def test_readingAndWritingViaTheStatsAttribute(self):
"""
Tests the writing with MSEED file attributes set via the attributes in
trace.stats.mseed.
"""
npts = 6000
np.random.seed(815) # make test reproducable
data = np.random.randint(-1000, 1000, npts).astype(np.int32)
# Test all possible combinations of record length, encoding and
# byte order.
record_lengths = [256, 512, 1024, 2048, 4096, 8192]
byteorders = ['>', '<']
# Only select encoding that have write support.
encodings = [value[0] for value in list(ENCODINGS.values()) if
value[3]]
np_encodings = {}
# Special handling for ASCII encoded files.
for value in list(ENCODINGS.values()):
if value[0] == 'ASCII':
np_encodings[value[0]] = np.dtype(native_str("|S1"))
else:
np_encodings[value[0]] = value[2]
st = Stream([Trace(data=data)])
st[0].stats.mseed = AttribDict()
st[0].stats.mseed.dataquality = 'D'
# Loop over all combinations.
for reclen in record_lengths:
for order in byteorders:
for encoding in encodings:
# Create new stream and change stats.
stream = copy.deepcopy(st)
stream[0].stats.mseed.record_length = reclen
stream[0].stats.mseed.byteorder = order
stream[0].stats.mseed.encoding = encoding
# Convert the data so that it is compatible with the
# encoding.
stream[0].data = np.require(
stream[0].data, np_encodings[encoding])
# Write it.
with NamedTemporaryFile() as tf:
tempfile = tf.name
stream.write(tempfile, format="MSEED")
# Open the file.
stream2 = read(tempfile)
# remove file specific stats
stream2[0].stats.mseed.pop('filesize')
stream2[0].stats.mseed.pop('number_of_records')
# compare stats
self.assertEqual(stream[0].stats.mseed,
stream2[0].stats.mseed)
del stream
del stream2
def test_readingAndWritingViaTheStatsAttribute(self):
"""
Tests the writing with MSEED file attributes set via the attributes in
trace.stats.mseed.
"""
npts = 6000
np.random.seed(815) # make test reproducable
data = np.random.randint(-1000, 1000, npts).astype(np.int32)
# Test all possible combinations of record length, encoding and
# byte order.
record_lengths = [256, 512, 1024, 2048, 4096, 8192]
byteorders = ['>', '<']
# Only select encoding that have write support.
encodings = [value[0] for value in ENCODINGS.values() if value[3]]
np_encodings = {}
# Special handling for ASCII encoded files.
for value in ENCODINGS.values():
if value[0] == 'ASCII':
np_encodings[value[0]] = np.dtype(native_str("|S1"))
else:
np_encodings[value[0]] = value[2]
st = Stream([Trace(data=data)])
st[0].stats.mseed = AttribDict()
st[0].stats.mseed.dataquality = 'D'
# Loop over all combinations.
for reclen in record_lengths:
for order in byteorders:
for encoding in encodings:
# Create new stream and change stats.
stream = copy.deepcopy(st)
stream[0].stats.mseed.record_length = reclen
stream[0].stats.mseed.byteorder = order
stream[0].stats.mseed.encoding = encoding
# Convert the data so that it is compatible with the
# encoding.
stream[0].data = np.require(stream[0].data,
np_encodings[encoding])
# Write it.
with NamedTemporaryFile() as tf:
tempfile = tf.name
stream.write(tempfile, format="MSEED")
# Open the file.
stream2 = read(tempfile)
# remove file specific stats
stream2[0].stats.mseed.pop('filesize')
stream2[0].stats.mseed.pop('number_of_records')
# compare stats
self.assertEqual(stream[0].stats.mseed,
stream2[0].stats.mseed)
del stream
del stream2
def test_writeAndReadDifferentEncodings(self):
"""
Writes and read a file with different encoding via the obspy.core
methods.
"""
npts = 1000
np.random.seed(815) # make test reproducable
data = np.random.randn(npts).astype('float64') * 1e3 + .5
st = Stream([Trace(data=data)])
# Loop over some record lengths.
for encoding, value in ENCODINGS.iteritems():
seed_dtype = value[2]
# Special handling for the ASCII dtype. NumPy 1.7 changes the
# default dtype of numpy.string_ from "|S1" to "|S32". Enforce
# "|S1|" here to be consistent across NumPy versions.
if encoding == 0:
seed_dtype = "|S1"
with NamedTemporaryFile() as tf:
tempfile = tf.name
# Write it once with the encoding key and once with the value.
st[0].data = data.astype(seed_dtype)
st.verify()
st.write(tempfile, format="MSEED", encoding=encoding)
st2 = read(tempfile)
del st2[0].stats.mseed
np.testing.assert_array_equal(st[0].data, st2[0].data,
"Arrays are not equal for encoding '%s'" %
ENCODINGS[encoding][0])
del st2
ms = _MSStruct(tempfile)
ms.read(-1, 1, 1, 0)
self.assertEqual(ms.msr.contents.encoding, encoding)
del ms # for valgrind
def _convert_and_check_encoding_for_writing(encoding):
"""
Helper function to handle and test encodings.
If encoding is a string, it will be converted to the appropriate
integer. It will furthermore be checked if the specified encoding can be
written using libmseed. Appropriate errors will be raised if necessary.
