test_mseed_special_issues.py

# -*- coding: utf-8 -*-
from obspy import UTCDateTime, Stream, Trace, read
from obspy.core.util import NamedTemporaryFile
from obspy.core.util.attribdict import AttribDict
from obspy.core.util.decorator import skipIf
from obspy.mseed import util
from obspy.mseed.core import readMSEED, writeMSEED
from obspy.mseed.headers import clibmseed, PyFile_FromFile
from obspy.mseed.msstruct import _MSStruct
from struct import unpack
import ctypes as C
import numpy as np
import os
import sys
import unittest
import warnings


# some Python version don't support negative timestamps
NO_NEGATIVE_TIMESTAMPS = False
try:
    UTCDateTime(-50000)
except:
    NO_NEGATIVE_TIMESTAMPS = True


class MSEEDSpecialIssueTestCase(unittest.TestCase):
    """
    """
    def setUp(self):
        # Directory where the test files are located
        self.path = os.path.dirname(__file__)
        # mseed steim compression is big endian
        if sys.byteorder == 'little':
            self.swap = 1
        else:
            self.swap = 0

    def test_invalidRecordLength(self):
        """
        An invalid record length should raise an exception.
        """
        npts = 6000
        tempfile = NamedTemporaryFile().name
        np.random.seed(815)  # make test reproducable
        data = np.random.randint(-1000, 1000, npts).astype('int32')
        st = Stream([Trace(data=data)])
        # Writing should fail with invalid record lengths.
        # Not a power of 2.
        self.assertRaises(ValueError, writeMSEED, st, tempfile, format="MSEED",
                          reclen=1000)
        # Too small.
        self.assertRaises(ValueError, writeMSEED, st, tempfile, format="MSEED",
                          reclen=8)
        # Not a number.
        self.assertRaises(ValueError, writeMSEED, st, tempfile, format="MSEED",
                          reclen='A')
        os.remove(tempfile)

    def test_invalidEncoding(self):
        """
        An invalid encoding should raise an exception.
        """
        npts = 6000
        tempfile = NamedTemporaryFile().name
        np.random.seed(815)  # make test reproducable
        data = np.random.randint(-1000, 1000, npts).astype('int32')
        st = Stream([Trace(data=data)])
        # Writing should fail with invalid record lengths.
        # Wrong number.
        self.assertRaises(ValueError, writeMSEED, st, tempfile, format="MSEED",
                          encoding=2)
        # Wrong Text.
        self.assertRaises(ValueError, writeMSEED, st, tempfile, format="MSEED",
                          encoding='FLOAT_64')
        os.remove(tempfile)

    def test_ctypesArgtypes(self):
        """
        Test that ctypes argtypes are set for type checking
        """
        ArgumentError = C.ArgumentError
        cl = clibmseed
        args = [C.pointer(C.pointer(C.c_int())), 'a', 1, 1.5, 1, 0, 0, 0, 0]
        self.assertRaises(ArgumentError, cl.ms_readtraces, *args)
        self.assertRaises(TypeError, cl.ms_readtraces, *args[:-1])
        self.assertRaises(ArgumentError, cl.ms_readmsr_r, *args)
        self.assertRaises(TypeError, cl.ms_readmsr_r, *args[:-1])
        self.assertRaises(ArgumentError, cl.mst_printtracelist, *args[:5])
        self.assertRaises(ArgumentError, PyFile_FromFile, *args[:5])
        self.assertRaises(ArgumentError, cl.ms_detect, *args[:4])
        args.append(1)  # 10 argument function
        self.assertRaises(ArgumentError, cl.mst_packgroup, *args)
        args = ['hallo']  # one argument functions
        self.assertRaises(ArgumentError, cl.msr_starttime, *args)
        self.assertRaises(ArgumentError, cl.msr_endtime, *args)
        self.assertRaises(ArgumentError, cl.mst_init, *args)
        self.assertRaises(ArgumentError, cl.mst_free, *args)
        self.assertRaises(ArgumentError, cl.mst_initgroup, *args)
        self.assertRaises(ArgumentError, cl.mst_freegroup, *args)
        self.assertRaises(ArgumentError, cl.msr_init, *args)

