pyacs.gts.Gts module¶
Geodetic Time Series Class & methods
A Geodetic time series (Gts) is a series of 3 components North,East,UP as a function of increasing dates
The Gts implemented in PYACS has the following structure:
- Basic data
data: a 2D numpy array with 7 columns including: dec.year, N, E, U, S_N, S_E, S_U
code: station 4-letters code
lon,lat,h: approximate longitude, latitude (geodetic, deg.dec) and ellipsoidal height (m)
X0,Y0,Z0 XYZ reference position in the Geocentric Frame. N,E,U are with respect to X0,Y0,Z0
t0 reference date in decimal year corresponding to the X0,Y0,Z0
- Optional data
data_xyz: a 2D numpy array with 7 columns including: dec.year, X, Y, Z, SX, SY, SZ, corr_XY, corr_XZ, corr_YZ
data_corr_neu a 2D numpy array with 4 columns including: dec.year, corr_ne,corr_nu,corr_eu
data_corr_xyz a 2D numpy array with 4 columns including: dec.year, corr_xy,corr_xz,corr_yz
- Analysis results
outliers: list of index of outliers in a time series (all components)
outliers_east list of index of outliers on the East component in a time series
outliers_north list of index of outliers on the North component in a time series
outliers_up list of index of outliers on the Up component in a time series
offsets_values: a 2D numpy array with 7 columns: dec.year N, E, U, S_N, S_E, S_U
offsets_dates: a list of dates for offsets
velocity: a 1D numpy array with 6 columns: vel_N, vel_E, vel_U, S_vel_N, S_vel_E, S_vel_U
annual: a 1D numpy array with 6 columns: Amplitude_N, Phase_N, Amplitude_E, Phase_E, Amplitude_U, Phase_U
semi_annual: a 1D numpy array with 6 columns: Amplitude_N, Phase_N, Amplitude_E, Phase_E, Amplitude_U, Phase_U
- Metadata
ifile: original input file of the time series
log: log of operations
metadata: any information the analyst would like to be recorded
- Units Conventions
dates are in decimal year
coordinates are in meters
phases are in radians
- Programming conventions
singular denotes single values, plural or name starting with l denotes lists or array
in_place=True in methods means that current content of the Gts will be overwritten; default is False
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pyacs.gts.Gts.
get_index_from_dates
(dates, data, tol=0.25)[source]¶ returns the list of index in data corresponding to given dates within tolerance
- Parameters
dates – list of dates in decimal year
data – a 2D numpy array with decimal dates in the first column
tol – date tolerance to decide that two dates are equal. (default 0.25 day)
:return : list of index
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class
pyacs.gts.Gts.
Gts
(code=None, lat=None, lon=None, h=None, X0=None, Y0=None, Z0=None, t0=None, data=None, data_xyz=None, data_corr_neu=None, data_corr_xyz=None, offsets_dates=[], offsets_values=None, outliers=[], annual=None, semi_annual=None, velocity=None, ifile=None, log=None, metadata=None)[source]¶ Bases:
object
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add_obs
(date, NEUSNSESUCNECNUCEU, in_place=False, check=True, verbose=False)¶ Adds observation(s) as DN,DE,DU to a time series
- Parameters
date – date in decimal year. float, a list or 1D numpy array
NEUSNSESUCNECNUCEU – value to be added in the Gts, provided as a list, a 1D numpy array or a 2D numpy array. requires at least NEU: North, East, UP values optional: SN, SE, SU, CNE, CNU, CEU: standard deviations and correlation coefficient between North, East and Up components. If not provided, SN=SE=SU=0.001 (1 mm) and CNE=CNU=CEU=0
in_place – boolean, if True add_obs to the current Gts, if False, returns a new Gts
check – check time order and duplicate dates
verbose – verbose mode
:return : new Gts or the modified Gts if in_place :note : if it exists, .data_xyz will be set to None for consistency.
