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SNIVEL_tools.py
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SNIVEL_tools.py
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#!/usr/bin/env python
import numpy
import datetime
import calendar
import math
import georinex as gr
import obspy
import scipy
import matplotlib.pyplot as plt
from scipy.signal import butter, lfilter, filtfilt
from obspy.io.sac import SACTrace
#####################################################################################
#SNIVEL_tools.py
#Written by Brendan Crowell, University of Washington
#Last edited January 11, 2019
#####################################################################################
c = 299792458.0 #speed of light
fL1 = 1575.42e6 #L1 frequency
fL2 = 1227.60e6 #L2 frequency
# Print iterations progress
def printProgressBar (iteration, total, prefix = '', suffix = '', decimals = 1, length = 100, fill = 'â–ˆ', printEnd = "\r"):
"""
Call in a loop to create terminal progress bar
@params:
iteration - Required : current iteration (Int)
total - Required : total iterations (Int)
prefix - Optional : prefix string (Str)
suffix - Optional : suffix string (Str)
decimals - Optional : positive number of decimals in percent complete (Int)
length - Optional : character length of bar (Int)
fill - Optional : bar fill character (Str)
printEnd - Optional : end character (e.g. "\r", "\r\n") (Str)
"""
percent = ("{0:." + str(decimals) + "f}").format(100 * (iteration / float(total)))
filledLength = int(length * iteration // total)
bar = fill * filledLength + '-' * (length - filledLength)
print('\r%s |%s| %s%% %s' % (prefix, bar, percent, suffix), end = printEnd)
# Print New Line on Complete
if iteration == total:
print()
def month_converter(month):
months = ['JAN', 'FEB', 'MAR', 'APR', 'MAY', 'JUN', 'JUL', 'AUG', 'SEP', 'OCT', 'NOV', 'DEC']
return months.index(month) + 1
def doy2month(doy,year):
isleap = calendar.isleap(year)
if str(isleap) == 'True':
dom = [31,29,31,30,31,30,31,31,30,31,30,31]
else:
dom = [31,28,31,30,31,30,31,31,30,31,30,31]
dayind = int(dom[0])
monind=1
for i in range (1, 12):
if (int(doy) < dayind):
month = monind
else:
dayind = dayind+dom[i]
monind=monind+1
return month
def doy_calc(year,month,day):
isleap = calendar.isleap(year)
if str(isleap) == 'True':
dom = [31,29,31,30,31,30,31,31,30,31,30,31]
else:
dom = [31,28,31,30,31,30,31,31,30,31,30,31]
doy = int(numpy.sum(dom[:(month-1)])+day)
return(doy)
def gpsweekdow(year,doy):
date = datetime.datetime(year, 1, 1) + datetime.timedelta(doy - 1)
gpstime = (numpy.datetime64(date) - numpy.datetime64('1980-01-06T00:00:00'))/ numpy.timedelta64(1, 's')
gpsweek = int(gpstime/604800)
gpsdow = math.floor((gpstime-gpsweek*604800)/86400)
return(gpsweek, gpsdow)
def gpsleapsec(gpssec):
leaptimes = numpy.array([46828800, 78364801, 109900802, 173059203, 252028804, 315187205, 346723206, 393984007, 425520008, 457056009, 504489610, 551750411, 599184012, 820108813, 914803214, 1025136015, 1119744016, 1167264017])
