zeropad(ndflip(tr2_d), fftlen), shape=[fftlen])
# end if
if (not np.isnan(rf).any()):
resl.append(rf)
windowCount += 1
# end if
# end if
wtr1s += int(
(window_samples_1 - 2 * window_buffer_seconds * sr1_orig) -
(window_samples_1 - 2 * window_buffer_seconds * sr1_orig) *
window_overlap)
wtr2s += int(
(window_samples_2 - 2 * window_buffer_seconds * sr2_orig) -
(window_samples_2 - 2 * window_buffer_seconds * sr2_orig) *
window_overlap)
# end while (windows within interval)
if (verbose > 1):
if (logger):
logger.info('\tProcessed %d windows in interval %d' %
(windowCount, intervalCount))
# end fi
intervalStartSeconds.append(itr1s / sr1_orig +
tr1.stats.starttime.timestamp)
intervalEndSeconds.append(itr1e / sr1_orig +
tr1.stats.starttime.timestamp)
itr1s = itr1e
itr2s = itr2e
intervalCount += 1
# Append an array of zeros if no windows were processed for the current interval
if (windowCount == 0):
resl.append(np.zeros(fftlen))
if (verbose > 1):
if (logger):
logger.info(
'\tWarning: No windows processed due to gaps in data in current interval'
)
# end if
# end if
windowsPerInterval.append(windowCount)
if (windowCount > 0):
mean = reduce((lambda tx, ty: tx + ty), resl) / float(windowCount)
else:
mean = reduce((lambda tx, ty: tx + ty), resl)
# end if
if (envelope_normalize):
step = np.sign(np.fft.fftfreq(fftlen, 1.0 / sr))
mean = mean + step * mean # compute analytic
# end if
mean = ifftn(mean)
if (envelope_normalize):
# Compute magnitude of mean
mean = np.abs(mean)
normFactor = np.max(mean)
# mean can be 0 for a null result
if (normFactor > 0):
mean /= normFactor
# end if
# end if
resll.append(mean[:xcorlen])
# end while (iteration over intervals)
if (len(resll)):
return np.array(resll), np.array(windowsPerInterval), \
np.array(intervalStartSeconds, dtype='i8'), \
np.array(intervalEndSeconds, dtype='i8'), \
sr
else:
return None, None, None, None, None
def readTSPAIR(filename, headonly=False, **kwargs): # @UnusedVariable
"""
Reads a ASCII TSPAIR file and returns an ObsPy Stream object.
.. warning::
This function should NOT be called directly, it registers via the
ObsPy :func:`~obspy.core.stream.read` function, call this instead.
:type filename: str
:param filename: ASCII file to be read.
:type headonly: bool, optional
:param headonly: If set to True, read only the headers. This is most useful
for scanning available data in huge (temporary) data sets.
:rtype: :class:`~obspy.core.stream.Stream`
:return: A ObsPy Stream object.
.. rubric:: Example
>>> from obspy import read
>>> st = read('/path/to/tspair.ascii')
"""
fh = open(filename, "rt")
# read file and split text into channels
headers = {}
key = None
for line in fh:
if line.isspace():
# blank line
continue
elif line.startswith("TIMESERIES"):
# new header line
key = line
headers[key] = StringIO()
elif headonly:
# skip data for option headonly
continue
elif key:
# data entry - may be written in multiple columns
headers[key].write(line.strip().split()[-1] + " ")
fh.close()
# create ObsPy stream object
stream = Stream()
for header, data in headers.iteritems():
# create Stats
stats = Stats()
parts = header.replace(",", "").split()
temp = parts[1].split("_")
stats.network = temp[0]
stats.station = temp[1]
stats.location = temp[2]
stats.channel = temp[3]
stats.sampling_rate = parts[4]
# quality only used in MSEED
stats.mseed = AttribDict({"dataquality": temp[4]})
stats.ascii = AttribDict({"unit": parts[-1]})
stats.starttime = UTCDateTime(parts[6])
stats.npts = parts[2]
if headonly:
# skip data
stream.append(Trace(header=stats))
else:
data = _parse_data(data, parts[8])
stream.append(Trace(data=data, header=stats))
return stream
def test_delta_zero(self):
"""
Make sure you can set delta = 0. for #1989
"""
stat = Stats()
stat.delta = 0
def create_esm_acc(folder, event, station, num):
"""
ESM recordings can be stored in advance or automatically downloaded from
