/
test_mseed_util.py
1284 lines (1164 loc) · 56.5 KB
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test_mseed_util.py
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# -*- coding: utf-8 -*-
import copy
import io
import os
import random
import shutil
import sys
from datetime import datetime
from struct import pack, unpack
import warnings
import numpy as np
from obspy import UTCDateTime
from obspy.core import Stream, Trace
from obspy.core.util import NamedTemporaryFile
from obspy.io.mseed import util
from obspy.io.mseed.core import _read_mseed
from obspy.io.mseed.headers import (FIXED_HEADER_ACTIVITY_FLAGS,
FIXED_HEADER_DATA_QUAL_FLAGS,
FIXED_HEADER_IO_CLOCK_FLAGS)
from obspy.io.mseed.util import set_flags_in_fixed_headers
import pytest
def _create_mseed_file(filename, record_count, sampling_rate=1.0,
starttime=UTCDateTime(0), flags=None, seed=None,
skiprecords=0):
"""
Helper function to create MiniSEED files with certain flags set for
testing purposes.
"""
all_flags = {
"data_quality_flags": {"offset": 38, "flags": [
"amplifier_saturation", "digitizer_clipping",
"spikes", "glitches", "missing_padded_data",
"telemetry_sync_error", "digital_filter_charging",
"suspect_time_tag"]},
"activity_flags": {"offset": 36, "flags": [
"calibration_signal", "time_correction_applied",
"event_begin", "event_end", "positive_leap", "negative_leap",
"event_in_progress"]},
"io_and_clock_flags": {"offset": 37, "flags": [
"station_volume", "long_record_read",
"short_record_read", "start_time_series", "end_time_series",
"clock_locked"]}
}
# With uncompressed float32 it is 50 samples per record.
data = np.arange(50 * record_count, dtype=np.float32)
tr = Trace(data=data,
header={"sampling_rate": sampling_rate, "starttime": starttime})
tr.write(filename, format="mseed", reclen=256, encoding="FLOAT32")
if not flags:
return
# Reproducibility!
if seed is not None:
np.random.seed(seed)
data = np.fromfile(filename, dtype=np.int8)
# Modify the flags to get the required statistics.
for key, value in all_flags.items():
if key not in flags:
continue
_f = value["flags"]
_flag_values = np.zeros(record_count - skiprecords, dtype=np.int8)
for _i, name in enumerate(_f):
if name not in flags[key]:
continue
# Create array with the correct number of flags set.
arr = np.zeros(record_count - skiprecords, dtype=np.int8)
arr[:flags[key][name]] = 1 << _i
np.random.shuffle(arr)
_flag_values |= arr
data[value["offset"]:: 256] = np.concatenate([
np.zeros(skiprecords, dtype=np.int8), _flag_values])
# Write again.
data.tofile(filename)
class TestMSEEDUtil():
"""
Tests suite for util module of obspy.io.mseed.
"""
@classmethod
def setup_class(cls):
cls.maxDiff = None
# mseed steim compression is big endian
if sys.byteorder == 'little':
cls.swap = 1
else:
cls.swap = 0
def test_convert_datetime(self):
"""
Tests all time conversion methods.
"""
# These values are created using the Linux "date -u -d @TIMESTRING"
# command. These values are assumed to be correct.
timesdict = {
1234567890: UTCDateTime(2009, 2, 13, 23, 31, 30),
1111111111: UTCDateTime(2005, 3, 18, 1, 58, 31),
1212121212: UTCDateTime(2008, 5, 30, 4, 20, 12),
1313131313: UTCDateTime(2011, 8, 12, 6, 41, 53),
100000: UTCDateTime(1970, 1, 2, 3, 46, 40),
100000.111112: UTCDateTime(1970, 1, 2, 3, 46, 40, 111112),
200000000: UTCDateTime(1976, 5, 3, 19, 33, 20),
# test rounding of 7th digit of microseconds
1388479508.871572: UTCDateTime(1388479508.8715718),
}
# Loop over timesdict.
for ts, dt in timesdict.items():
assert dt == util._convert_mstime_to_datetime(ts * 1000000)
assert ts * 1000000 == util._convert_datetime_to_mstime(dt)
