def remove_seasonals_by_german_load(Data, lsdm_dir):
station = Data.name;
files = glob.glob(lsdm_dir + station + '*.txt');
if not files: # found an empty array
print("Error! LSDM file not found for %s" % Data.name);
print("Returning placeholder object.");
wimpyObj = get_wimpy_object(Data);
return wimpyObj, wimpyObj;
else:
filename = files[0];
# Read the hydro model and pair it to the GPS
[hydro_data] = gps_io_functions.read_lsdm_file(filename);
# Clean up and pair data
Data = gps_ts_functions.remove_nans(Data);
hydro_data = gps_ts_functions.remove_nans(hydro_data); # this may or may not be necessary.
[gps_data, hydro_data] = gps_ts_functions.pair_gps_model(Data, hydro_data); # matched in terms of dtarray.
# Subtract the model from the data.
dE_filt, dN_filt, dU_filt = [], [], [];
for i in range(len(gps_data.dtarray)):
dE_filt.append(gps_data.dE[i] - hydro_data.dE[i]);
dN_filt.append(gps_data.dN[i] - hydro_data.dN[i]);
dU_filt.append(gps_data.dU[i] - hydro_data.dU[i]);
# A Simple detrending
decyear = gps_ts_functions.get_float_times(gps_data.dtarray);
dE_detrended = np.zeros(np.shape(decyear));
dN_detrended = np.zeros(np.shape(decyear));
dU_detrended = np.zeros(np.shape(decyear));
east_coef = np.polyfit(decyear, dE_filt, 1)[0];
for i in range(len(dE_filt)):
dE_detrended[i] = dE_filt[i] - east_coef * decyear[i] - (dE_filt[0] - east_coef * decyear[0]);
north_coef = np.polyfit(decyear, dN_filt, 1)[0];
for i in range(len(dN_filt)):
dN_detrended[i] = (dN_filt[i] - north_coef * decyear[i]) - (dN_filt[0] - north_coef * decyear[0]);
vert_coef = np.polyfit(decyear, dU_filt, 1)[0];
for i in range(len(dU_filt)):
dU_detrended[i] = (dU_filt[i] - vert_coef * decyear[i]) - (dU_filt[0] - vert_coef * decyear[0]);
detrended = gps_io_functions.Timeseries(name=gps_data.name, coords=gps_data.coords, dtarray=gps_data.dtarray,
dE=dE_detrended, dN=dN_detrended, dU=dU_detrended, Se=gps_data.Se,
Sn=gps_data.Sn, Su=gps_data.Su, EQtimes=gps_data.EQtimes);
trended = gps_io_functions.Timeseries(name=gps_data.name, coords=gps_data.coords, dtarray=gps_data.dtarray,
dE=dE_filt, dN=dN_filt, dU=dU_filt, Se=gps_data.Se, Sn=gps_data.Sn,
Su=gps_data.Su, EQtimes=gps_data.EQtimes);
return detrended, trended;
def remove_seasonals_by_notch(Data):
# Using Sang-Ho's notch filter script to remove power at frequencies corresponding to 1 year and 6 months.
# We are also removing a linear trend in this step.
Data = gps_ts_functions.remove_nans(Data);
# Parameters
# % x 1-D signal array
# % fs sampling frequency, Hz
# % fn notch frequency, Hz
# % Bn notch bandwidth, Hz
dt_interval = 1.0; # one day
fs = 1 / dt_interval;
fn1 = 1.0 / 365.24; # fn = notch frequency, annual
Bn1 = 0.1 * fn1;
fn2 = 2.0 / 365.24; # fn = notch frequency, semiannual
Bn2 = 0.1 * fn2; # a choice: 10% seems to work well.
