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test_read_rg16.py
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test_read_rg16.py
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# -*- coding: utf-8 -*-
"""
Tests for reading rg16 format.
"""
import io
import numpy as np
import pytest
import obspy
import obspy.io.rg16.core as rc
from obspy import read, UTCDateTime
class TestReadRG16():
@pytest.fixture(autouse=True, scope="function")
def setup(self, testdata):
self.one_chan_fcnt = testdata['one_channel_many_traces.fcnt']
self.three_chan_fcnt = testdata['three_chans_six_traces.fcnt']
self.bad_alias_filter = testdata['channel_set_bad_alias_filter.dat']
self.header_block_same_ru_code = testdata['header_3_chan_one_code.dat']
self.fcnt_files = [self.one_chan_fcnt, self.three_chan_fcnt]
def test_reading_rg16_files(self):
"""
Ensure that the rg16 files are read by the function
:func:`~obspy.core.stream.read` with or without specifying the format.
"""
for fcnt_file in self.fcnt_files:
st_1 = read(fcnt_file)
st_2 = read(fcnt_file, format="RG16")
st_3 = rc._read_rg16(fcnt_file)
# when the function read is called a key "_format" is introduced
# in the object stats. This key is not created when the function
# _read_rg16 is called. In order to check the stream equality, the
# key "_format" was removed.
for tr_1, tr_2 in zip(st_1, st_2):
del tr_1.stats._format
del tr_2.stats._format
assert st_1 == st_3
assert st_2 == st_3
def test_rg16_files_identified(self):
"""
Ensure the rg16 files are correctly labeled as such.
"""
for fcnt_file in self.fcnt_files:
assert rc._is_rg16(fcnt_file)
with open(fcnt_file, 'rb') as fi:
assert rc._is_rg16(fi)
def test_empty_buffer(self):
"""
Ensure an empty buffer returns false.
"""
buff = io.BytesIO()
assert not rc._is_rg16(buff)
def test_headonly_option(self):
"""
Ensure no data is returned when the option headonly is used.
"""
st = rc._read_rg16(self.three_chan_fcnt, headonly=True)
for tr in st:
assert len(tr.data) == 0
assert tr.stats.npts != 0
def test_starttime_endtime_option(self):
"""
Test the options starttime and endtime
"""
t1 = UTCDateTime(2017, 8, 9, 16, 0, 15)
t2 = UTCDateTime(2017, 8, 9, 16, 0, 45)
# read streams for testing. The three channel rg16 file has 6 traces
# but the streams may have less depending on the starttime/endtime
st = rc._read_rg16(self.three_chan_fcnt) # no time filtering
st1 = rc._read_rg16(self.three_chan_fcnt, starttime=t1, endtime=t2)
# test using starttime and endtime
assert len(st1) == len(st)
for tr, tr1 in zip(st, st1):
assert tr.stats.starttime == tr1.stats.starttime
assert tr.stats.endtime == tr1.stats.endtime
def test_intrablock_starttime_endtime(self):
"""
Test starttime/endtime options when starttime and endtime are comprised
in a data block.
"""
t1 = UTCDateTime(2017, 8, 9, 16, 0, 47)
t2 = UTCDateTime(2017, 8, 9, 16, 0, 58)
# read streams for testing
st = rc._read_rg16(self.three_chan_fcnt) # no time filtering
st1 = rc._read_rg16(self.three_chan_fcnt, starttime=t1, endtime=t2)
# test when starttime and endtime are comprised in a data packet.
assert len(st1) == 3
for tr, tr1 in zip(st[1::2], st1):
assert tr.stats.starttime == tr1.stats.starttime
assert tr.stats.endtime == tr1.stats.endtime
def test_merge(self):
"""
Ensure the merge option of read_rg16 merges all contiguous traces
together.
"""
for fcnt_file in self.fcnt_files:
st_merged = rc._read_rg16(fcnt_file, merge=True)
st = rc._read_rg16(fcnt_file).merge()
assert len(st) == len(st_merged)
assert st == st_merged
def test_contacts_north_and_merge(self):
"""
Ensure the "contacts_north" and "merge" parameters can be used
together. See #2198.
"""
for filename in self.fcnt_files:
st = rc._read_rg16(filename, contacts_north=True, merge=True)
assert isinstance(st, obspy.Stream)
def test_make_stats(self):
"""
Check function make_stats.
