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# -*- coding: utf-8 -*-
from __future__ import absolute_import
try:
from future_builtins import zip, map
except ImportError:
pass
from types import GeneratorType
import itertools
import filecmp
import shutil
import numpy as np
import numpy.testing as npt
import pytest
from pytest import approx
from . import tmpfiles, small, smallps
import segyio
from segyio import TraceField, BinField, TraceSortingFormat
from segyio.field import Field
from segyio.line import Line, HeaderLine
from segyio.trace import Trace, Header
small_sus = [
(segyio.su.open, { 'filename': 'test-data/small.su',
'iline': 5,
'xline': 21 }),
(segyio.su.open, { 'filename': 'test-data/small-lsb.su',
'iline': 5,
'xline': 21,
'endian': 'lsb' }),
]
small_segys = [
(segyio.open, { 'filename': 'test-data/small.sgy' }),
(segyio.open, { 'filename': 'test-data/small-lsb.sgy',
'endian': 'little' }),
]
smallfiles = small_segys + small_sus
@pytest.mark.parametrize(('openfn', 'kwargs'), smallfiles)
def test_inline_4(openfn, kwargs):
with openfn(**kwargs) as f:
sample_count = len(f.samples)
assert 50 == sample_count
data = f.iline[4]
assert 4.2 == approx(data[0, 0], abs=1e-6)
# middle sample
assert 4.20024 == approx(data[0, sample_count // 2 - 1], abs=1e-6)
# last sample
assert 4.20049 == approx(data[0, -1], abs=1e-6)
# middle xline
middle_line = 2
# first sample
assert 4.22 == approx(data[middle_line, 0], abs=1e-5)
# middle sample
assert 4.22024 == approx(data[middle_line, sample_count // 2 - 1], abs=1e-6)
# last sample
assert 4.22049 == approx(data[middle_line, -1], abs=1e-6)
# last xline
last_line = (len(f.xlines) - 1)
# first sample
assert 4.24 == approx(data[last_line, 0], abs=1e-5)
# middle sample
assert 4.24024 == approx(data[last_line, sample_count // 2 - 1], abs=1e-6)
# last sample
assert 4.24049 == approx(data[last_line, sample_count - 1], abs=1e-6)
def test_inline_4_seismic_unix():
with segyio.su.open('test-data/small.su',
iline = 5,
xline = 21,
endian = 'big',
) as f:
sample_count = len(f.samples)
assert 50 == sample_count
data = f.iline[4]
assert 4.2 == approx(data[0, 0], abs=1e-6)
# middle sample
assert 4.20024 == approx(data[0, sample_count // 2 - 1], abs=1e-6)
# last sample
assert 4.20049 == approx(data[0, -1], abs=1e-6)
# middle xline
middle_line = 2
# first sample
assert 4.22 == approx(data[middle_line, 0], abs=1e-5)
# middle sample
assert 4.22024 == approx(data[middle_line, sample_count // 2 - 1], abs=1e-6)
# last sample
assert 4.22049 == approx(data[middle_line, -1], abs=1e-6)
# last xline
last_line = (len(f.xlines) - 1)
# first sample
assert 4.24 == approx(data[last_line, 0], abs=1e-5)
# middle sample
assert 4.24024 == approx(data[last_line, sample_count // 2 - 1], abs=1e-6)
# last sample
assert 4.24049 == approx(data[last_line, sample_count - 1], abs=1e-6)
@pytest.mark.parametrize(('openfn', 'kwargs'), smallfiles)
def test_xline_22(openfn, kwargs):
with openfn(**kwargs) as f:
data = f.xline[22]
size = len(f.samples)
# first iline
# first sample
assert 1.22 == approx(data[0, 0], abs=1e-5)
# middle sample
assert 1.22024 == approx(data[0, size // 2 - 1], abs=1e-6)
# last sample
assert 1.22049 == approx(data[0, size - 1], abs=1e-6)
# middle iline
middle_line = 2
# first sample
assert 3.22 == approx(data[middle_line, 0], abs=1e-5)
# middle sample
assert 3.22024 == approx(data[middle_line, size // 2 - 1], abs=1e-6)
# last sample
assert 3.22049 == approx(data[middle_line, size - 1], abs=1e-6)
# last iline
last_line = len(f.ilines) - 1
# first sample
assert 5.22 == approx(data[last_line, 0], abs=1e-5)
# middle sample
assert 5.22024 == approx(data[last_line, size // 2 - 1], abs=1e-6)
# last sample
assert 5.22049 == approx(data[last_line, size - 1], abs=1e-6)
@pytest.mark.parametrize(('openfn', 'kwargs'), smallfiles)
def test_iline_slicing(openfn, kwargs):
with openfn(**kwargs) as f:
assert len(f.ilines) == sum(1 for _ in f.iline)
assert len(f.ilines) == sum(1 for _ in f.iline[1:6])
assert len(f.ilines) == sum(1 for _ in f.iline[5:0:-1])
assert len(f.ilines) // 2 == sum(1 for _ in f.iline[0::2])
assert len(f.ilines) == sum(1 for _ in f.iline[1:])
assert 3 == sum(1 for _ in f.iline[::2])
assert 0 == sum(1 for _ in f.iline[12:24])
assert 3 == sum(1 for _ in f.iline[:4])
assert 2 == sum(1 for _ in f.iline[2:6:2])
@pytest.mark.parametrize(('openfn', 'kwargs'), smallfiles)
def test_xline_slicing(openfn, kwargs):
with openfn(**kwargs) as f:
assert len(f.xlines) == sum(1 for _ in f.xline)
assert len(f.xlines) == sum(1 for _ in f.xline[20:25])
assert len(f.xlines) == sum(1 for _ in f.xline[25:19:-1])
assert 3 == sum(1 for _ in f.xline[0::2])
assert 3 == sum(1 for _ in f.xline[::2])
assert len(f.xlines) == sum(1 for _ in f.xline[20:])
assert 0 == sum(1 for _ in f.xline[12:18])
assert 5 == sum(1 for _ in f.xline[:25])
assert 2 == sum(1 for _ in f.xline[:25:3])
@pytest.mark.parametrize(('openfn', 'kwargs'), smallfiles)
def test_open_transposed_lines(openfn, kwargs):
with openfn(**kwargs) as f:
il = f.ilines
xl = f.xlines
with segyio.open("test-data/small.sgy", "r", segyio.TraceField.CROSSLINE_3D, segyio.TraceField.INLINE_3D) as f:
assert list(il) == list(f.xlines)
assert list(xl) == list(f.ilines)
# only run this test for the SEG-Ys, because the SU files are in IEEE float,
# not IBM float
@pytest.mark.parametrize(('openfn', 'kwargs'), small_segys)
def test_file_info(openfn, kwargs):
with openfn(**kwargs) as f:
assert 2 == f.sorting
assert 1 == f.offsets
assert 1 == int(f.format)
assert np.single == f.dtype
xlines = list(range(20, 25))
ilines = list(range(1, 6))
assert xlines == list(f.xlines)
assert ilines == list(f.ilines)
assert 25 == f.tracecount
assert len(f.trace) == f.tracecount
assert 50 == len(f.samples)
def test_open_nostrict():
