pylot/scripts/run_makeCF.py

#!/usr/bin/python
# -*- coding: utf-8 -*-

"""
   Script to run autoPyLoT-script "run_makeCF.py".
   Only for test purposes!
"""

from obspy.core import read
import matplotlib.pyplot as plt
import numpy as np
from pylot.core.pick.charfuns import CharacteristicFunction
from pylot.core.pick.picker import AutoPicker
from pylot.core.pick.utils import *
import glob
import argparse

def run_makeCF(project, database, event, iplot, station=None):
    #parameters for CF calculation
    t2 = 7                   #length of moving window for HOS calculation [sec]
    p = 4                    #order of HOS
    cuttimes = [10, 50]      #start and end time for CF calculation
    bpz = [2, 30]            #corner frequencies of bandpass filter, vertical component
    bph = [2, 15]            #corner frequencies of bandpass filter, horizontal components
    tdetz= 1.2               #length of AR-determination window [sec], vertical component
    tdeth= 0.8               #length of AR-determination window [sec], horizontal components
    tpredz = 0.4             #length of AR-prediction window [sec], vertical component
    tpredh = 0.4             #length of AR-prediction window [sec], horizontal components
    addnoise = 0.001         #add noise to seismogram for stable AR prediction
    arzorder = 2             #chosen order of AR process, vertical component
    arhorder = 4             #chosen order of AR process, horizontal components
    TSNRhos = [5, 0.5, 1, .6] #window lengths [s] for calculating SNR for earliest/latest pick and quality assessment
                             #from HOS-CF [noise window, safety gap, signal window, slope determination window]
    TSNRarz = [5, 0.5, 1, 1.0] #window lengths [s] for calculating SNR for earliest/lates pick and quality assessment
                             #from ARZ-CF
    #get waveform data
    if station:
       dpz = '/DATA/%s/EVENT_DATA/LOCAL/%s/%s/%s*HZ.msd' % (project, database, event, station)
       dpe = '/DATA/%s/EVENT_DATA/LOCAL/%s/%s/%s*HE.msd' % (project, database, event, station)
       dpn = '/DATA/%s/EVENT_DATA/LOCAL/%s/%s/%s*HN.msd' % (project, database, event, station)
       #dpz = '/DATA/%s/EVENT_DATA/LOCAL/%s/%s/%s*_z.gse' % (project, database, event, station)
       #dpe = '/DATA/%s/EVENT_DATA/LOCAL/%s/%s/%s*_e.gse' % (project, database, event, station)
       #dpn = '/DATA/%s/EVENT_DATA/LOCAL/%s/%s/%s*_n.gse' % (project, database, event, station)
    else:
       dpz = '/DATA/%s/EVENT_DATA/LOCAL/%s/%s/*HZ.msd' % (project, database, event)
       dpe = '/DATA/%s/EVENT_DATA/LOCAL/%s/%s/*HE.msd' % (project, database, event)
       dpn = '/DATA/%s/EVENT_DATA/LOCAL/%s/%s/*HN.msd' % (project, database, event)
    wfzfiles = glob.glob(dpz)
    wfefiles = glob.glob(dpe)
    wfnfiles = glob.glob(dpn)
    if wfzfiles:
       for i in range(len(wfzfiles)):
          print 'Vertical component data found ...'
          print wfzfiles[i]
          st = read('%s' % wfzfiles[i])
          st_copy = st.copy()
          #filter and taper data
          tr_filt = st[0].copy()
          tr_filt.filter('bandpass', freqmin=bpz[0], freqmax=bpz[1], zerophase=False)
          tr_filt.taper(max_percentage=0.05, type='hann')
          st_copy[0].data = tr_filt.data
          ##############################################################
          #calculate HOS-CF using subclass HOScf of class CharacteristicFunction
          hoscf = HOScf(st_copy, cuttimes, t2, p) #instance of HOScf
          ##############################################################
          #calculate AIC-HOS-CF using subclass AICcf of class CharacteristicFunction
          #class needs stream object => build it
          tr_aic = tr_filt.copy()
          tr_aic.data = hoscf.getCF()
          st_copy[0].data = tr_aic.data
          aiccf = AICcf(st_copy, cuttimes) #instance of AICcf
          ##############################################################
          #get prelimenary onset time from AIC-HOS-CF using subclass AICPicker of class AutoPicking
          aicpick = AICPicker(aiccf, TSNRhos, 3, 10, None, 0.1)
          ##############################################################
          #get refined onset time from HOS-CF using class Picker
          hospick = PragPicker(hoscf, TSNRhos, 2, 10, 0.001, 0.2, aicpick.getpick())
          #############################################################
          #get earliest and latest possible picks
          st_copy[0].data = tr_filt.data
          [lpickhos, epickhos, pickerrhos] = earllatepicker(st_copy, 1.5, TSNRhos, hospick.getpick(), 10)
          #############################################################
          #get SNR
          [SNR, SNRdB] = getSNR(st_copy, TSNRhos, hospick.getpick())
          print 'SNR:', SNR, 'SNR[dB]:', SNRdB
          ##########################################################
          #get first motion of onset
          hosfm = fmpicker(st, st_copy, 0.2, hospick.getpick(), 11)
          ##############################################################
          #calculate ARZ-CF using subclass ARZcf of class CharcteristicFunction
          arzcf = ARZcf(st, cuttimes, tpredz, arzorder, tdetz, addnoise) #instance of ARZcf
          ##############################################################
          #calculate AIC-ARZ-CF using subclass AICcf of class CharacteristicFunction
          #class needs stream object => build it
          tr_arzaic = tr_filt.copy()
          tr_arzaic.data = arzcf.getCF()
          st_copy[0].data = tr_arzaic.data
          araiccf = AICcf(st_copy, cuttimes, tpredz, 0, tdetz) #instance of AICcf
          ##############################################################
          #get onset time from AIC-ARZ-CF using subclass AICPicker of class AutoPicking
          aicarzpick = AICPicker(araiccf, TSNRarz, 2, 10, None, 0.1)
          ##############################################################
          #get refined onset time from ARZ-CF using class Picker
          arzpick = PragPicker(arzcf, TSNRarz, 2.0, 10, 0.1, 0.05, aicarzpick.getpick())
          #get earliest and latest possible picks
          st_copy[0].data = tr_filt.data
          [lpickarz, epickarz, pickerrarz] = earllatepicker(st_copy, 1.5, TSNRarz, arzpick.getpick(), 10)
    elif not wfzfiles:
       print 'No vertical component data found!'

