def _test_colocated():
eventid = "ci38445975"
datafiles, event = read_data_dir("fdsn", eventid, "*")
datadir = os.path.split(datafiles[0])[0]
raw_streams = StreamCollection.from_directory(datadir)
config_file = os.path.join(datadir, "test_config.yml")
with open(config_file, "r", encoding="utf-8") as f:
yaml = YAML()
yaml.preserve_quotes = True
config = yaml.load(f)
processed_streams = process_streams(raw_streams, event, config=config)
tdir = tempfile.mkdtemp()
try:
tfile = os.path.join(tdir, "test.hdf")
ws = StreamWorkspace(tfile)
ws.addEvent(event)
ws.addStreams(event, raw_streams, label="raw")
ws.addStreams(event, processed_streams, label="processed")
ws.calcMetrics(eventid, labels=["processed"], config=config)
stasum = ws.getStreamMetrics(eventid, "CI", "MIKB", "processed")
np.testing.assert_allclose(
stasum.get_pgm("duration", "geometric_mean"), 38.94480068)
ws.close()
except Exception as e:
raise (e)
finally:
shutil.rmtree(tdir)
def _test_colocated():
eventid = 'ci38445975'
datafiles, event = read_data_dir('fdsn', eventid, '*')
datadir = os.path.split(datafiles[0])[0]
raw_streams = StreamCollection.from_directory(datadir)
config_file = os.path.join(datadir, 'test_config.yml')
with open(config_file, 'r', encoding='utf-8') as f:
config = yaml.load(f, Loader=yaml.FullLoader)
processed_streams = process_streams(raw_streams, event, config=config)
tdir = tempfile.mkdtemp()
try:
tfile = os.path.join(tdir, 'test.hdf')
ws = StreamWorkspace(tfile)
ws.addEvent(event)
ws.addStreams(event, raw_streams, label='raw')
ws.addStreams(event, processed_streams, label='processed')
ws.calcMetrics(eventid, labels=['processed'], config=config)
stasum = ws.getStreamMetrics(eventid, 'CI', 'MIKB', 'processed')
np.testing.assert_allclose(
stasum.get_pgm('duration', 'geometric_mean'), 38.94480068)
ws.close()
except Exception as e:
raise (e)
finally:
shutil.rmtree(tdir)
def test_metrics():
eventid = 'usb000syza'
datafiles, event = read_data_dir('knet', eventid, '*')
datadir = os.path.split(datafiles[0])[0]
raw_streams = StreamCollection.from_directory(datadir)
config = get_config()
# turn off sta/lta check and snr checks
newconfig = drop_processing(config, ['check_sta_lta', 'compute_snr'])
processed_streams = process_streams(raw_streams, event, config=newconfig)
tdir = tempfile.mkdtemp()
try:
tfile = os.path.join(tdir, 'test.hdf')
workspace = StreamWorkspace(tfile)
workspace.addEvent(event)
workspace.addStreams(event, processed_streams, label='processed')
stream1 = processed_streams[0]
stream2 = processed_streams[1]
summary1 = StationSummary.from_config(stream1)
summary2 = StationSummary.from_config(stream2)
workspace.setStreamMetrics(event.id, 'processed', summary1)
workspace.setStreamMetrics(event.id, 'processed', summary2)
workspace.calcStationMetrics(event.id, labels=['processed'])
summary1_a = workspace.getStreamMetrics(event.id,
stream1[0].stats.station,
'processed')
s1_df_in = summary1.pgms.sort_values(['IMT', 'IMC'])
s1_df_out = summary1_a.pgms.sort_values(['IMT', 'IMC'])
array1 = s1_df_in['Result'].as_matrix()
array2 = s1_df_out['Result'].as_matrix()
np.testing.assert_almost_equal(array1, array2, decimal=4)