    def test_brokenLastRecord(self):
        """
        Test if Libmseed is able to read files with broken last record. Use
        both methods, readMSTracesViaRecords and readMSTraces
        """
        file = os.path.join(self.path, "data", "brokenlastrecord.mseed")
        # independent reading of the data
        data_string = open(file, 'rb').read()[128:]  # 128 Bytes header
        data = util._unpackSteim2(data_string, 5980, swapflag=self.swap,
                                  verbose=0)
        # test readMSTraces
        data_record = readMSEED(file)[0].data
        np.testing.assert_array_equal(data, data_record)

    def test_oneSampleOverlap(self):
        """
        Both methods readMSTraces and readMSTracesViaRecords should recognize a
        single sample overlap.
        """
        # create a stream with one sample overlapping
        trace1 = Trace(data=np.zeros(1000))
        trace2 = Trace(data=np.zeros(10))
        trace2.stats.starttime = UTCDateTime(999)
        st = Stream([trace1, trace2])
        # write into MSEED
        tempfile = NamedTemporaryFile().name
        writeMSEED(st, tempfile, format="MSEED")
        # read it again
        new_stream = readMSEED(tempfile)
        self.assertEquals(len(new_stream), 2)
        # clean up
        os.remove(tempfile)

    def test_bugWriteReadFloat32SEEDWin32(self):
        """
        Test case for issue #64.
        """
        # create stream object
        data = np.array([395.07809448, 395.0782, 1060.28112793, -1157.37487793,
                         -1236.56237793, 355.07028198, -1181.42175293],
                        dtype=np.float32)
        st = Stream([Trace(data=data)])
        tempfile = NamedTemporaryFile().name
        writeMSEED(st, tempfile, format="MSEED")
        # read temp file directly without libmseed
        bin_data = open(tempfile, "rb").read()
        bin_data = np.array(unpack(">7f", bin_data[56:84]))
        np.testing.assert_array_equal(data, bin_data)
        # read via ObsPy
        st2 = readMSEED(tempfile)
        os.remove(tempfile)
        # test results
        np.testing.assert_array_equal(data, st2[0].data)

    @skipIf(NO_NEGATIVE_TIMESTAMPS,
            'times before 1970 are not supported on this operation system')
    def test_writeWithDateTimeBefore1970(self):
        """
        Write an stream via libmseed with a datetime before 1970.

        This test depends on the platform specific localtime()/gmtime()
        function.
        """
        # create trace
        tr = Trace(data=np.empty(1000))
        tr.stats.starttime = UTCDateTime("1969-01-01T00:00:00")
        # write file
        tempfile = NamedTemporaryFile().name
        writeMSEED(Stream([tr]), tempfile, format="MSEED")
        # read again
        stream = readMSEED(tempfile)
        os.remove(tempfile)
        stream.verify()

    def test_invalidDataType(self):
        """
        Writing data of type int64 and int16 are not supported.
        """
        npts = 6000
        tempfile = NamedTemporaryFile().name
        np.random.seed(815)  # make test reproducable
        # int64
        data = np.random.randint(-1000, 1000, npts).astype('int64')
        st = Stream([Trace(data=data)])
        self.assertRaises(Exception, st.write, tempfile, format="MSEED")
        # int8
        data = np.random.randint(-1000, 1000, npts).astype('int8')
        st = Stream([Trace(data=data)])
        self.assertRaises(Exception, st.write, tempfile, format="MSEED")
        os.remove(tempfile)

    def test_writeWrongEncoding(self):
        """
        Test to write a floating point mseed file with encoding STEIM1.
        An exception should be raised.
        """
        file = os.path.join(self.path, "data", \
                            "BW.BGLD.__.EHE.D.2008.001.first_record")
        tempfile = NamedTemporaryFile().name
        # Read the data and convert them to float
        st = read(file)
        st[0].data = st[0].data.astype('float32') + .5
        # Type is not consistent float32 cannot be compressed with STEIM1,
        # therefore a exception should be raised.
        self.assertRaises(Exception, st.write, tempfile, format="MSEED",
                encoding=10)
        os.remove(tempfile)