# Additional sanity tests.
# Random date that previously failed.
dt = UTCDateTime(2017, 3, 6, 4, 12, 16, 260696)
assert dt == util._convert_mstime_to_datetime(
util._convert_datetime_to_mstime(dt))
# Some random date.
random.seed(815) # make test reproducible
timestring = random.randint(0, 2000000) * 1e6
assert timestring == util._convert_datetime_to_mstime(
util._convert_mstime_to_datetime(timestring))
def test_convert_datetime2(self):
"""
Some failing test discovered in #1670
"""
# 1
dt = UTCDateTime(ns=1487021451935737333)
assert str(dt) == "2017-02-13T21:30:51.935737Z"
assert util._convert_datetime_to_mstime(dt) == 1487021451935737
assert dt == util._convert_mstime_to_datetime(
util._convert_datetime_to_mstime(dt))
# 2
dt = UTCDateTime(ns=1487021451935736449)
assert str(dt) == "2017-02-13T21:30:51.935736Z"
assert util._convert_datetime_to_mstime(dt) == 1487021451935736
assert dt == util._convert_mstime_to_datetime(
util._convert_datetime_to_mstime(dt))
# 3
dt = UTCDateTime(ns=1487021451935736501)
assert str(dt) == "2017-02-13T21:30:51.935737Z"
assert util._convert_datetime_to_mstime(dt) == 1487021451935737
assert dt == util._convert_mstime_to_datetime(
util._convert_datetime_to_mstime(dt))
def test_get_record_information(self, testdata):
"""
Tests the util._get_ms_file_info method with known values.
"""
filename = testdata['BW.BGLD.__.EHE.D.2008.001.first_10_records']
# Simply reading the file.
info = util.get_record_information(filename)
assert info['filesize'] == 5120
assert info['record_length'] == 512
assert info['number_of_records'] == 10
assert info['excess_bytes'] == 0
# Now with an open file. This should work regardless of the current
# value of the file pointer and it should also not change the file
# pointer.
with open(filename, 'rb') as open_file:
open_file.seek(1234)
info = util.get_record_information(open_file)
assert info['filesize'] == 5120 - 1234
assert info['record_length'] == 512
assert info['number_of_records'] == 7
assert info['excess_bytes'] == 302
assert open_file.tell() == 1234
# Now test with a BytesIO with the first ten percent.
with open(filename, 'rb') as open_file:
open_file_string = io.BytesIO(open_file.read())
open_file_string.seek(111)
info = util.get_record_information(open_file_string)
assert info['filesize'] == 5120 - 111
assert info['record_length'] == 512
assert info['number_of_records'] == 9
assert info['excess_bytes'] == 401
assert open_file_string.tell() == 111
# One more file containing two records.
filename = testdata['test.mseed']
info = util.get_record_information(filename)
assert info['filesize'] == 8192
assert info['record_length'] == 4096
assert info['number_of_records'] == 2
assert info['excess_bytes'] == 0
def test_get_record_information_negative_sr_rate_and_mult(self, testdata):
"""
Tests the method for negative sampling rate factors and multipliers.
"""
filename = testdata['single_record_negative_sr_fact_and_mult.mseed']
info = util.get_record_information(filename)
assert info == {
'activity_flags': 0,
'byteorder': '>',
'channel': 'VHZ',
'data_quality_flags': 0,
'encoding': 10,
'endtime': UTCDateTime(1991, 2, 21, 23, 59, 50, 430000),
'excess_bytes': 0,
'filesize': 4096,
'io_and_clock_flags': 0,
'location': '',
'network': 'MN',
'npts': 60,
'number_of_records': 1,
'record_length': 4096,
'samp_rate': 0.1,
'starttime': UTCDateTime(1991, 2, 21, 23, 50, 0, 430000),
'station': 'TNV',
'time_correction': 0
}
def test_issue2069(self, testdata):
"""
Tests the util._get_ms_file_info method with sample rate of 0.
Reads a datafile and sets sr factor and multipier to 0 and and mseed
ASCII LOG file with a sample rate of 0.
"""
# Test with a file by setting sr = 0
filename = testdata['BW.BGLD.__.EHE.D.2008.001.first_10_records']
fmt = '>HHBBBxHHhhBBBxlxxH'
with open(filename, "rb") as fh:
with io.BytesIO(fh.read()) as buf:
buf.seek(20, 0)
data = buf.read(28)
values = list(unpack(fmt, data))
values[7] = 0
values[8] = 0
data = pack(fmt, *values)
buf.seek(20, 0)
buf.write(data)
buf.seek(0, 0)
info = util.get_record_information(buf)
assert info['samp_rate'] == 0
# Test with an actual sr = 0 file
filename = testdata['rt130_sr0_cropped.mseed']
info = util.get_record_information(filename)
assert info['samp_rate'] == 0
def test_get_data_quality(self, testdata):
"""
This test reads a self-made Mini-SEED file with set Data Quality Bits.
A real test file would be better as this test tests a file that was
created by the inverse method that reads the bits.
The method used to be called getTimingAndDataQuality() but has in
the meanwhile been replaced by a more general get_flags() method.
This test uses the general method but is otherwise not altered.
