# -*- coding: utf-8 -*-
"""
The obspy.segy core test suite.
"""
import numpy as np
from obspy import UTCDateTime, read
from obspy.core.util import NamedTemporaryFile
from obspy.segy.core import isSEGY, readSEGY, writeSEGY, SEGYCoreWritingError
from obspy.segy.core import SEGYSampleIntervalError
from obspy.segy.core import isSU, readSU, writeSU
from obspy.segy.segy import SEGYError
from obspy.segy.segy import readSEGY as readSEGYInternal
from obspy.segy.tests.header import FILES, DTYPES
import os
from struct import unpack
import unittest
class SEGYCoreTestCase(unittest.TestCase):
"""
Test cases for SEG Y reading and writing..
"""
def setUp(self):
# directory where the test files are located
self.dir = os.path.dirname(__file__)
self.path = os.path.join(self.dir, 'data')
# All the files and information about them. These files will be used in
# most tests. data_sample_enc is the encoding of the data value and
# sample_size the size in bytes of these samples.
self.files = FILES
self.dtypes = DTYPES
def test_isSEGYFile(self):
"""
Tests the isSEGY method.
"""
# Test all files in the test directory.
for file in self.files.keys():
file = os.path.join(self.path, file)
self.assertEqual(isSEGY(file), True)
# Also check all the other files in the test directory and they should
# not work. Just check certain files to ensure reproducibility.
files = ['test_core.py', 'test_segy.py', '__init__.py']
for file in files:
file = os.path.join(self.dir, file)
self.assertEqual(isSEGY(file), False)
def test_isSUFile(self):
"""
Tests the isSU method.
"""
# Test all SEG Y files in the test directory.
for file in self.files.keys():
file = os.path.join(self.path, file)
self.assertEqual(isSU(file), False)
# Also check all the other files in the test directory and they should
# not work. Just check certain files to ensure reproducibility.
files = ['test_core.py', 'test_segy.py', '__init__.py']
for file in files:
file = os.path.join(self.dir, file)
self.assertEqual(isSU(file), False)
# Check an actual Seismic Unix file.
file = os.path.join(self.path, '1.su_first_trace')
self.assertEqual(isSU(file), True)
def test_readHeadOnly(self):
"""
Tests headonly flag on readSEGY and readSU functions.
"""
# readSEGY
file = os.path.join(self.path, '1.sgy_first_trace')
st = readSEGY(file, headonly=True)
self.assertEquals(st[0].stats.npts, 8000)
self.assertEquals(len(st[0].data), 0)
# readSU
file = os.path.join(self.path, '1.su_first_trace')
st = readSU(file, headonly=True)
self.assertEquals(st[0].stats.npts, 8000)
self.assertEquals(len(st[0].data), 0)
def test_enforcingTextualHeaderEncodingWhileReading(self):
"""
Tests whether or not the enforcing of the encoding of the textual file
header actually works.
"""
# File ld0042_file_00018.sgy_first_trace has an EBCDIC encoding.
file = os.path.join(self.path, 'ld0042_file_00018.sgy_first_trace')
# Read once with EBCDIC encoding and check if it is correct.
st1 = readSEGY(file, textual_header_encoding='EBCDIC')
self.assertTrue(st1.stats.textual_file_header[3:21] \
== 'CLIENT: LITHOPROBE')
# This should also be written the stats dictionary.
self.assertEqual(st1.stats.textual_file_header_encoding,
'EBCDIC')
# Reading again with ASCII should yield bad results. Lowercase keyword
# argument should also work.
st2 = readSEGY(file, textual_header_encoding='ascii')
self.assertFalse(st2.stats.textual_file_header[3:21] \
== 'CLIENT: LITHOPROBE')
self.assertEqual(st2.stats.textual_file_header_encoding,
'ASCII')
# Autodection should also write the textual file header encoding to the
# stats dictionary.
st3 = readSEGY(file)
self.assertEqual(st3.stats.textual_file_header_encoding,
'EBCDIC')
def test_enforcingEndiannessWhileWriting(self):
"""
Tests whether or not the enforcing of the endianness while writing
works.
