def load_snuffling(win):
s = LassieSnuffling()
s.config = _lassie_config
s.setup()
win.pile_viewer.viewer.add_snuffling(s, reloaded=True)
win.pile_viewer.viewer.add_blacklist_pattern('*.SMAX.i.*')
for bl in _lassie_config.blacklist:
win.pile_viewer.viewer.add_blacklist_pattern('%s.*' % bl)
detections_path = _lassie_config.get_detections_path()
if os.path.exists(detections_path):
s.detections = detections_to_event_markers(detections_path)
s.add_markers(s.detections)
for _ifc in s.config.image_function_contributions:
if isinstance(_ifc, ifc.ManualPickIFC):
markers_path_extra = _ifc.picks_path
elif isinstance(_ifc, ifc.TemplateMatchingIFC):
markers_path_extra = _ifc.template_markers_path
else:
continue
if os.path.exists(markers_path_extra):
s.add_markers(pmarker.load_markers(markers_path_extra))
else:
logger.warn(
'No such file: %s (referenced in %s, named %s)' %
(markers_path_extra, _ifc.__class__.__name__, _ifc.name))
def test_writeread(self):
nslc_ids = [('', 'STA', '', '*')]
event = model.Event(lat=111., lon=111., depth=111., time=111.)
_marker = marker.Marker(nslc_ids=nslc_ids, tmin=1., tmax=10.)
emarker = marker.EventMarker(event=event)
pmarker = marker.PhaseMarker(nslc_ids=nslc_ids, tmin=1., tmax=10.)
pmarker.set_event(event)
emarker.set_alerted(True)
markers = [_marker, emarker, pmarker]
fn = tempfile.mkstemp()[1]
marker.save_markers(markers, fn)
in_markers = marker.load_markers(fn)
in__marker, in_emarker, in_pmarker = in_markers
for i, m in enumerate(in_markers):
if not isinstance(m, marker.EventMarker):
assert (m.tmax - m.tmin) == 9.
else:
assert not m.is_alerted()
marker.associate_phases_to_events([in_pmarker, in_emarker])
in_event = in_pmarker.get_event()
assert all((in_event.lat == 111., in_event.lon == 111.,
in_event.depth == 111., in_event.time == 111.))
assert in_pmarker.get_event_hash() == in_event.get_hash()
assert in_pmarker.get_event_time() == 111.
def setup(self):
self.data_pile = pile.make_pile(
self.data_paths, fileformat=self.data_format)
if self.data_pile.is_empty():
sys.exit('Data pile is empty!')
self.deltat_want = self.config.deltat_want or \
min(self.data_pile.deltats.keys())
self.n_samples = int(
(self.config.sample_length + self.config.tpad) / self.deltat_want)
logger.debug('loading marker file %s' % self.fn_markers)
# loads just plain markers:
markers = marker.load_markers(self.fn_markers)
if self.fn_events:
markers.extend(
[marker.EventMarker(e) for e in
load_events(self.fn_events)])
if self.sort_markers:
logger.info('sorting markers!')
markers.sort(key=lambda x: x.tmin)
marker.associate_phases_to_events(markers)
markers_by_nsl = {}
for m in markers:
if not m.match_nsl(self.config.reference_target.codes[:3]):
continue
if m.get_phasename().upper() != self.align_phase:
continue
markers_by_nsl.setdefault(m.one_nslc()[:3], []).append(m)
assert(len(markers_by_nsl) == 1)
# filter markers that do not have an event assigned:
self.markers = list(markers_by_nsl.values())[0]
if not self.labeled:
dummy_event = Event(lat=0., lon=0., depth=0.)
for m in self.markers:
if not m.get_event():
m.set_event(dummy_event)
self.markers = [m for m in self.markers if m.get_event() is not None]
if not len(self.markers):
raise Exception('No markers left in dataset')
self.config.channels = list(self.data_pile.nslc_ids.keys())
self.config.channels.sort()
def setup(self):
self.data_pile = pile.make_pile(
self.data_paths, fileformat=self.data_format)
if self.data_pile.is_empty():
sys.exit('Data pile is empty!')
