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_function_and_scanner_class(self):
"""
Test scan function and Scanner class (in one test to keep overhead of
copying files down)
"""
scanner = Scanner()
# Copy files to a temp folder to avoid wildcard scans.
with TemporaryWorkingDirectory():
for filename in self.all_files:
shutil.copy(filename, os.curdir)
scanner.parse(os.curdir)
with ImageComparison(self.path, 'scan.png') as ic:
scan(paths=os.curdir, plot=ic.name)
with ImageComparison(self.path, 'scan.png') as ic:
scanner.plot(ic.name)
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)