with segyio.open("test-data/small.sgy", strict=False):
pass
def test_open_ignore_geometry():
with segyio.open("test-data/small.sgy", ignore_geometry=True) as f:
with pytest.raises(ValueError):
_ = f.iline[0]
@pytest.mark.parametrize(('openfn', 'kwargs'), smallfiles)
def test_traces_slicing(openfn, kwargs):
with openfn(**kwargs) as f:
traces = list(map(np.copy, f.trace[0:6:2]))
assert len(traces) == 3
assert traces[0][49] == f.trace[0][49]
assert traces[1][49] == f.trace[2][49]
assert traces[2][49] == f.trace[4][49]
rev_traces = list(map(np.copy, f.trace[4::-2]))
assert rev_traces[0][49] == f.trace[4][49]
assert rev_traces[1][49] == f.trace[2][49]
assert rev_traces[2][49] == f.trace[0][49]
# make sure buffers can be reused
for i, trace in enumerate(f.trace[0:6:2]):
assert np.array_equal(trace, traces[i])
def test_traces_offset():
with segyio.open("test-data/small-ps.sgy") as f:
assert 2 == len(f.offsets)
assert [1, 2] == list(f.offsets)
# traces are laid out |l1o1 l1o2 l2o1 l2o2...|
# where l = iline number and o = offset number
# traces are not re-indexed according to offsets
# see make-ps-file.py for value formula
assert 101.01 == approx(f.trace[0][0], abs=1e-4)
assert 201.01 == approx(f.trace[1][0], abs=1e-4)
assert 101.02 == approx(f.trace[2][0], abs=1e-4)
assert 201.02 == approx(f.trace[3][0], abs=1e-4)
assert 102.01 == approx(f.trace[6][0], abs=1e-4)
def test_headers_offset():
with segyio.open("test-data/small-ps.sgy") as f:
il, xl = TraceField.INLINE_3D, TraceField.CROSSLINE_3D
assert f.header[0][il] == f.header[1][il]
assert f.header[1][il] == f.header[2][il]
assert f.header[0][xl] == f.header[1][xl]
assert not f.header[1][xl] == f.header[2][xl]
@pytest.mark.parametrize(('openfn', 'kwargs'), small_sus)
def test_disabled_methods_seismic_unix(openfn, kwargs):
with openfn(**kwargs) as f:
with pytest.raises(NotImplementedError):
_ = f.text[0]
with pytest.raises(NotImplementedError):
_ = f.bin
with pytest.raises(NotImplementedError):
f.bin = {}
@pytest.mark.parametrize(('openfn', 'kwargs'), small_segys)
def test_header_dict_methods(openfn, kwargs):
with openfn(**kwargs) as f:
assert 89 == len(list(f.header[0].keys()))
assert 89 == len(list(f.header[1].values()))
assert 89 == len(list(f.header[2].items()))
assert 89 == len(list(f.header[3]))
assert 0 not in f.header[0]
assert 1 in f.header[0]
assert segyio.su.cdpx in f.header[0]
iter(f.header[0])
assert 30 == len(f.bin.keys())
assert 30 == len(list(f.bin.values()))
assert 30 == len(list(f.bin.items()))
assert 30 == len(f.bin)
iter(f.bin)
def test_header_dropped_writes(small):
with segyio.open(small, mode='r+') as f:
f.header[10] = { 1: 5, 5: 10 }
with segyio.open(small, mode='r+') as f:
x, y = f.header[10], f.header[10]
assert x[1, 5] == { 1: 5, 5: 10 }
assert y[1, 5] == { 1: 5, 5: 10 }
# write to x[1] is invisible to y
x[1] = 6
assert x[1] == 6
assert y[1] == 5
y.reload()
assert x[1] == 6
assert y[1] == 6
x[1] = 5
assert x[1] == 5
assert y[1] == 6
# the write to x[1] is lost
y[5] = 1
assert x[1] == 5
assert x.reload()
assert x[1] == 6
assert y[1, 5] == { 1: 6, 5: 1 }
def test_headers_line_offset(smallps):
il, xl = TraceField.INLINE_3D, TraceField.CROSSLINE_3D
with segyio.open(smallps, "r+") as f:
f.header.iline[1, 2] = {il: 11}
f.header.iline[1, 2] = {xl: 13}
with segyio.open(smallps, strict=False) as f:
assert f.header[0][il] == 1
assert f.header[1][il] == 11
assert f.header[2][il] == 1
assert f.header[0][xl] == 1
assert f.header[1][xl] == 13
assert f.header[2][xl] == 2
@pytest.mark.parametrize(('openfn', 'kwargs'), smallfiles)
def test_attributes(openfn, kwargs):
with openfn(**kwargs) as f:
il = kwargs.get('iline', TraceField.INLINE_3D)
xl = kwargs.get('xline', TraceField.CROSSLINE_3D)
assert 1 == f.attributes(il)[0]
assert 20 == f.attributes(xl)[0]
assert f.tracecount == len(f.attributes(il))
assert iter(f.attributes(il))
ils = [(i // 5) + 1 for i in range(25)]
attrils = list(map(int, f.attributes(il)[:]))
assert ils == attrils
xls = [(i % 5) + 20 for i in range(25)]
attrxls = list(map(int, f.attributes(xl)[:]))
assert xls == attrxls
ils = [(i // 5) + 1 for i in range(25)][::-1]
attrils = list(map(int, f.attributes(il)[::-1]))
assert ils == attrils
xls = [(i % 5) + 20 for i in range(25)][::-1]
attrxls = list(map(int, f.attributes(xl)[::-1]))
assert xls == attrxls
assert f.header[0][il] == f.attributes(il)[0]
f.mmap()
assert f.header[0][il] == f.attributes(il)[0]
ils = [(i // 5) + 1 for i in range(25)][1:21:3]
attrils = list(map(int, f.attributes(il)[1:21:3]))
assert ils == attrils
xls = [(i % 5) + 20 for i in range(25)][2:17:5]
attrxls = list(map(int, f.attributes(xl)[2:17:5]))
assert xls == attrxls
ils = [1, 2, 3, 4, 5]
attrils = list(map(int, f.attributes(il)[[0, 5, 11, 17, 23]]))
assert ils == attrils
ils = [1, 2, 3, 4, 5]
indices = np.asarray([0, 5, 11, 17, 23])
attrils = list(map(int, f.attributes(il)[indices]))
assert ils == attrils
def test_iline_offset():
with segyio.open("test-data/small-ps.sgy") as f:
line1 = f.iline[1, 1]
assert 101.01 == approx(line1[0][0], abs=1e-4)
assert 101.02 == approx(line1[1][0], abs=1e-4)
assert 101.03 == approx(line1[2][0], abs=1e-4)
assert 101.01001 == approx(line1[0][1], abs=1e-4)
assert 101.01002 == approx(line1[0][2], abs=1e-4)
assert 101.02001 == approx(line1[1][1], abs=1e-4)
line2 = f.iline[1, 2]
assert 201.01 == approx(line2[0][0], abs=1e-4)
assert 201.02 == approx(line2[1][0], abs=1e-4)
assert 201.03 == approx(line2[2][0], abs=1e-4)
assert 201.01001 == approx(line2[0][1], abs=1e-4)
assert 201.01002 == approx(line2[0][2], abs=1e-4)
assert 201.02001 == approx(line2[1][1], abs=1e-4)
with pytest.raises(KeyError):
_ = f.iline[1, 0]
with pytest.raises(KeyError):
_ = f.iline[1, 3]
with pytest.raises(KeyError):
_ = f.iline[100, 1]