"""
filename = testdata['qualityflags.mseed']
# Read quality flags.
result = util.get_flags(filename, timing_quality=False,
io_flags=False, activity_flags=False,
data_quality_flags=True)
# The test file contains 18 records. The first record has no set bit,
# bit 0 of the second record is set, bit 1 of the third, ..., bit 7 of
# the 9th record is set. The last nine records have 0 to 8 set bits,
# starting with 0 bits, bit 0 is set, bits 0 and 1 are set...
# Altogether the file contains 44 set bits.
assert result['data_quality_flags_counts'] == {
"amplifier_saturation": 9,
"digitizer_clipping": 8,
"spikes": 7,
"glitches": 6,
"missing_padded_data": 5,
"telemetry_sync_error": 4,
"digital_filter_charging": 3,
"suspect_time_tag": 2}
# No set quality flags should result in a list of zeros.
filename = testdata['test.mseed']
result = util.get_flags(filename, timing_quality=False,
io_flags=False, activity_flags=False,
data_quality_flags=True)
assert result['data_quality_flags_counts'] == {
"amplifier_saturation": 0,
"digitizer_clipping": 0,
"spikes": 0,
"glitches": 0,
"missing_padded_data": 0,
"telemetry_sync_error": 0,
"digital_filter_charging": 0,
"suspect_time_tag": 0}
def test_get_flags(self):
"""
This test reads a real Mini-SEED file which has been
modified ad hoc.
"""
with NamedTemporaryFile() as tf:
_create_mseed_file(
tf.name, record_count=112, seed=3412,
starttime="2015-10-16T00:00:00", skiprecords=5, flags={
'data_quality_flags': {
"amplifier_saturation": 55,
"digitizer_clipping": 72,
"spikes": 55,
"glitches": 63,
"missing_padded_data": 55,
"telemetry_sync_error": 63,
"digital_filter_charging": 4,
"suspect_time_tag": 8},
'activity_flags': {
"calibration_signal": 1,
"time_correction_applied": 2,
"event_begin": 3,
"event_end": 53,
"positive_leap": 4,
"negative_leap": 11,
"event_in_progress": 5},
'io_and_clock_flags': {
"station_volume": 1,
"long_record_read": 33,
"short_record_read": 2,
"start_time_series": 3,
"end_time_series": 4,
"clock_locked": 32}})
result = util.get_flags(tf.name, timing_quality=False)
assert result["record_count"] == 112
assert result['data_quality_flags_counts'] == {
"amplifier_saturation": 55,
"digitizer_clipping": 72,
"spikes": 55,
"glitches": 63,
"missing_padded_data": 55,
"telemetry_sync_error": 63,
"digital_filter_charging": 4,
"suspect_time_tag": 8}
assert result['activity_flags_counts'] == {
"calibration_signal": 1,
"time_correction_applied": 2,
"event_begin": 3,
"event_end": 53,
"positive_leap": 4,
"negative_leap": 11,
"event_in_progress": 5}
assert result['io_and_clock_flags_counts'] == {
"station_volume": 1,
"long_record_read": 33,
"short_record_read": 2,
"start_time_series": 3,
"end_time_series": 4,
"clock_locked": 32}
# Test time settings. Everything is still present.
starttime = '2015-10-16T00:00:00'
result = util.get_flags(tf.name, starttime=starttime,
io_flags=False, activity_flags=False,
timing_quality=False)
assert result['data_quality_flags_counts'] == {
"amplifier_saturation": 55,
"digitizer_clipping": 72,
"spikes": 55,
"glitches": 63,
"missing_padded_data": 55,
"telemetry_sync_error": 63,
"digital_filter_charging": 4,
"suspect_time_tag": 8}
# Nothing is present.
starttime = '2015-10-17T00:00:00'
result = util.get_flags(tf.name, starttime=starttime,
io_flags=False, activity_flags=False,
timing_quality=False)
assert result['data_quality_flags_counts'] == {
"amplifier_saturation": 0,
"digitizer_clipping": 0,
"spikes": 0,
"glitches": 0,
"missing_padded_data": 0,
"telemetry_sync_error": 0,
"digital_filter_charging": 0,
"suspect_time_tag": 0}
# There are exactly 10 records at the front which have nothing.
# Thus reading until that point should yield nothing.
endtime = UTCDateTime('2015-10-15T00:00:00') + 50 * 10
result = util.get_flags(tf.name, endtime=endtime,
io_flags=False, activity_flags=False,
timing_quality=False)
assert result['data_quality_flags_counts'] == {
"amplifier_saturation": 0,
"digitizer_clipping": 0,
"spikes": 0,
"glitches": 0,
"missing_padded_data": 0,
"telemetry_sync_error": 0,
"digital_filter_charging": 0,
"suspect_time_tag": 0}
# Reading after that point should yield everything.
result = util.get_flags(tf.name, starttime=endtime,
io_flags=False, activity_flags=False,
timing_quality=False)
assert result['data_quality_flags_counts'] == {
"amplifier_saturation": 55,
"digitizer_clipping": 72,
"spikes": 55,
"glitches": 63,
"missing_padded_data": 55,
"telemetry_sync_error": 63,
"digital_filter_charging": 4,
"suspect_time_tag": 8}
def test_get_flags_from_files_and_file_like_objects(self):
"""
Similar to test_get_flags() but with file-like objects.
