Time slice extraction example program.

examples/timeslice.py

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+"""Extract a timeslice from a 3D seismic volume to a Numpy array.
+
+Usage: timeslice.py [-h] [--dtype DTYPE] [--null NULL]
+                    segy-file npy-file slice-index
+
+Positional arguments:
+  segy-file      Path to an existing SEG Y file of 3D seismic data
+  npy-file       Path to the Numpy array file to be created for the timeslice
+  slice-index    Zero based index of the time slice to be extracted
+
+Optional arguments:
+  -h, --help     show this help message and exit
+  --dtype DTYPE  Numpy data type. If not provided a dtype compatible with the
+                 SEG Y data will be used.
+  --null NULL    Sample value to use for missing or short traces.
+
+Example:
+
+  timeslice.py stack_final_int8.sgy slice_800.npy 800 --null=42.0 --dtype=f
+"""
+from __future__ import print_function
+
+import argparse
+
+import os
+
+import sys
+import traceback
+
+from segpy.reader import create_reader
+from segpy.ext.numpyext import make_dtype
+
+import numpy as np
+
+
+class DimensionalityError(Exception):
+    pass
+
+
+def extract_timeslice(segy_filename, out_filename, slice_index, dtype=None, null=0):
+    """Extract a timeslice from a 3D SEG Y file to a Numpy NPY file.
+
+    Args:
+        segy_filename: Filename of a SEG Y file.
+
+        out_filename: Filename of the NPY file.
+
+        slice_index: The zero-based index (increasing with depth) of the slice to be extracted.
+
+        dtype: Optional Numpy dtype for the result array. If not provided a dtype compatible with
+            the SEG Y data will be used.
+
+        null: Optional sample value to use for missing or short traces. Defaults to zero.
+    """
+    with open(segy_filename, 'rb') as segy_file:
+
+        segy_reader = create_reader(segy_file)
+
+        if dtype is None:
+            dtype = make_dtype(segy_reader.data_sample_format)
+
+        if segy_reader.dimensionality != 3:
+            raise DimensionalityError("Cannot slice {n} dimensional seismic.".format(segy_reader.dimensionality))
+
+        i_line_range = segy_reader.inline_range()
+        x_line_range = segy_reader.xline_range()
+
+        i_size = len(i_line_range)
+        x_size = len(x_line_range)
+        t_size = segy_reader.max_num_trace_samples()
+
+        if not (0 <= slice_index < t_size):
+            raise ValueError("Time slice index {0} out of range {} to {}".format(slice_index, 0, t_size))
+
+        timeslice = np.full((x_size, i_size), null, dtype)
+
+        for inline_num, xline_num in segy_reader.inline_xline_numbers():
+            trace_index = segy_reader.trace_index((inline_num, xline_num))
+            trace = segy_reader.trace_samples(trace_index)
+
+            try:
+                sample = trace[slice_index]
+            except IndexError:
+                sample = null
+
+            i_index = inline_num - i_line_range.start
+            x_index = xline_num - x_line_range.start
+            timeslice[x_index, i_index] = sample
+
+        np.save(out_filename, timeslice)
+
+
+def nullable_dtype(s):
+    return None if s == "" else np.dtype(s)
+
+
+def main(argv=None):
+    parser = argparse.ArgumentParser()
+    parser.add_argument("segy_file", metavar="segy-file",
+                        help="Path to an existing SEG Y file of 3D seismic data")
+
+    parser.add_argument("npy_file", metavar="npy-file",
+                        help="Path to the Numpy array file to be created for the timeslice")
+
+    parser.add_argument("slice_index", metavar="slice-index", type=int,
+                        help="Zero based index of the time slice to be extracted", )
+
+    parser.add_argument("--dtype", type=nullable_dtype, default="",
+                        help="Numpy data type. If not provided a dtype compatible with the SEG Y data will be used.")
+
+    parser.add_argument("--null",  type=float, default=0.0,
+                        help="Sample value to use for missing or short traces.")
+
+    if argv is None:
+        argv = sys.argv[1:]
+
+    args = parser.parse_args(argv)
+
+    try:
+        extract_timeslice(args.segy_file,
+                          args.npy_file,
+                          args.slice_index,
+                          args.dtype,
+                          args.null)
+    except (FileNotFoundError, IsADirectoryError) as e:
+        print(e, file=sys.stderr)
+        return os.EX_NOINPUT
+    except PermissionError as e:
+        print(e, file=sys.stderr)
+        return os.EX_NOPERM
+    except Exception as e:
+        traceback.print_exception(type(e), e, e.__traceback__, file=sys.stderr)
+        return os.EX_SOFTWARE
+    return os.EX_OK
+
+
+if __name__ == '__main__':
+    sys.exit(main())
+