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

from .header import (BINARY_FILE_HEADER_FORMAT,
                     DATA_SAMPLE_FORMAT_PACK_FUNCTIONS,
                     DATA_SAMPLE_FORMAT_SAMPLE_SIZE,
                     DATA_SAMPLE_FORMAT_UNPACK_FUNCTIONS, ENDIAN,
                     TRACE_HEADER_FORMAT, TRACE_HEADER_KEYS)
from .unpack import OnTheFlyDataUnpacker
from .util import unpack_header_value


[docs]class SEGYError(Exception): """ Base SEGY exception class. """ pass
[docs]class SEGYTraceHeaderTooSmallError(SEGYError): """ Raised if the trace header is not the required 240 byte long. """ pass
[docs]class SEGYTraceReadingError(SEGYError): """ Raised if there is not enough data left in the file to unpack the data according to the values read from the header. """ 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
[docs]class SEGYInvalidTextualHeaderWarning(SEGYWarning): """ 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, unpack_headers=False, headonly=False, read_traces=True): """ 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. :param textual_header_encoding: The encoding of the textual header. 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'. :type unpack_headers: bool :param unpack_headers: Determines whether or not all headers will be 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. :type headonly: bool :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. :type read_traces: bool :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. if textual_header_encoding is None: self.textual_header_encoding = 'ASCII' self.textual_header = b'' 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. self.textual_header_encoding = textual_header_encoding # Read the headers. self._read_headers() # Read the actual traces. if read_traces: [i for i in self._read_traces( unpack_headers=unpack_headers, headonly=headonly)]
[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() # Jump to the data sample format code. self.file.seek(3224, 1) format = unpack(b'>h', self.file.read(2))[0] # Check if valid. if format in DATA_SAMPLE_FORMAT_UNPACK_FUNCTIONS.keys(): self.endian = '>' # Else test little endian. else: self.file.seek(-2, 1) format = unpack(b'<h', self.file.read(2))[0] if format in DATA_SAMPLE_FORMAT_UNPACK_FUNCTIONS.keys(): self.endian = '<' else: msg = 'Unable to determine the endianness of the file. ' + \ 'Please specify it.' raise SEGYError(msg) # Jump to previous position. self.file.seek(pos, 0)
[docs] def _create_empty_segy_file_object(self): """ Creates an empty SEGYFile object. """ self.textual_file_header = b'' self.binary_file_header = None self.traces = []
[docs] def _read_textual_header(self): """ Reads the textual header. """ # The first 3200 byte are the textual header. textual_header = self.file.read(3200) # 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. if not self.textual_header_encoding: if not (b'C' in (textual_header[0:1], textual_header[3040:3041], textual_header[3120:3120])): try: textual_header = \ textual_header.decode('EBCDIC-CP-BE').encode('ascii') # If this worked, the encoding is EBCDIC. self.textual_header_encoding = 'EBCDIC' except UnicodeEncodeError: textual_header = textual_header # Otherwise it is ASCII. self.textual_header_encoding = 'ASCII' else: # Otherwise the encoding will also be ASCII. self.textual_header_encoding = 'ASCII' elif self.textual_header_encoding.upper() == 'EBCDIC': textual_header = \ textual_header.decode('EBCDIC-CP-BE').encode('ascii') elif self.textual_header_encoding.upper() != '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. self.textual_file_header = textual_header
[docs] def _read_headers(self): """ Reads the textual and binary file headers starting at the current file pointer position. """ # Read the textual header. self._read_textual_header() # The next 400 bytes are from the Binary File Header. binary_file_header = self.file.read(400) bfh = SEGYBinaryFileHeader(binary_file_header, self.endian) self.binary_file_header = bfh self.data_encoding = self.binary_file_header.data_sample_format_code # If bytes 3506-3506 are not zero, an extended textual header follows # which is not supported so far. if bfh.number_of_3200_byte_ext_file_header_records_following != 0: msg = 'Extended textual headers are not yet supported. ' + \ 'Please contact the developers.' 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 the textual header. self._write_textual_header(file) # 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! if self.binary_file_header.number_of_data_traces_per_ensemble <= 0: self.binary_file_header.number_of_data_traces_per_ensemble = \ len(self.traces) if self.binary_file_header.sample_interval_in_microseconds <= 0: self.binary_file_header.sample_interval_in_microseconds = \ self.traces[0].header.sample_interval_in_ms_for_this_trace if self.binary_file_header.number_of_samples_per_data_trace <= 0: self.binary_file_header.number_of_samples_per_data_trace = \ len(self.traces[0].data) # Always set the SEGY Revision number to 1.0 (hex-coded). self.binary_file_header.seg_y_format_revision_number = 256 # 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: self.binary_file_header.fixed_length_trace_flag = 0 # Extended textual headers are not supported by ObsPy so far. self.binary_file_header.\ number_of_3200_byte_ext_file_header_records_following = 0 # Enforce the encoding if data_encoding: self.binary_file_header.data_sample_format_code = data_encoding # Write the binary header. self.binary_file_header.write(file, endian=endian) # Write all traces. for trace in self.traces: trace.write(file, data_encoding=data_encoding, endian=endian)
