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test_scan.py
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test_scan.py
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# -*- coding: utf-8 -*-
"""
The obspy.imaging.scripts.scan / obspy-scan test suite.
"""
import os
import shutil
import warnings
from pathlib import Path
import matplotlib.pyplot as plt
import pytest
from obspy import read, UTCDateTime
from obspy.core.util.base import NamedTemporaryFile, get_example_file
from obspy.core.util.misc import TemporaryWorkingDirectory, CatchOutput
from obspy.imaging.scripts.scan import main as obspy_scan
from obspy.imaging.scripts.scan import scan, Scanner
class TestScan:
"""
Test cases for obspy-scan
"""
@pytest.fixture(scope='class')
def all_files(self, root):
"""return a list of all waveform files in the test suite."""
sac_files = ['LMOW.BHE.SAC', 'seism.sac', 'dis.G.SCZ.__.BHE_short',
'null_terminated.sac', 'test.sac', 'seism-longer.sac',
'test.sac.swap', 'seism-shorter.sac', 'testxy.sac']
gse2_files = ['STA2.testlines', 'STA2.testlines_out', 'acc.gse',
'loc_RJOB20050831023349.z',
'loc_RJOB20050831023349_first100_dos.z',
'loc_RNON20040609200559.z', 'loc_STAU20031119011659.z',
'sta2.gse2', 'twiceCHK2.gse2', 'y2000.gse']
all_files = [root / 'io' / 'sac' / 'tests' / 'data' / i
for i in sac_files]
all_files.extend([root / 'io' / 'gse2' / 'tests' / 'data' / i
for i in gse2_files])
return all_files
def test_scan_main_method(self, all_files, image_path):
"""
Run obspy-scan on selected tests/data directories
"""
# Copy files to a temp folder to avoid wildcard scans.
with TemporaryWorkingDirectory():
for filename in all_files:
shutil.copy(filename, os.curdir)
obspy_scan([os.curdir] + ['--output', str(image_path)])
def test_scan_dir_no_permission(self, all_files):
"""
Run obspy-scan on a directory without read permission.
Should just skip it and not raise an exception. see #3115
"""
# Copy files to a temp folder to avoid wildcard scans.
scanner = Scanner()
with TemporaryWorkingDirectory():
no_permission_dir = Path('no_permission_dir')
no_permission_dir.mkdir()
# copy one test file in
shutil.copy(all_files[0], no_permission_dir)
# take away read permissions
no_permission_dir.chmod(0o000)
# still sometimes even on Linux CI runners it seems that stripping
# read permission does not work and the scanner is able to process
# it, thus ending up with a higher counter than if properly making
# the directory not readable
try:
os.listdir(no_permission_dir)
# this is what we want, not being able to read the directory, thus
# the scanner only processing one item
except PermissionError:
pass
# this is unexpected, we weren't able to strip read permissions,
# and then in consequence this test is meaningless and we mark it
# as a skipped test
else:
pytest.skip(
"unable to remove read permission from a test file for "
"testing purposes")
scanner.parse(str(no_permission_dir))
# should not have been able to read test file but also not raised
# an error
assert scanner.counter == 1
assert not scanner.data
# now allow read permission and read again
no_permission_dir.chmod(0o777)
scanner.parse(str(no_permission_dir))
assert scanner.counter == 2
assert '.LMOW..BHE' in scanner.data
for child in no_permission_dir.iterdir():
child.unlink()
no_permission_dir.rmdir()
def test_scan_function_and_scanner_class(self, all_files, image_path):
"""
Test scan function and Scanner class (in one test to keep overhead of
copying files down)
"""
scanner = Scanner()
path1 = image_path.parent / 'scan1.png'
path2 = image_path.parent / 'scan2.png'
# Copy files to a temp folder to avoid wildcard scans.
with TemporaryWorkingDirectory():
for filename in all_files:
shutil.copy(filename, os.curdir)
scanner.parse(os.curdir)
scan(paths=os.curdir, plot=path1)
scanner.plot(path2)
def test_scan_plot_by_id_with_wildcard(self):
"""
Test selecting what to plot after scanning with wildcards in selected
SEED IDs
"""
files = [
"BW.UH1._.EHZ.D.2010.147.a.slist.gz",
"BW.UH1._.EHZ.D.2010.147.b.slist.gz",
"BW.UH1._.SHZ.D.2010.147.cut.slist.gz",
"BW.UH2._.SHZ.D.2010.147.cut.slist.gz",
"BW.UH3._.SHE.D.2010.147.cut.slist.gz",
"BW.UH3._.SHN.D.2010.147.cut.slist.gz",
"BW.UH3._.SHZ.D.2010.147.cut.slist.gz",
"BW.UH4._.EHZ.D.2010.147.cut.slist.gz",
"IUANMO.seed"]
scanner = Scanner()
for filename in files:
scanner.parse(get_example_file(filename))
expected = [
('*.UH[12]*',
['BW.UH2..SHZ\n100.0%',
'BW.UH1..SHZ\n100.0%',
'BW.UH1..EHZ\n10.7%']),
('*Z',
['IU.ANMO.00.LHZ\n100.0%',
'BW.UH4..EHZ\n100.0%',
'BW.UH3..SHZ\n100.0%',
'BW.UH2..SHZ\n100.0%',
'BW.UH1..SHZ\n100.0%',
'BW.UH1..EHZ\n10.7%'])]
for seed_id, expected_labels in expected:
fig, ax = plt.subplots()
fig = scanner.plot(fig=fig, show=False, seed_ids=[seed_id])
got = [label.get_text() for label in ax.get_yticklabels()]
assert got == expected_labels
plt.close(fig)
def test_scanner_manually_add_streams(self, all_files, image_path):
"""
Test Scanner class, manually adding streams of read data files
"""
scanner = Scanner()