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add_obs_xyz
(date, XYZSXSYSZCXYCXZCYZ, in_place=False, check=True, neu=True, verbose=False)¶ Adds observation(s) as XYZ to a time series
- Parameters
date – date in decimal year. float, a list or 1D numpy array
XYZSXSYSZCXYCXZCYZ – value to be added in the Gts, provided as a list, a 1D numpy array or a 2D numpy array. requires at least X,Y,Z
optional: SX, SY, SZ, CXY, CXZ, CYZ: standard deviations and correlation coefficients. If not provided, SX=SY=SZ=0.001 (1 mm) and CXY=CXZ=CYZ=0 :param in_place: boolean, if True add_obs to the current Gts, if False, returns a new Gts :param check: check time order , duplicate dates and re-generate NEU time series (.data) :param neu: regenerate .data from the updated .data_xyz :param verbose: verbose mode
:return : new Gts or the modified Gts if in_place :note 1: by default .data will be updated from .data_xyz, and X0,Y0,Z0 will be updated. :note 2:
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add_offsets_dates
(offsets_dates, in_place=False)¶ add_offsets_dates to a time series if in_place = True then replace the current time series
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add_vel_sigma
(in_place=False, b_fn=4, verbose=True)¶ calculates realistic sigma on velocity components assuming white & flicker using eq (19) & (23) from Williams (J. of Geodesy, 2003) b_fn is the value for flicker noise, taken as 4 mm/yr^1/4 model can be detrend, detrend_annual, detrend_seasonal if in_place = True then replace the current time series
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apply_offsets
(np_offset, opposite=False, in_place=False, verbose=False)¶ Applies given offsets to a times series np_offset is a 1D np.array with lines [dates,north,east,up] if in_place = True then replace the current time series
- Parameters
np_offset – 1D or 3D numpy array or list or list of list with column offset_dates, north, east, up, s_north, s_east, s_up
opposite – boolean, if True apply the oppsite of provided offsets
in_place – if True, will make change in place, if False, return s a new time series
verbose – boolean, verbose mode
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cdata
(data=False, data_xyz=False, tol=0.001, verbose=False)¶ Check data/data_xyz attributes
- Parameters
data – boolean, if True, data attribute will be checked
data_xyz – boolean, if True, data_xyz attribute will be checked
tol – tolerance in days for two dates to be considered as the same (default 0.001 of day)
verbose – boolean, verbose mode
:return : boolean, True if everything is OK, False otherwise
:note : in future, this routine should also whether .data and .data_xyz value are consistent
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copy
(data=True, data_xyz=True, loutliers=True)¶ makes a (deep) copy of the time series.
By default, all attributes are also copied, including .data, .data_xyz, loutliers etc.
Default behaviour can be modified for the following attribute:
- Parameters
data – can be set to None or a 2D numpy array of shape (n,10)
data_xyz – can be set to None or a 2D numpy array of shape (n,10)
loutliers – False will not copy the loutliers atrribute
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correct_duplicated_dates
(action='correct', tol=0.1, in_place=False, verbose=False)¶ Check or remove duplicated dates in a time series
- Parameters
action – ‘correct’ (default) or ‘check’
tol – tolerance for two dates to be considered as the same (default = 0.1 day)
in_place – boolean, if True,
verbose – verbose mode
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decimate
(time_step=30.0, dates=[], method='median', verbose=False)¶ decimate a time series
- Parameters
time_step – time step in days
dates – list of dates where point are forced to be written regardless time_step
method – method used to be used to calculated the position. choose among [‘median’,’mean’,’exact’]
verbose – verbose mode
:return : new Gts
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decyear2days
(ref_date='', in_place=False)¶ Converts the dates of a time series from decimal years to days after a reference date ref_date is read by guess_date
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delete_small_offsets
(offsets, del_by_pricise=False)¶ The aim for test_offset modul. Estimate the offsets with clean data. Then delete the offsets which their values are so small input: list of time offsets output: list of time offsets tested
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detrend
(method='L2', in_place=False, periods=[], exclude_periods=[])¶ detrends a time series and save velocity estimates in velocity attribute
:param periods : periods used to estimate the velocity :param exclude_periods : periods to be excluded for the velocity estimate :param in_place : if True then replace the current time series :return : the detrended time series :note : outliers from Gts.outliers are omitted in the estimation and offsets given Gts.offsets_dates are estimated simultaneously
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detrend_annual
(method='L2', in_place=False, periods=None, exclude_periods=None)¶ estimates a trend + annual terms in a time series and removes them velocity and annual attribute are saved in Gts.velocity & Gts.annual
:param periods : periods used for estimation :param exclude_periods : periods to be excluded from estimation :param in_place : if True then replace the current time series :return : the detrended time series :note : outliers from Gts.outliers are ommitted in the estimation and offsets given Gts.offsets_dates are estimated simultaneously
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detrend_median
(delta_day=None, in_place=False, periods=[], exclude_periods=[], verbose=False, auto=False)¶ Calculates a velocity using the median of pair of displacements exactly separated by one year, inspired from MIDAS If the time series has less than a year of data, then the time series is kept untouched.
- Parameters
delta_day – if None, it is one year, if 0 then it is the relax mode for campaign data, any integer is the time delta (in days) used to compute velocity.
in_place – boolean, if True, in_place, if False, returns a new Gts instance (default)
periods – periods (list of lists) to be included for trend calculation
exclude_periods – periods (list of lists) to be excluded for trend calculation
verbose – verbose mode
auto – if True, then start will delta_day=None, if it fails or found less than 100 pairs then use delta_day=0,
if fails then use regular detrend
- Note
returns None if time series is shorter than 1 year
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detrend_seasonal
(method='L2', in_place=False, periods=None, exclude_periods=None)¶ estimates a trend + annual + semi-annual terms in a time series and removes them velocity, annual and semi-annual attributes are saved in Gts.velocity, Gts.annual, Gts.semi_annual
:param periods : periods used for estimation :param exclude_periods : periods to be excluded from estimation :param in_place : if True then replace the current time series :return : the detrended time series :note : outliers from Gts.outliers are ommitted in the estimation and offsets given Gts.offsets_dates are estimated simultaneously
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detrend_seasonal_median
(wl=11, in_place=False, verbose=False)¶ Calculates a velocity using the median of pair of displacements exactly separated by one year, inspired from MIDAS and then removes repeating yearly signal If the time series has less than three years of data, then the time series is kept untouched.