[docs] def _write_textual_header(self, file): """ Write the textual header in various encodings. The encoding will depend on self.textual_header_encoding. If self.textual_file_header is too small it will be padded with zeros. If it is too long or an invalid encoding is specified an exception will be raised. """ textual_header = self.textual_file_header # 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. if hasattr(textual_header, "encode"): textual_header = textual_header.encode() length = len(textual_header) # Append spaces to the end if its too short. if length < 3200: textual_header = textual_header + b' ' * (3200 - length) elif length == 3200: textual_header = textual_header # 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. enc = self.textual_header_encoding.upper() # 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. # Make sure the textual header has the required fields. revision_number = textual_header[3200-160:3200-146].decode() end_header_mark = textual_header[3200-80:3200-58] if revision_number != "C39 SEG Y REV1": if revision_number.strip() in ("", "C", "C39"): textual_header = textual_header[:3200-160] + \ 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) warnings.warn(msg, SEGYInvalidTextualHeaderWarning) desired_end_header_mark = b"C40 END TEXTUAL HEADER" if enc == "ASCII" \ else b"C40 END EBCDIC " if end_header_mark != desired_end_header_mark: if end_header_mark.strip() in (b"", b"C", b"C40"): textual_header = textual_header[:3200-80] + \ desired_end_header_mark + textual_header[3200-58:] 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." % end_header_mark.decode()) warnings.warn(msg, SEGYInvalidTextualHeaderWarning) # Finally encode the header if necessary. if enc == 'ASCII': pass elif enc == 'EBCDIC': textual_header = \ textual_header.decode('ascii').encode('EBCDIC-CP-BE') # Should not happen. else: msg = 'self.textual_header_encoding has to be either ASCII or ' + \ 'EBCDIC.' raise SEGYWritingError(msg) file.write(textual_header)
[docs] def _read_traces(self, unpack_headers=False, headonly=False, yield_each_trace=False): """ Reads the actual traces starting at the current file pointer position to the end of the file. :type unpack_headers: bool :param unpack_headers: Determines whether or not all headers will be 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. :type headonly: bool :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 streaming interface to read SEG-Y files. Read traces will no 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, unpack_headers=unpack_headers, filesize=filesize, headonly=headonly) if yield_each_trace: yield trace else: self.traces.append(trace) except SEGYTraceHeaderTooSmallError: break
[docs]class SEGYBinaryFileHeader(object): """ Parses the binary file header at the given starting position. """
[docs] def __init__(self, header=None, endian='>'): """ """ self.endian = endian if header is None: self._create_empty_binary_file_header() return self._read_binary_file_header(header)
[docs] def _read_binary_file_header(self, header): """ Reads the binary file header and stores every value in a class attribute. """ pos = 0 for item in BINARY_FILE_HEADER_FORMAT: 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 = ["Binary File Header:"] for item in BINARY_FILE_HEADER_FORMAT: 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 for item in BINARY_FILE_HEADER_FORMAT: 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
[docs] def _create_empty_binary_file_header(self): """ 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='>', unpack_headers=False, filesize=None, headonly=False): """ 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 binary file header: 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. :type unpack_headers: bool :param unpack_headers: Determines whether or not all headers will be 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. :type filesize: int :param filesize: Filesize of the file. If not given it will be determined using fstat which is slow. :param headonly: bool :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] # Otherwise read the file. self._read_trace(unpack_headers=unpack_headers, headonly=headonly)
[docs] def _read_trace(self, unpack_headers=False, headonly=False): """ Reads the complete next header starting at the file pointer at self.file. :type unpack_headers: bool :param unpack_headers: Determines whether or not all headers will be 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. :type headonly: bool :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. """ trace_header = self.file.read(240) # Check if it is smaller than 240 byte. if len(trace_header) != 240: msg = 'The trace header needs to be 240 bytes long' raise SEGYTraceHeaderTooSmallError(msg) self.header = SEGYTraceHeader(trace_header, endian=self.endian, unpack_headers=unpack_headers) # The number of samples in the current trace. npts = self.header.number_of_samples_in_this_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() raise SEGYTraceReadingError(msg) if headonly: # skip reading the data, but still advance the file 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. self.header.number_of_samples_in_this_trace = len(self.data) # Write the header. self.header.write(file, endian=endian) 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) self.header = SEGYTraceHeader(header=None, endian=self.endian)
[docs] def __str__(self): """ Print some information about the trace. """ ret_val = 'Trace sequence number within line: %i\n' % \ self.header.trace_sequence_number_within_line ret_val += '%i samples, dtype=%s, %.2f Hz' % ( len(self.data), self.data.dtype, 1.0 / (self.header.sample_interval_in_ms_for_this_trace / 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)