with pytest.raises(TypeError):
_ = f.iline[1, {}]
def test_iline_slice_fixed_offset():
with segyio.open("test-data/small-ps.sgy") as f:
for i, ln in enumerate(f.iline[:, 1], 1):
assert i + 100.01 == approx(ln[0][0], abs=1e-4)
assert i + 100.02 == approx(ln[1][0], abs=1e-4)
assert i + 100.03 == approx(ln[2][0], abs=1e-4)
assert i + 100.01001 == approx(ln[0][1], abs=1e-4)
assert i + 100.01002 == approx(ln[0][2], abs=1e-4)
assert i + 100.02001 == approx(ln[1][1], abs=1e-4)
def test_iline_slice_fixed_line():
with segyio.open("test-data/small-ps.sgy") as f:
for i, ln in enumerate(f.iline[1, :], 1):
off = i * 100
assert off + 1.01 == approx(ln[0][0], abs=1e-4)
assert off + 1.02 == approx(ln[1][0], abs=1e-4)
assert off + 1.03 == approx(ln[2][0], abs=1e-4)
assert off + 1.01001 == approx(ln[0][1], abs=1e-4)
assert off + 1.01002 == approx(ln[0][2], abs=1e-4)
assert off + 1.02001 == approx(ln[1][1], abs=1e-4)
def test_iline_slice_all_offsets():
with segyio.open("test-data/small-ps.sgy") as f:
offs, ils = len(f.offsets), len(f.ilines)
assert offs * ils == sum(1 for _ in f.iline[:, :])
assert offs * ils == sum(1 for _ in f.iline[:, ::-1])
assert offs * ils == sum(1 for _ in f.iline[::-1, :])
assert offs * ils == sum(1 for _ in f.iline[::-1, ::-1])
assert 0 == sum(1 for _ in f.iline[:, 10:12])
assert 0 == sum(1 for _ in f.iline[10:12, :])
assert (offs // 2) * ils == sum(1 for _ in f.iline[::2, :])
assert offs * (ils // 2) == sum(1 for _ in f.iline[:, ::2])
assert (offs // 2) * ils == sum(1 for _ in f.iline[::-2, :])
assert offs * (ils // 2) == sum(1 for _ in f.iline[:, ::-2])
assert (offs // 2) * (ils // 2) == sum(1 for _ in f.iline[::2, ::2])
assert (offs // 2) * (ils // 2) == sum(1 for _ in f.iline[::2, ::-2])
assert (offs // 2) * (ils // 2) == sum(1 for _ in f.iline[::-2, ::2])
def test_gather_mode():
with segyio.open("test-data/small-ps.sgy") as f:
empty = np.empty(0, dtype=np.single)
# should raise
with pytest.raises(KeyError):
assert np.array_equal(empty, f.gather[2, 3, 3])
with pytest.raises(KeyError):
assert np.array_equal(empty, f.gather[2, 5, 1])
with pytest.raises(KeyError):
assert np.array_equal(empty, f.gather[5, 2, 1])
assert np.array_equal(f.trace[10], f.gather[2, 3, 1])
assert np.array_equal(f.trace[11], f.gather[2, 3, 2])
traces = segyio.tools.collect(f.trace[10:12])
gather = f.gather[2, 3, :]
assert np.array_equal(traces, gather)
assert np.array_equal(traces, f.gather[2, 3])
assert np.array_equal(empty, f.gather[2, 3, 1:0])
assert np.array_equal(empty, f.gather[2, 3, 3:4])
for g, line in zip(f.gather[1:3, 3, 1], f.iline[1:3]):
assert 10 == len(g)
assert (10,) == g.shape
assert np.array_equal(line[2], g)
for g, line in zip(f.gather[1:3, 3, :], f.iline[1:3]):
assert 2 == len(g)
assert (2, 10) == g.shape
assert np.array_equal(line[2], g[0])
for g, line in zip(f.gather[1, 1:3, 1], f.xline[1:3]):
assert 10 == len(g)
assert (10,) == g.shape
assert np.array_equal(line[0], g)
for g, line in zip(f.gather[1, 1:3, :], f.xline[1:3]):
assert 2 == len(g)
assert (2, 10) == g.shape
assert np.array_equal(line[0], g[0])
for g, line in zip(f.gather[1, 1:3, 3:4], f.xline[1:3]):
assert np.array_equal(empty, g)
def test_line_generators():
with segyio.open("test-data/small.sgy") as f:
for _ in f.iline:
pass
for _ in f.xline:
pass
@pytest.mark.parametrize(('openfn', 'kwargs'), smallfiles)
def test_fast_slow_dimensions(openfn, kwargs):
with openfn(**kwargs) as f:
for iline, fline in zip(f.iline, f.fast):
assert np.array_equal(iline, fline)
for xline, sline in zip(f.xline, f.slow):
assert np.array_equal(xline, sline)
@pytest.mark.parametrize(('openfn', 'kwargs'), smallfiles)
def test_traces_raw(openfn, kwargs):
with openfn(**kwargs) as f:
gen_traces = np.array(list(map(np.copy, f.trace)), dtype=np.single)
raw_traces = f.trace.raw[:]
assert np.array_equal(gen_traces, raw_traces)
assert len(gen_traces) == f.tracecount
assert len(raw_traces) == f.tracecount
assert gen_traces[0][49] == raw_traces[0][49]
assert gen_traces[1][49] == f.trace.raw[1][49]
assert gen_traces[2][49] == raw_traces[2][49]
assert np.array_equal(f.trace[10], f.trace.raw[10])
for raw, gen in zip(f.trace.raw[::2], f.trace[::2]):
assert np.array_equal(raw, gen)
for raw, gen in zip(f.trace.raw[::-1], f.trace[::-1]):
assert np.array_equal(raw, gen)
def test_read_text_sequence():
with segyio.open('test-data/multi-text.sgy', ignore_geometry = True) as f:
for text in f.text[:]:
assert text
assert iter(f.text)
with pytest.deprecated_call():
str(f.text)
@tmpfiles('test-data/multi-text.sgy')
def test_put_text_sequence(tmpdir):
lines = { 1: 'first line', 10: 'last line' }
ref = segyio.tools.create_text_header(lines)
fname = str(tmpdir / 'multi-text.sgy')
with segyio.open(fname, mode = 'r+', ignore_geometry = True) as f, \
segyio.open("test-data/small.sgy") as g:
f.text[0] = ref
f.text[1] = f.text
f.text[-1] = ref
f.text[2:4] = [g.text, f.text]
assert f.text[2] == g.text[0]
f.text[2:3] = [ref]
# ref doesn't have to be bytes for reading, but has to in order to compare
# with the returned object from text
ref = bytearray(ref, 'ascii')
ref = bytes(ref)
with segyio.open(fname, ignore_geometry = True) as f:
for text in f.text:
assert text == ref
@pytest.mark.parametrize(('openfn', 'kwargs'), smallfiles)
def test_header_getitem_intlikes(openfn, kwargs):
with openfn(**kwargs) as f:
h = f.header[0]
assert 1 == h[37]
assert 1 == h[segyio.su.offset]
assert 1 == h[TraceField.offset]
@pytest.mark.parametrize(('openfn', 'kwargs'), smallfiles)
def test_read_header(openfn, kwargs):
with openfn(**kwargs) as f:
il = kwargs.get('iline', TraceField.INLINE_3D)
assert 1 == f.header[0][il]
assert 5 == f.header[-1][il]
assert dict(f.header[-1]) == dict(f.header[24])
with pytest.raises(IndexError):
_ = f.header[30]