internet using a token file (:code:`token.txt`). To obtain the token file you need
at first to register at: `https://esm-db.eu/` and then you can run the command::
curl -X POST -F 'message={"user_email": "email","user_password": "******"}
' "https://esm-db.eu/esmws/generate-signed-message/1/query" > token.txt
"""
# Import libraries
import glob
from obspy.core import Stats
import numpy as np
import os
from zipfile import ZipFile
import requests
import sys
if not os.path.isdir(folder):
zip_output = 'output_' + str(num) + '.zip'
params = (
('eventid', event),
('data-type', 'ACC'),
('station', station),
('format', 'ascii'),
)
files = {
'message': ('path/to/token.txt', open('token.txt', 'rb')),
}
headers = {'Authorization': 'token {}'.format('token.txt')}
url = 'https://esm-db.eu/esmws/eventdata/1/query'
req = requests.post(url=url, params=params, files=files)
if req.status_code == 200:
with open(zip_output, "wb") as zf:
zf.write(req.content)
else:
if req.status_code == 403:
sys.exit(
'Problem with ESM download. Maybe the token is no longer valid'
)
else:
sys.exit('Problem with ESM download. Status code: ' +
str(req.status_code))
with ZipFile(zip_output, 'r') as zipObj:
zipObj.extractall(folder)
os.remove(zip_output)
time1 = []
time2 = []
inp_acc1 = []
inp_acc2 = []
npts1 = []
npts2 = []
filename_in = ''
for i in range(1, 3):
if folder.find('ESM/GR') > -1:
file_ew = folder + '/*2.D.*'
file_ns = folder + '/*3.D.*'
else:
file_ew = folder + '/*E.D.*'
file_ns = folder + '/*N.D.*'
if i == 1:
filename_in = glob.glob(file_ew)[0]
if i == 2:
filename_in = glob.glob(file_ns)[0]
headers = {}
# read file
fh = open(filename_in, 'rt')
for j in range(64):
key, value = fh.readline().strip().split(':', 1)
headers[key.strip()] = value.strip()
header = Stats()
header['dyna'] = {}
header['network'] = headers['NETWORK']
header['station'] = headers['STATION_CODE']
header['location'] = headers['LOCATION']
header['channel'] = headers['STREAM']
try:
# use toUTCDateTime to convert from DYNA format
header['starttime'] \
= to_utc_date_time(headers
['DATE_TIME_FIRST_SAMPLE_YYYYMMDD_HHMMSS'])
except ValueError:
header['starttime'] = to_utc_date_time('19700101_000000')
header['sampling_rate'] = 1 / float(headers['SAMPLING_INTERVAL_S'])
header['delta'] = float(headers['SAMPLING_INTERVAL_S'])
header['npts'] = int(headers['NDATA'])
header['calib'] = 1 # not in file header
# DYNA dict float data
header['dyna']['EVENT_LATITUDE_DEGREE'] = strtofloat(
headers['EVENT_LATITUDE_DEGREE'])
header['dyna']['EVENT_LONGITUDE_DEGREE'] = strtofloat(
headers['EVENT_LONGITUDE_DEGREE'])
header['dyna']['EVENT_DEPTH_KM'] = strtofloat(
headers['EVENT_DEPTH_KM'])
header['dyna']['HYPOCENTER_REFERENCE'] = headers[
'HYPOCENTER_REFERENCE']
header['dyna']['MAGNITUDE_W'] = strtofloat(headers['MAGNITUDE_W'])
header['dyna']['MAGNITUDE_L'] = strtofloat(headers['MAGNITUDE_L'])
header['dyna']['STATION_LATITUDE_DEGREE'] = strtofloat(
headers['STATION_LATITUDE_DEGREE'])
header['dyna']['STATION_LONGITUDE_DEGREE'] = strtofloat(
headers['STATION_LONGITUDE_DEGREE'])
header['dyna']['VS30_M_S'] = strtofloat(headers['VS30_M/S'])
header['dyna']['EPICENTRAL_DISTANCE_KM'] = strtofloat(
headers['EPICENTRAL_DISTANCE_KM'])
header['dyna']['EARTHQUAKE_BACKAZIMUTH_DEGREE'] = strtofloat(
headers['EARTHQUAKE_BACKAZIMUTH_DEGREE'])
header['dyna']['DURATION_S'] = strtofloat(headers['DURATION_S'])
header['dyna']['INSTRUMENTAL_FREQUENCY_HZ'] = strtofloat(
headers['INSTRUMENTAL_FREQUENCY_HZ'])
header['dyna']['INSTRUMENTAL_DAMPING'] = strtofloat(
headers['INSTRUMENTAL_DAMPING'])
header['dyna']['FULL_SCALE_G'] = strtofloat(headers['FULL_SCALE_G'])
# data type is acceleration
if headers['DATA_TYPE'] == "ACCELERATION" \
or headers['DATA_TYPE'] == "ACCELERATION RESPONSE SPECTRUM":
header['dyna']['PGA_CM_S_2'] = strtofloat(headers['PGA_CM/S^2'])
header['dyna']['TIME_PGA_S'] = strtofloat(headers['TIME_PGA_S'])