    if wfefiles and wfnfiles:
       for i in range(len(wfefiles)):
          print 'Horizontal component data found ...'
          print wfefiles[i]
          print wfnfiles[i]
          #merge streams
          H = read('%s' % wfefiles[i])
          H += read('%s' % wfnfiles[i])
          H_copy = H.copy()
          #filter and taper data
          trH1_filt = H[0].copy()
          trH2_filt = H[1].copy()
          trH1_filt.filter('bandpass', freqmin=bph[0], freqmax=bph[1], zerophase=False)
          trH2_filt.filter('bandpass', freqmin=bph[0], freqmax=bph[1], zerophase=False)
          trH1_filt.taper(max_percentage=0.05, type='hann')
          trH2_filt.taper(max_percentage=0.05, type='hann')
          H_copy[0].data = trH1_filt.data
          H_copy[1].data = trH2_filt.data

          ##############################################################
          #calculate ARH-CF using subclass ARHcf of class CharcteristicFunction
          arhcf = ARHcf(H_copy, cuttimes, tpredh, arhorder, tdeth, addnoise) #instance of ARHcf
          ##############################################################
          #calculate AIC-ARH-CF using subclass AICcf of class CharacteristicFunction
          #class needs stream object => build it
          tr_arhaic = trH1_filt.copy()
          tr_arhaic.data = arhcf.getCF()
          H_copy[0].data = tr_arhaic.data
          #calculate ARH-AIC-CF
          arhaiccf = AICcf(H_copy, cuttimes, tpredh, 0, tdeth) #instance of AICcf
          ##############################################################
          #get onset time from AIC-ARH-CF using subclass AICPicker of class AutoPicking
          aicarhpick = AICPicker(arhaiccf, TSNRarz, 4, 10, None, 0.1)
          ###############################################################
          #get refined onset time from ARH-CF using class Picker
          arhpick = PragPicker(arhcf, TSNRarz, 2.5, 10, 0.1, 0.05, aicarhpick.getpick())
          #get earliest and latest possible picks
          H_copy[0].data = trH1_filt.data
          [lpickarh1, epickarh1, pickerrarh1] = earllatepicker(H_copy, 1.5, TSNRarz, arhpick.getpick(), 10)
          H_copy[0].data = trH2_filt.data
          [lpickarh2, epickarh2, pickerrarh2] = earllatepicker(H_copy, 1.5, TSNRarz, arhpick.getpick(), 10)
          #get earliest pick of both earliest possible picks
          epick = [epickarh1, epickarh2]
          lpick = [lpickarh1, lpickarh2]
          pickerr = [pickerrarh1, pickerrarh2]
          ipick =np.argmin([epickarh1, epickarh2])
          epickarh = epick[ipick]
          lpickarh = lpick[ipick]
          pickerrarh = pickerr[ipick]