"""
# Check if encoding kwarg is set and catch invalid encodings.
encoding_strings = dict([(v[0], k) for (k, v) in ENCODINGS.items()])
try:
encoding = int(encoding)
except:
pass
if isinstance(encoding, int):
if (encoding in ENCODINGS and ENCODINGS[encoding][3] is False) or \
encoding in UNSUPPORTED_ENCODINGS:
msg = ("Encoding %i cannot be written with ObsPy. Please "
"use another encoding.") % encoding
raise ValueError(msg)
elif encoding not in ENCODINGS:
raise ValueError("Unknown encoding: %i." % encoding)
else:
if encoding not in encoding_strings:
raise ValueError("Unknown encoding: '%s'." % str(encoding))
elif ENCODINGS[encoding_strings[encoding]][3] is False:
msg = ("Encoding '%s' cannot be written with ObsPy. Please "
"use another encoding.") % encoding
raise ValueError(msg)
encoding = encoding_strings[encoding]
return encoding
def test_writeAndReadDifferentEncodings(self):
"""
Writes and read a file with different encoding via the obspy.core
methods.
"""
npts = 1000
np.random.seed(815) # make test reproducable
data = np.random.randn(npts).astype('float64') * 1e3 + .5
st = Stream([Trace(data=data)])
# Loop over some record lengths.
for encoding, value in ENCODINGS.iteritems():
seed_dtype = value[2]
tempfile = NamedTemporaryFile().name
# Write it once with the encoding key and once with the value.
st[0].data = data.astype(seed_dtype)
st.verify()
st.write(tempfile, format="MSEED", encoding=encoding)
st2 = read(tempfile)
del st2[0].stats.mseed
np.testing.assert_array_equal(st[0].data, st2[0].data)
del st2
ms = _MSStruct(tempfile)
ms.read(-1, 1, 1, 0)
self.assertEqual(ms.msr.contents.encoding, encoding)
del ms # for valgrind
os.remove(tempfile)
def _convert_and_check_encoding_for_writing(encoding):
"""
Helper function to handle and test encodings.
If encoding is a string, it will be converted to the appropriate
integer. It will furthermore be checked if the specified encoding can be
written using libmseed. Appropriate errors will be raised if necessary.
"""
# Check if encoding kwarg is set and catch invalid encodings.
encoding_strings = dict([(v[0], k) for (k, v) in ENCODINGS.items()])
try:
encoding = int(encoding)
except:
pass
if isinstance(encoding, int):
if (encoding in ENCODINGS and ENCODINGS[encoding][3] is False) or \
encoding in UNSUPPORTED_ENCODINGS:
msg = ("Encoding %i cannot be written with ObsPy. Please "
"use another encoding.") % encoding
raise ValueError(msg)
elif encoding not in ENCODINGS:
raise ValueError("Unknown encoding: %i." % encoding)
else:
if encoding not in encoding_strings:
raise ValueError("Unknown encoding: '%s'." % str(encoding))
elif ENCODINGS[encoding_strings[encoding]][3] is False:
msg = ("Encoding '%s' cannot be written with ObsPy. Please "
"use another encoding.") % encoding
raise ValueError(msg)
encoding = encoding_strings[encoding]
return encoding
def test_writeAndReadDifferentEncodings(self):
"""
Writes and read a file with different encoding via the obspy.core
methods.
"""
npts = 1000
np.random.seed(815) # make test reproducable
data = np.random.randn(npts).astype('float64') * 1e3 + .5
st = Stream([Trace(data=data)])
# Loop over some record lengths.
for encoding, value in ENCODINGS.iteritems():
seed_dtype = value[2]
tempfile = NamedTemporaryFile().name
# Write it once with the encoding key and once with the value.
st[0].data = data.astype(seed_dtype)
st.verify()
st.write(tempfile, format="MSEED", encoding=encoding)
st2 = read(tempfile)
del st2[0].stats.mseed
np.testing.assert_array_equal(st[0].data, st2[0].data)
del st2
ms = _MSStruct(tempfile)
ms.read(-1, 1, 1, 0)
self.assertEqual(ms.msr.contents.encoding, encoding)
del ms # for valgrind
os.remove(tempfile)
def test_writing_with_some_encoding_fails(self):
"""
Writing with some encoding fails as libmseed does not support those.
Make sure an appropriate error is raised.
"""
tr = read()[0]
tr.data = tr.data[:10]
for encoding, value in ENCODINGS.items():
# Convert the data to the appropriate type to make it does not
# fail because of that.
tr2 = tr.copy()
tr2.data = np.require(tr2.data, dtype=value[2])
buf = io.BytesIO()
# Test writing by forcing the encoding.
# Should not fail with write support.
if value[3]:
# Test with integer code and string name.
tr2.write(buf, format="mseed", encoding=encoding)
tr2.write(buf, format="mseed", encoding=value[0])
# Should fail without write support.
else:
# Test with integer code and string name.
self.assertRaises(ValueError,
tr2.write,
buf,
format="mseed",
encoding=encoding)
self.assertRaises(ValueError,
tr2.write,
buf,
format="mseed",
encoding=value[0])
# Test again by setting the encoding on the trace stats.
tr2.stats.mseed = AttribDict()
tr2.stats.mseed.encoding = encoding
if value[3]:
tr2.write(buf, format="mseed")
else:
self.assertRaises(ValueError, tr2.write, buf, format="mseed")
# Again with setting the string code.
tr2.stats.mseed.encoding = value[0]
if value[3]:
tr2.write(buf, format="mseed")
else:
self.assertRaises(ValueError, tr2.write, buf, format="mseed")
def test_getRecordInformation(self):
"""
Tests the reading of Mini-SEED record information.
