/
test_mseed_special_issues.py
1257 lines (1122 loc) · 49.5 KB
/
test_mseed_special_issues.py
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# -*- coding: utf-8 -*-
import ctypes as C # NOQA
import io
import multiprocessing
import os
import platform
import random
import signal
import sys
import unittest
import warnings
from unittest import mock
import numpy as np
from obspy import Stream, Trace, UTCDateTime, read
from obspy.core.compatibility import from_buffer
from obspy.core.util import NamedTemporaryFile
from obspy.core.util.attribdict import AttribDict
from obspy.core.util.testing import WarningsCapture
from obspy.io.mseed import (InternalMSEEDError, InternalMSEEDWarning,
ObsPyMSEEDFilesizeTooSmallError,
ObsPyMSEEDFilesizeTooLargeError)
from obspy.io.mseed import util
from obspy.io.mseed.core import _read_mseed, _write_mseed
from obspy.io.mseed.headers import clibmseed
from obspy.io.mseed.msstruct import _MSStruct
# some Python version don't support negative timestamps
NO_NEGATIVE_TIMESTAMPS = False
try:
UTCDateTime(-50000)
except Exception:
NO_NEGATIVE_TIMESTAMPS = True
def _test_function(filename):
"""
Internal function used by MSEEDSpecialIssueTestCase.test_infinite_loop
"""
with warnings.catch_warnings(record=True):
warnings.simplefilter("always")
try:
st = read(filename) # noqa @UnusedVariable
except (ValueError, InternalMSEEDError):
# Should occur with broken files
pass
class MSEEDSpecialIssueTestCase(unittest.TestCase):
"""
"""
def setUp(self):
# Directory where the test files are located
self.path = os.path.dirname(__file__)
# mseed steim compression is big endian
if sys.byteorder == 'little':
self.swap = 1
else:
self.swap = 0
def test_invalid_record_length(self):
"""
An invalid record length should raise an exception.
"""
npts = 6000
np.random.seed(815) # make test reproducible
with NamedTemporaryFile() as tf:
tempfile = tf.name
data = np.random.randint(-1000, 1000, npts).astype(np.int32)
st = Stream([Trace(data=data)])
# Writing should fail with invalid record lengths.
# Not a power of 2.
self.assertRaises(ValueError, _write_mseed, st, tempfile,
format="MSEED", reclen=1000)
# Too small.
self.assertRaises(ValueError, _write_mseed, st, tempfile,
format="MSEED", reclen=8)
# Not a number.
self.assertRaises(ValueError, _write_mseed, st, tempfile,
format="MSEED", reclen='A')
def test_invalid_encoding(self):
"""
An invalid encoding should raise an exception.
"""
npts = 6000
np.random.seed(815) # make test reproducible
with NamedTemporaryFile() as tf:
tempfile = tf.name
data = np.random.randint(-1000, 1000, npts).astype(np.int32)
st = Stream([Trace(data=data)])
# Writing should fail with invalid record lengths.
# Wrong number.
self.assertRaises(ValueError, _write_mseed, st, tempfile,
format="MSEED", encoding=2)
# Wrong Text.
self.assertRaises(ValueError, _write_mseed, st, tempfile,
format="MSEED", encoding='FLOAT_64')
def test_ctypes_arg_types(self):
"""
Test that ctypes argtypes are set for type checking
"""
argument_error = C.ArgumentError
cl = clibmseed
args = [C.pointer(C.pointer(C.c_int())), 'a', 1, 1.5, 1, 0, 0, 0, 0]
self.assertRaises(argument_error, cl.ms_readtraces, *args)
self.assertRaises(TypeError, cl.ms_readtraces, *args[:-1])
self.assertRaises(argument_error, cl.ms_readmsr_r, *args)
self.assertRaises(TypeError, cl.ms_readmsr_r, *args[:-1])
self.assertRaises(argument_error, cl.mst_printtracelist, *args[:5])
self.assertRaises(argument_error, cl.ms_detect, *args[:4])
args.append(1) # 10 argument function
self.assertRaises(argument_error, cl.mst_packgroup, *args)
args = ['hallo'] # one argument functions
self.assertRaises(argument_error, cl.msr_starttime, *args)
self.assertRaises(argument_error, cl.msr_endtime, *args)
self.assertRaises(argument_error, cl.mst_init, *args)
self.assertRaises(argument_error, cl.mst_free, *args)
self.assertRaises(argument_error, cl.mst_initgroup, *args)
self.assertRaises(argument_error, cl.mst_freegroup, *args)
self.assertRaises(argument_error, cl.msr_init, *args)
def test_broken_last_record(self):
"""
Test if Libmseed is able to read files with broken last record. Use
both methods, readMSTracesViaRecords and readMSTraces
"""
file = os.path.join(self.path, "data", "brokenlastrecord.mseed")
# independent reading of the data, 128 Bytes header
d = np.fromfile(file, dtype=np.uint8)[128:]
data = util._unpack_steim_2(d, 5980, swapflag=self.swap,
verbose=0)