leapseconds = numpy.array([1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18])
a1 = numpy.where(gpssec > leaptimes)[0]
leapsec = len(a1)
return(leapsec)
def ecef2lla(x,y,z):
a = 6378137
e = 8.1819190842622e-2
b = math.sqrt(math.pow(a,2)*(1-math.pow(e,2)))
ep = math.sqrt((math.pow(a,2)-math.pow(b,2))/math.pow(b,2))
p = math.sqrt(math.pow(x,2)+math.pow(y,2))
th = math.atan2(a*z,b*p)
lon = math.atan2(y,x)
lat = math.atan2((z+math.pow(ep,2)*b*math.pow(math.sin(th),3)),(p-math.pow(e,2)*a*math.pow(math.cos(th),3)))
N = a/math.sqrt(1-math.pow(e,2)*math.pow(math.sin(lat),2))
alt = p/math.cos(lat)-N
return (lat,lon,alt)
def azi_elev(xsta,ysta,zsta,xsat,ysat,zsat):
[latsta,lonsta,altsta]=ecef2lla(xsta,ysta,zsta)
[latsat,lonsat,altsat]=ecef2lla(xsat,ysat,zsat)
re = math.sqrt(math.pow(xsta,2)+math.pow(ysta,2)+math.pow(zsta,2))
rs = math.sqrt(math.pow(xsat,2)+math.pow(ysat,2)+math.pow(zsat,2))
gamma = math.acos(math.cos(latsta)*math.cos(latsat)*math.cos(lonsat-lonsta) + math.sin(latsta)*math.sin(latsat))
elev = math.acos(math.sin(gamma)/math.sqrt(1 + math.pow(re/rs,2) - 2*re/rs*math.cos(gamma)))
deltalon = lonsat-lonsta
azi = math.atan2(math.sin(deltalon)*math.cos(latsat),math.cos(latsta)*math.sin(latsat)-math.sin(latsta)*math.cos(latsat)*math.cos(deltalon))
azi = azi*180/math.pi
if (azi < 0):
azi = azi+360
elev = elev*180/math.pi
return(azi,elev)
def getklobucharvalues(navfile):
navhead = gr.rinexheader(navfile) #load navigation header to obtain klobuchar
alpha = navhead['ION ALPHA'] #klobuchar alphas
beta = navhead['ION BETA'] #klobuchar betas
alpha2 = alpha.replace("D", "E") #nav headers sometimes use D instead of E for power
beta2 = beta.replace("D", "E")
alp1= numpy.asarray(alpha2.split())
bet1= numpy.asarray(beta2.split())
alp = alp1.astype(numpy.float) #numpy array of klobuchar alphas
bet = bet1.astype(numpy.float) #numpy array of klobuchar betas
return(alp,bet)
#Klobuchar ionospheric correction
def klobuchar(latsta,lonsta,elev,azimuth,tow,alpha,beta):
a1 = float(alpha[0])
a2 = float(alpha[1])
a3 = float(alpha[2])
a4 = float(alpha[3])
b1 = float(beta[0])
b2 = float(beta[1])
b3 = float(beta[2])
b4 = float(beta[3])
elev = elev/180 #elevation angle in semicircles
azimuth = azimuth*math.pi/180
psi = 0.0137/(elev+0.11) - 0.022 #earth centered angle
lat_i = latsta/180 + psi*math.cos(azimuth) #subionospheric latitude
if (lat_i > 0.416):
lat_i = 0.416
if (lat_i < -0.416):
lat_i = -0.416
lon_i = lonsta/180 + psi*math.sin(azimuth)/math.cos(lat_i*math.pi) #subionospheric longitude
lat_m = lat_i + 0.064*math.cos((lon_i - 1.617)*math.pi) #geomagnetic lat
t = 4.32e4*lon_i + tow
t = t % 86400
if (t > 86400):
t = t - 86400
if (t < 0):
t = t + 86400
sF = 1 + 16*math.pow(0.53-elev,3) #slant factor
PER = b1 + b2*lat_m + b3*math.pow(lat_m,2) + b4*math.pow(lat_m,3)
if (PER < 72000):
PER = 72000
x = 2*math.pi*(t-50400)/PER
AMP = a1 + a2*lat_m + a3*math.pow(lat_m,2) + a4*math.pow(lat_m,3)
if (AMP < 0):
AMP = 0
if (abs(x) > 1.57):
dIon1 = sF*(5e-9)
else:
