def fromFiles(cls, directory, imcs=None, imts=None, process=True):
"""
Read files from a directory and return an EventSummary object.
Args:
directory (str): Path to input files.
imcs (list): List of intensity measurement components (str). Default
is None.
imts (list): List of intensity measurement types (str). Default
is None.
process (bool): Whether or not to process the streams.
Returns:
EventSummary: EventSummary object.
"""
streams = []
# gather streams so that they can be grouped
for file_path in glob.glob(directory + '/*'):
streams += [read_data(file_path)]
streams = group_channels(streams)
uncorrected_streams = {}
for stream in streams:
station = stream[0].stats['station']
uncorrected_streams[station] = stream
event = cls()
event.uncorrected_streams = uncorrected_streams
if process:
event.process()
# create dictionary of StationSummary objects for use by other methods
event.setStationDictionary(imcs, imts)
return event
def test_spectral():
homedir = os.path.dirname(
os.path.abspath(__file__)) # where is this script?
acc_file = os.path.join(homedir, '..', 'data', 'geonet',
'20161113_110259_WTMC_20.V2A')
acc = read_data(acc_file)
get_spectral(1.0, acc, 0.05, rotation='gm')
def from_files(cls, directory, imcs, imts):
"""
Read files from a directory and return an EventSummary object.
Args:
directory (str): Path to input files.
imcs (list): List of intensity measurement components (str).
imts (list): List of intensity measurement types (str).
Returns:
EventSummary: EventSummary object.
"""
streams = []
# gather streams
for file_path in glob.glob(directory + '/*'):
streams += [read_data(file_path)]
# group station traces
streams = group_channels(streams)
# process streams
#TODO separate into another method and add config for processing parameters
with warnings.catch_warnings():
warnings.simplefilter("ignore")
for idx, trace in enumerate(streams):
streams[idx] = filter_detrend(streams[idx])
# create dictionary of StationSummary objects
station_dict = OrderedDict()
for stream in streams:
station = stream[0].stats['station']
station_dict[station] = StationSummary(stream, imcs, imts)
event = cls(station_dict)
return event
def test_velocity():
homedir = os.path.dirname(
os.path.abspath(__file__)) # where is this script?
acc_file = os.path.join(homedir, '..', 'data', 'geonet',
'20161113_110259_WTMC_20.V2A')
acc = read_data(acc_file)
target_v = acc.copy().integrate()[0]
v = get_velocity(acc)
np.testing.assert_allclose(v[0], target_v)
def test_plot():
# read in data
homedir = os.path.dirname(os.path.abspath(__file__))
datadir = os.path.join(homedir, '..', 'data', 'cwb')
streams = []
for filename in glob.glob(datadir + '/*'):
streams += [read_data(filename)]
# One plot arias
axes = plot_arias(streams[3])
assert len(axes) == 3
# Multiplot arias
axs = matplotlib.pyplot.subplots(len(streams), 3, figsize=(15, 10))[1]
axs = axs.flatten()
idx = 0
for stream in streams:
axs = plot_arias(stream,
axes=axs,
axis_index=idx,
minfontsize=15,
show_maximum=False,
title="18km NNE of Hualian, Taiwan")
idx += 3
# One plot durations
durations = [(0.05, 0.75), (0.2, 0.8), (0.05, .95)]
axes = plot_durations(streams[3], durations)
assert len(axes) == 3
# Multiplot durations
axs = matplotlib.pyplot.subplots(len(streams), 3, figsize=(15, 10))[1]
axs = axs.flatten()
idx = 0
for stream in streams:
axs = plot_durations(stream,
durations,
axes=axs,
axis_index=idx,
minfontsize=15,
title="18km NNE of Hualian, Taiwan")
idx += 3
# Moveout plots
epicenter_lat = 24.14
epicenter_lon = 121.69
plot_moveout(streams,
epicenter_lat,
epicenter_lon,
'BN1',
cmap='nipy_spectral_r',
figsize=(15, 10),
minfontsize=16,
normalize=True,
scale=10)
def test_read():
homedir = os.path.dirname(
os.path.abspath(__file__)) #where is this script?