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differentiate
()¶ differentiate the current time series
- Returns
the differentiated time series as a new Gts object
:note : differentiation is made on .data. .data_xyz is set to None.
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displacement
(sdate=None, edate=None, window=None, method='median', speriod=[], eperiod=[], rounding='day', verbose=True)¶ Calculates displacements between two dates or two periods
- Parameters
sdate – start date in decimal year
edate – start date in decimal year
window – time window in days for searching available dates
method – method to calculate the position. ‘median’ or ‘mean’. default is ‘median’.
speriod – period for calculating the start position
eperiod – period for calculating the end position
rounding – rounding for dates. Choose among ‘day’,’hour’,’minute’ or ‘second’. default is ‘day’.
verbose – verbose mode
- Returns
displacement as np.array([dn,de,du,sdn,sde,sdu])
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edge_filter
(lbda, in_place=False, verbose=True)¶ Edge Gts filter using a L1 total variation filter. The signal is assumed to be piecewise constant.
- Parameters
lbda – lambda parameter
in_place – if True then replace the current time series
verbose – boolean, verbose mode
- Returns
the filtered time series
- Reference
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estimate_local_offset
(window_length=4, in_place=False)¶ Estimate the local offset, just used window_length positions before & window_length positions behind of offset output: amplitude of local offsets
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exclude_periods
(lperiod, in_place=False, verbose=False)¶ exclude periods of a Gts
- Parameters
lperiod – a list [start_date,end_date] or a list of periods e.g. periods=[[2000.1,2003.5],[2009.3,2010.8]]
in_place – if True, will make change in place, if False, return s a new time series
- Note 1
X0,Y0,Z0 attributes will be changed if necessary
- Note 2
handles both .data and .data_xyz
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extract_dates
(dates, tol=0.05, in_place=False, verbose=True)¶ Returns a time series extracted for a given list of dates
- Parameters
dates – dates either as a list or 1D numpy array of decimal dates
tol – date tolerance in days to assert that two dates are equal (default 0.05 day)
in_place – if True, will make change in place, if False, return s a new time series
verbose – boolean, verbose mode
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extract_ndates_after_date
(date, n, verbose=False)¶ Extract n values after a given date If n values are not available, returns all available values after date .data is set to None if no value at all is available
- Parameters
date – date in decimal year
n – number of observations to be extracted
- Returns
a new Gts
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extract_ndates_around_date
(date, n)¶ Extract n values before and n values after a given date If n values are not available, returns all available values .data is set to None if no value at all is available
- Parameters
date – date in decimal year
n – number of observations to be extracted
- Returns
a new Gts
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extract_ndates_before_date
(date, n, verbose=False)¶ Extract n values before a given date If n values are not available, returns all available values before date .data is set to None if no value at all is available
- Parameters
date – date in decimal year
n – number of observations to be extracted
- Returns
a new Gts
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extract_periods
(lperiod, in_place=False, verbose=False)¶ extract periods of a Gts
- Parameters
lperiod – a list [start_date,end_date] or a list of periods e.g. periods=[[2000.1,2003.5],[2009.3,2010.8]]
in_place – if True, will make change in place, if False, return s a new time series
- Note 1
X0,Y0,Z0 attributes will be changed if necessary
- Note 2
handles both .data and .data_xyz
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find_large_uncertainty
(sigma_thresold=10, verbose=True, lcomponent='NE')¶ Find dates with large uncertainty and flag them as outliers.
- Parameters
sigma_threshold – value (mm) for a date to be flagged.
verbose – verbose mode
lcomponent – list of components to be checked. default = ‘NE’
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find_offsets
(threshold=3, n_max_offsets=9, conf_level=95, lcomponent='NE', verbose=True, in_place=False)¶ A simple empirical procedure to find offsets.
- Parameters
threshold – threshold value for offset preliminary detection
n_max_offset – maximum number of offsets to be detected simultaneously
conf_level – confidence level for a suspected offset to be accepted
lcomponent – components used for offset detection
- Returns
a new Gts instance with offsets_dates and outliers now populated
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find_offsets_edge_filter
(threshold=0.6, search_lbda=[3, 5, 7, 10, 20, 50, 100, 200, 300], delta_day=100, in_place=False, lcomponent='NE', verbose=True, debug=True, log=False, eq_file=None)¶
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find_offsets_t_scan
(threshold=0.8, window=250, in_place=False, lcomponent='NE', verbose=True, debug=True)¶
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find_outlier_around_date
(date, conf_level=95, n=3, lcomponent='NE', verbose=True)¶ Find an outlier around a given date returns the index of the outlier, returns [] if no outlier found :param date : given date :param conf_level : confidence level for F_ratio test of outlier significance (default 95%%) :param n : number of dates either sides of date (default n=3) :param lcomponent : components ‘N’,’E’,’U’,’NE’,’NEU’ (default ‘NE’)
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find_outliers_and_offsets_through_differentiation
(th=100)¶ find outliers and offsets using differenciation
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find_outliers_by_RMS_ts
(ndays=7, th_detection=5, th_rejection=2)¶ - Find index of outliers in a time series, populate self.outliers.