# data type is velocity
if headers['DATA_TYPE'] == "VELOCITY" \
or headers['DATA_TYPE'] == "PSEUDO-VELOCITY RESPONSE SPECTRUM":
header['dyna']['PGV_CM_S'] = strtofloat(headers['PGV_CM/S'])
header['dyna']['TIME_PGV_S'] = strtofloat(headers['TIME_PGV_S'])
# data type is displacement
if headers['DATA_TYPE'] == "DISPLACEMENT" \
or headers['DATA_TYPE'] == "DISPLACEMENT RESPONSE SPECTRUM":
header['dyna']['PGD_CM'] = strtofloat(headers['PGD_CM'])
header['dyna']['TIME_PGD_S'] = strtofloat(headers['TIME_PGD_S'])
header['dyna']['LOW_CUT_FREQUENCY_HZ'] = strtofloat(
headers['LOW_CUT_FREQUENCY_HZ'])
header['dyna']['HIGH_CUT_FREQUENCY_HZ'] = strtofloat(
headers['HIGH_CUT_FREQUENCY_HZ'])
# DYNA dict int data
header['dyna']['STATION_ELEVATION_M'] = strtoint(
headers['STATION_ELEVATION_M'])
header['dyna']['SENSOR_DEPTH_M'] = strtoint(headers['SENSOR_DEPTH_M'])
header['dyna']['N_BIT_DIGITAL_CONVERTER'] = strtoint(
headers['N_BIT_DIGITAL_CONVERTER'])
header['dyna']['FILTER_ORDER'] = strtoint(headers['FILTER_ORDER'])
# DYNA dict string data
header['dyna']['EVENT_NAME'] = headers['EVENT_NAME']
header['dyna']['EVENT_ID'] = headers['EVENT_ID']
header['dyna']['EVENT_DATE_YYYYMMDD'] = headers['EVENT_DATE_YYYYMMDD']
header['dyna']['EVENT_TIME_HHMMSS'] = headers['EVENT_TIME_HHMMSS']
header['dyna']['MAGNITUDE_W_REFERENCE'] = headers[
'MAGNITUDE_W_REFERENCE']
header['dyna']['MAGNITUDE_L_REFERENCE'] = headers[
'MAGNITUDE_L_REFERENCE']
header['dyna']['FOCAL_MECHANISM'] = headers['FOCAL_MECHANISM']
header['dyna']['STATION_NAME'] = headers['STATION_NAME']
header['dyna']['SITE_CLASSIFICATION_EC8'] = headers[
'SITE_CLASSIFICATION_EC8']
header['dyna']['MORPHOLOGIC_CLASSIFICATION'] = headers[
'MORPHOLOGIC_CLASSIFICATION']
header['dyna']['DATE_TIME_FIRST_SAMPLE_PRECISION'] = headers[
'DATE_TIME_FIRST_SAMPLE_PRECISION']
header['dyna']['UNITS'] = headers['UNITS']
header['dyna']['INSTRUMENT'] = headers['INSTRUMENT']
header['dyna']['INSTRUMENT_ANALOG_DIGITAL'] = headers[
'INSTRUMENT_ANALOG/DIGITAL']
header['dyna']['BASELINE_CORRECTION'] = headers['BASELINE_CORRECTION']
header['dyna']['FILTER_TYPE'] = headers['FILTER_TYPE']
header['dyna']['LATE_NORMAL_TRIGGERED'] = headers[
'LATE/NORMAL_TRIGGERED']
header['dyna']['HEADER_FORMAT'] = headers['HEADER_FORMAT']
header['dyna']['DATABASE_VERSION'] = headers['DATABASE_VERSION']
header['dyna']['DATA_TYPE'] = headers['DATA_TYPE']
header['dyna']['PROCESSING'] = headers['PROCESSING']
header['dyna']['DATA_LICENSE'] = headers['DATA_LICENSE']
header['dyna']['DATA_TIMESTAMP_YYYYMMDD_HHMMSS'] = headers[
'DATA_TIMESTAMP_YYYYMMDD_HHMMSS']
header['dyna']['DATA_CITATION'] = headers['DATA_CITATION']
header['dyna']['DATA_CREATOR'] = headers['DATA_CREATOR']
header['dyna']['ORIGINAL_DATA_MEDIATOR_CITATION'] = headers[
'ORIGINAL_DATA_MEDIATOR_CITATION']
header['dyna']['ORIGINAL_DATA_MEDIATOR'] = headers[
'ORIGINAL_DATA_MEDIATOR']
header['dyna']['ORIGINAL_DATA_CREATOR_CITATION'] = headers[
'ORIGINAL_DATA_CREATOR_CITATION']
header['dyna']['ORIGINAL_DATA_CREATOR'] = headers[
'ORIGINAL_DATA_CREATOR']
header['dyna']['USER1'] = headers['USER1']
header['dyna']['USER2'] = headers['USER2']
header['dyna']['USER3'] = headers['USER3']
header['dyna']['USER4'] = headers['USER4']
header['dyna']['USER5'] = headers['USER5']
# read data
acc_data = np.loadtxt(fh, dtype='float32')
fh.close()
time = []
for j in range(0, header['npts']):
t = j * header['delta']
time.append(t)
if i == 1:
inp_acc1 = np.asarray(acc_data) / 981 # in g
# comp1=header['channel']
npts1 = header['npts']
time1 = time
if i == 2:
inp_acc2 = np.asarray(acc_data) / 981 # in g
# comp2=header['channel']
npts2 = header['npts']
time2 = time
return time1, time2, inp_acc1, inp_acc2, npts1, npts2
def _read_tspair(filename, headonly=False, **kwargs): # @UnusedVariable
"""
Reads a ASCII TSPAIR file and returns an ObsPy Stream object.