"""
with NamedTemporaryFile() as tf:
_create_mseed_file(
tf.name, record_count=112, seed=3412,
starttime="2015-10-16T00:00:00", skiprecords=5, flags={
'data_quality_flags': {
"amplifier_saturation": 55,
"digitizer_clipping": 72,
"spikes": 55,
"glitches": 63,
"missing_padded_data": 55,
"telemetry_sync_error": 63,
"digital_filter_charging": 4,
"suspect_time_tag": 8},
'activity_flags': {
"calibration_signal": 1,
"time_correction_applied": 2,
"event_begin": 3,
"event_end": 53,
"positive_leap": 4,
"negative_leap": 11,
"event_in_progress": 5},
'io_and_clock_flags': {
"station_volume": 1,
"long_record_read": 33,
"short_record_read": 2,
"start_time_series": 3,
"end_time_series": 4,
"clock_locked": 32}})
tf.seek(0, 0)
# Directly from the file.
result = util.get_flags(tf, timing_quality=False)
assert result["record_count"] == 112
assert result['data_quality_flags_counts'] == {
"amplifier_saturation": 55,
"digitizer_clipping": 72,
"spikes": 55,
"glitches": 63,
"missing_padded_data": 55,
"telemetry_sync_error": 63,
"digital_filter_charging": 4,
"suspect_time_tag": 8}
assert result['activity_flags_counts'] == {
"calibration_signal": 1,
"time_correction_applied": 2,
"event_begin": 3,
"event_end": 53,
"positive_leap": 4,
"negative_leap": 11,
"event_in_progress": 5}
assert result['io_and_clock_flags_counts'] == {
"station_volume": 1,
"long_record_read": 33,
"short_record_read": 2,
"start_time_series": 3,
"end_time_series": 4,
"clock_locked": 32}
# From a BytesIO objects.
tf.seek(0, 0)
with io.BytesIO(tf.read()) as buf:
result = util.get_flags(buf, timing_quality=False)
assert result["record_count"] == 112
assert result['data_quality_flags_counts'] == {
"amplifier_saturation": 55,
"digitizer_clipping": 72,
"spikes": 55,
"glitches": 63,
"missing_padded_data": 55,
"telemetry_sync_error": 63,
"digital_filter_charging": 4,
"suspect_time_tag": 8}
assert result['activity_flags_counts'] == {
"calibration_signal": 1,
"time_correction_applied": 2,
"event_begin": 3,
"event_end": 53,
"positive_leap": 4,
"negative_leap": 11,
"event_in_progress": 5}
assert result['io_and_clock_flags_counts'] == {
"station_volume": 1,
"long_record_read": 33,
"short_record_read": 2,
"start_time_series": 3,
"end_time_series": 4,
"clock_locked": 32}
def test_get_start_and_end_time(self, testdata):
"""
Tests getting the start- and endtime of a file.
The values are compared with the results of reading the full files.
"""
mseed_filenames = ['BW.BGLD.__.EHE.D.2008.001.first_10_records',
'test.mseed', 'timingquality.mseed']
for _i in mseed_filenames:
filename = testdata[_i]
# Get the start- and end time.
(start, end) = util.get_start_and_end_time(filename)
# Parse the whole file.
stream = _read_mseed(filename)
assert start == stream[0].stats.starttime
assert end == stream[0].stats.endtime
def test_get_timing_quality(self, testdata):
"""
This test reads a self-made Mini-SEED file with Timing Quality
information in Blockette 1001. A real test file would be better.
The test file contains 101 records with the timing quality ranging from
0 to 100 in steps of 1.
The result is compared to the result from the following R command:
V <- 0:100; min(V); max(V); mean(V); median(V); quantile(V, 0.75,
type = 3); quantile(V, 0.25, type = 3)
The method used to be called getTimingAndDataQuality() but has in
the meanwhile been replaced by a more general get_flags() method.
This test uses the general method but is otherwise not altered.
"""
filename = testdata['timingquality.mseed']
result = util.get_flags(filename, timing_quality=True,
io_flags=False, activity_flags=False,
data_quality_flags=False)
# Test all values separately.
np.testing.assert_allclose(
sorted(result["timing_quality"]["all_values"]),
np.arange(0, 101))
del result["timing_quality"]["all_values"]
assert result["timing_quality"] == {
'upper_quartile': 75.0,
'min': 0.0,
'lower_quartile': 25.0,
'mean': 50.0,
'median': 50.0,
'max': 100.0}
# No timing quality set should result in an empty dictionary.
filename = testdata['BW.BGLD.__.EHE.D.2008.001.first_10_records']
result = util.get_flags(filename, timing_quality=True,
io_flags=False, activity_flags=False,
data_quality_flags=False)
assert result["timing_quality"] == {}
def test_unpack_steim_1(self, testdata):
"""
Test decompression of Steim1 strings. Remove 64 Bytes of header
by hand, see SEEDManual_V2.4.pdf page 100.
