def test_issue_2222(self):
"""
Test that hour values of 24 don't break parser.
"""
# modify the example file to contain an hour 24 and second 60
with open(get_example_file('nlloc.hyp')) as f:
nll_str = f.read().splitlines()
# first add a line with hour 24
str_list = list(nll_str[-3])
str_list[37:41] = '2400'
nll_str[-3] = ''.join(str_list)
# then add a line with second 60
str_list = list(nll_str[-4])
str_list[46:48] = '60'
nll_str[-4] = ''.join(str_list)
# write to string io and read into catalog object
str_io = io.StringIO()
str_io.write('\n'.join(nll_str))
str_io.seek(0)
cat = read_nlloc_hyp(str_io)
# check catalog is populated and pick times are right
self.assertEqual(len(cat), 1)
pick1, pick2 = cat[0].picks[-1], cat[0].picks[-2]
self.assertEqual(pick1.time.hour, 0)
self.assertEqual(pick2.time.second, 0)
def test_issue_2222(self):
"""
Test that hour values of 24 don't break parser.
"""
# modify the example file to contain an hour 24 and second 60
nll_str = open(get_example_file('nlloc.hyp')).read().splitlines()
# first add a line with hour 24
str_list = list(nll_str[-3])
str_list[37:41] = '2400'
nll_str[-3] = ''.join(str_list)
# then add a line with second 60
str_list = list(nll_str[-4])
str_list[46:48] = '60'
nll_str[-4] = ''.join(str_list)
# write to string io and read into catalog object
str_io = io.StringIO()
str_io.write('\n'.join(nll_str))
str_io.seek(0)
cat = read_nlloc_hyp(str_io)
# check catalog is populated and pick times are right
self.assertEqual(len(cat), 1)
pick1, pick2 = cat[0].picks[-1], cat[0].picks[-2]
self.assertEqual(pick1.time.hour, 0)
self.assertEqual(pick2.time.second, 0)
def read_nlloc_sum(file_in):
"""
Function made to read a nlloc hypocenter-file and store it into a simple LOTOS_class Catalog
The ID is read from the event.comments part
"""
from obspy.io.nlloc.core import read_nlloc_hyp
from lotos.LOTOS_class import Catalog, Event, Phase
from general import util as gutil
#file_in='/media/baillard/Shared/Dropbox/_Moi/Projects/Axial/PROG/NLLOC_AXIAL/loc3/AXIAL.20170130.005908.grid0.loc.hyp'
#file_in='/media/baillard/Shared/Dropbox/_Moi/Projects/Axial/PROG/NLLOC_AXIAL/loc3/sum.nlloc'
Ray = Catalog()
cat = read_nlloc_hyp(file_in)
stations_dic = Ray.stations_realname
for event in cat:
id_event = event.comments[0].text
origin = event.preferred_origin()
OT = origin.time
#### Initialize Event
Event_p = Event()
Event_p.x = origin.longitude
Event_p.y = origin.latitude
Event_p.z = origin.depth / 1000
Event_p.id = id_event
Event_p.ot = OT
Event_p.num_phase = origin.quality.used_phase_count
Picks_p = event.picks
for arrival in origin.arrivals:
Phase_p = Phase()
if arrival.phase in ['P', 'Pn']:
Phase_p.type = 1
else:
Phase_p.type = 2
Pick_p = gutil.getPickForArrival(Picks_p, arrival)
Phase_p.station = stations_dic[Pick_p.waveform_id.station_code]
Phase_p.t_obs = Pick_p.time - OT
Phase_p.t_tho = Phase_p.t_obs - arrival.time_residual
Event_p.phases.append(Phase_p)
Ray.events.append(Event_p)
return Ray
def test_read_nlloc_6_beta_signature(self):
"""
SIGNATURE field of nlloc hypocenter output file was somehow changed at
some point after version 6.0 (it appears in 6.0.3 beta release for
example).