"""
# File ld0042_file_00018.sgy_first_trace is in big endian.
file = os.path.join(self.path, 'ld0042_file_00018.sgy_first_trace')
st1 = readSEGY(file)
# First write should be big endian.
out_file = NamedTemporaryFile().name
writeSEGY(st1, out_file)
st2 = readSEGY(out_file)
os.remove(out_file)
self.assertEqual(st2.stats.endian, '>')
# Do once again to enforce big endian.
writeSEGY(st1, out_file, byteorder='>')
st3 = readSEGY(out_file)
os.remove(out_file)
self.assertEqual(st3.stats.endian, '>')
# Enforce little endian.
writeSEGY(st1, out_file, byteorder='<')
st4 = readSEGY(out_file)
os.remove(out_file)
self.assertEqual(st4.stats.endian, '<')
def test_settingDataEncodingWorks(self):
"""
Test whether or not the enforcing the data encoding works.
"""
# File ld0042_file_00018.sgy_first_trace uses IBM floating point
# representation.
file = os.path.join(self.path, 'ld0042_file_00018.sgy_first_trace')
st = readSEGY(file)
# First test if it even works.
out_file = NamedTemporaryFile().name
writeSEGY(st, out_file)
with open(out_file, 'rb') as f:
data1 = f.read()
os.remove(out_file)
# Write again and enforce encoding one which should yield the same
# result.
writeSEGY(st, out_file, data_encoding=1)
with open(out_file, 'rb') as f:
data2 = f.read()
os.remove(out_file)
self.assertTrue(data1 == data2)
# Writing IEEE floats which should not require any dtype changes.
writeSEGY(st, out_file, data_encoding=5)
with open(out_file, 'rb') as f:
data3 = f.read()
os.remove(out_file)
self.assertFalse(data1 == data3)
def test_readingAndWritingDifferentDataEncodings(self):
"""
Writes and reads different data encodings and checks if the data
remains the same.
"""
# The file uses IBM data encoding.
file = os.path.join(self.path, 'ld0042_file_00018.sgy_first_trace')
st = readSEGY(file)
data = st[0].data
# All working encodings with corresponding dtypes.
encodings = {1: 'float32',
2: 'int32',
3: 'int16',
5: 'float32'}
out_file = NamedTemporaryFile().name
# Loop over all encodings.
for data_encoding, dtype in encodings.iteritems():
this_data = np.require(data.copy(), dtype)
st[0].data = this_data
writeSEGY(st, out_file, data_encoding=data_encoding)
# Read again and compare data.
this_stream = readSEGY(out_file)
os.remove(out_file)
# Both should now be equal. Usually converting from IBM to IEEE
# floating point numbers might result in small rouning errors but
# in this case it seems to work. Might be different on different
# computers.
np.testing.assert_array_equal(this_data, this_stream[0].data)
def test_notMatchingDataEncodingAndDtypeRaises(self):
"""
obspy.segy does not automatically convert to the corresponding dtype.
"""
encodings = [1, 2, 3, 5]
# The file uses IBM data encoding.
file = os.path.join(self.path, 'ld0042_file_00018.sgy_first_trace')
st = readSEGY(file)
# Use float64 as the wrong encoding in every case.
st[0].data = np.require(st[0].data, 'float64')
out_file = NamedTemporaryFile().name
# Loop over all encodings.
for data_encoding in encodings:
self.assertRaises(SEGYCoreWritingError, writeSEGY, st, out_file,
data_encoding=data_encoding)
os.remove(out_file)
def test_invalidDataEncodingRaises(self):
"""
Using an invalid data encoding raises an error.
"""
file = os.path.join(self.path, 'ld0042_file_00018.sgy_first_trace')
st = readSEGY(file)
out_file = NamedTemporaryFile().name
self.assertRaises(SEGYCoreWritingError, writeSEGY, st, out_file,
data_encoding=0)
self.assertRaises(SEGYCoreWritingError, writeSEGY, st, out_file,
data_encoding='')
os.remove(out_file)
def test_enforcingTextualHeaderEncodingWhileWriting(self):
"""
Tests whether or not the enforcing of the endianness while writing
works.