"""
steim1_file = testdata['BW.BGLD.__.EHE.D.2008.001.first_record']
# 64 Bytes header.
d = np.fromfile(steim1_file, dtype=np.uint8)[64:]
data = util._unpack_steim_1(d, 412, swapflag=self.swap,
verbose=0)
data_record = _read_mseed(steim1_file)[0].data
np.testing.assert_array_equal(data, data_record)
def test_unpack_steim_2(self, testdata):
"""
Test decompression of Steim2 strings. Remove 128 Bytes of header
by hand, see SEEDManual_V2.4.pdf page 100.
"""
steim2_file = testdata['steim2.mseed']
# 128 Bytes header.
d = np.fromfile(steim2_file, dtype=np.uint8)[128:]
data = util._unpack_steim_2(d, 5980, swapflag=self.swap,
verbose=0)
data_record = _read_mseed(steim2_file)[0].data
np.testing.assert_array_equal(data, data_record)
def test_time_shifting(self, testdata):
"""
Tests the shift_time_of_file() function.
"""
with NamedTemporaryFile() as tf:
output_filename = tf.name
# Test a normal file first.
filename = testdata['BW.BGLD.__.EHE.D.2008.001.first_10_records']
# Shift by one second.
util.shift_time_of_file(filename, output_filename, 10000)
st_before = _read_mseed(filename)
st_after = _read_mseed(output_filename)
st_before[0].stats.starttime += 1
assert st_before == st_after
# Shift by 22 seconds in the other direction.
util.shift_time_of_file(filename, output_filename, -220000)
st_before = _read_mseed(filename)
st_after = _read_mseed(output_filename)
st_before[0].stats.starttime -= 22
assert st_before == st_after
# Shift by 11.33 seconds.
util.shift_time_of_file(filename, output_filename, 113300)
st_before = _read_mseed(filename)
st_after = _read_mseed(output_filename)
st_before[0].stats.starttime += 11.33
assert st_before == st_after
# Test a special case with the time correction applied flag set but
# no actual time correction in the field.
filename = testdata[
'one_record_time_corr_applied_but_time_corr_is_zero.mseed']
# Positive shift.
util.shift_time_of_file(filename, output_filename, 22000)
st_before = _read_mseed(filename)
st_after = _read_mseed(output_filename)
st_before[0].stats.starttime += 2.2
assert st_before == st_after
# Negative shift.
util.shift_time_of_file(filename, output_filename, -333000)
st_before = _read_mseed(filename)
st_after = _read_mseed(output_filename)
st_before[0].stats.starttime -= 33.3
assert st_before == st_after
def test_time_shifting_special_case(self, testdata):
"""
Sometimes actually changing the time value is necessary. This works but
is considered experimental and thus emits a warning. Therefore Python
>= 2.6 only.
"""
with NamedTemporaryFile() as tf:
output_filename = tf.name
# This file was created only for testing purposes.
filename = testdata[
'one_record_already_applied_time_correction.mseed']
with warnings.catch_warnings(record=True):
warnings.simplefilter('error', UserWarning)
with pytest.raises(UserWarning):
util.shift_time_of_file(
input_file=filename, output_file=output_filename,
timeshift=123400)
# Now ignore the warnings and test the default values.
warnings.simplefilter('ignore', UserWarning)
util.shift_time_of_file(input_file=filename,
output_file=output_filename,
timeshift=123400)
st_before = _read_mseed(filename)
st_after = _read_mseed(output_filename)
