Source code for openquake.hmtk.parsers.catalogue.gcmt_ndk_parser

#!/usr/bin/env python

'''
Parser for moment tensor catalogue in GCMT format into a set of GCMT classes
'''
from __future__ import division
import re
import datetime
import numpy as np
from math import floor, fabs
from linecache import getlines

import openquake.hmtk.seismicity.gcmt_utils as utils
from openquake.hmtk.seismicity.gcmt_catalogue import (
    GCMTHypocentre, GCMTCentroid,  GCMTPrincipalAxes, GCMTNodalPlanes,
    GCMTMomentTensor, GCMTEvent, GCMTCatalogue)


def _read_date_from_string(str1):
    """
    Reads the date from a string in the format YYYY/MM/DD and returns
    :class: datetime.date
    """
    full_date = [int(x) for x in str1.split('/')]
    return datetime.date(full_date[0], full_date[1], full_date[2])


def _read_time_from_string(str1):
    """
    Reads the time from a string in the format HH:MM:SS.S and returns
    :class: datetime.time
    """
    full_time = [float(x) for x in str1.split(':')]
    hour = int(full_time[0])
    minute = int(full_time[1])
    if full_time[2] > 59.99:
        minute += 1
        second = 0
    else:
        second = int(full_time[2])
    microseconds = int((full_time[2] - floor(full_time[2])) * 1000000)
    return datetime.time(hour, minute, second, microseconds)


def _read_moment_tensor_from_ndk_string(ndk_string, system='USE'):
    """
    Reads the moment tensor from the ndk_string representation
    ndk_string = [Mrr, sigMrr, Mtt, sigMtt, Mpp, sigMpp, Mrt, sigMrt, Mrp,
                  sigMrp, Mtp, sigMtp]
    Output tensors should be of format:
        expected = [[Mtt, Mtp, Mtr],
                    [Mtp, Mpp, Mpr],
                    [Mtr, Mpr, Mrr]]
        sigma = [[sigMtt, sigMtp, sigMtr],
                 [sigMtp, sigMpp, sigMpr],
                 [sigMtr, sigMpr, sigMrr]]
    Exponent returned in Nm

    :param str ndk_string:
        String of data in ndk format (line 4 of event)
    :param str system:
        Reference frame of tensor Up, South, East {USE} or North, East, Down
        (NED)
    """
    exponent = float(ndk_string[0:2]) - 7.
    mkr = np.array([2, 9, 15], dtype=int)
    vector = []
    for i in range(0, 6):
        vector.extend([
            float(ndk_string[mkr[0]:mkr[1]]),
            float(ndk_string[mkr[1]:mkr[2]])])
        mkr = mkr + 13
    vector = np.array(vector)
    mrr, mtt, mpp, mrt, mrp, mtp = tuple(vector[np.arange(0, 12, 2)])
    sig_mrr, sig_mtt, sig_mpp, sig_mrt, sig_mrp, sig_mtp = \
        tuple(vector[np.arange(1, 13, 2)])

    tensor = utils.COORD_SYSTEM[system](mrr, mtt, mpp, mrt, mrp, mtp)
    tensor = (10. ** exponent) * tensor

    sigma = utils.COORD_SYSTEM[system](sig_mrr, sig_mtt, sig_mpp,
                                       sig_mrt, sig_mrp, sig_mtp)
    sigma = (10. ** exponent) * sigma