self.deltat_want = self.config.deltat_want or \
min(self.data_pile.deltats.keys())
self.n_samples = int(
(self.config.sample_length + self.config.tpad) / self.deltat_want)
logger.debug('loading marker file %s' % self.fn_markers)
# loads just plain markers:
markers = marker.load_markers(self.fn_markers)
if self.fn_events:
markers.extend(
[marker.EventMarker(e) for e in
load_events(self.fn_events)])
marker.associate_phases_to_events(markers)
markers = [m for m in markers if isinstance(m, marker.PhaseMarker)]
markers_dict = defaultdict(list)
for m in markers:
if m.get_phasename().upper() != self.align_phase:
continue
markers_dict[m.get_event()].append(m)
self.markers = []
for e, _markers in markers_dict.items():
first = min(_markers, key=lambda x: x.tmin)
self.markers.append(first)
if not self.labeled:
dummy_event = Event(lat=0., lon=0., depth=0.)
for m in self.markers:
if not m.get_event():
m.set_event(dummy_event)
self.markers = [m for m in self.markers if m.get_event() is not None]
if not len(self.markers):
raise Exception('No markers left in dataset')
self.config.channels = list(self.data_pile.nslc_ids.keys())
self.config.channels.sort()
def get_arv_time_from_pyrocko(self):
"""
Description:
------------
Get arrival times from pyrock format data.
Parameters/Input:
-----------
'tt_pyrockp.dat':
stream (obspy stream): Input 3 component waveform data
evid (int): Event id.
Returns/Modificatoins:
P_tt (dict): P travel time data
S_tt (dict): S travel time data
"""
evids = self.evlist.keys()
markers = mk.load_markers(self.maindir + '/input/tt_pyrocko.dat')
mk.associate_phases_to_events(markers)
indexs = [
i for i in range(len(markers))
if isinstance(markers[i], (mk.PhaseMarker))
]
evid_markers_index = [
j for i in evids for j in indexs if markers[j]._event.name == i
]
P_tt, S_tt = {}, {}
for i in evids:
P_tt[i] = []
S_tt[i] = []
for j in evid_markers_index:
if markers[j]._phasename == 'P':
P_tt[markers[j]._event.name].append([
UTCDateTime(util.time_to_str(markers[j].tmin)),
markers[j].get_nslc_ids()[0][1]
])
if markers[j]._phasename == 'S':
S_tt[markers[j]._event.name].append([
UTCDateTime(util.time_to_str(markers[j].tmin)),
markers[j].get_nslc_ids()[0][1]
])
self.P_tt = P_tt
self.S_tt = S_tt
return None
def snuffler_from_commandline(args=None):
if args is None:
args = sys.argv[1:]
usage = '''usage: %prog [options] waveforms ...'''
parser = OptionParser(usage=usage)
parser.add_option(
'--format',
dest='format',
default='detect',
choices=io.allowed_formats('load'),
help='assume input files are of given FORMAT. Choices: %s' %
io.allowed_formats('load', 'cli_help', 'detect'))
parser.add_option('--pattern',
dest='regex',
metavar='REGEX',
help='only include files whose paths match REGEX')
parser.add_option('--stations',
dest='station_fns',
action='append',
default=[],
metavar='STATIONS',
help='read station information from file STATIONS')
parser.add_option(
'--stationxml',
dest='stationxml_fns',
action='append',
default=[],
metavar='STATIONSXML',
help='read station information from XML file STATIONSXML')
parser.add_option('--event',
'--events',
dest='event_fns',
action='append',
default=[],
metavar='EVENT',
help='read event information from file EVENT')
parser.add_option('--markers',
dest='marker_fns',
action='append',
default=[],
metavar='MARKERS',
help='read marker information file MARKERS')
parser.add_option('--follow',
type='float',
dest='follow',
metavar='N',
help='follow real time with a window of N seconds')
parser.add_option('--cache',
dest='cache_dir',
default=config.config().cache_dir,
metavar='DIR',
help='use directory DIR to cache trace metadata '
'(default=\'%default\')')
parser.add_option(
'--force-cache',
dest='force_cache',
action='store_true',
default=False,
help='use the cache even when trace attribute spoofing is active '
'(may have silly consequences)')
parser.add_option(
'--store-path',
dest='store_path',
metavar='PATH_TEMPLATE',
