# Source code for obspy.io.segy.segy

# -*- coding: utf-8 -*-
# ------------------------------------------------------------------
#  Filename: seg.py
#  Purpose: Routines for reading and writing SEG Y files.
#   Author: Lion Krischer
#    Email: krischer@geophysik.uni-muenchen.de
#
# Copyright (C) 2010 Lion Krischer
# --------------------------------------------------------------------
"""
Routines to read and write SEG Y rev 1 encoded seismic data files.
"""
from __future__ import (absolute_import, division, print_function,
unicode_literals)
from future.builtins import *  # NOQA

import io
import os
from struct import pack, unpack
import warnings

import numpy as np

from obspy import Trace, UTCDateTime
from obspy.core import AttribDict

DATA_SAMPLE_FORMAT_PACK_FUNCTIONS,
DATA_SAMPLE_FORMAT_SAMPLE_SIZE,
DATA_SAMPLE_FORMAT_UNPACK_FUNCTIONS, ENDIAN,
from .unpack import OnTheFlyDataUnpacker

[docs]class SEGYError(Exception):
"""
Base SEGY exception class.
"""
pass

"""
Raised if the trace header is not the required 240 byte long.
"""
pass

"""
Raised if there is not enough data left in the file to unpack the data
"""
pass

[docs]class SEGYTraceOnTheFlyDataUnpackingError(SEGYError):
"""
Raised if attempting to unpack trace data but no unpack_data() function
exists.
"""
pass

[docs]class SEGYWritingError(SEGYError):
"""
Raised if the trace header is not the required 240 byte long.
"""
pass

[docs]class SEGYWarning(UserWarning):
"""
SEG Y warnings base class.
"""
pass

"""
Warning that is raised if an invalid textual header is about to be written.
"""
pass

[docs]class SEGYFile(object):
"""
Class that internally handles SEG Y files.
"""
[docs]    def __init__(self, file=None, endian=None, textual_header_encoding=None,
"""
Class that internally handles SEG Y files.

:param file: A file like object with the file pointer set at the
beginning of the SEG Y file. If file is None, an empty SEGYFile
object will be initialized.
:param endian: The endianness of the file. If None, autodetection will
be used.
Either 'EBCDIC', 'ASCII' or None. If it is None, autodetection will
be attempted. If it is None and file is also None, it will default
to 'ASCII'.
unpacked during reading the file. Has a huge impact on the memory
usage and the performance. They can be unpacked on-the-fly after
:param headonly: Determines whether or not the actual data records
will be read and unpacked. Has a huge impact on memory usage. Data
will not be unpackable on-the-fly. Defaults to False.
:param read_traces: Data traces will only be read if this is set to
True. The data will be completely ignored if this is set to
False.
"""
if file is None:
self._create_empty_segy_file_object()
# Set the endianness to big.
if endian is None:
self.endian = '>'
else:
self.endian = ENDIAN[endian]
# And the textual header encoding to ASCII.
return
self.file = file
# If endian is None autodetect is.
if not endian:
self._autodetect_endianness()
else:
self.endian = ENDIAN[endian]
# If the textual header encoding is None, autodetection will be used.

[docs]    def __str__(self):
"""
Prints some information about the SEG Y file.
"""
return '%i traces in the SEG Y structure.' % len(self.traces)

[docs]    def _repr_pretty_(self, p, cycle):
p.text(str(self))

[docs]    def _autodetect_endianness(self):
"""
Tries to automatically determine the endianness of the file at hand.
"""
pos = self.file.tell()
self.file.seek(3224, 1)
# Check if valid.
if format in DATA_SAMPLE_FORMAT_UNPACK_FUNCTIONS.keys():
self.endian = '>'
# Else test little endian.
else:
self.file.seek(-2, 1)
if format in DATA_SAMPLE_FORMAT_UNPACK_FUNCTIONS.keys():
self.endian = '<'
else:
msg = 'Unable to determine the endianness of the file. ' + \
raise SEGYError(msg)
self.file.seek(pos, 0)

[docs]    def _create_empty_segy_file_object(self):
"""
Creates an empty SEGYFile object.
"""
self.traces = []