"""
with open(self.three_chan_fcnt, 'rb') as fi:
stats = rc._make_stats(fi, 288, False, False)
assert isinstance(stats, obspy.core.trace.Stats)
assert abs(stats.sampling_rate-500) < 1e-5
assert stats.network == '1'
assert stats.station == '1'
assert stats.location == '1'
assert stats.channel == 'DP3'
assert stats.npts == 15000
assert stats.starttime == UTCDateTime('2017-08-09T16:00:00.380000Z')
assert stats.endtime == UTCDateTime('2017-08-09T16:00:30.378000Z')
with open(self.three_chan_fcnt, 'rb') as fi:
stats = rc._make_stats(fi, 288, True, False)
assert stats.channel == 'DPN'
class TestReadRG16Headers():
@pytest.fixture(autouse=True, scope="function")
def setup(self, testdata):
self.one_chan_fcnt = testdata['one_channel_many_traces.fcnt']
self.three_chan_fcnt = testdata['three_chans_six_traces.fcnt']
self.bad_alias_filter = testdata['channel_set_bad_alias_filter.dat']
self.header_block_same_ru_code = testdata['header_3_chan_one_code.dat']
self.fcnt_files = [self.one_chan_fcnt, self.three_chan_fcnt]
def test_cmp_nbr_headers(self):
"""
Test to check that the number of headers is correct.
"""
with open(self.three_chan_fcnt, 'rb') as fi:
(nbr_channel_set_headers, nbr_extended_headers,
nbr_external_headers) = rc._cmp_nbr_headers(fi)
assert nbr_channel_set_headers == 3
assert nbr_extended_headers == 3
assert nbr_external_headers == 1
def test_cmp_nbr_records(self):
"""
Check the number of records in the file.
"""
with open(self.three_chan_fcnt, 'rb') as fi:
nbr_records = rc._cmp_nbr_records(fi)
assert nbr_records == 6
with open(self.one_chan_fcnt, 'rb') as fi:
nbr_records = rc._cmp_nbr_records(fi)
assert nbr_records == 10
def test_cmp_jump(self):
"""
Check the number of bytes to jump to reach the next trace block.
"""
with open(self.three_chan_fcnt, 'rb') as fi:
jump = rc._cmp_jump(fi, 288)
assert jump == 60340
def test_read_trace_header(self):
"""
Test the reading of the trace header.
"""
with open(self.three_chan_fcnt, 'rb') as fi:
trace_header = rc._read_trace_header(fi, 288)
assert trace_header['trace_number'] == 1
assert trace_header['trace_edit_code'] == 0
def test_read_trace_header_1(self):
"""
Test the reading of the trace header 1.
"""
with open(self.three_chan_fcnt, 'rb') as fi:
trace_header_1 = rc._read_trace_header_1(fi, 288)
assert trace_header_1['extended_receiver_line_nbr'] == 65536
assert trace_header_1['extended_receiver_point_nbr'] == 65536
assert trace_header_1['sensor_type'] == 3
assert trace_header_1['trace_count_file'] == 1
def test_read_trace_header_2(self):
"""
Test the reading of the trace header 2.
"""
with open(self.three_chan_fcnt, 'rb') as fi:
trace_header_2 = rc._read_trace_header_2(fi, 288)
assert trace_header_2['shot_line_nbr'] == 2240
assert trace_header_2['shot_point'] == 1
assert trace_header_2['shot_point_index'] == 0
assert abs(trace_header_2['shot_point_pre_plan_x']-0) < 1e-5
assert abs(trace_header_2['shot_point_pre_plan_y']-0) < 1e-5
assert abs(trace_header_2['shot_point_final_x']-0) < 1e-5
assert abs(trace_header_2['shot_point_final_y']-0) < 1e-5
assert abs(trace_header_2['shot_point_final_depth']-0) < 1e-5
assert trace_header_2['source_of_final_shot_info'] == 'undefined'
assert trace_header_2['energy_source_type'] == 'undefined'
def test_read_trace_header_3(self):
"""
Test the reading of the trace header 3.
"""
with open(self.three_chan_fcnt, 'rb') as fi:
trace_header_3 = rc._read_trace_header_3(fi, 288)
assert trace_header_3['epoch_time'] == \
UTCDateTime('2017-08-09T16:00:00.380000Z')
assert abs(trace_header_3['shot_skew_time']-0) < 1e-5
assert abs(trace_header_3['time_shift_clock_correction']-0) < 1e-5
assert abs(trace_header_3['remaining_clock_correction']-0) < 1e-5
def test_read_trace_header_4(self):
"""
Test the reading of the trace header 4.