with pytest.raises(IndexError):
_ = f.header[-30]
with pytest.raises(KeyError):
_ = f.header[0][188] # between byte offsets
with pytest.raises(KeyError):
_ = f.header[0][-1]
with pytest.raises(KeyError):
_ = f.header[0][700]
def test_read_header_seismic_unix():
il = 5
with segyio.su.open('test-data/small.su',
ignore_geometry = True,
endian = 'big') as f:
assert 1 == f.header[0][il]
assert 1 == f.header[1][il]
assert 5 == f.header[-1][il]
assert 5 == f.header[24][il]
assert dict(f.header[-1]) == dict(f.header[24])
def test_write_header(small):
with segyio.open(small, "r+") as f:
# assign to a field in a header, write immediately
f.header[0][189] = 42
f.flush()
assert 42 == f.header[0][189]
assert 1 == f.header[1][189]
# accessing non-existing offsets raises exceptions
with pytest.raises(KeyError):
f.header[0][188] = 1 # between byte offsets
with pytest.raises(KeyError):
f.header[0][-1] = 1
with pytest.raises(KeyError):
f.header[0][700] = 1
d = {TraceField.INLINE_3D: 43,
TraceField.CROSSLINE_3D: 11,
TraceField.offset: 15}
# assign multiple fields at once by using a dict
f.header[1] = d
f.flush()
assert 43 == f.header[1][TraceField.INLINE_3D]
assert 11 == f.header[1][segyio.su.xline]
assert 15 == f.header[1][segyio.su.offset]
# looking up multiple values at once returns a { TraceField: value } dict
assert d == f.header[1][TraceField.INLINE_3D, TraceField.CROSSLINE_3D, TraceField.offset]
# slice-support over headers (similar to trace)
for _ in f.header[0:10]:
pass
assert 6 == len(list(f.header[10::-2]))
assert 5 == len(list(f.header[10:5:-1]))
assert 0 == len(list(f.header[10:5]))
d = {TraceField.INLINE_3D: 45,
TraceField.CROSSLINE_3D: 10,
TraceField.offset: 16}
# assign multiple values using alternative syntax
f.header[5].update(d)
f.flush()
assert 45 == f.header[5][TraceField.INLINE_3D]
assert 10 == f.header[5][segyio.su.xline]
assert 16 == f.header[5][segyio.su.offset]
# accept anything with a key-value structure
f.header[5].update([(segyio.su.ns, 12), (segyio.su.dt, 4)])
f.header[5].update(((segyio.su.muts, 3), (segyio.su.mute, 7)))
f.header[5].update([(segyio.su.muts, 3)], sx=7)
f.header[5].update(sy=8)
with pytest.raises(TypeError):
f.header[0].update(10)
with pytest.raises(TypeError):
f.header[0].update(None)
with pytest.raises(ValueError):
f.header[0].update('foo')
f.flush()
assert 12 == f.header[5][segyio.su.ns]
assert 4 == f.header[5][segyio.su.dt]
assert 3 == f.header[5][segyio.su.muts]
assert 7 == f.header[5][segyio.su.mute]
assert 7 == f.header[5][segyio.su.sx]
assert 8 == f.header[5][segyio.su.sy]
# for-each support
for _ in f.header:
pass
# copy a header
f.header[2] = f.header[1]
f.flush()
d = {TraceField.INLINE_3D: 12,
TraceField.CROSSLINE_3D: 13,
TraceField.offset: 14}
# assign multiple values with a slice
f.header[:5] = d
f.flush()
for i in range(5):
assert 12 == f.header[i][TraceField.INLINE_3D]
assert 13 == f.header[i][segyio.su.xline]
assert 14 == f.header[i][segyio.su.offset]
# don't use this interface in production code, it's only for testing
# i.e. don't access buf of treat it as a list
# assertEqual(list(f.header[2].buf), list(f.header[1].buf))
def test_write_binary(small):
with segyio.open(small, "r+") as f:
f.bin[3213] = 5
f.flush()
assert 5 == f.bin[3213]
# accessing non-existing offsets raises exceptions
with pytest.raises(KeyError):
_ = f.bin[0]
with pytest.raises(KeyError):
_ = f.bin[50000]
with pytest.raises(KeyError):
_ = f.bin[3214]
d = {BinField.Traces: 43,
BinField.SweepFrequencyStart: 11}
# assign multiple fields at once by using a dict
f.bin = d
f.flush()
assert 43 == f.bin[segyio.su.ntrpr]
assert 11 == f.bin[segyio.su.hsfs]
d = {BinField.Traces: 45,
BinField.SweepFrequencyStart: 10}
# assign multiple values using alternative syntax
f.bin.update(d)
f.flush()
assert 45 == f.bin[segyio.su.ntrpr]
assert 10 == f.bin[segyio.su.hsfs]
# accept anything with a key-value structure
f.bin.update([(segyio.su.jobid, 12), (segyio.su.lino, 4)])
f.bin.update(((segyio.su.reno, 3), (segyio.su.hdt, 7)))
f.flush()
assert 12 == f.bin[segyio.su.jobid]
assert 4 == f.bin[segyio.su.lino]
assert 3 == f.bin[segyio.su.reno]
assert 7 == f.bin[segyio.su.hdt]
# looking up multiple values at once returns a { TraceField: value } dict
assert d == f.bin[BinField.Traces, BinField.SweepFrequencyStart]
# copy a header
f.bin = f.bin
def test_write_header_update_atomic(small):
with segyio.open(small, "r+") as f:
orig = dict(f.header[10])
d = { 1: 10,
37: 4,
73: 15,
2: 10, # this key raises error
}
# use the same instance all the time, to also catch the case where
# update dirties the backing storage
header = f.header[10]
with pytest.raises(KeyError):
header.update(d)
assert orig == header
# flushing the header should just write a clean buffer
header.flush()
assert orig == header
del d[2]
header.update(d)
assert header[1] == 10
assert header[73] == 15
assert f.header[10][37] == 4
fresh = orig.copy()
fresh.update(d)
assert orig != header
assert orig != f.header[10]
assert fresh == f.header[10]
assert header == f.header[10]
def test_fopen_error():
# non-existent file
with pytest.raises(IOError):
segyio.open("no_dir/no_file")
# non-existant mode
with pytest.raises(ValueError):
segyio.open("test-data/small.sgy", "foo")
with pytest.raises(ValueError):
segyio.open("test-data/small.sgy", "r+b+toolong")
def test_wrong_lineno():
with pytest.raises(KeyError):
with segyio.open("test-data/small.sgy") as f:
_ = f.iline[3000]
with pytest.raises(KeyError):
with segyio.open("test-data/small.sgy") as f:
_ = f.xline[2]
def test_open_wrong_inline():
with pytest.raises(IndexError):
with segyio.open("test-data/small.sgy", "r", 2):
pass
with segyio.open("test-data/small.sgy", "r", 2, strict=False):
pass
def test_open_wrong_crossline():
with pytest.raises(IndexError):
