def main(argv=None):
parser = ArgumentParser(prog="obspy-plot", description=__doc__.strip())
parser.add_argument("-V", "--version", action="version", version="%(prog)s " + __version__)
parser.add_argument("-f", "--format", choices=ENTRY_POINTS["waveform"], help="Waveform format.")
parser.add_argument("-o", "--outfile", help="Output filename.")
parser.add_argument(
"-n",
"--no-automerge",
dest="automerge",
action="store_false",
help="Disable automatic merging of matching channels.",
)
parser.add_argument(
"--full",
dest="full",
action="store_true",
help="Disable min/max-plot, i.e. always plot every "
'single sample (Stream.plot(..., method="full"), '
"for interactive zooming).",
)
parser.add_argument("files", nargs="+", help="Files to plot.")
args = parser.parse_args(argv)
if args.outfile is not None:
MatplotlibBackend.switch_backend("AGG", sloppy=False)
st = Stream()
for f in args.files:
st += read(f, format=args.format)
kwargs = {"outfile": args.outfile, "automerge": args.automerge}
if args.full:
kwargs["method"] = "full"
st.plot(**kwargs)
def main(argv=None):
parser = ArgumentParser(prog='obspy-plot', description=__doc__.strip())
parser.add_argument('-V', '--version', action='version',
version='%(prog)s ' + __version__)
parser.add_argument('-f', '--format', choices=ENTRY_POINTS['waveform'],
help='Waveform format.')
parser.add_argument('-o', '--outfile',
help='Output filename.')
parser.add_argument('-n', '--no-automerge', dest='automerge',
action='store_false',
help='Disable automatic merging of matching channels.')
parser.add_argument('--full', dest='full', action='store_true',
help='Disable min/max-plot, i.e. always plot every '
'single sample (Stream.plot(..., method="full"), '
'for interactive zooming).')
parser.add_argument('files', nargs='+',
help='Files to plot.')
args = parser.parse_args(argv)
if args.outfile is not None:
MatplotlibBackend.switch_backend("AGG", sloppy=False)
st = Stream()
for f in args.files:
st += read(f, format=args.format)
kwargs = {"outfile": args.outfile,
"automerge": args.automerge}
if args.full:
kwargs['method'] = "full"
st.plot(**kwargs)
def main(argv=None):
parser = ArgumentParser(prog='obspy-plot', description=__doc__.strip())
parser.add_argument('-V',
'--version',
action='version',
version='%(prog)s ' + __version__)
parser.add_argument('-f',
'--format',
choices=ENTRY_POINTS['waveform'],
help='Waveform format.')
parser.add_argument('-o', '--outfile', help='Output filename.')
parser.add_argument('-n',
'--no-automerge',
dest='automerge',
action='store_false',
help='Disable automatic merging of matching channels.')
parser.add_argument('--full',
dest='full',
action='store_true',
help='Disable min/max-plot, i.e. always plot every '
'single sample (Stream.plot(..., method="full"), '
'for interactive zooming).')
parser.add_argument('files', nargs='+', help='Files to plot.')
args = parser.parse_args(argv)
if args.outfile is not None:
MatplotlibBackend.switch_backend("AGG", sloppy=False)
st = Stream()
for f in args.files:
st += read(f, format=args.format)
kwargs = {"outfile": args.outfile, "automerge": args.automerge}
if args.full:
kwargs['method'] = "full"
st.plot(**kwargs)
def main(argv=None):
parser = ArgumentParser(prog='obspy-plot', description=__doc__.strip())
parser.add_argument('-V',
'--version',
action='version',
version='%(prog)s ' + __version__)
parser.add_argument('-f',
'--format',
choices=ENTRY_POINTS['waveform'],
help='Waveform format.')
parser.add_argument('-o', '--outfile', help='Output filename.')
parser.add_argument('-n',
'--no-automerge',
dest='automerge',
action='store_false',
help='Disable automatic merging of matching channels.')
parser.add_argument('files', nargs='+', help='Files to plot.')
args = parser.parse_args(argv)
if args.outfile is not None:
MatplotlibBackend.switch_backend("AGG", sloppy=False)
st = Stream()
for f in args.files:
st += read(f, format=args.format)
st.plot(outfile=args.outfile, automerge=args.automerge)
def __enter__(self):
"""
Set matplotlib defaults.
"""
MatplotlibBackend.switch_backend("AGG", sloppy=False)
from matplotlib import font_manager, rcParams, rcdefaults
import locale
try:
locale.setlocale(locale.LC_ALL, native_str('en_US.UTF-8'))
except Exception:
try:
locale.setlocale(locale.LC_ALL,
native_str('English_United States.1252'))
except Exception:
msg = "Could not set locale to English/United States. " + \
"Some date-related tests may fail"
warnings.warn(msg)
# set matplotlib builtin default settings for testing
rcdefaults()
if self.style is not None:
self.style.__enter__()
if MATPLOTLIB_VERSION >= [2, 0, 0]:
default_font = 'DejaVu Sans'
else:
default_font = 'Bitstream Vera Sans'
rcParams['font.family'] = default_font
with warnings.catch_warnings(record=True) as w:
warnings.filterwarnings('always', 'findfont:.*')
font_manager.findfont(default_font)
if w:
warnings.warn('Unable to find the ' + default_font + ' font. '
'Plotting tests will likely fail.')
try:
rcParams['text.hinting'] = False
except KeyError:
warnings.warn("could not set rcParams['text.hinting']")
try:
rcParams['text.hinting_factor'] = 8
except KeyError:
warnings.warn("could not set rcParams['text.hinting_factor']")
if self.plt_close_all_enter:
import matplotlib.pyplot as plt
try:
plt.close("all")
except Exception:
pass
return self
def __enter__(self):
"""
Set matplotlib defaults.
"""
MatplotlibBackend.switch_backend("AGG", sloppy=False)
from matplotlib import font_manager, rcParams, rcdefaults
import locale
try:
locale.setlocale(locale.LC_ALL, native_str('en_US.UTF-8'))
except Exception:
try:
locale.setlocale(locale.LC_ALL,
native_str('English_United States.1252'))
except Exception:
msg = "Could not set locale to English/United States. " + \
"Some date-related tests may fail"
warnings.warn(msg)
# set matplotlib builtin default settings for testing
rcdefaults()
if self.style is not None:
self.style.__enter__()
if MATPLOTLIB_VERSION >= [2, 0, 0]:
default_font = 'DejaVu Sans'
else:
default_font = 'Bitstream Vera Sans'
rcParams['font.family'] = default_font
with warnings.catch_warnings(record=True) as w:
warnings.filterwarnings('always', 'findfont:.*')
font_manager.findfont(default_font)
if w:
warnings.warn('Unable to find the ' + default_font + ' font. '
'Plotting tests will likely fail.')
try:
rcParams['text.hinting'] = False
except KeyError:
warnings.warn("could not set rcParams['text.hinting']")
try:
rcParams['text.hinting_factor'] = 8
except KeyError:
warnings.warn("could not set rcParams['text.hinting_factor']")
if self.plt_close_all_enter:
import matplotlib.pyplot as plt
try:
plt.close("all")
except Exception:
pass
return self
def main(argv=None):
parser = ArgumentParser(prog='obspy-plot', description=__doc__.strip())
parser.add_argument('-V', '--version', action='version',
version='%(prog)s ' + __version__)
parser.add_argument('-f', '--format', choices=ENTRY_POINTS['waveform'],
help='Waveform format.')
parser.add_argument('-o', '--outfile',
help='Output filename.')
parser.add_argument('-n', '--no-automerge', dest='automerge',
action='store_false',
help='Disable automatic merging of matching channels.')
parser.add_argument('files', nargs='+',
help='Files to plot.')
args = parser.parse_args(argv)
if args.outfile is not None:
MatplotlibBackend.switch_backend("AGG", sloppy=False)
st = Stream()
for f in args.files:
st += read(f, format=args.format)
st.plot(outfile=args.outfile, automerge=args.automerge)
def __enter__(self):
"""
Set matplotlib defaults.