rms time series are first calculated over ndays
time windows are kept for further inspection if rms(t) > th_detection * median(rms(ts))
for each anomalous time windows, differentiate positions, find the max
test whether it is a true outlier (differentiated(t) > th_rejection * median(differentiated))
- output:
None
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find_outliers_by_residuals
(threshold=5, model='detrend_seasonal', component='NE', in_place=False)¶ Find index of outliers by trendline/trendline_annual/trendline_seasonal (the complete model) Then the outliers are detected if their residuals are greater than th_rejection*standard_deviation
- output:
Add the list of outlier index into self.outliers
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find_outliers_percentage
(percentage=0.03, in_place=False, verbose=False, component='NEU', periods=None, excluded_periods=None)¶ detrend a time series and ranks the residuals by increasing absolute value populate the outliers with the x % largest ones on each component
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find_outliers_simple
(threshold=100, window_length=10, in_place=False, verbose=False, component='NEU', periods=None, excluded_periods=None)¶
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find_outliers_sliding_window
(threshold=3, in_place=False, verbose=True, periods=[[]], excluded_periods=[[]], component='NE', window_len=15, automatic=True)¶ Find outliers using sliding windows
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find_outliers_vondrak
(threshold=10, fc=2.0, in_place=False, verbose=True, periods=[[]], excluded_periods=[[]], component='NE')¶ Find outliers using a Vondrak filter
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find_time_offsets
(option=None, ndays=7, th_detection_rms=3, th_detection_offset=3)¶ Find the time of suspected offsets by rms time series calculated over ndays Then check the time of offsets: if one offset is too small/None then it is removed input:
ndays: number of positions in the windows. rms time series are calculated over ndays.
th_detection_rms: the threshold for detecting the anomalous windows rms(t) > th_detection_rms*median(rms(ts)).
- th_detection_offset: the threshold for detecting the offsets,
for each anomalous time windows, differentiate positions then test whether it is a suspected offset (differentiated(t) > threshold * median(differentiated))
output:
add the time of offsets in to self.offsets
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force_daily
(in_place=False)¶ force a time series to be daily with dates at 12:00:00 of every day
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frame
(frame=None, in_place=False, verbose=False)¶ Rotates a time series according to an Euler pole Returns a new Gts instance
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get_coseismic
(eq_date, window_days=5, sample_after=1, method='median', in_place=False)¶ Get coseismic displacement at a given date. Coseismic displacement is estimated as the position difference between the median of window_days before the earthquake date and the median of sample_after samples after the earthquake date.
note: only median method implemented
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get_unr
(site, verbose=False)¶ Get a time series from http://geodesy.unr.edu/gps_timeseries/txyz/IGS14/ in PYACS
- Parameters
site – 4-letters code
verbose – verbose mode
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info
(info=2)¶ Print various informations about the time series
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insert_gts_data
(gts, in_place=False, verbose=False)¶ insert data (and/or) .data_xyz of a gts into the current gts
- Parameters
gts – tie series to be inserted
in_place – boolean, if True add_obs to the current Gts, if False, returns a new Gts
verbose – verbose mode
:return : new Gts or the modified Gts if in_place
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local_offset_robust
(date, n, verbose=False, debug=False)¶ estimate a local offset (no velocity) with a robust method
- Parameters
date – date in decimal year
n – number of dates before and after the dates used in the estimation
:return : a 1D numpy array with [date, north, east, up, s_north, s_east, s_up]
- Note
the offsets are estimated using the difference between the median position before and after the earthquake using i days
for all i <=n. Then the median of the estimates is returned.
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make_dynamic_apr
(apr, time_step=30.0, pos_tol=0.03, dates=[], gap=20.0, verbose=False)¶ Creates an apr file for GAMIT The created apr file has no velocity, but a series of coordinates at different time
- Parameters
apr – apr file (Globk format)
time_step – time step for writing dates (default 30 days)
pos_tol – position tolerance. If exceeded, a new date will be written. (default 0.03 m)
dates – a list of dates in decimal years where writing will be forced
gap – gap in days. If there is no data during a duration greater than gap, then observation is forced to be included and tested against pos_tol
verbose – verbose mode (boolean)
- Returns
Gts instance
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make_model
(option='detrend', method='L2', loutlier=None, in_place=False)¶ Estimate time series model parameters using least squares input: data: Gts format option are: ‘detrend’/’detrend_annual’/’detrend_seasonal’ output: new Gts object: time series is now the residuals wrt to the model and its associated values (vel, annual, semi-annual etc)
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median_filter
(n, in_place=False, verbose=True)¶ returns a filtered time series using scipy.signal.medfilt
- Parameters
n – size of the median filter window (must be odd)
in_place – if True then replace the current time series
verbose – boolean, verbose mode
- Returns
the filtered time series
- Note
the filter is applied to .data and .data_xyz is set to None
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minimum_component
(mask_period=[], p=1, fcut=None, Q=None, in_place=False, verbose=True)¶ Minimum component filtering for Gts.
