Source code for seispy.rf

import obspy
from obspy import UTCDateTime
from obspy.taup import TauPyModel
from import SACTrace
from obspy.core.event.catalog import read_events
import re
from os.path import join, exists
from os import makedirs
from import Query, _cat2df
from seispy.para import RFPara
from seispy import distaz
from seispy.eq import EQ
from seispy.setuplog import setuplog
from seispy.catalog import read_catalog_file
import glob
import numpy as np
from datetime import timedelta
import pandas as pd
import configparser
import argparse
import sys
import pickle

[docs]def pickphase(eqs, para, logger): from PySide6.QtWidgets import QApplication from seispy.pickseis.sviewerui import MatplotlibWidget app = QApplication(sys.argv) ui = MatplotlibWidget(eqs, para, logger) if app.exec() == 0: ui.exit_app() return
def _add_header(st, evt_time, stainfo): sta = stainfo.query.stations[0][0] for tr in st: header = SACTrace.from_obspy_trace(tr).to_obspy_trace().stats.sac channel = for ch in sta.channels: if ch.code == channel: header.cmpaz = ch.azimuth header.cmpinc = -ch.dip header.stla = stainfo.stla header.stlo = stainfo.stlo header.stel = stainfo.stel header.b = 0 header.o = evt_time - tr.stats.starttime tr.stats.__dict__['sac'] = header
[docs]class SACFileNotFoundError(Exception): def __init__(self, matchkey): self.matchkey = matchkey def __str__(self): print('No sac files found with {}'.format(self.matchkey))
[docs]def datestr2regex(datestr): pattern = datestr.replace('%y', r'\d{2}') pattern = pattern.replace('%Y', r'\d{4}') pattern = pattern.replace('%m', r'\d{2}') pattern = pattern.replace('%d', r'\d{2}') pattern = pattern.replace('%j', r'\d{3}') pattern = pattern.replace('%H', r'\d{2}') pattern = pattern.replace('%M', r'\d{2}') pattern = pattern.replace('%S', r'\d{2}') return pattern
[docs]def read_catalog(logpath:str, b_time, e_time, stla:float, stlo:float, magmin=5.5, magmax=10., dismin=30., dismax=90.): """Read local catalog with seispy or QUAKEML format :param logpath: Path to catalogs :type logpath: str :param b_time: Start time :type b_time: obspy.UTCDateTime :param e_time: End time :type e_time: obspy.UTCDateTime :param stla: Station latitude :type stla: float :param stlo: Station longitude :type stlo: float :param magmin: Minimum magnitude, defaults to 5.5 :type magmin: float, optional :param magmax: Maximum magnitude, defaults to 10 :type magmax: float, optional :param dismin: Minimum distance, defaults to 30 :type dismin: float, optional :param dismax: Maximum distance, defaults to 90 :type dismax: float, optional :return: list of earthquakes :rtype: pandas.DataFrame """ try: eq_lst = read_catalog_file(logpath) except: events = read_events(logpath, 'QUAKEML') eq_lst = _cat2df(events) dis = distaz(stla, stlo, eq_lst['evla'], eq_lst['evlo']).delta eq_lst = eq_lst[(eq_lst['date']>=b_time) & (eq_lst['date']<=e_time) & \ (eq_lst['mag']>=magmin) & (eq_lst['mag']<=magmax) & \ (dis>=dismin) & (dis<=dismax)] return eq_lst
[docs]def fetch_waveform(eq_lst, para, model, logger): tb = np.max([2*para.noiselen, 2*para.time_before]) te = np.max([2*para.noiselen, 2*para.time_after]) query = Query(para.data_server) new_col = ['dis', 'bazi', 'data', 'datestr'] eq_match = pd.DataFrame(columns=new_col) for i, row in eq_lst.iterrows(): datestr = row['date'].strftime('%Y.%j.%H.%M.