    return tensor, sigma, exponent


[docs]class ParseNDKtoGCMT(object): """ Implements the parser to read a file in ndk format to the GCMT catalogue """ def __init__(self, filename): """ :param str filename: Name of the catalogue file in ndk format """ self.filename = filename self.catalogue = GCMTCatalogue()
[docs] def read_file(self, start_year=None, end_year=None, use_centroid=None): """ Reads the file """ raw_data = getlines(self.filename) num_lines = len(raw_data) if ((float(num_lines) / 5.) - float(num_lines / 5)) > 1E-9: raise IOError('GCMT represented by 5 lines - number in file not' ' a multiple of 5!') self.catalogue.number_gcmts = num_lines // 5 self.catalogue.gcmts = [None] * self.catalogue.number_gcmts # Pre-allocates list id0 = 0 print('Parsing catalogue ...') for iloc in range(0, self.catalogue.number_gcmts): self.catalogue.gcmts[iloc] = self.read_ndk_event(raw_data, id0) id0 += 5 print('complete. Contains %s moment tensors' % self.catalogue.get_number_tensors()) if not start_year: min_years = [] min_years = [cent.centroid.date.year for cent in self.catalogue.gcmts] self.catalogue.start_year = np.min(min_years) if not end_year: max_years = [] max_years = [cent.centroid.date.year for cent in self.catalogue.gcmts] self.catalogue.end_year = np.max(max_years) self.to_hmtk(use_centroid) return self.catalogue
[docs] def read_ndk_event(self, raw_data, id0): """ Reads a 5-line batch of data into a set of GCMTs """ gcmt = GCMTEvent() # Get hypocentre ndkstring = raw_data[id0].rstrip('\n') gcmt.hypocentre = self._read_hypocentre_from_ndk_string(ndkstring) # GCMT metadata ndkstring = raw_data[id0 + 1].rstrip('\n') gcmt = self._get_metadata_from_ndk_string(gcmt, ndkstring) # Get Centroid ndkstring = raw_data[id0 + 2].rstrip('\n') gcmt.centroid = self._read_centroid_from_ndk_string(ndkstring, gcmt.hypocentre) # Get Moment Tensor ndkstring = raw_data[id0 + 3].rstrip('\n') gcmt.moment_tensor = self._get_moment_tensor_from_ndk_string(ndkstring) # Get principal axes ndkstring = raw_data[id0 + 4].rstrip('\n') gcmt.principal_axes = self._get_principal_axes_from_ndk_string( ndkstring[3:48], exponent=gcmt.moment_tensor.exponent) # Get Nodal Planes gcmt.nodal_planes = self._get_nodal_planes_from_ndk_string( ndkstring[57:]) # Get Moment and Magnitude gcmt.moment, gcmt.version, gcmt.magnitude = \ self._get_moment_from_ndk_string( ndkstring, gcmt.moment_tensor.exponent) return gcmt
[docs] def to_hmtk(self, use_centroid=True): ''' Convert the content of the GCMT catalogue to a HMTK catalogue. ''' self._preallocate_data_dict() for iloc, gcmt in enumerate(self.catalogue.gcmts): self.catalogue.data['eventID'][iloc] = iloc if use_centroid: self.catalogue.data['year'][iloc] = \ gcmt.centroid.date.year self.catalogue.data['month'][iloc] = \ gcmt.centroid.date.month self.catalogue.data['day'][iloc] = \ gcmt.centroid.date.day self.catalogue.data['hour'][iloc] = \ gcmt.centroid.time.hour self.catalogue.data['minute'][iloc] = \ gcmt.centroid.time.minute self.catalogue.data['second'][iloc] = \ gcmt.centroid.time.second self.catalogue.data['longitude'][iloc] = \ gcmt.centroid.longitude self.catalogue.data['latitude'][iloc] = \ gcmt.centroid.latitude self.catalogue.data['depth'][iloc] = \ gcmt.centroid.depth else: self.catalogue.data['year'][iloc] = \ gcmt.hypocentre.date.year