"""
# Build encoding strings.
encoding_strings = {}
for key, value in ENCODINGS.iteritems():
encoding_strings[value[0]] = key
# Test the encodings and byteorders.
path = os.path.join(self.path, "data", "encoding")
files = ['float32_Float32_bigEndian.mseed',
'float32_Float32_littleEndian.mseed',
'float64_Float64_bigEndian.mseed',
'float64_Float64_littleEndian.mseed',
'fullASCII_bigEndian.mseed', 'fullASCII_littleEndian.mseed',
'int16_INT16_bigEndian.mseed',
'int16_INT16_littleEndian.mseed',
'int32_INT32_bigEndian.mseed',
'int32_INT32_littleEndian.mseed',
'int32_Steim1_bigEndian.mseed',
'int32_Steim1_littleEndian.mseed',
'int32_Steim2_bigEndian.mseed',
'int32_Steim2_littleEndian.mseed']
for file in files:
info = util.getRecordInformation(os.path.join(path, file))
if not 'ASCII' in file:
encoding = file.split('_')[1].upper()
byteorder = file.split('_')[2].split('.')[0]
else:
encoding = 'ASCII'
byteorder = file.split('_')[1].split('.')[0]
if 'big' in byteorder:
byteorder = '>'
else:
byteorder = '<'
self.assertEqual(encoding_strings[encoding], info['encoding'])
self.assertEqual(byteorder, info['byteorder'])
# Also test the record length although it is equal for all files.
self.assertEqual(256, info['record_length'])
# No really good test files for the record length so just two files
# with known record lengths are tested.
info = util.getRecordInformation(os.path.join(self.path, 'data',
'timingquality.mseed'))
self.assertEqual(info['record_length'], 512)
info = util.getRecordInformation(os.path.join(self.path, 'data',
'steim2.mseed'))
self.assertEqual(info['record_length'], 4096)
def test_writing_with_some_encoding_fails(self):
"""
Writing with some encoding fails as libmseed does not support those.
Make sure an appropriate error is raised.
"""
tr = read()[0]
tr.data = tr.data[:10]
for encoding, value in ENCODINGS.items():
# Convert the data to the appropriate type to make it does not
# fail because of that.
tr2 = tr.copy()
tr2.data = np.require(tr2.data, dtype=value[2])
buf = io.BytesIO()
# Test writing by forcing the encoding.
# Should not fail with write support.
if value[3]:
# Test with integer code and string name.
tr2.write(buf, format="mseed", encoding=encoding)
tr2.write(buf, format="mseed", encoding=value[0])
# Should fail without write support.
else:
# Test with integer code and string name.
self.assertRaises(ValueError, tr2.write, buf,
format="mseed", encoding=encoding)
self.assertRaises(ValueError, tr2.write, buf,
format="mseed", encoding=value[0])
# Test again by setting the encoding on the trace stats.
tr2.stats.mseed = AttribDict()
tr2.stats.mseed.encoding = encoding
if value[3]:
tr2.write(buf, format="mseed")
else:
self.assertRaises(ValueError, tr2.write, buf, format="mseed")
# Again with setting the string code.
tr2.stats.mseed.encoding = value[0]
if value[3]:
tr2.write(buf, format="mseed")
else:
self.assertRaises(ValueError, tr2.write, buf, format="mseed")
def writeMSEED(stream,
filename,
encoding=None,
reclen=None,
byteorder=None,
flush=1,
verbose=0,
**_kwargs):
"""
Write Mini-SEED file from a Stream object.
.. warning::
This function should NOT be called directly, it registers via the
the :meth:`~obspy.core.stream.Stream.write` method of an
ObsPy :class:`~obspy.core.stream.Stream` object, call this instead.
:type stream: :class:`~obspy.core.stream.Stream`
:param stream: A Stream object.
:type filename: str
:param filename: Name of the output file
:type encoding: int or str, optional
:param encoding: Should be set to one of the following supported Mini-SEED
data encoding formats: ASCII (``0``)*, INT16 (``1``), INT32 (``3``),
FLOAT32 (``4``)*, FLOAT64 (``5``)*, STEIM1 (``10``) and STEIM2
(``11``)*. Default data types a marked with an asterisk. Currently
INT24 (``2``) is not supported due to lacking NumPy support.
:type reclen: int, optional
:param reclen: Should be set to the desired data record length in bytes
which must be expressible as 2 raised to the power of X where X is
between (and including) 8 to 20.
Defaults to 4096
:type byteorder: [``0`` or ``'<'`` | ``1`` or ``'>'`` | ``'='``], optional
:param byteorder: Must be either ``0`` or ``'<'`` for LSBF or
little-endian, ``1`` or ``'>'`` for MBF or big-endian. ``'='`` is the
native byteorder. If ``-1`` it will be passed directly to libmseed
which will also default it to big endian. Defaults to big endian.
:type flush: int, optional
:param flush: If it is not zero all of the data will be packed into
records, otherwise records will only be packed while there are
enough data samples to completely fill a record.
:type verbose: int, optional
:param verbose: Controls verbosity, a value of zero will result in no
diagnostic output.