Date is now seemingly always prepended with 'run:' without a space
afterwards.
"""
filename = os.path.join(self.datapath, 'nlloc_post_version_6.hyp')
cat = read_nlloc_hyp(filename)
# check that signature time-of-run part is correctly read
# (actually before the fix the above reading already fails..)
self.assertEqual(cat[0].creation_info.creation_time,
UTCDateTime(2017, 5, 9, 11, 0, 22))
def test_read_nlloc_6_beta_signature(self):
"""
SIGNATURE field of nlloc hypocenter output file was somehow changed at
some point after version 6.0 (it appears in 6.0.3 beta release for
example).
Date is now seemingly always prepended with 'run:' without a space
afterwards.
"""
filename = os.path.join(self.datapath, 'nlloc_post_version_6.hyp')
cat = read_nlloc_hyp(filename)
# check that signature time-of-run part is correctly read
# (actually before the fix the above reading already fails..)
self.assertEqual(
cat[0].creation_info.creation_time,
UTCDateTime(2017, 5, 9, 11, 0, 22))
def relocate(cat, root_name, in_file, pick_uncertainty=0.1):
"""
Run NonLinLoc relocations on a catalog. This is a function hardcoded for my laptop only.
:type cat: obspy.Catalog
:param cat: catalog of events with picks to relocate
:type root_name: str
:param root_name: String specifying where the nlloc.obs files will be written from the catalog
:type outfiles: str
:param outfiles: Output directory for location files
:type in_file: str
:param in_file: NLLoc input file
:return: same catalog with new origins appended to each event
"""
for ev in cat:
if len(ev.picks) < 5:
print('Fewer than 5 picks for %s. Will not locate.' %
str(ev.resource_id))
continue
for pk in ev.picks:
pk.time_errors.uncertainty = pick_uncertainty
id_str = str(ev.resource_id).split('/')[-1]
filename = root_name + 'obs/' + id_str + '.nll'
outfile = root_name + 'loc/' + id_str
# TODO This clause needs faster file existece check. Do 25-7.
if os.path.isfile(outfile):
if len(glob(outfile + '.????????.??????.grid0.loc.hyp')) > 0:
print('LOC file already written, reading output to catalog')
else:
ev.write(filename, format="NLLOC_OBS")
# Specify awk command to edit NLLoc .in file
cmnd = """awk '$1 == "LOCFILES" {$2 = "%s"; $5 = "%s"}1' %s > tmp.txt && mv tmp.txt %s""" % (
filename, outfile, in_file, in_file)
call(cmnd, shell=True)
# Call to NLLoc
call('NLLoc %s' % in_file, shell=True)
# Now reading NLLoc output back into catalog as new origin
# XXX BE MORE CAREFUL HERE. CANNOT GRAB BOTH SUM AND NON-SUM
out_w_ext = glob(outfile + '.????????.??????.grid0.loc.hyp')
try:
new_o = read_nlloc_hyp(out_w_ext[0],
coordinate_converter=my_conversion,
picks=ev.picks)
except ValueError as ve:
print(ve)
continue
ev.origins.append(new_o[0].origins[0])
ev.preferred_origin_id = str(new_o[0].origins[0].resource_id)
return cat
def relocate(cat, root_name, in_file):
"""
Run NonLinLoc relocations on a catalog. This is a function hardcoded for my laptop only.