"""
MatplotlibBackend.switch_backend("AGG", sloppy=False)
from matplotlib import font_manager, rcParams, rcdefaults
import locale
try:
locale.setlocale(locale.LC_ALL, native_str('en_US.UTF-8'))
except:
try:
locale.setlocale(locale.LC_ALL,
native_str('English_United States.1252'))
except:
msg = "Could not set locale to English/United States. " + \
"Some date-related tests may fail"
warnings.warn(msg)
# set matplotlib builtin default settings for testing
rcdefaults()
rcParams['font.family'] = 'Bitstream Vera Sans'
with warnings.catch_warnings(record=True) as w:
warnings.filterwarnings('always', 'findfont:.*')
font_manager.findfont('Bitstream Vera Sans')
if w:
warnings.warn('Unable to find the Bitstream Vera Sans font. '
'Plotting tests will likely fail.')
try:
rcParams['text.hinting'] = False
except KeyError:
warnings.warn("could not set rcParams['text.hinting']")
try:
rcParams['text.hinting_factor'] = 8
except KeyError:
warnings.warn("could not set rcParams['text.hinting_factor']")
return self
def __enter__(self):
"""
Set matplotlib defaults.
"""
MatplotlibBackend.switch_backend("AGG", sloppy=False)
from matplotlib import font_manager, rcParams, rcdefaults
import locale
try:
locale.setlocale(locale.LC_ALL, native_str('en_US.UTF-8'))
except:
try:
locale.setlocale(locale.LC_ALL,
native_str('English_United States.1252'))
except:
msg = "Could not set locale to English/United States. " + \
"Some date-related tests may fail"
warnings.warn(msg)
# set matplotlib builtin default settings for testing
rcdefaults()
rcParams['font.family'] = 'Bitstream Vera Sans'
with warnings.catch_warnings(record=True) as w:
warnings.filterwarnings('always', 'findfont:.*')
font_manager.findfont('Bitstream Vera Sans')
if w:
warnings.warn('Unable to find the Bitstream Vera Sans font. '
'Plotting tests will likely fail.')
try:
rcParams['text.hinting'] = False
except KeyError:
warnings.warn("could not set rcParams['text.hinting']")
try:
rcParams['text.hinting_factor'] = 8
except KeyError:
warnings.warn("could not set rcParams['text.hinting_factor']")
return self
def run(argv=None, interactive=True):
MatplotlibBackend.switch_backend("AGG", sloppy=False)
parser = ArgumentParser(prog='obspy-runtests',
description='A command-line program that runs all '
'ObsPy tests.')
parser.add_argument('-V', '--version', action='version',
version='%(prog)s ' + get_git_version())
parser.add_argument('-v', '--verbose', action='store_true',
help='verbose mode')
parser.add_argument('-q', '--quiet', action='store_true',
help='quiet mode')
parser.add_argument('--raise-all-warnings', action='store_true',
help='All warnings are raised as exceptions when this '
'flag is set. Only for debugging purposes.')
# filter options
filter = parser.add_argument_group('Module Filter',
'Providing no modules will test all '
'ObsPy modules which do not require an '
'active network connection.')
filter.add_argument('-a', '--all', action='store_true',
dest='test_all_modules',
help='test all modules (including network modules)')
filter.add_argument('-x', '--exclude', action='append',
help='exclude given module from test')
filter.add_argument('tests', nargs='*',
help='test modules to run')
# timing / profile options
timing = parser.add_argument_group('Timing/Profile Options')
timing.add_argument('-t', '--timeit', action='store_true',
help='shows accumulated run times of each module')
timing.add_argument('-s', '--slowest', default=0, type=int, dest='n',
help='lists n slowest test cases')
timing.add_argument('-p', '--profile', action='store_true',
help='uses cProfile, saves the results to file ' +
'obspy.pstats and prints some profiling numbers')
# reporting options
report = parser.add_argument_group('Reporting Options')
report.add_argument('-r', '--report', action='store_true',
help='automatically submit a test report')
report.add_argument('-d', '--dontask', action='store_true',
help="don't explicitly ask for submitting a test "
"report")
report.add_argument('-u', '--server', default='tests.obspy.org',
help='report server (default is tests.obspy.org)')
report.add_argument('-n', '--node', dest='hostname', default=HOSTNAME,
help='nodename visible at the report server')
report.add_argument('-l', '--log', default=None,
help='append log file to test report')
report.add_argument('--ci-url', default=None, dest="ci_url",
help='URL to Continuous Integration job page.')
report.add_argument('--pr-url', default=None,
dest="pr_url", help='Github (Pull Request) URL.')
# other options
others = parser.add_argument_group('Additional Options')
others.add_argument('--tutorial', action='store_true',
help='add doctests in tutorial')
others.add_argument('--no-flake8', action='store_true',
help='skip code formatting test')
others.add_argument('--keep-images', action='store_true',
help='store images created during image comparison '
'tests in subfolders of baseline images')
others.add_argument('--keep-only-failed-images', action='store_true',
help='when storing images created during testing, '
'only store failed images and the corresponding '
'diff images (but not images that passed the '
'corresponding test).')
args = parser.parse_args(argv)
# set correct verbosity level
if args.verbose:
verbosity = 2
# raise all NumPy warnings
np.seterr(all='warn')
elif args.quiet:
verbosity = 0
# ignore user and deprecation warnings
warnings.simplefilter("ignore", DeprecationWarning)
warnings.simplefilter("ignore", UserWarning)
# don't ask to send a report
args.dontask = True
else:
verbosity = 1
# show all NumPy warnings
np.seterr(all='print')
# ignore user warnings
warnings.simplefilter("ignore", UserWarning)
# whether to raise any warning that's appearing
if args.raise_all_warnings:
# raise all NumPy warnings
np.seterr(all='raise')
# raise user and deprecation warnings
warnings.simplefilter("error", UserWarning)
# check for send report option or environmental settings
if args.report or 'OBSPY_REPORT' in os.environ.keys():
report = True
else:
report = False
if 'OBSPY_REPORT_SERVER' in os.environ.keys():
args.server = os.environ['OBSPY_REPORT_SERVER']
# check interactivity settings
if interactive and args.dontask:
interactive = False
if args.keep_images:
os.environ['OBSPY_KEEP_IMAGES'] = ""
if args.keep_only_failed_images:
os.environ['OBSPY_KEEP_ONLY_FAILED_IMAGES'] = ""
if args.no_flake8:
os.environ['OBSPY_NO_FLAKE8'] = ""
# All arguments are used by the test runner and should not interfere
# with any other module that might also parse them, e.g. flake8.
sys.argv = sys.argv[:1]
return run_tests(verbosity, args.tests, report, args.log, args.server,
args.test_all_modules, args.timeit, interactive, args.n,
exclude=args.exclude, tutorial=args.tutorial,
hostname=args.hostname, ci_url=args.ci_url,
pr_url=args.pr_url)
def run(argv=None, interactive=True):
MatplotlibBackend.switch_backend("AGG", sloppy=False)
parser = ArgumentParser(prog='obspy-runtests',
description='A command-line program that runs all '
'ObsPy tests.')
parser.add_argument('-V',
'--version',
action='version',
version='%(prog)s ' + get_git_version())
parser.add_argument('-v',
'--verbose',
action='store_true',
help='verbose mode')
parser.add_argument('-q',
'--quiet',
action='store_true',
help='quiet mode')
parser.add_argument('--raise-all-warnings',
action='store_true',
help='All warnings are raised as exceptions when this '
'flag is set. Only for debugging purposes.')