"""
"""
# The first 3200 byte are the textual header.
# The data can either be saved as plain ASCII or EBCDIC. The first
# character always is mostly 'C' and therefore used to check the
# encoding. Sometimes is it not C but also cannot be decoded from
# EBCDIC so it is treated as ASCII and all empty symbols are removed.
#
# Also check the revision number and textual header end markers for
# the "C" as they might be set when the first byte is not.
try:
# If this worked, the encoding is EBCDIC.
except UnicodeEncodeError:
# Otherwise it is ASCII.
else:
# Otherwise the encoding will also be ASCII.
msg = """
The textual_header_encoding has to be either ASCII, EBCDIC or None
for autodetection. ASCII, EBCDIC or None for autodetection.
""".strip()
raise SEGYError(msg)
# Finally set it.

"""
Reads the textual and binary file headers starting at the current file
pointer position.
"""
# The next 400 bytes are from the Binary File Header.
# If bytes 3506-3506 are not zero, an extended textual header follows
# which is not supported so far.
msg = 'Extended textual headers are not yet supported. ' + \
raise NotImplementedError(msg)

[docs]    def write(self, file, data_encoding=None, endian=None):
"""
Write a SEG Y file to file which is either a file like object with a
write method or a filename string.

If data_encoding or endian is set, these values will be enforced.
"""
if not hasattr(file, 'write'):
with open(file, 'wb') as file:
self._write(file, data_encoding=data_encoding, endian=endian)
return
self._write(file, data_encoding=data_encoding, endian=endian)

[docs]    def _write(self, file, data_encoding=None, endian=None):
"""
Writes SEG Y to a file like object.

If data_encoding or endian is set, these values will be enforced.
"""

# Write certain fields in the binary header if they are not set. Most
# fields will be written using the data from the first trace. It is
# usually better to set the header manually!
len(self.traces)
len(self.traces[0].data)

# Always set the SEGY Revision number to 1.0 (hex-coded).
# Set the fixed length flag to zero if all traces have NOT the same
# length. Leave unchanged otherwise.
if len(set([len(tr.data) for tr in self.traces])) != 1:
# Extended textual headers are not supported by ObsPy so far.
# Enforce the encoding
if data_encoding:

# Write all traces.
for trace in self.traces:
trace.write(file, data_encoding=data_encoding, endian=endian)

"""
Write the textual header in various encodings. The encoding will depend
small it will be padded with zeros. If it is too long or an invalid
encoding is specified an exception will be raised.
"""

# Convert to ASCII bytes if necessary - this will raise an error in
# case the textual file header has no representation in ASCII - this
# is then the users responsibility.

# Append spaces to the end if its too short.
if length < 3200:
elif length == 3200:
# The length must not exceed 3200 byte.
else:
msg = 'self.textual_file_header is not allowed to be longer ' + \
'than 3200 bytes'
raise SEGYWritingError(msg)

# Assert the encoding.

# Make sure revision number and end header marker are present. If
# not: add them - if something else is already present, raise a
# warning but don't do anything.

if revision_number != "C39 SEG Y REV1":
if revision_number.strip() in ("", "C", "C39"):
b"C39 SEG Y REV1" + textual_header[3200-146:]
else:
# Raise warning but don't do anything.
msg = ("The revision number in the textual header should be "
"set as 'C39 SEG Y REV1' for a fully valid SEG-Y "
"file. It is set to '%s' which will be written to the "
"file. Please change it if you want a fully valid file."
% revision_number)

else b"C40 END EBCDIC        "

if end_header_mark.strip() in (b"", b"C", b"C40"):
else:
# Raise warning but don't do anything.
msg = ("The end header mark in the textual header should be "
"set as 'C40 END TEXTUAL HEADER' or as "
"'C40 END EBCDIC        ' for a fully valid "
"SEG-Y file. It is set to '%s' which will be written "
"to the file. Please change it if you want a fully "
"valid file."

# Finally encode the header if necessary.
if enc == 'ASCII':
pass
elif enc == 'EBCDIC':
# Should not happen.
else:
msg = 'self.textual_header_encoding has to be either ASCII or ' + \
'EBCDIC.'
raise SEGYWritingError(msg)

yield_each_trace=False):
"""
Reads the actual traces starting at the current file pointer position
to the end of the file.

unpacked during reading the file. Has a huge impact on the memory
usage and the performance. They can be unpacked on-the-fly after

:param headonly: Determines whether or not the actual data records
will be read and unpacked. Has a huge impact on memory usage. Data
will not be unpackable on-the-fly after reading the file.
Defaults to False.