.. warning::
This function should NOT be called directly, it registers via the
ObsPy :func:`~obspy.core.stream.read` function, call this instead.
:type filename: str
:param filename: ASCII file to be read.
:type headonly: bool, optional
:param headonly: If set to True, read only the headers. This is most useful
for scanning available data in huge (temporary) data sets.
:rtype: :class:`~obspy.core.stream.Stream`
:return: A ObsPy Stream object.
.. rubric:: Example
>>> from obspy import read
>>> st = read('/path/to/tspair.ascii')
"""
with open(filename, 'rt') as fh:
# read file and split text into channels
buf = []
key = False
for line in fh:
if line.isspace():
# blank line
continue
elif line.startswith('TIMESERIES'):
# new header line
key = True
buf.append((line, io.StringIO()))
elif headonly:
# skip data for option headonly
continue
elif key:
# data entry - may be written in multiple columns
buf[-1][1].write(line.strip().split()[-1] + ' ')
# create ObsPy stream object
stream = Stream()
for header, data in buf:
# create Stats
stats = Stats()
parts = header.replace(',', '').split()
temp = parts[1].split('_')
stats.network = temp[0]
stats.station = temp[1]
stats.location = temp[2]
stats.channel = temp[3]
stats.sampling_rate = parts[4]
# quality only used in MSEED
# don't put blank quality code into 'mseed' dictionary
# (quality code is mentioned as optional by format specs anyway)
if temp[4]:
stats.mseed = AttribDict({'dataquality': temp[4]})
stats.ascii = AttribDict({'unit': parts[-1]})
stats.starttime = UTCDateTime(parts[6])
stats.npts = parts[2]
if headonly:
# skip data
stream.append(Trace(header=stats))
else:
data = _parse_data(data, parts[8])
stream.append(Trace(data=data, header=stats))
return stream
def _single_corr_trace_to_obspy_trace(trace):
""" Convert a correlation trace dictionary to an obspy trace.
Convert a single correlation trace in an
:class:`~obspy.core.trace.Trace` object.
:type corr_trace: dictionary of type correlation trace
:param corr_trace: input date to be converted
:rtype: :class:`~obspy.core.trace.Trace`
:return: **tr**: the obspy object containing the data
"""
tr = Trace(data=np.squeeze(trace['corr_trace']))
stats_keys = ['network', 'station', 'location',
'channel', 'npts', 'sampling_rate']
sac_keys = ['baz', 'az', 'stla', 'stlo', 'stel',
'evla', 'evlo', 'evel', 'dist']
# copy stats
for key in stats_keys:
try:
tr.stats[key] = trace['stats'][key]
except:
print 'Error copying key: %s' % key
raise
# special keys
tr.stats['starttime'] = UTCDateTime(
convert_time([trace['stats']['starttime']])[0])
# test for presence of geo information
flag = 0
for key in sac_keys:
if not key in trace['stats']:
flag += 1
if flag == 0: # geo information present
tr.stats['sac'] = {}
for key in sac_keys:
tr.stats['sac'][key] = trace['stats'][key]
# copy stats_tr1
if 'stats_tr1' in trace:
tr.stats_tr1 = Stats()
tr.stats_tr1['starttime'] = UTCDateTime(
convert_time([trace['stats_tr1']['starttime']])[0])
for key in stats_keys:
try:
tr.stats_tr1[key] = trace['stats_tr1'][key]
except:
print 'Error copying key: %s' % key
raise
for key in sac_keys:
try:
tr.stats_tr1[key] = trace['stats_tr1'][key]
except:
pass
# copy stats_tr2
if 'stats_tr2' in trace:
tr.stats_tr2 = Stats()
tr.stats_tr2['starttime'] = UTCDateTime(
convert_time([trace['stats_tr2']['starttime']])[0])
for key in stats_keys:
try:
tr.stats_tr2[key] = trace['stats_tr2'][key]
except:
print 'Error copying key: %s' % key
raise
for key in sac_keys:
try:
tr.stats_tr2[key] = trace['stats_tr2'][key]
except:
pass
return tr
def sac_to_obspy_header(sacheader):
"""
Make an ObsPy Stats header dictionary from a SAC header dictionary.
:param sacheader: SAC header dictionary.
:type sacheader: dict
:rtype: :class:`~obspy.core.Stats`
:return: Filled ObsPy Stats header.