"""
with open(self.three_chan_fcnt, 'rb') as fi:
trace_header_4 = rc._read_trace_header_4(fi, 288)
assert abs(trace_header_4['pre_shot_guard_band']-0) < 1e-5
assert abs(trace_header_4['post_shot_guard_band']-0) < 1e-5
assert trace_header_4['preamp_gain'] == 24
assert trace_header_4['trace_clipped_flag'] == 'not clipped'
assert trace_header_4['record_type_code'] == \
'normal seismic data record'
assert trace_header_4['shot_status_flag'] == 'normal'
assert trace_header_4['external_shot_id'] == 0
key = 'post_processed_first_break_pick_time'
assert abs(trace_header_4[key]-0) < 1e-5
assert abs(trace_header_4['post_processed_rms_noise']-0) < 1e-5
def test_read_trace_header_5(self):
"""
Test the reading of the trace header 5.
"""
with open(self.three_chan_fcnt, 'rb') as fi:
trace_header_5 = rc._read_trace_header_5(fi, 288)
assert abs(trace_header_5['receiver_point_pre_plan_x']-469567.2) < 1e-5
assert \
abs(trace_header_5['receiver_point_pre_plan_y']-5280707.8) < 1e-5
assert abs(trace_header_5['receiver_point_final_x']-469565.2) < 1e-5
assert abs(trace_header_5['receiver_point_final_y']-5280709.7) < 1e-5
assert abs(trace_header_5['receiver_point_final_depth']-0) < 1e-5
assert trace_header_5['source_of_final_receiver_info'] == \
'as laid (no navigation sensor)'
def test_read_trace_header_6(self):
"""
Test the reading of the trace header 6.
"""
with open(self.three_chan_fcnt, 'rb') as fi:
trace_header_6 = rc._read_trace_header_6(fi, 288)
assert abs(trace_header_6['tilt_matrix_h1x']-0) < 1e-5
assert abs(trace_header_6['tilt_matrix_h2x']-0) < 1e-5
assert abs(trace_header_6['tilt_matrix_vx']-0) < 1e-5
assert abs(trace_header_6['tilt_matrix_h1y']-0) < 1e-5
assert abs(trace_header_6['tilt_matrix_h2y']-0) < 1e-5
assert abs(trace_header_6['tilt_matrix_vy']-0) < 1e-5
assert abs(trace_header_6['tilt_matrix_h1z']-0) < 1e-5
assert abs(trace_header_6['tilt_matrix_h2z']-0) < 1e-5
def test_read_trace_header_7(self):
"""
Test the reading of the trace header 7.
"""
with open(self.three_chan_fcnt, 'rb') as fi:
trace_header_7 = rc._read_trace_header_7(fi, 288)
assert abs(trace_header_7['tilt_matrix_vz']-0) < 1e-5
assert abs(trace_header_7['azimuth_degree']-0) < 1e-5
assert abs(trace_header_7['pitch_degree']-0) < 1e-5
assert abs(trace_header_7['roll_degree']-0) < 1e-5
assert abs(trace_header_7['remote_unit_temp']-0) < 1e-5
assert abs(trace_header_7['remote_unit_humidity']-0) < 1e-5
assert trace_header_7['orientation_matrix_version_nbr'] == 0
assert trace_header_7['gimbal_corrections'] == 0
def test_read_trace_header_8(self):
"""
Test the reading of the trace header 8.
"""
with open(self.three_chan_fcnt, 'rb') as fi:
trace_header_8 = rc._read_trace_header_8(fi, 288)
assert trace_header_8['fairfield_test_analysis_code'] == 0
assert trace_header_8['first_test_oscillator_attenuation'] == 0
assert trace_header_8['second_test_oscillator_attenuation'] == 0
assert abs(trace_header_8['start_delay']-0) < 1e-5
assert trace_header_8['dc_filter_flag'] == 0
assert abs(trace_header_8['dc_filter_frequency']-0) < 1e-5
assert trace_header_8['preamp_path'] == 'external input selected'
assert trace_header_8['test_oscillator_signal_type'] == \
'test oscillator path open'
def test_read_trace_header_9(self):
"""
Test the reading of the trace header 9.
