Source code for obspy.io.sh.core

# -*- coding: utf-8 -*-
"""
SH bindings to ObsPy core module.

:copyright:
    The ObsPy Development Team (devs@obspy.org)
:license:
    GNU Lesser General Public License, Version 3
    (https://www.gnu.org/copyleft/lesser.html)
"""
from __future__ import (absolute_import, division, print_function,
                        unicode_literals)
from future.builtins import *  # NOQA
from future.utils import native_str

import io
import os

import numpy as np

from obspy import Stream, Trace, UTCDateTime
from obspy.core import Stats
from obspy.core.compatibility import from_buffer
from obspy.core.util import loadtxt


MONTHS = ['JAN', 'FEB', 'MAR', 'APR', 'MAY', 'JUN', 'JUL', 'AUG', 'SEP',
          'OCT', 'NOV', 'DEC']

SH_IDX = {
    'LENGTH': 'L001',
    'SIGN': 'I011',
    'EVENTNO': 'I012',
    'MARK': 'I014',
    'DELTA': 'R000',
    'CALIB': 'R026',
    'DISTANCE': 'R011',
    'AZIMUTH': 'R012',
    'SLOWNESS': 'R018',
    'INCI': 'R013',
    'DEPTH': 'R014',
    'MAGNITUDE': 'R015',
    'LAT': 'R016',
    'LON': 'R017',
    'SIGNOISE': 'R022',
    'PWDW': 'R023',
    'DCVREG': 'R024',
    'DCVINCI': 'R025',
    'COMMENT': 'S000',
    'STATION': 'S001',
    'OPINFO': 'S002',
    'FILTER': 'S011',
    'QUAL': 'S012',
    'COMP': 'C000',
    'CHAN1': 'C001',
    'CHAN2': 'C002',
    'BYTEORDER': 'C003',
    'START': 'S021',
    'P-ONSET': 'S022',
    'S-ONSET': 'S023',
    'ORIGIN': 'S024'
}

STANDARD_ASC_HEADERS = ['START', 'COMP', 'CHAN1', 'CHAN2', 'STATION', 'CALIB']

SH_KEYS_INT = [k for (k, v) in SH_IDX.items() if v.startswith('I')]
SH_KEYS_FLOAT = [k for (k, v) in SH_IDX.items() if v.startswith('R')]
INVERTED_SH_IDX = {v: k for k, v in SH_IDX.items()}