    def test_writeWrongEncodingViaMseedStats(self):
        """
        Test to write a floating point mseed file with encoding STEIM1 with the
        encoding set in stats.mseed.encoding.
        This will just raise a warning.
        """
        file = os.path.join(self.path, "data", \
                            "BW.BGLD.__.EHE.D.2008.001.first_record")
        tempfile = NamedTemporaryFile().name
        # Read the data and convert them to float
        st = read(file)
        st[0].data = st[0].data.astype('float32') + .5
        # Type is not consistent float32 cannot be compressed with STEIM1,
        # therefore a warning should be raised.
        self.assertEqual(st[0].stats.mseed.encoding, 'STEIM1')
        with warnings.catch_warnings(record=True):
            warnings.simplefilter('error', UserWarning)
            self.assertRaises(UserWarning, st.write, tempfile, format="MSEED")
        os.remove(tempfile)

    def test_wrongRecordLengthAsArgument(self):
        """
        Specifying a wrong record length should raise an error.
        """
        file = os.path.join(self.path, 'data', 'libmseed',
                            'float32_Float32_bigEndian.mseed')
        self.assertRaises(Exception, read, file, reclen=4096)

    def test_readQualityInformationWarns(self):
        """
        Reading the quality information while reading the data files is no more
        supported in newer obspy.mseed versions. Check that a warning is
        raised.
        Similar functionality is included in obspy.mseed.util.
        """
        timingqual = os.path.join(self.path, 'data', 'timingquality.mseed')
        with warnings.catch_warnings(record=True):
            warnings.simplefilter('error', DeprecationWarning)
            # This should not raise a warning.
            read(timingqual)
            # This should warn.
            self.assertRaises(DeprecationWarning, read, timingqual,
                              quality=True)

    def test_readWithMissingBlockette010(self):
        """
        Reading a Full/Mini-SEED w/o blockette 010 but blockette 008.
        """
        # 1 - Mini-SEED
        file = os.path.join(self.path, 'data', 'blockette008.mseed')
        tr = read(file)[0]
        self.assertEqual('BW.PART..EHZ', tr.id)
        self.assertEqual(1642, tr.stats.npts)
        # 2 - full SEED
        file = os.path.join(self.path, 'data',
                            'RJOB.BW.EHZ.D.300806.0000.fullseed')
        tr = read(file)[0]
        self.assertEqual('BW.RJOB..EHZ', tr.id)
        self.assertEqual(412, tr.stats.npts)

    def test_issue160(self):
        """
        Tests issue #160.

        Reading the header of SEED file.
        """
        file = os.path.join(self.path, 'data',
                            'BW.BGLD.__.EHE.D.2008.001.first_10_records')
        tr_one = read(file)[0]
        tr_two = read(file, headonly=True)[0]
        ms = AttribDict({'record_length': 512, 'encoding': 'STEIM1',
                         'filesize': 5120, 'dataquality': 'D',
                         'number_of_records': 10, 'byteorder': '>'})
        for tr in tr_one, tr_two:
            self.assertEqual('BW.BGLD..EHE', tr.id)
            self.assertEqual(ms, tr.stats.mseed)
            self.assertEqual(4120, tr.stats.npts)
            self.assertEqual(UTCDateTime(2008, 1, 1, 0, 0, 20, 510000),
                             tr.stats.endtime)

    def test_issue217(self):
        """
        Tests issue #217.