cosmos_dir = os.path.join(homedir, '..', '..', 'data', 'cosmos')
cwb_dir = os.path.join(homedir, '..', '..', 'data', 'cwb')
dmg_dir = os.path.join(homedir, '..', '..', 'data', 'dmg')
geonet_dir = os.path.join(homedir, '..', '..', 'data', 'geonet')
knet_dir = os.path.join(homedir, '..', '..', 'data', 'knet')
smc_dir = os.path.join(homedir, '..', '..', 'data', 'smc')
file_dict = {}
file_dict['cosmos'] = os.path.join(cosmos_dir, 'Cosmos12TimeSeriesTest.v1')
file_dict['cwb'] = os.path.join(cwb_dir, '1-EAS.dat')
file_dict['dmg'] = os.path.join(dmg_dir, 'CE89146.V2')
file_dict['geonet'] = os.path.join(geonet_dir,
'20161113_110259_WTMC_20.V1A')
file_dict['knet'] = os.path.join(knet_dir, 'AOM0011801241951.EW')
file_dict['smc'] = os.path.join(smc_dir, '0111a.smc')
for file_format in file_dict:
file_path = file_dict[file_format]
assert _get_format(file_path) == file_format
assert _validate_format(file_path, file_format) == file_format
assert _validate_format(file_dict['knet'], 'smc') == 'knet'
assert _validate_format(file_dict['dmg'], 'cosmos') == 'dmg'
assert _validate_format(file_dict['cosmos'], 'invalid') == 'cosmos'
for file_format in file_dict:
stream = read_data(file_dict[file_format], file_format)
assert stream[0].stats.standard['source_format'] == file_format
stream = read_data(file_dict[file_format])
assert stream[0].stats.standard['source_format'] == file_format
# test exception
try:
file_path = os.path.join(smc_dir, 'not_a_file.smc')
read_data(file_path)
success = True
except AmptoolsException:
success = False
assert success == False
def test_arias():
homedir = os.path.dirname(
os.path.abspath(__file__)) # where is this script?
data_dir = os.path.join(homedir, '..', 'data',
'evolutionary_IM_examples.xlsx')
df = pd.read_excel(data_dir)
time = df.iloc[:, 0].values
# input output is m/s/s
acc = df.iloc[:, 1].values / 100
target_IA = df.iloc[:, 4].values[0]
delta = time[2] - time[1]
sr = 1 / delta
header = {
'delta': delta,
'sampling_rate': sr,
'npts': len(acc),
'units': 'm/s/s',
'channel': 'H1'
}
trace = Trace(data=acc, header=header)
stream = Stream([trace])
Ia = calculate_arias(stream, ['channels'])['H1']
# the target has only one decimal place and is in cm/s/s
Ia = Ia * 100
np.testing.assert_almost_equal(Ia, target_IA, decimal=1)
# input is cm/s/s output is m/s/s
trace = Trace(data=acc * 100, header=header)
stream = Stream([trace])
station = StationSummary.from_stream(stream, ['channels'], ['arias'])
Ia = station.pgms['ARIAS']['H1']
# the target has only one decimal place and is in cm/s/s
Ia = Ia * 100
np.testing.assert_almost_equal(Ia, target_IA, decimal=1)
# Test other components
data_file = os.path.join(homedir, '..', 'data', 'cwb', '2-ECU.dat')
stream = read_data(data_file)
station = StationSummary.from_stream(
stream, ['channels', 'gmrotd', 'rotd50', 'greater_of_two_horizontals'],
['arias'])
def test_acceleration():
homedir = os.path.dirname(
os.path.abspath(__file__)) # where is this script?