[docs]def _is_asc(filename): """ Checks whether a file is a Seismic Handler ASCII file or not. :type filename: str :param filename: Name of the ASCII file to be checked. :rtype: bool :return: ``True`` if a Seismic Handler ASCII file. .. rubric:: Example >>> _is_asc("/path/to/QFILE-TEST-ASC.ASC") #doctest: +SKIP True """ # first six chars should contain 'DELTA:' try: with open(filename, 'rb') as f: temp = f.read(6) except Exception: return False if temp != b'DELTA:': return False return True
[docs]def _read_asc(filename, headonly=False, skip=0, delta=None, length=None, **kwargs): # @UnusedVariable """ Reads a Seismic Handler ASCII file and returns an ObsPy Stream object. .. warning:: This function should NOT be called directly, it registers via the ObsPy :func:`~obspy.core.stream.read` function, call this instead. :type filename: str :param filename: ASCII file to be read. :type headonly: bool, optional :param headonly: If set to True, read only the head. This is most useful for scanning available data in huge (temporary) data sets. :type skip: int, optional :param skip: Number of lines to be skipped from top of file. If defined only one trace is read from file. :type delta: float, optional :param delta: If ``skip`` is used, ``delta`` defines sample offset in seconds. :type length: int, optional :param length: If ``skip`` is used, ``length`` defines the number of values to be read. :rtype: :class:`~obspy.core.stream.Stream` :return: A ObsPy Stream object. .. rubric:: Example >>> from obspy import read >>> st = read("/path/to/QFILE-TEST-ASC.ASC") >>> st # doctest: +ELLIPSIS <obspy.core.stream.Stream object at 0x...> >>> print(st) # doctest: +ELLIPSIS 3 Trace(s) in Stream: .TEST..BHN | 2009-10-01T12:46:01.000000Z - ... | 20.0 Hz, 801 samples .TEST..BHE | 2009-10-01T12:46:01.000000Z - ... | 20.0 Hz, 801 samples .WET..HHZ | 2010-01-01T01:01:05.999000Z - ... | 100.0 Hz, 4001 samples """ fh = open(filename, 'rt') # read file and split text into channels channels = [] headers = {} data = io.StringIO() for line in fh.readlines()[skip:]: if line.isspace(): # blank line # check if any data fetched yet if len(headers) == 0 and data.tell() == 0: continue # append current channel data.seek(0) channels.append((headers, data)) # create new channel headers = {} data = io.StringIO() if skip: # if skip is set only one trace is read, everything else makes # no sense. break continue elif line[0].isalpha(): # header entry key, value = line.split(':', 1) key = key.strip() value = value.strip() headers[key] = value elif not headonly: # data entry - may be written in multiple columns data.write(line.strip() + ' ') fh.close() # create ObsPy stream object stream = Stream() # custom header custom_header = {} if delta: custom_header["delta"] = delta if length: custom_header["npts"] = length for headers, data in channels: # create Stats header = Stats(custom_header) header['sh'] = {} channel = [' ', ' ', ' '] # generate headers for key, value in headers.items(): if key == 'DELTA': header['delta'] = float(value) elif key == 'LENGTH': header['npts'] = int(value) elif key == 'CALIB': header['calib'] = float(value) elif key == 'STATION': header['station'] = value elif key == 'COMP': channel[2] = value[0] elif key == 'CHAN1': channel[0] = value[0] elif key == 'CHAN2': channel[1] = value[0] elif key == 'START': # 01-JAN-2009_01:01:01.0 # 1-OCT-2009_12:46:01.000 header['starttime'] = to_utcdatetime(value) else: # everything else gets stored into sh entry if key in SH_KEYS_INT: header['sh'][key] = int(value) elif key in SH_KEYS_FLOAT: header['sh'][key] = float(value) else: header['sh'][key] = value # set channel code header['channel'] = ''.join(channel) if headonly: # skip data stream.append(Trace(header=header)) else: # read data data = loadtxt(data, dtype=np.float32, ndmin=1) # cut data if requested if skip and length: data = data[:length] # use correct value in any case header["npts"] = len(data) stream.append(Trace(data=data, header=header)) return stream