dIon1 = sF*(5e-9 + AMP*(1 - math.pow(x,2)/2 + math.pow(x,4)/24))
dIon1 = c*dIon1
dIon2 = math.pow(fL1/fL2,2)*dIon1
return(dIon1,dIon2)
def niell(elev,lat,alt,doy):
aht = 2.53e-5
bht = 5.49e-3
cht = 1.14e-3
aavg15 = 1.2769934e-3
bavg15 = 2.9153695e-3
cavg15 = 62.610505e-3
aamp15 = 0.0
bamp15 = 0.0
camp15 = 0.0
aavg30 = 1.2683230e-3
bavg30 = 2.9152299e-3
cavg30 = 62.837393e-3
aamp30 = 1.2709626e-5
bamp30 = 2.1414979e-5
camp30 = 9.0128400e-5
aavg45 = 1.2465397e-3
bavg45 = 2.9288445e-3
cavg45 = 63.721774e-3
aamp45 = 2.6523662e-5
bamp45 = 3.0160779e-5
camp45 = 4.3497037e-5
aavg60 = 1.2196049e-3
bavg60 = 2.9022565e-3
cavg60 = 63.824265e-3
aamp60 = 3.4000452e-5
bamp60 = 7.2562722e-5
camp60 = 84.795348e-5
aavg75 = 1.2045996e-3
bavg75 = 2.9024912e-3
cavg75 = 64.258455e-3
aamp75 = 4.1202191e-5
bamp75 = 11.723375e-5
camp75 = 170.37206e-5
if (abs(lat) <= 15):
aavg = aavg15
bavg = bavg15
cavg = cavg15
aamp = aamp15
bamp = bamp15
camp = camp15
if (abs(lat) > 15 and abs(lat) <= 30):
amavg = 15.0/(aavg30-aavg15)
aavg = (abs(lat) - 15)/amavg + aavg15
amamp = 15.0/(aamp30-aamp15)
aamp = (abs(lat) - 15)/amamp + aamp15
bmavg = 15.0/(bavg30-bavg15)
bavg = (abs(lat) - 15)/bmavg + bavg15
bmamp = 15.0/(bamp30-bamp15)
bamp = (abs(lat) - 15)/bmamp + bamp15
cmavg = 15.0/(cavg30-cavg15)
cavg = (abs(lat) - 15)/cmavg + cavg15
cmamp = 15.0/(camp30-camp15)
camp = (abs(lat) - 15)/cmamp + camp15
if (abs(lat) > 30 and abs(lat) <= 45):
amavg = 15.0/(aavg45-aavg30)
aavg = (abs(lat) - 30)/amavg + aavg30
amamp = 15.0/(aamp45-aamp30)
aamp = (abs(lat) - 30)/amamp + aamp30
bmavg = 15.0/(bavg45-bavg30)
bavg = (abs(lat) - 30)/bmavg + bavg30
bmamp = 15.0/(bamp45-bamp30)
bamp = (abs(lat) - 30)/bmamp + bamp30
cmavg = 15.0/(cavg45-cavg30)
cavg = (abs(lat) - 30)/cmavg + cavg30
cmamp = 15.0/(camp45-camp30)
camp = (abs(lat) - 30)/cmamp + camp30
if (abs(lat) > 45 and abs(lat) <= 60):
amavg = 15.0/(aavg60-aavg45)
aavg = (abs(lat) - 45)/amavg + aavg45
amamp = 15.0/(aamp60-aamp45)
aamp = (abs(lat) - 45)/amamp + aamp45
bmavg = 15.0/(bavg60-bavg45)
bavg = (abs(lat) - 45)/bmavg + bavg45
bmamp = 15.0/(bamp60-bamp45)
bamp = (abs(lat) - 45)/bmamp + bamp45
cmavg = 15.0/(cavg60-cavg45)
cavg = (abs(lat) - 45)/cmavg + cavg45
cmamp = 15.0/(camp60-camp45)
camp = (abs(lat) - 45)/cmamp + camp45
if (abs(lat) > 60 and abs(lat) <= 75):
amavg = 15.0/(aavg75-aavg60)
aavg = (abs(lat) - 60)/amavg + aavg60
amamp = 15.0/(aamp75-aamp60)
aamp = (abs(lat) - 60)/amamp + aamp60
bmavg = 15.0/(bavg75-bavg60)
bavg = (abs(lat) - 60)/bmavg + bavg60
bmamp = 15.0/(bamp75-bamp60)
bamp = (abs(lat) - 60)/bmamp + bamp60
cmavg = 15.0/(cavg75-cavg60)
cavg = (abs(lat) - 60)/cmavg + cavg60
cmamp = 15.0/(camp75-camp60)
camp = (abs(lat) - 60)/cmamp + camp60
if (abs(lat) > 75):
aavg = aavg75
bavg = bavg75
cavg = cavg75
aamp = aamp75
bamp = bamp75
camp = camp75
a = aavg - aamp*math.cos(2*math.pi*(doy-28)/365.25)
b = bavg - bamp*math.cos(2*math.pi*(doy-28)/365.25)
c = cavg - camp*math.cos(2*math.pi*(doy-28)/365.25)
el = math.sin(elev*math.pi/180)
