def new_func(*args, **kwargs):
prefix = '/path/to/'
# check kwargs
if arg_kwarg_name in kwargs:
if isinstance(kwargs[arg_kwarg_name], (str, native_str)):
if kwargs[arg_kwarg_name].startswith(prefix):
try:
kwargs[arg_kwarg_name] = \
getExampleFile(kwargs[arg_kwarg_name][9:])
# file not found by getExampleFile:
except IOError:
pass
# check args
else:
try:
ind = inspect.getargspec(func).args.index(arg_kwarg_name)
except ValueError:
pass
else:
if ind < len(args) and isinstance(args[ind], (str,
native_str)):
# need to check length of args from inspect
if args[ind].startswith(prefix):
try:
args = list(args)
args[ind] = getExampleFile(args[ind][9:])
args = tuple(args)
# file not found by getExampleFile:
except IOError:
pass
return func(*args, **kwargs)
def test_write_nlloc_obs(self):
"""
Test writing nonlinloc observations phase file.
"""
# load nlloc.qml QuakeML file to generate OBS file from it
filename = getExampleFile("nlloc.qml")
cat = readEvents(filename, "QUAKEML")
# adjust one pick time that got cropped by nonlinloc in NLLOC HYP file
# due to less precision in hypocenter file (that we used to create the
# reference QuakeML file)
for pick in cat[0].picks:
if pick.waveform_id.station_code == "UH4" and \
pick.phase_hint == "P":
pick.time -= 0.005
# read expected OBS file output
filename = getExampleFile("nlloc.obs")
with open(filename, "rb") as fh:
expected = fh.read().decode()
# write via plugin
with NamedTemporaryFile() as tf:
cat.write(tf, format="NLLOC_OBS")
tf.seek(0)
got = tf.read().decode()
self.assertEqual(expected, got)
# write manually
with NamedTemporaryFile() as tf:
write_nlloc_obs(cat, tf)
tf.seek(0)
got = tf.read().decode()
self.assertEqual(expected, got)
def test_write_nlloc_obs(self):
"""
Test writing nonlinloc observations phase file.
"""
# load nlloc.qml QuakeML file to generate OBS file from it
filename = getExampleFile("nlloc.qml")
cat = readEvents(filename, "QUAKEML")
# adjust one pick time that got cropped by nonlinloc in NLLOC HYP file
# due to less precision in hypocenter file (that we used to create the
# reference QuakeML file)
for pick in cat[0].picks:
if pick.waveform_id.station_code == "UH4" and \
pick.phase_hint == "P":
pick.time -= 0.005
# read expected OBS file output
filename = getExampleFile("nlloc.obs")
with open(filename, "rb") as fh:
expected = fh.read().decode()
# write via plugin
with NamedTemporaryFile() as tf:
cat.write(tf, format="NLLOC_OBS")
tf.seek(0)
got = tf.read().decode()
self.assertEqual(expected, got)
# write manually
with NamedTemporaryFile() as tf:
write_nlloc_obs(cat, tf)
tf.seek(0)
got = tf.read().decode()
self.assertEqual(expected, got)
def new_func(*args, **kwargs):
prefix = '/path/to/'
# check kwargs
if arg_kwarg_name in kwargs:
if isinstance(kwargs[arg_kwarg_name], (str, native_str)):
if kwargs[arg_kwarg_name].startswith(prefix):
try:
kwargs[arg_kwarg_name] = \
getExampleFile(kwargs[arg_kwarg_name][9:])
# file not found by getExampleFile:
except IOError:
pass
# check args
else:
try:
ind = inspect.getargspec(func).args.index(arg_kwarg_name)
except ValueError:
pass
else:
if ind < len(args) and isinstance(args[ind],
(str, native_str)):
# need to check length of args from inspect
if args[ind].startswith(prefix):
try:
args = list(args)
args[ind] = getExampleFile(args[ind][9:])
args = tuple(args)
# file not found by getExampleFile:
except IOError:
pass
return func(*args, **kwargs)
def test_is_nlloc_hyp(self):
# test positive
filename = getExampleFile("nlloc.hyp")
self.assertEqual(is_nlloc_hyp(filename), True)
# test some negatives
for filenames in ["nlloc.qml", "nlloc.obs", "gaps.mseed",
"BW_RJOB.xml", "QFILE-TEST-ASC.ASC", "LMOW.BHE.SAC"]:
filename = getExampleFile("nlloc.qml")
self.assertEqual(is_nlloc_hyp(filename), False)
def test_read_nlloc_with_picks(self):
"""
Test correct resource ID linking when reading NLLOC_HYP file with
providing original picks.