with segyio.open("test-data/small.sgy", "r", 189, 2):
pass
with segyio.open("test-data/small.sgy", "r", 189, 2, strict=False):
pass
def test_wonky_dimensions():
with segyio.open("test-data/Mx1.sgy"):
pass
with segyio.open("test-data/1xN.sgy"):
pass
with segyio.open("test-data/1x1.sgy"):
pass
def test_open_fails_unstructured():
with segyio.open("test-data/small.sgy", "r", 37, strict=False) as f:
with pytest.raises(ValueError):
_ = f.iline[10]
with pytest.raises(ValueError):
_ = f.iline[:, :]
with pytest.raises(ValueError):
_ = f.xline[:, :]
# operations that don't rely on geometry still works
assert f.header[2][189] == 1
assert (list(f.attributes(189)[:]) ==
[(i // 5) + 1 for i in range(len(f.trace))])
def test_write_with_narrowing(small):
with segyio.open(small, mode = 'r+') as f:
with pytest.warns(RuntimeWarning):
ones = np.ones(len(f.samples), dtype=np.float64)
f.trace[0] = ones
assert np.array_equal(f.trace[0], ones)
with pytest.warns(RuntimeWarning):
twos = [np.single(2.0) for _ in range(len(f.samples))]
f.trace[1] = twos
assert np.array_equal(f.trace[1], twos)
with pytest.warns(RuntimeWarning):
first = f.ilines[0]
shape = f.iline[first].shape
ones = np.ones(shape, dtype=np.float64)
f.iline[first] = ones
assert np.array_equal(f.iline[first], ones)
with pytest.warns(RuntimeWarning):
last = f.xlines[-1]
shape = f.xline[last].shape
threes = np.ones(shape, dtype=np.float64) * 3
f.xline[last] = threes
assert np.array_equal(f.xline[last], threes)
def test_write_with_array_likes(small):
with segyio.open(small, mode = 'r+') as f:
with pytest.warns(RuntimeWarning):
ones = np.ones(3 * len(f.samples), dtype='single')
# ::3 makes the array non-contiguous
f.trace[0] = ones[::3]
assert np.array_equal(f.trace[0], ones[::3])
with pytest.warns(RuntimeWarning):
ones = np.ones(len(f.samples), dtype='single')
f.trace[0] = (1 for _ in range(len(f.samples)))
assert np.array_equal(f.trace[0], ones)
def test_assign_all_traces(small):
orig = str(small.dirname + '/small.sgy')
copy = str(small.dirname + '/copy.sgy')
shutil.copy(orig, copy)
with segyio.open(orig) as f:
traces = f.trace.raw[:] * 2.0
with segyio.open(copy, 'r+') as f:
f.trace[:] = traces[:]
with segyio.open(copy) as f:
assert np.array_equal(f.trace.raw[:], traces)
def test_traceaccess_from_array():
a = np.arange(10, dtype=int)
b = np.arange(10, dtype=np.int32)
c = np.arange(10, dtype=np.int64)
d = np.arange(10, dtype=np.intc)
with segyio.open("test-data/small.sgy") as f:
_ = f.trace[a[0]]
_ = f.trace[b[1]]
_ = f.trace[c[2]]
_ = f.trace[d[3]]
def test_create_sgy(small):
orig = str(small.dirname + '/small.sgy')
fresh = str(small.dirname + '/fresh.sgy')
with segyio.open(orig) as src:
spec = segyio.spec()
spec.format = int(src.format)
spec.sorting = int(src.sorting)
spec.samples = src.samples
spec.ilines = src.ilines
spec.xlines = src.xlines
with segyio.create(fresh, spec) as dst:
dst.text[0] = src.text[0]
dst.bin = src.bin
# copy all headers
dst.header = src.header
for i, srctr in enumerate(src.trace):
dst.trace[i] = srctr
dst.trace = src.trace
# this doesn't work yet, some restructuring is necessary
# if it turns out to be a desired feature it's rather easy to do
# for dsth, srch in zip(dst.header, src.header):
# dsth = srch
# for dsttr, srctr in zip(dst.trace, src.trace):
# dsttr = srctr
assert filecmp.cmp(orig, fresh)
def test_ref_getitem(small):
with segyio.open(small, mode = 'r+') as f:
with f.trace.ref as ref:
expected = ref[10].copy()
x = ref[10]
y = ref[10]
x[5] = 0
# getting a new trace within the same with block should not
# invalidate other refs
y = ref[11]
x[6] = 1.6721
x[5] = 52
y[0] = 0
assert ref[10][5] == 52
assert ref[10][6] == approx(1.6721)
assert len(ref.refs) == 2
z = ref[12]
z[0] = 0
assert len(ref.refs) == 3
x, y = None, None
ref.flush()
assert len(ref.refs) == 1
with segyio.open(small) as f:
expected[5] = 52
expected[6] = 1.6721
npt.assert_array_almost_equal(expected, f.trace[10])
def test_ref_inplace_add_foreach(small):
with segyio.open(small, mode = 'r+') as f:
expected = f.trace.raw[:] + 1.617
with f.trace.ref as ref:
for x in ref[:]:
x += 1.617
with segyio.open(small) as f:
npt.assert_array_almost_equal(expected, f.trace.raw[:])
def test_ref_preserve_change_except_block(small):
with segyio.open(small, mode = 'r+') as f:
expected = f.trace.raw[:]
expected[10][0] = 0
with f.trace.ref as ref:
try:
for i, x in enumerate(ref[:]):
if i == 10: raise RuntimeError
except RuntimeError:
x[0] = 0
with segyio.open(small) as f:
result = f.trace.raw[:]
npt.assert_array_almost_equal(expected[10], result[10])
npt.assert_array_almost_equal(expected, result)
def test_ref_post_loop_var(small):
with segyio.open(small, mode = 'r+') as f:
expected = f.trace[-1]
expected[0] = 1.617
with f.trace.ref as ref:
for x in ref[:]: pass
x[0] = 1.617
with segyio.open(small) as f:
npt.assert_array_almost_equal(expected, f.trace[-1])
def test_ref_sliced(small):
with segyio.open(small, mode = 'r+') as f:
expected = f.trace.raw[:]
expected[10:15] += expected[:5]
with f.trace.ref as ref:
for x, y in zip(ref[10:15], f.trace[:]):
np.copyto(x, x + y)
with segyio.open(small) as f:
npt.assert_array_almost_equal(expected, f.trace.raw[:])
def test_ref_mixed_for_else(small):
with segyio.open(small, mode = 'r+') as f:
samples = len(f.samples)
zeros = np.zeros(samples, dtype = f.dtype)
ones = np.ones(samples, dtype = f.dtype)
expected = f.trace.raw[:]
expected[7] = zeros
expected[5:10] += 1.617
expected[9] = ones
with f.trace.ref as ref:
ref[7] = zeros
for x in ref[5:10]:
# break won't run, so enter else block
if len(x) == 0: break
x += 1.617
else: # else should preserve last x
np.copyto(x, ones)
with segyio.open(small) as f:
npt.assert_array_almost_equal(expected, f.trace.raw[:])
def test_ref_new_file(small):