"""
with open(self.three_chan_fcnt, 'rb') as fi:
trace_header_9 = rc._read_trace_header_9(fi, 288)
assert trace_header_9['test_signal_generator_signal_type'] == \
'pattern is address ramp'
key = 'test_signal_generator_frequency_1'
assert abs(trace_header_9[key]-0) < 1e-5
key = 'test_signal_generator_frequency_2'
assert abs(trace_header_9[key]-0) < 1e-5
assert trace_header_9['test_signal_generator_amplitude_1'] == 0
assert trace_header_9['test_signal_generator_amplitude_2'] == 0
key = 'test_signal_generator_duty_cycle_percentage'
assert abs(trace_header_9[key]-0) < 1e-5
key = 'test_signal_generator_active_duration'
assert abs(trace_header_9[key]-0) < 1e-5
key = 'test_signal_generator_activation_time'
assert abs(trace_header_9[key]-0) < 1e-5
def test_read_trace_header_10(self):
"""
Test the reading of the trace header 10.
"""
with open(self.three_chan_fcnt, 'rb') as fi:
trace_header_10 = rc._read_trace_header_10(fi, 288)
assert trace_header_10['test_signal_generator_idle_level'] == 0
assert trace_header_10['test_signal_generator_active_level'] == 0
assert trace_header_10['test_signal_generator_pattern_1'] == 0
assert trace_header_10['test_signal_generator_pattern_2'] == 0
def test_make_trace(self):
"""
Test if the ten first samples of the waveform are read correctly
and if the output is a Trace object.
"""
with open(self.three_chan_fcnt, 'rb') as fi:
trace_3 = rc._make_trace(fi, 288, False, False, False)
trace_z = rc._make_trace(fi, 241648, False, True, False)
expected = np.array([-0.18864873, -0.30852857, -0.35189095,
-0.22547323, -0.12023376, -0.14336781,
-0.11712314, 0.04060567, 0.18024819,
0.17769636])
all_close = np.allclose(trace_3.data[:len(expected)], expected)
assert all_close
assert isinstance(trace_3, obspy.core.trace.Trace)
expected = np.array([-0.673309, -0.71590775, -0.54966664, -0.33980238,
-0.29999766, -0.3031269, -0.12762846, 0.08782373,
0.11377038, 0.09888785])
all_close = np.allclose(trace_z.data[:len(expected)], expected)
assert all_close
def test_can_write(self):
"""
Ensure the result of _read_rg16 is a stream object and that
it can be written as mseed.
"""
st = rc._read_rg16(self.three_chan_fcnt)
assert isinstance(st, obspy.core.stream.Stream)
bytstr = io.BytesIO()
# test passes if this doesn't raise
try:
st.write(bytstr, 'mseed')
except Exception:
self.fail('Failed to write to mseed!')
def test_read_general_header_1(self):
"""
Test the reading of the general header 1.
"""
with open(self.three_chan_fcnt, 'rb') as fi:
header_1 = rc._read_general_header_1(fi)
assert header_1['base_scan_interval'] == 32
assert header_1['file_number'] == 1
assert header_1['general_constant'] == 0
assert header_1['julian_day'] == 221
assert header_1['manufacturer_code'] == 20
assert header_1['manufacturer_serial_number'] == 0
assert header_1['nbr_add_general_header'] == 1
assert header_1['nbr_channel_set'] == 3
assert header_1['nbr_skew_block'] == 0
assert header_1['polarity_code'] == 0
assert header_1['record_type'] == 0
assert header_1['sample_format_code'] == 8058
assert header_1['scan_type_per_record'] == 1
assert header_1['time_slice'] == 160000
assert header_1['time_slice_year'] == 17
def test_read_general_header_2(self):
"""
Test the reading of the general header 2.
"""
with open(self.three_chan_fcnt, 'rb') as fi:
header_2 = rc._read_general_header_2(fi)
assert header_2['extended_channel_sets_per_scan_type'] == 3
assert header_2['extended_file_number'] == 1
assert header_2['extended_header_blocks'] == 3
assert header_2['extended_record_length'] == 30
assert header_2['external_header_blocks'] == 1
assert header_2['general_header_block_number'] == 2
assert header_2['version_number'] == 262
def test_read_channel_sets(self):
"""
Test that all the channel sets are read.
"""
with open(self.three_chan_fcnt, 'rb') as fi:
channel_sets = rc._read_channel_sets(fi)
assert len(channel_sets) == 3
def test_read_channel_set(self):
"""
Test the reading of the first channel set.