          #create stream with 3 traces
          #merge streams
          AllC = read('%s' % wfefiles[i])
          AllC += read('%s' % wfnfiles[i])
          AllC += read('%s' % wfzfiles[i])
          #filter and taper data
          All1_filt = AllC[0].copy()
          All2_filt = AllC[1].copy()
          All3_filt = AllC[2].copy()
          All1_filt.filter('bandpass', freqmin=bph[0], freqmax=bph[1], zerophase=False)
          All2_filt.filter('bandpass', freqmin=bph[0], freqmax=bph[1], zerophase=False)
          All3_filt.filter('bandpass', freqmin=bpz[0], freqmax=bpz[1], zerophase=False)
          All1_filt.taper(max_percentage=0.05, type='hann')
          All2_filt.taper(max_percentage=0.05, type='hann')
          All3_filt.taper(max_percentage=0.05, type='hann')
          AllC[0].data = All1_filt.data
          AllC[1].data = All2_filt.data
          AllC[2].data = All3_filt.data
          #calculate AR3C-CF using subclass AR3Ccf of class CharacteristicFunction
          ar3ccf = AR3Ccf(AllC, cuttimes, tpredz, arhorder, tdetz, addnoise) #instance of AR3Ccf
          ##############################################################
          if iplot:
             #plot vertical trace
             plt.figure()
             tr = st[0]
             tdata = np.arange(0, tr.stats.npts / tr.stats.sampling_rate, tr.stats.delta)
             p1, = plt.plot(tdata, tr_filt.data/max(tr_filt.data), 'k')
             p2, = plt.plot(hoscf.getTimeArray(), hoscf.getCF() / max(hoscf.getCF()), 'r')
             p3, = plt.plot(aiccf.getTimeArray(), aiccf.getCF()/max(aiccf.getCF()), 'b')
             p4, = plt.plot(arzcf.getTimeArray(), arzcf.getCF()/max(arzcf.getCF()), 'g')
             p5, = plt.plot(araiccf.getTimeArray(), araiccf.getCF()/max(araiccf.getCF()), 'y')
             plt.plot([aicpick.getpick(), aicpick.getpick()], [-1, 1], 'b--')
             plt.plot([aicpick.getpick()-0.5, aicpick.getpick()+0.5], [1, 1], 'b')
             plt.plot([aicpick.getpick()-0.5, aicpick.getpick()+0.5], [-1, -1], 'b')
             plt.plot([hospick.getpick(), hospick.getpick()], [-1.3, 1.3], 'r', linewidth=2)
             plt.plot([hospick.getpick()-0.5, hospick.getpick()+0.5], [1.3, 1.3], 'r')
             plt.plot([hospick.getpick()-0.5, hospick.getpick()+0.5], [-1.3, -1.3], 'r')
             plt.plot([lpickhos, lpickhos], [-1.1, 1.1], 'r--')
             plt.plot([epickhos, epickhos], [-1.1, 1.1], 'r--')
             plt.plot([aicarzpick.getpick(), aicarzpick.getpick()], [-1.2, 1.2], 'y', linewidth=2)
             plt.plot([aicarzpick.getpick()-0.5, aicarzpick.getpick()+0.5], [1.2, 1.2], 'y')
             plt.plot([aicarzpick.getpick()-0.5, aicarzpick.getpick()+0.5], [-1.2, -1.2], 'y')
             plt.plot([arzpick.getpick(), arzpick.getpick()], [-1.4, 1.4], 'g', linewidth=2)
             plt.plot([arzpick.getpick()-0.5, arzpick.getpick()+0.5], [1.4, 1.4], 'g')
             plt.plot([arzpick.getpick()-0.5, arzpick.getpick()+0.5], [-1.4, -1.4], 'g')
             plt.plot([lpickarz, lpickarz], [-1.2, 1.2], 'g--')
             plt.plot([epickarz, epickarz], [-1.2, 1.2], 'g--')
             plt.yticks([])