# this is the case the trace.ref feature was designed to support, namely
# creating a file trace-by-trace based on some transformation of another
# file, or an operation on multiple, where the trace index itself is
# uninteresting.
orig = str(small.dirname + '/small.sgy')
fresh = str(small.dirname + '/fresh.sgy')
with segyio.open(orig) as src:
spec = segyio.tools.metadata(src)
with segyio.create(fresh, spec) as dst:
dst.text[0] = src.text[0]
dst.bin = src.bin
# copy all headers
dst.header = src.header
with dst.trace.ref as ref:
for x, y in zip(ref[:], src.trace):
# x default-inits to 0, so += is essentially copyto()
# since traces hasn't been written yet, this has to handle
# read miss errors
x += y
with segyio.open(fresh) as dst:
npt.assert_array_almost_equal(src.trace.raw[:], dst.trace.raw[:])
def test_create_sgy_truncate(small):
orig = str(small.dirname + '/small.sgy')
trunc = str(small.dirname + '/text-truncated.sgy')
with segyio.open(orig) as src:
spec = segyio.tools.metadata(src)
# repeat the text header 3 times
text = src.text[0]
text = text + text + text
with segyio.create(trunc, spec) as dst:
dst.bin = src.bin
dst.text[0] = text
dst.header = src.header
for i, srctr in enumerate(src.trace):
dst.trace[i] = srctr
dst.trace = src.trace
assert filecmp.cmp(orig, trunc)
def test_create_sgy_shorter_traces(small):
orig = str(small.dirname + '/small.sgy')
fresh = str(small.dirname + '/small_created_shorter.sgy')
with segyio.open(orig) as src:
spec = segyio.spec()
spec.format = int(src.format)
spec.sorting = int(src.sorting)
spec.samples = src.samples[:20] # reduces samples per trace
spec.ilines = src.ilines
spec.xlines = src.xlines
with segyio.create(fresh, spec) as dst:
for i, srch in enumerate(src.header):
dst.header[i] = srch
d = {TraceField.INLINE_3D: srch[TraceField.INLINE_3D] + 100}
dst.header[i] = d
for lineno in dst.ilines:
dst.iline[lineno] = src.iline[lineno]
# alternative form using left-hand-side slices
dst.iline[2:4] = src.iline
for lineno in dst.xlines:
dst.xline[lineno] = src.xline[lineno]
with segyio.open(fresh) as dst:
assert 20 == len(dst.samples)
assert [x + 100 for x in src.ilines] == list(dst.ilines)
@pytest.mark.parametrize('endian', ['lsb', 'msb'])
def test_create_from_naught(endian, tmpdir):
spec = segyio.spec()
spec.format = 5
spec.sorting = 1
spec.samples = range(150)
spec.ilines = range(1, 11)
spec.xlines = range(1, 6)
spec.endian = endian
with segyio.create(tmpdir / "mk.sgy", spec) as dst:
tr = np.arange(start=1.000, stop=1.151, step=0.001, dtype=np.single)
for i in range(len(dst.trace)):
dst.trace[i] = tr
tr += 1.000
for il in spec.ilines:
dst.header.iline[il] = {TraceField.INLINE_3D: il}
for xl in spec.xlines:
dst.header.xline[xl] = {TraceField.CROSSLINE_3D: xl}
# Set header field 'offset' to 1 in all headers
dst.header = {TraceField.offset: 1}
with segyio.open(tmpdir / "mk.sgy", endian = endian) as f:
assert 1 == approx(f.trace[0][0], abs=1e-4)
assert 1.001 == approx(f.trace[0][1], abs=1e-4)
assert 1.149 == approx(f.trace[0][-1], abs=1e-4)
assert 50.100 == approx(f.trace[-1][100], abs=1e-4)
assert f.header[0][TraceField.offset] == f.header[1][TraceField.offset]
assert 1 == f.header[1][TraceField.offset]
assert f.sorting == TraceSortingFormat.CROSSLINE_SORTING
@pytest.mark.parametrize('endian', ['lsb', 'msb'])
def test_create_from_naught_prestack(endian, tmpdir):
spec = segyio.spec()
spec.format = 5
#spec.sorting not set by test design
spec.samples = range(7)
spec.ilines = range(1, 4)
spec.xlines = range(1, 3)
spec.offsets = range(1, 6)
spec.endian = endian
with segyio.create(tmpdir / "mk-ps.sgy", spec) as dst:
arr = np.arange(start=0.000,
stop=0.007,
step=0.001,
dtype=np.single)
arr = np.concatenate([[arr + 0.01], [arr + 0.02]], axis=0)
lines = [arr + i for i in spec.ilines]
cube = [(off * 100) + line for line in lines for off in spec.offsets]
dst.iline[:, :] = cube
for of in spec.offsets:
for il in spec.ilines:
dst.header.iline[il, of] = {TraceField.INLINE_3D: il,
TraceField.offset: of
}
for xl in spec.xlines:
dst.header.xline[xl, of] = {TraceField.CROSSLINE_3D: xl}
with segyio.open(tmpdir / "mk-ps.sgy", endian = endian) as f:
assert 101.010 == approx(f.trace[0][0], abs=1e-4)
assert 101.011 == approx(f.trace[0][1], abs=1e-4)
assert 101.016 == approx(f.trace[0][-1], abs=1e-4)
assert 503.025 == approx(f.trace[-1][5], abs=1e-4)
assert f.header[0][TraceField.offset] != f.header[1][TraceField.offset]
assert 1 == f.header[0][TraceField.offset]
assert 2 == f.header[1][TraceField.offset]
for x, y in zip(f.iline[:, :], cube):
assert list(x.flatten()) == list(y.flatten())
assert f.sorting == TraceSortingFormat.INLINE_SORTING
@pytest.mark.parametrize('endian', ['lsb', 'msb'])
def test_create_unstructured_hasattrs(endian, tmpdir):
spec = segyio.spec()
spec.format = 5
spec.samples = range(150)
spec.tracecount = 50
spec.endian = endian
with segyio.create(tmpdir / "mk.sgy", spec) as dst:
# accessing the sorting, inline and crossline attributes should work,
# but not raise errors
assert not dst.sorting
assert not dst.ilines
assert not dst.xlines
assert dst.unstructured
@pytest.mark.parametrize('endian', ['lsb', 'msb'])
def test_create_from_naught_unstructured(endian, tmpdir):