st_before[0].stats.starttime += 12.34
assert st_before == st_after
# Test negative shifts.
with warnings.catch_warnings(record=True):
warnings.simplefilter('ignore', UserWarning)
util.shift_time_of_file(input_file=filename,
output_file=output_filename,
timeshift=-22222)
st_before = _read_mseed(filename)
st_after = _read_mseed(output_filename)
st_before[0].stats.starttime -= 2.2222
assert st_before == st_after
def test_check_flag_value(self):
"""
Test case for obspy.io.mseed.util._check_flag_value
"""
# Valid value for a boolean flag
corrected_flag = util._check_flag_value(True)
assert isinstance(corrected_flag, bool)
assert corrected_flag
corrected_flag = util._check_flag_value(False)
assert isinstance(corrected_flag, bool)
assert not corrected_flag
# Valid value for an instant flag #1
flag_value = {"INSTANT": UTCDateTime("2009-12-23T06:00:00.0")}
corrected_flag = util._check_flag_value(flag_value)
assert isinstance(corrected_flag, list)
assert corrected_flag[0][0] == UTCDateTime("2009-12-23T06:00:00.0")
assert corrected_flag[0][1] == UTCDateTime("2009-12-23T06:00:00.0")
# Valid value for an instant flag #2
flag_value = {"INSTANT": [UTCDateTime("2009-12-24T06:00:00.0")]}
corrected_flag = util._check_flag_value(flag_value)
assert isinstance(corrected_flag, list)
assert corrected_flag[0][0] == UTCDateTime("2009-12-24T06:00:00.0")
assert corrected_flag[0][1] == UTCDateTime("2009-12-24T06:00:00.0")
# Valid value for several instant flags
flag_value = {"INSTANT": [UTCDateTime("2009-12-24T06:00:00.0"),
UTCDateTime("2009-12-24T06:01:00.0")]}
corrected_flag = util._check_flag_value(flag_value)
assert isinstance(corrected_flag, list)
assert corrected_flag[0][0] == UTCDateTime("2009-12-24T06:00:00.0")
assert corrected_flag[0][1] == UTCDateTime("2009-12-24T06:00:00.0")
assert corrected_flag[1][0] == UTCDateTime("2009-12-24T06:01:00.0")
assert corrected_flag[1][1] == UTCDateTime("2009-12-24T06:01:00.0")
# Valid value for a duration #1
flag_value = {"DURATION": [UTCDateTime("2009-12-25T06:00:00.0"),
UTCDateTime("2009-12-25T06:10:00.0")]}
corrected_flag = util._check_flag_value(flag_value)
assert isinstance(corrected_flag, list)
assert corrected_flag[0][0] == UTCDateTime("2009-12-25T06:00:00.0")
assert corrected_flag[0][1] == UTCDateTime("2009-12-25T06:10:00.0")
# Valid value for a duration #2
flag_value = {"DURATION": [(UTCDateTime("2009-12-25T16:00:00.0"),
UTCDateTime("2009-12-25T16:10:00.0"))]}
corrected_flag = util._check_flag_value(flag_value)
assert isinstance(corrected_flag, list)
assert corrected_flag[0][0] == UTCDateTime("2009-12-25T16:00:00.0")
assert corrected_flag[0][1] == UTCDateTime("2009-12-25T16:10:00.0")
# Valid value for several durations #1
flag_value = {"DURATION": [UTCDateTime("2009-12-24T06:00:00.0"),
UTCDateTime("2009-12-24T06:10:00.0"),
UTCDateTime("2009-12-24T07:00:00.0"),
UTCDateTime("2009-12-24T07:10:00.0")]}
corrected_flag = util._check_flag_value(flag_value)
assert isinstance(corrected_flag, list)
assert corrected_flag[0][0] == UTCDateTime("2009-12-24T06:00:00.0")
assert corrected_flag[0][1] == UTCDateTime("2009-12-24T06:10:00.0")
assert corrected_flag[1][0] == UTCDateTime("2009-12-24T07:00:00.0")
assert corrected_flag[1][1] == UTCDateTime("2009-12-24T07:10:00.0")
# Valid value for several durations #2
flag_value = {"DURATION": [(UTCDateTime("2009-12-25T06:00:00.0"),
UTCDateTime("2009-12-25T06:10:00.0")),
(UTCDateTime("2009-12-25T07:00:00.0"),
UTCDateTime("2009-12-25T07:10:00.0"))]}
corrected_flag = util._check_flag_value(flag_value)
assert isinstance(corrected_flag, list)
assert corrected_flag[0][0] == UTCDateTime("2009-12-25T06:00:00.0")
assert corrected_flag[0][1] == UTCDateTime("2009-12-25T06:10:00.0")
assert corrected_flag[1][0] == UTCDateTime("2009-12-25T07:00:00.0")
assert corrected_flag[1][1] == UTCDateTime("2009-12-25T07:10:00.0")
# Test of the (valid) example 1 written in set_flags_in_fixed_headers's
# docstring
date1 = UTCDateTime("2009-12-23T06:00:00.0")
date2 = UTCDateTime("2009-12-23T06:30:00.0")
date3 = UTCDateTime("2009-12-24T10:00:00.0")
date4 = UTCDateTime("2009-12-24T10:30:00.0")
date5 = UTCDateTime("2009-12-26T18:00:00.0")
date6 = UTCDateTime("2009-12-26T18:04:00.0")