df = workspace.getMetricsTable(event.id)
cmp_series = {
'GREATER_OF_TWO_HORIZONTALS': 0.6787,
'H1': 0.3869,
'H2': 0.6787,
'Z': 0.7663
}
pga_dict = df.iloc[0]['PGA'].to_dict()
for key, value in pga_dict.items():
value2 = cmp_series[key]
np.testing.assert_almost_equal(value, value2, decimal=4)
workspace.close()
except Exception as e:
raise(e)
finally:
shutil.rmtree(tdir)
def test_metrics():
eventid = 'usb000syza'
datafiles, event = read_data_dir('knet',
eventid,
'*')
datadir = os.path.split(datafiles[0])[0]
raw_streams = StreamCollection.from_directory(datadir)
config = get_config()
# turn off sta/lta check and snr checks
newconfig = drop_processing(config, ['check_sta_lta', 'compute_snr'])
processed_streams = process_streams(raw_streams, event, config=newconfig)
tdir = tempfile.mkdtemp()
try:
tfile = os.path.join(tdir, 'test.hdf')
workspace = StreamWorkspace(tfile)
workspace.addEvent(event)
workspace.addStreams(event, processed_streams, label='processed')
stream1 = processed_streams[0]
stream2 = processed_streams[1]
summary1 = StationSummary.from_config(stream1)
summary2 = StationSummary.from_config(stream2)
workspace.setStreamMetrics(event.id, 'processed', summary1)
workspace.setStreamMetrics(event.id, 'processed', summary2)
summary1_a = workspace.getStreamMetrics(event.id,
stream1[0].stats.station,
'processed')
s1_df_in = summary1.pgms.sort_values(['IMT', 'IMC'])
s1_df_out = summary1_a.pgms.sort_values(['IMT', 'IMC'])
array1 = s1_df_in['Result'].as_matrix()
array2 = s1_df_out['Result'].as_matrix()
np.testing.assert_almost_equal(array1, array2, decimal=4)
df = workspace.getMetricsTable(event.id)
cmp_series = {'GREATER_OF_TWO_HORIZONTALS': 0.6787,
'HN1': 0.3869,
'HN2': 0.6787,
'HNZ': 0.7663}
pga_dict = df.iloc[0]['PGA'].to_dict()
for key, value in pga_dict.items():
value2 = cmp_series[key]
np.testing.assert_almost_equal(value, value2, decimal=4)
workspace.close()
except Exception as e:
raise(e)
finally:
shutil.rmtree(tdir)
def test_metrics():
eventid = "usb000syza"
datafiles, event = read_data_dir("knet", eventid, "*")
datadir = os.path.split(datafiles[0])[0]
raw_streams = StreamCollection.from_directory(datadir)
config = update_config(os.path.join(datadir, "config_min_freq_0p2.yml"))
# turn off sta/lta check and snr checks
# newconfig = drop_processing(config, ['check_sta_lta', 'compute_snr'])
# processed_streams = process_streams(raw_streams, event, config=newconfig)
newconfig = config.copy()
newconfig["processing"].append(
{"NNet_QA": {
"acceptance_threshold": 0.5,
"model_name": "CantWell"
}})
processed_streams = process_streams(raw_streams.copy(),
event,
config=newconfig)
tdir = tempfile.mkdtemp()
try:
tfile = os.path.join(tdir, "test.hdf")
workspace = StreamWorkspace(tfile)
workspace.addEvent(event)
workspace.addStreams(event, raw_streams, label="raw")
workspace.addStreams(event, processed_streams, label="processed")
stream1 = raw_streams[0]
# Get metrics from station summary for raw streams
summary1 = StationSummary.from_config(stream1)
s1_df_in = summary1.pgms.sort_values(["IMT", "IMC"])
array1 = s1_df_in["Result"].to_numpy()