Minimum component filtering is useful for determining the background component of a signal in the presence of spikes
- Parameters
mask_periods – periods (list or list of lists) which should be ignored for smoothing
p – integer (optional). polynomial degree to be used for the fit (default = 1)
fcut – float (optional). the cutoff frequency for the low-pass filter. Default value is f_nyq / sqrt(N)
Q – float (optional). the strength of the low-pass filter. Larger Q means a steeper cutoff. default value is 0.1 * fcut
in_place – if True then replace the current time series
verbose – boolean, verbose mode
- Returns
the filtered time series
- Note
This code follows the procedure explained in the book “Practical Statistics for Astronomers” by Wall & Jenkins book, as well as in Wall, J, A&A 122:371, 1997
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mmodel
()¶ Generates a modeled time series from the parameters read in self
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neu2xyz
(corr=False, verbose=False)¶ populates .data_xyz from .data requires X0,Y0,Z0 attributes to be set
- Parameters
corr – if True, then standard deviation and correlations will also be calculated
verbose – verbose mode
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np_datetime_2_eq_time
(leap_sec=0.0, eq_time=0.0)¶ takes a hash of python datetime.datetime object and return a numpy array of seconds with respect to eq_time if the input array is in GPS time, providing leap_sec correct for the GPS_time - UTC delta
- Parameters
leap_sec – number of seconds between GPS_time - UTC delta (leap_sec=17 that is GPS is ahead of UTC by 17 seconds on 13/02/2016)
eq_time – time of earthquake as a python datetime.datetime object (in UTC)
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np_yyyy_mm_dd_hh_mm_ss_2_datetime
()¶ converts a numpy array including year month mday hour minute sec to an array of python datetime.datetime object returns a hash
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np_yyyy_mm_dd_hh_mm_ss_2_decyear
()¶ converts a numpy array including year month mday hour minute sec to decimal year returns a 1D array
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plot
(title=None, loffset=True, loutliers=True, verbose=False, date=[], yaxis=None, yupaxis=None, xticks_minor_locator=1, lcomponent=['N', 'E', 'U'], error_scale=1.0, lperiod=[[]], lvline=[], save_dir_plots='.', save=None, show=True, unit='mm', date_unit='cal', date_ref=0.0, center=True, superimposed=None, lcolor=['r', 'g', 'c', 'm', 'y', 'k', 'b'], label=None, legend=False, set_zero_at_date=None, grid=True, plot_size=None, info=[], xlabel_fmt=None, **kwargs)¶ Create a plot of a North-East-Up time series and related info (offsets, outliers) using Matplotlib Coordinates of the time series are assumed to be in meters default plots units will be mm; Use unit=’m’ to get meters instead
- Parameters
title – string to be added to the site name as a plot title
loffset – boolean print a dash vertical line at offset dates
loutliers – boolean print outliers
verbose – boolean verbose mode
date – [sdate,edate] start and end date for plots sdate and edate in decimal years if date_unit is either ‘decyear’ or ‘cal’, or in days if date_unit is ‘days’
yaxis – [min_y,max_y] min and max value for the yaxis if not provided automatically adjusted
yupaxis – same as yaxis but applies to the up component only
xticks_minor_locator – where xticks_minor_locator will be placed. Float when date_unit is ‘decyear’ or ‘days’, a string ‘%Y’,’%m’,’%d’ is date_unit is ‘cal’.
lcomponent – list of components to be plotted (default =[‘N’,’E’,’U’])
error_scale – scaling factor for error bars (default = 1.0, 0 means no error bar)
lperiod – list of periods to be drawn in background (color=light salmon)
lvline – list of dates where vertical lines will be drawn in background (color=green)
save_dir_plots – directory used for saving the plots
save – name, save the plot into name, if simply True an automatic name is given
show – boolean, is True show the plot
unit – ‘m’,’cm’,’mm’, default=’mm’
date_unit – ‘decyear’ or ‘cal’ or ‘days’, default=’decyear’
date_ref – reference date, default=0.0
center – boolean, if True the y_axis is centered around the mean value for the plotted period
superimposed – if a gts is provided, it is superimposed to the master, default=None
lcolor – color list used for the superimposed time series, default=[‘r’,’g’,’c’,’m’,’y’,’k’,’b’]
label – label for superimposed time series to be displayed in legend, default=None
legend – boolean. Set true to display label for superimposed time series, default=False
set_zero_at_date – date at which the master and superimposed gts will be equal (default=None). date can also be a list with [date,offset_north,offset_east,offset_up]
plot_size – plot size as a tuple. Default, best guess.
grid – boolean
info – title to appear in time series subplots
**kwargs –
any argument to be passed to matplotlib.pyplot.errorbar
- Note
The list of kwargs are:
{ ‘linewidth’ : 0, ‘marker’ : marker_main_symbol , ‘markersize’ : marker_main_size, ‘markerfacecolor’ : marker_main_color, ‘markeredgecolor’ : marker_main_color, ‘markeredgewidth’ : marker_main_colorlw, ‘ecolor’ : error_bar_color, ‘elinewidth’ : error_bar_linewidth, ‘capsize’ : error_bar_capsize }
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pwlf
(component, n, in_place=False, verbose=False, output=False)¶ Perform a piecewise approximation of a time series. Since it the routine is 1D, the component E,N, or U needs to be specified.