decyear = gps_ts_functions.get_float_times(Data.dtarray);
dE_detrended = np.zeros(np.shape(Data.dE));
dN_detrended = np.zeros(np.shape(Data.dN));
dU_detrended = np.zeros(np.shape(Data.dU));
dE_trended = np.zeros(np.shape(Data.dE));
dN_trended = np.zeros(np.shape(Data.dN));
dU_trended = np.zeros(np.shape(Data.dU));
# East
x = Data.dE;
dE_filt = notch_filter.notchfilt(x, fs, fn1, Bn1, filtfiltopt=True);
dE_filt = notch_filter.notchfilt(dE_filt, fs, fn2, Bn2, filtfiltopt=True);
east_coef = np.polyfit(decyear, dE_filt, 1)[0];
for i in range(len(dE_filt)):
dE_detrended[i] = dE_filt[i] - east_coef * decyear[i] - (dE_filt[0] - east_coef * decyear[0]);
dE_trended[i] = dE_filt[i];
# North
x = Data.dN;
dN_filt = notch_filter.notchfilt(x, fs, fn1, Bn1, filtfiltopt=True);
dN_filt = notch_filter.notchfilt(dN_filt, fs, fn2, Bn2, filtfiltopt=True);
north_coef = np.polyfit(decyear, dN_filt, 1)[0];
for i in range(len(dN_filt)):
dN_detrended[i] = dN_filt[i] - north_coef * decyear[i] - (dN_filt[0] - north_coef * decyear[0]);
dN_trended[i] = dN_filt[i];
# Up
x = Data.dU;
dU_filt = notch_filter.notchfilt(x, fs, fn1, Bn1, filtfiltopt=True);
dU_filt = notch_filter.notchfilt(dU_filt, fs, fn2, Bn2, filtfiltopt=True);
vert_coef = np.polyfit(decyear, dU_filt, 1)[0];
for i in range(len(dU_filt)):
dU_detrended[i] = dU_filt[i] - vert_coef * decyear[i] - (dU_filt[0] - vert_coef * decyear[0]);
dU_trended[i] = dU_filt[i];
detrended = gps_io_functions.Timeseries(name=Data.name, coords=Data.coords, dtarray=Data.dtarray, dN=dN_detrended,
dE=dE_detrended, dU=dU_detrended, Sn=Data.Sn, Se=Data.Se, Su=Data.Su,
EQtimes=Data.EQtimes);
trended = gps_io_functions.Timeseries(name=Data.name, coords=Data.coords, dtarray=Data.dtarray, dN=dN_trended,
dE=dE_trended, dU=dU_trended, Sn=Data.Sn, Se=Data.Se, Su=Data.Su,
EQtimes=Data.EQtimes);
return detrended, trended;
def remove_seasonals_by_GRACE(Data, grace_dir):
# Here we use pre-computed GRACE load model time series to correct the GPS time series.
# We recognize that the horizontals will be bad, and that the resolution of GRACE is coarse.
# For these reasons, this is not an important part of the analysis.
# Read and interpolate GRACE loading model
# Subtract the GRACE model
# Remove a trend from the GPS data
# Return the object.
filename = grace_dir + "scaled_" + Data.name + "_PREM_model_ts.txt";
if not os.path.isfile(filename):
print("Error! GRACE not found for %s" % Data.name);
print("Returning placeholder object.");
wimpyObj = get_wimpy_object(Data)
return wimpyObj, wimpyObj;
# If the station has been pre-computed with GRACE:
Data = gps_ts_functions.remove_nans(Data);
[grace_model] = gps_io_functions.read_grace(filename);
my_paired_ts = grace_ts_functions.pair_GPSGRACE(Data, grace_model);
decyear = gps_ts_functions.get_float_times(my_paired_ts.dtarray);
# Subtract the GRACE object
dE_filt, dN_filt, dU_filt = [], [], [];
for i in range(len(my_paired_ts.dtarray)):
dE_filt.append(my_paired_ts.east[i] - my_paired_ts.u[i]);
dN_filt.append(my_paired_ts.north[i] - my_paired_ts.v[i]);
dU_filt.append(my_paired_ts.vert[i] - my_paired_ts.w[i]);
# A Simple detrending
dE_detrended = np.zeros(np.shape(decyear));
dN_detrended = np.zeros(np.shape(decyear));
dU_detrended = np.zeros(np.shape(decyear));
east_coef = np.polyfit(decyear, dE_filt, 1)[0];
for i in range(len(dE_filt)):
dE_detrended[i] = dE_filt[i] - east_coef * decyear[i] - (dE_filt[0] - east_coef * decyear[0]);
north_coef = np.polyfit(decyear, dN_filt, 1)[0];
for i in range(len(dN_filt)):
dN_detrended[i] = (dN_filt[i] - north_coef * decyear[i]) - (dN_filt[0] - north_coef * decyear[0]);
vert_coef = np.polyfit(decyear, dU_filt, 1)[0];
for i in range(len(dU_filt)):
