From 9c7ca04468a349237d0536e0587e7262700a5891 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Peter=20L=C3=BCnenschlo=C3=9F?= <peter.luenenschloss@ufz.de>
Date: Tue, 17 Jan 2023 20:59:05 +0100
Subject: [PATCH] Inter limit fix
---
CHANGELOG.md | 1 +
saqc/funcs/interpolation.py | 47 +++++-----
saqc/lib/ts_operators.py | 154 ++++++++++++++++++++-------------
tests/lib/test_ts_operators.py | 67 +++++++++++++-
4 files changed, 188 insertions(+), 81 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index f7334504d..6731aa25e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -29,6 +29,7 @@ SPDX-License-Identifier: GPL-3.0-or-later
### Removed
- python 3.7 support
### Fixed
+- Error for interpolations with limits set to be greater than 2 (`interpolateNANs`)
## [2.2.1](https://git.ufz.de/rdm-software/saqc/-/tags/v2.2.1) - 2022-10-29
[List of commits](https://git.ufz.de/rdm-software/saqc/-/compare/v2.2.0...v2.2.1)
diff --git a/saqc/funcs/interpolation.py b/saqc/funcs/interpolation.py
index e0907e261..d4b16bbd1 100644
--- a/saqc/funcs/interpolation.py
+++ b/saqc/funcs/interpolation.py
@@ -144,12 +144,12 @@ class InterpolationMixin:
method: _SUPPORTED_METHODS,
order: int = 2,
limit: int | None = None,
- downgrade: bool = False,
+ extrapolate: Literal["forward", "backward", "both"] = None,
flag: float = UNFLAGGED,
**kwargs,
) -> "SaQC":
"""
- Function to interpolate nan values in the data.
+ Function to interpolate nan values in data.
There are available all the interpolation methods from the pandas.interpolate method and they are applicable by
the very same key words, that you would pass to the ``pd.Series.interpolate``'s method parameter.
@@ -167,8 +167,11 @@ class InterpolationMixin:
If there your selected interpolation method can be performed at different 'orders' - here you pass the desired
order.
- limit : int, optional
- Maximum number of consecutive `nan` values to fill. Must be greater than 0.
+ limit : int or str, default None
+ Upper limit of missing index values (with respect to `freq`) to fill. The limit can either be expressed
+ as the number of consecutive missing values (integer) or temporal extension of the gaps to be filled
+ (Offset String).
+ If `None` is passed, no Limit is set.
flag : float or None, default UNFLAGGED
Flag that is set for interpolated values. If ``None``, no flags are set at all.
@@ -186,8 +189,8 @@ class InterpolationMixin:
self._data[field],
method,
order=order,
- inter_limit=limit,
- downgrade_interpolation=downgrade,
+ gap_limit=limit,
+ extrapolate=extrapolate,
)
interpolated = self._data[field].isna() & inter_data.notna()
@@ -209,15 +212,12 @@ class InterpolationMixin:
freq: str,
method: _SUPPORTED_METHODS,
order: int = 2,
- limit: int | None = None,
- downgrade: bool = False,
+ limit: int | None = 2,
+ extrapolate: Literal["forward", "backward", "both"] = None,
**kwargs,
) -> "SaQC":
"""
- Function to interpolate the data at regular (equidistant) timestamps (or Grid points).
-
- Note, that the interpolation will only be calculated, for grid timestamps that have a preceding AND a succeeding
- valid data value within "freq" range.
+ Function to interpolate the data at regular (äquidistant) timestamps (or Grid points).
Parameters
----------
@@ -233,17 +233,22 @@ class InterpolationMixin:
The interpolation method you want to apply.
order : int, default 2
- If there your selected interpolation method can be performed at different 'orders' - here you pass the desired
+ If your selected interpolation method can be performed at different 'orders' - here you pass the desired
order.
limit : int, optional
- Maximum number of missing index values (with respect to `freq`) to fill. Must be greater than 0.
+ Upper limit of missing index values (with respect to `freq`) to fill. The limit can either be expressed
+ as the number of consecutive missing values (integer) or temporal extension of the gaps to be filled
+ (Offset String).
