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test_segyio_c.py
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test_segyio_c.py
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import shutil
from unittest import TestCase
import numpy
import segyio._segyio as _segyio
ACTUAL_TEXT_HEADER = b"C 1 DATE: 2016-09-19 " \
b"C 2 AN INCREASE IN AMPLITUDE EQUALS AN INCREASE IN ACOUSTIC IMPEDANCE " \
b"C 3 Written by libsegyio (python) " \
b"C 4 " \
b"C 5 " \
b"C 6 " \
b"C 7 " \
b"C 8 " \
b"C 9 " \
b"C10 " \
b"C11 TRACE HEADER POSITION: " \
b"C12 INLINE BYTES 189-193 | OFFSET BYTES 037-041 " \
b"C13 CROSSLINE BYTES 193-197 | " \
b"C14 " \
b"C15 END EBCDIC HEADER " \
b"C16 " \
b"C17 " \
b"C18 " \
b"C19 " \
b"C20 " \
b"C21 " \
b"C22 " \
b"C23 " \
b"C24 " \
b"C25 " \
b"C26 " \
b"C27 " \
b"C28 " \
b"C29 " \
b"C30 " \
b"C31 " \
b"C32 " \
b"C33 " \
b"C34 " \
b"C35 " \
b"C36 " \
b"C37 " \
b"C38 " \
b"C39 " \
b"C40 \x80"
class _segyioTests(TestCase):
def setUp(self):
self.filename = "test-data/small.sgy"
def test_binary_header_size(self):
self.assertEqual(400, _segyio.binheader_size())
def test_textheader_size(self):
self.assertEqual(3200, _segyio.textheader_size())
def test_open_non_existing_file(self):
with self.assertRaises(IOError):
f = _segyio.open("non-existing", "r")
def test_close_non_existing_file(self):
with self.assertRaises(TypeError):
_segyio.close(None)
def test_open_and_close_file(self):
f = _segyio.open(self.filename, "r")
_segyio.close(f)
def test_open_flush_and_close_file(self):
_segyio.flush(None)
f = _segyio.open(self.filename, "r")
_segyio.flush(f)
_segyio.close(f)
# This does not fail for some reason.
# with self.assertRaises(IOError):
# _segyio.flush(f)
def test_read_text_header(self):
f = _segyio.open(self.filename, "r")
self.assertEqual(_segyio.read_textheader(f, 0), ACTUAL_TEXT_HEADER)
with self.assertRaises(Exception):
_segyio.read_texthdr(None, 0)
_segyio.close(f)
def test_write_text_header(self):
fname = self.filename.replace("small", "txt_hdr_wrt")
shutil.copyfile(self.filename, fname)
f = _segyio.open(fname, "r+")
with self.assertRaises(ValueError):
_segyio.write_textheader(f, 0, "")
self.assertEqual(_segyio.read_textheader(f, 0), ACTUAL_TEXT_HEADER)
_segyio.write_textheader(f, 0, "yolo" * 800)
textheader = _segyio.read_textheader(f, 0)
textheader = textheader.decode('ascii') # Because in Python 3.5 bytes are not comparable to strings
self.assertEqual(textheader, "yolo" * 800)
_segyio.close(f)
def test_read_and_write_binary_header(self):
with self.assertRaises(Exception):
hdr = _segyio.read_binaryheader(None)
with self.assertRaises(Exception):
_segyio.write_binaryheader(None, None)
fname = self.filename.replace("small", "bin_hdr_wrt")
shutil.copyfile(self.filename, fname)
f = _segyio.open(fname, "r+")
binary_header = _segyio.read_binaryheader(f)
with self.assertRaises(Exception):
_segyio.write_binaryheader(f, "Not the correct type")
_segyio.write_binaryheader(f, binary_header)
_segyio.close(f)
def test_read_binary_header_fields(self):
f = _segyio.open(self.filename, "r")
binary_header = _segyio.read_binaryheader(f)
with self.assertRaises(TypeError):
value = _segyio.get_field("s", 0)
with self.assertRaises(IndexError):
value = _segyio.get_field(binary_header, -1)
self.assertEqual(_segyio.get_field(binary_header, 3225), 1)
self.assertEqual(_segyio.get_field(binary_header, 3221), 50)
_segyio.close(f)
def test_line_metrics(self):
f = _segyio.open(self.filename, "r")
binary_header = _segyio.read_binaryheader(f)
ilb = 189
xlb = 193
metrics = _segyio.init_metrics(f, binary_header, ilb, xlb)
_segyio.close(f)
sorting = metrics['sorting']
trace_count = metrics['trace_count']