acc_file = os.path.join(homedir, '..', 'data', 'geonet',
'20161113_110259_WTMC_20.V2A')
acc = read_data(acc_file)
target_g = acc[0].data * GAL_TO_PCTG
target_m = acc[0].data / 100
target_cm = acc[0].data
acc_g = get_acceleration(acc, units='%%g')
assert acc_g[0].stats['units'] == '%%g'
np.testing.assert_allclose(acc_g[0], target_g)
acc_m = get_acceleration(acc, units='m/s/s')
assert acc_m[0].stats['units'] == 'm/s/s'
np.testing.assert_allclose(acc_m[0], target_m)
acc_cm = get_acceleration(acc, units='cm/s/s')
assert acc_cm[0].stats['units'] == 'cm/s/s'
np.testing.assert_allclose(acc_cm[0], target_cm)
def get_station_data(event, data_type):
"""
Reads in seismic data, groups by station, and creates a list of station
stats.
Args:
event (str): USGS event ID.
data_type (str): Seismic data format.
Options are:
knt
kik
smc
V2_V3
Returns:
stations (array): Combined streams of acceleration data for each station.
station_stats (list): Name, lat, lon, and elevation for each station.
"""
# Define filepath and selected stations to use (if there are any).
filepath = os.path.join('/Users/tnye/PROJECTS/Duration/data/events', event,
'ground_motion', data_type)
select_stns = os.path.join('/Users/tnye/PROJECTS/Duration/data/events',
event, 'select_stations', data_type + '.csv')
os.chdir(filepath)
# Select acceleration files and combine into a list.
files_grabbed = []
if data_type == 'knt':
types = ('*.EW', '*.NS', '*.UD')
for files in types:
files_grabbed.extend(glob.glob(files))
elif data_type == 'kik':
types = ('*.EW2', '*.NS2', '*.UD2')
for files in types:
files_grabbed.extend(glob.glob(files))
elif data_type == 'smc':
types = ('*a.smc')
for file in glob.glob(types):
files_grabbed.append(file)
elif data_type == 'v2':
types = ('*.V2')
for file in glob.glob(types):
files_grabbed.append(file)
# Read files using Amptools.
data = []
try:
for i in range(len(files_grabbed)):
data.append(read_data(files_grabbed[i]))
except:
print('Bad file', files_grabbed[i])
# Filter out stations with poor records using a dataframe of pre-selected
# station names for knet and kiknet events.
names = pd.read_csv(select_stns, usecols=(['X']), sep=",")
names_list = names.to_string(index=False)
filtered_files = []
for st in data:
for i in range(len(st)):
trace = st[i]
if trace.stats.station in names_list:
filtered_files.append([trace])
data = filtered_files
# Group all acceleration files by station if they are not already grouped.
if len(data[0]) == 3:
stations = data
else:
stations = group_channels(data)
# Obtain stats for each station using the stats from the first trace
# Also add station type to stats
# (read does not distinguish between knet and kik)
station_stats = []
for sta in stations:
for i in range(len(sta)):
trace = sta[0]
stn_type = trace.stats.standard['source_format']
name = trace.stats['station']
station_lat = trace.stats.coordinates['latitude']
station_lon = trace.stats.coordinates['longitude']
elev = trace.stats.coordinates['elevation']
station_stats.append(
[stn_type, name, station_lat, station_lon, elev])
return (stations, station_stats)
st = read(
'/Users/tnye/PROJECTS/Duration/data/events/us2000dwh6/ground_motion/kik/*.NS2'
)
elif data_type == 'smc':
# Read in one component of acceleration.
os.chdir(
'/Users/tnye/PROJECTS/Duration/data/events/nc216859/ground_motion/smc')
files_grabbed = []
for file in glob.glob('*a.smc'):
files_grabbed.append(file)
st_list = []
for file in files_grabbed:
data = read_data(file)
st_list.append(data)
flat_list = [item for sublist in st_list for item in sublist]
st = Stream([])
for trace in flat_list:
st.append(trace)
elif data_type == 'v2':