+ If `None` is passed, no Limit is set.
- downgrade : bool, default False
- If `True` and the interpolation can not be performed at current order, retry with a lower order.
- This can happen, because the chosen ``method`` does not support the passed ``order``, or
- simply because not enough values are present in a interval.
+ extraplate : {'forward', 'backward', 'both'}, default None
+ Use parameter to perform extrapolation instead of interpolation onto the trailing and/or leading chunks of
+ NaN values in data series.
+ * 'None' (default) - perform interpolation
+ * 'forward'/'backward' - perform forward/backward extrapolation
+ * 'both' - perform forward and backward extrapolation
Returns
-------
@@ -281,8 +286,8 @@ class InterpolationMixin:
data=datcol,
method=method,
order=order,
- inter_limit=limit,
- downgrade_interpolation=downgrade,
+ gap_limit=limit,
+ extrapolate=extrapolate,
)
# override falsely interpolated values:
@@ -305,7 +310,7 @@ class InterpolationMixin:
"method": method,
"order": order,
"limit": limit,
- "downgrade": downgrade,
+ "extrapolate": extrapolate,
**kwargs,
},
}
diff --git a/saqc/lib/ts_operators.py b/saqc/lib/ts_operators.py
index e63eb8b74..0c5533ec0 100644
--- a/saqc/lib/ts_operators.py
+++ b/saqc/lib/ts_operators.py
@@ -276,91 +276,129 @@ def meanQC(data, max_nan_total=np.inf, max_nan_consec=np.inf):
)
-def interpolateNANs(
- data, method, order=2, inter_limit=2, downgrade_interpolation=False
+def _interpolWrapper(
+ x, order=1, method="time", limit_area="inside", limit_direction=None
):
+ """
+ Function that automatically modifies the interpolation level or returns uninterpolated
+ input data if the data configuration breaks the interpolation method at the selected degree.
+ """
+
+ min_vals_dict = {
+ "nearest": 2,
+ "slinear": 2,
+ "quadratic": 3,
+ "cubic": 4,
+ "spline": order + 1,
+ "polynomial": order + 1,
+ "piecewise_polynomial": 2,
+ "pchip": 2,
+ "akima": 2,
+ "cubicspline": 2,
+ }
+ min_vals = min_vals_dict.get(method, 0)
+
+ if (x.size < 3) | (x.count() < min_vals):
+ return x
+ else:
+ return x.interpolate(
+ method=method,
+ order=order,
+ limit_area=limit_area,
+ limit_direction=limit_direction,
+ )
+
+
+def interpolateNANs(data, method, order=2, gap_limit=2, extrapolate=None):
"""
The function interpolates nan-values (and nan-grids) in timeseries data. It can
be passed all the method keywords from the pd.Series.interpolate method and will
than apply this very methods. Note, that the limit keyword really restricts
- the interpolation to chunks, not containing more than "limit" nan entries (
+ the interpolation to gaps, not containing more than "limit" nan entries (
thereby not being identical to the "limit" keyword of pd.Series.interpolate).
:param data: pd.Series or np.array. The data series to be interpolated
:param method: String. Method keyword designating interpolation method to use.
:param order: Integer. If your desired interpolation method needs an order to be passed -
here you pass it.
- :param inter_limit: Integer. Default = 2. Limit up to which consecutive nan - values in the data get
- replaced by interpolation.
+ :param gap_limit: Integer or Offset String. Default = 2.
+ Number up to which consecutive nan - values in the data get
+ replaced by interpolated values.
Its default value suits an interpolation that only will apply to points of an
inserted frequency grid. (regularization by interpolation)
- Gaps wider than "limit" will NOT be interpolated at all.
- :param downgrade_interpolation: Boolean. Default False. If True:
+ Gaps of size "limit" or greater will NOT be interpolated at all.
+ :param extrapolate: Str or None. Default None. If True:
If a data chunk not contains enough values for interpolation of the order "order",
the highest order possible will be selected for that chunks interpolation.