inline_count = metrics['iline_count']
crossline_count = metrics['xline_count']
offset_count = metrics['offset_count']
metrics = _segyio.init_line_metrics(sorting, trace_count, inline_count, crossline_count, offset_count)
self.assertEqual(metrics['xline_length'], 5)
self.assertEqual(metrics['xline_stride'], 5)
self.assertEqual(metrics['iline_length'], 5)
self.assertEqual(metrics['iline_stride'], 1)
# (sorting, trace_count, inline_count, crossline_count, offset_count)
metrics = _segyio.init_line_metrics(1, 15, 3, 5, 1)
self.assertEqual(metrics['xline_length'], 3)
self.assertEqual(metrics['xline_stride'], 1)
self.assertEqual(metrics['iline_length'], 5)
self.assertEqual(metrics['iline_stride'], 3)
metrics = _segyio.init_line_metrics(2, 15, 3, 5, 1)
self.assertEqual(metrics['xline_length'], 3)
self.assertEqual(metrics['xline_stride'], 5)
self.assertEqual(metrics['iline_length'], 5)
self.assertEqual(metrics['iline_stride'], 1)
def test_metrics(self):
f = _segyio.open(self.filename, "r")
binary_header = _segyio.read_binaryheader(f)
ilb = 189
xlb = 193
with self.assertRaises(TypeError):
metrics = _segyio.init_metrics("?", binary_header, ilb, xlb)
with self.assertRaises(TypeError):
metrics = _segyio.init_metrics(f, "?", ilb, xlb)
with self.assertRaises(IndexError):
metrics = _segyio.init_metrics(f, binary_header, ilb + 1, xlb)
metrics = _segyio.init_metrics(f, binary_header, ilb, xlb)
self.assertEqual(metrics['iline_field'], ilb)
self.assertEqual(metrics['xline_field'], xlb)
self.assertEqual(metrics['trace0'], _segyio.textheader_size() + _segyio.binheader_size())
self.assertEqual(metrics['sample_count'], 50)
self.assertEqual(metrics['format'], 1)
self.assertEqual(metrics['trace_bsize'], 200)
self.assertEqual(metrics['sorting'], 2) # inline sorting = 2, crossline sorting = 1
self.assertEqual(metrics['trace_count'], 25)
self.assertEqual(metrics['offset_count'], 1)
self.assertEqual(metrics['iline_count'], 5)
self.assertEqual(metrics['xline_count'], 5)
_segyio.close(f)
with self.assertRaises(IOError):
metrics = _segyio.init_metrics(f, binary_header, ilb, xlb)
def test_indices(self):
f = _segyio.open(self.filename, "r")
binary_header = _segyio.read_binaryheader(f)
ilb = 189
xlb = 193
metrics = _segyio.init_metrics(f, binary_header, ilb, xlb)
dmy = numpy.zeros(2, dtype=numpy.uintc)
dummy_metrics = {'xline_count': 2,
'iline_count': 2,
'offset_count': 1}
with self.assertRaises(TypeError):
_segyio.init_indices(".", {}, dmy, dmy, dmy)
with self.assertRaises(TypeError):
_segyio.init_indices(f, "-", dmy, dmy, dmy)
# with self.assertRaises(KeyError):
# _segyio.init_indices(f, {}, dmy, dmy, dmy)
with self.assertRaises(TypeError):
_segyio.init_indices(f, dummy_metrics, 1, dmy, dmy)
with self.assertRaises(TypeError):
_segyio.init_indices(f, dummy_metrics, dmy, 2, dmy)
with self.assertRaises(TypeError):
_segyio.init_indices(f, dummy_metrics, dmy, dmy, 2)
with self.assertRaises(TypeError):
fdmy = numpy.zeros(1, dtype=numpy.single)
_segyio.init_indices(f, dummy_metrics, fdmy, dmy, dmy)
one = numpy.zeros(1, dtype=numpy.uintc)
two = numpy.zeros(2, dtype=numpy.uintc)
off = numpy.zeros(1, dtype=numpy.uintc)
with self.assertRaises(ValueError):
_segyio.init_indices(f, dummy_metrics, one, two, off)
with self.assertRaises(ValueError):
_segyio.init_indices(f, dummy_metrics, two, one, off)
# Happy Path
iline_indexes = numpy.zeros(metrics['iline_count'], dtype=numpy.uintc)
xline_indexes = numpy.zeros(metrics['xline_count'], dtype=numpy.uintc)
offsets = numpy.zeros(metrics['offset_count'], dtype=numpy.uintc)
_segyio.init_indices(f, metrics, iline_indexes, xline_indexes, offsets)
self.assertListEqual([1, 2, 3, 4, 5], list(iline_indexes))
