FunctionDescriptions.md

Implemented QC functions

range

Signature

range(min, max)

Parameters

parameter	data type	default value	description
min	float
max	float

Description

missing

Signature

missing(nodata=NaN)

Parameters

parameter	data type	default value	description
nodata	any	NaN	Value indicating missing values in the passed data

Description

The function flags those values in the the passed data series, that are associated with "missing" data. The missing data indicator (default: NaN), can be altered to any other value by passing this new value to the parameter nodata.

seasonalRange

Signature

sesonalRange(min, max, startmonth=1, endmonth=12, startday=1, endday=31)

Parameters

parameter	data type	default value	description
min	float
max	float
startmonth	integer	1
endmonth	integer	12
startday	integer	1
endday	integer	31

Description

clear

Signature

clear()

Parameters

parameter	data type	default value	description

Description

Remove all previously set flags.

force

Signature

force()

Parameters

parameter	data type	default value	description

Description

sliding_outlier

Signature

sliding_outlier(winsz="1h", dx="1h", count=1, deg=1, z=3.5, method="modZ")

Parameters

parameter	data type	default value	description
winsz	string	"1h"
dx	string	"1h"
count	integer	1
deg	integer	1"
z	float	3.5
method	string	"modZ"

Description

mad

Signature

mad(length, z=3.5, freq=None)

Parameters

parameter	data type	default value	description
length
z	float	3.5
freq		None

Description

Spikes_Basic

Signature

Spikes_Basic(thresh, tolerance, window_size)

Parameters

parameter	data type	default value	description
thresh	float		Minimum jump margin for spikes. See condition (1).
tolerance	float		Range of area, containing al "valid return values". See condition (2).
window_size	ftring		An offset string, denoting the maximal length of "spikish" value courses. See condition (3).

Description

A basic outlier test, that is designed to work for harmonized, as well as raw (not-harmonized) data.

The values

$x_{n}, x_{n+1}, .... , x_{n+k}$

of a passed timeseries

$x$

, are considered spikes, if:

1. $|x_{n-1} - x_{n + s}| >$
   thresh,
   $s \in \{0,1,2,...,k\}$

2. $|x_{n-1} - x_{n+k+1}| <$
   tolerance

3. $|y_{n-1} - y_{n+k+1}| <$
   window_size, with
   $y$
   , denoting the series of timestamps associated with
   $x$
   .

By this definition, spikes are values, that, after a jump of margin thresh(1), are keeping that new value level they jumped to, for a timespan smaller than window_size (3), and do then return to the initial value level - within a tolerance margin of tolerance (2).

Note, that this characterization of a "spike", not only includes one-value outliers, but also plateau-ish value courses.

The implementation is a time-window based version of an outlier test from the UFZ Python library, that can be found here.

Spikes_SpektrumBased

Signature

Spikes_SpektrumBased(raise_factor=0.15, dev_cont_factor=0.2,
                     noise_barrier=1, noise_window_size="12h", noise_statistic="CoVar",
                     smooth_poly_order=2, filter_window_size=None)

Parameters

parameter	data type	default value	description
raise_factor	float	0.15	Minimum change margin for a datapoint to become a candidate for a spike. See condition (1).
dev_cont_factor	float	0.2	See condition (2).
noise_barrier	float	1	Upper bound for noisyness of data surrounding potential spikes. See condition (3).
noise_window_range	string	"12h"	Any offset string. Determines the range of the timewindow of the "surrounding" data of a potential spike. See condition (3).
noise_statistic	string	"CoVar"	Operator to calculate noisyness of data, surrounding potential spike. Either "Covar" (=Coefficient od Variation) or "rvar" (=relative Variance).
smooth_poly_order	integer	2	Order of the polynomial fit, applied for smoothing
filter_window_size	Nonetype or string	None	Options: - None - any offset string Controlls the range of the smoothing window applied with the Savitsky-Golay filter. If None is passed (default), the window size will be two times the sampling rate. (Thus, covering 3 values.) If you are not very well knowing what you are doing - do not change that value. Broader window sizes caused unexpected results during testing phase.

Description

The function detects and flags spikes in input data series by evaluating the the timeseries' derivatives and applying some conditions to them.

NOTE, that the dataseries-to-be flagged is supposed to be harmonized to an equadistant frequencie grid.