%S') daz = distaz(para.stainfo.stla, para.stainfo.stlo, row['evla'], row['evlo']) arrivals = model.get_travel_times(row['evdp'],, phase_list=[para.phase]) if not arrivals: logger.RFlog.error('The phase of {} with source depth {} and distance {} is not exists'.format( para.phase, row['evdp'], continue if len(arrivals) > 1: logger.RFlog.error('More than one phase were calculated with source depth of {} and distance of {}'.format( row['evdp'], else: arr_time = arrivals[0].time t1 = row['date']+arr_time-tb t2 = row['date']+arr_time+te try:'Fetch waveforms of ({}/{}) event {} from {}'.format( i+1, eq_lst.shape[0], datestr, para.data_server)) st = query.client.get_waveforms(, para.stainfo.station, para.stainfo.location,, t1, t2) _add_header(st, row['date'], para.stainfo) except Exception as e: logger.RFlog.error('Error in fetching waveforms of event {}: {}'.format(datestr, str(e).strip())) continue try: this_eq = EQ.from_stream(st) except Exception as e: logger.RFlog.error('{}'.format(e)) continue this_eq.get_time_offset(row['date']) this_df = pd.DataFrame([[, daz.baz, this_eq, datestr]], columns=new_col, index=[i]) eq_match = pd.concat([eq_match, this_df]) ind = eq_match.index.drop_duplicates(keep=False) eq_match = eq_match.loc[ind] return pd.concat([eq_lst, eq_match], axis=1, join='inner')
[docs]def match_eq(eq_lst, pathname, stla, stlo, logger, ref_comp='Z', suffix='SAC', offset=None, tolerance=210, dateformat='%Y.%j.%H.%M.%S'): pattern = datestr2regex(dateformat) ref_eqs = glob.glob(join(pathname, '*{0}*{1}'.format(ref_comp, suffix))) if len(ref_eqs) == 0: raise SACFileNotFoundError(join(pathname, '*{0}*{1}'.format(ref_comp, suffix))) sac_files = [] for ref_sac in ref_eqs: try: datestr = re.findall(pattern, ref_sac)[0] except IndexError: raise IndexError('Error data format of {} in {}'.format(pattern, ref_sac)) if isinstance(offset, (int, float)): sac_files.append([datestr, UTCDateTime.strptime(datestr, dateformat), -offset]) elif offset is None: try: tr =[0] except TypeError: continue sac_files.append([datestr, tr.stats.starttime-tr.stats.sac.b, tr.stats.sac.o]) else: raise TypeError('offset should be int or float type') new_col = ['dis', 'bazi', 'data', 'datestr'] eq_match = pd.DataFrame(columns=new_col) for datestr, b_time, offs in sac_files: date_range_begin = b_time + timedelta(seconds=offs - tolerance) date_range_end = b_time + timedelta(seconds=offs + tolerance) results = eq_lst[( > date_range_begin) & ( < date_range_end)] if len(results) != 1: continue try: this_eq = EQ(pathname, datestr, suffix) except Exception as e: logger.RFlog.error(''.format(e)) continue this_eq.get_time_offset(results.iloc[0]['date']) daz = distaz(stla, stlo, results.iloc[0]['evla'], results.iloc[0]['evlo']) this_df = pd.DataFrame([[, daz.baz, this_eq, datestr]], columns=new_col, index=results.index.values) eq_match = pd.concat([eq_match, this_df]) ind = eq_match.index.drop_duplicates(keep=False) eq_match = eq_match.loc[ind] return pd.concat([eq_lst, eq_match], axis=1, join='inner')
[docs]def CfgModify(cfg_file, session, key, value): cf = configparser.RawConfigParser() try: except Exception: raise FileNotFoundError('Cannot open configure file %s' % cfg_file) cf.set(session, key, value) cf.write(open(cfg_file, 'w'))