.. note::
The reclen, encoding and byteorder keyword arguments can be set
in the stats.mseed of each :class:`~obspy.core.trace.Trace` as well as
as kwargs of this function. If both are given the kwargs will be used.
.. rubric:: Example
>>> from obspy import read
>>> st = read()
>>> st.write('filename.mseed', format='MSEED') # doctest: +SKIP
"""
# Some sanity checks for the keyword arguments.
if reclen is not None and reclen not in VALID_RECORD_LENGTHS:
msg = 'Invalid record length. The record length must be a value\n' + \
'of 2 to the power of X where 8 <= X <= 20.'
raise ValueError(msg)
if byteorder is not None and byteorder not in [0, 1, -1]:
if byteorder == '=':
byteorder = NATIVE_BYTEORDER
# If not elif because NATIVE_BYTEORDER is '<' or '>'.
if byteorder == '<':
byteorder = 0
elif byteorder == '>':
byteorder = 1
else:
msg = "Invalid byteorder. It must be either '<', '>', '=', " + \
"0, 1 or -1"
raise ValueError(msg)
# Check if encoding kwarg is set and catch invalid encodings.
# XXX: Currently INT24 is not working due to lacking NumPy support.
encoding_strings = dict([(v[0], k) for (k, v) in ENCODINGS.items()])
if encoding is not None:
if isinstance(encoding, int) and encoding in ENCODINGS:
pass
elif encoding and isinstance(encoding, (str, native_str)) \
and encoding in encoding_strings:
encoding = encoding_strings[encoding]
else:
msg = 'Invalid encoding %s. Valid encodings: %s'
raise ValueError(msg % (encoding, encoding_strings))
trace_attributes = []
use_blkt_1001 = 0
# The data might need to be modified. To not modify the input data keep
# references of which data to finally write.
trace_data = []
# Loop over every trace and figure out the correct settings.
for _i, trace in enumerate(stream):
# Create temporary dict for storing information while writing.
trace_attr = {}
trace_attributes.append(trace_attr)
stats = trace.stats
# Figure out whether or not to use Blockette 1001. This check is done
# once to ensure that Blockette 1001 is either written for every record
# in the file or for none. It checks the starttime as well as the
# sampling rate. If either one has a precision of more than 100
# microseconds, Blockette 1001 will be written for every record.
starttime = util._convertDatetimeToMSTime(trace.stats.starttime)
if starttime % 100 != 0 or \
(1.0 / trace.stats.sampling_rate * HPTMODULUS) % 100 != 0:
use_blkt_1001 += 1
# Determine if a blockette 100 will be needed to represent the input
# sample rate or if the sample rate in the fixed section of the data
# header will suffice (see ms_genfactmult in libmseed/genutils.c)
if trace.stats.sampling_rate >= 32727.0 or \
trace.stats.sampling_rate <= (1.0 / 32727.0):
use_blkt_100 = True
else:
use_blkt_100 = False
# Set data quality to indeterminate (= D) if it is not already set.
try:
trace_attr['dataquality'] = \
trace.stats['mseed']['dataquality'].upper()
except:
trace_attr['dataquality'] = 'D'
# Sanity check for the dataquality to get a nice Python exception
# instead of a C error.
if trace_attr['dataquality'] not in ['D', 'R', 'Q', 'M']:
msg = 'Invalid dataquality in Stream[%i].stats' % _i + \
'.mseed.dataquality\n' + \
'The dataquality for Mini-SEED must be either D, R, Q ' + \
'or M. See the SEED manual for further information.'
raise ValueError(msg)
# Check that data is of the right type.
if not isinstance(trace.data, np.ndarray):
msg = "Unsupported data type %s" % type(trace.data) + \
" for Stream[%i].data." % _i
raise ValueError(msg)
# Check if ndarray is contiguous (see #192, #193)
if not trace.data.flags.c_contiguous:
msg = "Detected non contiguous data array in Stream[%i]" % _i + \
".data. Trying to fix array."
warnings.warn(msg)
trace.data = np.require(trace.data,
requirements=('C_CONTIGUOUS', ))
# Handle the record length.
if reclen is not None:
trace_attr['reclen'] = reclen
elif hasattr(stats, 'mseed') and \
hasattr(stats.mseed, 'record_length'):
if stats.mseed.record_length in VALID_RECORD_LENGTHS:
trace_attr['reclen'] = stats.mseed.record_length
else:
msg = 'Invalid record length in Stream[%i].stats.' % _i + \
'mseed.reclen.\nThe record length must be a value ' + \
'of 2 to the power of X where 8 <= X <= 20.'
raise ValueError(msg)
else:
trace_attr['reclen'] = 4096
# Handle the byteorder.
if byteorder is not None:
trace_attr['byteorder'] = byteorder
elif hasattr(stats, 'mseed') and \
hasattr(stats.mseed, 'byteorder'):
if stats.mseed.byteorder in [0, 1, -1]:
trace_attr['byteorder'] = stats.mseed.byteorder
elif stats.mseed.byteorder == '=':
if NATIVE_BYTEORDER == '<':
trace_attr['byteorder'] = 0
else:
trace_attr['byteorder'] = 1
elif stats.mseed.byteorder == '<':
trace_attr['byteorder'] = 0
elif stats.mseed.byteorder == '>':
trace_attr['byteorder'] = 1
else:
msg = "Invalid byteorder in Stream[%i].stats." % _i + \
"mseed.byteorder. It must be either '<', '>', '='," + \
" 0, 1 or -1"
raise ValueError(msg)
else:
trace_attr['byteorder'] = 1
if trace_attr['byteorder'] == -1:
if NATIVE_BYTEORDER == '<':
trace_attr['byteorder'] = 0
else:
trace_attr['byteorder'] = 1
# Handle the encoding.
trace_attr['encoding'] = None
if encoding is not None:
# Check if the dtype for all traces is compatible with the enforced
# encoding.
id, _, dtype = ENCODINGS[encoding]
if trace.data.dtype.type != dtype:
msg = """
Wrong dtype for Stream[%i].data for encoding %s.
