Пример #1
0
    def test_read_wavename(self):
        from eqcorrscan.utils.sfile_util import readwavename
        import os

        testing_path = os.path.join(os.path.abspath(os.path.dirname(__file__)),
                                    'test_data', 'REA', 'TEST_',
                                    '19-0926-59L.S201309')
        wavefiles = readwavename(testing_path)
        self.assertEqual(len(wavefiles), 1)
Пример #2
0
    def test_read_wavename(self):
        from eqcorrscan.utils.sfile_util import readwavename
        import os

        testing_path = os.path.join(os.path.abspath(os.path.dirname(__file__)),
                                    'test_data', 'REA', 'TEST_',
                                    '19-0926-59L.S201309')
        wavefiles = readwavename(testing_path)
        self.assertEqual(len(wavefiles), 1)
Пример #3
0
 def setUpClass(cls):
     cls.testing_path = os.path.join(
         os.path.abspath(os.path.dirname(__file__)), 'test_data')
     sfile = os.path.join(cls.testing_path, 'REA', 'TEST_',
                          '01-0411-15L.S201309')
     cls.event = read_event(sfile)
     cls.wavfiles = readwavename(sfile)
     cls.datapath = os.path.join(cls.testing_path, 'WAV', 'TEST_')
     cls.st = read(os.path.join(cls.datapath, cls.wavfiles[0]))
     cls.respdir = cls.testing_path
Пример #4
0
    def test_read_write(self):
        """
        Function to test the read and write capabilities of sfile_util.
        """
        import os
        from obspy.core.event import Catalog
        import obspy
        if int(obspy.__version__.split('.')[0]) >= 1:
            from obspy.core.event import read_events
        else:
            from obspy.core.event import readEvents as read_events

        # Set-up a test event
        test_event = basic_test_event()
        # Add the event to a catalogue which can be used for QuakeML testing
        test_cat = Catalog()
        test_cat += test_event
        # Write the catalog
        test_cat.write("Test_catalog.xml", format='QUAKEML')
        # Read and check
        read_cat = read_events("Test_catalog.xml")
        os.remove("Test_catalog.xml")
        self.assertEqual(read_cat[0].resource_id, test_cat[0].resource_id)
        self.assertEqual(read_cat[0].picks, test_cat[0].picks)
        self.assertEqual(read_cat[0].origins[0].resource_id,
                         test_cat[0].origins[0].resource_id)
        self.assertEqual(read_cat[0].origins[0].time,
                         test_cat[0].origins[0].time)
        # Note that time_residuel_RMS is not a quakeML format
        self.assertEqual(read_cat[0].origins[0].longitude,
                         test_cat[0].origins[0].longitude)
        self.assertEqual(read_cat[0].origins[0].latitude,
                         test_cat[0].origins[0].latitude)
        self.assertEqual(read_cat[0].origins[0].depth,
                         test_cat[0].origins[0].depth)
        self.assertEqual(read_cat[0].magnitudes, test_cat[0].magnitudes)
        self.assertEqual(read_cat[0].event_descriptions,
                         test_cat[0].event_descriptions)
        self.assertEqual(read_cat[0].amplitudes[0].resource_id,
                         test_cat[0].amplitudes[0].resource_id)
        self.assertEqual(read_cat[0].amplitudes[0].period,
                         test_cat[0].amplitudes[0].period)
        self.assertEqual(read_cat[0].amplitudes[0].unit,
                         test_cat[0].amplitudes[0].unit)
        self.assertEqual(read_cat[0].amplitudes[0].generic_amplitude,
                         test_cat[0].amplitudes[0].generic_amplitude)
        self.assertEqual(read_cat[0].amplitudes[0].pick_id,
                         test_cat[0].amplitudes[0].pick_id)
        self.assertEqual(read_cat[0].amplitudes[0].waveform_id,
                         test_cat[0].amplitudes[0].waveform_id)

        # Check the read-write s-file functionality
        sfile = eventtosfile(test_cat[0],
                             userID='TEST',
                             evtype='L',
                             outdir='.',
                             wavefiles='test',
                             explosion=True,
                             overwrite=True)
        del read_cat
        self.assertEqual(readwavename(sfile), ['test'])
        read_cat = Catalog()
        read_cat += readpicks(sfile)
        os.remove(sfile)
        self.assertEqual(read_cat[0].picks[0].time, test_cat[0].picks[0].time)
        self.assertEqual(read_cat[0].picks[0].backazimuth,
                         test_cat[0].picks[0].backazimuth)
        self.assertEqual(read_cat[0].picks[0].onset,
                         test_cat[0].picks[0].onset)
        self.assertEqual(read_cat[0].picks[0].phase_hint,
                         test_cat[0].picks[0].phase_hint)
        self.assertEqual(read_cat[0].picks[0].polarity,
                         test_cat[0].picks[0].polarity)
        self.assertEqual(read_cat[0].picks[0].waveform_id.station_code,
                         test_cat[0].picks[0].waveform_id.station_code)
        self.assertEqual(read_cat[0].picks[0].waveform_id.channel_code[-1],
                         test_cat[0].picks[0].waveform_id.channel_code[-1])
        # assert read_cat[0].origins[0].resource_id ==\
        #     test_cat[0].origins[0].resource_id
        self.assertEqual(read_cat[0].origins[0].time,
                         test_cat[0].origins[0].time)
        # Note that time_residuel_RMS is not a quakeML format
        self.assertEqual(read_cat[0].origins[0].longitude,
                         test_cat[0].origins[0].longitude)
        self.assertEqual(read_cat[0].origins[0].latitude,
                         test_cat[0].origins[0].latitude)
        self.assertEqual(read_cat[0].origins[0].depth,
                         test_cat[0].origins[0].depth)
        self.assertEqual(read_cat[0].magnitudes[0].mag,
                         test_cat[0].magnitudes[0].mag)
        self.assertEqual(read_cat[0].magnitudes[1].mag,
                         test_cat[0].magnitudes[1].mag)
        self.assertEqual(read_cat[0].magnitudes[2].mag,
                         test_cat[0].magnitudes[2].mag)
        self.assertEqual(read_cat[0].magnitudes[0].creation_info,
                         test_cat[0].magnitudes[0].creation_info)
        self.assertEqual(read_cat[0].magnitudes[1].creation_info,
                         test_cat[0].magnitudes[1].creation_info)
        self.assertEqual(read_cat[0].magnitudes[2].creation_info,
                         test_cat[0].magnitudes[2].creation_info)
        self.assertEqual(read_cat[0].magnitudes[0].magnitude_type,
                         test_cat[0].magnitudes[0].magnitude_type)
        self.assertEqual(read_cat[0].magnitudes[1].magnitude_type,
                         test_cat[0].magnitudes[1].magnitude_type)
        self.assertEqual(read_cat[0].magnitudes[2].magnitude_type,
                         test_cat[0].magnitudes[2].magnitude_type)
        self.assertEqual(read_cat[0].event_descriptions,
                         test_cat[0].event_descriptions)
        # assert read_cat[0].amplitudes[0].resource_id ==\
        #     test_cat[0].amplitudes[0].resource_id
        self.assertEqual(read_cat[0].amplitudes[0].period,
                         test_cat[0].amplitudes[0].period)
        self.assertEqual(read_cat[0].amplitudes[0].snr,
                         test_cat[0].amplitudes[0].snr)
        del read_cat
        # assert read_cat[0].amplitudes[0].pick_id ==\
        #     test_cat[0].amplitudes[0].pick_id
        # assert read_cat[0].amplitudes[0].waveform_id ==\
        #     test_cat[0].amplitudes[0].waveform_id

        # Test the wrappers for PICK and EVENTINFO classes
        picks, evinfo = eventtopick(test_cat)
        # Test the conversion back
        conv_cat = Catalog()
        conv_cat.append(picktoevent(evinfo, picks))
        self.assertEqual(conv_cat[0].picks[0].time, test_cat[0].picks[0].time)
        self.assertEqual(conv_cat[0].picks[0].backazimuth,
                         test_cat[0].picks[0].backazimuth)
        self.assertEqual(conv_cat[0].picks[0].onset,
                         test_cat[0].picks[0].onset)
        self.assertEqual(conv_cat[0].picks[0].phase_hint,
                         test_cat[0].picks[0].phase_hint)
        self.assertEqual(conv_cat[0].picks[0].polarity,
                         test_cat[0].picks[0].polarity)
        self.assertEqual(conv_cat[0].picks[0].waveform_id.station_code,
                         test_cat[0].picks[0].waveform_id.station_code)
        self.assertEqual(conv_cat[0].picks[0].waveform_id.channel_code[-1],
                         test_cat[0].picks[0].waveform_id.channel_code[-1])
        # self.assertEqual(read_cat[0].origins[0].resource_id,
        #                  test_cat[0].origins[0].resource_id)
        self.assertEqual(conv_cat[0].origins[0].time,
                         test_cat[0].origins[0].time)
        # Note that time_residuel_RMS is not a quakeML format
        self.assertEqual(conv_cat[0].origins[0].longitude,
                         test_cat[0].origins[0].longitude)
        self.assertEqual(conv_cat[0].origins[0].latitude,
                         test_cat[0].origins[0].latitude)
        self.assertEqual(conv_cat[0].origins[0].depth,
                         test_cat[0].origins[0].depth)
        self.assertEqual(conv_cat[0].magnitudes[0].mag,
                         test_cat[0].magnitudes[0].mag)
        self.assertEqual(conv_cat[0].magnitudes[1].mag,
                         test_cat[0].magnitudes[1].mag)
        self.assertEqual(conv_cat[0].magnitudes[2].mag,
                         test_cat[0].magnitudes[2].mag)
        self.assertEqual(conv_cat[0].magnitudes[0].creation_info,
                         test_cat[0].magnitudes[0].creation_info)
        self.assertEqual(conv_cat[0].magnitudes[1].creation_info,
                         test_cat[0].magnitudes[1].creation_info)
        self.assertEqual(conv_cat[0].magnitudes[2].creation_info,
                         test_cat[0].magnitudes[2].creation_info)
        self.assertEqual(conv_cat[0].magnitudes[0].magnitude_type,
                         test_cat[0].magnitudes[0].magnitude_type)
        self.assertEqual(conv_cat[0].magnitudes[1].magnitude_type,
                         test_cat[0].magnitudes[1].magnitude_type)
        self.assertEqual(conv_cat[0].magnitudes[2].magnitude_type,
                         test_cat[0].magnitudes[2].magnitude_type)
        self.assertEqual(conv_cat[0].event_descriptions,
                         test_cat[0].event_descriptions)
        # self.assertEqual(read_cat[0].amplitudes[0].resource_id,
        #                  test_cat[0].amplitudes[0].resource_id)
        self.assertEqual(conv_cat[0].amplitudes[0].period,
                         test_cat[0].amplitudes[0].period)
        self.assertEqual(conv_cat[0].amplitudes[0].snr,
                         test_cat[0].amplitudes[0].snr)
Пример #5
0
def from_sfile(sfile, lowcut, highcut, samp_rate, filt_order, length, swin,
               prepick=0.05, debug=0, plot=False):
    r"""Function to read in picks from sfile then generate the template from \
    the picks within this and the wavefile found in the pick file.

    :type sfile: string
    :param sfile: sfilename must be the \
        path to a seisan nordic type s-file containing waveform and pick \
        information.
    :type lowcut: float
    :param lowcut: Low cut (Hz), if set to None will look in template \
            defaults file
    :type highcut: float
    :param highcut: High cut (Hz), if set to None will look in template \
            defaults file
    :type samp_rate: float
    :param samp_rate: New sampling rate in Hz, if set to None will look in \
            template defaults file
    :type filt_order: int
    :param filt_order: Filter level, if set to None will look in \
            template defaults file
    :type swin: str
    :param swin: Either 'all', 'P' or 'S', to select which phases to output.
    :type length: float
    :param length: Extract length in seconds, if None will look in template \
            defaults file.
    :type prepick: float
    :param prepick: Length to extract prior to the pick in seconds.
    :type debug: int
    :param debug: Debug level, higher number=more output.
    :type plot: bool
    :param plot: Turns template plotting on or off.