"""
# 1. get required sac header values
try:
npts = sacheader['npts']
delta = sacheader['delta']
except KeyError:
msg = "Incomplete SAC header information to build an ObsPy header."
raise KeyError(msg)
assert npts != HD.INULL
assert delta != HD.FNULL
#
# 2. get time
try:
reftime = get_sac_reftime(sacheader)
except (SacError, ValueError, TypeError):
# ObsPy doesn't require a valid reftime
reftime = UTCDateTime(0.0)
b = sacheader.get('b', HD.FNULL)
#
# 3. get optional sac header values
calib = sacheader.get('scale', HD.FNULL)
kcmpnm = sacheader.get('kcmpnm', HD.SNULL)
kstnm = sacheader.get('kstnm', HD.SNULL)
knetwk = sacheader.get('knetwk', HD.SNULL)
khole = sacheader.get('khole', HD.SNULL)
#
# 4. deal with null values
b = b if (b != HD.FNULL) else 0.0
calib = calib if (calib != HD.FNULL) else 1.0
kcmpnm = kcmpnm if (kcmpnm != HD.SNULL) else ''
kstnm = kstnm if (kstnm != HD.SNULL) else ''
knetwk = knetwk if (knetwk != HD.SNULL) else ''
khole = khole if (khole != HD.SNULL) else ''
#
# 5. transform to obspy values
# nothing is null
stats = {}
stats['npts'] = npts
stats['sampling_rate'] = np.float32(1.) / np.float32(delta)
stats['network'] = _clean_str(knetwk)
stats['station'] = _clean_str(kstnm)
stats['channel'] = _clean_str(kcmpnm)
stats['location'] = _clean_str(khole)
stats['calib'] = calib
# store _all_ provided SAC header values
stats['sac'] = sacheader.copy()
# get first sample absolute time as UTCDateTime
# always add the begin time (if it's defined) to get the given
# SAC reference time, no matter which iztype is given
# b may be non-zero, even for iztype 'ib', especially if it was used to
# store microseconds from obspy_to_sac_header
stats['starttime'] = UTCDateTime(reftime) + b
return Stats(stats)
def _read_seisan(filename, headonly=False, **kwargs): # @UnusedVariable
"""
Reads a SEISAN file and returns an ObsPy Stream object.
.. warning::
This function should NOT be called directly, it registers via the
ObsPy :func:`~obspy.core.stream.read` function, call this instead.
:type filename: str
:param filename: SEISAN file to be read.
:rtype: :class:`~obspy.core.stream.Stream`
:return: A ObsPy Stream object.
.. rubric:: Example
>>> from obspy import read
>>> st = read("/path/to/2001-01-13-1742-24S.KONO__004")
>>> st # doctest: +ELLIPSIS
<obspy.core.stream.Stream object at 0x...>
>>> print(st) # doctest: +ELLIPSIS
4 Trace(s) in Stream:
.KONO.0.B0Z | 2001-01-13T17:45:01.999000Z - ... | 20.0 Hz, 6000 samples
.KONO.0.L0Z | 2001-01-13T17:42:24.924000Z - ... | 1.0 Hz, 3542 samples
.KONO.0.L0N | 2001-01-13T17:42:24.924000Z - ... | 1.0 Hz, 3542 samples
.KONO.0.L0E | 2001-01-13T17:42:24.924000Z - ... | 1.0 Hz, 3542 samples
"""
# get version info from event file header (at least 12*80 bytes)
fh = open(filename, 'rb')
data = fh.read(80 * 12)
(byteorder, arch, version) = _get_version(data)
dlen = arch // 8
dtype = np.dtype(native_str(byteorder + 'i' + str(dlen)))
stype = native_str('=i' + str(dlen))
def _readline(fh, version=version, dtype=dtype):
if version >= 7:
# On Sun, Linux, MaxOSX and PC from version 7.0 (using Digital
# Fortran), every write is preceded and terminated with 4
# additional bytes giving the number of bytes in the write.
# With 64 bit systems, 8 bytes is used to define number of bytes
# written.
start_bytes = fh.read(dtype.itemsize)
# convert to int32/int64
length = np.fromstring(start_bytes, dtype=dtype)[0]
data = fh.read(length)
end_bytes = fh.read(dtype.itemsize)