# Compare to metrics from getStreamMetrics for raw streams
workspace.calcMetrics(eventid, labels=["raw"])
summary1_a = workspace.getStreamMetrics(event.id,
stream1[0].stats.network,
stream1[0].stats.station,
"raw")
s1_df_out = summary1_a.pgms.sort_values(["IMT", "IMC"])
array2 = s1_df_out["Result"].to_numpy()
np.testing.assert_allclose(array1, array2, atol=1e-6, rtol=1e-6)
workspace.close()
except Exception as e:
raise (e)
finally:
shutil.rmtree(tdir)
def test_metrics():
eventid = 'usb000syza'
datafiles, event = read_data_dir('knet', eventid, '*')
datadir = os.path.split(datafiles[0])[0]
raw_streams = StreamCollection.from_directory(datadir)
config = update_config(os.path.join(datadir, 'config_min_freq_0p2.yml'))
# turn off sta/lta check and snr checks
# newconfig = drop_processing(config, ['check_sta_lta', 'compute_snr'])
# processed_streams = process_streams(raw_streams, event, config=newconfig)
newconfig = config.copy()
newconfig['processing'].append(
{'NNet_QA': {
'acceptance_threshold': 0.5,
'model_name': 'CantWell'
}})
processed_streams = process_streams(raw_streams.copy(),
event,
config=newconfig)
tdir = tempfile.mkdtemp()
try:
tfile = os.path.join(tdir, 'test.hdf')
workspace = StreamWorkspace(tfile)
workspace.addEvent(event)
workspace.addStreams(event, raw_streams, label='raw')
workspace.addStreams(event, processed_streams, label='processed')
stream1 = raw_streams[0]
# Get metrics from station summary for raw streams
summary1 = StationSummary.from_config(stream1)
s1_df_in = summary1.pgms.sort_values(['IMT', 'IMC'])
array1 = s1_df_in['Result'].to_numpy()
# Compare to metrics from getStreamMetrics for raw streams
workspace.calcMetrics(eventid, labels=['raw'])
summary1_a = workspace.getStreamMetrics(event.id,
stream1[0].stats.network,
stream1[0].stats.station,
'raw')
s1_df_out = summary1_a.pgms.sort_values(['IMT', 'IMC'])
array2 = s1_df_out['Result'].to_numpy()
np.testing.assert_allclose(array1, array2, atol=1e-6, rtol=1e-6)
workspace.close()
except Exception as e:
raise (e)
finally:
shutil.rmtree(tdir)
def test_metrics():
eventid = 'usb000syza'
datafiles, event = read_data_dir('knet', eventid, '*')
datadir = os.path.split(datafiles[0])[0]
raw_streams = StreamCollection.from_directory(datadir)
config = get_config()
# turn off sta/lta check and snr checks
# newconfig = drop_processing(config, ['check_sta_lta', 'compute_snr'])
# processed_streams = process_streams(raw_streams, event, config=newconfig)
newconfig = config.copy()
newconfig['processing'].append(
{'NNet_QA': {
'acceptance_threshold': 0.5,
'model_name': 'CantWell'
}})
processed_streams = process_streams(raw_streams, event, config=newconfig)
tdir = tempfile.mkdtemp()
try:
tfile = os.path.join(tdir, 'test.hdf')
workspace = StreamWorkspace(tfile)
workspace.addEvent(event)
workspace.addStreams(event, raw_streams, label='raw')
workspace.addStreams(event, processed_streams, label='processed')
stream1 = raw_streams[0]
summary1 = StationSummary.from_config(stream1)
s1_df_in = summary1.pgms.sort_values(['IMT', 'IMC'])
array1 = s1_df_in['Result'].as_matrix()
workspace.calcStreamMetrics(eventid, labels=['raw'])
workspace.calcStationMetrics(event.id, labels=['raw'])