[docs]def _write_asc(stream, filename, included_headers=None, npl=4, custom_format="%-.6e", append=False, **kwargs): # @UnusedVariable """ Writes a Seismic Handler ASCII file from given ObsPy Stream object. .. warning:: This function should NOT be called directly, it registers via the the :meth:`~obspy.core.stream.Stream.write` method of an ObsPy :class:`~obspy.core.stream.Stream` object, call this instead. :type stream: :class:`~obspy.core.stream.Stream` :param stream: The ObsPy Stream object to write. :type filename: str :param filename: Name of the ASCII file to write. :type npl: int, optional :param npl: Number of data columns in file, default to four. :type included_headers: list or None, optional :param included_headers: If set to a list, only these header entries will be written to file. DELTA and LENGTH are written in any case. If it's set to None, a basic set will be included. :type custom_format: str, optional :param custom_format: Parameter for number formatting of samples, defaults to "%-.6e". :type append: bool, optional :param append: If filename exists append all data to file, default False. """ if included_headers is None: included_headers = STANDARD_ASC_HEADERS sio = io.StringIO() for trace in stream: # write headers sio.write("DELTA: %-.6e\n" % (trace.stats.delta)) sio.write("LENGTH: %d\n" % trace.stats.npts) # additional headers for key, value in trace.stats.get('sh', {}).items(): if included_headers and key not in included_headers: continue sio.write("%s: %s\n" % (key, value)) # special format for start time if "START" in included_headers: dt = trace.stats.starttime sio.write("START: %s\n" % from_utcdatetime(dt)) # component must be split if len(trace.stats.channel) > 2 and "COMP" in included_headers: sio.write("COMP: %c\n" % trace.stats.channel[2]) if len(trace.stats.channel) > 0 and "CHAN1" in included_headers: sio.write("CHAN1: %c\n" % trace.stats.channel[0]) if len(trace.stats.channel) > 1 and "CHAN2" in included_headers: sio.write("CHAN2: %c\n" % trace.stats.channel[1]) if "STATION" in included_headers: sio.write("STATION: %s\n" % trace.stats.station) if "CALIB" in included_headers: sio.write("CALIB: %-.6e\n" % (trace.stats.calib)) # write data in npl columns mask = ([''] * (npl - 1)) + ['\n'] delimiter = mask * ((trace.stats.npts // npl) + 1) delimiter = delimiter[:trace.stats.npts - 1] delimiter.append('\n') for (sample, delim) in zip(trace.data, delimiter): value = custom_format % (sample) sio.write("%s %s" % (value, delim)) sio.write("\n") if append: mode = 'ab' else: mode = 'wb' with open(filename, mode=mode) as fh: sio.seek(0) fh.write(sio.read().encode('ascii', 'strict'))
[docs]def _is_q(filename): """ Checks whether a file is a Seismic Handler Q file or not. :type filename: str :param filename: Name of the Q file to be checked. :rtype: bool :return: ``True`` if a Seismic Handler Q file. .. rubric:: Example >>> _is_q("/path/to/QFILE-TEST.QHD") #doctest: +SKIP True """ # file must start with magic number 43981 try: with open(filename, 'rb') as f: temp = f.read(5) except Exception: return False if temp != b'43981': return False return True
[docs]def _read_q(filename, headonly=False, data_directory=None, byteorder='=', **kwargs): # @UnusedVariable """ Reads a Seismic Handler Q file and returns an ObsPy Stream object. .. warning:: This function should NOT be called directly, it registers via the ObsPy :func:`~obspy.core.stream.read` function, call this instead. :type filename: str :param filename: Q header file to be read. Must have a `QHD` file extension. :type headonly: bool, optional :param headonly: If set to True, read only the head. This is most useful for scanning available data in huge (temporary) data sets. :type data_directory: str, optional :param data_directory: Data directory where the corresponding QBN file can be found. :type byteorder: str, optional :param byteorder: Enforce byte order for data file. This is important for Q files written in older versions of Seismic Handler, which don't explicit state the `BYTEORDER` flag within the header file. Can be little endian (``'<'``), big endian (``'>'``), or native byte order (``'='``). Defaults to ``'='``. :rtype: :class:`~obspy.core.stream.Stream` :return: A ObsPy Stream object. Q files consists of two files per data set: * a ASCII header file with file extension `QHD` and the * binary data file with file extension `QBN`. The read method only accepts header files for the ``filename`` parameter. ObsPy assumes that the corresponding data file is within the same directory if the ``data_directory`` parameter is not set. Otherwise it will search in the given ``data_directory`` for a file with the `QBN` file extension. This function should NOT be called directly, it registers via the ObsPy :func:`~obspy.core.stream.read` function, call this instead. .. rubric:: Example >>> from obspy import read >>> st = read("/path/to/QFILE-TEST.QHD") >>> st #doctest: +ELLIPSIS <obspy.core.stream.Stream object at 0x...