# Read in one component of acceleration.
os.chdir(
'/Users/tnye/PROJECTS/Duration/data/events/nc72282711/ground_motion/v2'
)
files_grabbed = []
for file in glob.glob('*.V2'):
def test_grouping():
homedir = os.path.dirname(os.path.abspath(__file__))
# cwb
cwb_files = os.path.join(homedir, '..', 'data', 'cwb', '*')
cwb_streams = []
for filename in glob.glob(cwb_files):
cwb_streams += [read_data(filename)]
cwb_streams = group_channels(cwb_streams)
assert len(cwb_streams) == 5
for stream in cwb_streams:
assert len(stream) == 3
# dmg
dmg_files = os.path.join(homedir, '..', 'data', 'dmg', '*.V2')
dmg_streams = []
for filename in glob.glob(dmg_files):
if (not os.path.basename(filename).startswith('Bad')
and not os.path.basename(filename).startswith('CE58667')):
dmg_streams += [read_data(filename)]
dmg_streams = group_channels(dmg_streams)
assert len(dmg_streams) == 2
for stream in dmg_streams:
assert len(stream) == 3
# geonet
geonet_files = os.path.join(homedir, '..', 'data', 'geonet', '*')
geonet_streams = []
for filename in glob.glob(geonet_files):
geonet_streams += [read_data(filename)]
geonet_streams = group_channels(geonet_streams)
assert len(geonet_streams) == 7
for stream in geonet_streams:
assert len(stream) == 3
assert len(stream.select(station=stream[0].stats.station)) == 3
level = stream[0].stats.standard.process_level
for trace in stream:
assert trace.stats.standard.process_level == level
# kiknet
kiknet_files = os.path.join(homedir, '..', 'data', 'kiknet', '*')
kiknet_streams = []
for filename in glob.glob(kiknet_files):
kiknet_streams += [read_data(filename)]
kiknet_streams = group_channels(kiknet_streams)
assert len(kiknet_streams) == 1
for stream in kiknet_streams:
assert len(stream) == 3
assert len(stream.select(station=stream[0].stats.station)) == 3
# knet
knet_files = os.path.join(homedir, '..', 'data', 'knet', '*')
knet_streams = []
for filename in glob.glob(knet_files):
knet_streams += [read_data(filename)]
knet_streams = group_channels(knet_streams)
assert len(knet_streams) == 9
for stream in knet_streams:
assert len(stream) == 3
assert len(stream.select(station=stream[0].stats.station)) == 3
pl = stream[0].stats.standard.process_level
for trace in stream:
assert trace.stats.standard.process_level == pl
# obspy
obspy_files = os.path.join(homedir, '..', 'data', 'obspy', '*')
obspy_streams = []
for filename in glob.glob(obspy_files):
if not filename.endswith('.json'):
obspy_streams += [read_data(filename)]
obspy_streams = group_channels(obspy_streams)
assert len(obspy_streams) == 1
for stream in obspy_streams:
assert len(stream) == 3
assert len(stream.select(station=stream[0].stats.station)) == 3
# smc
smc_files = os.path.join(homedir, '..', 'data', 'smc', '*')
smc_streams = []
for filename in glob.glob(smc_files):
if not filename.endswith('.json'):
smc_streams += [read_data(filename, any_structure=True)]
smc_streams = group_channels(smc_streams)
assert len(smc_streams) == 6
for stream in smc_streams:
if stream[0].stats.station == 'DVD0':
assert len(stream) == 1
assert len(stream.select(station=stream[0].stats.station)) == 1
elif stream[0].stats.location == '01':
assert len(stream) == 2
assert len(stream.select(station=stream[0].stats.station)) == 2
else:
assert len(stream) == 3
assert len(stream.select(station=stream[0].stats.station)) == 3
# usc
usc_files = os.path.join(homedir, '..', 'data', 'usc', '*')
usc_streams = []
for filename in glob.glob(usc_files):
if not filename.endswith('.json'):
if os.path.basename(filename) != '017m30bt.s0a':
usc_streams += [read_data(filename)]
usc_streams = group_channels(usc_streams)
assert len(usc_streams) == 3
for stream in usc_streams:
if stream[0].stats.station == '57':
assert len(stream) == 1
else:
assert len(stream) == 3