:type yield_each_trace: bool
:param yield_each_trace: If True, it will yield each trace after it
has been read. This enables a simple implementation of a
longer be collected in self.traces list if this is set to
True.
"""
self.traces = []
# Determine the filesize once.
if isinstance(self.file, io.BytesIO):
pos = self.file.tell()
self.file.seek(0, 2)  # go t end of file
filesize = self.file.tell()
self.file.seek(pos, 0)
else:
filesize = os.fstat(self.file.fileno())[6]
# Big loop to read all data traces.
while True:
# Read and as soon as the trace header is too small abort.
try:
trace = SEGYTrace(self.file, self.data_encoding, self.endian,
if yield_each_trace:
yield trace
else:
self.traces.append(trace)
break

"""
Parses the binary file header at the given starting position.
"""
"""
"""
self.endian = endian
return

"""
Reads the binary file header and stores every value in a class
attribute.
"""
pos = 0
length, name, _ = item
string = header[pos: pos + length]
pos += length
# Unpack according to different lengths.
if length == 2:
format = ('%sh' % self.endian).encode('ascii', 'strict')
# Set the class attribute.
setattr(self, name, unpack(format, string)[0])
# Update: Seems to be correct. Two's complement integers seem to be
# the common way to store integer values.
elif length == 4:
format = ('%si' % self.endian).encode('ascii', 'strict')
# Set the class attribute.
setattr(self, name, unpack(format, string)[0])
# The other value are the unassigned values. As it is unclear how
# these are formatted they will be stored as strings.
elif name.startswith('unassigned'):
# These are only the unassigned fields.
format = 'h' * (length // 2)
# Set the class attribute.
setattr(self, name, string)
# Should not happen.
else:
raise Exception

[docs]    def __str__(self):
"""
Convenience method to print the binary file header.
"""
final_str.append("\t%s: %s" % (item[1],
str(getattr(self, item[1]))))
return "\n".join(final_str)

[docs]    def _repr_pretty_(self, p, cycle):
p.text(str(self))

[docs]    def write(self, file, endian=None):
"""
Writes the header to an open file like object.
"""
if endian is None:
endian = self.endian
length, name, _ = item
# Unpack according to different lengths.
if length == 2:
format = ('%sh' % endian).encode('ascii', 'strict')
# Write to file.
file.write(pack(format, getattr(self, name)))
# Update: Seems to be correct. Two's complement integers seem to be
# the common way to store integer values.
elif length == 4:
format = ('%si' % endian).encode('ascii', 'strict')
# Write to file.
file.write(pack(format, getattr(self, name)))
# These are the two unassigned values in the binary file header.
elif name.startswith('unassigned'):
temp = getattr(self, name)
if not isinstance(temp, bytes):
temp = str(temp).encode('ascii', 'strict')
temp_length = len(temp)
# Pad to desired length if necessary.
if temp_length != length:
temp += b'\x00' * (length - temp_length)
file.write(temp)
# Should not happen.
else:
raise Exception

"""
Just fills all necessary class attributes with zero.
"""
for _, name, _ in BINARY_FILE_HEADER_FORMAT:
setattr(self, name, 0)

[docs]class SEGYTrace(object):
"""
Convenience class that internally handles a single SEG Y trace.
"""
[docs]    def __init__(self, file=None, data_encoding=4, endian='>',
"""
Convenience class that internally handles a single SEG Y trace.

:param file: Open file like object with the file pointer of the
beginning of a trace. If it is None, an empty trace will be
created.
:param data_encoding: The data sample format code as defined in the

1:
4 byte IBM floating point
2:
4 byte Integer, two's complement
3:
2 byte Integer, two's complement
4:
4 byte Fixed point with gain
5:
4 byte IEEE floating point
8:
1 byte Integer, two's complement