> >>> print(st) # doctest: +ELLIPSIS 3 Trace(s) in Stream: .TEST..BHN | 2009-10-01T12:46:01.000000Z - ... | 20.0 Hz, 801 samples .TEST..BHE | 2009-10-01T12:46:01.000000Z - ... | 20.0 Hz, 801 samples .WET..HHZ | 2010-01-01T01:01:05.999000Z - ... | 100.0 Hz, 4001 samples """ if not headonly: if not data_directory: data_file = os.path.splitext(filename)[0] + '.QBN' else: data_file = os.path.basename(os.path.splitext(filename)[0]) data_file = os.path.join(data_directory, data_file + '.QBN') if not os.path.isfile(data_file): msg = "Can't find corresponding QBN file at %s." raise IOError(msg % data_file) fh_data = open(data_file, 'rb') # loop through read header file with open(filename, 'rt') as fh: lines = fh.read().splitlines() # number of comment lines cmtlines = int(lines[0][5:7]) # trace lines traces = {} i = -1 id = '' for line in lines[cmtlines:]: cid = int(line[0:2]) if cid != id: id = cid i += 1 traces.setdefault(i, '') traces[i] += line[3:] # create stream object stream = Stream() for id in sorted(traces.keys()): # fetch headers header = {} header['sh'] = { "FROMQ": True, "FILE": os.path.splitext(os.path.split(filename)[1])[0], } channel = ['', '', ''] npts = 0 for item in traces[id].split('~'): key = item.lstrip()[0:4] value = item.lstrip()[5:] if key == 'L001': npts = header['npts'] = int(value) elif key == 'L000': continue elif key == 'R000': header['delta'] = float(value) elif key == 'R026': header['calib'] = float(value) elif key == 'S001': header['station'] = value elif key == 'C000' and value: channel[2] = value[0] elif key == 'C001' and value: channel[0] = value[0] elif key == 'C002' and value: channel[1] = value[0] elif key == 'C003': if value == '<' or value == '>': byteorder = header['sh']['BYTEORDER'] = value elif key == 'S021': # 01-JAN-2009_01:01:01.0 # 1-OCT-2009_12:46:01.000 header['starttime'] = to_utcdatetime(value) elif key == 'S022': header['sh']['P-ONSET'] = to_utcdatetime(value) elif key == 'S023': header['sh']['S-ONSET'] = to_utcdatetime(value) elif key == 'S024': header['sh']['ORIGIN'] = to_utcdatetime(value) elif key: key = INVERTED_SH_IDX.get(key, key) if key in SH_KEYS_INT: header['sh'][key] = int(value) elif key in SH_KEYS_FLOAT: header['sh'][key] = float(value) else: header['sh'][key] = value # set channel code header['channel'] = ''.join(channel) # remember record number header['sh']['RECNO'] = len(stream) + 1 if headonly: # skip data stream.append(Trace(header=header)) else: if not npts: stream.append(Trace(header=header)) continue # read data data = fh_data.read(npts * 4) dtype = native_str(byteorder + 'f4') data = from_buffer(data, dtype=dtype) # convert to system byte order data = np.require(data, native_str('=f4')) stream.append(Trace(data=data, header=header)) if not headonly: fh_data.close() return stream
[docs]def _write_q(stream, filename, data_directory=None, byteorder='=', append=False, **kwargs): # @UnusedVariable """ Writes a Seismic Handler Q file from given ObsPy Stream object. .. warning:: This function should NOT be called directly, it registers via the the :meth:`~obspy.core.stream.Stream.write` method of an ObsPy :class:`~obspy.core.stream.Stream` object, call this instead. :type stream: :class:`~obspy.core.stream.Stream` :param stream: The ObsPy Stream object to write. :type filename: str :param filename: Name of the Q file to write. :type data_directory: str, optional :param data_directory: Data directory where the corresponding QBN will be written. :type byteorder: str, optional :param byteorder: Enforce byte order for data file. Can be little endian (``'<'``), big endian (``'>'``), or native byte order (``'='``). Defaults to ``'='``. :type append: bool, optional :param append: If filename exists append all data to file, default False. """ if