# test readMSTraces. Will raise an internal warning.
with WarningsCapture() as w:
data_record = _read_mseed(file)[0].data
# This will raise 18 (!) warnings. It will skip 17 * 128 bytes due
# to it not being a SEED records and then complain that the remaining
# 30 bytes are not enough to constitute a full SEED record.
self.assertEqual(len(w), 18)
self.assertEqual(w[0].category, InternalMSEEDWarning)
# Test against reference data.
self.assertEqual(len(data_record), 5980)
last10samples = [2862, 2856, 2844, 2843, 2851,
2853, 2853, 2854, 2857, 2863]
np.testing.assert_array_equal(data_record[-10:], last10samples)
# Also test against independently unpacked data.
np.testing.assert_allclose(data_record, data)
def test_one_sample_overlap(self):
"""
Both methods readMSTraces and readMSTracesViaRecords should recognize a
single sample overlap.
"""
# create a stream with one sample overlapping
trace1 = Trace(data=np.zeros(1000))
trace2 = Trace(data=np.zeros(10))
trace2.stats.starttime = UTCDateTime(999)
st = Stream([trace1, trace2])
# write into MSEED
with NamedTemporaryFile() as tf:
tempfile = tf.name
_write_mseed(st, tempfile, format="MSEED")
# read it again
new_stream = _read_mseed(tempfile)
self.assertEqual(len(new_stream), 2)
def test_bug_write_read_float32_seed_win32(self):
"""
Test case for issue #64.
"""
# create stream object
data = np.array([395.07809448, 395.0782, 1060.28112793, -1157.37487793,
-1236.56237793, 355.07028198, -1181.42175293],
dtype=np.float32)
st = Stream([Trace(data=data)])
with NamedTemporaryFile() as tf:
tempfile = tf.name
_write_mseed(st, tempfile, format="MSEED")
# read temp file directly without libmseed
with open(tempfile, 'rb') as fp:
fp.seek(56)
dtype = np.dtype('>f4')
bin_data = from_buffer(fp.read(7 * dtype.itemsize),
dtype=dtype)
np.testing.assert_array_equal(data, bin_data)
# read via ObsPy
st2 = _read_mseed(tempfile)
# test results
np.testing.assert_array_equal(data, st2[0].data)
@unittest.skipIf(NO_NEGATIVE_TIMESTAMPS,
'times before 1970 are not supported on this operation '
'system')
def test_write_with_date_time_before_1970(self):
"""
Write an stream via libmseed with a datetime before 1970.
This test depends on the platform specific localtime()/gmtime()
function.
"""
# create trace
tr = Trace(data=np.empty(1000))
tr.stats.starttime = UTCDateTime("1969-01-01T00:00:00")
# write file
with NamedTemporaryFile() as tf:
tempfile = tf.name
_write_mseed(Stream([tr]), tempfile, format="MSEED")
# read again
stream = _read_mseed(tempfile)
stream.verify()
def test_invalid_data_type(self):
"""
Writing data of type int64 and int8 are not supported.
int64 data can now be written since #2356 if it can be downcast to
int32.
"""
npts = 6000
np.random.seed(815) # make test reproducible
with NamedTemporaryFile() as tf:
tempfile = tf.name
# int64
data = np.random.randint(-1000, 1000, npts).astype(np.int64)
# add a data point that can not be downcast (even though we have a
# separate test for this)
data[4] = np.iinfo(np.int32).max + 2
st = Stream([Trace(data=data)])
self.assertRaises(Exception, st.write, tempfile, format="MSEED")
# int8
data = np.random.randint(-1000, 1000, npts).astype(np.int8)
st = Stream([Trace(data=data)])
self.assertRaises(Exception, st.write, tempfile, format="MSEED")
def test_write_wrong_encoding(self):
"""
Test to write a floating point mseed file with encoding STEIM1.
An exception should be raised.