# filter options
filter = parser.add_argument_group(
'Module Filter', 'Providing no modules will test all '
'ObsPy modules which do not require an '
'active network connection.')
filter.add_argument('-a',
'--all',
action='store_true',
dest='test_all_modules',
help='test all modules (including network modules)')
filter.add_argument('-x',
'--exclude',
action='append',
help='exclude given module from test')
filter.add_argument('tests', nargs='*', help='test modules to run')
# timing / profile options
timing = parser.add_argument_group('Timing/Profile Options')
timing.add_argument('-t',
'--timeit',
action='store_true',
help='shows accumulated run times of each module')
timing.add_argument('-s',
'--slowest',
default=0,
type=int,
dest='n',
help='lists n slowest test cases')
timing.add_argument('-p',
'--profile',
action='store_true',
help='uses cProfile, saves the results to file ' +
'obspy.pstats and prints some profiling numbers')
# reporting options
report = parser.add_argument_group('Reporting Options')
report.add_argument('-r',
'--report',
action='store_true',
help='automatically submit a test report')
report.add_argument('-d',
'--dontask',
action='store_true',
help="don't explicitly ask for submitting a test "
"report")
report.add_argument('-u',
'--server',
default='tests.obspy.org',
help='report server (default is tests.obspy.org)')
report.add_argument('-n',
'--node',
dest='hostname',
default=HOSTNAME,
help='nodename visible at the report server')
report.add_argument('-l',
'--log',
default=None,
help='append log file to test report')
report.add_argument('--ci-url',
default=None,
dest="ci_url",
help='URL to Continuous Integration job page.')
report.add_argument('--pr-url',
default=None,
dest="pr_url",
help='Github (Pull Request) URL.')
# other options
others = parser.add_argument_group('Additional Options')
others.add_argument('--tutorial',
action='store_true',
help='add doctests in tutorial')
others.add_argument('--no-flake8',
action='store_true',
help='skip code formatting test')
others.add_argument('--keep-images',
action='store_true',
help='store images created during image comparison '
'tests in subfolders of baseline images')
others.add_argument('--keep-only-failed-images',
action='store_true',
help='when storing images created during testing, '
'only store failed images and the corresponding '
'diff images (but not images that passed the '
'corresponding test).')
args = parser.parse_args(argv)
# set correct verbosity level
if args.verbose:
verbosity = 2
# raise all NumPy warnings
np.seterr(all='warn')
elif args.quiet:
verbosity = 0
# ignore user and deprecation warnings
warnings.simplefilter("ignore", DeprecationWarning)
warnings.simplefilter("ignore", UserWarning)
# don't ask to send a report
args.dontask = True
else:
verbosity = 1
# show all NumPy warnings
np.seterr(all='print')
# ignore user warnings
warnings.simplefilter("ignore", UserWarning)
# whether to raise any warning that's appearing
if args.raise_all_warnings:
# raise all NumPy warnings
np.seterr(all='raise')
# raise user and deprecation warnings
warnings.simplefilter("error", UserWarning)
# ignore specific warnings
msg = ('Matplotlib is currently using agg, which is a non-GUI backend, '
'so cannot show the figure.')
warnings.filterwarnings("ignore", message=msg)
# check for send report option or environmental settings
if args.report or 'OBSPY_REPORT' in os.environ.keys():
report = True
else:
report = False
if 'OBSPY_REPORT_SERVER' in os.environ.keys():
args.server = os.environ['OBSPY_REPORT_SERVER']
# check interactivity settings
if interactive and args.dontask:
interactive = False
if args.keep_images:
os.environ['OBSPY_KEEP_IMAGES'] = ""
if args.keep_only_failed_images:
os.environ['OBSPY_KEEP_ONLY_FAILED_IMAGES'] = ""
if args.no_flake8:
os.environ['OBSPY_NO_FLAKE8'] = ""
# All arguments are used by the test runner and should not interfere
# with any other module that might also parse them, e.g. flake8.
sys.argv = sys.argv[:1]
return run_tests(verbosity,
args.tests,
report,
args.log,
args.server,
args.test_all_modules,
args.timeit,
interactive,
args.n,
exclude=args.exclude,
tutorial=args.tutorial,
hostname=args.hostname,
ci_url=args.ci_url,
pr_url=args.pr_url)
def main(argv=None):
parser = ArgumentParser(prog='obspy-scan',
description=__doc__.strip(),
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('-V',
'--version',
action='version',
version='%(prog)s ' + __version__)
parser.add_argument('-f',
'--format',
choices=ENTRY_POINTS['waveform'],
help='Optional, the file format.\n' +
' '.join(__doc__.split('\n')[-4:]))
parser.add_argument('-v',
'--verbose',
action='store_true',
help='Optional. Verbose output.')
parser.add_argument('-q',
'--quiet',
action='store_true',
help='Optional. Be quiet. Overwritten by --verbose '
'flag.')
parser.add_argument('-n',
'--non-recursive',
action='store_false',
dest='recursive',
help='Optional. Do not descend into directories.')
parser.add_argument('-i',
'--ignore-links',
action='store_true',
help='Optional. Do not follow symbolic links.')
parser.add_argument('--start-time',
default=None,
type=UTCDateTime,
help='Optional, a UTCDateTime compatible string. ' +
'Only visualize data after this time and set ' +
'time-axis axis accordingly.')
parser.add_argument('--end-time',
default=None,
type=UTCDateTime,
help='Optional, a UTCDateTime compatible string. ' +
'Only visualize data before this time and set ' +
'time-axis axis accordingly.')
parser.add_argument('--id',
action='append',
help='Optional, a SEED channel identifier '
"(e.g. 'GR.FUR..HHZ'). You may provide this " +
'option multiple times. Only these ' +
'channels will be plotted.')
parser.add_argument('-t',
'--event-time',
default=None,
type=UTCDateTime,
action='append',
help='Optional, a UTCDateTime compatible string ' +
"(e.g. '2010-01-01T12:00:00'). You may provide " +
'this option multiple times. These times get ' +
'marked by vertical lines in the plot. ' +
'Useful e.g. to mark event origin times.')
parser.add_argument('-w',
'--write',
default=None,
help='Optional, npz file for writing data '
'after scanning waveform files')
parser.add_argument('-l',
'--load',
default=None,
help='Optional, npz file for loading data '
'before scanning waveform files')
parser.add_argument('--no-x',
action='store_true',
help='Optional, Do not plot crosses.')
parser.add_argument('--no-gaps',
action='store_true',
help='Optional, Do not plot gaps.')
parser.add_argument('-o',
'--output',
default=None,
help='Save plot to image file (e.g. out.pdf, ' +
'out.png) instead of opening a window.')
parser.add_argument('--print-gaps',
action='store_true',
help='Optional, prints a list of gaps at the end.')
parser.add_argument('paths',
nargs='*',
help='Files or directories to scan.')
args = parser.parse_args(argv)
if args.output is not None:
MatplotlibBackend.switch_backend("AGG", sloppy=False)
# Print help and exit if no arguments are given
if len(args.paths) == 0 and args.load is None:
parser.error('No paths specified.')