Defaults to 4.
:type big_endian: bool
:param big_endian: True means the header is encoded in big endian and
False corresponds to a little endian header.
unpacked during reading the file. Has a huge impact on the memory
usage and the performance. They can be unpacked on-the-fly after
:type filesize: int
:param filesize: Filesize of the file. If not given it will be
determined using fstat which is slow.
:param headonly: Determines whether or not the actual data records
will be read and unpacked. Has a huge impact on memory usage. Data
will not be unpackable on-the-fly after reading the file.
Defaults to False.
"""
self.endian = endian
self.data_encoding = data_encoding
# If None just return empty structure.
if file is None:
self._create_empty_trace()
return
self.file = file
# Set the filesize if necessary.
if filesize:
self.filesize = filesize
else:
if isinstance(self.file, io.BytesIO):
_pos = self.file.tell()
self.file.seek(0, 2)
self.filesize = self.file.tell()
self.file.seek(_pos)
else:
self.filesize = os.fstat(self.file.fileno())[6]

"""
self.file.

unpacked during reading the file. Has a huge impact on the memory
usage and the performance. They can be unpacked on-the-fly after
:param headonly: Determines whether or not the actual data records
will be read and unpacked. Has a huge impact on memory usage. Data
will not be unpackable on-the-fly after reading the file.
Defaults to False.
"""
# Check if it is smaller than 240 byte.
msg = 'The trace header needs to be 240 bytes long'
endian=self.endian,
# The number of samples in the current trace.
self.npts = npts
# Do a sanity check if there is enough data left.
pos = self.file.tell()
data_left = self.filesize - pos
data_needed = DATA_SAMPLE_FORMAT_SAMPLE_SIZE[self.data_encoding] * \
npts
if npts < 1 or data_needed > data_left:
msg = """
Too little data left in the file to unpack it according to
its trace header. This is most likely either due to a wrong
byte order or a corrupt file.
""".strip()
self.file.seek(data_needed, 1)
# build a function for reading data from the disk on the fly
self.unpack_data = OnTheFlyDataUnpacker(
DATA_SAMPLE_FORMAT_UNPACK_FUNCTIONS[self.data_encoding],
self.file.name, self.file.mode, pos, npts, endian=self.endian)
else:
# Unpack the data.
self.data = DATA_SAMPLE_FORMAT_UNPACK_FUNCTIONS[
self.data_encoding](self.file, npts, endian=self.endian)

[docs]    def write(self, file, data_encoding=None, endian=None):
"""
Writes the Trace to a file like object.

If endian or data_encoding is set, these values will be enforced.
Otherwise use the values of the SEGYTrace object.
"""
# Set the data length in the header before writing it.

if data_encoding is None:
data_encoding = self.data_encoding
if endian is None:
endian = self.endian
# Write the data.
if self.data is None:
msg = "No data in the SEGYTrace."
raise SEGYWritingError(msg)
DATA_SAMPLE_FORMAT_PACK_FUNCTIONS[data_encoding](file, self.data,
endian=endian)

[docs]    def _create_empty_trace(self):
"""
Creates an empty trace with an empty header.
"""
self.data = np.zeros(0, dtype=np.float32)

[docs]    def __str__(self):
"""
Print some information about the trace.
"""
ret_val = 'Trace sequence number within line: %i\n' % \
ret_val += '%i samples, dtype=%s, %.2f Hz' % (
len(self.data),
self.data.dtype, 1.0 /
float(1E6)))
return ret_val

[docs]    def _repr_pretty_(self, p, cycle):
p.text(str(self))

[docs]    def __getattr__(self, name):
"""
This method is only called if the attribute is not found in the usual
places (i.e. not an instance attribute or not found in the class tree
for self).
"""
if name == 'data':
# Use data unpack function to unpack data on the fly
if hasattr(self, 'unpack_data'):
return self.unpack_data()
else:
msg = """
Attempted to unpack trace data on the fly with
self.unpack_data(), but function does not exist.
""".strip()
raise SEGYTraceOnTheFlyDataUnpackingError(msg)
else:
msg = "'%s' object has no attribute '%s'" % \
(self.__class__.__name__, name)
raise AttributeError(msg)

"""
Convert the current Trace to an ObsPy Trace object.