"""
# File ld0042_file_00018.sgy_first_trace has an EBCDIC encoding.
file = os.path.join(self.path, 'ld0042_file_00018.sgy_first_trace')
st1 = readSEGY(file)
# Save the header to compare it later on.
with open(file, 'rb') as f:
header = f.read(3200)
# First write should remain EBCDIC.
out_file = NamedTemporaryFile().name
writeSEGY(st1, out_file)
st2 = readSEGY(out_file)
# Compare header.
with open(out_file, 'rb') as f:
new_header = f.read(3200)
self.assertTrue(header == new_header)
os.remove(out_file)
self.assertEqual(st2.stats.textual_file_header_encoding,
'EBCDIC')
# Do once again to enforce EBCDIC.
writeSEGY(st1, out_file, textual_header_encoding='EBCDIC')
st3 = readSEGY(out_file)
# Compare header.
with open(out_file, 'rb') as f:
new_header = f.read(3200)
self.assertTrue(header == new_header)
os.remove(out_file)
self.assertEqual(st3.stats.textual_file_header_encoding,
'EBCDIC')
# Enforce ASCII
writeSEGY(st1, out_file, textual_header_encoding='ASCII')
st4 = readSEGY(out_file)
# Compare header. Should not be equal this time.
with open(out_file, 'rb') as f:
new_header = f.read(3200)
self.assertFalse(header == new_header)
os.remove(out_file)
self.assertEqual(st4.stats.textual_file_header_encoding,
'ASCII')
def test_enforcingEndiannessWhileReading(self):
"""
Tests whether or not enforcing the endianness while reading a file
works. It will actually just deactivate the autodetection in case it
produced a wrong result. Using a wrong endianness while reading a file
will still produce an error because the data format will most likely be
wrong and therefore obspy.segy cannot unpack the data.
"""
# File ld0042_file_00018.sgy_first_trace is in big endian.
file = os.path.join(self.path, 'ld0042_file_00018.sgy_first_trace')
# This should work and write big endian to the stats dictionary.
st1 = readSEGY(file)
self.assertEqual(st1.stats.endian, '>')
# Doing the same with the right endianness should still work.
st2 = readSEGY(file, byteorder='>')
self.assertEqual(st2.stats.endian, '>')
# The wrong endianness should yield an key error because the routine to
# unpack the wrong data format code cannot be found.
self.assertRaises(KeyError, readSEGY, file, byteorder='<')
def test_readingUsingCore(self):
"""
This tests checks whether or not all necessary information is read
during reading with core. It actually just assumes the internal
SEGYFile object, which is thoroughly tested in
obspy.segy.tests.test_segy, is correct and compared all values to it.
This seems to be the easiest way to test everything.
"""
for file, _ in self.files.iteritems():
file = os.path.join(self.path, file)
# Read the file with the internal SEGY representation.
segy_file = readSEGYInternal(file)
# Read again using core.
st = readSEGY(file)
# They all should have length one because all additional traces
# have been removed.
self.assertEqual(len(st), 1)
# Assert the data is the same.
np.testing.assert_array_equal(segy_file.traces[0].data, st[0].data)
# Textual header.
self.assertEqual(segy_file.textual_file_header,
st.stats.textual_file_header)
# Textual_header_encoding.
self.assertEqual(segy_file.textual_header_encoding,
st.stats.textual_file_header_encoding)
# Endianness.
self.assertEqual(segy_file.endian, st.stats.endian)
# Data encoding.
self.assertEqual(segy_file.data_encoding,
st.stats.data_encoding)
# Test the file and trace binary headers.
for key, value in \
segy_file.binary_file_header.__dict__.iteritems():
self.assertEqual(getattr(st.stats.binary_file_header,
key), value)
for key, value in \
segy_file.traces[0].header.__dict__.iteritems():
self.assertEqual(getattr(st[0].stats.segy.trace_header, key),
value)
def test_writingUsingCore(self):
"""
Tests the writing of SEGY rev1 files using obspy.core. It just compares
the output of writing using obspy.core with the output of writing the
files using the internal SEGY object which is thoroughly tested in
obspy.segy.tests.test_segy.
"""
for file, _ in self.files.iteritems():
file = os.path.join(self.path, file)
# Read the file with the internal SEGY representation.
segy_file = readSEGYInternal(file)
# Read again using core.
st = readSEGY(file)
# Create two temporary files to write to.
out_file1 = NamedTemporaryFile().name
out_file2 = NamedTemporaryFile().name
# Write twice.
segy_file.write(out_file1)
writeSEGY(st, out_file2)
# Read and delete files.
with open(out_file1, 'rb') as f1:
data1 = f1.read()
with open(out_file2, 'rb') as f2:
data2 = f2.read()
os.remove(out_file1)
os.remove(out_file2)
# Test if they are equal.
self.assertEqual(data1[3200:3600], data2[3200:3600])
def test_invalidValuesForTextualHeaderEncoding(self):
"""
Invalid keyword arguments should be caught gracefully.