flag_value = {"INSTANT": [date5, date6],
"DURATION": [(date1, date2), (date3, date4)]}
corrected_flag = util._check_flag_value(flag_value)
assert isinstance(corrected_flag, list)
assert len(corrected_flag) == 4
# Sort by start date to ensure uniqueness of the list
corrected_flag.sort(key=lambda val: val[0])
assert len(corrected_flag) == 4
assert corrected_flag[0][0] == UTCDateTime("2009-12-23T06:00:00.0")
assert corrected_flag[0][1] == UTCDateTime("2009-12-23T06:30:00.0")
assert corrected_flag[1][0] == UTCDateTime("2009-12-24T10:00:00.0")
assert corrected_flag[1][1] == UTCDateTime("2009-12-24T10:30:00.0")
assert corrected_flag[2][0] == UTCDateTime("2009-12-26T18:00:00.0")
assert corrected_flag[2][1] == UTCDateTime("2009-12-26T18:00:00.0")
assert corrected_flag[3][0] == UTCDateTime("2009-12-26T18:04:00.0")
assert corrected_flag[3][1] == UTCDateTime("2009-12-26T18:04:00.0")
# Test of the (valid) example 2 written in set_flags_in_fixed_headers's
# docstring
flag_value = {"INSTANT": [date5, date6],
"DURATION": [date1, date2, date3, date4]}
assert len(corrected_flag) == 4
# Sort by start date to ensure uniqueness of the list
corrected_flag.sort(key=lambda val: val[0])
assert len(corrected_flag) == 4
assert corrected_flag[0][0] == UTCDateTime("2009-12-23T06:00:00.0")
assert corrected_flag[0][1] == UTCDateTime("2009-12-23T06:30:00.0")
assert corrected_flag[1][0] == UTCDateTime("2009-12-24T10:00:00.0")
assert corrected_flag[1][1] == UTCDateTime("2009-12-24T10:30:00.0")
assert corrected_flag[2][0] == UTCDateTime("2009-12-26T18:00:00.0")
assert corrected_flag[2][1] == UTCDateTime("2009-12-26T18:00:00.0")
assert corrected_flag[3][0] == UTCDateTime("2009-12-26T18:04:00.0")
assert corrected_flag[3][1] == UTCDateTime("2009-12-26T18:04:00.0")
# Invalid type for datation flag
flag_value = "invalid because str"
with pytest.raises(ValueError):
util._check_flag_value(flag_value)
# Invalid key (neither "INSTANT" nor "DURATION") for datation dict
flag_value = {"INVALID_KEY": [UTCDateTime("2009-12-25T07:10:00.0")]}
with pytest.raises(ValueError):
util._check_flag_value(flag_value)
# Invalid value type for key "INSTANT"
flag_value = {"INSTANT": "invalid because str"}
with pytest.raises(ValueError):
util._check_flag_value(flag_value)
# Invalid value type for key "DURATION"
flag_value = {"DURATION": "invalid because str"}
with pytest.raises(ValueError):
util._check_flag_value(flag_value)
# Invalid len for key DURATION #1
flag_value = {"DURATION": [UTCDateTime("2009-12-25T06:00:00.0"),
UTCDateTime("2009-12-25T06:10:00.0"),
UTCDateTime("2009-12-25T06:20:00.0")]}
with pytest.raises(ValueError):
util._check_flag_value(flag_value)
# Invalid type in DURATION
flag_value = {"DURATION": [UTCDateTime("2009-12-25T06:00:00.0"),
UTCDateTime("2009-12-25T06:10:00.0"),
UTCDateTime("2009-12-25T06:20:00.0"),
"invalid because str"]}
with pytest.raises(ValueError):
util._check_flag_value(flag_value)
# Start after end in DURATION
flag_value = {"DURATION": [UTCDateTime("2010-12-27T19:50:59.0"),
UTCDateTime("2009-12-25T06:00:00.0")]}
with pytest.raises(ValueError):
util._check_flag_value(flag_value)
def test_search_flag_in_blockette(self):
"""
Test case for obspy.io.mseed.util._search_flag_in_blockette
"""
# Write dummy file
npts = 2000
np.random.seed(42) # make test reproducible
data = np.random.randint(-1000, 1000, npts).astype(np.int32)
# This header ensures presence of blockettes 1000 and 1001
stat_header = {'network': 'NE', 'station': 'STATI', 'location': 'LO',
'channel': 'CHA', 'npts': len(data), 'sampling_rate': 1,
'mseed': {'dataquality': 'D',
'blkt1001': {'timing_quality': 63}}}
stat_header['starttime'] = UTCDateTime(datetime(2012, 8, 1,
12, 0, 0, 42))
trace1 = Trace(data=data, header=stat_header)
st = Stream([trace1])
with NamedTemporaryFile() as tf:
st.write(tf, format="mseed", encoding=11, reclen=512)
tf.seek(0, os.SEEK_SET)
file_name = tf.name
with open(file_name, "rb") as file_desc:
file_desc.seek(0, os.SEEK_SET)
# Test from file start
read_bytes = util._search_flag_in_blockette(
file_desc, 48, 1001, 4, 1)
assert not (read_bytes is None)
assert unpack(">B", read_bytes)[0] == 63