m = (1 + a/(1+b/(1+c)))/(el + a/(el+b/(el+c)))
mh = (1 + aht/(1+bht/(1+cht)))/(el + aht/(el+bht/(el+cht)))
dm = (1/el - mh)*alt/1000
Mdry = m + dm
Tropdelay = 2.3*math.exp(-0.116e-3*alt)*Mdry
return(Tropdelay)
#This takes displacements in x, y, z and converts them to north, east up
def dxyz2dneu(dx,dy,dz,lat,lon):
lat = lat*math.pi/180
lon = lon*math.pi/180
dn = -numpy.sin(lat)*numpy.cos(lon)*dx-numpy.sin(lat)*numpy.sin(lon)*dy+numpy.cos(lat)*dz
de = -numpy.sin(lon)*dx+numpy.cos(lon)*dy
du = numpy.cos(lat)*numpy.cos(lon)*dx+numpy.cos(lat)*numpy.sin(lon)*dy+numpy.sin(lat)*dz
return (dn, de, du)
def niell_wet(elev, lat):
aavg15 = 5.8021897e-4
bavg15 = 1.4275268e-3
cavg15 = 4.3472961e-2
aavg30 = 5.6794847e-4
bavg30 = 1.5138625e-3
cavg30 = 4.6729510e-2
aavg45 = 5.8118019e-4
bavg45 = 1.4572752e-3
cavg45 = 4.3908931e-2
aavg60 = 5.9727542e-4
bavg60 = 1.5007428e-3
cavg60 = 4.4626982e-2
aavg75 = 6.1641693e-4
bavg75 = 1.7599082e-3
cavg75 = 5.4736038e-2
if (abs(lat) <= 15):
aavg = aavg15
bavg = bavg15
cavg = cavg15
if (abs(lat) > 15 and abs(lat) <= 30):
amavg = 15.0/(aavg30-aavg15)
aavg = (abs(lat) - 15)/amavg + aavg15
bmavg = 15.0/(bavg30-bavg15)
bavg = (abs(lat) - 15)/bmavg + bavg15
cmavg = 15.0/(cavg30-cavg15)
cavg = (abs(lat) - 15)/cmavg + cavg15
if (abs(lat) > 30 and abs(lat) <= 45):
amavg = 15.0/(aavg45-aavg30)
aavg = (abs(lat) - 30)/amavg + aavg30
bmavg = 15.0/(bavg45-bavg30)
bavg = (abs(lat) - 30)/bmavg + bavg30
cmavg = 15.0/(cavg45-cavg30)
cavg = (abs(lat) - 30)/cmavg + cavg30
if (abs(lat) > 45 and abs(lat) <= 60):
amavg = 15.0/(aavg60-aavg45)
aavg = (abs(lat) - 45)/amavg + aavg45
bmavg = 15.0/(bavg60-bavg45)
bavg = (abs(lat) - 45)/bmavg + bavg45
cmavg = 15.0/(cavg60-cavg45)
cavg = (abs(lat) - 45)/cmavg + cavg45
if (abs(lat) > 60 and abs(lat) <= 75):
amavg = 15.0/(aavg75-aavg60)
aavg = (abs(lat) - 60)/amavg + aavg60
bmavg = 15.0/(bavg75-bavg60)
bavg = (abs(lat) - 60)/bmavg + bavg60
cmavg = 15.0/(cavg75-cavg60)
cavg = (abs(lat) - 60)/cmavg + cavg60
if (abs(lat) > 75):
aavg = aavg75
bavg = bavg75
cavg = cavg75
a = aavg
b = bavg
c = cavg
el = math.sin(elev*math.pi/180)
m = (1 + a/(1+b/(1+c)))/(el + a/(el+b/(el+c)))
Mwet = m
return(Mwet)
def writesac(velfile,site,stalat,stalon,doy,year,samprate,event):
a = numpy.loadtxt(velfile)
tind = a[:,0]
gtime = a[:,1]
leapsec = gpsleapsec(gtime[0])
#Get the start time of the file in UTC
date = datetime.datetime(int(year), 1, 1) + datetime.timedelta(int(doy) - 1)
gpstime = (numpy.datetime64(date) - numpy.datetime64('1980-01-06T00:00:00'))/ numpy.timedelta64(1, 's')
stime = (gtime[0]-leapsec)*numpy.timedelta64(1, 's')+ numpy.datetime64('1980-01-06T00:00:00')
sitem = stime.item()
print(sitem)
styr = sitem.year
stdy = sitem.day
stmon = sitem.month
sthr = sitem.hour
stmin = sitem.minute
stsec = sitem.second
nunf = a[:,2]-numpy.nanmean(a[:,2])
eunf = a[:,3]-numpy.nanmean(a[:,3])
uunf = a[:,4]-numpy.nanmean(a[:,4])
t = gtime-gtime[0]
print(samprate)
samplerate = float(samprate)
bf, af = butter(4, 1/4/samplerate/0.5*samplerate,btype='low')