    :returns: obspy.Stream Newly cut template

    .. warning:: This will use whatever data is pointed to in the s-file, if \
        this is not the coninuous data, we recommend using other functions. \
        Differences in processing between short files and day-long files \
        (inherent to resampling) will produce lower cross-correlations.
    """
    # Perform some checks first
    import os
    if not os.path.isfile(sfile):
        raise IOError('sfile does not exist')

    from eqcorrscan.utils import pre_processing
    from eqcorrscan.utils import sfile_util
    from obspy import read as obsread
    # Read in the header of the sfile
    wavefiles = sfile_util.readwavename(sfile)
    pathparts = sfile.split('/')[0:-1]
    new_path_parts = []
    for part in pathparts:
        if part == 'REA':
            part = 'WAV'
        new_path_parts.append(part)
    # * argument to allow .join() to accept a list
    wavpath = os.path.join(*new_path_parts) + '/'
    # In case of absolute paths (not handled with .split() --> .join())
    if sfile[0] == '/':
        wavpath = '/' + wavpath
    # Read in waveform file
    for wavefile in wavefiles:
        print(''.join(["I am going to read waveform data from: ", wavpath,
                       wavefile]))
        if 'st' not in locals():
            st = obsread(wavpath + wavefile)
        else:
            st += obsread(wavpath + wavefile)
    for tr in st:
        if tr.stats.sampling_rate < samp_rate:
            print('Sampling rate of data is lower than sampling rate asked ' +
                  'for')
            print('Not good practice for correlations: I will not do this')
            raise ValueError("Trace: " + tr.stats.station +
                             " sampling rate: " + str(tr.stats.sampling_rate))
    # Read in pick info
    catalog = sfile_util.readpicks(sfile)
    # Read the list of Picks for this event
    picks = catalog[0].picks
    print("I have found the following picks")
    for pick in picks:
        print(' '.join([pick.waveform_id.station_code,
                        pick.waveform_id.channel_code, pick.phase_hint,
                        str(pick.time)]))

    # Process waveform data
    st.merge(fill_value='interpolate')
    st = pre_processing.shortproc(st, lowcut, highcut, filt_order,
                                  samp_rate, debug)
    st1 = _template_gen(picks=picks, st=st, length=length, swin=swin,
                        prepick=prepick, plot=plot)
    return st1
Пример #6
0
    def test_read_write(self):
        """
        Function to test the read and write capabilities of sfile_util.
        """
        import os
        from obspy.core.event import Catalog
        import obspy
        if int(obspy.__version__.split('.')[0]) >= 1:
            from obspy.core.event import read_events
        else:
            from obspy.core.event import readEvents as read_events

        # Set-up a test event
        test_event = full_test_event()
        # Add the event to a catalogue which can be used for QuakeML testing
        test_cat = Catalog()
        test_cat += test_event
        # Write the catalog
        test_cat.write("Test_catalog.xml", format='QUAKEML')
        # Read and check
        read_cat = read_events("Test_catalog.xml")
        os.remove("Test_catalog.xml")
        self.assertEqual(read_cat[0].resource_id, test_cat[0].resource_id)
        for i in range(len(read_cat[0].picks)):
            for key in read_cat[0].picks[i].keys():
                # Ignore backazimuth errors and horizontal_slowness_errors
                if key in ['backazimuth_errors', 'horizontal_slowness_errors']:
                    continue
                self.assertEqual(read_cat[0].picks[i][key],
                                 test_cat[0].picks[i][key])
        self.assertEqual(read_cat[0].origins[0].resource_id,
                         test_cat[0].origins[0].resource_id)
        self.assertEqual(read_cat[0].origins[0].time,
                         test_cat[0].origins[0].time)
        # Note that time_residual_RMS is not a quakeML format
        self.assertEqual(read_cat[0].origins[0].longitude,
                         test_cat[0].origins[0].longitude)
        self.assertEqual(read_cat[0].origins[0].latitude,
                         test_cat[0].origins[0].latitude)
        self.assertEqual(read_cat[0].origins[0].depth,
                         test_cat[0].origins[0].depth)
        # Check magnitudes
        self.assertEqual(read_cat[0].magnitudes, test_cat[0].magnitudes)
        self.assertEqual(read_cat[0].event_descriptions,
                         test_cat[0].event_descriptions)
        # Check local magnitude amplitude
        self.assertEqual(read_cat[0].amplitudes[0].resource_id,
                         test_cat[0].amplitudes[0].resource_id)
        self.assertEqual(read_cat[0].amplitudes[0].period,
                         test_cat[0].amplitudes[0].period)
        self.assertEqual(read_cat[0].amplitudes[0].unit,
                         test_cat[0].amplitudes[0].unit)
        self.assertEqual(read_cat[0].amplitudes[0].generic_amplitude,
                         test_cat[0].amplitudes[0].generic_amplitude)
        self.assertEqual(read_cat[0].amplitudes[0].pick_id,
                         test_cat[0].amplitudes[0].pick_id)
        self.assertEqual(read_cat[0].amplitudes[0].waveform_id,
                         test_cat[0].amplitudes[0].waveform_id)
        # Check coda magnitude pick
        self.assertEqual(read_cat[0].amplitudes[1].resource_id,
                         test_cat[0].amplitudes[1].resource_id)
        self.assertEqual(read_cat[0].amplitudes[1].type,
                         test_cat[0].amplitudes[1].type)
        self.assertEqual(read_cat[0].amplitudes[1].unit,
                         test_cat[0].amplitudes[1].unit)
        self.assertEqual(read_cat[0].amplitudes[1].generic_amplitude,
                         test_cat[0].amplitudes[1].generic_amplitude)
        self.assertEqual(read_cat[0].amplitudes[1].pick_id,
                         test_cat[0].amplitudes[1].pick_id)
        self.assertEqual(read_cat[0].amplitudes[1].waveform_id,
                         test_cat[0].amplitudes[1].waveform_id)
        self.assertEqual(read_cat[0].amplitudes[1].magnitude_hint,
                         test_cat[0].amplitudes[1].magnitude_hint)
        self.assertEqual(read_cat[0].amplitudes[1].snr,
                         test_cat[0].amplitudes[1].snr)
        self.assertEqual(read_cat[0].amplitudes[1].category,
                         test_cat[0].amplitudes[1].category)

        # Check the read-write s-file functionality
        sfile = eventtosfile(test_cat[0],
                             userID='TEST',
                             evtype='L',
                             outdir='.',
                             wavefiles='test',
                             explosion=True,
                             overwrite=True)
        del read_cat
        self.assertEqual(readwavename(sfile), ['test'])
        read_cat = Catalog()
        read_cat += readpicks(sfile)
        os.remove(sfile)
        for i in range(len(read_cat[0].picks)):
            self.assertEqual(read_cat[0].picks[i].time,
                             test_cat[0].picks[i].time)
            self.assertEqual(read_cat[0].picks[i].backazimuth,
                             test_cat[0].picks[i].backazimuth)
            self.assertEqual(read_cat[0].picks[i].onset,
                             test_cat[0].picks[i].onset)
            self.assertEqual(read_cat[0].picks[i].phase_hint,
                             test_cat[0].picks[i].phase_hint)
            self.assertEqual(read_cat[0].picks[i].polarity,
                             test_cat[0].picks[i].polarity)
            self.assertEqual(read_cat[0].picks[i].waveform_id.station_code,
                             test_cat[0].picks[i].waveform_id.station_code)
            self.assertEqual(read_cat[0].picks[i].waveform_id.channel_code[-1],
                             test_cat[0].picks[i].waveform_id.channel_code[-1])
        # assert read_cat[0].origins[0].resource_id ==\
        #     test_cat[0].origins[0].resource_id
        self.assertEqual(read_cat[0].origins[0].time,
                         test_cat[0].origins[0].time)
        # Note that time_residual_RMS is not a quakeML format
        self.assertEqual(read_cat[0].origins[0].longitude,
                         test_cat[0].origins[0].longitude)
        self.assertEqual(read_cat[0].origins[0].latitude,
                         test_cat[0].origins[0].latitude)
        self.assertEqual(read_cat[0].origins[0].depth,
                         test_cat[0].origins[0].depth)
        self.assertEqual(read_cat[0].magnitudes[0].mag,
                         test_cat[0].magnitudes[0].mag)
        self.assertEqual(read_cat[0].magnitudes[1].mag,
                         test_cat[0].magnitudes[1].mag)
        self.assertEqual(read_cat[0].magnitudes[2].mag,
                         test_cat[0].magnitudes[2].mag)
        self.assertEqual(read_cat[0].magnitudes[0].creation_info,
                         test_cat[0].magnitudes[0].creation_info)
        self.assertEqual(read_cat[0].magnitudes[1].creation_info,
                         test_cat[0].magnitudes[1].creation_info)
        self.assertEqual(read_cat[0].magnitudes[2].creation_info,
                         test_cat[0].magnitudes[2].creation_info)
        self.assertEqual(read_cat[0].magnitudes[0].magnitude_type,
                         test_cat[0].magnitudes[0].magnitude_type)
        self.assertEqual(read_cat[0].magnitudes[1].magnitude_type,
                         test_cat[0].magnitudes[1].magnitude_type)
        self.assertEqual(read_cat[0].magnitudes[2].magnitude_type,
                         test_cat[0].magnitudes[2].magnitude_type)
        self.assertEqual(read_cat[0].event_descriptions,
                         test_cat[0].event_descriptions)
        # assert read_cat[0].amplitudes[0].resource_id ==\
        #     test_cat[0].amplitudes[0].resource_id
        self.assertEqual(read_cat[0].amplitudes[0].period,
                         test_cat[0].amplitudes[0].period)
        self.assertEqual(read_cat[0].amplitudes[0].snr,
                         test_cat[0].amplitudes[0].snr)
        # Check coda magnitude pick
        # Resource ids get overwritten because you can't have two the same in
        # memory
        # self.assertEqual(read_cat[0].amplitudes[1].resource_id,
        #                  test_cat[0].amplitudes[1].resource_id)
        self.assertEqual(read_cat[0].amplitudes[1].type,
                         test_cat[0].amplitudes[1].type)
        self.assertEqual(read_cat[0].amplitudes[1].unit,
                         test_cat[0].amplitudes[1].unit)
        self.assertEqual(read_cat[0].amplitudes[1].generic_amplitude,
                         test_cat[0].amplitudes[1].generic_amplitude)
        # Resource ids get overwritten because you can't have two the same in
        # memory
        # self.assertEqual(read_cat[0].amplitudes[1].pick_id,
        #                  test_cat[0].amplitudes[1].pick_id)
        self.assertEqual(read_cat[0].amplitudes[1].waveform_id.station_code,
                         test_cat[0].amplitudes[1].waveform_id.station_code)
        self.assertEqual(
            read_cat[0].amplitudes[1].waveform_id.channel_code,
            test_cat[0].amplitudes[1].waveform_id.channel_code[0] +
            test_cat[0].amplitudes[1].waveform_id.channel_code[-1])
        self.assertEqual(read_cat[0].amplitudes[1].magnitude_hint,
                         test_cat[0].amplitudes[1].magnitude_hint)
        # snr is not supported in s-file
        # self.assertEqual(read_cat[0].amplitudes[1].snr,
        #                  test_cat[0].amplitudes[1].snr)
        self.assertEqual(read_cat[0].amplitudes[1].category,
                         test_cat[0].amplitudes[1].category)
        del read_cat