:type cat: obspy.Catalog
:param cat: catalog of events with picks to relocate
:type root_name: str
:param root_name: String specifying where the nlloc.obs files will be written from the catalog
:type outfiles: str
:param outfiles: Output directory for location files
:type in_file: str
:param in_file: NLLoc input file
:return:
"""
# root_name = '/media/chet/hdd/seismic/NZ/NLLoc/mrp/2015_Rawlinson_spicks/obs/'
for ev in cat:
if len(ev.picks) < 6:
print('Fewer than 8 picks for %s. Will not locate.' %
str(ev.resource_id))
continue
id_str = str(ev.resource_id).split('/')[-1]
filename = root_name + 'obs/' + id_str + '.nll'
ev.write(filename, format="NLLOC_OBS")
# Specify awk command to edit NLLoc .in file
outfile = root_name + 'loc/' + id_str
cmnd = """awk '$1 == "LOCFILES" {$2 = "%s"; $5 = "%s"}1' %s > tmp && mv tmp %s""" % (
filename, outfile, in_file, in_file)
call(cmnd, shell=True)
# Call to NLLoc
call('NLLoc %s' % in_file, shell=True)
# Now reading NLLoc output back into catalog as new origin
# XXX BE MORE CAREFUL HERE. CANNOT GRAB BOTH SUM AND NON-SUM
out_w_ext = glob(outfile + '.????????.??????.grid0.loc.hyp')
try:
new_o = read_nlloc_hyp(out_w_ext[0],
coordinate_converter=my_conversion,
picks=ev.picks)
except ValueError as ve:
print(ve)
continue
ev.origins.append(new_o[0].origins[0])
ev.preferred_origin_id = str(new_o[0].origins[0].resource_id)
return cat
def test_read_nlloc_hyp(self):
"""
Test reading nonlinloc hypocenter phase file.
"""
filename = get_example_file("nlloc_custom.hyp")
cat = read_nlloc_hyp(filename,
coordinate_converter=_mock_coordinate_converter)
# reset pick channel codes, these got automatically mapped upon reading
for pick in cat[0].picks:
pick.waveform_id.channel_code = None
with open(get_example_file("nlloc_custom.qml"), 'rb') as tf:
quakeml_expected = tf.read().decode()
with NamedTemporaryFile() as tf:
cat.write(tf, format="QUAKEML")
tf.seek(0)
quakeml_got = tf.read().decode()
# test creation times manually as they get omitted in the overall test
creation_time = UTCDateTime("2014-10-17T16:30:08.000000Z")
self.assertEqual(cat[0].creation_info.creation_time, creation_time)
self.assertEqual(cat[0].origins[0].creation_info.creation_time,
creation_time)
quakeml_expected = remove_unique_ids(quakeml_expected,
remove_creation_time=True)
quakeml_got = remove_unique_ids(quakeml_got, remove_creation_time=True)
# In python 3 float.__str__ outputs 5 decimals of precision more.
# We use it in writing QuakeML, so files look different on Py2/3.
# We use regex to cut off floats in the xml such that we only compare
# 7 digits.
pattern = r'(<.*?>[0-9]*?\.[0-9]{7})[0-9]*?(</.*?>)'
quakeml_expected = re.sub(pattern, r'\1\2', quakeml_expected)
quakeml_got = re.sub(pattern, r'\1\2', quakeml_got)
# remove (changing) obspy version number from output
re_pattern = '<version>ObsPy .*?</version>'
quakeml_expected = re.sub(re_pattern, '', quakeml_expected, 1)
quakeml_got = re.sub(re_pattern, '', quakeml_got, 1)
compare_xml_strings(quakeml_expected, quakeml_got)
def test_read_nlloc_hyp(self):
"""
Test reading nonlinloc hypocenter phase file.
"""
filename = get_example_file("nlloc_custom.hyp")
cat = read_nlloc_hyp(filename,
coordinate_converter=_mock_coordinate_converter)
with open(get_example_file("nlloc_custom.qml"), 'rb') as tf:
quakeml_expected = tf.read().decode()
with NamedTemporaryFile() as tf:
cat.write(tf, format="QUAKEML")
tf.seek(0)
quakeml_got = tf.read().decode()
# test creation times manually as they get omitted in the overall test
creation_time = UTCDateTime("2014-10-17T16:30:08.000000Z")
self.assertEqual(cat[0].creation_info.creation_time, creation_time)
self.assertEqual(cat[0].origins[0].creation_info.creation_time,
creation_time)
quakeml_expected = remove_unique_ids(quakeml_expected,
remove_creation_time=True)
quakeml_got = remove_unique_ids(quakeml_got, remove_creation_time=True)