             plt.ylim([-1.5, 1.5])
             plt.xlabel('Time [s]')
             plt.ylabel('Normalized Counts')
             plt.title('%s, %s, CF-SNR=%7.2f, CF-Slope=%12.2f' % (tr.stats.station,
                                                                  tr.stats.channel, aicpick.getSNR(), aicpick.getSlope()))
             plt.suptitle(tr.stats.starttime)
             plt.legend([p1, p2, p3, p4, p5], ['Data', 'HOS-CF', 'HOSAIC-CF', 'ARZ-CF', 'ARZAIC-CF'])
             #plot horizontal traces
             plt.figure(2)
             plt.subplot(2,1,1)
             tsteph = tpredh / 4
             th1data = np.arange(0, trH1_filt.stats.npts / trH1_filt.stats.sampling_rate, trH1_filt.stats.delta)
             th2data = np.arange(0, trH2_filt.stats.npts / trH2_filt.stats.sampling_rate, trH2_filt.stats.delta)
             tarhcf = np.arange(0, len(arhcf.getCF()) * tsteph, tsteph) + cuttimes[0] + tdeth +tpredh
             p21, = plt.plot(th1data, trH1_filt.data/max(trH1_filt.data), 'k')
             p22, = plt.plot(arhcf.getTimeArray(), arhcf.getCF()/max(arhcf.getCF()), 'r')
             p23, = plt.plot(arhaiccf.getTimeArray(), arhaiccf.getCF()/max(arhaiccf.getCF()))
             plt.plot([aicarhpick.getpick(), aicarhpick.getpick()], [-1, 1], 'b')
             plt.plot([aicarhpick.getpick()-0.5, aicarhpick.getpick()+0.5], [1, 1], 'b')
             plt.plot([aicarhpick.getpick()-0.5, aicarhpick.getpick()+0.5], [-1, -1], 'b')
             plt.plot([arhpick.getpick(), arhpick.getpick()], [-1, 1], 'r')
             plt.plot([arhpick.getpick()-0.5, arhpick.getpick()+0.5], [1, 1], 'r')
             plt.plot([arhpick.getpick()-0.5, arhpick.getpick()+0.5], [-1, -1], 'r')
             plt.plot([lpickarh, lpickarh], [-0.8, 0.8], 'r--')
             plt.plot([epickarh, epickarh], [-0.8, 0.8], 'r--')
             plt.plot([arhpick.getpick() + pickerrarh, arhpick.getpick() + pickerrarh], [-0.2, 0.2], 'r--')
             plt.plot([arhpick.getpick() - pickerrarh, arhpick.getpick() - pickerrarh], [-0.2, 0.2], 'r--')
             plt.yticks([])
             plt.ylim([-1.5, 1.5])
             plt.ylabel('Normalized Counts')
             plt.title([trH1_filt.stats.station, trH1_filt.stats.channel])
             plt.suptitle(trH1_filt.stats.starttime)
             plt.legend([p21, p22, p23], ['Data', 'ARH-CF', 'ARHAIC-CF'])
             plt.subplot(2,1,2)
             plt.plot(th2data, trH2_filt.data/max(trH2_filt.data), 'k')
             plt.plot(arhcf.getTimeArray(), arhcf.getCF()/max(arhcf.getCF()), 'r')
             plt.plot(arhaiccf.getTimeArray(), arhaiccf.getCF()/max(arhaiccf.getCF()))
             plt.plot([aicarhpick.getpick(), aicarhpick.getpick()], [-1, 1], 'b')
             plt.plot([aicarhpick.getpick()-0.5, aicarhpick.getpick()+0.5], [1, 1], 'b')
             plt.plot([aicarhpick.getpick()-0.5, aicarhpick.getpick()+0.5], [-1, -1], 'b')
             plt.plot([arhpick.getpick(), arhpick.getpick()], [-1, 1], 'r')
             plt.plot([arhpick.getpick()-0.5, arhpick.getpick()+0.5], [1, 1], 'r')
             plt.plot([arhpick.getpick()-0.5, arhpick.getpick()+0.5], [-1, -1], 'r')
             plt.plot([lpickarh, lpickarh], [-0.8, 0.8], 'r--')