:return:
"""
- inter_limit = int(inter_limit or len(data) + 1)
- data = pd.Series(data, copy=True)
- gap_mask = data.isna().rolling(inter_limit, min_periods=0).sum() != inter_limit
- if inter_limit == 2:
- gap_mask = gap_mask & gap_mask.shift(-1, fill_value=True)
+ # helper variable for checking numerical value of gap limit, if its a numeric value (to avoid comparison to str)
+ gap_check = np.nan if isinstance(gap_limit, str) else gap_limit
+ data = pd.Series(data, copy=True)
+ limit_area = "inside" if not extrapolate else "outside"
+ if gap_check is None:
+ # if there is actually no limit set to the gaps to-be interpolated, generate a dummy mask for the gaps
+ gap_mask = pd.Series(True, index=data.index, name=data.name)
else:
- gap_mask = (
- gap_mask.replace(True, np.nan)
- .fillna(method="bfill", limit=inter_limit)
- .replace(np.nan, True)
- .astype(bool)
- )
+ if gap_check < 2:
+ # breaks execution down the line and is thus catched here since it basically means "do nothing"
+ return data
+ else:
+ # if there is a limit to the gaps to be interpolated, generate a mask that evaluates to False at the right
+ # side of each too-large gap with a rolling.sum combo
+ gap_mask = data.rolling(gap_limit, min_periods=0).count() > 0
+
+ # correction for initial gap
+ if isinstance(gap_limit, int):
+ gap_mask.iloc[:gap_limit] = True
+
+ if gap_limit == 2:
+ # for the common case of gap_limit=2 (default "harmonisation"), we efficiently back propagate the False
+ # value to fill the whole too-large gap by a shift and a conjunction.
+ gap_mask = gap_mask & gap_mask.shift(-1, fill_value=True)
+ else:
+ # If the gap_size is bigger we make a flip-rolling combo to backpropagate the False values
+ gap_mask = ~(
+ (~gap_mask[::-1]).rolling(gap_limit, min_periods=0).sum() > 0
+ )[::-1]
+ # memorizing the index for later reindexing
pre_index = data.index
-
- if data[gap_mask].empty:
+ # drop the gaps that are too large with regard to the gap_limit from the data-to-be interpolated
+ data = data[gap_mask]
+ if data.empty:
return data
- else:
- data = data[gap_mask]
-
if method in ["linear", "time"]:
-
+ # in the case of linear interpolation, not much can go wrong/break so this conditional branch has efficient
+ # finish by just calling pandas interpolation routine to fill the gaps remaining in the data:
data.interpolate(
- method=method, inplace=True, limit=inter_limit - 1, limit_area="inside"
+ method=method,
+ inplace=True,
+ limit_area=limit_area,
+ limit_direction=extrapolate,
)
else:
- dat_name = data.name
- gap_mask = (~gap_mask).cumsum()
- data = pd.merge(gap_mask, data, how="inner", left_index=True, right_index=True)
-
- def _interpolWrapper(x, wrap_order=order, wrap_method=method):
- if wrap_order < 0:
- return x
- elif x.count() > wrap_order:
- try:
- return x.interpolate(method=wrap_method, order=int(wrap_order))
- except (NotImplementedError, ValueError):
- warnings.warn(
- f"Interpolation with method {method} is not supported at order "
- f"{wrap_order}. and will be performed at order {wrap_order - 1}"
- )
- return _interpolWrapper(x, int(wrap_order - 1), wrap_method)
- elif x.size < 3:
- return x
- else:
- if downgrade_interpolation:
- return _interpolWrapper(x, int(x.count() - 1), wrap_method)
- else:
- return x
-
- data = data.groupby(data.columns[0]).transform(_interpolWrapper)
- # squeezing the 1-dimensional frame resulting from groupby for consistency
- # reasons
- data = data.squeeze(axis=1)
- data.name = dat_name
+ # if the method that is interpolated with, depends on not only the left and right border points of any gap,
+ # but includes more points, it has to be applied on any data chunk seperated by the too-big gaps individually.
+ # So we use the gap_mask to group the data into chunks and perform the interpolation on every chunk seperatly
+ # with the .transform method of the grouper.