# Use recursively parsing function?
if args.recursive:
parse_func = recursive_parse
else:
parse_func = parse_file_to_dict
from matplotlib.dates import date2num, num2date
from matplotlib.ticker import FuncFormatter
from matplotlib.patches import Rectangle
from matplotlib.collections import PatchCollection
import matplotlib.pyplot as plt
fig = plt.figure()
ax = fig.add_subplot(111)
# Plot vertical lines if option 'event_time' was specified
if args.event_time:
times = [date2num(t.datetime) for t in args.event_time]
for time in times:
ax.axvline(time, color='k')
if args.start_time:
args.start_time = date2num(args.start_time.datetime)
if args.end_time:
args.end_time = date2num(args.end_time.datetime)
# Generate dictionary containing nested lists of start and end times per
# station
data = {}
samp_int = {}
counter = 1
if args.load:
load_npz(args.load, data, samp_int)
for path in args.paths:
counter = parse_func(data,
samp_int,
path,
counter,
args.format,
verbose=args.verbose,
quiet=args.quiet,
ignore_links=args.ignore_links)
if not data:
if args.verbose or not args.quiet:
print("No waveform data found.")
return
if args.write:
write_npz(args.write, data, samp_int)
# either use ids specified by user or use ids based on what data we have
# parsed
ids = args.id or list(data.keys())
ids = sorted(ids)[::-1]
labels = [""] * len(ids)
if args.verbose or not args.quiet:
print('\n')
for _i, _id in enumerate(ids):
labels[_i] = ids[_i]
# sort data list and sampling rate list
if _id in data:
startend = np.array(data[_id])
_samp_int = np.array(samp_int[_id])
indices = np.lexsort((startend[:, 1], startend[:, 0]))
startend = startend[indices]
_samp_int = _samp_int[indices]
else:
startend = np.array([])
_samp_int = np.array([])
if len(startend) == 0:
if not (args.start_time and args.end_time):
continue
if not args.no_gaps:
rects = [
Rectangle((args.start_time, _i - 0.4),
args.end_time - args.start_time, 0.8)
]
ax.add_collection(PatchCollection(rects, color="r"))
if args.print_gaps and (args.verbose or not args.quiet):
print("%s %s %s %.3f" % (_id, args.start_time, args.end_time,
args.end_time - args.start_time))
continue
# restrict plotting of results to given start/end time
if args.start_time:
indices = startend[:, 1] > args.start_time
startend = startend[indices]
_samp_int = _samp_int[indices]
if len(startend) == 0:
continue
if args.end_time:
indices = startend[:, 0] < args.end_time
startend = startend[indices]
_samp_int = _samp_int[indices]
if len(startend) == 0:
continue
data_start = startend[:, 0].min()
data_end = startend[:, 1].max()
timerange_start = args.start_time or data_start
timerange_end = args.end_time or data_end
timerange = timerange_end - timerange_start
if timerange == 0.0:
warnings.warn('Zero sample long data for _id=%s, skipping' % _id)
continue
startend_compressed = compress_start_end(startend, 1000)
offset = np.ones(len(startend)) * _i # generate list of y values
if not args.no_x:
ax.plot(startend[:, 0], offset, 'x', linewidth=2)
ax.hlines(offset[:len(startend_compressed)],
startend_compressed[:, 0],
startend_compressed[:, 1],
'b',
linewidth=2,
zorder=3)
# find the gaps
diffs = startend[1:, 0] - startend[:-1, 1] # currend.start - last.end
gapsum = diffs[diffs > 0].sum()
# if start- and/or endtime is specified, add missing data at start/end
# to gap sum
has_gap = False
gap_at_start = (args.start_time and data_start > args.start_time
and data_start - args.start_time)
gap_at_end = (args.end_time and args.end_time > data_end
and args.end_time - data_end)
if args.start_time and gap_at_start:
gapsum += gap_at_start
has_gap = True
if args.end_time and gap_at_end:
gapsum += gap_at_end
has_gap = True
perc = (timerange - gapsum) / timerange
labels[_i] = labels[_i] + "\n%.1f%%" % (perc * 100)
gap_indices = diffs > 1.8 * _samp_int[:-1]
gap_indices = np.append(gap_indices, False)
has_gap |= any(gap_indices)
if has_gap:
# don't handle last end time as start of gap
gaps_start = startend[gap_indices, 1]
gaps_end = startend[np.roll(gap_indices, 1), 0]
if args.start_time and gap_at_start:
gaps_start = np.append(gaps_start, args.start_time)
gaps_end = np.append(gaps_end, data_start)
if args.end_time and gap_at_end:
gaps_start = np.append(gaps_start, data_end)
gaps_end = np.append(gaps_end, args.end_time)
if not args.no_gaps:
rects = [
Rectangle((start_, offset[0] - 0.4), end_ - start_, 0.8)
for start_, end_ in zip(gaps_start, gaps_end)
]
ax.add_collection(PatchCollection(rects, color="r"))
if args.print_gaps:
for start_, end_ in zip(gaps_start, gaps_end):
start_, end_ = num2date((start_, end_))
start_ = UTCDateTime(start_.isoformat())
end_ = UTCDateTime(end_.isoformat())
if args.verbose or not args.quiet:
print("%s %s %s %.3f" %
(_id, start_, end_, end_ - start_))
# Pretty format the plot
ax.set_ylim(0 - 0.5, len(ids) - 0.5)
ax.set_yticks(np.arange(len(ids)))
ax.set_yticklabels(labels, family="monospace", ha="right")
fig.autofmt_xdate() # rotate date
ax.xaxis_date()
# set custom formatters to always show date in first tick
formatter = ObsPyAutoDateFormatter(ax.xaxis.get_major_locator())
formatter.scaled[1 / 24.] = \
FuncFormatter(decimal_seconds_format_date_first_tick)
formatter.scaled.pop(1 / (24. * 60.))
ax.xaxis.set_major_formatter(formatter)
plt.subplots_adjust(left=0.2)
# set x-axis limits according to given start/end time
if args.start_time and args.end_time:
ax.set_xlim(left=args.start_time, right=args.end_time)
elif args.start_time:
ax.set_xlim(left=args.start_time, auto=None)
elif args.end_time:
ax.set_xlim(right=args.end_time, auto=None)
else:
left, right = ax.xaxis.get_data_interval()
x_axis_range = right - left
ax.set_xlim(left - 0.05 * x_axis_range, right + 0.05 * x_axis_range)
if args.output is None:
plt.show()
else:
fig.set_dpi(72)
height = len(ids) * 0.5
height = max(4, height)
fig.set_figheight(height)
plt.tight_layout()
if not args.start_time or not args.end_time:
days = ax.get_xlim()
days = days[1] - days[0]
else:
days = args.end_time - args.start_time
width = max(6, days / 30.)
width = min(width, height * 4)
fig.set_figwidth(width)
plt.subplots_adjust(top=1, bottom=0, left=0, right=1)
plt.tight_layout()
fig.savefig(args.output)
if args.verbose and not args.quiet:
sys.stdout.write('\n')
def main(argv=None):
MatplotlibBackend.switch_backend("AGG", sloppy=False)
parser = ArgumentParser(
prog='obspy-sds-report', description=__doc__,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument(
'-r', '--sds-root', dest='sds_root', required=True,
help='Root folder of SDS archive.')
parser.add_argument(
'-o', '--output', dest='output', required=True,
help='Full path (absolute or relative) of output files, without '
'suffix (e.g. ``/tmp/sds_report``).')
parser.add_argument(
'-u', '--update', dest='update', default=False, action="store_true",
help='Only update latency information, reuse previously computed list '
'of streams to check and data percentage and gap count. Many '
'other options e.g. regarding stream selection (``--id``, '
' ``--location``, ..) and time span of data quality checks '
'(``--check-quality-days``) will be without effect if this '
'option is specified. Only updating latency is significantly '
'faster than a full analysis run, a normal use case is to do a '
'full run once or twice per day and update latency every 5 or '
'ten minutes. An exception is raised if an update is specified '
'but the necessary file is not yet present.')