"""
picks = readEvents(getExampleFile("nlloc.qml"))[0].picks
arrivals = readEvents(getExampleFile("nlloc.hyp"), format="NLLOC_HYP",
picks=picks)[0].origins[0].arrivals
expected = [p.resource_id for p in picks]
got = [a.pick_id for a in arrivals]
self.assertEqual(expected, got)
def test_is_nlloc_hyp(self):
# test positive
filename = getExampleFile("nlloc.hyp")
self.assertEqual(is_nlloc_hyp(filename), True)
# test some negatives
for filenames in [
"nlloc.qml", "nlloc.obs", "gaps.mseed", "BW_RJOB.xml",
"QFILE-TEST-ASC.ASC", "LMOW.BHE.SAC"
]:
filename = getExampleFile("nlloc.qml")
self.assertEqual(is_nlloc_hyp(filename), False)
def test_read_nlloc_with_picks(self):
"""
Test correct resource ID linking when reading NLLOC_HYP file with
providing original picks.
"""
picks = readEvents(getExampleFile("nlloc.qml"))[0].picks
arrivals = readEvents(getExampleFile("nlloc.hyp"),
format="NLLOC_HYP",
picks=picks)[0].origins[0].arrivals
expected = [p.resource_id for p in picks]
got = [a.pick_id for a in arrivals]
self.assertEqual(expected, got)
def test_read_nlloc_hyp(self):
"""
Test reading nonlinloc hypocenter phase file.
"""
filename = getExampleFile("nlloc.hyp")
cat = read_nlloc_hyp(filename,
coordinate_converter=_mock_coordinate_converter)
with open(getExampleFile("nlloc.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 = getExampleFile("nlloc.hyp")
cat = read_nlloc_hyp(filename,
coordinate_converter=_mock_coordinate_converter)
with open(getExampleFile("nlloc.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_map_example_filename(self):
"""
Tests the @map_example_filename decorator
"""
dummy = "abc"
example_file = "example.npz"
path = "/path/to/" + example_file
path_mapped = getExampleFile(example_file)
def unchanged(a, b="", **kwargs):
return list(map(str, (a, b, kwargs)))
@map_example_filename("a")
def changed1(a, b="", **kwargs):
return list(map(str, (a, b, kwargs)))
self.assertEqual(changed1(dummy, dummy), unchanged(dummy, dummy))
self.assertEqual(changed1(path, dummy), unchanged(path_mapped, dummy))
self.assertEqual(changed1(dummy, path), unchanged(dummy, path))
self.assertEqual(changed1(a=path, b=dummy),
unchanged(path_mapped, dummy))
self.assertEqual(changed1(path, b=dummy),
unchanged(path_mapped, dummy))
self.assertEqual(changed1(path, b=path, x=path),
unchanged(path_mapped, path, x=path))
@map_example_filename("b")
def changed2(a, b="", **kwargs):
return list(map(str, (a, b, kwargs)))
self.assertEqual(changed2(dummy, dummy), unchanged(dummy, dummy))
self.assertEqual(changed2(path, dummy), unchanged(path, dummy))
self.assertEqual(changed2(dummy, path), unchanged(dummy, path_mapped))
self.assertEqual(changed2(a=path, b=dummy), unchanged(path, dummy))
self.assertEqual(changed2(path, b=path), unchanged(path, path_mapped))
self.assertEqual(changed2(path, b=path, x=path),
unchanged(path, path_mapped, x=path))
@map_example_filename("x")
def changed3(a, b="", **kwargs):
return list(map(str, (a, b, kwargs)))
self.assertEqual(changed3(dummy, dummy), unchanged(dummy, dummy))
self.assertEqual(changed3(path, dummy), unchanged(path, dummy))
self.assertEqual(changed3(dummy, path), unchanged(dummy, path))
self.assertEqual(changed3(a=path, b=dummy), unchanged(path, dummy))
self.assertEqual(changed3(path, b=dummy), unchanged(path, dummy))
self.assertEqual(changed3(path, b=path, x=path),
unchanged(path, path, x=path_mapped))
def read_inventory(path_or_file_object, format=None):
"""
Function to read inventory files.
:param path_or_file_object: Filename or file like object.