"""
file = os.path.join(self.path, "data",
"BW.BGLD.__.EHE.D.2008.001.first_record")
with NamedTemporaryFile() as tf:
tempfile = tf.name
# Read the data and convert them to float
st = read(file)
st[0].data = st[0].data.astype(np.float32) + .5
# Type is not consistent float32 cannot be compressed with STEIM1,
# therefore a exception should be raised.
self.assertRaises(Exception, st.write, tempfile, format="MSEED",
encoding=10)
def test_write_wrong_encoding_via_mseed_stats(self):
"""
Test to write a floating point mseed file with encoding STEIM1 with the
encoding set in stats.mseed.encoding.
This will just raise a warning.
"""
file = os.path.join(self.path, "data",
"BW.BGLD.__.EHE.D.2008.001.first_record")
with NamedTemporaryFile() as tf:
tempfile = tf.name
# Read the data and convert them to float
st = read(file)
st[0].data = st[0].data.astype(np.float32) + .5
# Type is not consistent float32 cannot be compressed with STEIM1,
# therefore a warning should be raised.
self.assertEqual(st[0].stats.mseed.encoding, 'STEIM1')
with warnings.catch_warnings(record=True):
warnings.simplefilter('error', UserWarning)
self.assertRaises(UserWarning, st.write, tempfile,
format="MSEED")
def test_wrong_record_length_as_argument(self):
"""
Specifying a wrong record length should raise an error.
"""
file = os.path.join(self.path, 'data', 'encoding',
'float32_Float32_bigEndian.mseed')
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
# invalid reclen
read(file, reclen=111)
self.assertTrue('Invalid record length' in str(w[0].message))
self.assertEqual(w[0].category, UserWarning)
# wrong reclen - raises and also displays a warning
self.assertRaises(Exception, read, file, reclen=4096)
self.assertTrue('reclen exceeds buflen' in str(w[1].message))
self.assertEqual(w[1].category, InternalMSEEDWarning)
def test_read_with_missing_blockette010(self):
"""
Reading a Full/Mini-SEED w/o blockette 010 but blockette 008.
"""
# 1 - Mini-SEED
file = os.path.join(self.path, 'data', 'blockette008.mseed')
tr = read(file)[0]
self.assertEqual('BW.PART..EHZ', tr.id)
self.assertEqual(1642, tr.stats.npts)
# 2 - full SEED
file = os.path.join(self.path, 'data',
'RJOB.BW.EHZ.D.300806.0000.fullseed')
tr = read(file)[0]
self.assertEqual('BW.RJOB..EHZ', tr.id)
self.assertEqual(412, tr.stats.npts)
def test_issue160(self):
"""
Tests issue #160.
Reading the header of SEED file.
"""
file = os.path.join(self.path, 'data',
'BW.BGLD.__.EHE.D.2008.001.first_10_records')
tr_one = read(file)[0]
tr_two = read(file, headonly=True)[0]
ms = AttribDict({'record_length': 512, 'encoding': 'STEIM1',
'filesize': 5120, 'dataquality': 'D',
'number_of_records': 10, 'byteorder': '>'})
for tr in tr_one, tr_two:
self.assertEqual('BW.BGLD..EHE', tr.id)
self.assertEqual(ms, tr.stats.mseed)
self.assertEqual(4120, tr.stats.npts)
self.assertEqual(UTCDateTime(2008, 1, 1, 0, 0, 20, 510000),
tr.stats.endtime)
def test_issue217(self):
"""
Tests issue #217.
Reading a MiniSEED file without sequence numbers and a record length of
1024.
"""
file = os.path.join(self.path, 'data',
'reclen_1024_without_sequence_numbers.mseed')
tr = read(file)[0]
ms = AttribDict({'record_length': 1024, 'encoding': 'STEIM1',
'filesize': 2048, 'dataquality': 'D',
'number_of_records': 2, 'byteorder': '>'})
self.assertEqual('XX.STF1..HHN', tr.id)
self.assertEqual(ms, tr.stats.mseed)
self.assertEqual(932, tr.stats.npts)
self.assertEqual(UTCDateTime(2007, 5, 31, 22, 45, 46, 720000),
tr.stats.endtime)
def test_issue296(self):
"""
Tests issue #296.