help='store data received through streams to PATH_TEMPLATE')
parser.add_option(
'--store-interval',
type='float',
dest='store_interval',
default=600,
metavar='N',
help='dump stream data to file every N seconds [default: %default]')
parser.add_option(
'--ntracks',
type='int',
dest='ntracks',
default=24,
metavar='N',
help='initially use N waveform tracks in viewer [default: %default]')
parser.add_option('--opengl',
dest='opengl',
action='store_true',
default=False,
help='use OpenGL for drawing')
parser.add_option('--qt5',
dest='gui_toolkit_qt5',
action='store_true',
default=False,
help='use Qt5 for the GUI')
parser.add_option('--qt4',
dest='gui_toolkit_qt4',
action='store_true',
default=False,
help='use Qt4 for the GUI')
parser.add_option('--debug',
dest='debug',
action='store_true',
default=False,
help='print debugging information to stderr')
options, args = parser.parse_args(list(args))
if options.debug:
util.setup_logging('snuffler', 'debug')
else:
util.setup_logging('snuffler', 'warning')
if options.gui_toolkit_qt4:
config.override_gui_toolkit = 'qt4'
if options.gui_toolkit_qt5:
config.override_gui_toolkit = 'qt5'
this_pile = pile.Pile()
stations = []
for stations_fn in extend_paths(options.station_fns):
stations.extend(model.station.load_stations(stations_fn))
for stationxml_fn in extend_paths(options.stationxml_fns):
stations.extend(
stationxml.load_xml(filename=stationxml_fn).get_pyrocko_stations())
events = []
for event_fn in extend_paths(options.event_fns):
events.extend(model.load_events(event_fn))
markers = []
for marker_fn in extend_paths(options.marker_fns):
markers.extend(marker.load_markers(marker_fn))
return snuffle(this_pile,
stations=stations,
events=events,
markers=markers,
ntracks=options.ntracks,
follow=options.follow,
controls=True,
opengl=options.opengl,
paths=args,
cache_dir=options.cache_dir,
regex=options.regex,
format=options.format,
force_cache=options.force_cache,
store_path=options.store_path,
store_interval=options.store_interval)
from markers import lookPattern
###Command line arguments
# 1: number of the day
# 2: number of the marker
if len(sys.argv) < 2:
sys.exit("Day number and markers number were not introduced.")
# set input file (which day to work on and which channel)
day = sys.argv[1]
dayCMD = formatDay(day)
filename = dict[int(sys.argv[2])] + dayCMD
stream = obspy.read(filename)
markers = pm.load_markers("../Markers/" + dayCMD + ".mk")
trace = stream[0]
interval = 30 #seconds for window width
overlap = 15
tzero = trace.stats.starttime
traces = []
maxTime = 24 * 60 * 60 - interval
#maxTime = 50 #for testing
#fileToSave = open(, 'w')
def snuffler_from_commandline(args=None):
if args is None:
args = sys.argv[1:]
usage = '''usage: %prog [options] waveforms ...'''
parser = OptionParser(usage=usage)
parser.add_option(
'--format',
dest='format',
default='detect',
choices=io.allowed_formats('load'),
help='assume input files are of given FORMAT. Choices: %s'
% io.allowed_formats('load', 'cli_help', 'detect'))
parser.add_option(
'--pattern',
dest='regex',
metavar='REGEX',
help='only include files whose paths match REGEX')
parser.add_option(
'--stations',
dest='station_fns',
action='append',
default=[],
metavar='STATIONS',
help='read station information from file STATIONS')
parser.add_option(
'--stationxml',
dest='stationxml_fns',
action='append',
default=[],
metavar='STATIONSXML',
help='read station information from XML file STATIONSXML')
parser.add_option(
'--event', '--events',
dest='event_fns',
action='append',
default=[],
metavar='EVENT',
help='read event information from file EVENT')
parser.add_option(
'--markers',
dest='marker_fns',
action='append',
default=[],
metavar='MARKERS',
help='read marker information file MARKERS')
parser.add_option(
'--follow',
type='float',
dest='follow',
metavar='N',
help='follow real time with a window of N seconds')
parser.add_option(
'--cache',
dest='cache_dir',
default=config.config().cache_dir,