- Parameters
component – component used for the decomposition. Must be ‘E’,’N’ or ‘U’
n – number of segments
in_place – if True then replace the current time series
verbose – boolean, verbose mode
- Output
if False, the predicted time series is returned. If True, then a list of dates is returned.
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read_cats_file
(idir='.', ifile=None, gmt=True, verbose=False)¶ Read cats files in a directory and actually loads the time series
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read_eq_rename
(eq_rename, in_place=False, verbose=False)¶ Reads the information for the current site (code) from an eq_rename globk file.
Populates loutliers and offsets_dates Found excluded periods in the eq_rename file are added to loutliers
- Parameters
eq_rename – eq_rename (globk format) file to be read
in_place – boolean. If True then the Gts instance is modified, if False the Gts instance is preserved and a new Gts instance is return
verbose – verbose mode (boolean)
- Returns
Gts instance
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read_kenv
(ifile, date_type='jd')¶ Read kenv file (magnet) format for time series
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read_lon_lat
(gmt_file, verbose=False)¶ Reads a gmt psvelo file and populates Gts.lon & Gts.lat
- Parameters
gmt_file – gmt psvelo file
verbose – verbose mode (boolean)
- Returns
the current Gts instance
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read_mb_file
(idir='.', ifile=None, gmt=True, verbose=False)¶ Read GAMIT/GLOBK mb_files in a directory and actually loads the time series
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read_offset_dates
(offset_file)¶ Reads an offset file and populates offsets_dates (pyacs format) attribute of the current Gts instance. format is simply a code dates. dates can be any format read by pyacs.guess_date
- Parameters
offset_file – offset_file to be read
- Returns
the current Gts instance
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read_pos
(tsdir='.', tsfile=None, xyz=True, verbose=False)¶ Read GAMIT/GLOBK PBO pos file in a directory and actually loads the time series
- Parameters
tsdir – directory of pos file
tsfile – pos file to be loaded
xyz – reads xyz sx sy sz corr_xy corr_xz corr_yz columns
verbose – verbose mode
- Return Nothing
- Raises
Nothing –
- Note
Since a pos file includes (almost) all the information, data, code, X0,Y0,Z0,t0 will be populated
If file=None, then read_pos will look for a file named CODE*.pos
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read_pride
(tsdir='.', tsfile=None, xyz=True, verbose=False)¶ Read PRIDE-PPPAR kinematic result file
- Parameters
tsdir – directory of pride-pppar kinematic files
tsfile – pride-pppar kinematic file to be loaded
verbose – verbose mode
- Return Nothing
- Raises
Nothing –
If file=None, then read_pride will look for a files named kin_*code
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read_pride_pos
(tsdir='.', tsfile=None, verbose=False)¶ Read PRIDE-PPPAR static result file
- Parameters
tsdir – directory of pride-pppar pos static files
tsfile – pride-pppar pos static file to be loaded
verbose – verbose mode
If file=None, then read_pride will look for a files named pos_*code
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read_tdp
(idir='.', ifile=None, gmt=True, verbose=False)¶ Read tdp (Gipsy kinematics provided by Cedric Twardzik 17/04/2018) format for time series
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read_track_NEU
(tsdir='.', tsfile=None, leap_sec=0.0, eq_time=None, verbose=False)¶ Read a GAMIT/GLOBK Track output file generated with the option out_type NEU in this case dates are seconds by default the seconds are with respect to the first epoch of measurements If option leap_sec is provided with a value > 0.0, then GPS time is corrected for the difference between GPTS time and UTC If eq_time is provided, it is assumed to be UTC. Expected format is YYYY:MM:MD:HH:MM:SS.S
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realistic_sigma
(option='tsfit', in_place=False, verbose=False)¶ Calculates realistic sigmas on velocity components :param option:
tsfit: globk T. Herring realistic sigma
cats_pl: CATS estimates with noise type estimated (i.e. –model=pl:)
cats_seasonal_pl: CATS estimates with seasonal terms and noise type estimated (i.e. –model=pl: –sinusoid=1y1)
cats_flicker: CATS estimates assuming flicker noise (i.e. –model=pl:k-1)
cats_seasonal_flicker: CATS estimates with seasonal terms and assuming flicker noise (i.e. –model=pl:k-1 –sinusoid=1y1)
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remove_outliers
(periods=None, in_place=False)¶ removes outliers provided in self.outliers return a new Gts without the outliers if in_place = True then self has the outliers removed as well (in _place)
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remove_pole
(pole, pole_type='euler', in_place=False, verbose=True)¶ remove velocity predicted by an Euler pole or a rotation rate vector from a time series pole is a 1D array with 3 values requires self.lon & self.lat attributes to have been filled before if in_place = True then replace the current time series
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remove_velocity
(vel_neu, in_place=False)¶ remove velocity from a time series vel_neu is a 1D array of any arbitrary length, but with the velocities (NEU) to be removed in the first 3 columns if in_place = True then replace the current time series
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reorder
(verbose=False)¶ reorder data and/or data_xyz by increasing dates always in place
- Parameters
verbose – verbose mode
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rotate
(angle, in_place=False)¶ rotates the axis by an angle
- Parameters