[docs]class RF(object): def __init__(self, cfg_file=None, log=None): if log is None: self.logger = setuplog() else: self.logger = log if cfg_file is None: self.para = RFPara() elif isinstance(cfg_file, str): if not exists(cfg_file): self.logger.RFlog.error('No such file of {}.'.format(cfg_file)) sys.exit(1) self.para = RFPara.read_para(cfg_file) else: raise TypeError('cfg should be in \'str\' format rather than \'{0}\''.format(type(cfg_file))) if not isinstance(self.para, RFPara): raise TypeError('Input value should be class seispy.rf.para') self.eq_lst = pd.DataFrame() self.eqs = pd.DataFrame() self.model = TauPyModel(self.para.velmod) self.stainfo = self.para.stainfo self.baz_shift = 0 @property def date_begin(self): return self.para.date_begin @date_begin.setter def date_begin(self, value): self.para.date_begin = value @property def date_end(self): return self.para.date_end @date_end.setter def date_end(self, value): self.para.date_end = value
[docs] def load_stainfo(self): try: if self.para.use_remote_data:'Load station info of {}.{} from {} web-service'.format(, self.para.stainfo.station, self.para.data_server)) self.para.stainfo.get_station_from_ws(self.para.data_server) try: self.para._check_date_range() except Exception as e: self.logger.RFlog.error('{}'.format(e)) sys.exit(1) else:'Load station info from {0}'.format(self.para.datapath)) self.para.stainfo.load_stainfo(self.para.datapath, self.para.ref_comp, self.para.suffix) except Exception as e: self.logger.RFlog.error('Error in loading station info: {0}'.format(e)) sys.exit(1)
[docs] def search_eq(self, local=False, catalog=None): if not local: try:'Searching earthquakes from {}'.format(self.para.cata_server)) if self.para.date_end > UTCDateTime(): self.para.date_end = UTCDateTime() query = Query(self.para.cata_server) query.get_events(starttime=self.para.date_begin, endtime=self.para.date_end, latitude=self.para.stainfo.stla, longitude=self.para.stainfo.stlo, minmagnitude=self.para.magmin, maxmagnitude=self.para.magmax, minradius=self.para.dismin, maxradius=self.para.dismax, catalog=catalog) self.eq_lst = except Exception as e: raise ConnectionError(e) else: try: 'Searching earthquakes from {0} to {1}'.format(self.date_begin.strftime('%Y.%m.%dT%H:%M:%S'), self.date_end.strftime('%Y.%m.%dT%H:%M:%S'))) self.eq_lst = read_catalog(self.para.catalogpath, self.para.date_begin, self.para.date_end, self.para.stainfo.stla, self.para.stainfo.stlo, magmin=self.para.magmin, magmax=self.para.magmax, dismin=self.para.dismin, dismax=self.para.dismax) except Exception as e: self.logger.RFlog.error('{0}'.format(e)) raise e'{} earthquakes are found'.format(self.eq_lst.shape[0]))
[docs] def match_eq(self): try: if self.para.use_remote_data:'Fetch seismic data from {}'.format(self.para.data_server)) self.eqs = fetch_waveform(self.eq_lst, self.para, self.model, self.logger) else:'Associating SAC files with earthquakes') self.eqs = match_eq(self.eq_lst, self.para.datapath, self.para.stainfo.stla, self.para.stainfo.stlo, self.logger, ref_comp=self.para.ref_comp, suffix=self.para.suffix, offset=self.para.offset, tolerance=self.para.tolerance, dateformat=self.para.dateformat) except Exception as e: self.logger.RFlog.error('{0}'.format(e)) raise e if self.eqs.shape[0] == 0: self.logger.RFlog.warning('No earthquakes associated, please check configurations.'.format(self.eqs.shape[0])) sys.exit(1) else:'{0} earthquakes are associated'.format(self.eqs.shape[0]))
[docs] def save_raw_data(self): if not exists(self.para.datapath): makedirs(self.para.datapath) for i, row in self.eqs.iterrows(): row['data'].write(self.para.datapath, row['date'])
[docs] def savepjt(self): eqs = self.eqs.copy() for _, row in eqs.iterrows(): row['data'].cleanstream() try:'Saving project to {0}'.format(self.para.pjtpath)) with open(self.para.pjtpath, 'wb') as f: pickle.dump({'para': self.para, 'eqs': eqs}, f, -1) except Exception as e: self.logger.RFlog.error('{0}'.format(e)) raise IOError(e)
