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General cleanup.
This commit is contained in:
Robert Smallshire
@@ -0,0 +1,383 @@
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from __future__ import print_function
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from portability import seekable
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from util import file_length, filename_from_handle
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from datatypes import DATA_SAMPLE_FORMAT, CTYPE_DESCRIPTION, CTYPES
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from toolkit import (extract_revision, bytes_per_sample, read_reel_header, catalog_traces, read_binary_values,
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compile_trace_header_format, TraceHeader, REEL_HEADER_NUM_BYTES, TRACE_HEADER_NUM_BYTES)
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def create_reader(fh, endian='>'):
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"""Create a SegYReader (or one of its subclasses) based on performing a scan of SEG Y data.
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This function is the preferred method for creating SegYReader objects. It reads basic header
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information and attempts to build indexes for traces, CDP numbers (for 2D surveys), and inline
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and cross line co-ordinates (for 3D surveys) to facilitate subsequent random-access to traces.
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Args:
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fh: A file-like-object open in binary mode positioned such that the
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beginning of the reel header will be the next byte to be read. For disk-based
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SEG Y files, this is the beginning of the file.
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endian: '>' for big-endian data (the standard and default), '<' for
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little-endian (non-standard)
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Returns:
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A SegYReader object. Depending on the exact type of the SegYReader returned different capabilities may be
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available. Inspect the returned object to determine these capabilities, or be prepared for capabilities not
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defined in the SegYReader base class to be unavailable. The underlying file-like object must remain open
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for the duration of use of the returned reader object. It is the caller's responsibility to close the
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underlying file.
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Example:
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with open('my_seismic_data.sgy', 'rb') as fh:
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reader = create_reader(fh)
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print(reader.num_traces())
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"""
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if fh.encoding is not None:
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raise TypeError("SegYReader must be provided with a binary mode file object")
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if not seekable(fh):
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raise TypeError("SegYReader must be provided with a seekable file object")
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if fh.closed:
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raise ValueError("SegYReader must be provided with an open file object")
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num_file_bytes = file_length(fh)
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if num_file_bytes < REEL_HEADER_NUM_BYTES:
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raise ValueError("SEG Y file {!r} of {} bytes is too short".format(filename_from_handle(fh),
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num_file_bytes))
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if endian not in ('<', '>'):
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raise ValueError("Unrecognised endian value {!r}".format(endian))
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reel_header = read_reel_header(fh, endian)
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revision = extract_revision(reel_header)
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bps = bytes_per_sample(reel_header, revision)
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trace_catalog, cdp_catalog, line_catalog = catalog_traces(fh, bps, endian)
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if cdp_catalog is not None and line_catalog is None:
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return SegYReader2D(fh, reel_header, trace_catalog, cdp_catalog, endian)
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if cdp_catalog is None and line_catalog is not None:
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return SegYReader3D(fh, reel_header, trace_catalog, line_catalog, endian)
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return SegYReader(fh, reel_header, trace_catalog, endian)
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class SegYReader(object):
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"""A basic SEG Y reader.
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Use to obtain read the reel header, the trace headers or trace values. Traces can be accessed
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only by trace index.
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"""
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def __init__(self, fh, reel_header, trace_catalog, endian='>'):
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"""Initialize a SegYReader around a file-like-object.
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Note:
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Usually a SegYReader is most easily constructed using the create_reader() function.
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Args:
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fh: A file-like object, which must support seeking and support binary reading.
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reel_header: A dictionary containing reel header data.
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trace_catalog: A mapping from zero-based trace index to the byte-offset to
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individual traces within the file.
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endian: '>' for big-endian data (the standard and default), '<' for
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little-endian (non-standard)
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"""
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self._fh = fh
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self._endian = endian
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self._trace_header_format = compile_trace_header_format(self._endian)
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self._reel_header = reel_header
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self._trace_catalog = trace_catalog
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self._revision = extract_revision(self._reel_header)
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self._bytes_per_sample = bytes_per_sample(self._reel_header, self.revision)
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def trace_indexes(self):
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"""An iterator over zero-based trace indexes.