angle – angle in decimal degrees clockwise
if in_place = True then replace the current time series
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save_apr
(apr, epoch=None, verbose=False, excluded_periods=None)¶ save results of a Gts analysis in globk format apr file
- Parameters
apr – apr file (Globk format)
epoch – epoch in decimal year for coordinates in apr
verbose – verbose mode (boolean)
exluded_periods – periods to be excluded
- Returns
Gts instance
- Note
following Globk’s convention, site will be named XXXX_1PS, XXXX_2PS etc between offset dates
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save_eq_rename
(eq_rename, verbose=False, excluded_periods=None)¶ save results of a Gts analysis in globk format eq_rename
- Parameters
eq_rename – output eq_rename file (Golbk format)
verbose – verbose mode (boolean)
exluded_periods – periods to be excluded
- Returns
Gts instance
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save_offsets
(ofile, verbose=True, comment='', up=False, info=False)¶ Appends offsets values to a given text file (gmt psvelo format)
- Parameters
ofile – output offset file
verbose – verbose mode (boolean)
comment – comment as a string. ‘# ‘ is pre-prended to comment if not provided
up – boolean. If True, then Ve, SVe and SVen are set to 0 and Vu and Vu are written as 4-th and 6-th fields
- Returns
the current Gts instance
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save_velocity
(gmt_file, verbose=True, comment=None, up=False)¶ Appends velocity estimates (with uncertainties) to a gmt psvelo file
- Parameters
gmt_file – output gmt psvelo file (will append if gmt_file already exists)
verbose – verbose mode (boolean)
comment – comment as a string. ‘# ‘ is pre-prended to comment if not provided
up – boolean. If True, then Ve, SVe and SVen are set to 0 and Vu and Vu are written as 4-th and 6-th fields
- Returns
the current Gts instance
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savitzky_golay
(in_place=False, verbose=True, window_length=15, polyorder=3, deriv=0, delta=1.0, mode='interp', cval=0.0)¶ returns a filtered time series using scipy.signal.savgol_filter
See documentation for the filter parameters. http://https://docs.scipy.org/doc/scipy/reference/generated/scipy.signal.savgol_filter.html#scipy.signal.savgol_filter
- Parameters
in_place – if True then replace the current time series
verbose – boolean, verbose mode
- Returns
the filtered time series
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set_zero_at_date
(date, offset=None, in_place=False)¶ make a translation of a time series, setting to 0 at a given date if the provided date does not exist, uses the next date available
- Parameters
date – date in decimal year
offset – an offset (in mm) to be added. Could be a float, a list or 1D numpy array with 3 elements
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sigma_cats
(in_place=False, verbose=False, k='k-1', seasonal='')¶ runs CATS for getting realistic sigma
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sigma_vel_tsfit
(in_place=False, verbose=False)¶ runs tsfit for getting realistic sigma
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smooth
(window_len=11, window='hanning', in_place=False, verbose=False, component='NEU')¶ smooth a time series
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spline
(smoothing=1, degree=5, date=None)¶ - Parameters
smoothing – Positive smoothing factor used to choose the number of knots. Number of knots will be increased
until the smoothing condition is satisfied:
sum((w[i] * (y[i]-spl(x[i])))**2, axis=0) <= s
- Parameters
degree – Degree of the smoothing spline. Must be <= 5. Default is k=3, a cubic spline.
date – 1D array of interpolation dates in decimal year, or ‘day’ for every day. defualt None will interpolate
at data date only. :return: new gts instance
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substract_ts
(ts, tol=0.05, verbose=True)¶ substract the ts provided as argument to the current time series
- Parameters
ts – time series to be substracted as a Gts instance
tol – date tolerance to decide whether two dates are identical in both time series. default = 1/4 day
verbose – verbose mode
:return : new Gts
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substract_ts_daily
(ts, verbose=True)¶ substract the ts provided as argument to the current time series
- Parameters
ts – time series to be substracted as a Gts instance
verbose – verbose mode
:return : new Gts
- Note
this method assumes daily time series
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suspect_offsets
(threshold=3, verbose=True, lcomponent='NE', n_max_offsets=10, in_place=False)¶ Tries to find offsets in a time series
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suspect_offsets_mf
(threshold=3, verbose=True, lcomponent='NE', n_max_offsets=5, in_place=False, debug=False)¶ Tries to find offsets in a time series using a median filter
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test_offset_significance
(date, conf_level=95, lcomponent='NE', verbose=True, debug=False, mode='local')¶ test the significance of an offset
- Param
date : date of the offset to be tested
- Param
conf_level : confidence level in percent (default=95)
- Param
lcomponent : component to be tested (default=’NE’)
- Param
mode : choose among ‘local’,’detrend’,’detrend_seasonal’ to test significance
- Param
verbose : verbose mode
- Returns
: True if significant, else False
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test_offsets
(verbose=False, debug=True, window_length=None)¶ - Test the offset:
delete the small offset (1mm for East/North, 2mm for Up)
then make a F ratio test
re-check to delete the small offsets
-
to_pandas_df
()¶ - Parameters
self –
- Returns
pandas DataFrame
- Note
uncertainties are not imported.