A datapoint

$x_k$

of a dataseries

$x$

, is considered a spike, if:

1. The quotient to its preceeding datapoint exceeds a certain bound:
   • $|\frac{x_k}{x_{k-1}}| > 1 +$
     raise_factor, or:
   • $|\frac{x_k}{x_{k-1}}| < 1 -$
     raise_factor
2. The quotient of the datas second derivate
   $x''$
   , at the preceeding and subsequent timestamps is close enough to 1:
   • $|\frac{x''_{k-1}}{x''_{k+1}} | > 1 -$
     dev_cont_factor, and
   • $|\frac{x''_{k-1}}{x''_{k+1}} | < 1 +$
     dev_cont_factor
3. The dataset,
   $X_k$
   , surrounding
   $x_{k}$
   , within noise_window_range range, but excluding
   $x_{k}$
   , is not too noisy. Wheras the noisyness gets measured by noise_statistic:
   • noise_statistic
     $(X_k) <$
     noise_barrier

NOTE, that the derivative is calculated after applying a savitsky-golay filter to

$x$

.

This Function is a generalization of the Spectrum based Spike flagging mechanism as presented in:

Dorigo, W. et al: Global Automated Quality Control of In Situ Soil Moisture Data from the international Soil Moisture Network. 2013. Vadoze Zone J. doi:10.2136/vzj2012.0097.

constant

Signature

constant(eps, length, thmin=None)

Parameters

parameter	data type	default value	description
eps
length
thmin		None

Description

constants_varianceBased

Signature

constants_varianceBased(plateau_window_min="12h", plateau_var_limit=0.0005,
                        var_total_nans=Inf, var_consec_nans=Inf)

Parameters

parameter	data type	default value	description
plateau_window_min	string		Options - any offset string Minimum barrier for the duration, values have to be continouos to be plateau canditaes. See condition (1).
plateau_var_limit	float	0.0005	Barrier, the variance of a group of values must not exceed to be flagged a plateau. See condition (2).
var_total_nans	integer	Inf	Maximum number of nan values allowed, for a calculated variance to be valid. (Default skips the condition.)
var_consec_nans	integer	Inf	Maximum number of consecutive nan values allowed, for a calculated variance to be valid. (Default skips the condition.)

Description

Function flags plateaus/series of constant values. Any set of consecutive values

$x_k,..., x_{k+n}$

of a timeseries

$x$

is flagged, if:

1. $n >$
   plateau_window_min
2. $\sigma(x_k,..., x_{k+n})$
   < plateau_var_limit

NOTE, that the dataseries-to-be flagged is supposed to be harmonized to an equadistant frequency grid.

NOTE, that when var_total_nans or var_consec_nans are set to a value < Inf , plateaus that can not be calculated the variance of, due to missing values, will never be flagged. (Test not applicable rule.)

constant

Signature

soilMoisture_plateaus(plateau_window_min="12h", plateau_var_limit=0.0005,
                      rainfall_window_range="12h", var_total_nans=np.inf, 
                      var_consec_nans=np.inf, derivative_max_lb=0.0025, 
                      derivative_min_ub=0, data_max_tolerance=0.95, 
                      filter_window_size=None, smooth_poly_order=2, **kwargs)

Parameters

parameter	data type	default value	description
plateau_window_min	string	"12h"	Options - any offset string Minimum barrier for the duration, values have to be continouos to be plateau canditaes. See condition (1).
plateau_var_limit	float	0.0005	Barrier, the variance of a group of values must not exceed to be flagged a plateau. See condition (2).
rainfall_range	string	"12h"	An Offset string. See condition (3) and (4)
var_total_nans	int or 'inf'	np.inf	Maximum number of nan values allowed, for a calculated variance to be valid. (Default skips the condition.)
var_consec_nans	int or 'inf'	np.inf	Maximum number of consecutive nan values allowed, for a calculated variance to be valid. (Default skips the condition.)
derivative_max_lb	float	0.0025	Lower bound for the second derivatives maximum in rainfall_range range. See condition (3)
derivative_min_ub	float	0	Upper bound for the second derivatives minimum in rainfall_range range. See condition (4)
data_max_tolerance	flaot	0.95	Factor for data max barrier of condition (5).
filter_window_size	Nonetype or string	None	Options: - None - any offset string Controlls the range of the smoothing window applied with the Savitsky-Golay filter. If None is passed (default), the window size will be two times the sampling rate. (Thus, covering 3 values.) If you are not very well knowing what you are doing - do not change that value. Broader window sizes caused unexpected results during testing phase.
smooth_poly_order	int	2	Order of the polynomial used for fitting while smoothing.