dU_detrended[i] = (dU_filt[i] - vert_coef * decyear[i]) - (dU_filt[0] - vert_coef * decyear[0]);
detrended = gps_io_functions.Timeseries(name=Data.name, coords=Data.coords, dtarray=my_paired_ts.dtarray,
dN=dN_detrended, dE=dE_detrended, dU=dU_detrended, Sn=my_paired_ts.N_err,
Se=my_paired_ts.E_err, Su=my_paired_ts.V_err, EQtimes=Data.EQtimes);
trended = gps_io_functions.Timeseries(name=Data.name, coords=Data.coords, dtarray=my_paired_ts.dtarray, dN=dN_filt,
dE=dE_filt, dU=dU_filt, Sn=my_paired_ts.N_err, Se=my_paired_ts.E_err,
Su=my_paired_ts.V_err, EQtimes=Data.EQtimes);
return detrended, trended; # 0 = successful completion
def remove_seasonals_by_hydro(Data, hydro_dir, scaling=False):
station = Data.name;
files = glob.glob(hydro_dir + station.lower() + '*.hyd');
if not files: # found an empty array
print("Error! Hydro file not found for %s" % Data.name);
print("Returning placeholder object.");
wimpyObj = get_wimpy_object(Data);
return wimpyObj, wimpyObj;
else:
filename = files[0];
# Read the hydro model and pair it to the GPS
[hydro_data] = gps_io_functions.read_pbo_hydro_file(filename);
# Clean up and pair data
Data = gps_ts_functions.remove_nans(Data);
# hydro_data=gps_ts_functions.remove_nans(hydro_data); # this may or may not be necessary.
[gps_data, hydro_data] = gps_ts_functions.pair_gps_model(Data, hydro_data); # matched in terms of dtarray.
if scaling is True:
[_, _, vert_gps] = gps_ts_functions.get_linear_annual_semiannual(gps_data);
[_, _, vert_hydro] = gps_ts_functions.get_linear_annual_semiannual(hydro_data);
gps_amp = np.sqrt(vert_gps[1] * vert_gps[1] + vert_gps[2] * vert_gps[2]);
hydro_amp = np.sqrt(vert_hydro[1] * vert_hydro[1] + vert_hydro[2] * vert_hydro[2]);
if hydro_amp == 0.0:
print("ERROR! NLDAS amplitude is exactly 0!! You should probably fix this. ");
wimpyObj = get_wimpy_object(Data);
print("Returning placeholder object.");
return wimpyObj, wimpyObj;
scale_factor = gps_amp / hydro_amp;
# print("GPS Amplitude is %.2f mm" % gps_amp);
# print("NLDAS Amplitude is %.2f mm" % hydro_amp);
print("NLDAS scaling factor is %.2f" % scale_factor);
else:
scale_factor = 1;
# Subtract the model from the data.
dE_filt, dN_filt, dU_filt = [], [], [];
for i in range(len(gps_data.dtarray)):
dE_filt.append(gps_data.dE[i] - scale_factor * hydro_data.dE[i]);
dN_filt.append(gps_data.dN[i] - scale_factor * hydro_data.dN[i]);
dU_filt.append(gps_data.dU[i] - scale_factor * hydro_data.dU[i]);
# A Simple detrending
decyear = gps_ts_functions.get_float_times(gps_data.dtarray);
dE_detrended = np.zeros(np.shape(decyear));
dN_detrended = np.zeros(np.shape(decyear));
dU_detrended = np.zeros(np.shape(decyear));
east_coef = np.polyfit(decyear, dE_filt, 1)[0];
for i in range(len(dE_filt)):
dE_detrended[i] = dE_filt[i] - east_coef * decyear[i] - (dE_filt[0] - east_coef * decyear[0]);
north_coef = np.polyfit(decyear, dN_filt, 1)[0];
for i in range(len(dN_filt)):
dN_detrended[i] = (dN_filt[i] - north_coef * decyear[i]) - (dN_filt[0] - north_coef * decyear[0]);
vert_coef = np.polyfit(decyear, dU_filt, 1)[0];
for i in range(len(dU_filt)):
dU_detrended[i] = (dU_filt[i] - vert_coef * decyear[i]) - (dU_filt[0] - vert_coef * decyear[0]);
corrected_object = gps_io_functions.Timeseries(name=gps_data.name, coords=gps_data.coords, dtarray=gps_data.dtarray,
dE=dE_detrended, dN=dN_detrended, dU=dU_detrended, Se=gps_data.Se,
Sn=gps_data.Sn, Su=gps_data.Su, EQtimes=gps_data.EQtimes);
trended = gps_io_functions.Timeseries(name=gps_data.name, coords=gps_data.coords, dtarray=gps_data.dtarray,
dE=dE_filt, dN=dN_filt, dU=dU_filt, Se=gps_data.Se, Sn=gps_data.Sn,
Su=gps_data.Su, EQtimes=gps_data.EQtimes);
return corrected_object, trended;
def remove_seasonals_by_STL(Data, STL_dir):