Please change the dtype of your data or use an appropriate
encoding. See the obspy.mseed documentation for more
information.
""" % (_i, id)
raise Exception(msg)
trace_attr['encoding'] = encoding
elif hasattr(trace.stats, 'mseed') and hasattr(trace.stats.mseed,
'encoding'):
mseed_encoding = stats.mseed.encoding
# Check if the encoding is valid.
if isinstance(mseed_encoding, int) and mseed_encoding in ENCODINGS:
trace_attr['encoding'] = mseed_encoding
elif isinstance(mseed_encoding, (str, native_str)) and \
mseed_encoding in encoding_strings:
trace_attr['encoding'] = encoding_strings[mseed_encoding]
else:
msg = 'Invalid encoding %s in ' + \
'Stream[%i].stats.mseed.encoding. Valid encodings: %s'
raise ValueError(msg % (mseed_encoding, _i, encoding_strings))
# Check if the encoding matches the data's dtype.
if trace.data.dtype.type != ENCODINGS[trace_attr['encoding']][2]:
msg = 'The encoding specified in ' + \
'trace.stats.mseed.encoding does not match the ' + \
'dtype of the data.\nA suitable encoding will ' + \
'be chosen.'
warnings.warn(msg, UserWarning)
trace_attr['encoding'] = None
# automatically detect encoding if no encoding is given.
if not trace_attr['encoding']:
if trace.data.dtype.type == np.dtype("int32"):
trace_attr['encoding'] = 11
elif trace.data.dtype.type == np.dtype("float32"):
trace_attr['encoding'] = 4
elif trace.data.dtype.type == np.dtype("float64"):
trace_attr['encoding'] = 5
elif trace.data.dtype.type == np.dtype("int16"):
trace_attr['encoding'] = 1
elif trace.data.dtype.type == np.dtype('|S1').type:
trace_attr['encoding'] = 0
else:
msg = "Unsupported data type %s in Stream[%i].data" % \
(trace.data.dtype, _i)
raise Exception(msg)
# Convert data if necessary, otherwise store references in list.
if trace_attr['encoding'] == 1:
# INT16 needs INT32 data type
trace_data.append(trace.data.copy().astype(np.int32))
else:
trace_data.append(trace.data)
# Do some final sanity checks and raise a warning if a file will be written
# with more than one different encoding, record length or byteorder.
encodings = set([_i['encoding'] for _i in trace_attributes])
reclens = set([_i['reclen'] for _i in trace_attributes])
byteorders = set([_i['byteorder'] for _i in trace_attributes])
msg = 'File will be written with more than one different %s.\n' + \
'This might have a negative influence on the compatibility ' + \
'with other programs.'
if len(encodings) != 1:
warnings.warn(msg % 'encodings')
if len(reclens) != 1:
warnings.warn(msg % 'record lengths')
if len(byteorders) != 1:
warnings.warn(msg % 'byteorders')
# Open filehandler or use an existing file like object.
if not hasattr(filename, 'write'):
f = open(filename, 'wb')
else:
f = filename
# Loop over every trace and finally write it to the filehandler.
for trace, data, trace_attr in zip(stream, trace_data, trace_attributes):
if not len(data):
msg = 'Skipping empty trace "%s".' % (trace)
warnings.warn(msg)
continue
# Create C struct MSTrace.
mst = MST(trace, data, dataquality=trace_attr['dataquality'])
# Initialize packedsamples pointer for the mst_pack function
packedsamples = C.c_int()
# Callback function for mst_pack to actually write the file
def record_handler(record, reclen, _stream):
f.write(record[0:reclen])
# Define Python callback function for use in C function
recHandler = C.CFUNCTYPE(C.c_void_p, C.POINTER(C.c_char), C.c_int,
C.c_void_p)(record_handler)
# Fill up msr record structure, this is already contained in
# mstg, however if blk1001 is set we need it anyway
msr = clibmseed.msr_init(None)
msr.contents.network = trace.stats.network.encode('ascii', 'strict')
msr.contents.station = trace.stats.station.encode('ascii', 'strict')
msr.contents.location = trace.stats.location.encode('ascii', 'strict')
msr.contents.channel = trace.stats.channel.encode('ascii', 'strict')
msr.contents.dataquality = trace_attr['dataquality'].\
encode('ascii', 'strict')
# Only use Blockette 1001 if necessary.
if use_blkt_1001:
size = C.sizeof(blkt_1001_s)
blkt1001 = C.c_char(b' ')
C.memset(C.pointer(blkt1001), 0, size)
ret_val = clibmseed.msr_addblockette(msr, C.pointer(blkt1001),
size, 1001, 0)