self.assertListEqual([20, 21, 22, 23, 24], list(xline_indexes))
self.assertListEqual([1], list(offsets))
_segyio.close(f)
def test_fread_trace0(self):
f = _segyio.open(self.filename, "r")
binary_header = _segyio.read_binaryheader(f)
ilb = 189
xlb = 193
metrics = _segyio.init_metrics(f, binary_header, ilb, xlb)
sorting = metrics['sorting']
trace_count = metrics['trace_count']
inline_count = metrics['iline_count']
crossline_count = metrics['xline_count']
offset_count = metrics['offset_count']
line_metrics = _segyio.init_line_metrics(sorting, trace_count, inline_count, crossline_count, offset_count)
iline_indexes = numpy.zeros(metrics['iline_count'], dtype=numpy.uintc)
xline_indexes = numpy.zeros(metrics['xline_count'], dtype=numpy.uintc)
offsets = numpy.zeros(metrics['offset_count'], dtype=numpy.uintc)
_segyio.init_indices(f, metrics, iline_indexes, xline_indexes, offsets)
with self.assertRaises(KeyError):
_segyio.fread_trace0(0, len(xline_indexes), line_metrics['iline_stride'], offset_count, iline_indexes, "inline")
with self.assertRaises(KeyError):
_segyio.fread_trace0(2, len(iline_indexes), line_metrics['xline_stride'], offset_count, xline_indexes, "crossline")
value = _segyio.fread_trace0(1, len(xline_indexes), line_metrics['iline_stride'], offset_count, iline_indexes, "inline")
self.assertEqual(value, 0)
value = _segyio.fread_trace0(2, len(xline_indexes), line_metrics['iline_stride'], offset_count, iline_indexes, "inline")
self.assertEqual(value, 5)
value = _segyio.fread_trace0(21, len(iline_indexes), line_metrics['xline_stride'], offset_count, xline_indexes, "crossline")
self.assertEqual(value, 1)
value = _segyio.fread_trace0(22, len(iline_indexes), line_metrics['xline_stride'], offset_count, xline_indexes, "crossline")
self.assertEqual(value, 2)
_segyio.close(f)
def test_get_and_set_field(self):
hdr = _segyio.empty_traceheader()
with self.assertRaises(TypeError):
_segyio.get_field(".", 0)
with self.assertRaises(TypeError):
_segyio.set_field(".", 0, 1)
with self.assertRaises(IndexError):
_segyio.get_field(hdr, 0)
with self.assertRaises(IndexError):
_segyio.set_field(hdr, 0, 1)
_segyio.set_field(hdr, 1, 127)
_segyio.set_field(hdr, 5, 67)
_segyio.set_field(hdr, 9, 19)
self.assertEqual(_segyio.get_field(hdr, 1), 127)
self.assertEqual(_segyio.get_field(hdr, 5), 67)
self.assertEqual(_segyio.get_field(hdr, 9), 19)
def test_read_and_write_traceheader(self):
fname = self.filename.replace("small", "bin_hdr_wrt")
shutil.copyfile(self.filename, fname)
f = _segyio.open(fname, "r+")
binary_header = _segyio.read_binaryheader(f)
ilb = 189
xlb = 193
metrics = _segyio.init_metrics(f, binary_header, ilb, xlb)
empty = _segyio.empty_traceheader()
with self.assertRaises(TypeError):
trace_header = _segyio.read_traceheader("+", )
with self.assertRaises(TypeError):
trace_header = _segyio.read_traceheader(f, 0, None)
trace_header = _segyio.read_traceheader(f, 0, _segyio.empty_traceheader(), metrics['trace0'], metrics['trace_bsize'])
self.assertEqual(_segyio.get_field(trace_header, ilb), 1)
self.assertEqual(_segyio.get_field(trace_header, xlb), 20)
trace_header = _segyio.read_traceheader(f, 1, _segyio.empty_traceheader(), metrics['trace0'], metrics['trace_bsize'])
self.assertEqual(_segyio.get_field(trace_header, ilb), 1)
self.assertEqual(_segyio.get_field(trace_header, xlb), 21)
_segyio.set_field(trace_header, ilb, 99)
_segyio.set_field(trace_header, xlb, 42)
_segyio.write_traceheader(f, 0, trace_header, metrics['trace0'], metrics['trace_bsize'])
trace_header = _segyio.read_traceheader(f, 0, _segyio.empty_traceheader(), metrics['trace0'], metrics['trace_bsize'])
self.assertEqual(_segyio.get_field(trace_header, ilb), 99)