# Has an issue: Not sure if it returns trended data.
# Right now only returns detrended data.
filename = STL_dir + Data.name + "_STL_30.txt";
if os.path.isfile(filename):
# If a precomputed file exists...
[dtstrings, dE, dN, dU, Se, Sn, Su] = np.loadtxt(filename, unpack=True, usecols=(0, 1, 2, 3, 4, 5, 6),
dtype={'names': ('dt', 'dE', 'dN', 'dU', 'Se', 'Sn', 'Su'),
'formats': ('U8', np.float, np.float, np.float,
np.float, np.float, np.float)});
final_dtarray = [dt.datetime.strptime(x, "%Y%m%d") for x in dtstrings];
Data = gps_io_functions.Timeseries(name=Data.name, coords=Data.coords, dtarray=final_dtarray, dN=dN,
dE=dE, dU=dU, Sn=Sn, Se=Se, Su=Su, EQtimes=Data.EQtimes);
else: # ELSE: WE NEED TO RECOMPUTE
print("Warning! STL not found for %s" % Data.name);
print("We did not find a pre-computed array, so we are re-computing STL. ");
# Preprocess data: remove nans, fill in gaps.
Data = gps_ts_functions.remove_nans(Data);
[_, dE, Se] = preprocess_stl(Data.dtarray, Data.dE, Data.Se);
[_, dN, Sn] = preprocess_stl(Data.dtarray, Data.dN, Data.Sn);
[new_dtarray, dU, Su] = preprocess_stl(Data.dtarray, Data.dU, Data.Su);
# Write E, N, U
ofile = open('raw_ts_data.txt', 'w');
for i in range(len(dE)):
mystring = dt.datetime.strftime(new_dtarray[i], "%Y%m%d");
ofile.write('%s %f %f %f\n' % (mystring, dE[i], dN[i], dU[i]));
ofile.close();
# Call driver in matlab (read, STL, write)
subprocess.call(['matlab', '-nodisplay', '-nosplash', '-r', 'stl_driver'], shell=False);
# Read / Detrended data
[dE, dN, dU] = np.loadtxt('filtered_ts_data.txt', unpack=True, usecols=(1, 2, 3));
# East, North, Up Detrending
decyear = gps_ts_functions.get_float_times(new_dtarray);
dE_detrended = np.zeros(np.shape(dE));
dN_detrended = np.zeros(np.shape(dN));
dU_detrended = np.zeros(np.shape(dU));
east_coef = np.polyfit(decyear, dE, 1)[0];
for i in range(len(dE)):
dE_detrended[i] = dE[i] - east_coef * decyear[i] - (dE[0] - east_coef * decyear[0]);
north_coef = np.polyfit(decyear, dN, 1)[0];
for i in range(len(dN)):
dN_detrended[i] = (dN[i] - north_coef * decyear[i]) - (dN[0] - north_coef * decyear[0]);
vert_coef = np.polyfit(decyear, dU, 1)[0];
for i in range(len(dU)):
dU_detrended[i] = (dU[i] - vert_coef * decyear[i]) - (dU[0] - vert_coef * decyear[0]);
# Put the gaps back in:
final_dtarray, final_dE, final_dN, final_dU = [], [], [], [];
final_Se, final_Sn, final_Su = [], [], [];
for i in range(len(new_dtarray)):
if new_dtarray[i] in Data.dtarray:
final_dtarray.append(new_dtarray[i]);
final_dE.append(dE_detrended[i]);
final_dN.append(dN_detrended[i]);
final_dU.append(dU_detrended[i]);
final_Se.append(Se[i]);
final_Sn.append(Sn[i]);
final_Su.append(Su[i]);
final_dE = np.array(final_dE);
final_dN = np.array(final_dN);
final_dU = np.array(final_dU);
final_Se = np.array(final_Se);
final_Sn = np.array(final_Sn);
final_Su = np.array(final_Su);
# Return data
Data = gps_io_functions.Timeseries(name=Data.name, coords=Data.coords, dtarray=final_dtarray, dN=final_dN,
dE=final_dE, dU=final_dU, Sn=final_Sn, Se=final_Se, Su=final_Su,
EQtimes=Data.EQtimes);