             plt.plot([epickarh, epickarh], [-0.8, 0.8], 'r--')
             plt.plot([arhpick.getpick() + pickerrarh, arhpick.getpick() + pickerrarh], [-0.2, 0.2], 'r--')
             plt.plot([arhpick.getpick() - pickerrarh, arhpick.getpick() - pickerrarh], [-0.2, 0.2], 'r--')
             plt.title([trH2_filt.stats.station, trH2_filt.stats.channel])
             plt.yticks([])
             plt.ylim([-1.5, 1.5])
             plt.xlabel('Time [s]')
             plt.ylabel('Normalized Counts')
             #plot 3-component window
             plt.figure(3)
             plt.subplot(3,1,1)
             p31, = plt.plot(tdata, tr_filt.data/max(tr_filt.data), 'k')
             p32, = plt.plot(ar3ccf.getTimeArray(), ar3ccf.getCF()/max(ar3ccf.getCF()), 'r')
             plt.plot([arhpick.getpick(), arhpick.getpick()], [-1, 1], 'b')
             plt.plot([arhpick.getpick()-0.5, arhpick.getpick()+0.5], [-1, -1], 'b')
             plt.plot([arhpick.getpick()-0.5, arhpick.getpick()+0.5], [1, 1], 'b')
             plt.yticks([])
             plt.xticks([])
             plt.ylabel('Normalized Counts')
             plt.title([tr.stats.station, tr.stats.channel])
             plt.suptitle(trH1_filt.stats.starttime)
             plt.legend([p31, p32], ['Data', 'AR3C-CF'])
             plt.subplot(3,1,2)
             plt.plot(th1data, trH1_filt.data/max(trH1_filt.data), 'k')
             plt.plot(ar3ccf.getTimeArray(), ar3ccf.getCF()/max(ar3ccf.getCF()), 'r')
             plt.plot([arhpick.getpick(), arhpick.getpick()], [-1, 1], 'b')
             plt.plot([arhpick.getpick()-0.5, arhpick.getpick()+0.5], [-1, -1], 'b')
             plt.plot([arhpick.getpick()-0.5, arhpick.getpick()+0.5], [1, 1], 'b')
             plt.yticks([])
             plt.xticks([])
             plt.ylabel('Normalized Counts')
             plt.title([trH1_filt.stats.station, trH1_filt.stats.channel])
             plt.subplot(3,1,3)
             plt.plot(th2data, trH2_filt.data/max(trH2_filt.data), 'k')
             plt.plot(ar3ccf.getTimeArray(), ar3ccf.getCF()/max(ar3ccf.getCF()), 'r')
             plt.plot([arhpick.getpick(), arhpick.getpick()], [-1, 1], 'b')
             plt.plot([arhpick.getpick()-0.5, arhpick.getpick()+0.5], [-1, -1], 'b')
             plt.plot([arhpick.getpick()-0.5, arhpick.getpick()+0.5], [1, 1], 'b')
             plt.yticks([])
             plt.ylabel('Normalized Counts')
             plt.title([trH2_filt.stats.station, trH2_filt.stats.channel])
             plt.xlabel('Time [s]')
             plt.show()
             raw_input()
             plt.close()

parser = argparse.ArgumentParser()
parser.add_argument('--project', type=str, help='project name (e.g. Insheim)')
parser.add_argument('--database', type=str, help='event data base (e.g. 2014.09_Insheim)')
parser.add_argument('--event', type=str, help='event ID (e.g. e0010.015.14)')
parser.add_argument('--iplot', help='anything, if set, figure occurs')
parser.add_argument('--station', type=str, help='Station ID (e.g. INS3) (optional)')
args = parser.parse_args()

run_makeCF(args.project, args.database, args.event, args.iplot, args.station)