"""
# Import here to avoid circular imports.
from .core import LazyTraceHeaderAttribDict  # NOQA

# Create new Trace object for every segy trace and append to the Stream
# object.
trace = Trace()
# skip data if headonly is set
trace.stats.npts = self.npts
else:
trace.data = self.data
trace.stats.segy = AttribDict()
# If all values will be unpacked create a normal dictionary.
else:
# The sampling rate should be set for every trace. It is a sample
# interval in microseconds. The only sanity check is that is should be
# larger than 0.
trace.stats.delta = \
1E6
# If the year is not zero, calculate the start time. The end time is
# then calculated from the start time and the sampling rate.
# The SEG Y rev 0 standard specifies the year to be a 4 digit
# number.  Before that it was unclear if it should be a 2 or 4
# digit number. Old or wrong software might still write 2 digit
# years. Every number <30 will be mapped to 2000-2029 and every
# number between 30 and 99 will be mapped to 1930-1999.
if year < 100:
if year < 30:
year += 2000
else:
year += 1900
# work around some strange SEGY files that don't store proper
# start date/time but only a year (see #1722)
if julday == 0 and hour == 0 and minute == 0 and second == 0:
msg = ('Trace starttime does not store a proper date (day '
'of year is zero). Using January 1st 00:00 as '
'trace start time.')
warnings.warn(msg)
julday = 1
trace.stats.starttime = UTCDateTime(
year=year, julday=julday, hour=hour, minute=minute,
second=second)
return trace

"""
"""
"""
Will take the 240 byte of the trace header and unpack all values with
the given endianness.

If header is None, a trace header with all values set to 0 will be
created
:type big_endian: bool
:param big_endian: True means the header is encoded in big endian and
False corresponds to a little endian header.
unpacked during reading the file. Has a huge impact on the memory
usage and the performance. They can be unpacked on-the-fly after
"""
self.endian = endian
return
# Check the length of the string,
msg = 'The trace header needs to be 240 bytes long'
# Either unpack the header or just append the unpacked header. This is
# much faster and can later be unpacked on the fly.
else:

"""
corresponding class attributes.
"""
# Set the start position.
pos = 0
# Loop over all items in the TRACE_HEADER_FORMAT list which is supposed
# to be in the correct order.
length, name, special_format, _ = item
string = header[pos: pos + length]
pos += length
length, special_format))

[docs]    def write(self, file, endian=None):
"""
Writes the header to an open file like object.
"""
if endian is None:
endian = self.endian
length, name, special_format, _ = item
# Use special format if necessary.
if special_format:
format = ('%s%s' % (endian,
special_format)).encode('ascii',
'strict')
file.write(pack(format, getattr(self, name)))
# Pack according to different lengths.
elif length == 2:
format = ('%sh' % endian).encode('ascii', 'strict')
file.write(pack(format, getattr(self, name)))
# Update: Seems to be correct. Two's complement integers seem to be
# the common way to store integer values.
elif length == 4:
format = ('%si' % endian).encode('ascii', 'strict')
file.write(pack(format, getattr(self, name)))
# Just the one unassigned field.
elif length == 8:
field = getattr(self, name)
# An empty field will have a zero.
if field == 0:
field = 2 * pack(('%si' % endian).encode('ascii',
'strict'), 0)
file.write(field)
# Should not happen.
else:
raise Exception

[docs]    def __getattr__(self, name):
"""
This method is only called if the attribute is not found in the usual
places (i.e. not an instance attribute or not found in the class tree
for self).
"""
try:
except ValueError:
msg = "'%s' object has no attribute '%s'" % \
(self.__class__.__name__, name)
raise AttributeError(msg)
# Unpack the one value and set the class attribute so it will does not
# have to unpacked again if accessed in the future.
length, name, special_format, start = TRACE_HEADER_FORMAT[index]
string = self.unpacked_header[start: start + length]
special_format)
setattr(self, name, attribute)
return attribute

[docs]    def __str__(self):
"""
"""
retval = ''
for _, name, _, _ in TRACE_HEADER_FORMAT:
# Do not print the unassigned value.
if name == 'unassigned':
continue
retval += '%s: %i\n' % (name, getattr(self, name))
return retval

[docs]    def _repr_pretty_(self, p, cycle):
p.text(str(self))

"""
Init the trace header with zeros.
"""
# First set all fields to zero.
setattr(self, field[1], 0)

"""
Reads a SEG Y file and returns a SEGYFile object.