# Write the file so that we don't recompute it next time.
output_stl(Data, STL_dir);
return Data, Data;
def remove_seasonals_by_GRACE(Data, grace_dir):
# Here we use pre-computed GRACE load model time series to correct the GPS time series.
# We recognize that the horizontals will be bad, and that the resolution of GRACE is coarse.
# For these reasons, this is not an important part of the analysis.
# Read and interpolate GRACE loading model
# Subtract the GRACE model
# Remove a trend from the GPS data
# Return the object.
filename = grace_dir + "scaled_" + Data.name + "_PREM_model_ts.txt"
try:
ifile = open(filename)
except FileNotFoundError:
print("Error! GRACE not found for %s" % Data.name)
placeholder = np.full_like(Data.dtarray, np.nan, dtype=np.double)
wimpyObj = Timeseries(name=Data.name,
coords=Data.coords,
dtarray=Data.dtarray,
dN=[1.0000],
dE=placeholder,
dU=placeholder,
Sn=Data.Sn,
Se=Data.Se,
Su=Data.Su,
EQtimes=Data.EQtimes)
print("returning placeholder object")
return wimpyObj
# 1 = error code.
# If the station has been pre-computed with GRACE:
Data = gps_ts_functions.remove_nans(Data)
grace_model = grace_ts_functions.input_GRACE_individual_station(
grace_dir + "scaled_" + Data.name + "_PREM_model_ts.txt")
my_paired_ts = grace_ts_functions.pair_GPSGRACE(Data, grace_model)
decyear = gps_ts_functions.get_float_times(my_paired_ts.dtarray)
# Subtract the GRACE object
dE_filt = []
dN_filt = []
dU_filt = []
for i in range(len(my_paired_ts.dtarray)):
dE_filt.append(my_paired_ts.east[i] - my_paired_ts.u[i])
dN_filt.append(my_paired_ts.north[i] - my_paired_ts.v[i])
dU_filt.append(my_paired_ts.vert[i] - my_paired_ts.w[i])
# A Simple detrending
dE_detrended = np.zeros(np.shape(decyear))
dN_detrended = np.zeros(np.shape(decyear))
dU_detrended = np.zeros(np.shape(decyear))
east_coef = np.polyfit(decyear, dE_filt, 1)[0]
for i in range(len(dE_filt)):
dE_detrended[i] = dE_filt[i] - east_coef * decyear[i] - (
dE_filt[0] - east_coef * decyear[0])
north_coef = np.polyfit(decyear, dN_filt, 1)[0]
for i in range(len(dN_filt)):
dN_detrended[i] = (dN_filt[i] - north_coef * decyear[i]) - (
dN_filt[0] - north_coef * decyear[0])
vert_coef = np.polyfit(decyear, dU_filt, 1)[0]
for i in range(len(dU_filt)):
dU_detrended[i] = (dU_filt[i] - vert_coef * decyear[i]) - (
dU_filt[0] - vert_coef * decyear[0])
newData = Timeseries(name=Data.name,
coords=Data.coords,
dtarray=my_paired_ts.dtarray,
dN=dN_detrended,
dE=dE_detrended,
dU=dU_detrended,
Sn=my_paired_ts.N_err,
Se=my_paired_ts.E_err,
Su=my_paired_ts.V_err,
EQtimes=Data.EQtimes)
return newData
def remove_seasonals_by_STL(Data, STL_dir):
# First check if a pre-computed file exists
filename = STL_dir + Data.name + "_STL_30.txt"
recompute = 0
try:
ifile = open(filename)
except FileNotFoundError:
print("Warning! STL not found for %s" % Data.name)
recompute = 1
if recompute == 0:
# If a precomputed file exists...
[dE, dN, dU, Se, Sn, Su] = np.loadtxt(filename,
unpack=True,
usecols=(1, 2, 3, 4, 5, 6))
final_dtarray = []
for line in ifile:
dtstring = line.split()[0]
final_dtarray.append(dt.datetime.strptime(dtstring, "%Y%m%d"))
Data = Timeseries(name=Data.name,
coords=Data.coords,
dtarray=final_dtarray,
dN=dN,
dE=dE,
dU=dU,
Sn=Sn,
Se=Se,
Su=Su,
EQtimes=Data.EQtimes)
# ELSE: WE NEED TO RECOMPUTE
else:
print(
"We did not find a pre-computed array, so we are re-computing STL. "
)
# Preprocess data: remove nans, fill in gaps.
Data = gps_ts_functions.remove_nans(Data)
[new_dtarray, dE, Se] = preprocess_stl(Data.dtarray, Data.dE, Data.Se)
[new_dtarray, dN, Sn] = preprocess_stl(Data.dtarray, Data.dN, Data.Sn)
[new_dtarray, dU, Su] = preprocess_stl(Data.dtarray, Data.dU, Data.Su)
# Write E, N, U
ofile = open('raw_ts_data.txt', 'w')
for i in range(len(dE)):
mystring = dt.datetime.strftime(new_dtarray[i], "%Y%m%d")
ofile.write('%s %f %f %f\n' % (mystring, dE[i], dN[i], dU[i]))
ofile.close()
# Call driver in matlab (read, STL, write)
subprocess.call(
['matlab', '-nodisplay', '-nosplash', '-r', 'stl_driver'],
shell=False)
# Read / Detrended data
[dE, dN, dU] = np.loadtxt('filtered_ts_data.txt',
unpack=True,
usecols=(1, 2, 3))
# East, North, Up Detrending
decyear = gps_ts_functions.get_float_times(new_dtarray)
dE_detrended = np.zeros(np.shape(dE))
dN_detrended = np.zeros(np.shape(dN))
dU_detrended = np.zeros(np.shape(dU))
east_coef = np.polyfit(decyear, dE, 1)[0]
for i in range(len(dE)):
dE_detrended[i] = dE[i] - east_coef * decyear[i] - (
dE[0] - east_coef * decyear[0])
north_coef = np.polyfit(decyear, dN, 1)[0]
for i in range(len(dN)):
dN_detrended[i] = (dN[i] - north_coef * decyear[i]) - (
dN[0] - north_coef * decyear[0])
vert_coef = np.polyfit(decyear, dU, 1)[0]
for i in range(len(dU)):
dU_detrended[i] = (dU[i] - vert_coef * decyear[i]) - (
dU[0] - vert_coef * decyear[0])
# Put the gaps back in:
final_dtarray = []
final_dE = []
final_dN = []
final_dU = []
final_Se = []
final_Sn = []
final_Su = []
for i in range(len(new_dtarray)):
if new_dtarray[i] in Data.dtarray:
final_dtarray.append(new_dtarray[i])
final_dE.append(dE_detrended[i])
final_dN.append(dN_detrended[i])
final_dU.append(dU_detrended[i])
final_Se.append(Se[i])
final_Sn.append(Sn[i])
final_Su.append(Su[i])
final_dE = np.array(final_dE)
final_dN = np.array(final_dN)
final_dU = np.array(final_dU)
final_Se = np.array(final_Se)
final_Sn = np.array(final_Sn)
final_Su = np.array(final_Su)
# Return data
Data = Timeseries(name=Data.name,
coords=Data.coords,
dtarray=final_dtarray,
dN=final_dN,
dE=final_dE,
dU=final_dU,
Sn=final_Sn,
Se=final_Se,
Su=final_Su,
EQtimes=Data.EQtimes)
# Write the file so that we don't recompute it next time.
output_stl(Data, STL_dir)
return Data