        Reading a MiniSEED file without sequence numbers and a record length of
        1024.
        """
        file = os.path.join(self.path, 'data',
                            'reclen_1024_without_sequence_numbers.mseed')
        tr = read(file)[0]
        ms = AttribDict({'record_length': 1024, 'encoding': 'STEIM1',
                         'filesize': 2048, 'dataquality': 'D',
                         'number_of_records': 2, 'byteorder': '>'})
        self.assertEqual('XX.STF1..HHN', tr.id)
        self.assertEqual(ms, tr.stats.mseed)
        self.assertEqual(932, tr.stats.npts)
        self.assertEqual(UTCDateTime(2007, 5, 31, 22, 45, 46, 720000),
                         tr.stats.endtime)

    def test_issue296(self):
        """
        Tests issue #296.
        """
        tempfile = NamedTemporaryFile().name
        # 1 - transform to np.float64 values
        st = read()
        for tr in st:
            tr.data = tr.data.astype('float64')
        # write a single trace automatically detecting encoding
        st[0].write(tempfile, format="MSEED")
        # write a single trace automatically detecting encoding
        st.write(tempfile, format="MSEED")
        # write a single trace with encoding 5
        st[0].write(tempfile, format="MSEED", encoding=5)
        # write a single trace with encoding 5
        st.write(tempfile, format="MSEED", encoding=5)
        # 2 - transform to np.float32 values
        st = read()
        for tr in st:
            tr.data = tr.data.astype('float32')
        # write a single trace automatically detecting encoding
        st[0].write(tempfile, format="MSEED")
        # write a single trace automatically detecting encoding
        st.write(tempfile, format="MSEED")
        # write a single trace with encoding 4
        st[0].write(tempfile, format="MSEED", encoding=4)
        # write a single trace with encoding 4
        st.write(tempfile, format="MSEED", encoding=4)
        # 3 - transform to np.int32 values
        st = read()
        for tr in st:
            tr.data = tr.data.astype('int32')
        # write a single trace automatically detecting encoding
        st[0].write(tempfile, format="MSEED")
        # write a single trace automatically detecting encoding
        st.write(tempfile, format="MSEED")
        # write a single trace with encoding 3
        st[0].write(tempfile, format="MSEED", encoding=3)
        # write the whole stream with encoding 3
        st.write(tempfile, format="MSEED", encoding=3)
        # write a single trace with encoding 10
        st[0].write(tempfile, format="MSEED", encoding=10)
        # write the whole stream with encoding 10
        st.write(tempfile, format="MSEED", encoding=10)
        # write a single trace with encoding 11
        st[0].write(tempfile, format="MSEED", encoding=11)
        # write the whole stream with encoding 11
        st.write(tempfile, format="MSEED", encoding=11)
        # 4 - transform to np.int16 values
        st = read()
        for tr in st:
            tr.data = tr.data.astype('int16')
        # write a single trace automatically detecting encoding
        st[0].write(tempfile, format="MSEED")
        # write a single trace automatically detecting encoding
        st.write(tempfile, format="MSEED")
        # write a single trace with encoding 1
        st[0].write(tempfile, format="MSEED", encoding=1)
        # write the whole stream with encoding 1
        st.write(tempfile, format="MSEED", encoding=1)
        # 5 - transform to ASCII values
        st = read()
        for tr in st:
            tr.data = tr.data.astype('|S1')
        # write a single trace automatically detecting encoding
        st[0].write(tempfile, format="MSEED")
        # write a single trace automatically detecting encoding
        st.write(tempfile, format="MSEED")
        # write a single trace with encoding 0
        st[0].write(tempfile, format="MSEED", encoding=0)
        # write the whole stream with encoding 0
        st.write(tempfile, format="MSEED", encoding=0)
        # cleanup
        os.remove(tempfile)

    def test_issue289(self):
        """
        Tests issue #289.

        Reading MiniSEED using start-/endtime outside of data should result in
        an empty Stream object.
        """
        # 1
        file = os.path.join(self.path, 'data', 'steim2.mseed')
        st = read(file, starttime=UTCDateTime() - 10, endtime=UTCDateTime())
        self.assertEqual(len(st), 0)
        # 2
        file = os.path.join(self.path, 'data', 'fullseed.mseed')
        st = read(file, starttime=UTCDateTime() - 10, endtime=UTCDateTime())
        self.assertEqual(len(st), 0)