"""
with NamedTemporaryFile() as tf:
tempfile = tf.name
# 1 - transform to np.float64 values
st = read()
for tr in st:
tr.data = tr.data.astype(np.float64)
# write a single trace automatically detecting encoding
st[0].write(tempfile, format="MSEED")
# write a single trace automatically detecting encoding
st.write(tempfile, format="MSEED")
# write a single trace with encoding 5
st[0].write(tempfile, format="MSEED", encoding=5)
# write a single trace with encoding 5
st.write(tempfile, format="MSEED", encoding=5)
# 2 - transform to np.float32 values
st = read()
for tr in st:
tr.data = tr.data.astype(np.float32)
# write a single trace automatically detecting encoding
st[0].write(tempfile, format="MSEED")
# write a single trace automatically detecting encoding
st.write(tempfile, format="MSEED")
# write a single trace with encoding 4
st[0].write(tempfile, format="MSEED", encoding=4)
# write a single trace with encoding 4
st.write(tempfile, format="MSEED", encoding=4)
# 3 - transform to np.int32 values
st = read()
for tr in st:
tr.data = tr.data.astype(np.int32)
# write a single trace automatically detecting encoding
st[0].write(tempfile, format="MSEED")
# write a single trace automatically detecting encoding
st.write(tempfile, format="MSEED")
# write a single trace with encoding 3
st[0].write(tempfile, format="MSEED", encoding=3)
# write the whole stream with encoding 3
st.write(tempfile, format="MSEED", encoding=3)
# write a single trace with encoding 10
st[0].write(tempfile, format="MSEED", encoding=10)
# write the whole stream with encoding 10
st.write(tempfile, format="MSEED", encoding=10)
# write a single trace with encoding 11
st[0].write(tempfile, format="MSEED", encoding=11)
# write the whole stream with encoding 11
st.write(tempfile, format="MSEED", encoding=11)
# 4 - transform to np.int16 values
st = read()
for tr in st:
tr.data = tr.data.astype(np.int16)
# write a single trace automatically detecting encoding
st[0].write(tempfile, format="MSEED")
# write a single trace automatically detecting encoding
st.write(tempfile, format="MSEED")
# write a single trace with encoding 1
st[0].write(tempfile, format="MSEED", encoding=1)
# write the whole stream with encoding 1
st.write(tempfile, format="MSEED", encoding=1)
# 5 - transform to ASCII values
st = read()
for tr in st:
tr.data = tr.data.astype('|S1')
# write a single trace automatically detecting encoding
st[0].write(tempfile, format="MSEED")
# write a single trace automatically detecting encoding
st.write(tempfile, format="MSEED")
# write a single trace with encoding 0
st[0].write(tempfile, format="MSEED", encoding=0)
# write the whole stream with encoding 0
st.write(tempfile, format="MSEED", encoding=0)
def test_issue289(self):
"""
Tests issue #289.
Reading MiniSEED using start/end time outside of data should result in
an empty Stream object.
"""
# 1
file = os.path.join(self.path, 'data', 'steim2.mseed')
st = read(file, starttime=UTCDateTime() - 10, endtime=UTCDateTime())
self.assertEqual(len(st), 0)
# 2
file = os.path.join(self.path, 'data', 'fullseed.mseed')
st = read(file, starttime=UTCDateTime() - 10, endtime=UTCDateTime())
self.assertEqual(len(st), 0)
def test_issue312(self):
"""
Tests issue #312
The blkt_link struct was defined wrong.
"""
filename = os.path.join(self.path, 'data',
'BW.BGLD.__.EHE.D.2008.001.first_10_records')
# start and end time
ms = _MSStruct(filename)
ms.read(-1, 0, 1, 0)
blkt_link = ms.msr.contents.blkts.contents
# The first blockette usually begins after 48 bytes. In the test file
# it does.
self.assertEqual(blkt_link.blktoffset, 48)
# The first blockette is blockette 1000 in this file.
self.assertEqual(blkt_link.blkt_type, 1000)
# Only one blockette.
self.assertEqual(blkt_link.next_blkt, 0)
# Blockette data is 8 bytes - 4 bytes for the blockette header.
self.assertEqual(blkt_link.blktdatalen, 4)
del ms
def test_issue272(self):
"""
Tests issue #272
Option headonly should not read the actual waveform data.
"""
filename = os.path.join(self.path, 'data',
'BW.BGLD.__.EHE.D.2008.001.first_10_records')
# everything
st = read(filename)
self.assertEqual(st[0].stats.npts, 4120)
self.assertEqual(len(st[0].data), 4120)
# headers only
st = read(filename, headonly=True)
self.assertEqual(st[0].stats.npts, 4120)
self.assertEqual(len(st[0].data), 0)
def test_issue325(self):
"""
Tests issue #325: Use selection with non default dataquality flag.