print(1/4/samplerate/0.5*samplerate)
nv = filtfilt(bf,af,nunf)
ev = filtfilt(bf,af,eunf)
uv = filtfilt(bf,af,uunf)
plotvelocities(event,site,t,nunf*100,eunf*100,uunf*100)
sr = "{0:.2f}".format(float(samprate))
print('Writing SAC file ' + 'output/' + event + '.' + site + '.' + sr + '.LXN.sac')
headN = {'kstnm': site, 'kcmpnm': 'LXN', 'stla': float(stalat),'stlo': float(stalon),
'nzyear': int(year), 'nzjday': int(doy), 'nzhour': int(sthr), 'nzmin': int(stmin),
'nzsec': int(stsec), 'nzmsec': int(0), 'delta': float(samprate)}
sacn = SACTrace(data=nv, **headN)
sacn.write('output/sacfilt/'+event+'/'+ event + '.' + site.upper() + '.' + sr + '.filt.LXN.sac')
sacn = SACTrace(data=nunf, **headN)
sacn.write('output/sac/'+event+'/' + event + '.' + site.upper() + '.' + sr + '.LXN.sac')
print('Writing SAC file ' + 'output/' + event + '.' + site + '.' + sr + '.LXE.sac')
headE = {'kstnm': site, 'kcmpnm': 'LXE', 'stla': float(stalat),'stlo': float(stalon),
'nzyear': int(year), 'nzjday': int(doy), 'nzhour': int(sthr), 'nzmin': int(stmin),
'nzsec': int(stsec), 'nzmsec': int(0), 'delta': float(samprate)}
sace = SACTrace(data=ev, **headE)
sace.write('output/sacfilt/'+event+'/' + event + '.' + site.upper() + '.' + sr + '.filt.LXE.sac')
sace = SACTrace(data=eunf, **headE)
sace.write('output/sac/'+event+'/' + event + '.' + site.upper() + '.' + sr + '.LXE.sac')
print('Writing SAC file ' + 'output/' + event + '.' + site + '.' + sr + '.LXZ.sac')
headZ = {'kstnm': site, 'kcmpnm': 'LXZ', 'stla': float(stalat),'stlo': float(stalon),
'nzyear': int(year), 'nzjday': int(doy), 'nzhour': int(sthr), 'nzmin': int(stmin),
'nzsec': int(stsec), 'nzmsec': int(0), 'delta': float(samprate)}
sacu = SACTrace(data=uv, **headZ)
sacu.write('output/sacfilt/'+event+'/' + event + '.' + site.upper() + '.' + sr + '.filt.LXZ.sac')
sacu = SACTrace(data=uunf, **headZ)
sacu.write('output/sac/'+event+'/' + event + '.' + site.upper() + '.' + sr + '.LXZ.sac')
def plotvelocities(event,site,t,n,e,v):
fname = 'output/fig/'+event+'/'+event+'_'+site+'.png'
ax1 = plt.subplot(311)
plt.plot(t,n)
plt.title(event+' '+site)
plt.ylabel('North (cm/s)')
ax2 = plt.subplot(312)
plt.plot(t,e)
plt.ylabel('East (cm/s)')
ax3 = plt.subplot(313)
plt.plot(t,v)
plt.xlabel('Seconds after OT')
plt.ylabel('Vertical (cm/s)')
plt.savefig(fname)
plt.clf()
plt.close()
return
def getpeakvals(velfile,site,samprate,event):
a = numpy.loadtxt(velfile)
tind = a[:,0]
gtime = a[:,1]
nunf = a[:,2]-numpy.nanmean(a[:,2])
eunf = a[:,3]-numpy.nanmean(a[:,3])
uunf = a[:,4]-numpy.nanmean(a[:,4])
bf, af = butter(4, 1.25/0.5*0.2,btype='low')
nv = filtfilt(bf,af,nunf)
ev = filtfilt(bf,af,eunf)
uv = filtfilt(bf,af,uunf)
peakn = numpy.amax(numpy.absolute(nv))*100
peake = numpy.amax(numpy.absolute(ev))*100
peaku = numpy.amax(numpy.absolute(uv))*100
print (peakn,peake,peaku)
return(peakn,peake,peaku)
#getpeakvals('output/velocities_mom0_111_2022.txt','mom0',0.2,'masachapa')
#writesac('output/velocities_boar_130_2012.txt','boar','35','-120','130','2012',30,'pig')