    def test_issue312(self):
        """
        Tests issue #312

        The blkt_link struct was defined wrong.
        """
        filename = os.path.join(self.path, 'data',
                                'BW.BGLD.__.EHE.D.2008.001.first_10_records')
        # start and endtime
        ms = _MSStruct(filename)
        ms.read(-1, 0, 1, 0)
        blkt_link = ms.msr.contents.blkts.contents
        # The first blockette usually begins after 48 bytes. In the test file
        # it does.
        self.assertEqual(blkt_link.blktoffset, 48)
        # The first blockette is blockette 1000 in this file.
        self.assertEqual(blkt_link.blkt_type, 1000)
        # Only one blockette.
        self.assertEqual(blkt_link.next_blkt, 0)
        # Blockette data is 8 bytes - 4 bytes for the blockette header.
        self.assertEqual(blkt_link.blktdatalen, 4)
        del ms

    def test_issue272(self):
        """
        Tests issue #272

        Option headonly should not read the actual waveform data.
        """
        filename = os.path.join(self.path, 'data',
                                'BW.BGLD.__.EHE.D.2008.001.first_10_records')
        # everything
        st = read(filename)
        self.assertEqual(st[0].stats.npts, 4120)
        self.assertEqual(len(st[0].data), 4120)
        # headers only
        st = read(filename, headonly=True)
        self.assertEqual(st[0].stats.npts, 4120)
        self.assertEqual(len(st[0].data), 0)

    def test_issue325(self):
        """
        Tests issue #325: Use selection with non default dataquality flag.
        """
        filename = os.path.join(self.path, 'data', 'dataquality-m.mseed')
        # 1 - read all
        st = read(filename)
        self.assertEquals(len(st), 3)
        t1 = st[0].stats.starttime
        t2 = st[0].stats.endtime
        # 2 - select full time window
        st2 = read(filename, starttime=t1, endtime=t2)
        self.assertEquals(len(st2), 3)
        self.assertEquals(st, st2)
        # 3 - use selection
        st2 = read(filename, starttime=t1, endtime=t2, sourcename='*.*.*.*')
        self.assertEquals(len(st2), 3)
        self.assertEquals(st, st2)
        st2 = read(filename, starttime=t1, endtime=t2, sourcename='*')
        self.assertEquals(len(st2), 3)
        self.assertEquals(st, st2)
        # 4 - selection without times
        st2 = read(filename, sourcename='*.*.*.*')
        self.assertEquals(len(st2), 3)
        self.assertEquals(st, st2)
        st2 = read(filename, sourcename='*')
        self.assertEquals(len(st2), 3)
        self.assertEquals(st, st2)

    def test_issue332(self):
        """
        Tests issue #332

        Writing traces with wrong encoding in stats should raise only a user
        warning.
        """
        tempfile = NamedTemporaryFile().name
        st = read()
        tr = st[0]
        tr.data = tr.data.astype('float64') + .5
        tr.stats.mseed = {'encoding': 0}
        with warnings.catch_warnings(record=True):
            warnings.simplefilter('error', UserWarning)
            self.assertRaises(UserWarning, st.write, tempfile, format="MSEED")
        # clean up
        os.remove(tempfile)

    def test_issue341(self):
        """
        Tests issue #341

        Read/write of MiniSEED files with huge sampling rates/delta values.
        """
        tempfile = NamedTemporaryFile().name
        # 1 - sampling rate
        st = read()
        tr = st[0]
        tr.stats.sampling_rate = 1000000000.0
        tr.write(tempfile, format="MSEED")
        # read again
        st = read(tempfile)
        self.assertEquals(st[0].stats.sampling_rate, 1000000000.0)
        # 2 - delta
        st = read()
        tr = st[0]
        tr.stats.delta = 10000000.0
        tr.write(tempfile, format="MSEED")
        # read again
        st = read(tempfile)
        self.assertAlmostEquals(st[0].stats.delta, 10000000.0, 0)
        # clean up
        os.remove(tempfile)


def suite():
    return unittest.makeSuite(MSEEDSpecialIssueTestCase, 'test')


if __name__ == '__main__':
    unittest.main(defaultTest='suite')