"""
# if pathname starts with /path/to/ try to search in examples
if isinstance(path_or_file_object, (str, native_str)) and \
path_or_file_object.startswith('/path/to/'):
try:
path_or_file_object = getExampleFile(path_or_file_object[9:])
except:
# otherwise just try to read the given /path/to folder
pass
return _readFromPlugin("inventory", path_or_file_object, format=format)[0]
def test_map_example_filename(self):
"""
Tests the @map_example_filename decorator
"""
dummy = "abc"
example_file = "example.npz"
path = "/path/to/" + example_file
path_mapped = getExampleFile(example_file)
def unchanged(a, b="", **kwargs):
return list(map(str, (a, b, kwargs)))
@map_example_filename("a")
def changed1(a, b="", **kwargs):
return list(map(str, (a, b, kwargs)))
self.assertEqual(changed1(dummy, dummy), unchanged(dummy, dummy))
self.assertEqual(changed1(path, dummy), unchanged(path_mapped, dummy))
self.assertEqual(changed1(dummy, path), unchanged(dummy, path))
self.assertEqual(changed1(a=path, b=dummy), unchanged(path_mapped, dummy))
self.assertEqual(changed1(path, b=dummy), unchanged(path_mapped, dummy))
self.assertEqual(changed1(path, b=path, x=path), unchanged(path_mapped, path, x=path))
@map_example_filename("b")
def changed2(a, b="", **kwargs):
return list(map(str, (a, b, kwargs)))
self.assertEqual(changed2(dummy, dummy), unchanged(dummy, dummy))
self.assertEqual(changed2(path, dummy), unchanged(path, dummy))
self.assertEqual(changed2(dummy, path), unchanged(dummy, path_mapped))
self.assertEqual(changed2(a=path, b=dummy), unchanged(path, dummy))
self.assertEqual(changed2(path, b=path), unchanged(path, path_mapped))
self.assertEqual(changed2(path, b=path, x=path), unchanged(path, path_mapped, x=path))
@map_example_filename("x")
def changed3(a, b="", **kwargs):
return list(map(str, (a, b, kwargs)))
self.assertEqual(changed3(dummy, dummy), unchanged(dummy, dummy))
self.assertEqual(changed3(path, dummy), unchanged(path, dummy))
self.assertEqual(changed3(dummy, path), unchanged(dummy, path))
self.assertEqual(changed3(a=path, b=dummy), unchanged(path, dummy))
self.assertEqual(changed3(path, b=dummy), unchanged(path, dummy))
self.assertEqual(changed3(path, b=path, x=path), unchanged(path, path, x=path_mapped))
def read(self, data):
"""
General parser method for XML-SEED and Dataless SEED files.
:type data: Filename, URL, Basestring or StringIO object.
:param data: Filename, URL or XSEED/SEED string as file pointer or
StringIO.
"""
if getattr(self, "_format", None):
warnings.warn("Clearing parser before every subsequent read()")
self.__init__()
# try to transform everything into StringIO object
if isinstance(data, basestring):
# if it starts with /path/to/ try to search in examples
if data.startswith("/path/to/"):
try:
data = getExampleFile(data[9:])
except:
# otherwise just try to read the given /path/to folder
pass
if "://" in data:
# some URL
data = urllib2.urlopen(data).read()
elif os.path.isfile(data):
# looks like a file - read it
data = open(data, "rb").read()
# but could also be a big string with data
data = StringIO(data)
elif not hasattr(data, "read"):
raise TypeError
# check first byte of data StringIO object
first_byte = data.read(1)
data.seek(0)
if first_byte.isdigit():
# SEED volumes starts with a number
self._parseSEED(data)
self._format = "SEED"
elif first_byte == "<":
# XML files should always starts with an '<'
self._parseXSEED(data)
self._format = "XSEED"
else:
raise IOError
def read(self, data):
"""
General parser method for XML-SEED and Dataless SEED files.
:type data: Filename, URL, Basestring or StringIO object.
:param data: Filename, URL or XSEED/SEED string as file pointer or
StringIO.
"""
if getattr(self, "_format", None):
warnings.warn("Clearing parser before every subsequent read()")
self.__init__()
# try to transform everything into StringIO object
if isinstance(data, basestring):
# if it starts with /path/to/ try to search in examples
if data.startswith('/path/to/'):
try:
data = getExampleFile(data[9:])
except:
# otherwise just try to read the given /path/to folder
pass
if "://" in data:
# some URL
data = urllib2.urlopen(data).read()
elif os.path.isfile(data):
# looks like a file - read it
data = open(data, 'rb').read()
# but could also be a big string with data
data = StringIO(data)
elif not hasattr(data, "read"):
raise TypeError
# check first byte of data StringIO object
first_byte = data.read(1)
data.seek(0)
if first_byte.isdigit():
# SEED volumes starts with a number
self._parseSEED(data)
self._format = 'SEED'
elif first_byte == '<':
# XML files should always starts with an '<'
self._parseXSEED(data)
self._format = 'XSEED'
else:
raise IOError
from obspy.core.util import getExampleFile
from obspy.segy.segy import readSU
from obspy.segy.benchmark import plotBenchmark
files = [getExampleFile('seismic01_fdmpi_vz.su'),
getExampleFile('seismic01_gemini_vz.su'),
getExampleFile('seismic01_sofi2D_transformed_vz.su'),
getExampleFile('seismic01_specfem_vz.su')]
sufiles = [readSU(file) for file in files]
plotBenchmark(sufiles, title="Homogenous halfspace", xmax=0.14)
def test_read_nlloc_hyp_via_plugin(self):
filename = getExampleFile("nlloc.hyp")
cat = readEvents(filename)
self.assertEqual(len(cat), 1)
cat = readEvents(filename, format="NLLOC_HYP")
self.assertEqual(len(cat), 1)
def test_read_nlloc_hyp_via_plugin(self):
filename = getExampleFile("nlloc.hyp")
cat = readEvents(filename)
self.assertEqual(len(cat), 1)
cat = readEvents(filename, format="NLLOC_HYP")
self.assertEqual(len(cat), 1)