assert start_bytes == end_bytes
return data
else: # version <= 6
# Every write is preceded and terminated with one byte giving the
# number of bytes in the write. If the write contains more than 128
# bytes, it is blocked in records of 128 bytes, each with the start
# and end byte which in this case is the number 128. Each record is
# thus 130 bytes long.
data = b''
while True:
start_byte = fh.read(1)
if not start_byte:
# end of file
break
# convert to unsigned int8
length = np.fromstring(start_byte, np.uint8)[0]
data += fh.read(length)
end_byte = fh.read(1)
assert start_byte == end_byte
if length == 128:
# blocked data - repeat loop
continue
# end of blocked data
break
return data
# reset file pointer
if version >= 7:
fh.seek(0)
else:
# version <= 6 starts with first byte K
fh.seek(1)
# event file header
# line 1
data = _readline(fh)
number_of_channels = int(data[30:33])
# calculate number of lines with channels
number_of_lines = number_of_channels // 3 + (number_of_channels % 3 and 1)
if number_of_lines < 10:
number_of_lines = 10
# line 2 - always empty
data = _readline(fh)
# line 3
for _i in range(0, number_of_lines):
data = _readline(fh)
# now parse each event file channel header + data
stream = Stream()
for _i in range(number_of_channels):
# get channel header
temp = _readline(fh).decode()
# create Stats
header = Stats()
header['network'] = (temp[16] + temp[19]).strip()
header['station'] = temp[0:5].strip()
header['location'] = (temp[7] + temp[12]).strip()
header['channel'] = (temp[5:7] + temp[8]).strip()
header['sampling_rate'] = float(temp[36:43])
header['npts'] = int(temp[43:50])
# create start and end times
year = int(temp[9:12]) + 1900
month = int(temp[17:19])
day = int(temp[20:22])
hour = int(temp[23:25])
mins = int(temp[26:28])
secs = float(temp[29:35])
header['starttime'] = UTCDateTime(year, month, day, hour, mins) + secs
if headonly:
# skip data
from_buffer(_readline(fh), dtype=dtype)
stream.append(Trace(header=header))
else:
# fetch data
data = from_buffer(_readline(fh), dtype=dtype)
# convert to system byte order
data = np.require(data, stype)
if header['npts'] != len(data):
msg = "Mismatching byte size %d != %d"
warnings.warn(msg % (header['npts'], len(data)))
stream.append(Trace(data=data, header=header))
fh.close()
return stream
def readSLIST(filename, headonly=False, **kwargs): # @UnusedVariable
"""
Reads a ASCII SLIST file and returns an ObsPy Stream object.
.. warning::
This function should NOT be called directly, it registers via the
ObsPy :func:`~obspy.core.stream.read` function, call this instead.
:type filename: str
:param filename: ASCII file to be read.
:type headonly: bool, optional
:param headonly: If set to True, read only the head. This is most useful
for scanning available data in huge (temporary) data sets.
:rtype: :class:`~obspy.core.stream.Stream`
:return: A ObsPy Stream object.
.. rubric:: Example
>>> from obspy.core import read
>>> st = read('/path/to/slist.ascii')
"""
fh = open(filename, 'rt')
# read file and split text into channels
headers = {}
key = None
for line in fh:
if line.isspace():
# blank line
continue
elif line.startswith('TIMESERIES'):
# new header line
key = line
headers[key] = StringIO()
elif headonly:
# skip data for option headonly
continue
elif key:
# data entry - may be written in multiple columns
headers[key].write(line.strip() + ' ')
fh.close()
# create ObsPy stream object
stream = Stream()
for header, data in headers.iteritems():
# create Stats
stats = Stats()
parts = header.replace(',', '').split()
temp = parts[1].split('_')
stats.network = temp[0]
stats.station = temp[1]
stats.location = temp[2]
stats.channel = temp[3]
stats.sampling_rate = parts[4]
# quality only used in MSEED
stats.mseed = AttribDict({'dataquality': temp[4]})
stats.ascii = AttribDict({'unit': parts[-1]})
stats.starttime = UTCDateTime(parts[6])
stats.npts = parts[2]
if headonly:
# skip data
stream.append(Trace(header=stats))
else:
# parse data
data.seek(0)
if parts[8] == 'INTEGER':
data = loadtxt(data, dtype='int', ndlim=1)
elif parts[8] == 'FLOAT':
data = loadtxt(data, dtype='float32', ndlim=1)
else:
raise NotImplementedError
stream.append(Trace(data=data, header=stats))
return stream
#plt.savefig("lin688_similarity2.png", dpi=250)
#trace = extract_trace(segy, 688, 390).data
#%%
################################### Write data ###########################
#write
from obspy.core import AttribDict
from obspy.core import Stats
from obspy.core import Trace, Stream
from obspy.io.segy.segy import SEGYBinaryFileHeader
from obspy.io.segy.segy import SEGYTraceHeader
out = Stream(Trace(t, header=dict(delta=dt)) for t in data)
out.stats = Stats(dict(textual_file_header=segy.textual_file_header))
# out.stats.textual_file_header += """energy volume.
# Generated: 18 Sep 2016 by Matt Hall [email protected].
# Algorithm: github.com/agile-geoscience/bruges.attribute.similarity.
# Parameters: duration=0.16 s, dt=0.002 s.""".encode('utf-8')
out.write('out1.sgy', format='SEGY', data_encoding=1)
#encode 1 for IBM,5 for IEEE
#%%
##################### Validate the output data ##########################
s = _read_segy('out1.sgy', headonly=True)
s.textual_file_header[:15 * 80] # First 15 lines.
s.traces[0].header
segy.traces[0].data.shape
d = np.arange(751)
def test_ppsd_restricted_stacks(self):
"""
Test PPSD.calculate_histogram() with restrictions to what data should
be stacked. Also includes image tests.