Description

NOTE, that the dataseries-to-be flagged is supposed to be harmonized to an equadistant frequency grid.

The function represents a stricter version of the constant_varianceBased test from the constants detection library. The added constraints for values to be flagged (3)-(5), are designed to match the special case of constant value courses of soil moisture meassurements and basically check the derivative for being determined by preceeding rainfall events ((3) and (4)), as well as the plateau for being sufficiently high in value (5).

Any set of consecutive values

$x_k,..., x_{k+n}$

, of a timeseries

$x$

is flagged, if:

1. $n >$
   plateau_window_min
2. $\sigma(x_k, x_{k+1},..., x_{k+n}) <$
   plateau_var_limit
3. $\max(x'_{k-n-s}, x'_{k-n-s+1},..., x'_{k-n+s}) \geq$
   derivative_max_lb, with
   $s$
   denoting periods per rainfall_range
4. $\min(x'_{k-n-s}, x'_{k-n-s+1},..., x'_{k-n+s}) \leq$
   derivative_min_ub, with
   $s$
   denoting periods per rainfall_range
5. $\mu(x_k, x_{k+1},..., x_{k+n}) < \max(x) \times$
   plateau_var_limit

This Function is an implementation of the soil temperature based Soil Moisture flagging, as presented in:

Dorigo, W. et al: Global Automated Quality Control of In Situ Soil Moisture Data from the international Soil Moisture Network. 2013. Vadoze Zone J. doi:10.2136/vzj2012.0097.

All parameters default to the values, suggested in this publication.

SoilMoistureSpikes

Signature

SoilMoistureSpikes(filter_window_size="3h", raise_factor=0.15, dev_cont_factor=0.2,
                   noise_barrier=1, noise_window_size="12h", noise_statistic="CoVar")

Parameters

parameter	data type	default value	description
filter_window_size	string	"3h"
raise_factor	float	0.15
dev_cont_factor	float	0.2
noise_barrier	integer	1
noise_window_size	string	"12h"
noise_statistic	string	"CoVar"

Description

The Function is just a wrapper around flagSpikes_spektrumBased, from the spike detection library and performs a call to this function with a parameter set, referring to:

Dorigo, W. et al: Global Automated Quality Control of In Situ Soil Moisture Data from the international Soil Moisture Network. 2013. Vadoze Zone J. doi:10.2136/vzj2012.0097.

SoilMoistureBreaks

Signature

SoilMoistureBreaks(diff_method="raw", filter_window_size="3h",
                   rel_change_rate_min=0.1, abs_change_min=0.01, first_der_factor=10,
                   first_der_window_size="12h", scnd_der_ratio_margin_1=0.05,
                   scnd_der_ratio_margin_2=10, smooth_poly_order=2)

Parameters

parameter	data type	default value	description
diff_method	string	"raw"
filter_window_size	string	"3h"
rel_change_rate_min	float	0.1
abs_change_min	float	0.01
first_der_factor	integer	10
first_der_window_size	string	"12h"
scnd_der_ratio_margin_1	float	0.05
scnd_der_ratio_margin_2	float	10.0
smooth_poly_order	integer	2

Description

The Function is just a wrapper around flagBreaks_spektrumBased, from the breaks detection library and performs a call to this function with a parameter set, referring to:

Dorigo, W. et al: Global Automated Quality Control of In Situ Soil Moisture Data from the international Soil Moisture Network. 2013. Vadoze Zone J. doi:10.2136/vzj2012.0097.

SoilMoistureByFrost

Signature

SoilMoistureByFrost(soil_temp_reference, tolerated_deviation="1h", frost_level=0)

Parameters

parameter	data type	default value	description
soil_temp_reference	string		A string, denoting the fields name in data, that holds the data series of soil temperature values, the to-be-flagged values shall be checked against.
tolerated_deviation	string	"1h"	An offset string, denoting the maximal temporal deviation, the soil frost states timestamp is allowed to have, relative to the data point to be flagged.
frost_level	integer	0	Value level, the flagger shall check against, when evaluating soil frost level.