parser.add_argument(
'-l', '--location', dest='locations', action="append",
help='Location codes to look for (e.g. ``""`` for empty location code '
'or ``"00"``). This option can be provided multiple times and '
'must be specified at least once for a full run (i.e. without '
'``--update`` option). While network/station combinations are '
'automatically discovered, only streams whose location codes are '
'provided here will be discovered and taken into account and '
'ultimately displayed.')
parser.add_argument(
'-c', '--channel', dest='channels', action="append",
help='Channel codes to look for (e.g. specified three times with '
'``HHZ``, ``EHZ`` and ``ELZ`` to cover all stations that serve '
'a broad-band, short-period or low gain vertical channel). '
'This option can be provided multiple times and must be '
'specified at least once for a full run (i.e. without '
'``--update`` option). Only one stream per '
'network/station/location combination will be displayed, '
'selected by the lowest latency.')
parser.add_argument(
'-i', '--id', dest='ids', action="append", default=[],
help='SEED IDs of streams that should be included in addition to the '
'autodiscovery of streams controlled by ``--location`` and '
'``--channel`` options (e.g. ``IU.ANMO..LHZ``). '
'This option can be provided multiple times.')
parser.add_argument(
'--skip', dest='skip', action="append", default=[],
help='Networks or stations that should be skipped (e.g. ``IU`` or '
'``IU.ANMO``). This option can be provided multiple times.')
parser.add_argument(
'-f', '--format', default="MSEED", choices=ENTRY_POINTS['waveform'],
help='Waveform format of SDS archive. Should be "MSEED" in most '
'cases. Use ``None`` or empty string for format autodection '
'(slower and should not be necessary in most all cases). '
'Warning: formats that do not support ``headonly`` '
'option in ``read()`` operation will be significantly slower).')
parser.add_argument(
'--check-backwards-days', dest='check_back_days', default=30,
type=int, help='Check for latency backwards for this many days.')
parser.add_argument(
'--check-quality-days', dest='check_quality_days', default=7,
type=int, help='Calculate and plot data availability and number of '
'gaps for a period of this many days.')
parser.add_argument(
'--latency-warn', dest='latency_warn', default=3600,
type=float, help='Latency warning threshold in seconds.')
parser.add_argument(
'--latency-warn-color', dest='latency_warn_color', default="#FFFF33",
help='Latency warning threshold color (valid HTML color string).')
parser.add_argument(
'--latency-error', dest='latency_error', default=24*3600,
type=float, help='Latency error threshold in seconds.')
parser.add_argument(
'--latency-error-color', dest='latency_error_color', default="#E41A1C",
help='Latency error threshold color (valid HTML color string).')
parser.add_argument(
'--percentage-warn', dest='percentage_warn', default=99.5, type=float,
help='Data availability percentage warning threshold (``0`` to '
'``100``).')
parser.add_argument(
'--gaps-warn', dest='gaps_warn', default=20, type=int,
help='Gap/overlap number warning threshold.')
parser.add_argument(
'--data-quality-warn-color', dest='data_quality_warn_color',
default="#377EB8",
help='Data quality (percentage/gap count) warning color '
'(valid HTML color string).')
parser.add_argument(
'--outdated-color', dest='outdated_color', default="#808080",
help='Color for streams that have no data in check range '
'(valid HTML color string).')
parser.add_argument(
'--ok-color', dest='ok_color', default="#4DAF4A",
help='Color for streams that pass all checks (valid HTML color '
'string).')
parser.add_argument(
'--background-color', dest='background_color', default="#999999",
help='Color for background of page (valid HTML color string).')
parser.add_argument(
'-V', '--version', action='version', version='%(prog)s ' + __version__)
args = parser.parse_args(argv)
now = UTCDateTime()
stop_time = now - args.check_back_days * 24 * 3600
client = Client(args.sds_root)
dtype_streamfile = np.dtype("U10, U30, U10, U10, f8, f8, i8")
availability_check_endtime = now - 3600
availability_check_starttime = (
availability_check_endtime - (args.check_quality_days * 24 * 3600))
streams_file = args.output + ".txt"
html_file = args.output + ".html"
scan_file = args.output + ".png"
if args.format.upper() == "NONE" or args.format == "":
args.format = None
# check whether to set up list of streams to check or use existing list
# update list of streams once per day at nighttime
if args.update:
if not os.path.isfile(streams_file):
msg = ("Update flag specified, but no output of previous full run "
"was present in the expected location (as determined by "
"``--output`` flag: {})").format(streams_file)
raise IOError(msg)
# use existing list of streams and availability information, just
# update latency
nslc = np.loadtxt(streams_file, delimiter=",", dtype=dtype_streamfile)
else:
if not args.locations or not args.channels:
msg = ("At least one location code ``--location`` and at least "
"one channel code ``--channel`` must be specified.")
raise ObsPyException(msg)
nsl = set()
# get all network/station combinations in SDS archive
for net, sta in client.get_all_stations():
if net in args.skip or ".".join((net, sta)) in args.skip:
continue
# for all combinations of user specified location and channel codes
# check if data is in SDS archive
for loc in args.locations:
for cha in args.channels:
if client.has_data(net, sta, loc, cha):
# for now omit channel information, we only include the
# channel with lowest latency later on
nsl.add((net, sta, loc))
break
nsl = sorted(nsl)
nslc = []
# determine which channel to check for each network/station/location
# combination
for net, sta, loc in nsl:
latency = []
# check latency of all channels that should be checked
for cha in args.channels:
latency_ = client.get_latency(net, sta, loc, cha,
stop_time=stop_time)
latency.append(latency_ or np.inf)
# only include the channel with lowest latency in our stream list
cha = args.channels[np.argmin(latency)]
latency = np.min(latency)
nslc.append((net, sta, loc, cha, latency))
for id in args.ids:
net, sta, loc, cha = id.split(".")
latency = client.get_latency(net, sta, loc, cha,
stop_time=stop_time)
latency = latency or np.inf
nslc.append((net, sta, loc, cha, latency))
nslc_ = []
# request and assemble availability information.
# this takes pretty long (on network/slow file systems),
# so we only do it during a full run here, not during update
for net, sta, loc, cha, latency in nslc:
percentage, gap_count = client.get_availability_percentage(
net, sta, loc, cha, availability_check_starttime,
availability_check_endtime)
nslc_.append((net, sta, loc, cha, latency, percentage, gap_count))
nslc = nslc_
# write stream list and availability information to file
nslc = np.array(sorted(nslc), dtype=dtype_streamfile)
np.savetxt(streams_file, nslc, delimiter=",",
fmt=["%s", "%s", "%s", "%s", "%f", "%f", "%d"])
# generate obspy-scan image
files = []
seed_ids = set()
for nslc_ in nslc:
net, sta, loc, cha, latency, _, _ = nslc_
if np.isinf(latency) or latency > args.check_back_days * 24 * 3600:
continue
seed_ids.add(".".join((net, sta, loc, cha)))
files += client._get_filenames(
net, sta, loc, cha, availability_check_starttime,
availability_check_endtime)
scan(files, format=args.format, starttime=availability_check_starttime,
endtime=availability_check_endtime, plot=scan_file, verbose=False,
recursive=True, ignore_links=False, seed_ids=seed_ids,
print_gaps=False)
# request and assemble current latency information
data = []
for net, sta, loc, cha, latency, percentage, gap_count in nslc:
if args.update:
latency = client.get_latency(net, sta, loc, cha,
stop_time=stop_time)
latency = latency or np.inf
data.append((net, sta, loc, cha, latency, percentage, gap_count))
# separate out the long dead streams
data_normal = []
data_outdated = []
for data_ in data:
latency = data_[4]
if np.isinf(latency) or latency > args.check_back_days * 24 * 3600:
data_outdated.append(data_)
else:
data_normal.append(data_)
# write html output to file
html = _format_html(args, data_normal, data_outdated)
with open(html_file, "wt") as fh:
fh.write(html)
def main(argv=None):
MatplotlibBackend.switch_backend("AGG", sloppy=False)
parser = ArgumentParser(
prog='obspy-sds-report', description=__doc__,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument(
'-r', '--sds-root', dest='sds_root', required=True,
help='Root folder of SDS archive.')