self.assertEqual(_segyio.get_field(trace_header, xlb), 42)
_segyio.close(f)
def test_read_and_write_trace(self):
f = _segyio.open("test-data/trace-wrt.sgy", "w+")
buf = numpy.ones(25, dtype=numpy.single)
buf[11] = 3.1415
_segyio.write_trace(f, 0, buf, 0, 100, 1, 25)
buf[:] = 42.0
_segyio.write_trace(f, 1, buf, 0, 100, 1, 25)
_segyio.flush(f)
buf = numpy.zeros(25, dtype=numpy.single)
_segyio.read_trace(f, 0, 25, buf, 0, 100, 1, 25)
self.assertAlmostEqual(buf[10], 1.0, places=4)
self.assertAlmostEqual(buf[11], 3.1415, places=4)
_segyio.read_trace(f, 1, 25, buf, 0, 100, 1, 25)
self.assertAlmostEqual(sum(buf), 42.0 * 25, places=4)
_segyio.close(f)
def read_small(self, mmap = False):
f = _segyio.open(self.filename, "r")
if mmap: _segyio.mmap(f)
binary_header = _segyio.read_binaryheader(f)
ilb = 189
xlb = 193
metrics = _segyio.init_metrics(f, binary_header, ilb, xlb)
sorting = metrics['sorting']
trace_count = metrics['trace_count']
inline_count = metrics['iline_count']
crossline_count = metrics['xline_count']
offset_count = metrics['offset_count']
line_metrics = _segyio.init_line_metrics(sorting, trace_count, inline_count, crossline_count, offset_count)
metrics.update(line_metrics)
iline_indexes = numpy.zeros(metrics['iline_count'], dtype=numpy.uintc)
xline_indexes = numpy.zeros(metrics['xline_count'], dtype=numpy.uintc)
offsets = numpy.zeros(metrics['offset_count'], dtype=numpy.uintc)
_segyio.init_indices(f, metrics, iline_indexes, xline_indexes, offsets)
return f, metrics, iline_indexes, xline_indexes
def test_read_line(self):
f, metrics, iline_idx, xline_idx = self.read_small()
tr0 = metrics['trace0']
bsz = metrics['trace_bsize']
samples = metrics['sample_count']
xline_stride = metrics['xline_stride']
iline_stride = metrics['iline_stride']
offsets = metrics['offset_count']
xline_trace0 = _segyio.fread_trace0(20, len(iline_idx), xline_stride, offsets, xline_idx, "crossline")
iline_trace0 = _segyio.fread_trace0(1, len(xline_idx), iline_stride, offsets, iline_idx, "inline")
buf = numpy.zeros((len(iline_idx), samples), dtype=numpy.single)
_segyio.read_line(f, xline_trace0, len(iline_idx), xline_stride, offsets, buf, tr0, bsz, 1, samples)
self.assertAlmostEqual(sum(sum(buf)), 800.061169624, places=6)
_segyio.read_line(f, iline_trace0, len(xline_idx), iline_stride, offsets, buf, tr0, bsz, 1, samples)
self.assertAlmostEqual(sum(sum(buf)), 305.061146736, places=6)
_segyio.close(f)
def test_read_line_mmap(self):
f, metrics, iline_idx, xline_idx = self.read_small(True)
tr0 = metrics['trace0']
bsz = metrics['trace_bsize']
samples = metrics['sample_count']
xline_stride = metrics['xline_stride']
iline_stride = metrics['iline_stride']
offsets = metrics['offset_count']
xline_trace0 = _segyio.fread_trace0(20, len(iline_idx), xline_stride, offsets, xline_idx, "crossline")
iline_trace0 = _segyio.fread_trace0(1, len(xline_idx), iline_stride, offsets, iline_idx, "inline")
buf = numpy.zeros((len(iline_idx), samples), dtype=numpy.single)
_segyio.read_line(f, xline_trace0, len(iline_idx), xline_stride, offsets, buf, tr0, bsz, 1, samples)
self.assertAlmostEqual(sum(sum(buf)), 800.061169624, places=6)
_segyio.read_line(f, iline_trace0, len(xline_idx), iline_stride, offsets, buf, tr0, bsz, 1, samples)
self.assertAlmostEqual(sum(sum(buf)), 305.061146736, places=6)
_segyio.close(f)
def test_fread_trace0_for_depth(self):
elements = list(range(25))
indices = numpy.asarray(elements, dtype=numpy.uintc)
for index in indices:
d = _segyio.fread_trace0(index, 1, 1, 1, indices, "depth")
self.assertEqual(d, index)
with self.assertRaises(KeyError):
d = _segyio.fread_trace0(25, 1, 1, 1, indices, "depth")