Description

The function flags Soil moisture measurements by evaluating the soil-frost-level in the moment of measurement (+/- tolerated deviation). Soil temperatures below "frost_level" are regarded as denoting frozen soil state and result in the checked soil moisture value to get flagged.

This Function is an implementation of the soil temperature based Soil Moisture flagging, as presented in:

Dorigo, W. et al: Global Automated Quality Control of In Situ Soil Moisture Data from the international Soil Moisture Network. 2013. Vadoze Zone J. doi:10.2136/vzj2012.0097.

All parameters default to the values, suggested in this publication.

SoilMoistureByPrecipitation

Signature

SoilMoistureByPrecipitation(prec_reference, sensor_meas_depth=0,
                            sensor_accuracy=0, soil_porosity=0,
                            std_factor=2, std_factor_range="24h"
                            ignore_missing=False)

Parameters

parameter	data type	default value	description
prec_reference	string		A string, denoting the fields name in data, that holds the data series of precipitation values, the to-be-flagged values shall be checked against.
sensor_meas_depth	integer	0	Depth of the soil moisture sensor in meter.
sensor_accuracy	integer	0	Soil moisture sensor accuracy in $\frac{m^3}{m^{-3}}$
soil_porosity	integer	0	Porosoty of the soil, surrounding the soil moisture sensor
std_factor	integer	2	See condition (2)
std_factor_range	string	"24h"	See condition (2)
ignore_missing	bool	False	If True, the variance of condition (2), will also be calculated if there is a value missing in the time window. Selcting Flase (default) results in values that succeed a time window containing a missing value never being flagged (test not applicable rule)

Description

Function flags Soil moisture measurements by flagging moisture rises that do not follow up a sufficient precipitation event. If measurement depth, sensor accuracy of the soil moisture sensor and the porosity of the surrounding soil is passed to the function, an inferior level of precipitation, that has to preceed a significant moisture raise within 24 hours, can be estimated. If those values are not delivered, this inferior bound is set to zero. In that case, any non zero precipitation count will justify any soil moisture raise.

Thus, a data point

$x_k$

with sampling rate

$f$

is flagged an invalid soil moisture raise, if:

1. The value to be flagged has to signify a rise. This means, for the quotient
   $s =$
   (raise_reference /
   $f$
   ):
   • $x_k > x_{k-s}$
2. The rise must be sufficient. Meassured in terms of the standart deviation
   $V$
   , of the values in the preceeding std_factor_range - window. This means, with
   $h =$
   std_factor_range /
   $f$
   :
   • $x_k - x_{k-s} >$
     std_factor
     $\times V(x_{t-h},...,x_k{k})$
3. Depending on some sensor specifications, there can be calculated a bound
   $>0$
   , the rainfall has to exceed to justify the eventual soil moisture raise. For the series of the precipitation meassurements
   $y$
   , and the quotient
   $j =$
   "24h" /
   $f$
   , this means:
   • $y_{k-j} + y_{k-j+1} + ... + y_{k} <$
     sensor_meas_depth
     $\times$
     sensor_accuracy \times soil_porosity

Function flags Soil moisture measurements by flagging moisture rises that do not follow up a sufficient precipitation event. If measurement depth, sensor accuracy of the soil moisture sensor and the porosity of the surrounding soil is passed to the function, an inferior level of precipitation, that has to preceed a significant moisture raise within 24 hours, can be estimated. If those values are not delivered, this inferior bound is set to zero. In that case, any non zero precipitation count will justify any soil moisture raise.

This Function is an implementation of the precipitation based Soil Moisture flagging, as presented in:

Dorigo, W. et al: Global Automated Quality Control of In Situ Soil Moisture Data from the international Soil Moisture Network. 2013. Vadoze Zone J. doi:10.2136/vzj2012.0097.

All parameters default to the values, suggested in this publication.