parser.add_argument(
'-o', '--output', dest='output', required=True,
help='Full path (absolute or relative) of output files, without '
'suffix (e.g. ``/tmp/sds_report``).')
parser.add_argument(
'-u', '--update', dest='update', default=False, action="store_true",
help='Only update latency information, reuse previously computed list '
'of streams to check and data percentage and gap count. Many '
'other options e.g. regarding stream selection (``--id``, '
' ``--location``, ..) and time span of data quality checks '
'(``--check-quality-days``) will be without effect if this '
'option is specified. Only updating latency is significantly '
'faster than a full analysis run, a normal use case is to do a '
'full run once or twice per day and update latency every 5 or '
'ten minutes. An exception is raised if an update is specified '
'but the necessary file is not yet present.')
parser.add_argument(
'-l', '--location', dest='locations', action="append",
help='Location codes to look for (e.g. ``""`` for empty location code '
'or ``"00"``). This option can be provided multiple times and '
'must be specified at least once for a full run (i.e. without '
'``--update`` option). While network/station combinations are '
'automatically discovered, only streams whose location codes are '
'provided here will be discovered and taken into account and '
'ultimately displayed.')
parser.add_argument(
'-c', '--channel', dest='channels', action="append",
help='Channel codes to look for (e.g. specified three times with '
'``HHZ``, ``EHZ`` and ``ELZ`` to cover all stations that serve '
'a broad-band, short-period or low gain vertical channel). '
'This option can be provided multiple times and must be '
'specified at least once for a full run (i.e. without '
'``--update`` option). Only one stream per '
'network/station/location combination will be displayed, '
'selected by the lowest latency.')
parser.add_argument(
'-i', '--id', dest='ids', action="append", default=[],
help='SEED IDs of streams that should be included in addition to the '
'autodiscovery of streams controlled by ``--location`` and '
'``--channel`` options (e.g. ``IU.ANMO..LHZ``). '
'This option can be provided multiple times.')
parser.add_argument(
'--skip', dest='skip', action="append", default=[],
help='Networks or stations that should be skipped (e.g. ``IU`` or '
'``IU.ANMO``). This option can be provided multiple times.')
parser.add_argument(
'-f', '--format', default="MSEED", choices=ENTRY_POINTS['waveform'],
help='Waveform format of SDS archive. Should be "MSEED" in most '
'cases. Use ``None`` or empty string for format autodection '
'(slower and should not be necessary in most all cases). '
'Warning: formats that do not support ``headonly`` '
'option in ``read()`` operation will be significantly slower).')
parser.add_argument(
'--check-backwards-days', dest='check_back_days', default=30,
type=int, help='Check for latency backwards for this many days.')
parser.add_argument(
'--check-quality-days', dest='check_quality_days', default=7,
type=int, help='Calculate and plot data availability and number of '
'gaps for a period of this many days.')
parser.add_argument(
'--latency-warn', dest='latency_warn', default=3600,
type=float, help='Latency warning threshold in seconds.')
parser.add_argument(
'--latency-warn-color', dest='latency_warn_color', default="#FFFF33",
help='Latency warning threshold color (valid HTML color string).')
parser.add_argument(
'--latency-error', dest='latency_error', default=24 * 3600,
type=float, help='Latency error threshold in seconds.')
parser.add_argument(
'--latency-error-color', dest='latency_error_color', default="#E41A1C",
help='Latency error threshold color (valid HTML color string).')
parser.add_argument(
'--percentage-warn', dest='percentage_warn', default=99.5, type=float,
help='Data availability percentage warning threshold (``0`` to '
'``100``).')
parser.add_argument(
'--gaps-warn', dest='gaps_warn', default=20, type=int,
help='Gap/overlap number warning threshold.')
parser.add_argument(
'--data-quality-warn-color', dest='data_quality_warn_color',
default="#377EB8",
help='Data quality (percentage/gap count) warning color '
'(valid HTML color string).')
parser.add_argument(
'--outdated-color', dest='outdated_color', default="#808080",
help='Color for streams that have no data in check range '
'(valid HTML color string).')
parser.add_argument(
'--ok-color', dest='ok_color', default="#4DAF4A",
help='Color for streams that pass all checks (valid HTML color '
'string).')
parser.add_argument(
'--background-color', dest='background_color', default="#999999",
help='Color for background of page (valid HTML color string).')
parser.add_argument(
'-V', '--version', action='version', version='%(prog)s ' + __version__)
args = parser.parse_args(argv)
now = UTCDateTime()
stop_time = now - args.check_back_days * 24 * 3600
client = Client(args.sds_root)
dtype_streamfile = np.dtype("U10, U30, U10, U10, f8, f8, i8")
availability_check_endtime = now - 3600
availability_check_starttime = (
availability_check_endtime - (args.check_quality_days * 24 * 3600))
streams_file = args.output + ".txt"
html_file = args.output + ".html"
scan_file = args.output + ".png"
if args.format.upper() == "NONE" or args.format == "":
args.format = None
# check whether to set up list of streams to check or use existing list
# update list of streams once per day at nighttime
if args.update:
if not Path(streams_file).is_file():
msg = ("Update flag specified, but no output of previous full run "
"was present in the expected location (as determined by "
"``--output`` flag: {})").format(streams_file)
raise IOError(msg)
# use existing list of streams and availability information, just
# update latency
nslc = np.loadtxt(streams_file, delimiter=",", dtype=dtype_streamfile)
else:
if not args.locations or not args.channels:
msg = ("At least one location code ``--location`` and at least "
"one channel code ``--channel`` must be specified.")
raise ObsPyException(msg)
nsl = set()
# get all network/station combinations in SDS archive
for net, sta in client.get_all_stations():
if net in args.skip or ".".join((net, sta)) in args.skip:
continue
# for all combinations of user specified location and channel codes
# check if data is in SDS archive
for loc in args.locations:
for cha in args.channels:
if client.has_data(net, sta, loc, cha):
# for now omit channel information, we only include the
# channel with lowest latency later on
nsl.add((net, sta, loc))
break
nsl = sorted(nsl)
nslc = []
# determine which channel to check for each network/station/location
# combination
for net, sta, loc in nsl:
latency = []
# check latency of all channels that should be checked
for cha in args.channels:
latency_ = client.get_latency(
net, sta, loc, cha, stop_time=stop_time,
check_has_no_data=False)
latency.append(latency_ or np.inf)
# only include the channel with lowest latency in our stream list
cha = args.channels[np.argmin(latency)]
latency = np.min(latency)
nslc.append((net, sta, loc, cha, latency))
for id in args.ids:
net, sta, loc, cha = id.split(".")