        # Test a deliberate fail
        test_cat.append(full_test_event())
        with self.assertRaises(IOError):
            # Raises error due to multiple events in catalog
            sfile = eventtosfile(test_cat,
                                 userID='TEST',
                                 evtype='L',
                                 outdir='.',
                                 wavefiles='test',
                                 explosion=True,
                                 overwrite=True)
            # Raises error due to too long userID
            sfile = eventtosfile(test_cat[0],
                                 userID='TESTICLE',
                                 evtype='L',
                                 outdir='.',
                                 wavefiles='test',
                                 explosion=True,
                                 overwrite=True)
            # Raises error due to unrecognised event type
            sfile = eventtosfile(test_cat[0],
                                 userID='TEST',
                                 evtype='U',
                                 outdir='.',
                                 wavefiles='test',
                                 explosion=True,
                                 overwrite=True)
            # Raises error due to no output directory
            sfile = eventtosfile(test_cat[0],
                                 userID='TEST',
                                 evtype='L',
                                 outdir='albatross',
                                 wavefiles='test',
                                 explosion=True,
                                 overwrite=True)
            # Raises error due to incorrect wavefil formatting
            sfile = eventtosfile(test_cat[0],
                                 userID='TEST',
                                 evtype='L',
                                 outdir='.',
                                 wavefiles=1234,
                                 explosion=True,
                                 overwrite=True)
        with self.assertRaises(IndexError):
            invalid_origin = test_cat[0].copy()
            invalid_origin.origins = []
            sfile = eventtosfile(invalid_origin,
                                 userID='TEST',
                                 evtype='L',
                                 outdir='.',
                                 wavefiles='test',
                                 explosion=True,
                                 overwrite=True)
        with self.assertRaises(ValueError):
            invalid_origin = test_cat[0].copy()
            invalid_origin.origins[0].time = None
            sfile = eventtosfile(invalid_origin,
                                 userID='TEST',
                                 evtype='L',
                                 outdir='.',
                                 wavefiles='test',
                                 explosion=True,
                                 overwrite=True)
        # Write a near empty origin
        valid_origin = test_cat[0].copy()
        valid_origin.origins[0].latitude = None
        valid_origin.origins[0].longitude = None
        valid_origin.origins[0].depth = None
        sfile = eventtosfile(valid_origin,
                             userID='TEST',
                             evtype='L',
                             outdir='.',
                             wavefiles='test',
                             explosion=True,
                             overwrite=True)
        self.assertTrue(os.path.isfile(sfile))
        os.remove(sfile)
Пример #7
0
    def test_read_write(self):
        """
        Function to test the read and write capabilities of sfile_util.
        """
        import os
        from obspy.core.event import Catalog
        import obspy
        if int(obspy.__version__.split('.')[0]) >= 1:
            from obspy.core.event import read_events
        else:
            from obspy.core.event import readEvents as read_events

        # Set-up a test event
        test_event = full_test_event()
        # Add the event to a catalogue which can be used for QuakeML testing
        test_cat = Catalog()
        test_cat += test_event
        # Write the catalog
        test_cat.write("Test_catalog.xml", format='QUAKEML')
        # Read and check
        read_cat = read_events("Test_catalog.xml")
        os.remove("Test_catalog.xml")
        self.assertEqual(read_cat[0].resource_id, test_cat[0].resource_id)
        for i in range(len(read_cat[0].picks)):
            for key in read_cat[0].picks[i].keys():
                # Ignore backazimuth errors and horizontal_slowness_errors
                if key in ['backazimuth_errors', 'horizontal_slowness_errors']:
                    continue
                self.assertEqual(read_cat[0].picks[i][key],
                                 test_cat[0].picks[i][key])
        self.assertEqual(read_cat[0].origins[0].resource_id,
                         test_cat[0].origins[0].resource_id)
        self.assertEqual(read_cat[0].origins[0].time,
                         test_cat[0].origins[0].time)
        # Note that time_residual_RMS is not a quakeML format
        self.assertEqual(read_cat[0].origins[0].longitude,
                         test_cat[0].origins[0].longitude)
        self.assertEqual(read_cat[0].origins[0].latitude,
                         test_cat[0].origins[0].latitude)
        self.assertEqual(read_cat[0].origins[0].depth,
                         test_cat[0].origins[0].depth)
        # Check magnitudes
        self.assertEqual(read_cat[0].magnitudes, test_cat[0].magnitudes)
        self.assertEqual(read_cat[0].event_descriptions,
                         test_cat[0].event_descriptions)
        # Check local magnitude amplitude
        self.assertEqual(read_cat[0].amplitudes[0].resource_id,
                         test_cat[0].amplitudes[0].resource_id)
        self.assertEqual(read_cat[0].amplitudes[0].period,
                         test_cat[0].amplitudes[0].period)
        self.assertEqual(read_cat[0].amplitudes[0].unit,
                         test_cat[0].amplitudes[0].unit)
        self.assertEqual(read_cat[0].amplitudes[0].generic_amplitude,
                         test_cat[0].amplitudes[0].generic_amplitude)
        self.assertEqual(read_cat[0].amplitudes[0].pick_id,
                         test_cat[0].amplitudes[0].pick_id)
        self.assertEqual(read_cat[0].amplitudes[0].waveform_id,
                         test_cat[0].amplitudes[0].waveform_id)
        # Check coda magnitude pick
        self.assertEqual(read_cat[0].amplitudes[1].resource_id,
                         test_cat[0].amplitudes[1].resource_id)
        self.assertEqual(read_cat[0].amplitudes[1].type,
                         test_cat[0].amplitudes[1].type)
        self.assertEqual(read_cat[0].amplitudes[1].unit,
                         test_cat[0].amplitudes[1].unit)
        self.assertEqual(read_cat[0].amplitudes[1].generic_amplitude,
                         test_cat[0].amplitudes[1].generic_amplitude)
        self.assertEqual(read_cat[0].amplitudes[1].pick_id,
                         test_cat[0].amplitudes[1].pick_id)
        self.assertEqual(read_cat[0].amplitudes[1].waveform_id,
                         test_cat[0].amplitudes[1].waveform_id)
        self.assertEqual(read_cat[0].amplitudes[1].magnitude_hint,
                         test_cat[0].amplitudes[1].magnitude_hint)
        self.assertEqual(read_cat[0].amplitudes[1].snr,
                         test_cat[0].amplitudes[1].snr)
        self.assertEqual(read_cat[0].amplitudes[1].category,
                         test_cat[0].amplitudes[1].category)

        # Check the read-write s-file functionality
        sfile = eventtosfile(test_cat[0], userID='TEST',
                             evtype='L', outdir='.',
                             wavefiles='test', explosion=True, overwrite=True)
        del read_cat
        self.assertEqual(readwavename(sfile), ['test'])
        read_cat = Catalog()
        read_cat += readpicks(sfile)
        os.remove(sfile)
        for i in range(len(read_cat[0].picks)):
            self.assertEqual(read_cat[0].picks[i].time,
                             test_cat[0].picks[i].time)
            self.assertEqual(read_cat[0].picks[i].backazimuth,
                             test_cat[0].picks[i].backazimuth)
            self.assertEqual(read_cat[0].picks[i].onset,
                             test_cat[0].picks[i].onset)
            self.assertEqual(read_cat[0].picks[i].phase_hint,
                             test_cat[0].picks[i].phase_hint)
            self.assertEqual(read_cat[0].picks[i].polarity,
                             test_cat[0].picks[i].polarity)
            self.assertEqual(read_cat[0].picks[i].waveform_id.station_code,
                             test_cat[0].picks[i].waveform_id.station_code)
            self.assertEqual(read_cat[0].picks[i].waveform_id.channel_code[-1],
                             test_cat[0].picks[i].waveform_id.channel_code[-1])
        # assert read_cat[0].origins[0].resource_id ==\
        #     test_cat[0].origins[0].resource_id
        self.assertEqual(read_cat[0].origins[0].time,
                         test_cat[0].origins[0].time)
        # Note that time_residual_RMS is not a quakeML format
        self.assertEqual(read_cat[0].origins[0].longitude,
                         test_cat[0].origins[0].longitude)
        self.assertEqual(read_cat[0].origins[0].latitude,
                         test_cat[0].origins[0].latitude)
        self.assertEqual(read_cat[0].origins[0].depth,
                         test_cat[0].origins[0].depth)
        self.assertEqual(read_cat[0].magnitudes[0].mag,
                         test_cat[0].magnitudes[0].mag)
        self.assertEqual(read_cat[0].magnitudes[1].mag,
                         test_cat[0].magnitudes[1].mag)
        self.assertEqual(read_cat[0].magnitudes[2].mag,
                         test_cat[0].magnitudes[2].mag)
        self.assertEqual(read_cat[0].magnitudes[0].creation_info,
                         test_cat[0].magnitudes[0].creation_info)
        self.assertEqual(read_cat[0].magnitudes[1].creation_info,
                         test_cat[0].magnitudes[1].creation_info)
        self.assertEqual(read_cat[0].magnitudes[2].creation_info,
                         test_cat[0].magnitudes[2].creation_info)
        self.assertEqual(read_cat[0].magnitudes[0].magnitude_type,
                         test_cat[0].magnitudes[0].magnitude_type)
        self.assertEqual(read_cat[0].magnitudes[1].magnitude_type,
                         test_cat[0].magnitudes[1].magnitude_type)
        self.assertEqual(read_cat[0].magnitudes[2].magnitude_type,
                         test_cat[0].magnitudes[2].magnitude_type)
        self.assertEqual(read_cat[0].event_descriptions,
                         test_cat[0].event_descriptions)
        # assert read_cat[0].amplitudes[0].resource_id ==\
        #     test_cat[0].amplitudes[0].resource_id
        self.assertEqual(read_cat[0].amplitudes[0].period,
                         test_cat[0].amplitudes[0].period)
        self.assertEqual(read_cat[0].amplitudes[0].snr,
                         test_cat[0].amplitudes[0].snr)
        # Check coda magnitude pick
        # Resource ids get overwritten because you can't have two the same in
        # memory
        # self.assertEqual(read_cat[0].amplitudes[1].resource_id,
        #                  test_cat[0].amplitudes[1].resource_id)
        self.assertEqual(read_cat[0].amplitudes[1].type,
                         test_cat[0].amplitudes[1].type)
        self.assertEqual(read_cat[0].amplitudes[1].unit,
                         test_cat[0].amplitudes[1].unit)
        self.assertEqual(read_cat[0].amplitudes[1].generic_amplitude,
                         test_cat[0].amplitudes[1].generic_amplitude)
        # Resource ids get overwritten because you can't have two the same in
        # memory
        # self.assertEqual(read_cat[0].amplitudes[1].pick_id,
        #                  test_cat[0].amplitudes[1].pick_id)
        self.assertEqual(read_cat[0].amplitudes[1].waveform_id.station_code,
                         test_cat[0].amplitudes[1].waveform_id.station_code)
        self.assertEqual(read_cat[0].amplitudes[1].waveform_id.channel_code,
                         test_cat[0].amplitudes[1].
                         waveform_id.channel_code[0] +
                         test_cat[0].amplitudes[1].
                         waveform_id.channel_code[-1])
        self.assertEqual(read_cat[0].amplitudes[1].magnitude_hint,
                         test_cat[0].amplitudes[1].magnitude_hint)
        # snr is not supported in s-file
        # self.assertEqual(read_cat[0].amplitudes[1].snr,
        #                  test_cat[0].amplitudes[1].snr)
        self.assertEqual(read_cat[0].amplitudes[1].category,
                         test_cat[0].amplitudes[1].category)
        del read_cat

        # Test a deliberate fail
        test_cat.append(full_test_event())
        with self.assertRaises(IOError):
            # Raises error due to multiple events in catalog
            sfile = eventtosfile(test_cat, userID='TEST',
                                 evtype='L', outdir='.',
                                 wavefiles='test', explosion=True,
                                 overwrite=True)
            # Raises error due to too long userID
            sfile = eventtosfile(test_cat[0], userID='TESTICLE',
                                 evtype='L', outdir='.',
                                 wavefiles='test', explosion=True,
                                 overwrite=True)
            # Raises error due to unrecognised event type
            sfile = eventtosfile(test_cat[0], userID='TEST',
                                 evtype='U', outdir='.',
                                 wavefiles='test', explosion=True,
                                 overwrite=True)
            # Raises error due to no output directory
            sfile = eventtosfile(test_cat[0], userID='TEST',
                                 evtype='L', outdir='albatross',
                                 wavefiles='test', explosion=True,
                                 overwrite=True)
            # Raises error due to incorrect wavefil formatting
            sfile = eventtosfile(test_cat[0], userID='TEST',
                                 evtype='L', outdir='.',
                                 wavefiles=1234, explosion=True,
                                 overwrite=True)
        with self.assertRaises(IndexError):
            invalid_origin = test_cat[0].copy()
            invalid_origin.origins = []
            sfile = eventtosfile(invalid_origin, userID='TEST',
                                 evtype='L', outdir='.',
                                 wavefiles='test', explosion=True,
                                 overwrite=True)
        with self.assertRaises(ValueError):
            invalid_origin = test_cat[0].copy()
            invalid_origin.origins[0].time = None
            sfile = eventtosfile(invalid_origin, userID='TEST',
                                 evtype='L', outdir='.',
                                 wavefiles='test', explosion=True,
                                 overwrite=True)
        # Write a near empty origin
        valid_origin = test_cat[0].copy()
        valid_origin.origins[0].latitude = None
        valid_origin.origins[0].longitude = None
        valid_origin.origins[0].depth = None
        sfile = eventtosfile(valid_origin, userID='TEST',
                             evtype='L', outdir='.',
                             wavefiles='test', explosion=True,
                             overwrite=True)
        self.assertTrue(os.path.isfile(sfile))
        os.remove(sfile)
Пример #8
0
def write_correlations(event_list, wavbase, extract_len, pre_pick, shift_len,
                       lowcut=1.0, highcut=10.0, max_sep=4, min_link=8,
                       coh_thresh=0.0, coherence_weight=True, plotvar=False):
    """
    Function to write a dt.cc file for hypoDD input - takes an input list of
    events and computes pick refienements by correlation.