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Returns:
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An iterator which yields integers in the range zero to num_traces() - 1
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"""
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return iter(self._trace_catalog)
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def num_traces(self):
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"""The number of traces"""
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return len(self._trace_catalog)
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def read_trace(self, trace_index):
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"""Read a specific trace.
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Args:
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trace_index: An integer in the range zero to num_traces() - 1
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Returns:
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A 2-tuple containing a TraceHeader as the first item and a sequence of numeric trace samples
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as the second item.
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Example:
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first_trace_header, first_trace_samples = segy_reader.read_trace(0)
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"""
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if not (0 <= trace_index < self.num_traces()):
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raise ValueError("Trace index out of range.")
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trace_header = self.read_trace_header(trace_index)
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num_samples = trace_header.ns
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dsf = self._reel_header['DataSampleFormat']
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ctype = DATA_SAMPLE_FORMAT[dsf]
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pos = self._trace_catalog[trace_index] + TRACE_HEADER_NUM_BYTES
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trace_values = read_binary_values(self._fh, pos, ctype, num_samples, self._endian)
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return trace_header, trace_values
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def read_trace_header(self, trace_index):
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"""Read a specific trace.
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Args:
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trace_index: An integer in the range zero to num_traces() - 1
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Returns:
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A TraceHeader corresponding to the requested trace.
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Example:
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first_trace_header, first_trace_samples = segy_reader.read_trace(0)
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"""
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if not (0 <= trace_index < self.num_traces()):
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raise ValueError("Trace index out of range.")
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pos = self._trace_catalog[trace_index]
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self._fh.seek(pos)
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data = self._fh.read(TRACE_HEADER_NUM_BYTES)
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trace_header = TraceHeader._make(self._trace_header_format.unpack(data))
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return trace_header
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@property
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def dimensionality(self):
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"""The spatial dimensionality of the data.
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Returns:
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3 for 3D seismic volumes, 2 for 2D seismic lines, 1 for a single trace, otherwise 0.
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"""
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return self._dimensionality()
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def _dimensionality(self):
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return 1 if self.num_traces() == 1 else 0
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@property
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def reel_header(self):
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"""The reel header, sometimes known as the binary header.
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Returns:
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A dictionary containing data from the reel header.
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"""
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return self._reel_header
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@property
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def filename(self):
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"""The filename.
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Returns:
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The filename if it could be determined, otherwise '<unknown>'
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"""
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return filename_from_handle(self._fh)
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@property
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def revision(self):
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"""The SEG Y revision.
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Returns:
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Either datatypes.SEGY_REVISION_0 or datatypes.SEGY_REVISION_1
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"""
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return self._revision
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@property
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def bytes_per_sample(self):
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"""The number of bytes per trace sample.
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"""
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return self._bytes_per_sample
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@property
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def data_sample_format(self):
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"""The data type of the samples in machine-readable form.
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Returns:
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One of the values from datatypes.DATA_SAMPLE_FORMAT
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"""
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return DATA_SAMPLE_FORMAT[self._reel_header['DataSampleFormat']]
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@property
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def data_sample_format_description(self):
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"""A descriptive human-readable description of the data sample format
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"""
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return CTYPE_DESCRIPTION[CTYPES[self.data_sample_format]]
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class SegYReader3D(SegYReader):
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"""A reader for 3D seismic data.
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In addition to the capabilities provided by the SegYReader base class, this reader
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provides an index to facilitate random access to individual traces via crossline and
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inline co-ordinates.
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"""
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def __init__(self, fh, reel_header, trace_catalog, line_catalog, endian='>'):
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"""Initialize a SegYReader3D around a file-like-object.
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Note:
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Usually a SegYReader is most easily constructed using the create_reader() function.
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Args:
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fh: A file-like object, which must support seeking and support binary reading.
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reel_header: A dictionary containing reel header data.
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trace_catalog: A mapping from zero-based trace indexes to the byte-offset to
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individual traces within the file.