pstreams2 = workspace.getStreams(event.id, labels=['processed'])
assert pstreams2[0].getStreamParamKeys() == ['nnet_qa']
summary1_a = workspace.getStreamMetrics(event.id,
stream1[0].stats.network,
stream1[0].stats.station,
'raw')
s1_df_out = summary1_a.pgms.sort_values(['IMT', 'IMC'])
array2 = s1_df_out['Result'].as_matrix()
np.testing.assert_almost_equal(array1, array2, decimal=4)
workspace.close()
except Exception as e:
raise (e)
finally:
shutil.rmtree(tdir)
def _test_vs30_dist_metrics():
KNOWN_DISTANCES = {
"epicentral": 5.1,
"hypocentral": 10.2,
"rupture": 2.21,
"rupture_var": np.nan,
"joyner_boore": 2.21,
"joyner_boore_var": np.nan,
"gc2_rx": 2.66,
"gc2_ry": 3.49,
"gc2_ry0": 0.00,
"gc2_U": 34.34,
"gc2_T": 2.66,
}
KNOWN_BAZ = 239.46
KNOWN_VS30 = 331.47
eventid = "ci38457511"
datafiles, event = read_data_dir("fdsn", eventid, "*")
datadir = os.path.split(datafiles[0])[0]
raw_streams = StreamCollection.from_directory(datadir)
config = update_config(os.path.join(datadir, "config_min_freq_0p2.yml"))
processed_streams = process_streams(raw_streams, event, config=config)
rupture_file = get_rupture_file(datadir)
grid_file = os.path.join(datadir, "test_grid.grd")
config["metrics"]["vs30"] = {
"vs30": {
"file": grid_file,
"column_header": "GlobalVs30",
"readme_entry": "GlobalVs30",
"units": "m/s",
}
}
tdir = tempfile.mkdtemp()
try:
tfile = os.path.join(tdir, "test.hdf")
ws = StreamWorkspace(tfile)
ws.addEvent(event)
ws.addStreams(event, raw_streams, label="raw")
ws.addStreams(event, processed_streams, label="processed")
ws.calcMetrics(event.id,
rupture_file=rupture_file,
labels=["processed"],
config=config)
sta_sum = ws.getStreamMetrics(event.id, "CI", "CLC", "processed")
for dist in sta_sum.distances:
np.testing.assert_allclose(sta_sum.distances[dist],
KNOWN_DISTANCES[dist],
rtol=0.01)
np.testing.assert_allclose(sta_sum._back_azimuth, KNOWN_BAZ, rtol=0.01)
np.testing.assert_allclose(sta_sum._vs30["vs30"]["value"],
KNOWN_VS30,
rtol=0.01)
event_df, imc_tables, readme_tables = ws.getTables("processed")
ws.close()
check_cols = set([
"EpicentralDistance",
"HypocentralDistance",
"RuptureDistance",
"RuptureDistanceVar",
"JoynerBooreDistance",
"JoynerBooreDistanceVar",
"GC2_rx",
"GC2_ry",
"GC2_ry0",
"GC2_U",
"GC2_T",
"GlobalVs30",
"BackAzimuth",
])
assert check_cols.issubset(set(readme_tables["Z"]["Column header"]))
assert check_cols.issubset(set(imc_tables["Z"].columns))
except Exception as e:
raise (e)
finally:
shutil.rmtree(tdir)
def _test_vs30_dist_metrics():
KNOWN_DISTANCES = {
'epicentral': 5.1,
'hypocentral': 10.2,
'rupture': 2.21,
'rupture_var': np.nan,
'joyner_boore': 2.21,
'joyner_boore_var': np.nan,
'gc2_rx': 2.66,
'gc2_ry': 3.49,
'gc2_ry0': 0.00,
'gc2_U': 34.34,
'gc2_T': 2.66
}
KNOWN_BAZ = 239.46
KNOWN_VS30 = 331.47
eventid = 'ci38457511'
datafiles, event = read_data_dir('fdsn', eventid, '*')
datadir = os.path.split(datafiles[0])[0]
raw_streams = StreamCollection.from_directory(datadir)
config = update_config(os.path.join(datadir, 'config_min_freq_0p2.yml'))
processed_streams = process_streams(raw_streams, event, config=config)
rupture_file = get_rupture_file(datadir)