[docs] def to_obspy_trace(self, unpack_trace_headers=False, headonly=False): """ Convert the current Trace to an ObsPy Trace object. :param unpack_trace_headers: """ # 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 if headonly: trace.stats.npts = self.npts else: trace.data = self.data trace.stats.segy = AttribDict() # If all values will be unpacked create a normal dictionary. if unpack_trace_headers: # Add the trace header as a new attrib dictionary. header = AttribDict() for key, value in self.header.__dict__.items(): setattr(header, key, value) # Otherwise use the LazyTraceHeaderAttribDict. else: # Add the trace header as a new lazy attrib dictionary. header = LazyTraceHeaderAttribDict(self.header.unpacked_header, self.header.endian) trace.stats.segy.trace_header = header # 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. tr_header = trace.stats.segy.trace_header if tr_header.sample_interval_in_ms_for_this_trace > 0: trace.stats.delta = \ float(self.header.sample_interval_in_ms_for_this_trace) / \ 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. if tr_header.year_data_recorded > 0: year = tr_header.year_data_recorded # 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 julday = tr_header.day_of_year hour = tr_header.hour_of_day minute = tr_header.minute_of_hour second = tr_header.second_of_minute # 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
[docs]class SEGYTraceHeader(object): """ Convenience class that handles reading and writing of the trace headers. """
[docs] def __init__(self, header=None, endian='>', unpack_headers=False): """ Will take the 240 byte of the trace header and unpack all values with the given endianness. :type header: str :param header: String that contains the packed binary header values. 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. :type unpack_headers: bool :param unpack_headers: Determines whether or not all headers will be 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. """ self.endian = endian if header is None: self._create_empty_trace_header() return # Check the length of the string, if len(header) != 240: msg = 'The trace header needs to be 240 bytes long' raise SEGYTraceHeaderTooSmallError(msg) # Either unpack the header or just append the unpacked header. This is # much faster and can later be unpacked on the fly. if not unpack_headers: self.unpacked_header = header else: self.unpacked_header = None self._read_trace_header(header)
[docs] def _read_trace_header(self, header): """ Reads the 240 byte long header and unpacks all values into 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. for item in TRACE_HEADER_FORMAT: length, name, special_format, _ = item string = header[pos: pos + length] pos += length setattr(self, name, unpack_header_value(self.endian, string, 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 for item in TRACE_HEADER_FORMAT: 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: index = TRACE_HEADER_KEYS.index(name) # If not found raise an attribute error. 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] attribute = unpack_header_value(self.endian, string, length, special_format) setattr(self, name, attribute) return attribute
[docs] def __str__(self): """ Just returns all header values. """ 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))
[docs] def _create_empty_trace_header(self): """ Init the trace header with zeros. """ # First set all fields to zero. for field in TRACE_HEADER_FORMAT: setattr(self, field[1], 0)
[docs]def _read_segy(file, endian=None, textual_header_encoding=None, unpack_headers=False, headonly=False): """ 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. :param textual_header_encoding: The encoding of the textual header. Either 'EBCDIC', 'ASCII' or None. If it is None, autodetection will be attempted. :type unpack_headers: bool :param unpack_headers: Determines whether or not all headers will be 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. :type headonly: bool :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: return _internal_read_segy( open_file, endian=endian, textual_header_encoding=textual_header_encoding, unpack_headers=unpack_headers, headonly=headonly) # Otherwise just read it. return _internal_read_segy(file, endian=endian, textual_header_encoding=textual_header_encoding, unpack_headers=unpack_headers, headonly=headonly)
[docs]def _internal_read_segy(file, endian=None, textual_header_encoding=None, unpack_headers=False, headonly=False): """ 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. :param textual_header_encoding: The encoding of the textual header. Either 'EBCDIC', 'ASCII' or None. If it is None, autodetection will be attempted. :type unpack_headers: bool :param unpack_headers: Determines whether or not all headers will be 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. :type headonly: bool :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, textual_header_encoding=textual_header_encoding, unpack_headers=unpack_headers, headonly=headonly)
[docs]def iread_segy(file, endian=None, textual_header_encoding=None, unpack_headers=False, headonly=False): """ 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") >>> from obspy.io.segy.segy import iread_segy >>> for tr in iread_segy(filename): ... # Each Trace's stats attribute will have references to the file ... # headers and some more information. ... tf = tr.stats.segy.textual_file_header ... bf = tr.stats.segy.binary_file_header ... tfe = tr.stats.segy.textual_file_header_encoding ... 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. :param textual_header_encoding: The encoding of the textual header. Either 'EBCDIC', 'ASCII' or None. If it is None, autodetection will be attempted. :type unpack_headers: bool :param unpack_headers: Determines whether or not all headers will be 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. :type headonly: bool :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: for tr in _internal_iread_segy( open_file, endian=endian, textual_header_encoding=textual_header_encoding, unpack_headers=unpack_headers, headonly=headonly): yield tr return # Otherwise just read it. for tr in _internal_iread_segy( file, endian=endian, textual_header_encoding=textual_header_encoding, unpack_headers=unpack_headers, headonly=headonly): yield tr