    :type event_list: list of tuple
    :param event_list: List of tuples of event_id (int) and sfile (String)
    :type wavbase: str
    :param wavbase: Path to the seisan wave directory that the wavefiles in the
                    S-files are stored
    :type extract_len: float
    :param extract_len: Length in seconds to extract around the pick
    :type pre_pick: float
    :param pre_pick: Time before the pick to start the correlation window
    :type shift_len: float
    :param shift_len: Time to allow pick to vary
    :type lowcut: float
    :param lowcut: Lowcut in Hz - default=1.0
    :type highcut: float
    :param highcut: Highcut in Hz - deafult=10.0
    :type max_sep: float
    :param max_sep: Maximum seperation between event pairs in km
    :type min_link: int
    :param min_link: Minimum links for an event to be paired
    :type coherence_weight: bool
    :param coherence_weight: Use coherence to weight the dt.cc file, or the \
        raw cross-correlation value, defaults to false which uses the cross-\
        correlation value.
    :type plotvar: bool
    :param plotvar: To show the pick-correction plots, defualts to False.

    .. warning:: This is not a fast routine!

    .. warning:: In contrast to seisan's \
        corr routine, but in accordance with the hypoDD manual, this outputs \
        corrected differential time.

    .. note:: Currently we have not implemented a method for taking \
        unassociated event objects and wavefiles.  As such if you have events \
        with associated wavefiles you are advised to generate Sfiles for each \
        event using the sfile_util module prior to this step.
    """
    import obspy
    if int(obspy.__version__.split('.')[0]) > 0:
        from obspy.signal.cross_correlation import xcorr_pick_correction
    else:
        from obspy.signal.cross_correlation import xcorrPickCorrection \
            as xcorr_pick_correction
    import matplotlib.pyplot as plt
    from obspy import read
    from eqcorrscan.utils.mag_calc import dist_calc
    import glob
    import warnings

    corr_list = []
    f = open('dt.cc', 'w')
    f2 = open('dt.cc2', 'w')
    for i, master in enumerate(event_list):
        master_sfile = master[1]
        master_event_id = master[0]
        master_picks = sfile_util.readpicks(master_sfile).picks
        master_event = sfile_util.readheader(master_sfile)
        master_ori_time = master_event.origins[0].time
        master_location = (master_event.origins[0].latitude,
                           master_event.origins[0].longitude,
                           master_event.origins[0].depth)
        master_wavefiles = sfile_util.readwavename(master_sfile)
        masterpath = glob.glob(wavbase + os.sep + master_wavefiles[0])
        if masterpath:
            masterstream = read(masterpath[0])
        if len(master_wavefiles) > 1:
            for wavefile in master_wavefiles:
                try:
                    masterstream += read(os.join(wavbase, wavefile))
                except:
                    continue
                    raise IOError("Couldn't find wavefile")
        for j in range(i+1, len(event_list)):
            # Use this tactic to only output unique event pairings
            slave_sfile = event_list[j][1]
            slave_event_id = event_list[j][0]
            slave_wavefiles = sfile_util.readwavename(slave_sfile)
            try:
                # slavestream=read(wavbase+'/*/*/'+slave_wavefiles[0])
                slavestream = read(wavbase + os.sep + slave_wavefiles[0])
            except:
                # print(slavestream)
                raise IOError('No wavefile found: '+slave_wavefiles[0]+' ' +
                              slave_sfile)
            if len(slave_wavefiles) > 1:
                for wavefile in slave_wavefiles:
                    # slavestream+=read(wavbase+'/*/*/'+wavefile)
                    try:
                        slavestream += read(wavbase+'/'+wavefile)
                    except:
                        continue
            # Write out the header line
            event_text = '#'+str(master_event_id).rjust(10) +\
                str(slave_event_id).rjust(10)+' 0.0   \n'
            event_text2 = '#'+str(master_event_id).rjust(10) +\
                str(slave_event_id).rjust(10)+' 0.0   \n'
            slave_picks = sfile_util.readpicks(slave_sfile).picks
            slave_event = sfile_util.readheader(slave_sfile)
            slave_ori_time = slave_event.origins[0].time
            slave_location = (slave_event.origins[0].latitude,
                              slave_event.origins[0].longitude,
                              slave_event.origins[0].depth)
            if dist_calc(master_location, slave_location) > max_sep:
                continue
            links = 0
            phases = 0
            for pick in master_picks:
                if pick.phase_hint[0].upper() not in ['P', 'S']:
                    continue
                    # Only use P and S picks, not amplitude or 'other'
                # Find station, phase pairs
                # Added by Carolin
                slave_matches = [p for p in slave_picks
                                 if p.phase_hint == pick.phase_hint
                                 and p.waveform_id.station_code ==
                                 pick.waveform_id.station_code]

                if masterstream.select(station=pick.waveform_id.station_code,
                                       channel='*' +
                                       pick.waveform_id.channel_code[-1]):
                    mastertr = masterstream.\
                        select(station=pick.waveform_id.station_code,
                               channel='*' +
                               pick.waveform_id.channel_code[-1])[0]
                else:
                    print('No waveform data for ' +
                          pick.waveform_id.station_code + '.' +
                          pick.waveform_id.channel_code)
                    print(pick.waveform_id.station_code +
                          '.' + pick.waveform_id.channel_code +
                          ' ' + slave_sfile+' ' + master_sfile)
                    break
                # Loop through the matches
                for slave_pick in slave_matches:
                    if slavestream.select(station=slave_pick.waveform_id.
                                          station_code,
                                          channel='*'+slave_pick.waveform_id.
                                          channel_code[-1]):
                        slavetr = slavestream.\
                            select(station=slave_pick.waveform_id.station_code,
                                   channel='*'+slave_pick.waveform_id.
                                   channel_code[-1])[0]
                    else:
                        print('No slave data for ' +
                              slave_pick.waveform_id.station_code + '.' +
                              slave_pick.waveform_id.channel_code)
                        print(pick.waveform_id.station_code +
                              '.' + pick.waveform_id.channel_code +
                              ' ' + slave_sfile + ' ' + master_sfile)
                        break
                    # Correct the picks
                    try:
                        correction, cc =\
                            xcorr_pick_correction(pick.time, mastertr,
                                                  slave_pick.time,
                                                  slavetr, pre_pick,
                                                  extract_len - pre_pick,
                                                  shift_len, filter="bandpass",
                                                  filter_options={'freqmin':
                                                                  lowcut,
                                                                  'freqmax':
                                                                  highcut},
                                                  plot=plotvar)
                        # Get the differntial travel time using the
                        # corrected time.
                        # Check that the correction is within the allowed shift
                        # This can occur in the obspy routine when the
                        # correlation function is increasing at the end of the
                        # window.
                        if abs(correction) > shift_len:
                            warnings.warn('Shift correction too large, ' +
                                          'will not use')
                            continue
                        correction = (pick.time - master_ori_time) -\
                            (slave_pick.time + correction - slave_ori_time)
                        links += 1
                        if cc * cc >= coh_thresh:
                            if coherence_weight:
                                weight = cc * cc
                            else:
                                weight = cc
                            phases += 1
                            # added by Caro
                            event_text += pick.waveform_id.station_code.\
                                ljust(5) + _cc_round(correction, 3).\
                                rjust(11) + _cc_round(weight, 3).rjust(8) +\
                                ' '+pick.phase_hint+'\n'
                            event_text2 += pick.waveform_id.station_code\
                                .ljust(5).upper() +\
                                _cc_round(correction, 3).rjust(11) +\
                                _cc_round(weight, 3).rjust(8) +\
                                ' '+pick.phase_hint+'\n'

                            # links+=1
                        corr_list.append(cc*cc)
                    except:
                        # Should warn here
                        msg = "Couldn't compute correlation correction"
                        warnings.warn(msg)
                        continue
            if links >= min_link and phases > 0:
                f.write(event_text)
                f2.write(event_text2)
    if plotvar:
        plt.hist(corr_list, 150)
        plt.show()
    # f.write('\n')
    f.close()
    f2.close()
    return
Пример #9
0
def Amp_pick_sfile(sfile, datapath, respdir, chans=['Z'], var_wintype=True,
                   winlen=0.9, pre_pick=0.2, pre_filt=True, lowcut=1.0,
                   highcut=20.0, corners=4):
    """
    Function to read information from a SEISAN s-file, load the data and the \
    picks, cut the data for the channels given around the S-window, simulate \
    a Wood Anderson seismometer, then pick the maximum peak-to-trough \
    amplitude.

    Output will be put into a mag_calc.out file which will be in full S-file \
    format and can be copied to a REA database.

    :type sfile: string
    :type datapath: string
    :param datapath: Path to the waveform files - usually the path to the WAV \
        directory
    :type respdir: string
    :param respdir: Path to the response information directory
    :type chans: List of strings
    :param chans: List of the channels to pick on, defaults to ['Z'] - should \
        just be the orientations, e.g. Z,1,2,N,E
    :type var_wintype: bool
    :param var_wintype: If True, the winlen will be \
        multiplied by the P-S time if both P and S picks are \
        available, otherwise it will be multiplied by the \
        hypocentral distance*0.34 - dervided using a p-s ratio of \
        1.68 and S-velocity of 1.5km/s to give a large window, \
        defaults to True
    :type winlen: float
    :param winlen: Length of window, see above parameter, if var_wintype is \
        False then this will be in seconds, otherwise it is the \
        multiplier to the p-s time, defaults to 0.5.
    :type pre_pick: float
    :param pre_pick: Time before the s-pick to start the cut window, defaults \
        to 0.2
    :type pre_filt: bool
    :param pre_filt: To apply a pre-filter or not, defaults to True
    :type lowcut: float
    :param lowcut: Lowcut in Hz for the pre-filter, defaults to 1.0
    :type highcut: float
    :param highcut: Highcut in Hz for the pre-filter, defaults to 20.0
    :type corners: int
    :param corners: Number of corners to use in the pre-filter
    """
    # Hardwire a p-s multiplier of hypocentral distance based on p-s ratio of
    # 1.68 and an S-velocity 0f 1.5km/s, deliberately chosen to be quite slow
    ps_multiplier = 0.34
    from eqcorrscan.utils import sfile_util
    from obspy import read
    from scipy.signal import iirfilter
    from obspy.signal.invsim import paz2AmpValueOfFreqResp
    import warnings
    # First we need to work out what stations have what picks
    event = sfile_util.readpicks(sfile)[0]
    # Convert these picks into a lists
    stations = []  # List of stations
    channels = []  # List of channels
    picktimes = []  # List of pick times
    picktypes = []  # List of pick types
    distances = []  # List of hypocentral distances
    picks_out = []
    for pick in event.picks:
        if pick.phase_hint in ['P', 'S']:
            picks_out.append(pick)  # Need to be able to remove this if there
            # isn't data for a station!
            stations.append(pick.waveform_id.station_code)
            channels.append(pick.waveform_id.channel_code)
            picktimes.append(pick.time)
            picktypes.append(pick.phase_hint)
            arrival = [arrival for arrival in event.origins[0].arrivals
                       if arrival.pick_id == pick.resource_id]
            distances.append(arrival.distance)
    # Read in waveforms
    stream = read(datapath+'/'+sfile_util.readwavename(sfile)[0])
    if len(sfile_util.readwavename(sfile)) > 1:
        for wavfile in sfile_util.readwavename(sfile):
            stream += read(datapath+'/'+wavfile)
    stream.merge()  # merge the data, just in case!
    # For each station cut the window
    uniq_stas = list(set(stations))
    del arrival
    for sta in uniq_stas:
        for chan in chans:
            print('Working on '+sta+' '+chan)
            tr = stream.select(station=sta, channel='*'+chan)
            if not tr:
                # Remove picks from file
                # picks_out=[picks_out[i] for i in xrange(len(picks))\
                # if picks_out[i].station+picks_out[i].channel != \
                # sta+chan]
                warnings.warn('There is no station and channel match in the ' +
                              'wavefile!')
                break
            else:
                tr = tr[0]
            # Apply the pre-filter
            if pre_filt:
                try:
                    tr.detrend('simple')
                except:
                    dummy = tr.split()
                    dummy.detrend('simple')
                    tr = dummy.merge()[0]
                tr.filter('bandpass', freqmin=lowcut, freqmax=highcut,
                          corners=corners)
            sta_picks = [i for i in xrange(len(stations))
                         if stations[i] == sta]
            pick_id = event.picks[sta_picks[0]].resource_id
            arrival = [arrival for arrival in event.origins[0].arrivals
                       if arrival.pick_id == pick_id]
            hypo_dist = arrival.distance
            CAZ = arrival.azimuth
            if var_wintype:
                if 'S' in [picktypes[i] for i in sta_picks] and\
                   'P' in [picktypes[i] for i in sta_picks]:
                    # If there is an S-pick we can use this :D
                    S_pick = [picktimes[i] for i in sta_picks
                              if picktypes[i] == 'S']
                    S_pick = min(S_pick)
                    P_pick = [picktimes[i] for i in sta_picks
                              if picktypes[i] == 'P']
                    P_pick = min(P_pick)
                    try:
                        tr.trim(starttime=S_pick-pre_pick,
                                endtime=S_pick+(S_pick-P_pick)*winlen)
                    except:
                        break
                elif 'S' in [picktypes[i] for i in sta_picks]:
                    S_pick = [picktimes[i] for i in sta_picks
                              if picktypes[i] == 'S']
                    S_pick = min(S_pick)
                    P_modelled = S_pick - hypo_dist * ps_multiplier
                    try:
                        tr.trim(starttime=S_pick-pre_pick,
                                endtime=S_pick + (S_pick - P_modelled) *
                                winlen)
                    except:
                        break
                else:
                    # In this case we only have a P pick
                    P_pick = [picktimes[i] for i in sta_picks
                              if picktypes[i] == 'P']
                    P_pick = min(P_pick)
                    S_modelled = P_pick + hypo_dist * ps_multiplier
                    try:
                        tr.trim(starttime=S_modelled - pre_pick,
                                endtime=S_modelled + (S_modelled - P_pick) *
                                winlen)
                    except:
                        break
                # Work out the window length based on p-s time or distance
            elif 'S' in [picktypes[i] for i in sta_picks]:
                # If the window is fixed we still need to find the start time,
                # which can be based either on the S-pick (this elif), or
                # on the hypocentral distance and the P-pick