"""
filename = os.path.join(self.path, 'data', 'dataquality-m.mseed')
# 1 - read all
st = read(filename)
self.assertEqual(len(st), 3)
t1 = st[0].stats.starttime
t2 = st[0].stats.endtime
# 2 - select full time window
st2 = read(filename, starttime=t1, endtime=t2)
self.assertEqual(len(st2), 3)
for tr in st2:
del tr.stats.processing
self.assertEqual(st, st2)
# 3 - use selection
st2 = read(filename, starttime=t1, endtime=t2, sourcename='*.*.*.*')
self.assertEqual(len(st2), 3)
for tr in st2:
del tr.stats.processing
self.assertEqual(st, st2)
st2 = read(filename, starttime=t1, endtime=t2, sourcename='*')
self.assertEqual(len(st2), 3)
for tr in st2:
del tr.stats.processing
self.assertEqual(st, st2)
# 4 - selection without times
st2 = read(filename, sourcename='*.*.*.*')
self.assertEqual(len(st2), 3)
self.assertEqual(st, st2)
st2 = read(filename, sourcename='*')
self.assertEqual(len(st2), 3)
self.assertEqual(st, st2)
def test_issue332(self):
"""
Tests issue #332
Writing traces with wrong encoding in stats should raise only a user
warning.
"""
with NamedTemporaryFile() as tf:
tempfile = tf.name
st = read()
tr = st[0]
tr.data = tr.data.astype(np.float64) + .5
tr.stats.mseed = {'encoding': 0}
with warnings.catch_warnings(record=True):
warnings.simplefilter('error', UserWarning)
self.assertRaises(UserWarning, st.write, tempfile,
format="MSEED")
def test_issue341(self):
"""
Tests issue #341
Read/write of MiniSEED files with huge sampling rates/delta values.
"""
with NamedTemporaryFile() as tf:
tempfile = tf.name
# 1 - sampling rate
st = read()
tr = st[0]
tr.stats.sampling_rate = 1000000000.0
tr.write(tempfile, format="MSEED")
# read again
st = read(tempfile)
self.assertEqual(st[0].stats.sampling_rate, 1000000000.0)
# 2 - delta
st = read()
tr = st[0]
tr.stats.delta = 10000000.0
tr.write(tempfile, format="MSEED")
# read again
st = read(tempfile)
self.assertAlmostEqual(st[0].stats.delta, 10000000.0, 0)
def test_issue485(self):
"""
Test reading floats and doubles, which are bytswapped nans
"""
ref = [-1188.07800293, 638.16400146, 395.07809448, 1060.28112793]
for filename in ('nan_float32.mseed', 'nan_float64.mseed'):
filename = os.path.join(self.path, 'data', 'encoding', filename)
data = read(filename)[0].data.tolist()
np.testing.assert_array_almost_equal(
data, ref, decimal=8, err_msg='Data of file %s not equal' %
filename)
def test_enforcing_reading_byteorder(self):
"""
Tests if setting the byte order of the header for reading is passed to
the C functions.
Quite simple. It just checks if reading with the correct byte order
works and reading with the wrong byte order fails.
"""
tr = Trace(data=np.arange(10, dtype=np.int32))
# Test with little endian.
memfile = io.BytesIO()
tr.write(memfile, format="mseed", byteorder="<")
memfile.seek(0, 0)
# Reading little endian should work just fine.
tr2 = read(memfile, header_byteorder="<")[0]
memfile.seek(0, 0)
self.assertEqual(tr2.stats.mseed.byteorder, "<")
# Remove the mseed specific header fields. These are obviously not
# equal.
del tr2.stats.mseed
del tr2.stats._format
self.assertEqual(tr, tr2)
# Wrong byte order raises.
self.assertRaises(ValueError, read, memfile, header_byteorder=">")
# Same test with big endian
memfile = io.BytesIO()
tr.write(memfile, format="mseed", byteorder=">")
memfile.seek(0, 0)
# Reading big endian should work just fine.
tr2 = read(memfile, header_byteorder=">")[0]
memfile.seek(0, 0)
self.assertEqual(tr2.stats.mseed.byteorder, ">")
# Remove the mseed specific header fields. These are obviously not
# equal.
del tr2.stats.mseed
del tr2.stats._format
self.assertEqual(tr, tr2)
# Wrong byte order raises.
self.assertRaises(ValueError, read, memfile, header_byteorder="<")
def test_long_year_range(self):
"""
Tests reading and writing years 1900 to 2100.