# Test from middle of a record header
file_desc.seek(14, os.SEEK_CUR)
file_pos = file_desc.tell()
read_bytes = util._search_flag_in_blockette(
file_desc, 34, 1000, 6, 1)
assert not (read_bytes is None)
assert unpack(">B", read_bytes)[0] == 9
# Check that file_desc position has not changed
assert file_desc.tell() == file_pos
# Test from middle of a record data
file_desc.seek(60, os.SEEK_CUR)
read_bytes = util._search_flag_in_blockette(
file_desc, -26, 1001, 5, 1)
assert not (read_bytes is None)
assert unpack(">B", read_bytes)[0] == 42
# Test another record. There is at least 3 records in a
# mseed with 2000 data points and 512 bytes record length
file_desc.seek(1040, os.SEEK_SET)
read_bytes = util._search_flag_in_blockette(file_desc,
32, 1001, 4, 1)
assert unpack(">B", read_bytes)[0] == 63
# Test missing blockette
read_bytes = util._search_flag_in_blockette(file_desc,
32, 201, 4, 4)
assert read_bytes is None
def test_convert_flags_to_raw_bytes(self):
"""
Test case for obspy.io.mseed.util._convert_flags_to_raw_byte
"""
recstart = UTCDateTime("2009-12-25T06:00:00.0")
recend = UTCDateTime("2009-12-26T06:00:00.0")
user_flags = {
# boolean flags
'calib_signal': True,
'time_correction': False,
# instant value
'begin_event': [(UTCDateTime("2009-12-25T07:00:00.0"),
UTCDateTime("2009-12-25T07:00:00.0"))],
# duration value (inside record)
'end_event': [(UTCDateTime("2009-12-25T07:00:00.0"),
UTCDateTime("2009-12-25T07:04:00.0"))],
# instant value at the end of the record
'positive_leap': [(UTCDateTime("2009-12-26T06:00:00.0"),
UTCDateTime("2009-12-26T06:00:00.0"))],
# value before record start
'negative_leap': [(UTCDateTime("2001-12-25T06:00:00.0"),
UTCDateTime("2001-12-25T06:00:00.0"))],
# value after record end
'event_in_progress': [(UTCDateTime("2020-12-25T06:00:00.0"),
UTCDateTime("2020-12-25T06:00:00.0"))]}
act_flags = util._convert_flags_to_raw_byte(
FIXED_HEADER_ACTIVITY_FLAGS, user_flags, recstart, recend)
assert act_flags == 13
user_flags = {
# duration value (across record start)
'sta_vol_parity_error_possible':
[(UTCDateTime("2009-12-25T00:00:00.0"),
UTCDateTime("2009-12-26T00:00:00.0"))],
# duration value (across record end)
'long_record_read': [(UTCDateTime("2009-12-26T00:00:00.0"),
UTCDateTime("2009-12-27T00:00:00.0"))],
# duration value (record inside duration)
'short_record_read': [(UTCDateTime("2009-12-25T00:00:00.0"),
UTCDateTime("2009-12-27T00:00:00.0"))],
# several datation periods, one matching the record
'start_of_time_series': [(UTCDateTime("2008-12-25T00:00:00.0"),
UTCDateTime("2008-12-27T00:00:00.0")),
(UTCDateTime("2009-12-26T00:00:00.0"),
UTCDateTime("2009-12-26T00:00:00.0")),
(UTCDateTime("2010-12-25T00:00:00.0"),
UTCDateTime("2010-12-27T00:00:00.0"))]}
io_clock = util._convert_flags_to_raw_byte(
FIXED_HEADER_IO_CLOCK_FLAGS, user_flags, recstart, recend)
assert io_clock == 15
# Quick check of data quality flags
user_flags = {'amplifier_sat_detected': True,
'digitizer_clipping_detected': False,
'spikes_detected': True,
'glitches_detected': False,
'missing_padded_data_present': True,
'telemetry_sync_error': False,
'digital_filter_maybe_charging': True,
'time_tag_questionable': False}
data_qual = util._convert_flags_to_raw_byte(
FIXED_HEADER_DATA_QUAL_FLAGS, user_flags, recstart, recend)
assert data_qual == 85
def test_set_flags_in_fixed_header(self):
"""
Test case for obspy.io.mseed.util.set_flags_in_fixed_headers
"""
# Write mseed file with several traces
npts = 1000
np.random.seed(42) # make test reproducible
data = np.random.randint(-1000, 1000, npts).astype(np.int32)
# Test valid data
stat_header = {'network': 'NE', 'station': 'STATI', 'location': 'LO',
'channel': 'CHA', 'npts': len(data), 'sampling_rate': 1,
'mseed': {'dataquality': 'D',
'blkt1001': {'timing_quality': 63}}}
stat_header['starttime'] = UTCDateTime(datetime(2012, 8, 1,
12, 0, 0, 0))
trace1 = Trace(data=data, header=stat_header)
stat_header['channel'] = 'CHB'
trace2 = Trace(data=data, header=stat_header)
stat_header['station'] = 'STATJ'
trace3 = Trace(data=data, header=stat_header)
st = Stream([trace1, trace2, trace3])
with NamedTemporaryFile() as tf:
st.write(tf, format="mseed", encoding=11, reclen=512)
tf.seek(0, os.SEEK_SET)