                # Take the minimum S-pick time if more than one S-pick is
                # available
                S_pick = [picktimes[i] for i in sta_picks
                          if picktypes[i] == 'S']
                S_pick = min(S_pick)
                try:
                    tr.trim(starttime=S_pick - pre_pick,
                            endtime=S_pick + winlen)
                except:
                    break
            else:
                # In this case, there is no S-pick and the window length is
                # fixed we need to calculate an expected S_pick based on the
                # hypocentral distance, this will be quite hand-wavey as we
                # are not using any kind of velocity model.
                P_pick = [picktimes[i] for i in sta_picks
                          if picktypes[i] == 'P']
                P_pick = min(P_pick)
                hypo_dist = [distances[i] for i in sta_picks
                             if picktypes[i] == 'P'][0]
                S_modelled = P_pick + hypo_dist * ps_multiplier
                try:
                    tr.trim(starttime=S_modelled - pre_pick,
                            endtime=S_modelled + winlen)
                except:
                    break
            # Find the response information
            resp_info = _find_resp(tr.stats.station, tr.stats.channel,
                                   tr.stats.network, tr.stats.starttime,
                                   tr.stats.delta, respdir)
            PAZ = []
            seedresp = []
            if resp_info and 'gain' in resp_info:
                PAZ = resp_info
            elif resp_info:
                seedresp = resp_info
            # Simulate a Wood Anderson Seismograph
            if PAZ and len(tr.data) > 10:
                # Set ten data points to be the minimum to pass
                tr = _sim_WA(tr, PAZ, None, 10)
            elif seedresp and len(tr.data) > 10:
                tr = _sim_WA(tr, None, seedresp, 10)
            elif len(tr.data) > 10:
                warnings.warn('No PAZ for '+tr.stats.station+' ' +
                              tr.stats.channel+' at time: ' +
                              str(tr.stats.starttime))
                continue
            if len(tr.data) <= 10:
                # Should remove the P and S picks if len(tr.data)==0
                warnings.warn('No data found for: '+tr.stats.station)
                # print 'No data in miniseed file for '+tr.stats.station+\
                # ' removing picks'
                # picks_out=[picks_out[i] for i in xrange(len(picks_out))\
                # if i not in sta_picks]
                break
            # Get the amplitude
            amplitude, period, delay = _max_p2t(tr.data, tr.stats.delta)
            if amplitude == 0.0:
                break
            print('Amplitude picked: ' + str(amplitude))
            # Note, amplitude should be in meters at the moment!
            # Remove the pre-filter response
            if pre_filt:
                # Generate poles and zeros for the filter we used earlier: this
                # is how the filter is designed in the convenience methods of
                # filtering in obspy.
                z, p, k = iirfilter(corners, [lowcut / (0.5 *
                                                        tr.stats.
                                                        sampling_rate),
                                              highcut / (0.5 *
                                                         tr.stats.
                                                         sampling_rate)],
                                    btype='band', ftype='butter', output='zpk')
                filt_paz = {'poles': list(p),
                            'zeros': list(z),
                            'gain': k,
                            'sensitivity':  1.0}
                amplitude /= (paz2AmpValueOfFreqResp(filt_paz, 1 / period) *
                              filt_paz['sensitivity'])
            # Convert amplitude to mm
            if PAZ:  # Divide by Gain to get to nm (returns pm? 10^-12)
                # amplitude *=PAZ['gain']
                amplitude /= 1000
            if seedresp:  # Seedresp method returns mm
                amplitude *= 1000000
            # Write out the half amplitude, approximately the peak amplitude as
            # used directly in magnitude calculations
            # Page 343 of Seisan manual:
            #   Amplitude (Zero-Peak) in units of nm, nm/s, nm/s^2 or counts
            amplitude *= 0.5
            # Generate a PICK type object for this pick
            picks_out.append(sfile_util.PICK(station=tr.stats.station,
                                             channel=tr.stats.channel,
                                             impulsivity=' ',
                                             phase='IAML',
                                             weight='', polarity=' ',
                                             time=tr.stats.starttime+delay,
                                             coda=999, amplitude=amplitude,
                                             peri=period, azimuth=float('NaN'),
                                             velocity=float('NaN'), AIN=999,
                                             SNR='',
                                             azimuthres=999,
                                             timeres=float('NaN'),
                                             finalweight=999,
                                             distance=hypo_dist,
                                             CAZ=CAZ))
    # Copy the header from the sfile to a new local S-file
    fin = open(sfile, 'r')
    fout = open('mag_calc.out', 'w')
    for line in fin:
        if not line[79] == '7':
            fout.write(line)
        else:
            fout.write(line)
            break
    fin.close()
    for pick in picks_out:
        fout.write(pick)
        # Note this uses the legacy pick class
    fout.close()
    # Write picks out to new s-file
    for pick in picks_out:
        print(pick)
    # sfile_util.populatesfile('mag_calc.out', picks_out)
    return picks_out
Пример #10
0
def from_sfile(sfile, lowcut, highcut, samp_rate, filt_order, length, swin,
               prepick=0.05, debug=0, plot=False):
    r"""Function to read in picks from sfile then generate the template from \
    the picks within this and the wavefile found in the pick file.

    :type sfile: string
    :param sfile: sfilename must be the \
        path to a seisan nordic type s-file containing waveform and pick \
        information.
    :type lowcut: float
    :param lowcut: Low cut (Hz), if set to None will look in template \
            defaults file
    :type highcut: float
    :param highcut: High cut (Hz), if set to None will look in template \
            defaults file
    :type samp_rate: float
    :param samp_rate: New sampling rate in Hz, if set to None will look in \
            template defaults file
    :type filt_order: int
    :param filt_order: Filter level, if set to None will look in \
            template defaults file
    :type swin: str
    :param swin: Either 'all', 'P' or 'S', to select which phases to output.
    :type length: float
    :param length: Extract length in seconds, if None will look in template \
            defaults file.
    :type prepick: float
    :param prepick: Length to extract prior to the pick in seconds.
    :type debug: int
    :param debug: Debug level, higher number=more output.
    :type plot: bool
    :param plot: Turns template plotting on or off.

    :returns: obspy.Stream Newly cut template

    .. warning:: This will use whatever data is pointed to in the s-file, if \
        this is not the coninuous data, we recommend using other functions. \
        Differences in processing between short files and day-long files \
        (inherent to resampling) will produce lower cross-correlations.
    """
    # Perform some checks first
    import os
    if not os.path.isfile(sfile):
        raise IOError('sfile does not exist')

    from eqcorrscan.utils import pre_processing
    from eqcorrscan.utils import sfile_util
    from obspy import read as obsread
    # Read in the header of the sfile
    wavefiles = sfile_util.readwavename(sfile)
    pathparts = sfile.split('/')[0:-1]
    new_path_parts = []
    for part in pathparts:
        if part == 'REA':
            part = 'WAV'
        new_path_parts.append(part)
    # * argument to allow .join() to accept a list
    wavpath = os.path.join(*new_path_parts) + '/'
    # In case of absolute paths (not handled with .split() --> .join())
    if sfile[0] == '/':
        wavpath = '/' + wavpath
    # Read in waveform file
    for wavefile in wavefiles:
        print(''.join(["I am going to read waveform data from: ", wavpath,
                       wavefile]))
        if 'st' not in locals():
            st = obsread(wavpath + wavefile)
        else:
            st += obsread(wavpath + wavefile)
    for tr in st:
        if tr.stats.sampling_rate < samp_rate:
            print('Sampling rate of data is lower than sampling rate asked ' +
                  'for')
            print('Not good practice for correlations: I will not do this')
            raise ValueError("Trace: " + tr.stats.station +
                             " sampling rate: " + str(tr.stats.sampling_rate))
    # Read in pick info
    catalog = sfile_util.readpicks(sfile)
    # Read the list of Picks for this event
    picks = catalog[0].picks
    print("I have found the following picks")
    for pick in picks:
        print(' '.join([pick.waveform_id.station_code,
                        pick.waveform_id.channel_code, pick.phase_hint,
                        str(pick.time)]))

    # Process waveform data
    st.merge(fill_value='interpolate')
    st = pre_processing.shortproc(st, lowcut, highcut, filt_order,
                                  samp_rate, debug)
    st1 = _template_gen(picks=picks, st=st, length=length, swin=swin,
                        prepick=prepick, plot=plot, debug=debug)
    return st1
Пример #11
0
def write_correlations(event_list,
                       wavbase,
                       extract_len,
                       pre_pick,
                       shift_len,
                       lowcut=1.0,
                       highcut=10.0,
                       max_sep=8,
                       min_link=8,
                       cc_thresh=0.0,
                       plotvar=False,
                       debug=0):
    """
    Write a dt.cc file for hypoDD input for a given list of events.

    Takes an input list of events and computes pick refinements by correlation.
    Outputs two files, dt.cc and dt.cc2, each provides a different weight,
    dt.cc uses weights of the cross-correlation, and dt.cc2 provides weights
    as the square of the cross-correlation.

    :type event_list: list
    :param event_list: List of tuples of event_id (int) and sfile (String)
    :type wavbase: str
    :param wavbase: Path to the seisan wave directory that the wavefiles in the
                    S-files are stored
    :type extract_len: float
    :param extract_len: Length in seconds to extract around the pick
    :type pre_pick: float
    :param pre_pick: Time before the pick to start the correlation window
    :type shift_len: float
    :param shift_len: Time to allow pick to vary
    :type lowcut: float
    :param lowcut: Lowcut in Hz - default=1.0
    :type highcut: float
    :param highcut: Highcut in Hz - default=10.0
    :type max_sep: float
    :param max_sep: Maximum separation between event pairs in km
    :type min_link: int
    :param min_link: Minimum links for an event to be paired
    :type cc_thresh: float
    :param cc_thresh: Threshold to include cross-correlation results.
    :type plotvar: bool
    :param plotvar: To show the pick-correction plots, defualts to False.
    :type debug: int
    :param debug: Variable debug levels from 0-5, higher=more output.