"""
tr = Trace(np.arange(5, dtype=np.float32))
# Year 2056 is non-deterministic for days 1, 256 and 257. These three
# dates are simply simply not supported right now. See the libmseed
# documentation for more details.
# Use every 5th year. Otherwise the test takes too long. Use 1901 as
# start to get year 2056.
years = range(1901, 2101, 5)
for year in years:
for byteorder in ["<", ">"]:
memfile = io.BytesIO()
# Get some random time with the year and the byte order as the
# seed.
random.seed(year + ord(byteorder))
tr.stats.starttime = UTCDateTime(
year,
julday=random.randrange(1, 365),
hour=random.randrange(0, 24),
minute=random.randrange(0, 60),
second=random.randrange(0, 60))
if year == 2056:
tr.stats.starttime = UTCDateTime(2056, 2, 1)
tr.write(memfile, format="mseed")
st2 = read(memfile)
self.assertEqual(len(st2), 1)
tr2 = st2[0]
# Remove the mseed specific header fields. These are obviously
# not equal.
del tr2.stats.mseed
del tr2.stats._format
self.assertEqual(tr, tr2)
def test_full_seed_with_non_default_dataquality(self):
"""
Tests the reading of full SEED files with dataqualities other then D.
"""
# Test the normal one first.
filename = os.path.join(self.path, 'data', 'fullseed.mseed')
st = read(filename)
self.assertEqual(st[0].stats.mseed.dataquality, "D")
# Test the others. They should also have identical data.
filename = os.path.join(self.path, 'data',
'fullseed_dataquality_M.mseed')
st = read(filename)
data_m = st[0].data
self.assertEqual(len(st), 1)
self.assertEqual(st[0].stats.mseed.dataquality, "M")
filename = os.path.join(self.path, 'data',
'fullseed_dataquality_R.mseed')
st = read(filename)
data_r = st[0].data
self.assertEqual(len(st), 1)
self.assertEqual(st[0].stats.mseed.dataquality, "R")
filename = os.path.join(self.path, 'data',
'fullseed_dataquality_Q.mseed')
st = read(filename)
data_q = st[0].data
self.assertEqual(len(st), 1)
self.assertEqual(st[0].stats.mseed.dataquality, "Q")
# Assert that the data is the same.
np.testing.assert_array_equal(data_m, data_r)
np.testing.assert_array_equal(data_m, data_q)
@unittest.skipIf(
"CONDAFORGE" in os.environ and
os.environ.get("APPVEYOR", "false").lower() == "true",
'Test is known to fail when building conda package in Appveyor.')
def test_infinite_loop(self):
"""
Tests that libmseed doesn't enter an infinite loop on buggy files.
"""
filename = os.path.join(self.path, 'data', 'infinite-loop.mseed')
process = multiprocessing.Process(target=_test_function,
args=(filename, ))
process.start()
process.join(60)
fail = process.is_alive()
process.terminate()
if process.is_alive():
if platform.system() == 'Windows':
os.kill(process.pid, signal.CTRL_BREAK_EVENT)
else:
os.kill(process.pid, signal.SIGKILL)
self.assertFalse(fail)
def test_microsecond_accuracy_reading_and_writing_before_1970(self):
"""
Tests that reading and writing data with microsecond accuracy and
before 1970 works as expected.
"""
# Test a couple of timestamps. Positive and negative ones.
timestamps = [123456.789123, -123456.789123, 1.123400, 1.123412,
1.123449, 1.123450, 1.123499, -1.123400, -1.123412,
-1.123449, -1.123450, -1.123451, -1.123499]
for timestamp in timestamps:
starttime = UTCDateTime(timestamp)
self.assertEqual(starttime.timestamp, timestamp)
tr = Trace(data=np.linspace(0, 100, 101))
tr.stats.starttime = starttime
with io.BytesIO() as fh:
tr.write(fh, format="mseed")
fh.seek(0, 0)
tr2 = read(fh)[0]
del tr2.stats.mseed
del tr2.stats._format
self.assertEqual(tr2.stats.starttime, starttime)
self.assertEqual(tr2, tr)
def test_reading_noise_records(self):
"""
Tests reading a noise record. See #1495.
"""
file = os.path.join(self.path, "data",
"single_record_plus_noise_record.mseed")
st = read(file)
self.assertEqual(len(st), 1)
tr = st[0]
self.assertEqual(tr.id, "IM.NV32..BHE")
self.assertEqual(tr.stats.npts, 277)
self.assertEqual(tr.stats.sampling_rate, 40.0)
def test_read_file_with_various_noise_records(self):
"""
Tests reading a custom made file with noise records.