:param file: Open file like object or a string which will be assumed to be
a filename.
:type endian: str
:param endian: String that determines the endianness of the file. Either
'>' for big endian or '<' for little endian. If it is None,
obspy.io.segy will try to autodetect the endianness. The endianness
is always valid for the whole file.
Either 'EBCDIC', 'ASCII' or None. If it is None, autodetection will
be attempted.
unpacked during reading the file. Has a huge impact on the memory usage
and the performance. They can be unpacked on-the-fly after being read.
Defaults to False.
:param headonly: Determines whether or not the actual data records will be
read and unpacked. Has a huge impact on memory usage. Data will not be
unpackable on-the-fly after reading the file. Defaults to False.
"""
# Open the file if it is not a file like object.
if not hasattr(file, 'read') or not hasattr(file, 'tell') or not \
hasattr(file, 'seek'):
with open(file, 'rb') as open_file:
open_file, endian=endian,

"""
Reads on open file object and returns a SEGYFile object.

:param file: Open file like object.
:type endian: str
:param endian: String that determines the endianness of the file. Either
'>' for big endian or '<' for little endian. If it is None,
obspy.io.segy will try to autodetect the endianness. The endianness
is always valid for the whole file.
Either 'EBCDIC', 'ASCII' or None. If it is None, autodetection will
be attempted.
unpacked during reading the file. Has a huge impact on the memory usage
and the performance. They can be unpacked on-the-fly after being read.
Defaults to False.
:param headonly: Determines whether or not the actual data records will be
read and unpacked. Has a huge impact on memory usage. Data will not be
unpackable on-the-fly after reading the file. Defaults to False.
"""
return SEGYFile(file, endian=endian,

"""
Iteratively read a SEG-Y field and yield single ObsPy Traces.

The function iteratively loops over the whole file and yields single
ObsPy Traces. The next Trace will be read after the current loop has
finished - this function is thus suitable for reading arbitrarily large
SEG-Y files without running into memory problems.

>>> from obspy.core.util import get_example_file
>>> filename = get_example_file("00001034.sgy_first_trace")
...     # Each Trace's stats attribute will have references to the file
...     de = tr.stats.segy.data_encoding
...     e = tr.stats.segy.endian
...     # Also do something meaningful with each Trace.
...     print(int(tr.data.sum() * 1E9))
-5

:param file: Open file like object or a string which will be assumed to be
a filename.
:type endian: str
:param endian: String that determines the endianness of the file. Either
'>' for big endian or '<' for little endian. If it is None,
obspy.io.segy will try to autodetect the endianness. The endianness
is always valid for the whole file.
Either 'EBCDIC', 'ASCII' or None. If it is None, autodetection will
be attempted.
unpacked during reading the file. Has a huge impact on the memory usage
and the performance. They can be unpacked on-the-fly after being read.
Defaults to False.
:param headonly: Determines whether or not the actual data records will be
read and unpacked. Has a huge impact on memory usage. Data will not be
unpackable on-the-fly after reading the file. Defaults to False.
"""
# Open the file if it is not a file like object.
if not hasattr(file, 'read') or not hasattr(file, 'tell') or not \
hasattr(file, 'seek'):
with open(file, 'rb') as open_file:
open_file, endian=endian,
yield tr
return
file, endian=endian,
yield tr

"""
Iteratively read a SEG-Y field and yield single ObsPy Traces.
"""
segy_file = SEGYFile(
yield_each_trace=True):
# Fill stats that are normally attached to the stream stats.
tr.stats.segy.data_encoding = trace.data_encoding
tr.stats.segy.endian = trace.endian
tr.stats._format = "SEGY"
yield tr

"""
Iteratively read a SU field and yield single ObsPy Traces.

The function iteratively loops over the whole file and yields single
ObsPy Traces. The next Trace will be read after the current loop has
finished - this function is thus suitable for reading arbitrarily large
SU files without running into memory problems.