latency = client.get_latency(
net, sta, loc, cha, stop_time=stop_time,
check_has_no_data=False)
latency = latency or np.inf
nslc.append((net, sta, loc, cha, latency))
nslc_ = []
# request and assemble availability information.
# this takes pretty long (on network/slow file systems),
# so we only do it during a full run here, not during update
for net, sta, loc, cha, latency in nslc:
percentage, gap_count = client.get_availability_percentage(
net, sta, loc, cha, availability_check_starttime,
availability_check_endtime)
nslc_.append((net, sta, loc, cha, latency, percentage, gap_count))
nslc = nslc_
# write stream list and availability information to file
nslc = np.array(sorted(nslc), dtype=dtype_streamfile)
np.savetxt(streams_file, nslc, delimiter=",",
fmt=["%s", "%s", "%s", "%s", "%f", "%f", "%d"])
# generate obspy-scan image
files = []
seed_ids = set()
for nslc_ in nslc:
net, sta, loc, cha, latency, _, _ = nslc_
if np.isinf(latency) or latency > args.check_back_days * 24 * 3600:
continue
seed_ids.add(".".join((net, sta, loc, cha)))
files += client._get_filenames(
net, sta, loc, cha, availability_check_starttime,
availability_check_endtime)
scan(files, format=args.format, starttime=availability_check_starttime,
endtime=availability_check_endtime, plot=scan_file, verbose=False,
recursive=True, ignore_links=False, seed_ids=seed_ids,
print_gaps=False)
# request and assemble current latency information
data = []
for net, sta, loc, cha, latency, percentage, gap_count in nslc:
if args.update:
latency = client.get_latency(
net, sta, loc, cha, stop_time=stop_time,
check_has_no_data=False)
latency = latency or np.inf
data.append((net, sta, loc, cha, latency, percentage, gap_count))
# separate out the long dead streams
data_normal = []
data_outdated = []
for data_ in data:
latency = data_[4]
if np.isinf(latency) or latency > args.check_back_days * 24 * 3600:
data_outdated.append(data_)
else:
data_normal.append(data_)
# write html output to file
html = _format_html(args, data_normal, data_outdated)
with open(html_file, "wt") as fh:
fh.write(html)
def main(argv=None):
parser = ArgumentParser(prog='obspy-scan', description=__doc__.strip(),
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('-V', '--version', action='version',
version='%(prog)s ' + __version__)
parser.add_argument('-f', '--format', choices=ENTRY_POINTS['waveform'],
help='Optional, the file format.\n' +
' '.join(__doc__.split('\n')[-4:]))
parser.add_argument('-v', '--verbose', action='store_true',
help='Optional. Verbose output.')
parser.add_argument('-q', '--quiet', action='store_true',
help='Optional. Be quiet. Overwritten by --verbose '
'flag.')
parser.add_argument('-n', '--non-recursive',
action='store_false', dest='recursive',
help='Optional. Do not descend into directories.')
parser.add_argument('-i', '--ignore-links', action='store_true',
help='Optional. Do not follow symbolic links.')
parser.add_argument('--start-time', default=None, type=UTCDateTime,
help='Optional, a UTCDateTime compatible string. ' +
'Only visualize data after this time and set ' +
'time-axis axis accordingly.')
parser.add_argument('--end-time', default=None, type=UTCDateTime,
help='Optional, a UTCDateTime compatible string. ' +
'Only visualize data before this time and set ' +
'time-axis axis accordingly.')
parser.add_argument('--id', action='append',
help='Optional, a SEED channel identifier '
"(e.g. 'GR.FUR..HHZ'). You may provide this " +
'option multiple times. Only these ' +
'channels will be plotted.')
parser.add_argument('-t', '--event-time', default=None, type=UTCDateTime,
action='append',
help='Optional, a UTCDateTime compatible string ' +
"(e.g. '2010-01-01T12:00:00'). You may provide " +
'this option multiple times. These times get ' +
'marked by vertical lines in the plot. ' +
'Useful e.g. to mark event origin times.')
parser.add_argument('-w', '--write', default=None,
help='Optional, npz file for writing data '
'after scanning waveform files')
parser.add_argument('-l', '--load', default=None,
help='Optional, npz file for loading data '
'before scanning waveform files')
parser.add_argument('--no-x', action='store_true',
help='Optional, Do not plot crosses.')
parser.add_argument('--no-gaps', action='store_true',
help='Optional, Do not plot gaps.')
parser.add_argument('-o', '--output', default=None,
help='Save plot to image file (e.g. out.pdf, ' +
'out.png) instead of opening a window.')
parser.add_argument('--print-gaps', action='store_true',
help='Optional, prints a list of gaps at the end.')
parser.add_argument('paths', nargs='*',
help='Files or directories to scan.')
args = parser.parse_args(argv)
if args.output is not None:
MatplotlibBackend.switch_backend("AGG", sloppy=False)
# Print help and exit if no arguments are given
if len(args.paths) == 0 and args.load is None:
parser.error('No paths specified.')
# Use recursively parsing function?
if args.recursive:
parse_func = recursive_parse
else:
parse_func = parse_file_to_dict
from matplotlib.dates import date2num, num2date
from matplotlib.ticker import FuncFormatter
from matplotlib.patches import Rectangle
from matplotlib.collections import PatchCollection
import matplotlib.pyplot as plt
fig = plt.figure()
ax = fig.add_subplot(111)
# Plot vertical lines if option 'event_time' was specified
if args.event_time:
times = [date2num(t.datetime) for t in args.event_time]
for time in times:
ax.axvline(time, color='k')
if args.start_time:
args.start_time = date2num(args.start_time.datetime)
if args.end_time:
args.end_time = date2num(args.end_time.datetime)
# Generate dictionary containing nested lists of start and end times per
# station
data = {}
samp_int = {}
counter = 1
if args.load:
load_npz(args.load, data, samp_int)
for path in args.paths:
counter = parse_func(data, samp_int, path, counter, args.format,
verbose=args.verbose, quiet=args.quiet,
ignore_links=args.ignore_links)
if not data:
if args.verbose or not args.quiet:
print("No waveform data found.")
return
if args.write:
write_npz(args.write, data, samp_int)
# either use ids specified by user or use ids based on what data we have
# parsed
ids = args.id or list(data.keys())
ids = sorted(ids)[::-1]
labels = [""] * len(ids)
if args.verbose or not args.quiet:
print('\n')
for _i, _id in enumerate(ids):
labels[_i] = ids[_i]
# sort data list and sampling rate list
if _id in data:
startend = np.array(data[_id])
_samp_int = np.array(samp_int[_id])
indices = np.lexsort((startend[:, 1], startend[:, 0]))
startend = startend[indices]
_samp_int = _samp_int[indices]
else:
startend = np.array([])
_samp_int = np.array([])
if len(startend) == 0:
if not (args.start_time and args.end_time):
continue
if not args.no_gaps:
rects = [Rectangle((args.start_time, _i - 0.4),
args.end_time - args.start_time, 0.8)]
ax.add_collection(PatchCollection(rects, color="r"))
if args.print_gaps and (args.verbose or not args.quiet):
print("%s %s %s %.3f" % (
_id, args.start_time, args.end_time,
args.end_time - args.start_time))
continue
# restrict plotting of results to given start/end time
if args.start_time:
indices = startend[:, 1] > args.start_time
startend = startend[indices]
_samp_int = _samp_int[indices]
if len(startend) == 0:
continue
if args.end_time:
indices = startend[:, 0] < args.end_time
startend = startend[indices]
_samp_int = _samp_int[indices]
if len(startend) == 0:
continue
data_start = startend[:, 0].min()
data_end = startend[:, 1].max()
timerange_start = args.start_time or data_start
timerange_end = args.end_time or data_end
timerange = timerange_end - timerange_start
if timerange == 0.0:
warnings.warn('Zero sample long data for _id=%s, skipping' % _id)