    .. warning:: This is not a fast routine!

    .. warning::
        In contrast to seisan's corr routine, but in accordance with the
        hypoDD manual, this outputs corrected differential time.

    .. note::
        Currently we have not implemented a method for taking
        unassociated event objects and wavefiles.  As such if you have events \
        with associated wavefiles you are advised to generate Sfiles for each \
        event using the sfile_util module prior to this step.

    .. note::
        There is no provision to taper waveforms within these functions, if you
        desire this functionality, you should apply the taper before calling
        this.  Note the :func:`obspy.Trace.taper` functions.
    """
    from obspy.signal.cross_correlation import xcorr_pick_correction
    warnings.filterwarnings(action="ignore",
                            message="Maximum of cross correlation " +
                            "lower than 0.8: *")
    corr_list = []
    f = open('dt.cc', 'w')
    f2 = open('dt.cc2', 'w')
    k_events = len(list(event_list))
    for i, master in enumerate(event_list):
        master_sfile = master[1]
        if debug > 1:
            print('Computing correlations for master: %s' % master_sfile)
        master_event_id = master[0]
        master_picks = sfile_util.readpicks(master_sfile).picks
        master_event = sfile_util.readheader(master_sfile)
        master_ori_time = master_event.origins[0].time
        master_location = (master_event.origins[0].latitude,
                           master_event.origins[0].longitude,
                           master_event.origins[0].depth / 1000.0)
        master_wavefiles = sfile_util.readwavename(master_sfile)
        masterpath = glob.glob(wavbase + os.sep + master_wavefiles[0])
        if masterpath:
            masterstream = read(masterpath[0])
        if len(master_wavefiles) > 1:
            for wavefile in master_wavefiles:
                try:
                    masterstream += read(os.join(wavbase, wavefile))
                except:
                    raise IOError("Couldn't find wavefile")
                    continue
        for j in range(i + 1, k_events):
            # Use this tactic to only output unique event pairings
            slave_sfile = event_list[j][1]
            if debug > 2:
                print('Comparing to event: %s' % slave_sfile)
            slave_event_id = event_list[j][0]
            slave_wavefiles = sfile_util.readwavename(slave_sfile)
            try:
                slavestream = read(wavbase + os.sep + slave_wavefiles[0])
            except:
                raise IOError('No wavefile found: ' + slave_wavefiles[0] +
                              ' ' + slave_sfile)
            if len(slave_wavefiles) > 1:
                for wavefile in slave_wavefiles:
                    try:
                        slavestream += read(wavbase + os.sep + wavefile)
                    except IOError:
                        print('No waveform found: %s' %
                              (wavbase + os.sep + wavefile))
                        continue
            # Write out the header line
            event_text = '#' + str(master_event_id).rjust(10) +\
                str(slave_event_id).rjust(10) + ' 0.0   \n'
            event_text2 = '#' + str(master_event_id).rjust(10) +\
                str(slave_event_id).rjust(10) + ' 0.0   \n'
            slave_picks = sfile_util.readpicks(slave_sfile).picks
            slave_event = sfile_util.readheader(slave_sfile)
            slave_ori_time = slave_event.origins[0].time
            slave_location = (slave_event.origins[0].latitude,
                              slave_event.origins[0].longitude,
                              slave_event.origins[0].depth / 1000.0)
            if dist_calc(master_location, slave_location) > max_sep:
                if debug > 0:
                    print('Seperation exceeds max_sep: %s' %
                          (dist_calc(master_location, slave_location)))
                continue
            links = 0
            phases = 0
            for pick in master_picks:
                if not hasattr(pick, 'phase_hint') or \
                                len(pick.phase_hint) == 0:
                    warnings.warn('No phase-hint for pick:')
                    print(pick)
                    continue
                if pick.phase_hint[0].upper() not in ['P', 'S']:
                    warnings.warn('Will only use P or S phase picks')
                    print(pick)
                    continue
                    # Only use P and S picks, not amplitude or 'other'
                # Find station, phase pairs
                # Added by Carolin
                slave_matches = [
                    p for p in slave_picks if hasattr(p, 'phase_hint')
                    and p.phase_hint == pick.phase_hint and
                    p.waveform_id.station_code == pick.waveform_id.station_code
                ]

                if masterstream.select(station=pick.waveform_id.station_code,
                                       channel='*' +
                                       pick.waveform_id.channel_code[-1]):
                    mastertr = masterstream.\
                        select(station=pick.waveform_id.station_code,
                               channel='*' +
                               pick.waveform_id.channel_code[-1])[0]
                elif debug > 1:
                    print('No waveform data for ' +
                          pick.waveform_id.station_code + '.' +
                          pick.waveform_id.channel_code)
                    print(pick.waveform_id.station_code + '.' +
                          pick.waveform_id.channel_code + ' ' + slave_sfile +
                          ' ' + master_sfile)
                    break
                # Loop through the matches
                for slave_pick in slave_matches:
                    if slavestream.select(
                            station=slave_pick.waveform_id.station_code,
                            channel='*' +
                            slave_pick.waveform_id.channel_code[-1]):
                        slavetr = slavestream.\
                            select(station=slave_pick.waveform_id.station_code,
                                   channel='*' + slave_pick.waveform_id.
                                   channel_code[-1])[0]
                    else:
                        print('No slave data for ' +
                              slave_pick.waveform_id.station_code + '.' +
                              slave_pick.waveform_id.channel_code)
                        print(pick.waveform_id.station_code + '.' +
                              pick.waveform_id.channel_code + ' ' +
                              slave_sfile + ' ' + master_sfile)
                        break
                    # Correct the picks
                    try:
                        correction, cc =\
                            xcorr_pick_correction(
                                pick.time, mastertr, slave_pick.time,
                                slavetr, pre_pick, extract_len - pre_pick,
                                shift_len, filter="bandpass",
                                filter_options={'freqmin': lowcut,
                                                'freqmax': highcut},
                                plot=plotvar)
                        # Get the differential travel time using the
                        # corrected time.
                        # Check that the correction is within the allowed shift
                        # This can occur in the obspy routine when the
                        # correlation function is increasing at the end of the
                        # window.
                        if abs(correction) > shift_len:
                            warnings.warn('Shift correction too large, ' +
                                          'will not use')
                            continue
                        correction = (pick.time - master_ori_time) -\
                            (slave_pick.time + correction - slave_ori_time)
                        links += 1
                        if cc >= cc_thresh:
                            weight = cc
                            phases += 1
                            # added by Caro
                            event_text += pick.waveform_id.station_code.\
                                ljust(5) + _cc_round(correction, 3).\
                                rjust(11) + _cc_round(weight, 3).rjust(8) +\
                                ' ' + pick.phase_hint + '\n'
                            event_text2 += pick.waveform_id.station_code\
                                .ljust(5) + _cc_round(correction, 3).\
                                rjust(11) +\
                                _cc_round(weight * weight, 3).rjust(8) +\
                                ' ' + pick.phase_hint + '\n'
                            if debug > 3:
                                print(event_text)
                        else:
                            print('cc too low: %s' % cc)
                        corr_list.append(cc * cc)
                    except:
                        msg = "Couldn't compute correlation correction"
                        warnings.warn(msg)
                        continue
            if links >= min_link and phases > 0:
                f.write(event_text)
                f2.write(event_text2)
    if plotvar:
        plt.hist(corr_list, 150)
        plt.show()
    # f.write('\n')
    f.close()
    f2.close()
    return
Пример #12
0
    def test_read_write(self):
        """
        Function to test the read and write capabilities of sfile_util.
        """
        import os
        from obspy.core.event import Catalog
        import obspy
        if int(obspy.__version__.split('.')[0]) >= 1:
            from obspy.core.event import read_events
        else:
            from obspy.core.event import readEvents as read_events

        # Set-up a test event
        test_event = basic_test_event()
        # Add the event to a catalogue which can be used for QuakeML testing
        test_cat = Catalog()
        test_cat += test_event
        # Write the catalog
        test_cat.write("Test_catalog.xml", format='QUAKEML')
        # Read and check
        read_cat = read_events("Test_catalog.xml")
        os.remove("Test_catalog.xml")
        self.assertEqual(read_cat[0].resource_id, test_cat[0].resource_id)
        self.assertEqual(read_cat[0].picks, test_cat[0].picks)
        self.assertEqual(read_cat[0].origins[0].resource_id,
                         test_cat[0].origins[0].resource_id)
        self.assertEqual(read_cat[0].origins[0].time,
                         test_cat[0].origins[0].time)
        # Note that time_residuel_RMS is not a quakeML format
        self.assertEqual(read_cat[0].origins[0].longitude,
                         test_cat[0].origins[0].longitude)
        self.assertEqual(read_cat[0].origins[0].latitude,
                         test_cat[0].origins[0].latitude)
        self.assertEqual(read_cat[0].origins[0].depth,
                         test_cat[0].origins[0].depth)
        self.assertEqual(read_cat[0].magnitudes, test_cat[0].magnitudes)
        self.assertEqual(read_cat[0].event_descriptions,
                         test_cat[0].event_descriptions)
        self.assertEqual(read_cat[0].amplitudes[0].resource_id,
                         test_cat[0].amplitudes[0].resource_id)
        self.assertEqual(read_cat[0].amplitudes[0].period,
                         test_cat[0].amplitudes[0].period)
        self.assertEqual(read_cat[0].amplitudes[0].unit,
                         test_cat[0].amplitudes[0].unit)
        self.assertEqual(read_cat[0].amplitudes[0].generic_amplitude,
                         test_cat[0].amplitudes[0].generic_amplitude)
        self.assertEqual(read_cat[0].amplitudes[0].pick_id,
                         test_cat[0].amplitudes[0].pick_id)
        self.assertEqual(read_cat[0].amplitudes[0].waveform_id,
                         test_cat[0].amplitudes[0].waveform_id)

        # Check the read-write s-file functionality
        sfile = eventtosfile(test_cat[0], userID='TEST',
                             evtype='L', outdir='.',
                             wavefiles='test', explosion=True, overwrite=True)
        del read_cat
        self.assertEqual(readwavename(sfile), ['test'])
        read_cat = Catalog()
        read_cat += readpicks(sfile)
        os.remove(sfile)
        self.assertEqual(read_cat[0].picks[0].time,
                         test_cat[0].picks[0].time)
        self.assertEqual(read_cat[0].picks[0].backazimuth,
                         test_cat[0].picks[0].backazimuth)
        self.assertEqual(read_cat[0].picks[0].onset,
                         test_cat[0].picks[0].onset)
        self.assertEqual(read_cat[0].picks[0].phase_hint,
                         test_cat[0].picks[0].phase_hint)
        self.assertEqual(read_cat[0].picks[0].polarity,
                         test_cat[0].picks[0].polarity)
        self.assertEqual(read_cat[0].picks[0].waveform_id.station_code,
                         test_cat[0].picks[0].waveform_id.station_code)
        self.assertEqual(read_cat[0].picks[0].waveform_id.channel_code[-1],
                         test_cat[0].picks[0].waveform_id.channel_code[-1])
        # assert read_cat[0].origins[0].resource_id ==\
        #     test_cat[0].origins[0].resource_id
        self.assertEqual(read_cat[0].origins[0].time,
                         test_cat[0].origins[0].time)
        # Note that time_residuel_RMS is not a quakeML format
        self.assertEqual(read_cat[0].origins[0].longitude,
                         test_cat[0].origins[0].longitude)
        self.assertEqual(read_cat[0].origins[0].latitude,
                         test_cat[0].origins[0].latitude)
        self.assertEqual(read_cat[0].origins[0].depth,
                         test_cat[0].origins[0].depth)
        self.assertEqual(read_cat[0].magnitudes[0].mag,
                         test_cat[0].magnitudes[0].mag)
        self.assertEqual(read_cat[0].magnitudes[1].mag,
                         test_cat[0].magnitudes[1].mag)
        self.assertEqual(read_cat[0].magnitudes[2].mag,
                         test_cat[0].magnitudes[2].mag)
        self.assertEqual(read_cat[0].magnitudes[0].creation_info,
                         test_cat[0].magnitudes[0].creation_info)
        self.assertEqual(read_cat[0].magnitudes[1].creation_info,
                         test_cat[0].magnitudes[1].creation_info)
        self.assertEqual(read_cat[0].magnitudes[2].creation_info,
                         test_cat[0].magnitudes[2].creation_info)
        self.assertEqual(read_cat[0].magnitudes[0].magnitude_type,
                         test_cat[0].magnitudes[0].magnitude_type)
        self.assertEqual(read_cat[0].magnitudes[1].magnitude_type,
                         test_cat[0].magnitudes[1].magnitude_type)
        self.assertEqual(read_cat[0].magnitudes[2].magnitude_type,
                         test_cat[0].magnitudes[2].magnitude_type)
        self.assertEqual(read_cat[0].event_descriptions,
                         test_cat[0].event_descriptions)
        # assert read_cat[0].amplitudes[0].resource_id ==\
        #     test_cat[0].amplitudes[0].resource_id
        self.assertEqual(read_cat[0].amplitudes[0].period,
                         test_cat[0].amplitudes[0].period)
        self.assertEqual(read_cat[0].amplitudes[0].snr,
                         test_cat[0].amplitudes[0].snr)
        del read_cat
        # assert read_cat[0].amplitudes[0].pick_id ==\
        #     test_cat[0].amplitudes[0].pick_id
        # assert read_cat[0].amplitudes[0].waveform_id ==\
        #     test_cat[0].amplitudes[0].waveform_id