filename.endswith('.QHD') or filename.endswith('.QBN'): filename = os.path.splitext(filename)[0] if data_directory: temp = os.path.basename(filename) filename_data = os.path.join(data_directory, temp) else: filename_data = filename filename_header = filename + '.QHD' # if the header file exists its assumed that the data is also there if os.path.exists(filename_header) and append: try: trcs = _read_q(filename_header, headonly=True) mode = 'ab' count_offset = len(trcs) except Exception: raise Exception("Target filename '%s' not readable!" % filename) else: append = False mode = 'wb' count_offset = 0 fh = open(filename_header, mode) fh_data = open(filename_data + '.QBN', mode) # build up header strings headers = [] minnol = 4 cur_npts = 0 for trace in stream: temp = "L000:%d~ " % cur_npts cur_npts += trace.stats.npts temp += "L001:%d~ R000:%f~ R026:%f~ " % (trace.stats.npts, trace.stats.delta, trace.stats.calib) if trace.stats.station: temp += "S001:%s~ " % trace.stats.station # component must be split if len(trace.stats.channel) > 2: temp += "C000:%c~ " % trace.stats.channel[2] if len(trace.stats.channel) > 0: temp += "C001:%c~ " % trace.stats.channel[0] if len(trace.stats.channel) > 1: temp += "C002:%c~ " % trace.stats.channel[1] # special format for start time dt = trace.stats.starttime temp += "S021:%s~ " % from_utcdatetime(dt) for key, value in trace.stats.get('sh', {}).items(): # skip unknown keys if not key or key not in SH_IDX.keys(): continue # convert UTCDateTimes into strings if isinstance(value, UTCDateTime): value = from_utcdatetime(value) temp += "%s:%s~ " % (SH_IDX[key], value) headers.append(temp) # get maximal number of trclines nol = len(temp) // 74 + 1 if nol > minnol: minnol = nol # first line: magic number, cmtlines, trclines # XXX: comment lines are ignored if not append: line = "43981 1 %d\n" % minnol fh.write(line.encode('ascii', 'strict')) for i, trace in enumerate(stream): # write headers temp = [headers[i][j:j + 74] for j in range(0, len(headers[i]), 74)] for j in range(0, minnol): try: line = "%02d|%s\n" % ((i + 1 + count_offset) % 100, temp[j]) fh.write(line.encode('ascii', 'strict')) except Exception: line = "%02d|\n" % ((i + 1 + count_offset) % 100) fh.write(line.encode('ascii', 'strict')) # write data in given byte order dtype = native_str(byteorder + 'f4') data = np.require(trace.data, dtype=dtype) fh_data.write(data.data) fh.close() fh_data.close()
[docs]def to_utcdatetime(value): """ Converts time string used within Seismic Handler into a UTCDateTime. :type value: str :param value: A Date time string. :return: Converted :class:`~obspy.core.utcdatetime.UTCDateTime` object. .. rubric:: Example >>> to_utcdatetime(' 2-JAN-2008_03:04:05.123') UTCDateTime(2008, 1, 2, 3, 4, 5, 123000) >>> to_utcdatetime('2-JAN-2008') UTCDateTime(2008, 1, 2, 0, 0) >>> to_utcdatetime('2-JAN-08') UTCDateTime(2008, 1, 2, 0, 0) >>> to_utcdatetime('2-JAN-99') UTCDateTime(1999, 1, 2, 0, 0) >>> to_utcdatetime('2-JAN-2008_1') UTCDateTime(2008, 1, 2, 1, 0) >>> to_utcdatetime('2-JAN-2008_1:1') UTCDateTime(2008, 1, 2, 1, 1) """ try: date, time = value.split('_') except ValueError: date = value time = "0:0:0" day, month, year = date.split('-') time = time.split(':') try: hour, mins, secs = time except ValueError: hour = time[0] mins = "0" secs = "0" if len(time) == 2: mins = time[1] day = int(day) month = MONTHS.index(month.upper()) + 1 if len(year) == 2: if int(year) < 70: year = "20" + year else: year = "19" + year year = int(year) hour = int(hour) mins = int(mins) secs = float(secs) return UTCDateTime(year, month, day, hour, mins) + secs
[docs]def from_utcdatetime(dt): """ Converts UTCDateTime object into a time string used within Seismic Handler. :type dt: :class:`~obspy.core.utcdatetime.UTCDateTime` :param dt: A UTCDateTime object. :return: Converted date time string usable by Seismic Handler. .. rubric:: Example >>> from obspy import UTCDateTime >>> dt = UTCDateTime(2008, 1, 2, 3, 4, 5, 123456) >>> print(from_utcdatetime(dt)) 2-JAN-2008_03:04:05.123 """ pattern = "%2d-%3s-%4d_%02d:%02d:%02d.%03d" return pattern % (dt.day, MONTHS[dt.month - 1], dt.year, dt.hour, dt.minute, dt.second, dt.microsecond / 1000)
if __name__ == '__main__': import doctest doctest.testmod(exclude_empty=True)