# In python 3 float.__str__ outputs 5 decimals of precision more.
# We use it in writing QuakeML, so files look different on Py2/3.
# We use regex to cut off floats in the xml such that we only compare
# 7 digits.
pattern = r'(<.*?>[0-9]*?\.[0-9]{7})[0-9]*?(</.*?>)'
quakeml_expected = re.sub(pattern, r'\1\2', quakeml_expected)
quakeml_got = re.sub(pattern, r'\1\2', quakeml_got)
# remove (changing) obspy version number from output
re_pattern = '<version>ObsPy .*?</version>'
quakeml_expected = re.sub(re_pattern, '', quakeml_expected, 1)
quakeml_got = re.sub(re_pattern, '', quakeml_got, 1)
compare_xml_strings(quakeml_expected, quakeml_got)
def test_read_nlloc_hyp_with_builtin_projection(self):
"""
Test reading nonlinloc hyp file without a coordinate_converter.
"""
cat = read_nlloc_hyp(get_example_file("nlloc.hyp"))
cat_expected = read_events(get_example_file("nlloc.qml"))
# test event
ev = cat[0]
ev_expected = cat_expected[0]
self.assertAlmostEqual(ev.creation_info.creation_time,
ev_expected.creation_info.creation_time)
# test origin
orig = ev.origins[0]
orig_expected = ev_expected.origins[0]
self.assertAlmostEqual(orig.time, orig_expected.time)
self.assertAlmostEqual(orig.longitude, orig_expected.longitude)
self.assertAlmostEqual(orig.longitude_errors.uncertainty,
orig_expected.longitude_errors.uncertainty)
self.assertAlmostEqual(orig.latitude, orig_expected.latitude)
self.assertAlmostEqual(orig.latitude_errors.uncertainty,
orig_expected.latitude_errors.uncertainty)
self.assertAlmostEqual(orig.depth, orig_expected.depth)
self.assertAlmostEqual(orig.depth_errors.uncertainty,
orig_expected.depth_errors.uncertainty)
self.assertAlmostEqual(orig.depth_errors.confidence_level,
orig_expected.depth_errors.confidence_level)
self.assertEqual(orig.depth_type, orig_expected.depth_type)
self.assertEqual(orig.quality.associated_phase_count,
orig_expected.quality.associated_phase_count)
self.assertEqual(orig.quality.used_phase_count,
orig_expected.quality.used_phase_count)
self.assertEqual(orig.quality.associated_station_count,
orig_expected.quality.associated_station_count)
self.assertEqual(orig.quality.used_station_count,
orig_expected.quality.used_station_count)
self.assertAlmostEqual(orig.quality.standard_error,
orig_expected.quality.standard_error)
self.assertAlmostEqual(orig.quality.azimuthal_gap,
orig_expected.quality.azimuthal_gap)
self.assertAlmostEqual(orig.quality.secondary_azimuthal_gap,
orig_expected.quality.secondary_azimuthal_gap)
self.assertEqual(orig.quality.ground_truth_level,
orig_expected.quality.ground_truth_level)
self.assertAlmostEqual(orig.quality.minimum_distance,
orig_expected.quality.minimum_distance)
self.assertAlmostEqual(orig.quality.maximum_distance,
orig_expected.quality.maximum_distance)
self.assertAlmostEqual(orig.quality.median_distance,
orig_expected.quality.median_distance)
self.assertAlmostEqual(
orig.origin_uncertainty.min_horizontal_uncertainty,
orig_expected.origin_uncertainty.min_horizontal_uncertainty)
self.assertAlmostEqual(
orig.origin_uncertainty.max_horizontal_uncertainty,
orig_expected.origin_uncertainty.max_horizontal_uncertainty)
self.assertAlmostEqual(
orig.origin_uncertainty.azimuth_max_horizontal_uncertainty,
orig_expected.origin_uncertainty.