grid_file = os.path.join(datadir, 'test_grid.grd')
config['metrics']['vs30'] = {
'vs30': {
'file': grid_file,
'column_header': 'GlobalVs30',
'readme_entry': 'GlobalVs30',
'units': 'm/s'
}
}
tdir = tempfile.mkdtemp()
try:
tfile = os.path.join(tdir, 'test.hdf')
ws = StreamWorkspace(tfile)
ws.addEvent(event)
ws.addStreams(event, raw_streams, label='raw')
ws.addStreams(event, processed_streams, label='processed')
ws.calcMetrics(event.id,
rupture_file=rupture_file,
labels=['processed'],
config=config)
sta_sum = ws.getStreamMetrics(event.id, 'CI', 'CLC', 'processed')
for dist in sta_sum.distances:
np.testing.assert_allclose(sta_sum.distances[dist],
KNOWN_DISTANCES[dist],
rtol=0.01)
np.testing.assert_allclose(sta_sum._back_azimuth, KNOWN_BAZ, rtol=0.01)
np.testing.assert_allclose(sta_sum._vs30['vs30']['value'],
KNOWN_VS30,
rtol=0.01)
event_df, imc_tables, readme_tables = ws.getTables('processed')
ws.close()
check_cols = set([
'EpicentralDistance', 'HypocentralDistance', 'RuptureDistance',
'RuptureDistanceVar', 'JoynerBooreDistance',
'JoynerBooreDistanceVar', 'GC2_rx', 'GC2_ry', 'GC2_ry0', 'GC2_U',
'GC2_T', 'GlobalVs30', 'BackAzimuth'
])
assert check_cols.issubset(set(readme_tables['Z']['Column header']))
assert check_cols.issubset(set(imc_tables['Z'].columns))
except Exception as e:
raise (e)
finally:
shutil.rmtree(tdir)
def test_workspace():
eventid = 'us1000778i'
datafiles, origin = read_data_dir('geonet', eventid, '*.V1A')
event = get_event_object(origin)
tdir = tempfile.mkdtemp()
try:
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=H5pyDeprecationWarning)
warnings.filterwarnings("ignore", category=YAMLLoadWarning)
warnings.filterwarnings("ignore", category=FutureWarning)
config = get_config()
tfile = os.path.join(tdir, 'test.hdf')
raw_streams = []
for dfile in datafiles:
raw_streams += read_data(dfile)
workspace = StreamWorkspace(tfile)
t1 = time.time()
workspace.addStreams(event, raw_streams, label='raw')
t2 = time.time()
print('Adding %i streams took %.2f seconds' % (len(raw_streams),
(t2 - t1)))
str_repr = workspace.__repr__()
assert str_repr == 'Events: 1 Stations: 3 Streams: 3'
eventobj = workspace.getEvent(eventid)
assert eventobj.origins[0].latitude == event.origins[0].latitude
assert eventobj.magnitudes[0].mag == event.magnitudes[0].mag
stations = workspace.getStations()
assert sorted(stations) == ['hses', 'thz', 'wtmc']
stations = workspace.getStations(eventid=eventid)
assert sorted(stations) == ['hses', 'thz', 'wtmc']
# test retrieving tags for an event that doesn't exist
try:
workspace.getStreamTags('foo')
except KeyError:
assert 1 == 1
# test retrieving event that doesn't exist
try:
workspace.getEvent('foo')
except KeyError:
assert 1 == 1
instream = None
for stream in raw_streams:
if stream[0].stats.station.lower() == 'hses':
instream = stream
break
if instream is None:
assert 1 == 2
outstream = workspace.getStreams(eventid,
stations=['hses'],
labels=['raw'])[0]
compare_streams(instream, outstream)
label_summary = workspace.summarizeLabels()
assert label_summary.iloc[0]['Label'] == 'raw'
assert label_summary.iloc[0]['Software'] == 'gmprocess'