# Usually returns a pointer to the added blockette in the
# blockette link chain and a NULL pointer if it fails.
# NULL pointers have a false boolean value according to the
# ctypes manual.
if bool(ret_val) is False:
clibmseed.msr_free(C.pointer(msr))
del msr
raise Exception('Error in msr_addblockette')
# Only use Blockette 100 if necessary.
if use_blkt_100:
size = C.sizeof(blkt_100_s)
blkt100 = C.c_char(b' ')
C.memset(C.pointer(blkt100), 0, size)
ret_val = clibmseed.msr_addblockette(msr, C.pointer(blkt100), size,
100, 0) # NOQA
# Usually returns a pointer to the added blockette in the
# blockette link chain and a NULL pointer if it fails.
# NULL pointers have a false boolean value according to the
# ctypes manual.
if bool(ret_val) is False:
clibmseed.msr_free(C.pointer(msr)) # NOQA
del msr # NOQA
raise Exception('Error in msr_addblockette')
# Pack mstg into a MSEED file using the callback record_handler as
# write method.
errcode = clibmseed.mst_pack(mst.mst, recHandler, None,
trace_attr['reclen'],
trace_attr['encoding'],
trace_attr['byteorder'],
C.byref(packedsamples), flush, verbose,
msr) # NOQA
if errcode == 0:
msg = ("Did not write any data for trace '%s' even though it "
"contains data values.") % trace
raise ValueError(msg)
if errcode == -1:
clibmseed.msr_free(C.pointer(msr)) # NOQA
del mst, msr # NOQA
raise Exception('Error in mst_pack')
# Deallocate any allocated memory.
clibmseed.msr_free(C.pointer(msr)) # NOQA
del mst, msr # NOQA
# Close if its a file handler.
if not hasattr(filename, 'write'):
f.close()
def writeMSEED(stream, filename, encoding=None, reclen=None, byteorder=None,
flush=1, verbose=0, **_kwargs):
"""
Write Mini-SEED file from a Stream object.
.. warning::
This function should NOT be called directly, it registers via the
the :meth:`~obspy.core.stream.Stream.write` method of an
ObsPy :class:`~obspy.core.stream.Stream` object, call this instead.
:type stream: :class:`~obspy.core.stream.Stream`
:param stream: A Stream object.
:type filename: str
:param filename: Name of the output file
:type encoding: int or str, optional
:param encoding: Should be set to one of the following supported Mini-SEED
data encoding formats: ASCII (``0``)*, INT16 (``1``), INT32 (``3``),
FLOAT32 (``4``)*, FLOAT64 (``5``)*, STEIM1 (``10``) and STEIM2
(``11``)*. Default data types a marked with an asterisk. Currently
INT24 (``2``) is not supported due to lacking NumPy support.
:type reclen: int, optional
:param reclen: Should be set to the desired data record length in bytes
which must be expressible as 2 raised to the power of X where X is
between (and including) 8 to 20.
Defaults to 4096
:type byteorder: [``0`` or ``'<'`` | ``1`` or ``'>'`` | ``'='``], optional
:param byteorder: Must be either ``0`` or ``'<'`` for LSBF or
little-endian, ``1`` or ``'>'`` for MBF or big-endian. ``'='`` is the
native byteorder. If ``-1`` it will be passed directly to libmseed
which will also default it to big endian. Defaults to big endian.
:type flush: int, optional
:param flush: If it is not zero all of the data will be packed into
records, otherwise records will only be packed while there are
enough data samples to completely fill a record.
:type verbose: int, optional
:param verbose: Controls verbosity, a value of zero will result in no
diagnostic output.
.. note::
The reclen, encoding and byteorder keyword arguments can be set
in the stats.mseed of each :class:`~obspy.core.trace.Trace` as well as
as kwargs of this function. If both are given the kwargs will be used.
.. rubric:: Example
>>> from obspy import read
>>> st = read()
>>> st.write('filename.mseed', format='MSEED') # doctest: +SKIP
"""
# Some sanity checks for the keyword arguments.
if reclen is not None and reclen not in VALID_RECORD_LENGTHS:
msg = 'Invalid record length. The record length must be a value\n' + \
'of 2 to the power of X where 8 <= X <= 20.'
raise ValueError(msg)
if byteorder is not None and byteorder not in [0, 1, -1]:
if byteorder == '=':
byteorder = NATIVE_BYTEORDER
# If not elif because NATIVE_BYTEORDER is '<' or '>'.
if byteorder == '<':
byteorder = 0
elif byteorder == '>':
byteorder = 1
else:
msg = "Invalid byteorder. It must be either '<', '>', '=', " + \
"0, 1 or -1"
raise ValueError(msg)