self.catalogue.data['month'][iloc] = \ gcmt.hypocentre.date.month self.catalogue.data['day'][iloc] = \ gcmt.hypocentre.date.day self.catalogue.data['hour'][iloc] = \ gcmt.hypocentre.time.hour self.catalogue.data['minute'][iloc] = \ gcmt.hypocentre.time.minute self.catalogue.data['second'][iloc] = \ gcmt.hypocentre.time.second self.catalogue.data['longitude'][iloc] = \ gcmt.hypocentre.longitude self.catalogue.data['latitude'][iloc] = \ gcmt.hypocentre.latitude self.catalogue.data['depth'][iloc] = \ gcmt.hypocentre.depth # Moment, magnitude and relative errors self.catalogue.data['moment'][iloc] = gcmt.moment self.catalogue.data['magnitude'][iloc] = gcmt.magnitude self.catalogue.data['f_clvd'][iloc] = gcmt.f_clvd self.catalogue.data['e_rel'][iloc] = gcmt.e_rel self.catalogue.data['centroidID'][iloc] = gcmt.identifier # Nodal planes self.catalogue.data['strike1'][iloc] = \ gcmt.nodal_planes.nodal_plane_1['strike'] self.catalogue.data['dip1'][iloc] = \ gcmt.nodal_planes.nodal_plane_1['dip'] self.catalogue.data['rake1'][iloc] = \ gcmt.nodal_planes.nodal_plane_1['rake'] self.catalogue.data['strike2'][iloc] = \ gcmt.nodal_planes.nodal_plane_2['strike'] self.catalogue.data['dip2'][iloc] = \ gcmt.nodal_planes.nodal_plane_2['dip'] self.catalogue.data['rake2'][iloc] = \ gcmt.nodal_planes.nodal_plane_2['rake'] # Principal axes self.catalogue.data['eigenvalue_b'][iloc] = \ gcmt.principal_axes.b_axis['eigenvalue'] self.catalogue.data['azimuth_b'][iloc] = \ gcmt.principal_axes.b_axis['azimuth'] self.catalogue.data['plunge_b'][iloc] = \ gcmt.principal_axes.b_axis['plunge'] self.catalogue.data['eigenvalue_p'][iloc] = \ gcmt.principal_axes.p_axis['eigenvalue'] self.catalogue.data['azimuth_p'][iloc] = \ gcmt.principal_axes.p_axis['azimuth'] self.catalogue.data['plunge_p'][iloc] = \ gcmt.principal_axes.p_axis['plunge'] self.catalogue.data['eigenvalue_t'][iloc] = \ gcmt.principal_axes.t_axis['eigenvalue'] self.catalogue.data['azimuth_t'][iloc] = \ gcmt.principal_axes.t_axis['azimuth'] self.catalogue.data['plunge_t'][iloc] = \ gcmt.principal_axes.t_axis['plunge'] return self.catalogue
def _preallocate_data_dict(self): """ """ nvals = self.catalogue.get_number_tensors() for key in self.catalogue.TOTAL_ATTRIBUTE_LIST: if key in self.catalogue.STRING_ATTRIBUTE_LIST: self.catalogue.data[key] = [None for i in range(0, nvals)] elif key in self.catalogue.INT_ATTRIBUTE_LIST: self.catalogue.data[key] = np.zeros(nvals, dtype=int) else: self.catalogue.data[key] = np.zeros(nvals, dtype=float) def _read_hypocentre_from_ndk_string(self, linestring): """ Reads the hypocentre data from the ndk string to return an instance of the GCMTHypocentre class """ hypo = GCMTHypocentre() hypo.source = linestring[0:4] hypo.date = _read_date_from_string(linestring[5:15]) hypo.time = _read_time_from_string(linestring[16:26]) hypo.latitude = float(linestring[27:33]) hypo.longitude = float(linestring[34:41]) hypo.depth = float(linestring[42:47]) magnitudes = [float(x) for x in linestring[48:55].split(' ')] if magnitudes[0] > 0.: hypo.m_b = magnitudes[0] if magnitudes[1] > 0.: hypo.m_s = magnitudes[1] hypo.location = linestring[56:] return hypo def _get_metadata_from_ndk_string(self, gcmt, ndk_string): """ Reads the GCMT metadata from line 2 of the ndk batch """ gcmt.identifier = ndk_string[:16] inversion_data = re.split('[A-Z:]+', ndk_string[17:61]) gcmt.metadata['BODY'] = [float(x) for x in inversion_data[1].split()] gcmt.metadata['SURFACE'] = [ float(x) for x in inversion_data[2].split()] gcmt.metadata['MANTLE'] = [float(x) for x in inversion_data[3].split()] further_meta = re.split('[: ]+', ndk_string[62:]) gcmt.metadata['CMT'] = int(further_meta[1]) gcmt.metadata['FUNCTION'] = {'TYPE': further_meta[2], 'DURATION': float(further_meta[3])} return gcmt def _read_centroid_from_ndk_string(self, ndk_string, hypocentre): """ Reads the centroid data from the ndk string to return an instance of the GCMTCentroid class :param str ndk_string: String of data (line 3 of ndk format) :param hypocentre: Instance of the GCMTHypocentre class """ centroid = GCMTCentroid(hypocentre.date, hypocentre.time) data = ndk_string[:58].split() centroid.centroid_type = data[0].rstrip(':') data = [float(x) for x in data[1:]] time_diff = data[0] if fabs(time_diff) > 1E-6: centroid._get_centroid_time(time_diff) centroid.time_error = data[1] centroid.latitude = data[2] centroid.latitude_error = data[3] centroid.longitude = data[4] centroid.longitude_error = data[5] centroid.depth = data[6] centroid.depth_error = data[7] centroid.depth_type = ndk_string[59:63] centroid.centroid_id = ndk_string[64:] return centroid def _get_moment_tensor_from_ndk_string(self, ndk_string): """ Reads the moment tensor from the ndk_string and returns an instance of the GCMTMomentTensor class. By default the ndk format uses the Up, South, East (USE) reference system. """ moment_tensor = GCMTMomentTensor('USE') tensor_data = _read_moment_tensor_from_ndk_string(ndk_string, 'USE') moment_tensor.tensor = tensor_data[0] moment_tensor.tensor_sigma = tensor_data[1] moment_tensor.exponent = tensor_data[2] return moment_tensor def _get_principal_axes_from_ndk_string(self, ndk_string, exponent): """ Gets the principal axes from the ndk string and returns an instance of the GCMTPrincipalAxes class """ axes = GCMTPrincipalAxes() # The principal axes is defined in characters 3:48 of the 5th line exponent = 10. ** exponent axes.t_axis = {'eigenvalue': exponent * float(ndk_string[0:8]), 'plunge': float(ndk_string[8:11]), 'azimuth': float(ndk_string[11:15])} axes.b_axis = {'eigenvalue': exponent * float(ndk_string[15:23]), 'plunge': float(ndk_string[23:26]), 'azimuth': float(ndk_string[26:30])} axes.p_axis = {'eigenvalue': exponent * float(ndk_string[30:38]), 'plunge': float(ndk_string[38:41]), 'azimuth': float(ndk_string[41:])} return axes def _get_nodal_planes_from_ndk_string(self, ndk_string): """ Reads the nodal plane information (represented by 5th line [57:] of the tensor representation) and returns an instance of the GCMTNodalPlanes class """ planes = GCMTNodalPlanes() planes.nodal_plane_1 = {'strike': float(ndk_string[0:3]), 'dip': float(ndk_string[3:6]), 'rake': float(ndk_string[6:11])} planes.nodal_plane_2 = {'strike': float(ndk_string[11:15]), 'dip': float(ndk_string[15:18]), 'rake': float(ndk_string[18:])} return planes def _get_moment_from_ndk_string(self, ndk_string, exponent): """ Returns the moment and the moment magnitude """ moment = float(ndk_string[49:56]) * (10. ** exponent) version = ndk_string[:3] magnitude = utils.moment_magnitude_scalar(moment) return moment, version, magnitude