"""
# set up a bogus PPSD, with fixed random psds but with real start times
# of psd pieces, to facilitate testing the stack selection.
ppsd = PPSD(stats=Stats(dict(sampling_rate=150)),
metadata=None,
db_bins=(-200, -50, 20.),
period_step_octaves=1.4)
# change data to nowadays used nanoseconds POSIX timestamp
ppsd._times_processed = [
UTCDateTime(t)._ns for t in np.load(
os.path.join(self.path, "ppsd_times_processed.npy")).tolist()
]
np.random.seed(1234)
ppsd._binned_psds = [
arr for arr in np.random.uniform(-200, -50, (
len(ppsd._times_processed), len(ppsd.period_bin_centers)))
]
# Test callback function that selects a fixed random set of the
# timestamps. Also checks that we get passed the type we expect,
# which is 1D numpy ndarray of int type.
def callback(t_array):
self.assertIsInstance(t_array, np.ndarray)
self.assertEqual(t_array.shape, (len(ppsd._times_processed), ))
self.assertTrue(np.issubdtype(t_array.dtype, np.integer))
np.random.seed(1234)
res = np.random.randint(0, 2, len(t_array)).astype(np.bool)
return res
# test several different sets of stack criteria, should cover
# everything, even with lots of combined criteria
stack_criteria_list = [
dict(starttime=UTCDateTime(2015, 3, 8), month=[2, 3, 5, 7, 8]),
dict(endtime=UTCDateTime(2015, 6, 7),
year=[2015],
time_of_weekday=[(1, 0, 24), (2, 0, 24), (-1, 0, 11)]),
dict(year=[2013, 2014, 2016, 2017], month=[2, 3, 4]),
dict(month=[1, 2, 5, 6, 8], year=2015),
dict(isoweek=[4, 5, 6, 13, 22, 23, 24, 44, 45]),
dict(time_of_weekday=[(5, 22, 24), (6, 0, 2), (6, 22, 24)]),
dict(callback=callback, month=[1, 3, 5, 7]),
dict(callback=callback)
]
expected_selections = np.load(
os.path.join(self.path, "ppsd_stack_selections.npy"))
# test every set of criteria
for stack_criteria, expected_selection in zip(stack_criteria_list,
expected_selections):
selection_got = ppsd._stack_selection(**stack_criteria)
np.testing.assert_array_equal(selection_got, expected_selection)
# test one particular selection as an image test
plot_kwargs = dict(max_percentage=15,
xaxis_frequency=True,
period_lim=(0.01, 50))
ppsd.calculate_histogram(**stack_criteria_list[1])
with ImageComparison(self.path_images,
'ppsd_restricted_stack.png',
reltol=1.5) as ic:
fig = ppsd.plot(show=False, **plot_kwargs)
# some matplotlib/Python version combinations lack the left-most
# tick/label "Jan 2015". Try to circumvent and get the (otherwise
# OK) test by changing the left x limit a bit further out (by two
# days, axis is in mpl days). See e.g.
# https://tests.obspy.org/30657/#1
fig.axes[1].set_xlim(left=fig.axes[1].get_xlim()[0] - 2)
with np.errstate(under='ignore'):
fig.savefig(ic.name)
# test it again, checking that updating an existing plot with different
# stack selection works..
# a) we start with the stack for the expected image and test that it
# matches (like above):
ppsd.calculate_histogram(**stack_criteria_list[1])
with ImageComparison(self.path_images,
'ppsd_restricted_stack.png',
reltol=1.5,
plt_close_all_exit=False) as ic:
fig = ppsd.plot(show=False, **plot_kwargs)
# some matplotlib/Python version combinations lack the left-most
# tick/label "Jan 2015". Try to circumvent and get the (otherwise
# OK) test by changing the left x limit a bit further out (by two
# days, axis is in mpl days). See e.g.
# https://tests.obspy.org/30657/#1
fig.axes[1].set_xlim(left=fig.axes[1].get_xlim()[0] - 2)
with np.errstate(under='ignore'):
fig.savefig(ic.name)
# b) now reuse figure and set the histogram with a different stack,
# image test should fail:
ppsd.calculate_histogram(**stack_criteria_list[3])
try:
with ImageComparison(self.path_images,
'ppsd_restricted_stack.png',
adjust_tolerance=False,
plt_close_all_enter=False,
plt_close_all_exit=False) as ic:
# rms of the valid comparison above is ~31,
# rms of the invalid comparison we test here is ~36
if MATPLOTLIB_VERSION == [1, 1, 1]:
ic.tol = 33
ppsd._plot_histogram(fig=fig, draw=True)
with np.errstate(under='ignore'):
fig.savefig(ic.name)
except ImageComparisonException:
pass
else:
msg = "Expected ImageComparisonException was not raised."