# Check if encoding kwarg is set and catch invalid encodings.
# XXX: Currently INT24 is not working due to lacking NumPy support.
encoding_strings = dict([(v[0], k) for (k, v) in ENCODINGS.items()])
if encoding is not None:
if isinstance(encoding, int) and encoding in ENCODINGS:
pass
elif encoding and isinstance(encoding, (str, native_str)) \
and encoding in encoding_strings:
encoding = encoding_strings[encoding]
else:
msg = 'Invalid encoding %s. Valid encodings: %s'
raise ValueError(msg % (encoding, encoding_strings))
trace_attributes = []
use_blkt_1001 = 0
# The data might need to be modified. To not modify the input data keep
# references of which data to finally write.
trace_data = []
# Loop over every trace and figure out the correct settings.
for _i, trace in enumerate(stream):
# Create temporary dict for storing information while writing.
trace_attr = {}
trace_attributes.append(trace_attr)
stats = trace.stats
# Figure out whether or not to use Blockette 1001. This check is done
# once to ensure that Blockette 1001 is either written for every record
# in the file or for none. It checks the starttime as well as the
# sampling rate. If either one has a precision of more than 100
# microseconds, Blockette 1001 will be written for every record.
starttime = util._convertDatetimeToMSTime(trace.stats.starttime)
if starttime % 100 != 0 or \
(1.0 / trace.stats.sampling_rate * HPTMODULUS) % 100 != 0:
use_blkt_1001 += 1
# Determine if a blockette 100 will be needed to represent the input
# sample rate or if the sample rate in the fixed section of the data
# header will suffice (see ms_genfactmult in libmseed/genutils.c)
if trace.stats.sampling_rate >= 32727.0 or \
trace.stats.sampling_rate <= (1.0 / 32727.0):
use_blkt_100 = True
else:
use_blkt_100 = False
# Set data quality to indeterminate (= D) if it is not already set.
try:
trace_attr['dataquality'] = \
trace.stats['mseed']['dataquality'].upper()
except:
trace_attr['dataquality'] = 'D'
# Sanity check for the dataquality to get a nice Python exception
# instead of a C error.
if trace_attr['dataquality'] not in ['D', 'R', 'Q', 'M']:
msg = 'Invalid dataquality in Stream[%i].stats' % _i + \
'.mseed.dataquality\n' + \
'The dataquality for Mini-SEED must be either D, R, Q ' + \
'or M. See the SEED manual for further information.'
raise ValueError(msg)
# Check that data is of the right type.
if not isinstance(trace.data, np.ndarray):
msg = "Unsupported data type %s" % type(trace.data) + \
" for Stream[%i].data." % _i
raise ValueError(msg)
# Check if ndarray is contiguous (see #192, #193)
if not trace.data.flags.c_contiguous:
msg = "Detected non contiguous data array in Stream[%i]" % _i + \
".data. Trying to fix array."
warnings.warn(msg)
trace.data = np.require(trace.data, requirements=('C_CONTIGUOUS',))
# Handle the record length.
if reclen is not None:
trace_attr['reclen'] = reclen
elif hasattr(stats, 'mseed') and \
hasattr(stats.mseed, 'record_length'):
if stats.mseed.record_length in VALID_RECORD_LENGTHS:
trace_attr['reclen'] = stats.mseed.record_length
else:
msg = 'Invalid record length in Stream[%i].stats.' % _i + \
'mseed.reclen.\nThe record length must be a value ' + \
'of 2 to the power of X where 8 <= X <= 20.'
raise ValueError(msg)
else:
trace_attr['reclen'] = 4096
# Handle the byteorder.
if byteorder is not None:
trace_attr['byteorder'] = byteorder
elif hasattr(stats, 'mseed') and \
hasattr(stats.mseed, 'byteorder'):
if stats.mseed.byteorder in [0, 1, -1]:
trace_attr['byteorder'] = stats.mseed.byteorder
elif stats.mseed.byteorder == '=':
if NATIVE_BYTEORDER == '<':
trace_attr['byteorder'] = 0
else:
trace_attr['byteorder'] = 1
elif stats.mseed.byteorder == '<':
trace_attr['byteorder'] = 0
elif stats.mseed.byteorder == '>':
trace_attr['byteorder'] = 1
else:
msg = "Invalid byteorder in Stream[%i].stats." % _i + \
"mseed.byteorder. It must be either '<', '>', '='," + \
" 0, 1 or -1"
raise ValueError(msg)
else:
trace_attr['byteorder'] = 1
if trace_attr['byteorder'] == -1:
if NATIVE_BYTEORDER == '<':
trace_attr['byteorder'] = 0
else:
trace_attr['byteorder'] = 1
# Handle the encoding.
trace_attr['encoding'] = None
if encoding is not None:
# Check if the dtype for all traces is compatible with the enforced
# encoding.
id, _, dtype = ENCODINGS[encoding]
if trace.data.dtype.type != dtype:
msg = """
Wrong dtype for Stream[%i].data for encoding %s.
Please change the dtype of your data or use an appropriate
encoding. See the obspy.mseed documentation for more
information.
""" % (_i, id)
raise Exception(msg)
trace_attr['encoding'] = encoding
elif hasattr(trace.stats, 'mseed') and hasattr(trace.stats.mseed,
'encoding'):
mseed_encoding = stats.mseed.encoding
# Check if the encoding is valid.
if isinstance(mseed_encoding, int) and mseed_encoding in ENCODINGS:
trace_attr['encoding'] = mseed_encoding
elif isinstance(mseed_encoding, (str, native_str)) and \
mseed_encoding in encoding_strings:
trace_attr['encoding'] = encoding_strings[mseed_encoding]
else:
msg = 'Invalid encoding %s in ' + \
'Stream[%i].stats.mseed.encoding. Valid encodings: %s'
raise ValueError(msg % (mseed_encoding, _i, encoding_strings))
# Check if the encoding matches the data's dtype.
if trace.data.dtype.type != ENCODINGS[trace_attr['encoding']][2]:
msg = 'The encoding specified in ' + \
'trace.stats.mseed.encoding does not match the ' + \
'dtype of the data.\nA suitable encoding will ' + \
'be chosen.'