[docs]def _internal_iread_segy(file, endian=None, textual_header_encoding=None, unpack_headers=False, headonly=False): """ Iteratively read a SEG-Y field and yield single ObsPy Traces. """ segy_file = SEGYFile( file, endian=endian, textual_header_encoding=textual_header_encoding, unpack_headers=unpack_headers, headonly=headonly, read_traces=False) for trace in segy_file._read_traces(unpack_headers=unpack_headers, headonly=headonly, yield_each_trace=True): tr = trace.to_obspy_trace(unpack_trace_headers=unpack_headers, headonly=headonly) # Fill stats that are normally attached to the stream stats. tr.stats.segy.textual_file_header = segy_file.textual_file_header tr.stats.segy.binary_file_header = segy_file.binary_file_header tr.stats.segy.textual_file_header_encoding = \ segy_file.textual_header_encoding.upper() tr.stats.segy.data_encoding = trace.data_encoding tr.stats.segy.endian = trace.endian tr.stats._format = "SEGY" yield tr
[docs]def iread_su(file, endian=None, unpack_headers=False, headonly=False): """ 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") >>> from obspy.io.segy.segy import iread_su >>> for tr in iread_su(filename): ... # 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. :type unpack_headers: bool :param unpack_headers: Determines whether or not all headers will be 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. :type headonly: bool :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: for tr in _internal_iread_su( open_file, endian=endian, unpack_headers=unpack_headers, headonly=headonly): yield tr return # Otherwise just read it. for tr in _internal_iread_su( file, endian=endian, unpack_headers=unpack_headers, headonly=headonly): yield tr
[docs]def _internal_iread_su(file, endian=None, unpack_headers=False, headonly=False): """ Iteratively read a SU field and yield single ObsPy Traces. """ su_file = SUFile( file, endian=endian, unpack_headers=unpack_headers, headonly=headonly, read_traces=False) for trace in su_file._read_traces(unpack_headers=unpack_headers, headonly=headonly, yield_each_trace=True): tr = trace.to_obspy_trace(unpack_trace_headers=unpack_headers, headonly=headonly) 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, headonly=False, read_traces=True): """ :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. :type unpack_header: bool :param unpack_header: Determines whether or not all headers will be 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. :type headonly: bool :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 read_traces: bool :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] if read_traces: # Read the actual traces. [i for i in self._read_traces(unpack_headers=unpack_headers, headonly=headonly)]
[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))
[docs] def _read_traces(self, unpack_headers=False, headonly=False, yield_each_trace=False): """ Reads the actual traces starting at the current file pointer position to the end of the file. :type unpack_header: bool :param unpack_header: Determines whether or not all headers will be 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. :type headonly: bool :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 streaming interface to read SEG-Y files. Read traces will no 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, unpack_headers=unpack_headers, headonly=headonly) if yield_each_trace: yield trace else: self.traces.append(trace) except SEGYTraceHeaderTooSmallError: 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)
[docs]def _read_su(file, endian=None, unpack_headers=False, headonly=False): """ 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. :type unpack_header: bool :param unpack_header: Determines whether or not all headers will be 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. :type headonly: bool :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: return _internal_read_su(open_file, endian=endian, unpack_headers=unpack_headers, headonly=headonly) # Otherwise just read it. return _internal_read_su(file, endian=endian, unpack_headers=unpack_headers, headonly=headonly)
[docs]def _internal_read_su(file, endian=None, unpack_headers=False, headonly=False): """ 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. :type unpack_header: bool :param unpack_header: Determines whether or not all headers will be 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. :type headonly: bool :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. """ return SUFile(file, endian=endian, unpack_headers=unpack_headers, headonly=headonly)
[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 the Trace header. """ 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 # Jump to the number of samples field in the trace header. file.seek(114, 0) sample_count = file.read(2) interval = file.read(2) # Jump to the beginning of the year fields. file.seek(156, 0) year = file.read(2) jul_day = file.read(2) hour = file.read(2) minute = file.read(2) second = file.read(2) # Jump to previous position. 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 = """ Both possible byte orders passed all sanity checks. Please contact the ObsPy developers so they can implement additional tests. """.strip() raise Exception(msg)