>>> from obspy.core.util import get_example_file
>>> filename = get_example_file("1.su_first_trace")
...     # Each Trace's stats attribute will have some file-wide
...     # information.
...     de = tr.stats.su.data_encoding
...     e = tr.stats.su.endian
...     # Also do something meaningful with each Trace.
...     print(int(tr.data.sum()))
-26121

:param file: Open file like object or a string which will be assumed to be
a filename.
:type endian: str
:param endian: String that determines the endianness of the file. Either
'>' for big endian or '<' for little endian. If it is None,
obspy.io.segy will try to autodetect the endianness. The endianness
is always valid for the whole file.
unpacked during reading the file. Has a huge impact on the memory usage
and the performance. They can be unpacked on-the-fly after being read.
Defaults to False.
:param headonly: Determines whether or not the actual data records will be
read and unpacked. Has a huge impact on memory usage. Data will not be
unpackable on-the-fly after reading the file. Defaults to False.
"""
# Open the file if it is not a file like object.
if not hasattr(file, 'read') or not hasattr(file, 'tell') or not \
hasattr(file, 'seek'):
with open(file, 'rb') as open_file:
open_file, endian=endian,
yield tr
return
file, endian=endian,
yield tr

"""
Iteratively read a SU field and yield single ObsPy Traces.
"""
su_file = SUFile(
yield_each_trace=True):
tr.stats.su = tr.stats.segy
del tr.stats.segy
# Fill stats that are normally attached to the stream stats.
tr.stats.su.data_encoding = trace.data_encoding
tr.stats.su.endian = trace.endian
tr.stats._format = "SU"
yield tr

[docs]class SUFile(object):
"""
Convenience class that internally handles Seismic Unix data files. It
currently can only read IEEE 4 byte float encoded SU data files.
"""
[docs]    def __init__(self, file=None, endian=None, unpack_headers=False,
"""
:param file: A file like object with the file pointer set at the
beginning of the SEG Y file. If file is None, an empty SEGYFile
object will be initialized.

:param endian: The endianness of the file. If None, autodetection will
be used.
unpacked during reading the file. Has a huge impact on the memory
usage and the performance. They can be unpacked on-the-fly after
:param headonly: Determines whether or not the actual data records
will be read and unpacked. Has a huge impact on memory usage. Data
will not be unpackable on-the-fly after reading the file.
Defaults to False.
:param read_traces: Data traces will only be read if this is set to
True. The data will be completely ignored if this is set to
False.
"""
if file is None:
self._create_empty_su_file_object()
return
# Set the endianness to big.
if endian is None:
self.endian = '>'
else:
self.endian = ENDIAN[endian]
return
self.file = file
# If endian is None autodetect is.
if not endian:
self._autodetect_endianness()
else:
self.endian = ENDIAN[endian]

[docs]    def _autodetect_endianness(self):
"""
Tries to automatically determine the endianness of the file at hand.
"""
self.endian = autodetect_endian_and_sanity_check_su(self.file)
if self.endian is False:
msg = 'Autodetection of Endianness failed. Please specify it ' + \
'by hand or contact the developers.'
raise Exception(msg)

[docs]    def _create_empty_su_file_object(self):
"""
Creates an empty SUFile object.
"""
self.traces = []

[docs]    def __str__(self):
"""
Prints some information about the SU file.
"""
return '%i traces in the SU structure.' % len(self.traces)

[docs]    def _repr_pretty_(self, p, cycle):
p.text(str(self))

yield_each_trace=False):
"""
Reads the actual traces starting at the current file pointer position
to the end of the file.

unpacked during reading the file. Has a huge impact on the memory
usage and the performance. They can be unpacked on-the-fly after
:param headonly: Determines whether or not the actual data records
will be unpacked. Useful if one is just interested in the headers.
Data will not be unpackable on-the-fly after reading the file.
Defaults to False.
:type yield_each_trace: bool
:param yield_each_trace: If True, it will yield each trace after it
has been read. This enables a simple implementation of a
longer be collected in self.traces list if this is set to
True.
"""
self.traces = []
# Big loop to read all data traces.
while True:
# Read and as soon as the trace header is too small abort.
try:
# Always unpack with IEEE
trace = SEGYTrace(self.file, 5, self.endian,
if yield_each_trace:
yield trace
else:
self.traces.append(trace)
break

[docs]    def write(self, file, endian=None):
"""
Write a SU Y file to file which is either a file like object with a
write method or a filename string.

If endian is set it will be enforced.
"""
if not hasattr(file, 'write'):
with open(file, 'wb') as file:
self._write(file, endian=endian)
return
self._write(file, endian=endian)

[docs]    def _write(self, file, endian=None):
"""
Write a SU Y file to file which is either a file like object with a
write method or a filename string.