self.fail(msg)
# c) now reuse figure and set the original histogram stack again,
# image test should pass agin:
ppsd.calculate_histogram(**stack_criteria_list[1])
with ImageComparison(self.path_images,
'ppsd_restricted_stack.png',
reltol=1.5,
plt_close_all_enter=False) as ic:
ppsd._plot_histogram(fig=fig, draw=True)
with np.errstate(under='ignore'):
fig.savefig(ic.name)
def test_delta_zero(self):
"""
Make sure you can set delta = 0. for #1989
"""
stat = Stats()
stat.delta = 0
def readSLIST(filename, headonly=False, **kwargs): # @UnusedVariable
"""
Reads a ASCII SLIST file and returns an ObsPy Stream object.
.. warning::
This function should NOT be called directly, it registers via the
ObsPy :func:`~obspy.core.stream.read` function, call this instead.
:type filename: str
:param filename: ASCII file to be read.
:type headonly: bool, optional
:param headonly: If set to True, read only the head. This is most useful
for scanning available data in huge (temporary) data sets.
:rtype: :class:`~obspy.core.stream.Stream`
:return: A ObsPy Stream object.
.. rubric:: Example
>>> from obspy import read
>>> st = read('/path/to/slist.ascii')
"""
with open(filename, 'rt') as fh:
# read file and split text into channels
buf = []
key = False
for line in fh:
if line.isspace():
# blank line
continue
elif line.startswith('TIMESERIES'):
# new header line
key = True
buf.append((line, StringIO()))
elif headonly:
# skip data for option headonly
continue
elif key:
# data entry - may be written in multiple columns
buf[-1][1].write(line.strip() + ' ')
# create ObsPy stream object
stream = Stream()
for header, data in buf:
# create Stats
stats = Stats()
parts = header.replace(',', '').split()
temp = parts[1].split('_')
stats.network = temp[0]
stats.station = temp[1]
stats.location = temp[2]
stats.channel = temp[3]
stats.sampling_rate = parts[4]
# quality only used in MSEED
stats.mseed = AttribDict({'dataquality': temp[4]})
stats.ascii = AttribDict({'unit': parts[-1]})
stats.starttime = UTCDateTime(parts[6])
stats.npts = parts[2]
if headonly:
# skip data
stream.append(Trace(header=stats))
else:
data = _parse_data(data, parts[8])
stream.append(Trace(data=data, header=stats))
return stream
def combine_stats(tr1, tr2):
""" Combine the meta-information of two ObsPy Trace objects
This function returns a ObsPy :class:`~obspy.core.trace.Stats` object
obtained combining the two associated with the input Traces.
Namely ``tr1.stats`` and ``tr2.stats``.
The fields ['network','station','location','channel'] are combined in
a ``-`` separated fashion to create a "pseudo" SEED like ``id``.
For all the others fields, only "common" information are retained: This
means that only keywords that exist in both dictionaries will be included
in the resulting one.
:type tr1: :class:`~obspy.core.trace.Trace`
:param tr1: First Trace
:type tr2: :class:`~obspy.core.trace.Trace`
:param tr2: Second Trace
:rtype: :class:`~obspy.core.trace.Stats`
:return: **stats**: combined Stats object
"""
if not isinstance(tr1, Trace):
raise TypeError("tr1 must be an obspy Trace object.")
if not isinstance(tr2, Trace):
raise TypeError("tr2 must be an obspy Trace object.")
tr1_keys = tr1.stats.keys()
tr2_keys = tr2.stats.keys()
stats = Stats()
# Adjust the information to create a new SEED like id
keywords = ['network', 'station', 'location', 'channel']
sac_keywords = ['sac']
for key in keywords:
if key in tr1_keys and key in tr2_keys:
stats[key] = tr1.stats[key] + '-' + tr2.stats[key]
for key in tr1_keys:
if key not in keywords and key not in sac_keywords:
if key in tr2_keys:
if tr1.stats[key] == tr2.stats[key]:
# in the stats object there are read only objects
try:
stats[key] = tr1.stats[key]
except AttributeError:
pass
try:
stats['sac'] = {}
stats.sac['stla'] = tr1.stats.sac.stla
stats.sac['stlo'] = tr1.stats.sac.stlo
stats.sac['stel'] = tr1.stats.sac.stel
stats.sac['evla'] = tr2.stats.sac.stla
stats.sac['evlo'] = tr2.stats.sac.stlo
stats.sac['evel'] = tr2.stats.sac.stel
az, baz, dist = trace_calc_az_baz_dist(tr1, tr2)
stats.sac['dist'] = dist / 1000
stats.sac['az'] = az
stats.sac['baz'] = baz
except AttributeError:
stats.pop('sac')
print "No station coordinates provided."
return stats