"""
# This file has the following layout:
# 1. 256 byte NOISE record
# 2. 512 byte normal record - station NV30
# 3. 128 byte NOISE record
# 4. 512 byte normal record - station NV31
# 5. 512 byte NOISE record
# 6. 512 byte NOISE record
# 7. 512 byte normal record - station NV32
# 8. 1024 byte NOISE record
# 9. 512 byte normal record - station NV33
file = os.path.join(self.path, "data", "various_noise_records.mseed")
st = read(file)
self.assertTrue(len(st), 4)
self.assertTrue(st[0].stats.station, "NV30")
self.assertTrue(st[1].stats.station, "NV31")
self.assertTrue(st[2].stats.station, "NV32")
self.assertTrue(st[3].stats.station, "NV33")
# Data is the same across all records.
np.testing.assert_allclose(st[0].data, st[1].data)
np.testing.assert_allclose(st[0].data, st[2].data)
np.testing.assert_allclose(st[0].data, st[3].data)
def test_mseed_zero_data_offset(self):
"""
Tests that a data offset of zero in the fixed header does not
confuse ObsPy.
The file contains three records: a normal one, followed by one with
a data-offset of zero, followed by another normal one.
This currently results in three returned traces:
* CH.PANIX..LHZ |
2016-08-21T01:41:19.000000Z - 2016-08-21T01:45:30.000000Z |
1.0 Hz, 252 samples
* CH.PANIX..LHZ |
2016-08-21T01:43:37.000000Z - 2016-08-21T01:43:37.000000Z |
1.0 Hz, 0 samples
* CH.PANIX..LHZ |
2016-08-21T01:45:31.000000Z - 2016-08-21T01:49:52.000000Z |
1.0 Hz, 262 samples
"""
file = os.path.join(self.path, "data", "bizarre",
"mseed_data_offset_0.mseed")
st = read(file)
self.assertEqual(len(st), 3)
tr = st[0]
self.assertEqual(tr.id, "CH.PANIX..LHZ")
self.assertEqual(tr.stats.starttime,
UTCDateTime("2016-08-21T01:41:19.000000Z"))
self.assertEqual(tr.stats.endtime,
UTCDateTime("2016-08-21T01:45:30.000000Z"))
self.assertEqual(tr.stats.npts, len(tr.data))
self.assertEqual(tr.stats.npts, 252)
tr = st[1]
self.assertEqual(tr.id, "CH.PANIX..LHZ")
self.assertEqual(tr.stats.starttime,
UTCDateTime("2016-08-21T01:43:37.000000Z"))
self.assertEqual(tr.stats.endtime,
UTCDateTime("2016-08-21T01:43:37.000000Z"))
self.assertEqual(tr.stats.npts, len(tr.data))
self.assertEqual(tr.stats.npts, 0)
tr = st[2]
self.assertEqual(tr.id, "CH.PANIX..LHZ")
self.assertEqual(tr.stats.starttime,
UTCDateTime("2016-08-21T01:45:31.000000Z"))
self.assertEqual(tr.stats.endtime,
UTCDateTime("2016-08-21T01:49:52.000000Z"))
self.assertEqual(tr.stats.npts, len(tr.data))
self.assertEqual(tr.stats.npts, 262)
def test_mseed_zero_data_headonly(self):
"""
Tests that records with no data correctly work in headonly mode.
"""
file = os.path.join(self.path, "data",
"three_records_zero_data_in_middle.mseed")
expected = [
("BW.BGLD..EHE", UTCDateTime("2007-12-31T23:59:59.765000Z"),
UTCDateTime("2008-01-01T00:00:01.820000Z"), 200.0, 412),
("BW.BGLD..EHE", UTCDateTime("2008-01-01T00:00:01.825000Z"),
UTCDateTime("2008-01-01T00:00:01.825000Z"), 200.0, 0),
("BW.BGLD..EHE", UTCDateTime("2008-01-01T00:00:03.885000Z"),
UTCDateTime("2008-01-01T00:00:05.940000Z"), 200.0, 412)]
# Default full read.
st = read(file)
self.assertEqual(len(st), 3)
for tr, exp in zip(st, expected):
self.assertEqual(tr.id, exp[0])
self.assertEqual(tr.stats.starttime, exp[1])
self.assertEqual(tr.stats.endtime, exp[2])
self.assertEqual(tr.stats.sampling_rate, exp[3])
self.assertEqual(tr.stats.npts, exp[4])
# Headonly read.
st = read(file, headonly=True)
self.assertEqual(len(st), 3)
for tr, exp in zip(st, expected):
self.assertEqual(tr.id, exp[0])
self.assertEqual(tr.stats.starttime, exp[1])
self.assertEqual(tr.stats.endtime, exp[2])
self.assertEqual(tr.stats.sampling_rate, exp[3])
self.assertEqual(tr.stats.npts, exp[4])
def test_read_file_with_microsecond_wrap(self):
"""
This is not strictly valid but I encountered such a file in practice
so I guess it happens. Libmseed can also correctly deal with it.