If endian is set it will be enforced.
"""
# Write all traces.
for trace in self.traces:
trace.write(file, data_encoding=5, endian=endian)

"""
Reads a Seismic Unix (SU) file and returns a SUFile object.

:param file: Open file like object or a string which will be assumed to be
a filename.
:type endian: str
:param endian: String that determines the endianness of the file. Either
'>' for big endian or '<' for little endian. If it is None,
obspy.io.segy will try to autodetect the endianness. The endianness
is always valid for the whole file.
unpacked during reading the file. Has a huge impact on the memory usage
and the performance. They can be unpacked on-the-fly after being read.
Defaults to False.
:param headonly: Determines whether or not the actual data records will be
unpacked. Useful if one is just interested in the headers. Defaults to
False.
"""
# Open the file if it is not a file like object.
if not hasattr(file, 'read') or not hasattr(file, 'tell') or not \
hasattr(file, 'seek'):
with open(file, 'rb') as open_file:

"""
Reads on open file object and returns a SUFile object.

:param file: Open file like object.
:type endian: str
:param endian: String that determines the endianness of the file. Either
'>' for big endian or '<' for little endian. If it is None,
obspy.io.segy will try to autodetect the endianness. The endianness
is always valid for the whole file.
unpacked during reading the file. Has a huge impact on the memory usage
and the performance. They can be unpacked on-the-fly after being read.
Defaults to False.
:param headonly: Determines whether or not the actual data records will be
unpacked. Useful if one is just interested in the headers. Defaults to
False.
"""

[docs]def autodetect_endian_and_sanity_check_su(file):
"""
Takes an open file and tries to determine the endianness of a Seismic
Unix data file by doing some sanity checks with the unpacked header values.

Returns False if the sanity checks failed and the endianness otherwise.

It is assumed that the data is written as 32bit IEEE floating points in
either little or big endian.

The test currently can only identify SU files in which all traces have the
same length. It basically just makes a sanity check for various fields in
"""
pos = file.tell()
if isinstance(file, io.BytesIO):
file.seek(0, 2)
size = file.tell()
file.seek(pos, 0)
else:
size = os.fstat(file.fileno())[6]
if size < 244:
return False
# Also has to be a multiple of 4 in length because every header is 400 long
# and every data value 4 byte long.
elif (size % 4) != 0:
return False
file.seek(114, 0)
file.seek(156, 0)
file.seek(pos, 0)
# Unpack in little and big endian.
le_sample_count = unpack(b'<h', sample_count)[0]
be_sample_count = unpack(b'>h', sample_count)[0]
# Check if both work.
working_byteorders = []
if le_sample_count > 0:
length = 240 + (le_sample_count * 4)
if (size % length) == 0:
working_byteorders.append('<')
if be_sample_count > 0:
length = 240 + (be_sample_count * 4)
if (size % length) == 0:
working_byteorders.append('>')
# If None works return False.
if len(working_byteorders) == 0:
return False
# Check if the other header values make sense.
still_working_byteorders = []
for bo in working_byteorders:
fmt = ("%sh" % bo).encode('ascii', 'strict')
this_interval = unpack(fmt, interval)[0]
this_year = unpack(fmt, year)[0]
this_julday = unpack(fmt, jul_day)[0]
this_hour = unpack(fmt, hour)[0]
this_minute = unpack(fmt, minute)[0]
this_second = unpack(fmt, second)[0]
# Make a sanity check for each.
# XXX: The arbitrary maximum of the sample interval is 10 seconds.
if this_interval <= 0 or this_interval > 10E7:
continue
# Some programs write two digit years.
if this_year != 0 and (this_year < 1930 or this_year >= 2030) and \
(this_year < 0 or this_year >= 100):
continue
# 9999 is often used as a placeholder
if (this_julday > 366 or this_julday < 0) and this_julday != 9999:
continue
if this_hour > 24 or this_hour < 0:
continue
if this_minute > 60 or this_minute < 0:
continue
if this_second > 60 or this_second < 0:
continue
still_working_byteorders.append(bo)
length = len(still_working_byteorders)
if not length:
return False
elif length == 1:
return still_working_byteorders[0]
else:
# XXX: In the unlikely case both byte orders pass the sanity checks
# something else should be checked. Currently it is not.
msg = """