Work in progress on extraction to numpy data structures.

examples/extract_trace_header_field.py

@@ -0,0 +1,113 @@
+#!/usr/bin/env python3
+
+"""Extract a single field from the trace headers of  3D seismic volume to a 2D Numpy array.
+
+This utility assumes the inline and crossline numbers are evenly spaced.
+Each inline of the source data will be represented as a single row, and
+each crossline as a single column in the resulting 2D array.
+
+Usage: extract_trace_header_field.py [-h] [--null NULL]
+                    segy-file npy-file field-name
+
+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
+  field-name     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:
+
+  extract_trace_header_field.py stack_final_int8.sgy slice_800.npy ensemble_num
+"""
+
+import argparse
+import os
+import sys
+import traceback
+
+import numpy as np
+
+from numpy import s_
+
+from segpy.reader import create_reader
+from segpy.trace_header import TraceHeaderRev1
+from segpy_numpy.dtypes import make_dtype
+from segpy_numpy.extract import extract_inline_3d, extract_trace_header_field_3d
+
+
+class DimensionalityError(Exception):
+    pass
+
+
+
+def extract_header_field(segy_filename, out_filename, field_name, null=None):
+    """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.
+
+        inline_index: The zero-based index (increasing with depth) of the slice to be extracted.
+
+        null: Optional sample value to use for missing or short traces. Defaults to zero.
+    """
+    header_field = getattr(TraceHeaderRev1, field_name)
+
+    with open(segy_filename, 'rb') as segy_file:
+
+        segy_reader = create_reader(segy_file)
+        header_field_array = extract_trace_header_field_3d(segy_reader, header_field, null=null)
+        return header_field_array
+
+
+def nullable_int(s):
+    return None if not bool(s) else int(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("field_name", metavar="field-name", type=str,
+                        help="Name of the trace header field to be extracted", )
+
+    parser.add_argument("--null",  type=nullable_int, default="",
+                        help="Header value to use for missing or short traces.")
+
+    if argv is None:
+        argv = sys.argv[1:]
+
+    args = parser.parse_args(argv)
+
+    try:
+        extract_header_field(
+            segy_filename=args.segy_file,
+            out_filename=args.npy_file,
+            field_name=args.field_name,
+            null=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())
+
+

examples/inline.py

@@ -22,7 +22,7 @@ Optional arguments:
 
 Example:
 
-  timeslice.py stack_final_int8.sgy slice_800.npy 800 --null=42.0 --dtype=f
+  inline.py stack_final_int8.sgy slice_800.npy 800 --null=42.0 --dtype=f
 """
 
 import argparse
@@ -58,8 +58,8 @@ def extract_inline(segy_filename, out_filename, inline_number, null=None):
     with open(segy_filename, 'rb') as segy_file:
 
         segy_reader = create_reader(segy_file)
-        inline_array = extract_inline_3d(segy_reader, inline_number, sample_numbers=s_[::2], null=null)
-        return inline_number
+        inline_array = extract_inline_3d(segy_reader, inline_number, null=null)
+        return inline_array
 
 
 def nullable_float(s):