azimuth_max_horizontal_uncertainty)
self.assertEqual(
orig.origin_uncertainty.preferred_description,
orig_expected.origin_uncertainty.preferred_description)
self.assertAlmostEqual(
orig.origin_uncertainty.confidence_level,
orig_expected.origin_uncertainty.confidence_level)
self.assertEqual(orig.creation_info.creation_time,
orig_expected.creation_info.creation_time)
self.assertEqual(orig.comments[0].text, orig_expected.comments[0].text)
# test a couple of arrivals
for n in range(2):
arriv = orig.arrivals[n]
arriv_expected = orig_expected.arrivals[n]
self.assertEqual(arriv.phase, arriv_expected.phase)
self.assertAlmostEqual(arriv.azimuth, arriv_expected.azimuth)
self.assertAlmostEqual(arriv.distance, arriv_expected.distance)
self.assertAlmostEqual(arriv.takeoff_angle,
arriv_expected.takeoff_angle)
self.assertAlmostEqual(arriv.time_residual,
arriv_expected.time_residual)
self.assertAlmostEqual(arriv.time_weight,
arriv_expected.time_weight)
# test a couple of picks
for n in range(2):
pick = ev.picks[n]
pick_expected = ev_expected.picks[n]
self.assertAlmostEqual(pick.time, pick_expected.time)
self.assertEqual(pick.waveform_id.station_code,
pick_expected.waveform_id.station_code)
self.assertEqual(pick.onset, pick_expected.onset)
self.assertEqual(pick.phase_hint, pick_expected.phase_hint)
self.assertEqual(pick.polarity, pick_expected.polarity)
continue
id_str = str(ev.resource_id).split('/')[-1]
filename = root_name + id_str + '.nll'
ev.write(filename, format="NLLOC_OBS")
# Specify awk command to edit NLLoc .in file
in_file = '/Users/home/hoppche/NLLoc/mrp/run/nlloc_mrp.in'
outfile = '/Users/home/hoppche/NLLoc/mrp/loc/' + id_str
cmnd = """awk '$1 == "LOCFILES" {$2 = "%s"; $5 = "%s"}1' %s > tmp && mv tmp %s""" % (
filename, outfile, in_file, in_file)
call(cmnd, shell=True)
# Call to NLLoc
call('NLLoc /Users/home/hoppche/NLLoc/mrp/run/nlloc_mrp.in', shell=True)
# Now reading NLLoc output back into catalog as new origin
out_w_ext = glob(outfile + '*.grid0.loc.hyp')
new_o = read_nlloc_hyp(out_w_ext[0],
coordinate_converter=my_conversion,
picks=ev.picks)
ev.origins.append(new_o[0].origins[0])
ev.preferred_origin_id = str(new_o[0].origins[0].resource_id)
# Cut templates for each new event based on new picks
for event in refined_cat:
ev_name = str(event.resource_id).split('/')[2]
st = template_dict[event.resource_id]
st1 = pre_processing.shortproc(st,
lowcut=1.0,
highcut=20.0,
filt_order=3,
samp_rate=50,
debug=0)
print('Feeding stream to _template_gen...')
def test_read_nlloc_hyp_with_builtin_projection(self):
"""
Test reading nonlinloc hyp file without a coordinate_converter.