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trajectory
(model_type, offset_dates=[], eq_dates=[], H_fix={}, H_constraints={}, H_bounds={}, component='NEU', verbose=False)¶ Calculates the parameters of a (non-linear) trajectory model for a Geodetic Time Series. The trajectory model is:
y(t) =
trend : trend_cst + trend * ( t - t0 ) +
annual: a_annual * cos( 2*pi + phi_annual ) +
semi-annual: a_semi_annual * cos( 2*pi + phi_semi_annual ) +
offset : Heaviside( t - t_offset_i ) * offset_i +
post-seismic_deformation as decaying log (psd_log): psd_eq_i * np.log( 1 + Heaveside( t - eq_i )/tau_i )
- Parameters
model_type – string made of the key-word the parameters to be estimated.
Key-word parameters are
‘trend’,’annual’,’semi-annual’,’seasonal’,’offset’,’psd_log’.
‘trend-seasonal-offset-psd_log’ will do the full trajectory model.
- Parameters
offset_dates – a list of offset_dates in decimal year
eq_dates – a list of earthquake dates for which post-seismic deformation (psd_log) will be estimated
H_fix – a dictionary including the name of the parameter to be hold fixed and the value.
For instance to impose the co-seismic offset (North-East-Up) and relaxation time of 100 days for the first earthquake use:
H_fix = { ‘psd_log_offset_00’:[10., 15., 0.] , ‘psd_log_tau_00’:[100., 100., 100.]}
- Parameters
H_constraints – a dictionary including the name of the parameter to be constrained.
For instance to impose a 50 days constraints around 500 days on the relaxation time of the second earthquake for all NEU components use: H_fix = { ‘psd_log_tau_01’:[[500.,50], [500.,50] , [500.,50]]}
- Parameters
H_bounds – a dictionary including the bounds.
For instance to impose a relaxation time for the third earthquake to be in the range of 2 to 3 years, for all NEU components use: H_bounds = { ‘psd_log_tau_02’:[[2*365.,3*365.], [[2*365.,3*365.] , [[2*365.,3*365.]]}
- Parameters
component – string , component for which the trajectory model will be estimated.
verbose – verbose mode
- Note
Unlike most pyacs.gts functions, trajectory returns 4 elements: the results as a dictionary, the model Gts,
the residual Gts and a Gts with model predictions at every day.
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tv_l2_filter
(lbda, in_place=False, verbose=True)¶ Gts filter using a L2 total variation filter. The signal is assumed to be detrended.
- Parameters
lbda – lambda parameter
in_place – if True then replace the current time series
verbose – boolean, verbose mode
- Returns
the filtered time series
- Reference
-
vondrak
(fc, in_place=False, verbose=True, component='NEU')¶ returned a filtered Gts using a Vondrak filter
- Parameters
fc – cutoff frequence in cycle per year
in_place – if True then replace the current time series
verbose – boolean, verbose mode
- Returns
the filtered time series
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wiener
(in_place=False, verbose=True, my_size=15, noise=None)¶ returns a filtered time series using scipy.signal.wiener
See documentation for the filter parameters.
- Parameters
in_place – if True then replace the current time series
verbose – boolean, verbose mode
- Returns
the filtered time series
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write_cats
(idir, offsets_dates=None, add_key='')¶ Writes a file for a cats analysis if offsets_dates is not None then offsets are added at the beginning of the file
-
write_mb_file
(idir, add_key='')¶
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write_pos
(idir, add_key='', force=None, verbose=False)¶ Write a time series in GAMIT/GLOBK PBO pos format
- Parameters
idir – output directory
add_key – if not blank then the output pos file will be CODE_add_key.pos, CODE.pos otherwise.
force – set force to ‘data’ or ‘data_xyz’ to force pos to be written from .data or .data_xyz
- Note1
default behaviour (force = None) if data and data_xyz are not None, then print them independently if there are data only, then uses X0,Y0,Z0 to write data_xyz if there are data_xyz only, recreate data and write it
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wrms
()¶ Return the wrms
- Return wrms
return(np.array([wrms_n,wrms_e,wrms_up]))
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xyz2neu
(corr=False, ref_xyz=None, verbose=False)¶ populates neu (data) using xyz (data_xyz) lon, lat and h will also be set.
- Parameters
corr – if True, then standard deviation and correlations will also be calculated
ref_xyz – [X,Y,Z] corresponding to the 0 of the local NEU frame. If not provided, the first position is used as a reference
verbose – verbose mode
- Note
this method is always in place
-