"""
file = os.path.join(self.path, 'ld0042_file_00018.sgy_first_trace')
self.assertRaises(SEGYError, readSEGY, file,
textual_header_encoding='BLUB')
def test_settingDeltaandSamplingRateinStats(self):
"""
Just checks if the delta and sampling rate attributes are correctly
set.
Testing the delta value is enough because the stats attribute takes
care that delta/sampling rate always match.
"""
file = os.path.join(self.path, '1.sgy_first_trace')
segy = readSEGY(file)
self.assertEqual(segy[0].stats.delta, 250E-6)
# The same with the Seismic Unix file.
file = os.path.join(self.path, '1.su_first_trace')
su = readSU(file)
self.assertEqual(su[0].stats.delta, 250E-6)
def test_writingNewSamplingRate(self):
"""
Setting a new sample rate works.
"""
file = os.path.join(self.path, '1.sgy_first_trace')
segy = readSEGY(file)
segy[0].stats.sampling_rate = 20
outfile = NamedTemporaryFile().name
writeSEGY(segy, outfile)
new_segy = readSEGY(outfile)
os.remove(outfile)
self.assertEqual(new_segy[0].stats.sampling_rate, 20)
# The same with the Seismic Unix file.
file = os.path.join(self.path, '1.su_first_trace')
_su = readSU(file)
def test_readingDate(self):
"""
Reads one file with a set date. The date has been read with SeisView 2
by the DMNG.
"""
# Date as read by SeisView 2.
date = UTCDateTime(year=2005, julday=353, hour=15, minute=7, second=54)
file = os.path.join(self.path, '1.sgy_first_trace')
segy = readSEGY(file)
self.assertEqual(date, segy[0].stats.starttime)
# The same with the Seismic Unix file.
file = os.path.join(self.path, '1.su_first_trace')
su = readSU(file)
self.assertEqual(date, su[0].stats.starttime)
def test_largeSampleRateIntervalRaises(self):
"""
SEG Y supports a sample interval from 1 to 65535 microseconds in steps
of 1 microsecond. Larger intervals cannot be supported due to the
definition of the SEG Y format. Therefore the smallest possible
sampling rate is ~ 15.26 Hz.
"""
outfile = NamedTemporaryFile().name
# Test for SEG Y.
file = os.path.join(self.path, '1.sgy_first_trace')
segy = readSEGY(file)
# Set the largest possible delta value which should just work.
segy[0].stats.delta = 0.065535
writeSEGY(segy, outfile)
os.remove(outfile)
# Slightly larger should raise.
segy[0].stats.delta = 0.065536
self.assertRaises(SEGYSampleIntervalError, writeSEGY, segy, outfile)
# Same for SU.
file = os.path.join(self.path, '1.su_first_trace')
su = readSU(file)
# Set the largest possible delta value which should just work.
su[0].stats.delta = 0.065535
writeSU(su, outfile)
os.remove(outfile)
# Slightly larger should raise.
su[0].stats.delta = 0.065536
self.assertRaises(SEGYSampleIntervalError, writeSU, su, outfile)
def test_writingSUFileWithNoHeader(self):
"""
If the trace has no trace.su attribute, one should still be able to
write a SeismicUnix file.
This is not recommended because most Trace.stats attributes will be
lost while writing SU.
"""
st = read()
del st[1:]
st[0].data = np.require(st[0].data, 'float32')
outfile = NamedTemporaryFile().name
st.write(outfile, format='SU')
st2 = read(outfile)
os.remove(outfile)
# Compare new and old stream objects. All the other header attributes
# will not be set.
np.testing.assert_array_equal(st[0].data, st2[0].data)
self.assertEqual(st[0].stats.starttime, st2[0].stats.starttime)
self.assertEqual(st[0].stats.endtime, st2[0].stats.endtime)
self.assertEqual(st[0].stats.sampling_rate, st2[0].stats.sampling_rate)
# Writing and reading this new stream object should not change
# anything.
st2.write(outfile, format='SU')
st3 = read(outfile)
os.remove(outfile)
np.testing.assert_array_equal(st2[0].data, st3[0].data)
# Remove the su attributes because they will not be equal due to lazy
# header attributes.
del st2[0].stats.su
del st3[0].stats.su
self.assertEqual(st2[0].stats, st3[0].stats)
def test_writingModifiedDate(self):
"""
Tests if the date in Trace.stats.starttime is correctly written in SU
and SEGY files.