spec = segyio.spec()
spec.format = 5
spec.samples = range(150)
spec.tracecount = 50
spec.endian = endian
with segyio.create(tmpdir / "unstructured.sgy", spec) as dst:
tr = np.array(range(150), dtype = np.single)
for i in range(len(dst.trace)):
dst.trace[i] = tr
tr += 1
# Set header field 'offset' to 1 in all headers
dst.header = {TraceField.offset: 1}
with segyio.open(tmpdir / "unstructured.sgy",
ignore_geometry=True,
endian=endian) as f:
assert 1 == approx(f.trace[1][0], abs=1e-4)
assert 2 == approx(f.trace[1][1], abs=1e-4)
assert 150 == approx(f.trace[1][-1], abs=1e-4)
assert 149 == approx(f.trace[-1][100], abs=1e-4)
assert f.header[10][TraceField.offset] == f.header[25][TraceField.offset]
assert 1 == f.header[1][TraceField.offset]
def test_create_write_lines(tmpdir):
mklines(tmpdir / "mklines.sgy")
with segyio.open(tmpdir / "mklines.sgy") as f:
assert 1 == approx(f.iline[1][0][0], abs=1e-4)
assert 2.004 == approx(f.iline[2][0][4], abs=1e-4)
assert 2.014 == approx(f.iline[2][1][4], abs=1e-4)
assert 8.043 == approx(f.iline[8][4][3], abs=1e-4)
def test_create_sgy_skip_lines(tmpdir):
mklines(tmpdir / "lines.sgy")
with segyio.open(tmpdir / "lines.sgy") as src:
spec = segyio.spec()
spec.format = int(src.format)
spec.sorting = int(src.sorting)
spec.samples = src.samples
spec.ilines = src.ilines[::2]
spec.xlines = src.xlines[::2]
with segyio.create(tmpdir / "lines-halved.sgy", spec) as dst:
# use the inline headers as base
dst.header.iline = src.header.iline[::2]
# then update crossline numbers from the crossline headers
for xl in dst.xlines:
f = next(src.header.xline[xl])[TraceField.CROSSLINE_3D]
dst.header.xline[xl] = {TraceField.CROSSLINE_3D: f}
# but we override the last xline to be 6, not 5
dst.header.xline[5] = {TraceField.CROSSLINE_3D: 6}
dst.iline = src.iline[::2]
with segyio.open(tmpdir / "lines-halved.sgy") as f:
assert list(f.ilines) == list(spec.ilines)
assert list(f.xlines) == [1, 3, 6]
assert 1 == approx(f.iline[1][0][0], abs=1e-4)
assert 3.004 == approx(f.iline[3][0][4], abs=1e-4)
assert 3.014 == approx(f.iline[3][1][4], abs=1e-4)
assert 7.023 == approx(f.iline[7][2][3], abs=1e-4)
def mklines(fname):
spec = segyio.spec()
spec.format = 5
spec.sorting = 2
spec.samples = range(10)
spec.ilines = range(1, 11)
spec.xlines = range(1, 6)
# create a file with 10 inlines, with values on the form l.0tv where
# l = line no
# t = trace number (within line)
# v = trace value
# i.e. 2.043 is the value at inline 2's fourth trace's third value
with segyio.create(fname, spec) as dst:
ln = np.arange(start=0,
stop=0.001 * (5 * 10),
step=0.001,
dtype=np.single).reshape(5, 10)
for il in spec.ilines:
ln += 1
dst.header.iline[il] = {TraceField.INLINE_3D: il}
dst.iline[il] = ln
for xl in spec.xlines:
dst.header.xline[xl] = {TraceField.CROSSLINE_3D: xl}
def test_create_bad_specs(tmpdir):
class C:
pass
c = C()
mandatory = [('iline', 189),
('xline', 193),
('samples', [10, 11, 12]),
('format', 1),
('t0', 10.2)]
for attr, val in mandatory:
setattr(c, attr, val)
with pytest.raises(AttributeError):
with segyio.create(tmpdir / 'foo' + attr, c):
pass
c.tracecount = 10
with segyio.create(tmpdir / 'tracecount', c):
pass
del c.tracecount
c.ilines = [1, 2, 3]
with pytest.raises(AttributeError):
with segyio.create(tmpdir / 'ilines', c):
pass
c.xlines = [4, 6, 8]
with pytest.raises(AttributeError):
with segyio.create(tmpdir / 'xlines', c):
pass
c.offsets = [1]
with segyio.create(tmpdir / 'ok.sgy', c):
pass
@pytest.mark.parametrize(('openfn', 'kwargs'), smallfiles)
def test_segyio_types(openfn, kwargs):
with openfn(**kwargs) as f:
assert isinstance(f.sorting, int)
assert isinstance(f.ext_headers, int)
assert isinstance(f.tracecount, int)
assert isinstance(f.samples, np.ndarray)
from segyio.depth import Depth
assert isinstance(f.depth_slice, Depth)
assert isinstance(f.depth_slice[1], np.ndarray)
assert isinstance(f.depth_slice[1:23], GeneratorType)
assert isinstance(f.ilines, np.ndarray)
assert isinstance(f.iline, Line)
assert isinstance(f.iline[1], np.ndarray)
assert isinstance(f.iline[1:3], GeneratorType)
assert isinstance(f.iline[1][0], np.ndarray)
assert isinstance(f.iline[1][0:2], np.ndarray)
assert isinstance(float(f.iline[1][0][0]), float)
assert isinstance(f.iline[1][0][0:3], np.ndarray)
assert isinstance(f.xlines, np.ndarray)
assert isinstance(f.xline, Line)
assert isinstance(f.xline[21], np.ndarray)
assert isinstance(f.xline[21:23], GeneratorType)
assert isinstance(f.xline[21][0], np.ndarray)
assert isinstance(f.xline[21][0:2], np.ndarray)
assert isinstance(float(f.xline[21][0][0]), float)
assert isinstance(f.xline[21][0][0:3], np.ndarray)
assert isinstance(f.header, Header)
assert isinstance(f.header.iline, HeaderLine)
assert isinstance(f.header.iline[1], GeneratorType)
assert isinstance(next(f.header.iline[1]), Field)
assert isinstance(f.header.xline, HeaderLine)
assert isinstance(f.header.xline[21], GeneratorType)
assert isinstance(next(f.header.xline[21]), Field)
assert isinstance(f.trace, Trace)
assert isinstance(f.trace[0], np.ndarray)
@pytest.mark.parametrize(('openfn', 'kwargs'), small_segys)
def test_segyio_segy_only_types(openfn, kwargs):
with openfn(**kwargs) as f:
assert isinstance(f.bin, Field)
assert isinstance(f.text, object) # inner TextHeader instance
@pytest.mark.parametrize(('openfn', 'kwargs'), smallfiles)
def test_depth_slice_reading(openfn, kwargs):
from itertools import islice
with openfn(**kwargs) as f:
assert len(f.depth_slice) == len(f.samples)
for depth_sample in range(len(f.samples))[::5]:
depth_slice = f.depth_slice[depth_sample]
assert isinstance(depth_slice, np.ndarray)
assert depth_slice.shape == (5, 5)
for x, y in itertools.product(f.ilines, f.xlines):
i, j = x - f.ilines[0], y - f.xlines[0]
assert depth_slice[i][j] == approx(f.iline[x][j][depth_sample], abs=1e-6)
itr = iter(enumerate(f.depth_slice))
for index, depth_slice in itr:
assert isinstance(depth_slice, np.ndarray)
assert depth_slice.shape == (5, 5)
for x, y in itertools.product(f.ilines, f.xlines):
i, j = x - f.ilines[0], y - f.xlines[0]
assert depth_slice[i][j] == approx(f.iline[x][j][index], abs=1e-6)
next(islice(itr, 5, 5), None)
with pytest.raises(IndexError):
_ = f.depth_slice[len(f.samples)]
def test_depth_slice_array_shape():
with segyio.open("test-data/1xN.sgy") as f:
shape = (len(f.fast), len(f.slow))
assert f.depth_slice.shape == shape
@pytest.mark.parametrize(('openfn', 'kwargs'), smallfiles)
def test_depth_slice_unstructured(openfn, kwargs):
with openfn(ignore_geometry = True, **kwargs) as f:
traces = f.trace.raw[:]
shape = len(f.trace)
assert f.depth_slice.shape == shape
np.testing.assert_almost_equal(f.depth_slice[0], traces[:,0])
def test_depth_slice_writing(small):
from itertools import islice
buf = np.empty(shape=(5, 5), dtype=np.single)
def value(x, y):
return x + (1.0 // 5) * y
for x, y in itertools.product(range(5), range(5)):
buf[x][y] = value(x, y)
with segyio.open(small, "r+") as f:
f.depth_slice[7] = buf * 3.14 # assign to depth 7
assert np.allclose(f.depth_slice[7], buf * 3.14)
f.depth_slice = [buf * i for i in range(len(f.depth_slice))] # assign to all depths
itr = iter(enumerate(f.depth_slice))
for index, depth_slice in itr:
assert np.allclose(depth_slice, buf * index)
next(islice(itr, 3, 3), None)
@pytest.mark.parametrize('endian', ['little', 'big'])
def test_no_16bit_overflow_tracecount(endian, tmpdir):
spec = segyio.spec()
spec.format = 1
spec.sorting = 2
spec.samples = np.arange(501)
spec.ilines = np.arange(345)
spec.xlines = np.arange(250)
spec.endian = endian
# build a file with more than 65k traces, which would cause a 16bit int to
# overflow.
# see https://github.com/Statoil/segyio/issues/235
ones = np.ones(len(spec.samples), dtype = np.single)
with segyio.create(tmpdir / 'foo.sgy', spec) as f:
assert f.tracecount > 0
assert f.tracecount > 2**16 - 1
f.trace[-1] = ones
f.header[-1] = {
segyio.TraceField.INLINE_3D: 10,
segyio.TraceField.CROSSLINE_3D: 10,
segyio.TraceField.offset: 1,
}
def test_open_2byte_int_format():
with segyio.open('test-data/f3.sgy') as f:
assert int(f.format) == 3
assert len(f.samples) == 75
assert f.tracecount == 414
assert list(f.ilines) == list(range(111, 111 + 23))
assert list(f.xlines) == list(range(875, 875 + 18))
assert f.dtype == np.dtype(np.int16)
def test_readtrace_int16():
with segyio.open('test-data/f3.sgy') as f:
tr = f.trace[10]
assert list(tr[20:45: 5]) == [0, -1170, 5198, -2213, -888]
assert list(tr[40:19:-5]) == [-888, -2213, 5198, -1170, 0]
assert list(tr[53:50:-1]) == [-2609, -2625, 681]
@tmpfiles('test-data/f3.sgy')
def test_writetrace_int16(tmpdir):
with segyio.open(tmpdir / 'f3.sgy', mode = 'r+') as f:
tr = np.asarray(range(len(f.samples)), dtype = np.int16)
f.trace[0] = tr
f.trace[1] = tr + 1
with segyio.open(tmpdir / 'f3.sgy') as f:
# read both with trace and raw-with-slice, since sliced raw allocates
# and internal buffer that must match the type
assert np.array_equal(f.trace[0], tr)
assert np.array_equal(f.trace[1], tr + 1)
assert np.array_equal(f.trace.raw[:2], [tr, tr+1])
@tmpfiles('test-data/f3.sgy')
def test_write_iline_int16(tmpdir):
with segyio.open(tmpdir / 'f3.sgy', mode = 'r+') as f:
shape = f.iline[f.ilines[0]].shape
il = np.arange(np.prod(shape), dtype = np.int16).reshape(shape)
f.iline[f.ilines[0]] = il
with segyio.open(tmpdir / 'f3.sgy') as f:
assert np.array_equal(f.iline[f.ilines[0]], il)
def test_missing_format_ibmfloat_fallback(small):
with segyio.open(small, mode = 'r+') as f:
f.bin[segyio.su.format] = 0
with pytest.warns(UserWarning):
with segyio.open(small) as f:
assert int(f.format) == 1
assert f.dtype == np.dtype(np.float32)
def test_utf8_filename():
with segyio.open('test-data/小文件.sgy') as f:
assert list(f.ilines) == [1, 2, 3, 4, 5]
@tmpfiles(u'test-data/小文件.sgy')
def test_utf8_filename_pypath(tmpdir):
with segyio.open(tmpdir / '小文件.sgy') as f:
assert list(f.ilines) == [1, 2, 3, 4, 5]
def test_interpret_invalid_args():
with segyio.open("test-data/small.sgy", ignore_geometry=True) as f:
with pytest.raises(ValueError):
il = [1, 2, 3, 4]
xl = [20, 21, 22, 23, 24]
f.interpret(il, xl)
with pytest.raises(ValueError):
il = [1, 2, 3, 4, 5]
xl = [20, 21, 22, 23, 24]
f.interpret(il, xl, sorting=0)
with pytest.raises(ValueError):
il = [1, 2, 3, 4, 4]
xl = [20, 21, 22, 23, 24]
f.interpret(il, xl, sorting=0)
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