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line_catalog: A mapping from (xline, inline) tuples to trace_indexes.
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endian: '>' for big-endian data (the standard and default), '<' for
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little-endian (non-standard)
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"""
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super(SegYReader3D, self).__init__(fh, reel_header, trace_catalog, endian)
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self._line_catalog = line_catalog
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def _dimensionality(self):
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return 3
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def num_inlines(self):
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"""The number of distinct inlines in the survey
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"""
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try:
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return self._line_catalog.j_max - self._line_catalog.j_min
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except AttributeError:
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# TODO: Memoize
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return len(set(j for i, j in self._line_catalog))
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def num_xlines(self):
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"""The number of distinct crosslines in the survey
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"""
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try:
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return self._line_catalog.i_max - self._line_catalog.i_min
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except AttributeError:
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# TODO: Memoize
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return len(set(i for i, j in self._line_catalog))
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def inline_xlines(self):
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"""An iterator over all (xline_number, inline_number) tuples corresponding to traces.
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"""
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return iter(self._line_catalog)
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def trace_index(self, xline, inline):
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"""Obtain the trace index given an xline and a inline.
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Note:
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Do not assume that all combinations of crossline and inline co-ordinates are valid.
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The volume may not be rectangular. Valid values can be obtained from the
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inline_xlines() iterator.
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Furthermore, inline and crossline numbers should not be relied upon to be zero- or one-based
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indexes (although they may be).
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Args:
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xline: A crossline number.
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inline: An inline number.
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Returns:
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A trace index which can be used with read_trace().
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"""
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return self._line_catalog[(xline, inline)]
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class SegYReader2D(SegYReader):
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def __init__(self, fh, reel_header, trace_catalog, cdp_catalog, endian='>'):
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"""Initialize a SegYReader2D around a file-like-object.
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Note:
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Usually a SegYReader is most easily constructed using the create_reader() function.
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Args:
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fh: A file-like object, which must support seeking and support binary reading.
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reel_header: A dictionary containing reel header data.
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trace_catalog: A mapping from zero-based trace index to the byte-offset to
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individual traces within the file.
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cdp_catalog: A mapping from CDP numbers to trace_indexes.
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endian: '>' for big-endian data (the standard and default), '<' for
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little-endian (non-standard)
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"""
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super(SegYReader2D, self).__init__(fh, reel_header, trace_catalog, endian)
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self._cdp_catalog = cdp_catalog
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def _dimensionality(self):
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return 2
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def cdp_numbers(self):
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"""An iterator over all cdp numbers corresponding to traces.
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"""
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return iter(self._cdp_catalog)
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def num_cdps(self):
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return len(self._cdp_catalog)
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def trace_index(self, cdp_number):
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"""Obtain the trace index given an xline and a inline.
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Note:
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Do not assume that all combinations of crossline and inline co-ordinates are valid.
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The volume may not be rectangular. Valid values can be obtained from the
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inline_xlines() iterator.
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Furthermore, inline and crossline numbers should not be relied upon to be zero- or one-based
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indexes (although they may be).
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Args:
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xline: A crossline number.
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inline: An inline number.
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Returns:
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A trace index which can be used with read_trace().
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"""
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return self._cdp_catalog[cdp_number]
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def main(argv=None):
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import sys
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if argv is None:
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argv = sys.argv[1:]
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filename = argv[0]
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with open(filename, 'rb') as segy_file:
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segy_reader = create_reader(segy_file)
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print("Filename: ", segy_reader.filename)
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print("SEG Y revision: ", segy_reader.revision)
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print("Number of traces: ", segy_reader.num_traces())
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print("Data format: ", segy_reader.data_sample_format_description)
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print("Dimensionality: ", segy_reader.dimensionality)
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try:
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print("Number of CDPs: ", segy_reader.num_cdps())
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except AttributeError:
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pass
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try:
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print("Number of inlines: ", segy_reader.num_inlines())
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print("Number of crosslines: ", segy_reader.num_xlines())
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except AttributeError:
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pass
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if __name__ == '__main__':
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main()
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