[docs] @classmethod def loadpjt(cls, path): with open(path, 'rb') as f: rfdata = pickle.load(f) pjt = cls(phase=rfdata['para'].phase) pjt.para = rfdata['para'] if not exists(pjt.para.datapath): pjt.logger.RFlog.error('Data path {} was not found'.format(pjt.para.datapath)) sys.exit(1) pjt.load_stainfo() pjt.eqs = rfdata['eqs'] for _, row in pjt.eqs.iterrows(): try: row['data'].readstream() except Exception as e: pjt.logger.RFlog.warning('Cannot read {}, skipping'.format(row['data'].filestr)) continue return pjt
[docs] def channel_correct(self): if self.para.switchEN or self.para.reverseN or self.para.reverseE:'Correct components with switchEN: {}, reverseE: {}, reverseN: {}'.format( self.para.switchEN, self.para.reverseE, self.para.reverseN)) for _, row in self.eqs.iterrows(): row['data'].channel_correct(self.para.switchEN, self.para.reverseE, self.para.reverseN)
[docs] def detrend(self):'Detrend all data') drop_idx = [] for i, row in self.eqs.iterrows(): try: row['data'].detrend() except: self.logger.RFlog.error('Data error in {}'.format(row['date'].strftime('%Y.%j.%H.%M.%S'))) drop_idx.append(i) self.eqs.drop(drop_idx, inplace=True)
[docs] def filter(self, freqmin=None, freqmax=None, order=4): if freqmin is None: freqmin = self.para.freqmin if freqmax is None: freqmax = self.para.freqmax'Filter all data from {0} to {1}'.format(freqmin, freqmax)) for _, row in self.eqs.iterrows(): row['data'].filter(freqmin=freqmin, freqmax=freqmax, order=order)
[docs] def cal_phase(self):'Calculate {} arrivals and ray parameters for all data'.format(self.para.phase)) for _, row in self.eqs.iterrows(): row['data'].get_arrival(self.model, row['evdp'], row['dis'], phase=self.para.phase)
[docs] def baz_correct(self, time_b=10, time_e=20, offset=90, correct_angle=None): if correct_angle is not None:'correct back-azimuth with {} deg.'.format(correct_angle)) self.eqs['bazi'] = np.mod(self.eqs['bazi'] + correct_angle, 360) else:'correct back-azimuth with T energy minimization') y = np.arange(self.eqs.shape[0]) shift_all = np.array([]) x = np.arange(-offset, offset) ampt_all = np.empty([0, x.shape[0]]) for i, row in self.eqs.iterrows(): curr_baz, ampt = row['data'].search_baz(row['bazi'], time_b=time_b, time_e=time_e, offset=offset) shift_all = np.append(shift_all, curr_baz) ampt_all = np.vstack((ampt_all, ampt)) if None in shift_all: self.logger.RFlog.error('Range of searching bazi is too small.') sys.exit(1) self.baz_shift = np.mean(shift_all[np.where(np.logical_not(np.isnan(shift_all)))])'Average {:.1f} deg offset in back-azimuth'.format(self.baz_shift))
[docs] def rotate(self, search_inc=False): targ_comp = ''.join(sorted(self.para.comp.upper())) if targ_comp == 'RTZ': method='NE->RT' elif targ_comp == 'LQT': method='ZNE->LQT' else: raise ValueError('comp must be in RTZ or LQT.')'Rotate {0} phase to {1}'.format(self.para.phase, method)) drop_idx = [] for i, row in self.eqs.iterrows(): try: row['data'].rotate(row['bazi'], method=method, search_inc=search_inc, baz_shift=self.baz_shift) except Exception as e: self.logger.RFlog.error('{}: {}'.format(row['data'].datestr, e)) drop_idx.append(i) continue if search_inc:'The incidence angle of {} was corrected by {:.1f} deg'.format( row['data'].datestr, row['data'].inc_correction)) self.eqs.drop(drop_idx, inplace=True)