"""
cat = read_nlloc_hyp(get_example_file("nlloc.hyp"))
cat_expected = read_events(get_example_file("nlloc.qml"))
# test event
ev = cat[0]
ev_expected = cat_expected[0]
self.assertAlmostEqual(ev.creation_info.creation_time,
ev_expected.creation_info.creation_time)
# test origin
orig = ev.origins[0]
orig_expected = ev_expected.origins[0]
self.assertAlmostEqual(orig.time, orig_expected.time)
self.assertAlmostEqual(orig.longitude, orig_expected.longitude)
self.assertAlmostEqual(orig.longitude_errors.uncertainty,
orig_expected.longitude_errors.uncertainty)
self.assertAlmostEqual(orig.latitude, orig_expected.latitude)
self.assertAlmostEqual(orig.latitude_errors.uncertainty,
orig_expected.latitude_errors.uncertainty)
self.assertAlmostEqual(orig.depth, orig_expected.depth)
self.assertAlmostEqual(orig.depth_errors.uncertainty,
orig_expected.depth_errors.uncertainty)
self.assertAlmostEqual(orig.depth_errors.confidence_level,
orig_expected.depth_errors.confidence_level)
self.assertEqual(orig.depth_type, orig_expected.depth_type)
self.assertEqual(orig.quality.associated_phase_count,
orig_expected.quality.associated_phase_count)
self.assertEqual(orig.quality.used_phase_count,
orig_expected.quality.used_phase_count)
self.assertEqual(orig.quality.associated_station_count,
orig_expected.quality.associated_station_count)
self.assertEqual(orig.quality.used_station_count,
orig_expected.quality.used_station_count)
self.assertAlmostEqual(orig.quality.standard_error,
orig_expected.quality.standard_error)
self.assertAlmostEqual(orig.quality.azimuthal_gap,
orig_expected.quality.azimuthal_gap)
self.assertAlmostEqual(orig.quality.secondary_azimuthal_gap,
orig_expected.quality.secondary_azimuthal_gap)
self.assertEqual(orig.quality.ground_truth_level,
orig_expected.quality.ground_truth_level)
self.assertAlmostEqual(orig.quality.minimum_distance,
orig_expected.quality.minimum_distance)
self.assertAlmostEqual(orig.quality.maximum_distance,
orig_expected.quality.maximum_distance)
self.assertAlmostEqual(orig.quality.median_distance,
orig_expected.quality.median_distance)
self.assertAlmostEqual(
orig.origin_uncertainty.min_horizontal_uncertainty,
orig_expected.origin_uncertainty.min_horizontal_uncertainty)
self.assertAlmostEqual(
orig.origin_uncertainty.max_horizontal_uncertainty,
orig_expected.origin_uncertainty.max_horizontal_uncertainty)
self.assertAlmostEqual(
orig.origin_uncertainty.azimuth_max_horizontal_uncertainty,
orig_expected.origin_uncertainty.azimuth_max_horizontal_uncertainty
)
self.assertEqual(
orig.origin_uncertainty.preferred_description,
orig_expected.origin_uncertainty.preferred_description)
self.assertAlmostEqual(
orig.origin_uncertainty.confidence_level,
orig_expected.origin_uncertainty.confidence_level)
self.assertEqual(orig.creation_info.creation_time,
orig_expected.creation_info.creation_time)
self.assertEqual(orig.comments[0].text, orig_expected.comments[0].text)
# test a couple of arrivals
for n in range(2):
arriv = orig.arrivals[n]
arriv_expected = orig_expected.arrivals[n]
self.assertEqual(arriv.phase, arriv_expected.phase)
self.assertAlmostEqual(arriv.azimuth, arriv_expected.azimuth)
self.assertAlmostEqual(arriv.distance, arriv_expected.distance)
self.assertAlmostEqual(arriv.takeoff_angle,
arriv_expected.takeoff_angle)
self.assertAlmostEqual(arriv.time_residual,
arriv_expected.time_residual)
self.assertAlmostEqual(arriv.time_weight,
arriv_expected.time_weight)
# test a couple of picks
for n in range(2):
pick = ev.picks[n]
pick_expected = ev_expected.picks[n]
self.assertAlmostEqual(pick.time, pick_expected.time)
self.assertEqual(pick.waveform_id.station_code,
pick_expected.waveform_id.station_code)
self.assertEqual(pick.onset, pick_expected.onset)
self.assertEqual(pick.phase_hint, pick_expected.phase_hint)
self.assertEqual(pick.polarity, pick_expected.polarity)