+ gap_mask = (~gap_mask).cumsum()[data.index]
+ chunk_groups = data.groupby(by=gap_mask)
+ data = chunk_groups.transform(
+ _interpolWrapper,
+ **{
+ "order": order,
+ "method": method,
+ "limit_area": limit_area,
+ "limit_direction": extrapolate,
+ },
+ )
+ # finally reinsert the dropped data gaps
data = data.reindex(pre_index)
-
return data
@@ -599,10 +637,8 @@ def linearDriftModel(x, origin, target):
def linearInterpolation(data, inter_limit=2):
- return interpolateNANs(data, "time", inter_limit=inter_limit)
+ return interpolateNANs(data, "time", gap_limit=inter_limit)
def polynomialInterpolation(data, inter_limit=2, inter_order=2):
- return interpolateNANs(
- data, "polynomial", inter_limit=inter_limit, order=inter_order
- )
+ return interpolateNANs(data, "polynomial", gap_limit=inter_limit, order=inter_order)
diff --git a/tests/lib/test_ts_operators.py b/tests/lib/test_ts_operators.py
index f5f8b3ef2..c7288ce2e 100644
--- a/tests/lib/test_ts_operators.py
+++ b/tests/lib/test_ts_operators.py
@@ -1,13 +1,15 @@
# SPDX-FileCopyrightText: 2021 Helmholtz-Zentrum für Umweltforschung GmbH - UFZ
#
# SPDX-License-Identifier: GPL-3.0-or-later
+from __future__ import annotations
+
import numpy as np
import pandas as pd
import pytest
-from numpy.testing import assert_array_equal, assert_equal
from pandas.testing import assert_series_equal
import saqc.lib.ts_operators as tsops
+from saqc.lib.ts_operators import interpolateNANs
def test_butterFilter():
@@ -193,3 +195,66 @@ def test_rateOfChange(data, expected):
result = rateOfChange(data)
assert_series_equal(result, expected, check_names=False)
+
+
+@pytest.mark.parametrize(
+ "limit,extrapolate,data,expected",
+ [
+ (
+ 1,
+ None,
+ [np.nan, 0, np.nan, np.nan, np.nan, 4, np.nan],
+ [np.nan, 0, np.nan, np.nan, np.nan, 4, np.nan],
+ ),
+ (
+ 2,
+ "backward",
+ [np.nan, 0, np.nan, np.nan, np.nan, 4, np.nan],
+ [0, 0, np.nan, np.nan, np.nan, 4, np.nan],
+ ),
+ (
+ 2,
+ None,
+ [np.nan, 0, np.nan, np.nan, np.nan, 4, np.nan],
+ [np.nan, 0, np.nan, np.nan, np.nan, 4, np.nan],
+ ),
+ (
+ 3,
+ None,
+ [np.nan, 0, np.nan, np.nan, np.nan, 4, np.nan],
+ [np.nan, 0, np.nan, np.nan, np.nan, 4, np.nan],
+ ),
+ (
+ 3,
+ "forward",
+ [np.nan, 0, np.nan, np.nan, np.nan, 4, np.nan],
+ [np.nan, 0, np.nan, np.nan, np.nan, 4, 4],
+ ),
+ (
+ 4,
+ None,
+ [np.nan, 0, np.nan, np.nan, np.nan, 4, np.nan],
+ [np.nan, 0, 1, 2, 3, 4, np.nan],
+ ),
+ (
+ 4,
+ "both",
+ [np.nan, 0, np.nan, np.nan, np.nan, 4, np.nan],
+ [np.nan, 0, 1, 2, 3, 4, np.nan],
+ ),
+ (
+ None,
+ None,
+ [np.nan, 0, np.nan, np.nan, np.nan, 4, np.nan],
+ [np.nan, 0, 1, 2, 3, 4, np.nan],
+ ),
+ ],
+)
+def test_interpolatNANs(limit, extrapolate, data, expected):
+ got = interpolateNANs(
+ pd.Series(data), gap_limit=limit, method="linear", extrapolate=extrapolate
+ )
+ try:
+ assert got.equals(pd.Series(expected, dtype=float))
+ except AssertionError:
+ print("stop")
--
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