# Copy files to a temp folder to avoid wildcard scans.
with TemporaryWorkingDirectory():
for filename in all_files:
shutil.copy(filename, os.curdir)
for file_ in os.listdir(os.curdir):
# some files used in the test cases actually can not
# be read with obspy..
if file_ in ('STA2.testlines_out', 'STA2.testlines',
'seism-shorter.sac', 'seism-longer.sac'):
continue
st = read(file_, headonly=True)
scanner.add_stream(st)
scanner.plot(str(image_path))
def test_scan_save_load_npz(self, all_files, image_path):
"""
Run obspy-scan on selected tests/data directories, saving/loading
to/from npz.
Tests both the command line script and the Scanner class.
"""
scanner = Scanner()
# Copy files to a temp folder to avoid wildcard scans.
with TemporaryWorkingDirectory():
for filename in all_files:
shutil.copy(filename, os.curdir)
# save via command line
obspy_scan([os.curdir, '--write', 'scan.npz'])
# save via Python
scanner.parse(os.curdir)
scanner.save_npz('scanner.npz')
scanner = Scanner()
path1 = image_path.parent / 'scan_load_npz_1.png'
path2 = image_path.parent / 'scan_load_npz_2.png'
# version string of '0.0.0+archive' raises UserWarning - ignore
with warnings.catch_warnings(record=True):
warnings.simplefilter('ignore', UserWarning)
# load via Python
scanner.load_npz('scanner.npz')
scanner.plot(path1)
# load via command line
obspy_scan(['--load', 'scan.npz', '--output', str(path2)])
def test_scan_times(self, all_files, image_path):
"""
Checks for timing related options
"""
# Copy files to a temp folder to avoid wildcard scans.
with TemporaryWorkingDirectory():
for filename in all_files:
shutil.copy(filename, os.curdir)
obspy_scan([os.curdir] + ['--output', str(image_path)] +
['--start-time', '2004-01-01'] +
['--end-time', '2004-12-31'] +
['--event-time', '2004-03-14T15:09:26'] +
['--event-time', '2004-02-07T18:28:18'])
def test_multiple_sampling_rates(self, image_path):
"""
Check for multiple sampling rates
"""
lines = [
"TIMESERIES XX_TEST__BHZ_R, 200 samples, 200 sps, "
"2008-01-15T00:00:00.000000, SLIST, INTEGER, Counts",
"TIMESERIES XX_TEST__BHZ_R, 50 samples, 50 sps, "
"2008-01-15T00:00:00.900000, SLIST, INTEGER, Counts",
"TIMESERIES XX_TEST__BHZ_R, 200 samples, 200 sps, "
"2008-01-15T00:00:02.000000, SLIST, INTEGER, Counts",
]
files = []
expected = [
"XX.TEST..BHZ 2008-01-15T00:00:01.000000Z "
"2008-01-15T00:00:00.899995Z -0.100",
"XX.TEST..BHZ 2008-01-15T00:00:01.899999Z "
"2008-01-15T00:00:02.000000Z 0.100"
]
with NamedTemporaryFile() as f1, NamedTemporaryFile() as f2, \
NamedTemporaryFile() as f3:
for i, fp in enumerate([f1, f2, f3]):
fp.write(("%s\n" % lines[i]).encode('ascii',
'strict'))
fp.flush()
fp.seek(0)
files.append(fp.name)
# make image comparison instance and set manual rms (see #2089)
with CatchOutput() as out:
cmds = ['--output', str(image_path), '--print-gaps']
obspy_scan(files + cmds)
# read output and compare with expected
# only check if datetime objects are close, not exact
output = out.stdout.splitlines()
for ex_line, out_line in zip(expected, output):
ex_split = ex_line.split(' ')
out_split = out_line.split(' ')
for ex_str, out_str in zip(ex_split, out_split):
try:
utc1 = UTCDateTime(ex_str)
utc2 = UTCDateTime(out_str)
except (ValueError, TypeError):
# if str is not a datetime it should be equal
assert ex_str == out_str
else:
# datetimes just need to be close
t1, t2 = utc1.timestamp, utc2.timestamp
assert abs(t1 - t2) < .001