"""
# Define new date!
new_date = UTCDateTime(2010, 7, 7, 2, 2, 2)
outfile = NamedTemporaryFile().name
# Test for SEGY.
file = os.path.join(self.path, 'example.y_first_trace')
segy = readSEGY(file)
segy[0].stats.starttime = new_date
writeSEGY(segy, outfile)
segy_new = readSEGY(outfile)
os.remove(outfile)
self.assertEqual(new_date, segy_new[0].stats.starttime)
# Test for SU.
file = os.path.join(self.path, '1.su_first_trace')
su = readSU(file)
su[0].stats.starttime = new_date
writeSU(su, outfile)
su_new = readSU(outfile)
os.remove(outfile)
self.assertEqual(new_date, su_new[0].stats.starttime)
def test_writingStarttimeTimestamp0(self):
"""
If the starttime of the Trace is UTCDateTime(0) it will be interpreted
as a missing starttime is not written. Test if this holds True.
"""
file = os.path.join(self.path, '1.sgy_first_trace')
# This file has a set date!
with open(file, 'rb') as f:
f.seek(3600 + 156, 0)
date_time = f.read(10)
year, julday, hour, minute, second = unpack('>5h', date_time)
self.assertEqual([year == 2005, julday == 353, hour == 15, minute == 7,
second == 54], 5 * [True])
# Read and set zero time.
segy = readSEGY(file)
segy[0].stats.starttime = UTCDateTime(0)
outfile = NamedTemporaryFile().name
writeSEGY(segy, outfile)
# Check the new date.
with open(outfile, 'rb') as f:
f.seek(3600 + 156, 0)
date_time = f.read(10)
os.remove(outfile)
year, julday, hour, minute, second = unpack('>5h', date_time)
self.assertEqual([year == 0, julday == 0, hour == 0, minute == 0,
second == 0], 5 * [True])
# The same for SU.
file = os.path.join(self.path, '1.su_first_trace')
# This file has a set date!
with open(file, 'rb') as f:
f.seek(156, 0)
date_time = f.read(10)
year, julday, hour, minute, second = unpack('<5h', date_time)
self.assertEqual([year == 2005, julday == 353, hour == 15, minute == 7,
second == 54], 5 * [True])
# Read and set zero time.
su = readSU(file)
su[0].stats.starttime = UTCDateTime(0)
outfile = NamedTemporaryFile().name
writeSU(su, outfile)
# Check the new date.
with open(outfile, 'rb') as f:
f.seek(156, 0)
date_time = f.read(10)
os.remove(outfile)
year, julday, hour, minute, second = unpack('<5h', date_time)
self.assertEqual([year == 0, julday == 0, hour == 0, minute == 0,
second == 0], 5 * [True])
def test_TwoDigitYearsSEGY(self):
"""
Even tough not specified in the 1975 SEG Y rev 1 standard, 2 digit
years should be read correctly. Some programs produce them.
Every two digit year < 30 will be mapped to 2000-2029 and every two
digit year >=30 <100 will be mapped to 1930-1999.
"""
# Read two artificial test files and check the years.
filename = os.path.join(self.path, 'one_trace_year_11.sgy')
st = readSEGY(filename)
self.assertEqual(2011, st[0].stats.starttime.year)
filename = os.path.join(self.path, 'one_trace_year_99.sgy')
st = readSEGY(filename)
self.assertEqual(1999, st[0].stats.starttime.year)
def test_TwoDigitYearsSU(self):
"""
Same test as test_TwoDigitYearsSEGY just for Seismic Unix files.
"""
# Read two artificial test files and check the years.
filename = os.path.join(self.path, 'one_trace_year_11.su')
st = readSU(filename)
self.assertEqual(2011, st[0].stats.starttime.year)
filename = os.path.join(self.path, 'one_trace_year_99.su')
st = readSU(filename)
self.assertEqual(1999, st[0].stats.starttime.year)
def test_issue377(self):
"""
Tests that readSEGY() and stream.write() should handle negative trace
header values.
"""
filename = os.path.join(self.path, 'one_trace_year_11.sgy')
st = readSEGY(filename)
st[0].stats.segy.trace_header['source_coordinate_x'] = -1
outfile = NamedTemporaryFile().name
st.write(outfile, format='SEGY')
os.remove(outfile)
def suite():
return unittest.makeSuite(SEGYCoreTestCase, 'test')
if __name__ == '__main__':
unittest.main(defaultTest='suite')
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