continue
startend_compressed = compress_start_end(startend, 1000)
offset = np.ones(len(startend)) * _i # generate list of y values
if not args.no_x:
ax.plot(startend[:, 0], offset, 'x', linewidth=2)
ax.hlines(offset[:len(startend_compressed)], startend_compressed[:, 0],
startend_compressed[:, 1], 'b', linewidth=2, zorder=3)
# find the gaps
diffs = startend[1:, 0] - startend[:-1, 1] # currend.start - last.end
gapsum = diffs[diffs > 0].sum()
# if start- and/or endtime is specified, add missing data at start/end
# to gap sum
has_gap = False
gap_at_start = (
args.start_time and
data_start > args.start_time and
data_start - args.start_time)
gap_at_end = (
args.end_time and
args.end_time > data_end and
args.end_time - data_end)
if args.start_time and gap_at_start:
gapsum += gap_at_start
has_gap = True
if args.end_time and gap_at_end:
gapsum += gap_at_end
has_gap = True
perc = (timerange - gapsum) / timerange
labels[_i] = labels[_i] + "\n%.1f%%" % (perc * 100)
gap_indices = diffs > 1.8 * _samp_int[:-1]
gap_indices = np.append(gap_indices, False)
has_gap |= any(gap_indices)
if has_gap:
# don't handle last end time as start of gap
gaps_start = startend[gap_indices, 1]
gaps_end = startend[np.roll(gap_indices, 1), 0]
if args.start_time and gap_at_start:
gaps_start = np.append(gaps_start, args.start_time)
gaps_end = np.append(gaps_end, data_start)
if args.end_time and gap_at_end:
gaps_start = np.append(gaps_start, data_end)
gaps_end = np.append(gaps_end, args.end_time)
if not args.no_gaps:
rects = [Rectangle((start_, offset[0] - 0.4), end_ - start_,
0.8)
for start_, end_ in zip(gaps_start, gaps_end)]
ax.add_collection(PatchCollection(rects, color="r"))
if args.print_gaps:
for start_, end_ in zip(gaps_start, gaps_end):
start_, end_ = num2date((start_, end_))
start_ = UTCDateTime(start_.isoformat())
end_ = UTCDateTime(end_.isoformat())
if args.verbose or not args.quiet:
print("%s %s %s %.3f" % (_id, start_, end_,
end_ - start_))
# Pretty format the plot
ax.set_ylim(0 - 0.5, len(ids) - 0.5)
ax.set_yticks(np.arange(len(ids)))
ax.set_yticklabels(labels, family="monospace", ha="right")
fig.autofmt_xdate() # rotate date
ax.xaxis_date()
# set custom formatters to always show date in first tick
formatter = ObsPyAutoDateFormatter(ax.xaxis.get_major_locator())
formatter.scaled[1 / 24.] = \
FuncFormatter(decimal_seconds_format_date_first_tick)
formatter.scaled.pop(1/(24.*60.))
ax.xaxis.set_major_formatter(formatter)
plt.subplots_adjust(left=0.2)
# set x-axis limits according to given start/end time
if args.start_time and args.end_time:
ax.set_xlim(left=args.start_time, right=args.end_time)
elif args.start_time:
ax.set_xlim(left=args.start_time, auto=None)
elif args.end_time:
ax.set_xlim(right=args.end_time, auto=None)
else:
left, right = ax.xaxis.get_data_interval()
x_axis_range = right - left
ax.set_xlim(left - 0.05 * x_axis_range, right + 0.05 * x_axis_range)
if args.output is None:
plt.show()
else:
fig.set_dpi(72)
height = len(ids) * 0.5
height = max(4, height)
fig.set_figheight(height)
plt.tight_layout()
if not args.start_time or not args.end_time:
days = ax.get_xlim()
days = days[1] - days[0]
else:
days = args.end_time - args.start_time
width = max(6, days / 30.)
width = min(width, height * 4)
fig.set_figwidth(width)
plt.subplots_adjust(top=1, bottom=0, left=0, right=1)
plt.tight_layout()
fig.savefig(args.output)
if args.verbose and not args.quiet:
sys.stdout.write('\n')
def run(argv=None, interactive=True):
MatplotlibBackend.switch_backend("AGG", sloppy=False)
parser = ArgumentParser(prog="obspy-runtests", description="A command-line program that runs all " "ObsPy tests.")
parser.add_argument("-V", "--version", action="version", version="%(prog)s " + get_git_version())
parser.add_argument("-v", "--verbose", action="store_true", help="verbose mode")
parser.add_argument("-q", "--quiet", action="store_true", help="quiet mode")
# filter options
filter = parser.add_argument_group(
"Module Filter",
"Providing no modules will test all " "ObsPy modules which do not require an " "active network connection.",
)
filter.add_argument("-a", "--all", action="store_true", help="test all modules (including network modules)")
filter.add_argument("-x", "--exclude", action="append", help="exclude given module from test")
filter.add_argument("tests", nargs="*", help="test modules to run")
# timing / profile options
timing = parser.add_argument_group("Timing/Profile Options")
timing.add_argument("-t", "--timeit", action="store_true", help="shows accumulated run times of each module")
timing.add_argument("-s", "--slowest", default=0, type=int, dest="n", help="lists n slowest test cases")
timing.add_argument(
"-p",
"--profile",
action="store_true",
help="uses cProfile, saves the results to file " + "obspy.pstats and prints some profiling numbers",
)
# reporting options
report = parser.add_argument_group("Reporting Options")
report.add_argument("-r", "--report", action="store_true", help="automatically submit a test report")
report.add_argument(
"-d", "--dontask", action="store_true", help="don't explicitly ask for submitting a test " "report"
)
report.add_argument("-u", "--server", default="tests.obspy.org", help="report server (default is tests.obspy.org)")
report.add_argument("-n", "--node", dest="hostname", default=HOSTNAME, help="nodename visible at the report server")
report.add_argument("-l", "--log", default=None, help="append log file to test report")
report.add_argument("--ci-url", default=None, dest="ci_url", help="URL to Continuous Integration job page.")
report.add_argument("--pr-url", default=None, dest="pr_url", help="Github (Pull Request) URL.")
# other options
others = parser.add_argument_group("Additional Options")
others.add_argument("--tutorial", action="store_true", help="add doctests in tutorial")
others.add_argument("--no-flake8", action="store_true", help="skip code formatting test")
others.add_argument(
"--keep-images",
action="store_true",
help="store images created during image comparison " "tests in subfolders of baseline images",
)
others.add_argument(
"--keep-only-failed-images",
action="store_true",
help="when storing images created during testing, "
"only store failed images and the corresponding "
"diff images (but not images that passed the "
"corresponding test).",
)
args = parser.parse_args(argv)
# set correct verbosity level
if args.verbose:
verbosity = 2
# raise all NumPy warnings
np.seterr(all="raise")
# raise user and deprecation warnings
warnings.simplefilter("error", UserWarning)
elif args.quiet:
verbosity = 0
# ignore user and deprecation warnings
warnings.simplefilter("ignore", DeprecationWarning)
warnings.simplefilter("ignore", UserWarning)
# don't ask to send a report
args.dontask = True
else:
verbosity = 1
# show all NumPy warnings
np.seterr(all="print")
# ignore user warnings
warnings.simplefilter("ignore", UserWarning)
# check for send report option or environmental settings
if args.report or "OBSPY_REPORT" in os.environ.keys():
report = True
else:
report = False
if "OBSPY_REPORT_SERVER" in os.environ.keys():
args.server = os.environ["OBSPY_REPORT_SERVER"]
# check interactivity settings
if interactive and args.dontask:
interactive = False
if args.keep_images:
os.environ["OBSPY_KEEP_IMAGES"] = ""
if args.keep_only_failed_images:
os.environ["OBSPY_KEEP_ONLY_FAILED_IMAGES"] = ""
if args.no_flake8:
os.environ["OBSPY_NO_FLAKE8"] = ""
return run_tests(
verbosity,
args.tests,
report,
args.log,
args.server,
args.all,
args.timeit,
interactive,
args.n,
exclude=args.exclude,
tutorial=args.tutorial,
hostname=args.hostname,
ci_url=args.ci_url,
pr_url=args.pr_url,
)