warnings.warn(msg, UserWarning)
trace_attr['encoding'] = None
# automatically detect encoding if no encoding is given.
if not trace_attr['encoding']:
if trace.data.dtype.type == np.dtype("int32"):
trace_attr['encoding'] = 11
elif trace.data.dtype.type == np.dtype("float32"):
trace_attr['encoding'] = 4
elif trace.data.dtype.type == np.dtype("float64"):
trace_attr['encoding'] = 5
elif trace.data.dtype.type == np.dtype("int16"):
trace_attr['encoding'] = 1
elif trace.data.dtype.type == np.dtype('|S1').type:
trace_attr['encoding'] = 0
else:
msg = "Unsupported data type %s in Stream[%i].data" % \
(trace.data.dtype, _i)
raise Exception(msg)
# Convert data if necessary, otherwise store references in list.
if trace_attr['encoding'] == 1:
# INT16 needs INT32 data type
trace_data.append(trace.data.copy().astype(np.int32))
else:
trace_data.append(trace.data)
# Do some final sanity checks and raise a warning if a file will be written
# with more than one different encoding, record length or byteorder.
encodings = set([_i['encoding'] for _i in trace_attributes])
reclens = set([_i['reclen'] for _i in trace_attributes])
byteorders = set([_i['byteorder'] for _i in trace_attributes])
msg = 'File will be written with more than one different %s.\n' + \
'This might have a negative influence on the compatibility ' + \
'with other programs.'
if len(encodings) != 1:
warnings.warn(msg % 'encodings')
if len(reclens) != 1:
warnings.warn(msg % 'record lengths')
if len(byteorders) != 1:
warnings.warn(msg % 'byteorders')
# Open filehandler or use an existing file like object.
if not hasattr(filename, 'write'):
f = open(filename, 'wb')
else:
f = filename
# Loop over every trace and finally write it to the filehandler.
for trace, data, trace_attr in zip(stream, trace_data, trace_attributes):
if not len(data):
msg = 'Skipping empty trace "%s".' % (trace)
warnings.warn(msg)
continue
# Create C struct MSTrace.
mst = MST(trace, data, dataquality=trace_attr['dataquality'])
# Initialize packedsamples pointer for the mst_pack function
packedsamples = C.c_int()
# Callback function for mst_pack to actually write the file
def record_handler(record, reclen, _stream):
f.write(record[0:reclen])
# Define Python callback function for use in C function
recHandler = C.CFUNCTYPE(C.c_void_p, C.POINTER(C.c_char), C.c_int,
C.c_void_p)(record_handler)
# Fill up msr record structure, this is already contained in
# mstg, however if blk1001 is set we need it anyway
msr = clibmseed.msr_init(None)
msr.contents.network = trace.stats.network.encode('ascii', 'strict')
msr.contents.station = trace.stats.station.encode('ascii', 'strict')
msr.contents.location = trace.stats.location.encode('ascii', 'strict')
msr.contents.channel = trace.stats.channel.encode('ascii', 'strict')
msr.contents.dataquality = trace_attr['dataquality'].\
encode('ascii', 'strict')
# Only use Blockette 1001 if necessary.
if use_blkt_1001:
size = C.sizeof(blkt_1001_s)
blkt1001 = C.c_char(b' ')
C.memset(C.pointer(blkt1001), 0, size)
ret_val = clibmseed.msr_addblockette(msr, C.pointer(blkt1001),
size, 1001, 0)
# Usually returns a pointer to the added blockette in the
# blockette link chain and a NULL pointer if it fails.
# NULL pointers have a false boolean value according to the
# ctypes manual.
if bool(ret_val) is False:
clibmseed.msr_free(C.pointer(msr))
del msr
raise Exception('Error in msr_addblockette')
# Only use Blockette 100 if necessary.
if use_blkt_100:
size = C.sizeof(blkt_100_s)
blkt100 = C.c_char(b' ')
C.memset(C.pointer(blkt100), 0, size)
ret_val = clibmseed.msr_addblockette(
msr, C.pointer(blkt100), size, 100, 0) # NOQA
# Usually returns a pointer to the added blockette in the
# blockette link chain and a NULL pointer if it fails.
# NULL pointers have a false boolean value according to the
# ctypes manual.
if bool(ret_val) is False:
clibmseed.msr_free(C.pointer(msr)) # NOQA
del msr # NOQA
raise Exception('Error in msr_addblockette')
# Pack mstg into a MSEED file using the callback record_handler as
# write method.
errcode = clibmseed.mst_pack(
mst.mst, recHandler, None, trace_attr['reclen'],
trace_attr['encoding'], trace_attr['byteorder'],
C.byref(packedsamples), flush, verbose, msr) # NOQA
if errcode == 0:
msg = ("Did not write any data for trace '%s' even though it "
"contains data values.") % trace
raise ValueError(msg)
if errcode == -1:
clibmseed.msr_free(C.pointer(msr)) # NOQA
del mst, msr # NOQA
raise Exception('Error in mst_pack')
# Deallocate any allocated memory.
clibmseed.msr_free(C.pointer(msr)) # NOQA
del mst, msr # NOQA
# Close if its a file handler.
if not hasattr(filename, 'write'):
f.close()