[docs] def drop_eq_snr(self, length=None): if length is None: length = self.para.noiselen'Reject data record with SNR less than {0}'.format(self.para.noisegate)) drop_lst = [] for i, row in self.eqs.iterrows(): snr_E, snr_N, snr_Z = row['data'].snr(length=length) mean_snr = np.mean([snr_E, snr_N, snr_Z]) if mean_snr < self.para.noisegate: drop_lst.append(i) self.eqs.drop(drop_lst, inplace=True)'{0} events left after SNR calculation'.format(self.eqs.shape[0]))
[docs] def trim(self):'Trim waveforms from {0:.2f} before {2} to {1:.2f} after {2}'.format( self.para.time_before, self.para.time_after, self.para.phase)) for _, row in self.eqs.iterrows(): row['data'].trim(self.para.time_before, self.para.time_after)
[docs] def pick(self, prepick=True, stl=5, ltl=10): if prepick:'Pre-pick {} arrival using STA/LTA method'.format(self.para.phase)) for _, row in self.eqs.iterrows(): row['data'].phase_trigger(self.para.time_before, self.para.time_after, stl=stl, ltl=ltl)'{0} events left after virtual checking'.format(self.eqs.shape[0])) pickphase(self.eqs, self.para, self.logger)
[docs] def deconv(self): shift = self.para.time_before time_after = self.para.time_after drop_lst = [] count = 0 for i, row in self.eqs.iterrows(): count += 1 try: row['data'].deconvolute(shift, time_after, method=self.para.decon_method, f0=self.para.gauss, only_r=self.para.only_r, itmax=self.para.itmax, minderr=self.para.minderr, wlevel=self.para.wlevel, target_dt=self.para.target_dt) if self.para.decon_method == 'iter':'Iterative Decon {0} ({3}/{4}) iterations: {1}; final RMS: {2:.4f}'.format( row['data'].datestr, row['data'].rf[0].stats.iter, row['data'].rf[0].stats.rms[-1], count, self.eqs.shape[0])) elif self.para.decon_method == 'water':'Water level Decon {} ({}/{}); RMS: {:.4f}'.format( row['data'].datestr, count, self.eqs.shape[0], row['data'].rf[0].stats.rms)) except Exception as e: self.logger.RFlog.error('{}: {}'.format(row['data'].datestr, e)) drop_lst.append(i) self.eqs.drop(drop_lst, inplace=True)
[docs] def saverf(self, gauss=None): npts = int((self.para.time_before + self.para.time_after)/self.para.target_dt+1) if self.para.phase[-1] == 'P': shift = self.para.time_before elif self.para.phase[-1] == 'S': shift = self.para.time_after else: pass good_lst = [] if isinstance(self.para.gauss, (int, float)): gauss = self.para.gauss elif gauss is None: gauss = self.para.gauss[0] else: if gauss in self.para.gauss: pass else: raise ValueError('gauss should be a element in the seispy.para.RFPara.gauss') if self.para.rmsgate is not None:'Save RFs with final RMS less than {:.2f} and criterion of {}'.format(self.para.rmsgate, self.para.criterion)) else:'Save RFs with and criterion of {}'.format(self.para.criterion)) for i, row in self.eqs.iterrows(): if row['data'].judge_rf(gauss, shift, npts, criterion=self.para.criterion, rmsgate=self.para.rmsgate): row['data'].saverf(self.para.rfpath, evtstr=row['date'].strftime('%Y.%j.%H.%M.%S'), shift=shift, evla=row['evla'], evlo=row['evlo'], evdp=row['evdp'], baz=row['bazi'], mag=row['mag'], gcarc=row['dis'], gauss=gauss, only_r=self.para.only_r, user9=self.baz_shift) good_lst.append(i)'{} PRFs are saved.'.format(len(good_lst))) self.eqs = self.eqs.loc[good_lst]
[docs]def setpar(): parser = argparse.ArgumentParser(description="Set parameters to configure file") parser.add_argument('cfg_file', type=str, help='Path to configure file') parser.add_argument('session', type=str, help='session name') parser.add_argument('key', type=str, help='key name') parser.add_argument('value', type=str, help='value') arg = parser.parse_args() CfgModify(arg.cfg_file, arg.session, arg.key, arg.value)
if __name__ == '__main__': pass # get_events_test() # prf() # proj_test()