sc = StreamCollection(raw_streams)
processed_streams = process_streams(sc, origin, config=config)
workspace.addStreams(event, processed_streams, 'processed')
idlist = workspace.getEventIds()
assert idlist[0] == eventid
event_tags = workspace.getStreamTags(eventid)
assert sorted(event_tags) == [
'hses_processed', 'hses_raw', 'thz_processed', 'thz_raw',
'wtmc_processed', 'wtmc_raw'
]
outstream = workspace.getStreams(eventid,
stations=['hses'],
labels=['processed'])[0]
provenance = workspace.getProvenance(eventid, labels=['processed'])
first_row = pd.Series({
'Record': 'NZ.HSES.HN1',
'Processing Step': 'Remove Response',
'Step Attribute': 'input_units',
'Attribute Value': 'counts'
})
last_row = pd.Series({
'Record': 'NZ.WTMC.HNZ',
'Processing Step': 'Detrend',
'Step Attribute': 'detrending_method',
'Attribute Value': 'baseline_sixth_order'
})
assert provenance.iloc[0].equals(first_row)
assert provenance.iloc[-1].equals(last_row)
# compare the parameters from the input processed stream
# to it's output equivalent
instream = None
for stream in processed_streams:
if stream[0].stats.station.lower() == 'hses':
instream = stream
break
if instream is None:
assert 1 == 2
compare_streams(instream, outstream)
workspace.close()
# read in data from a second event and stash it in the workspace
eventid = 'nz2018p115908'
datafiles, origin = read_data_dir('geonet', eventid, '*.V2A')
raw_streams = []
for dfile in datafiles:
raw_streams += read_data(dfile)
event = get_event_object(origin)
workspace = StreamWorkspace.open(tfile)
workspace.addStreams(event, raw_streams, label='foo')
stations = workspace.getStations(eventid)
eventids = workspace.getEventIds()
assert eventids == ['us1000778i', 'nz2018p115908']
instation = raw_streams[0][0].stats.station
this_stream = workspace.getStreams(eventid,
stations=[instation],
labels=['foo'])[0]
assert instation == this_stream[0].stats.station
# set and retrieve waveform metrics in the file
imclist = [
'greater_of_two_horizontals', 'channels', 'rotd50', 'rotd100'
]
imtlist = ['sa1.0', 'PGA', 'pgv', 'fas2.0', 'arias']
usid = 'us1000778i'
tags = workspace.getStreamTags(usid)
workspace.setStreamMetrics(eventid,
labels=['foo'],
imclist=imclist,
imtlist=imtlist)
summary = workspace.getStreamMetrics(eventid, instation, 'foo')
summary_series = summary.toSeries()['ARIAS']
cmpseries = pd.Series({
'GEOMETRIC_MEAN': np.NaN,
'GREATER_OF_TWO_HORIZONTALS': 0.0005,
'HN1': 0.0001,
'HN2': 0.0005,
'HNZ': 0.0000,
'ROTD100.0': 0.0005,
'ROTD50.0': 0.0003
})
assert cmpseries.equals(summary_series)
workspace.setStreamMetrics(usid, labels=['processed'])
df = workspace.getMetricsTable(usid, labels=['processed'])
cmpdict = {
'GREATER_OF_TWO_HORIZONTALS': [26.8906, 4.9415, 94.6646],
'HN1': [24.5105, 4.9415, 94.6646],
'HN2': [26.8906, 4.0758, 86.7877],
'HNZ': [16.0941, 2.5401, 136.7054]
}
cmpframe = pd.DataFrame(cmpdict)
assert df['PGA'].equals(cmpframe)
inventory = workspace.getInventory(usid)
codes = [
station.code for station in inventory.networks[0].stations
]
assert sorted(codes) == ['HSES', 'THZ', 'WPWS', 'WTMC']
except Exception as e:
raise (e)
finally:
shutil.rmtree(tdir)