The test file is a single record with the .0001 seconds field set to
10000. SEED strictly allows only 0-9999 in this field.
"""
file = os.path.join(self.path, "data",
"microsecond_wrap.mseed")
with warnings.catch_warnings(record=True) as w_1:
warnings.simplefilter("always")
info = util.get_record_information(file)
self.assertEqual(w_1[0].message.args[0],
'Record contains a fractional seconds (.0001 secs) '
'of 10000 - the maximum strictly allowed value is '
'9999. It will be interpreted as one or more '
'additional seconds.')
with warnings.catch_warnings(record=True) as w_2:
warnings.simplefilter("always")
tr = read(file)[0]
# First warning is identical.
self.assertEqual(w_1[0].message.args[0], w_2[0].message.args[0])
# Second warning is raised by libmseed.
self.assertEqual(w_2[1].message.args[0],
'readMSEEDBuffer(): Record with offset=0 has a '
'fractional second (.0001 seconds) of 10000. This '
'is not strictly valid but will be interpreted as '
'one or more additional seconds.')
# Make sure libmseed and the internal ObsPy record parser produce
# the same result.
self.assertEqual(info["starttime"], tr.stats.starttime)
self.assertEqual(info["endtime"], tr.stats.endtime)
# Read with a hex-editor.
ref_time = UTCDateTime(year=2008, julday=8, hour=4, minute=58,
second=5 + 1)
self.assertEqual(ref_time, info["starttime"])
self.assertEqual(ref_time, tr.stats.starttime)
def test_reading_miniseed_with_no_blockette_1000(self):
"""
Blockette 1000 was only introduced with SEED version 2.3.
"""
file = os.path.join(self.path, "data", "bizarre",
"mseed_no_blkt_1000.mseed")
st = read(file)
self.assertEqual(len(st), 1)
tr = st[0]
self.assertEqual(tr.stats.npts, 7536)
np.testing.assert_allclose(tr.stats.sampling_rate, 20.0)
self.assertEqual(tr.stats.starttime,
UTCDateTime(1976, 3, 10, 3, 28))
self.assertEqual(tr.id, ".GRA1..BHZ")
# Also test the data to make sure the unpacking was successful.
np.testing.assert_equal(
st[0].data[:10],
[-185, -200, -209, -220, -228, -246, -252, -262, -262, -269])
def test_writing_of_blockette_100(self):
"""
Tests the writing of blockette 100 if necessary.
"""
def has_blkt_100(filename):
ms = _MSStruct(filename)
ms.read(-1, 0, 1, 0)
blkt_link = ms.msr.contents.blkts
has_blkt_100 = False
while True:
try:
if blkt_link.contents.blkt_type == 100:
has_blkt_100 = True
break
blkt_link = blkt_link.contents.next
except ValueError:
break
del ms
return has_blkt_100
tr = read()[0]
tr.data = tr.data[:10]
with NamedTemporaryFile() as tf:
tempfile = tf.name
# A "clean" sampling rate does not require blockette 100.
sr = 200.0
tr.stats.sampling_rate = sr
tr.write(tempfile, format="mseed")
self.assertEqual(
np.float32(read(tempfile)[0].stats.sampling_rate),
np.float32(sr))
self.assertFalse(has_blkt_100(tempfile))
# A more detailed one does.
sr = 199.9997
tr.stats.sampling_rate = sr
tr.write(tempfile, format="mseed")
self.assertEqual(
np.float32(read(tempfile)[0].stats.sampling_rate),
np.float32(sr))
self.assertTrue(has_blkt_100(tempfile))
# A very large (but "clean") one does not need it.
sr = 1E6
tr.stats.sampling_rate = sr
tr.write(tempfile, format="mseed")
self.assertEqual(
np.float32(read(tempfile)[0].stats.sampling_rate),
np.float32(sr))
self.assertFalse(has_blkt_100(tempfile))
# Same for a very small but "clean" one.
sr = 1E-6
tr.stats.sampling_rate = sr
tr.write(tempfile, format="mseed")
self.assertEqual(
np.float32(read(tempfile)[0].stats.sampling_rate),
np.float32(sr))
self.assertFalse(has_blkt_100(tempfile))
# But small perturbations resulting in "unclean" sampling rates
# will cause blockette 100 to be written.
sr = 1E6 + 0.123456
tr.stats.sampling_rate = sr
tr.write(tempfile, format="mseed")