Breaks_SpektrumBased

Signature

Breaks_SpektrumBased(rel_change_min=0.1, abs_change_min=0.01, first_der_factor=10,
                     first_der_window_size="12h", scnd_der_ratio_margin_1=0.05,
                     scnd_der_ratio_margin_2=10, smooth_poly_order=2,
                     diff_method="raw", filter_window_size="3h")

Parameters

parameter	data type	default value	description
rel_change_rate_min	float	0.1	Lower bound for the relative difference, a value has to have to its preceeding value, to be a candidate for being break-flagged. See condition (2).
abs_change_min	float	0.01	Lower bound for the absolute difference, a value has to have to its preceeding value, to be a candidate for being break-flagged. See condition (1).
first_der_factor	float	10	Factor of the second derivates "arithmetic middle bound". See condition (3).
first_der_window_size	string	"12h"	Options: - any offset String Determining the size of the window, covering all the values included in the the arithmetic middle calculation of condition (3).
scnd_der_ratio_margin_1	float	0.05	Range of the area, covering all the values of the second derivatives quotient, that are regarded "sufficiently close to 1" for signifying a break. See condition (5).
scnd_der_ratio_margin_2	float	10.0	Lower bound for the break succeeding second derivatives quotients. See condition (5).
smooth_poly_order	integer	2	When calculating derivatives from smoothed timeseries (diff_method="savgol"), this value gives the order of the fitting polynomial calculated in the smoothing process.
diff_method	string	`"savgol"	Options: - "savgol" - "raw" Select "raw", to skip smoothing before differenciation.
filter_window_size	Nonetype or string	None	Options: - None - any offset string Controlls the range of the smoothing window applied with the Savitsky-Golay filter. If None is passed (default), the window size will be two times the sampling rate. (Thus, covering 3 values.) If you are not very well knowing what you are doing - do not change that value. Broader window sizes caused unexpected results during testing phase.

Description

The function flags breaks (jumps/drops) in input measurement series by evaluating its derivatives.

NOTE, that the dataseries-to-be flagged is supposed to be harmonized to an equadistant frequencie grid.

NOTE, that the derivatives are calculated after applying a savitsky-golay filter to x.

A value x_k of a data series x, is flagged a break, if:

1. x_k represents a sufficient absolute jump in the course of data values:
   • |x_k - x_{k-1}| > abs_change_min
2. x_k represents a sufficient relative jump in the course of data values:
   • |\frac{x_k - x_{k-1}}{x_k}| > rel_change_min
3. Let X_k be the set of all values that lie within a first_der_window_range range around x_k. Then, for its arithmetic mean \bar{X_k}, following equation has to hold:
   • |x'_k| > first_der_factor \times \bar{X_k}
4. The second derivations quatients are "sufficiently equalling 1":
   • 1 - scnd_der_ratio_margin_1 < |\frac{x''_{k-1}}{x_{k''}}| < 1 + scnd_der_ratio_margin_1
5. The the succeeding second derivatives values quotient has to be sufficiently high:
   • |\frac{x''_{k}}{x''_{k+1}}| > scnd_der_ratio_margin_2

This Function is a generalization of the Spectrum based Spike flagging mechanism as presented in:

Dorigo,W. et al.: Global Automated Quality Control of In Situ Soil Moisture Data from the international Soil Moisture Network. 2013. Vadoze Zone J. doi:10.2136/vzj2012.0097.

machinelearning

Signature

machinelearning(references, window_values, window_flags, path)

Parameters

parameter	data type	default value	description
references	string or list of strings		the fieldnames of the data series that should be used as reference variables
window_values	integer		Window size that is used to derive the gradients of both the field- and reference-series inside the moving window
window_flags	integer		Window size that is used to count the surrounding automatic flags that have been set before
path	string		Path to the respective model object, i.e. its name and the respective value of the grouping variable. e.g. "models/model_0.2.pkl"

Description

This Function uses pre-trained machine-learning model objects for flagging. This requires training a model by use of the training script provided. For flagging, inputs to the model are the data of the variable of interest, data of reference variables and the automatic flags that were assigned by other tests inside SaQC. Internally, context information for each point is gathered in form of moving windows. The size of the moving windows for counting of the surrounding automatic flags and for calculation of gradients in the data is specified by the user during model training. For the model to work, the parameters 'references', 'window_values' and 'window_flags' have to be set to the same values as during training. For a more detailed description of the modeling aproach see the training script.