metavar='DIR',
help='use directory DIR to cache trace metadata '
'(default=\'%default\')')
parser.add_option(
'--force-cache',
dest='force_cache',
action='store_true',
default=False,
help='use the cache even when trace attribute spoofing is active '
'(may have silly consequences)')
parser.add_option(
'--store-path',
dest='store_path',
metavar='PATH_TEMPLATE',
help='store data received through streams to PATH_TEMPLATE')
parser.add_option(
'--store-interval',
type='float',
dest='store_interval',
default=600,
metavar='N',
help='dump stream data to file every N seconds [default: %default]')
parser.add_option(
'--ntracks',
type='int',
dest='ntracks',
default=24,
metavar='N',
help='initially use N waveform tracks in viewer [default: %default]')
parser.add_option(
'--opengl',
dest='opengl',
action='store_true',
default=False,
help='use OpenGL for drawing')
parser.add_option(
'--qt5',
dest='gui_toolkit_qt5',
action='store_true',
default=False,
help='use Qt5 for the GUI')
parser.add_option(
'--qt4',
dest='gui_toolkit_qt4',
action='store_true',
default=False,
help='use Qt4 for the GUI')
parser.add_option(
'--debug',
dest='debug',
action='store_true',
default=False,
help='print debugging information to stderr')
options, args = parser.parse_args(list(args))
if options.debug:
util.setup_logging('snuffler', 'debug')
else:
util.setup_logging('snuffler', 'warning')
if options.gui_toolkit_qt4:
config.override_gui_toolkit = 'qt4'
if options.gui_toolkit_qt5:
config.override_gui_toolkit = 'qt5'
this_pile = pile.Pile()
stations = []
for stations_fn in extend_paths(options.station_fns):
stations.extend(model.station.load_stations(stations_fn))
for stationxml_fn in extend_paths(options.stationxml_fns):
stations.extend(
stationxml.load_xml(
filename=stationxml_fn).get_pyrocko_stations())
events = []
for event_fn in extend_paths(options.event_fns):
events.extend(model.load_events(event_fn))
markers = []
for marker_fn in extend_paths(options.marker_fns):
markers.extend(marker.load_markers(marker_fn))
return snuffle(
this_pile,
stations=stations,
events=events,
markers=markers,
ntracks=options.ntracks,
follow=options.follow,
controls=True,
opengl=options.opengl,
paths=args,
cache_dir=options.cache_dir,
regex=options.regex,
format=options.format,
force_cache=options.force_cache,
store_path=options.store_path,
store_interval=options.store_interval)
#Filtering the data to the ones that are not noise
lastColumn = np.append(lastColumn, label)
return lastColumn
if len(sys.argv) < 2:
sys.exit("Day was not introduced")
day = formatDay(int(sys.argv[1]))
# set input file (which day to work on and which channel)
df = 50 #sampling rate
interval = 30 #seconds for window width
overlap = 15
markers = pm.load_markers("../Markers/" + day + ".pf")
#header = 'MEAN_E,MEDIAN_E,STDV_E,MAXIMUM_E,REP_FREQ_E,SUM_ENERGY_E,ENERGY_PREV_E,ENERGY_NEXT_E,MEAN_N,MEDIAN_N,STDV_N,MAXIMUM_N,REP_FREQ_N,SUM_ENERGY_N,ENERGY_PREV_N,ENERGY_NEXT_N,MEAN_Z,MEDIAN_Z,STDV_Z' #,MAXIMUM_Z,REP_FREQ_Z,SUM_ENERGY_Z,ENERGY_PREV_Z,ENERGY_NEXT_Z, CLASS'
filenames = filenames = [prefix + day for prefix in dict.values()]
##BMAS
station1 = processFile(filenames[0], markers)
station2 = processFile(filenames[1], markers)
station3 = processFile(filenames[2], markers, lastFile=True)
#classes = computeClasess(filenames[0], markers)
#classes = np.reshape(classes,(-1,1))
bmas = np.hstack((station1, station2, station3))
from pyrocko import util
from pyrocko.gui import marker as pm
from pyrocko.example import get_example_data
# Download example markers
get_example_data('my_markers.pf')
markers = pm.load_markers('my_markers.pf')
pm.associate_phases_to_events(markers)
for marker in markers:
print(util.time_to_str(marker.tmin), util.time_to_str(marker.tmax))
# only event and phase markers have an event attached
if isinstance(marker, (pm.EventMarker, pm.PhaseMarker)):
ev = marker.get_event()
print(ev) # may be shared between markers