"""
with open(self.three_chan_fcnt, 'rb') as fi:
channel_set_1 = rc._read_channel_set(fi, 64)
assert channel_set_1['RU_channel_number'] == 1
assert channel_set_1['alias_filter_frequency'] == 207
assert channel_set_1['alias_filter_slope'] == 320
assert channel_set_1['array_forming'] == 0
assert abs(channel_set_1['channel_set_end_time']-30) < 1e-5
assert channel_set_1['channel_set_number'] == 1
assert abs(channel_set_1['channel_set_start_time']-0) < 1e-5
assert channel_set_1['channel_type_code'] == 1
assert channel_set_1['extended_channel_set_number'] == 1
assert channel_set_1['extended_header_flag'] == 0
assert channel_set_1['gain_control_type'] == 3
assert channel_set_1['low_cut_filter_freq'] == 0
assert channel_set_1['low_cut_filter_slope'] == 6
assert channel_set_1['mp_factor_descaler_multiplier'] == 0
assert channel_set_1['nbr_32_byte_trace_header_extension'] == 10
assert channel_set_1['nbr_channels_in_channel_set'] == 2
assert abs(channel_set_1['notch_2_filter_freq']-0) < 1e-5
assert abs(channel_set_1['notch_3_filter_freq']-0) < 1e-5
assert abs(channel_set_1['notch_filter_freq']-0) < 1e-5
assert channel_set_1['optionnal_MP_factor'] == 0
assert channel_set_1['scan_type_number'] == 1
assert channel_set_1['vertical_stack_size'] == 1
def test_read_extended_header_1(self):
"""
Test the reading of the extended header 1.
"""
with open(self.three_chan_fcnt, 'rb') as fi:
extended_header_1 = rc._read_extended_header_1(fi, 160)
assert extended_header_1['deployment_time'] == \
UTCDateTime('2017-08-09T15:46:32.230000Z')
assert extended_header_1['id_ru'] == 1219770716358969536
assert extended_header_1['pick_up_time'] == \
UTCDateTime('2017-08-09T20:06:58.120000Z')
assert extended_header_1['start_time_ru'] == \
UTCDateTime('2017-08-09T15:52:31.366000Z')
def test_read_extended_header_2(self):
"""
Test the reading of the extended header 2.
"""
with open(self.three_chan_fcnt, 'rb') as fi:
extended_header_2 = rc._read_extended_header_2(fi, 192)
assert abs(extended_header_2['acquisition_drift_window']-0) < 1e-5
assert abs(extended_header_2['clock_drift']-0) < 1e-5
assert extended_header_2['clock_stop_method'] == 'normal'
assert extended_header_2['data_collection_method'] == 'continuous'
assert extended_header_2['data_decimation'] == 'not decimated'
assert extended_header_2['file_number'] == 1
assert extended_header_2['frequency_drift'] == 'within specification'
assert extended_header_2['nbr_files'] == 1
assert extended_header_2['nbr_time_slices'] == 2
key = 'nbr_decimation_filter_coef'
assert extended_header_2[key] == 0
assert extended_header_2['original_base_scan_interval'] == 0
assert extended_header_2['oscillator_type'] == 'disciplined'
def test_read_extended_header_3(self):
"""
Test the reading of the extended header 3.
"""
with open(self.three_chan_fcnt, 'rb') as fi:
extended_header_3 = rc._read_extended_header_3(fi, 224)
assert extended_header_3['first_shot_line'] == 0
assert extended_header_3['first_shot_point'] == 0
assert extended_header_3['first_shot_point_index'] == 0
assert extended_header_3['last_shot_line'] == 0
assert extended_header_3['last_shot_point'] == 0
assert extended_header_3['last_shot_point_index'] == 0
assert extended_header_3['receiver_line_number'] == 1
assert extended_header_3['receiver_point'] == 1
assert extended_header_3['receiver_point_index'] == 1
def test_bad_alias_filter(self):
"""
Tests for when alias filter is written as an int32 rather than BSD in
the channel descriptor block.
"""
with open(self.bad_alias_filter, 'rb') as fi:
out = rc._read_channel_set(fi, 0)
alias_freq = out['alias_filter_frequency']
assert alias_freq == 207
def test_3_channel_header(self):
"""
Tests for header which has three traces but identical RU channel
number.
"""
with open(self.header_block_same_ru_code, 'rb') as fi:
num_records = rc._cmp_nbr_records(fi)
assert num_records == 2180 * 3