        # Test the wrappers for PICK and EVENTINFO classes
        picks, evinfo = eventtopick(test_cat)
        # Test the conversion back
        conv_cat = Catalog()
        conv_cat.append(picktoevent(evinfo, picks))
        self.assertEqual(conv_cat[0].picks[0].time, test_cat[0].picks[0].time)
        self.assertEqual(conv_cat[0].picks[0].backazimuth,
                         test_cat[0].picks[0].backazimuth)
        self.assertEqual(conv_cat[0].picks[0].onset,
                         test_cat[0].picks[0].onset)
        self.assertEqual(conv_cat[0].picks[0].phase_hint,
                         test_cat[0].picks[0].phase_hint)
        self.assertEqual(conv_cat[0].picks[0].polarity,
                         test_cat[0].picks[0].polarity)
        self.assertEqual(conv_cat[0].picks[0].waveform_id.station_code,
                         test_cat[0].picks[0].waveform_id.station_code)
        self.assertEqual(conv_cat[0].picks[0].waveform_id.channel_code[-1],
                         test_cat[0].picks[0].waveform_id.channel_code[-1])
        # self.assertEqual(read_cat[0].origins[0].resource_id,
        #                  test_cat[0].origins[0].resource_id)
        self.assertEqual(conv_cat[0].origins[0].time,
                         test_cat[0].origins[0].time)
        # Note that time_residuel_RMS is not a quakeML format
        self.assertEqual(conv_cat[0].origins[0].longitude,
                         test_cat[0].origins[0].longitude)
        self.assertEqual(conv_cat[0].origins[0].latitude,
                         test_cat[0].origins[0].latitude)
        self.assertEqual(conv_cat[0].origins[0].depth,
                         test_cat[0].origins[0].depth)
        self.assertEqual(conv_cat[0].magnitudes[0].mag,
                         test_cat[0].magnitudes[0].mag)
        self.assertEqual(conv_cat[0].magnitudes[1].mag,
                         test_cat[0].magnitudes[1].mag)
        self.assertEqual(conv_cat[0].magnitudes[2].mag,
                         test_cat[0].magnitudes[2].mag)
        self.assertEqual(conv_cat[0].magnitudes[0].creation_info,
                         test_cat[0].magnitudes[0].creation_info)
        self.assertEqual(conv_cat[0].magnitudes[1].creation_info,
                         test_cat[0].magnitudes[1].creation_info)
        self.assertEqual(conv_cat[0].magnitudes[2].creation_info,
                         test_cat[0].magnitudes[2].creation_info)
        self.assertEqual(conv_cat[0].magnitudes[0].magnitude_type,
                         test_cat[0].magnitudes[0].magnitude_type)
        self.assertEqual(conv_cat[0].magnitudes[1].magnitude_type,
                         test_cat[0].magnitudes[1].magnitude_type)
        self.assertEqual(conv_cat[0].magnitudes[2].magnitude_type,
                         test_cat[0].magnitudes[2].magnitude_type)
        self.assertEqual(conv_cat[0].event_descriptions,
                         test_cat[0].event_descriptions)
        # self.assertEqual(read_cat[0].amplitudes[0].resource_id,
        #                  test_cat[0].amplitudes[0].resource_id)
        self.assertEqual(conv_cat[0].amplitudes[0].period,
                         test_cat[0].amplitudes[0].period)
        self.assertEqual(conv_cat[0].amplitudes[0].snr,
                         test_cat[0].amplitudes[0].snr)
Пример #13
0
def from_sfile(sfile, lowcut, highcut, samp_rate, filt_order, length, swin,
               prepick=0.05, debug=0, plot=False):
    """
    Generate multiplexed template from a Nordic (Seisan) s-file.
    Function to read in picks from sfile then generate the template from \
    the picks within this and the wavefile found in the pick file.

    :type sfile: str
    :param sfile: sfilename must be the \
        path to a seisan nordic type s-file containing waveform and pick \
        information.
    :type lowcut: float
    :param lowcut: Low cut (Hz), if set to None will look in template \
            defaults file
    :type highcut: float
    :param highcut: High cut (Hz), if set to None will look in template \
            defaults file
    :type samp_rate: float
    :param samp_rate: New sampling rate in Hz, if set to None will look in \
            template defaults file
    :type filt_order: int
    :param filt_order: Filter level, if set to None will look in \
            template defaults file
    :type swin: str
    :param swin: Either 'all', 'P' or 'S', to select which phases to output.
    :type length: float
    :param length: Extract length in seconds, if None will look in template \
            defaults file.
    :type prepick: float
    :param prepick: Length to extract prior to the pick in seconds.
    :type debug: int
    :param debug: Debug level, higher number=more output.
    :type plot: bool
    :param plot: Turns template plotting on or off.

    :returns: obspy.core.stream.Stream Newly cut template

    .. warning:: This will use whatever data is pointed to in the s-file, if \
        this is not the coninuous data, we recommend using other functions. \
        Differences in processing between short files and day-long files \
        (inherent to resampling) will produce lower cross-correlations.

    .. rubric:: Example

    >>> from eqcorrscan.core.template_gen import from_sfile
    >>> sfile = 'eqcorrscan/tests/test_data/REA/TEST_/01-0411-15L.S201309'
    >>> template = from_sfile(sfile=sfile, lowcut=5.0, highcut=15.0,
    ...                       samp_rate=50.0, filt_order=4, swin='P',
    ...                       prepick=0.2, length=6)
    >>> print(len(template))
    15
    >>> print(template[0].stats.sampling_rate)
    50.0
    >>> template.plot(equal_scale=False, size=(800,600)) # doctest: +SKIP

    .. plot::

        from eqcorrscan.core.template_gen import from_sfile
        import os
        sfile = os.path.realpath('../../..') + \
            '/tests/test_data/REA/TEST_/01-0411-15L.S201309'
        template = from_sfile(sfile=sfile, lowcut=5.0, highcut=15.0,
                              samp_rate=50.0, filt_order=4, swin='P',
                              prepick=0.2, length=6)
        template.plot(equal_scale=False, size=(800, 600))
    """
    # Perform some checks first
    import os
    if not os.path.isfile(sfile):
        raise IOError('sfile does not exist')

    from eqcorrscan.utils import pre_processing
    from eqcorrscan.utils import sfile_util
    from obspy import read as obsread
    # Read in the header of the sfile
    wavefiles = sfile_util.readwavename(sfile)
    pathparts = sfile.split('/')[0:-1]
    new_path_parts = []
    for part in pathparts:
        if part == 'REA':
            part = 'WAV'
        new_path_parts.append(part)
    main_wav_parts = []
    for part in new_path_parts:
        main_wav_parts.append(part)
        if part == 'WAV':
            break
    mainwav = os.path.join(*main_wav_parts) + os.path.sep
    # * argument to allow .join() to accept a list
    wavpath = os.path.join(*new_path_parts) + os.path.sep
    # In case of absolute paths (not handled with .split() --> .join())
    if sfile[0] == os.path.sep:
        wavpath = os.path.sep + wavpath
        mainwav = os.path.sep + mainwav
    # Read in waveform file
    for wavefile in wavefiles:
        if debug > 0:
            print(''.join(["I am going to read waveform data from: ", wavpath,
                           wavefile]))
        if 'st' not in locals():
            if os.path.isfile(wavpath + wavefile):
                st = obsread(wavpath + wavefile)
            elif os.path.isfile(wavefile):
                st = obsread(wavefile)
            else:
                # Read from the main WAV directory
                st = obsread(mainwav + wavefile)
        else:
            if os.path.isfile(wavpath + wavefile):
                st += obsread(wavpath + wavefile)
            elif os.path.isfile(wavefile):
                st += obsread(wavefile)
            else:
                st += obsread(mainwav + wavefile)
    for tr in st:
        if tr.stats.sampling_rate < samp_rate:
            print('Sampling rate of data is lower than sampling rate asked ' +
                  'for')
            print('Not good practice for correlations: I will not do this')
            raise ValueError("Trace: " + tr.stats.station +
                             " sampling rate: " + str(tr.stats.sampling_rate))
    # Read in pick info
    event = sfile_util.readpicks(sfile)
    # Read the list of Picks for this event
    picks = event.picks
    if debug > 0:
        print("I have found the following picks")
        for pick in picks:
            print(' '.join([pick.waveform_id.station_code,
                            pick.waveform_id.channel_code, pick.phase_hint,
                            str(pick.time)]))
    # Process waveform data
    st.merge(fill_value='interpolate')
    st = pre_processing.shortproc(st, lowcut, highcut, filt_order,
                                  samp_rate, debug)
    st1 = _template_gen(picks=picks, st=st, length=length, swin=swin,
                        prepick=prepick, plot=plot, debug=debug)
    return st1
Пример #14
0
def amp_pick_sfile(sfile, datapath, respdir, chans=['Z'], var_wintype=True,
                   winlen=0.9, pre_pick=0.2, pre_filt=True, lowcut=1.0,
                   highcut=20.0, corners=4):
    """
    Function to pick amplitudes for local magnitudes from NORDIC s-files.

    Reads information from a SEISAN s-file, load the data and the \
    picks, cut the data for the channels given around the S-window, simulate \
    a Wood Anderson seismometer, then pick the maximum peak-to-trough \
    amplitude.

    Output will be put into a mag_calc.out file which will be in full S-file \
    format and can be copied to a REA database.

    :type sfile: str
    :param sfile: Path to NORDIC format s-file
    :type datapath: str
    :param datapath: Path to the waveform files - usually the path to the WAV \
        directory
    :type respdir: str
    :param respdir: Path to the response information directory
    :type chans: list
    :param chans: List of the channels to pick on, defaults to ['Z'] - should \
        just be the orientations, e.g. Z,1,2,N,E
    :type var_wintype: bool
    :param var_wintype: If True, the winlen will be \
        multiplied by the P-S time if both P and S picks are \
        available, otherwise it will be multiplied by the \
        hypocentral distance*0.34 - derived using a p-s ratio of \
        1.68 and S-velocity of 1.5km/s to give a large window, \
        defaults to True
    :type winlen: float
    :param winlen: Length of window, see above parameter, if var_wintype is \
        False then this will be in seconds, otherwise it is the \
        multiplier to the p-s time, defaults to 0.5.
    :type pre_pick: float
    :param pre_pick: Time before the s-pick to start the cut window, defaults \
        to 0.2
    :type pre_filt: bool
    :param pre_filt: To apply a pre-filter or not, defaults to True
    :type lowcut: float
    :param lowcut: Lowcut in Hz for the pre-filter, defaults to 1.0
    :type highcut: float
    :param highcut: Highcut in Hz for the pre-filter, defaults to 20.0
    :type corners: int
    :param corners: Number of corners to use in the pre-filter

    :returns: obspy.core.event
    """
    from eqcorrscan.utils import sfile_util
    from obspy import read
    import shutil
    # First we need to work out what stations have what picks
    event = sfile_util.readpicks(sfile)
    # Read in waveforms
    stream = read(datapath+'/'+sfile_util.readwavename(sfile)[0])
    if len(sfile_util.readwavename(sfile)) > 1:
        for wavfile in sfile_util.readwavename(sfile):
            stream += read(datapath+'/'+wavfile)
    stream.merge()  # merge the data, just in case!
    event_picked = amp_pick_event(event=event, st=stream, respdir=respdir,
                                  chans=chans, var_wintype=var_wintype,
                                  winlen=winlen, pre_pick=pre_pick,
                                  pre_filt=pre_filt, lowcut=lowcut,
                                  highcut=highcut, corners=corners)
    new_sfile = sfile_util.eventtosfile(event=event, userID=str('EQCO'),
                                        evtype=str('L'), outdir=str('.'),
                                        wavefiles=sfile_util.
                                        readwavename(sfile))
    shutil.move(new_sfile, 'mag_calc.out')
    return event
Пример #15
0
def amp_pick_sfile(sfile,
                   datapath,
                   respdir,
                   chans=['Z'],
                   var_wintype=True,
                   winlen=0.9,
                   pre_pick=0.2,
                   pre_filt=True,
                   lowcut=1.0,
                   highcut=20.0,
                   corners=4):
    """
    Function to pick amplitudes for local magnitudes from NORDIC s-files.

    Reads information from a SEISAN s-file, load the data and the \
    picks, cut the data for the channels given around the S-window, simulate \
    a Wood Anderson seismometer, then pick the maximum peak-to-trough \
    amplitude.

    Output will be put into a mag_calc.out file which will be in full S-file \
    format and can be copied to a REA database.

    :type sfile: str
    :param sfile: Path to NORDIC format s-file
    :type datapath: str
    :param datapath: Path to the waveform files - usually the path to the WAV \
        directory
    :type respdir: str
    :param respdir: Path to the response information directory
    :type chans: list
    :param chans: List of the channels to pick on, defaults to ['Z'] - should \
        just be the orientations, e.g. Z,1,2,N,E
    :type var_wintype: bool
    :param var_wintype: If True, the winlen will be \
        multiplied by the P-S time if both P and S picks are \
        available, otherwise it will be multiplied by the \
        hypocentral distance*0.34 - derived using a p-s ratio of \
        1.68 and S-velocity of 1.5km/s to give a large window, \
        defaults to True
    :type winlen: float
    :param winlen: Length of window, see above parameter, if var_wintype is \
        False then this will be in seconds, otherwise it is the \
        multiplier to the p-s time, defaults to 0.5.
    :type pre_pick: float
    :param pre_pick: Time before the s-pick to start the cut window, defaults \
        to 0.2
    :type pre_filt: bool
    :param pre_filt: To apply a pre-filter or not, defaults to True
    :type lowcut: float
    :param lowcut: Lowcut in Hz for the pre-filter, defaults to 1.0
    :type highcut: float
    :param highcut: Highcut in Hz for the pre-filter, defaults to 20.0
    :type corners: int
    :param corners: Number of corners to use in the pre-filter

    :returns: obspy.core.event
    """
    from eqcorrscan.utils import sfile_util
    from obspy import read
    import shutil
    # First we need to work out what stations have what picks
    event = sfile_util.readpicks(sfile)
    # Read in waveforms
    stream = read(datapath + '/' + sfile_util.readwavename(sfile)[0])
    if len(sfile_util.readwavename(sfile)) > 1:
        for wavfile in sfile_util.readwavename(sfile):
            stream += read(datapath + '/' + wavfile)
    stream.merge()  # merge the data, just in case!
    event_picked = amp_pick_event(event=event,
                                  st=stream,
                                  respdir=respdir,
                                  chans=chans,
                                  var_wintype=var_wintype,
                                  winlen=winlen,
                                  pre_pick=pre_pick,
                                  pre_filt=pre_filt,
                                  lowcut=lowcut,
                                  highcut=highcut,
                                  corners=corners)
    new_sfile = sfile_util.eventtosfile(
        event=event,
        userID=str('EQCO'),
        evtype=str('L'),
        outdir=str('.'),
        wavefiles=sfile_util.readwavename(sfile))
    shutil.move(new_sfile, 'mag_calc.out')
    return event
Пример #16
0
def write_correlations(event_list,
                       wavbase,
                       extract_len,
                       pre_pick,
                       shift_len,
                       lowcut=1.0,
                       highcut=10.0,
                       max_sep=4,
                       min_link=8,
                       coh_thresh=0.0,
                       coherence_weight=True,
                       plotvar=False):
    """
    Function to write a dt.cc file for hypoDD input - takes an input list of
    events and computes pick refienements by correlation.

    :type event_list: list of tuple
    :param event_list: List of tuples of event_id (int) and sfile (String)
    :type wavbase: str
    :param wavbase: Path to the seisan wave directory that the wavefiles in the
                    S-files are stored
    :type extract_len: float
    :param extract_len: Length in seconds to extract around the pick
    :type pre_pick: float
    :param pre_pick: Time before the pick to start the correlation window
    :type shift_len: float
    :param shift_len: Time to allow pick to vary
    :type lowcut: float
    :param lowcut: Lowcut in Hz - default=1.0
    :type highcut: float
    :param highcut: Highcut in Hz - deafult=10.0
    :type max_sep: float
    :param max_sep: Maximum seperation between event pairs in km
    :type min_link: int
    :param min_link: Minimum links for an event to be paired
    :type coherence_weight: bool
    :param coherence_weight: Use coherence to weight the dt.cc file, or the \
        raw cross-correlation value, defaults to false which uses the cross-\
        correlation value.
    :type plotvar: bool
    :param plotvar: To show the pick-correction plots, defualts to False.

    .. warning:: This is not a fast routine!

    .. warning:: In contrast to seisan's \
        corr routine, but in accordance with the hypoDD manual, this outputs \
        corrected differential time.

    .. note:: Currently we have not implemented a method for taking \
        unassociated event objects and wavefiles.  As such if you have events \
        with associated wavefiles you are advised to generate Sfiles for each \
        event using the sfile_util module prior to this step.
    """
    import obspy
    if int(obspy.__version__.split('.')[0]) > 0:
        from obspy.signal.cross_correlation import xcorr_pick_correction
    else:
        from obspy.signal.cross_correlation import xcorrPickCorrection \
            as xcorr_pick_correction
    import matplotlib.pyplot as plt
    from obspy import read
    from eqcorrscan.utils.mag_calc import dist_calc
    import glob
    import warnings

    corr_list = []
    f = open('dt.cc', 'w')
    f2 = open('dt.cc2', 'w')
    for i, master in enumerate(event_list):
        master_sfile = master[1]
        master_event_id = master[0]
        master_picks = sfile_util.readpicks(master_sfile).picks
        master_event = sfile_util.readheader(master_sfile)
        master_ori_time = master_event.origins[0].time
        master_location = (master_event.origins[0].latitude,
                           master_event.origins[0].longitude,
                           master_event.origins[0].depth)
        master_wavefiles = sfile_util.readwavename(master_sfile)
        masterpath = glob.glob(wavbase + os.sep + master_wavefiles[0])
        if masterpath:
            masterstream = read(masterpath[0])
        if len(master_wavefiles) > 1:
            for wavefile in master_wavefiles:
                try:
                    masterstream += read(os.join(wavbase, wavefile))
                except:
                    continue
                    raise IOError("Couldn't find wavefile")
        for j in range(i + 1, len(event_list)):
            # Use this tactic to only output unique event pairings
            slave_sfile = event_list[j][1]
            slave_event_id = event_list[j][0]
            slave_wavefiles = sfile_util.readwavename(slave_sfile)
            try:
                # slavestream=read(wavbase+'/*/*/'+slave_wavefiles[0])
                slavestream = read(wavbase + os.sep + slave_wavefiles[0])
            except:
                # print(slavestream)
                raise IOError('No wavefile found: ' + slave_wavefiles[0] +
                              ' ' + slave_sfile)
            if len(slave_wavefiles) > 1:
                for wavefile in slave_wavefiles:
                    # slavestream+=read(wavbase+'/*/*/'+wavefile)
                    try:
                        slavestream += read(wavbase + '/' + wavefile)
                    except:
                        continue
            # Write out the header line
            event_text = '#'+str(master_event_id).rjust(10) +\
                str(slave_event_id).rjust(10)+' 0.0   \n'
            event_text2 = '#'+str(master_event_id).rjust(10) +\
                str(slave_event_id).rjust(10)+' 0.0   \n'
            slave_picks = sfile_util.readpicks(slave_sfile).picks
            slave_event = sfile_util.readheader(slave_sfile)
            slave_ori_time = slave_event.origins[0].time
            slave_location = (slave_event.origins[0].latitude,
                              slave_event.origins[0].longitude,
                              slave_event.origins[0].depth)
            if dist_calc(master_location, slave_location) > max_sep:
                continue
            links = 0
            phases = 0
            for pick in master_picks:
                if pick.phase_hint[0].upper() not in ['P', 'S']:
                    continue
                    # Only use P and S picks, not amplitude or 'other'
                # Find station, phase pairs
                # Added by Carolin
                slave_matches = [
                    p for p in slave_picks
                    if p.phase_hint == pick.phase_hint and
                    p.waveform_id.station_code == pick.waveform_id.station_code
                ]

                if masterstream.select(station=pick.waveform_id.station_code,
                                       channel='*' +
                                       pick.waveform_id.channel_code[-1]):
                    mastertr = masterstream.\
                        select(station=pick.waveform_id.station_code,
                               channel='*' +
                               pick.waveform_id.channel_code[-1])[0]
                else:
                    print('No waveform data for ' +
                          pick.waveform_id.station_code + '.' +
                          pick.waveform_id.channel_code)
                    print(pick.waveform_id.station_code + '.' +
                          pick.waveform_id.channel_code + ' ' + slave_sfile +
                          ' ' + master_sfile)
                    break
                # Loop through the matches
                for slave_pick in slave_matches:
                    if slavestream.select(
                            station=slave_pick.waveform_id.station_code,
                            channel='*' +
                            slave_pick.waveform_id.channel_code[-1]):
                        slavetr = slavestream.\
                            select(station=slave_pick.waveform_id.station_code,
                                   channel='*'+slave_pick.waveform_id.
                                   channel_code[-1])[0]
                    else:
                        print('No slave data for ' +
                              slave_pick.waveform_id.station_code + '.' +
                              slave_pick.waveform_id.channel_code)
                        print(pick.waveform_id.station_code + '.' +
                              pick.waveform_id.channel_code + ' ' +
                              slave_sfile + ' ' + master_sfile)
                        break
                    # Correct the picks
                    try:
                        correction, cc =\
                            xcorr_pick_correction(pick.time, mastertr,
                                                  slave_pick.time,
                                                  slavetr, pre_pick,
                                                  extract_len - pre_pick,
                                                  shift_len, filter="bandpass",
                                                  filter_options={'freqmin':
                                                                  lowcut,
                                                                  'freqmax':
                                                                  highcut},
                                                  plot=plotvar)
                        # Get the differntial travel time using the
                        # corrected time.
                        # Check that the correction is within the allowed shift
                        # This can occur in the obspy routine when the
                        # correlation function is increasing at the end of the
                        # window.
                        if abs(correction) > shift_len:
                            warnings.warn('Shift correction too large, ' +
                                          'will not use')
                            continue
                        correction = (pick.time - master_ori_time) -\
                            (slave_pick.time + correction - slave_ori_time)
                        links += 1
                        if cc * cc >= coh_thresh:
                            if coherence_weight:
                                weight = cc * cc
                            else:
                                weight = cc
                            phases += 1
                            # added by Caro
                            event_text += pick.waveform_id.station_code.\
                                ljust(5) + _cc_round(correction, 3).\
                                rjust(11) + _cc_round(weight, 3).rjust(8) +\
                                ' '+pick.phase_hint+'\n'
                            event_text2 += pick.waveform_id.station_code\
                                .ljust(5).upper() +\
                                _cc_round(correction, 3).rjust(11) +\
                                _cc_round(weight, 3).rjust(8) +\
                                ' '+pick.phase_hint+'\n'

                            # links+=1
                        corr_list.append(cc * cc)
                    except:
                        # Should warn here
                        msg = "Couldn't compute correlation correction"
                        warnings.warn(msg)
                        continue
            if links >= min_link and phases > 0:
                f.write(event_text)
                f2.write(event_text2)
    if plotvar:
        plt.hist(corr_list, 150)
        plt.show()
    # f.write('\n')
    f.close()
    f2.close()
    return