diff --git a/mlair/configuration/defaults.py b/mlair/configuration/defaults.py
index 85cf433427655484f1a29be562245144ae6c9e07..51d4beafbbc0b346331db80567946c3acc702b8e 100644
--- a/mlair/configuration/defaults.py
+++ b/mlair/configuration/defaults.py
@@ -1,6 +1,7 @@
__author__ = "Lukas Leufen"
__date__ = '2020-06-25'
+from mlair.helpers.statistics import TransformationClass
DEFAULT_STATIONS = ['DEBW107', 'DEBY081', 'DEBW013', 'DEBW076', 'DEBW087']
DEFAULT_VAR_ALL_DICT = {'o3': 'dma8eu', 'relhum': 'average_values', 'temp': 'maximum', 'u': 'average_values',
@@ -13,8 +14,7 @@ DEFAULT_START = "1997-01-01"
DEFAULT_END = "2017-12-31"
DEFAULT_WINDOW_HISTORY_SIZE = 13
DEFAULT_OVERWRITE_LOCAL_DATA = False
-# DEFAULT_TRANSFORMATION = {"scope": "data", "method": "standardise", "mean": "estimate"}
-DEFAULT_TRANSFORMATION = {"scope": "data", "method": "standardise"}
+DEFAULT_TRANSFORMATION = TransformationClass(inputs_method="standardise", targets_method="standardise")
DEFAULT_HPC_LOGIN_LIST = ["ju", "hdfmll"] # ju[wels} #hdfmll(ogin)
DEFAULT_HPC_HOST_LIST = ["jw", "hdfmlc"] # first part of node names for Juwels (jw[comp], hdfmlc(ompute).
DEFAULT_CREATE_NEW_MODEL = True
diff --git a/mlair/data_handler/data_handler_single_station.py b/mlair/data_handler/data_handler_single_station.py
index e4a3f857a01f3f8464fe102a020ba5ee82543d95..60ee28f42acb2a5b29c64dfbec8a1b359f56bf77 100644
--- a/mlair/data_handler/data_handler_single_station.py
+++ b/mlair/data_handler/data_handler_single_station.py
@@ -3,6 +3,7 @@
__author__ = 'Lukas Leufen, Felix Kleinert'
__date__ = '2020-07-20'
+import copy
import datetime as dt
import logging
import os
@@ -53,7 +54,8 @@ class DataHandlerSingleStation(AbstractDataHandler):
self.station = helpers.to_list(station)
self.path = os.path.abspath(data_path)
self.statistics_per_var = statistics_per_var
- self.transformation = self.setup_transformation(transformation)
+ self.do_transformation = transformation is not None
+ self.input_data, self.target_data = self.setup_transformation(transformation)
self.station_type = station_type
self.network = network
@@ -74,20 +76,13 @@ class DataHandlerSingleStation(AbstractDataHandler):
self.end = end
# internal
- self.data: xr.DataArray = None
+ self._data: xr.DataArray = None # loaded raw data
self.meta = None
self.variables = list(statistics_per_var.keys()) if variables is None else variables
self.history = None
self.label = None
self.observation = None
- # internal for transformation
- self.mean = None
- self.std = None
- self.max = None
- self.min = None
- self._transform_method = None
-
# create samples
self.setup_samples()
@@ -100,7 +95,7 @@ class DataHandlerSingleStation(AbstractDataHandler):
@property
def shape(self):
- return self.data.shape, self.get_X().shape, self.get_Y().shape
+ return self._data.shape, self.get_X().shape, self.get_Y().shape
def __repr__(self):
return f"StationPrep(station={self.station}, data_path='{self.path}', " \
@@ -109,24 +104,7 @@ class DataHandlerSingleStation(AbstractDataHandler):
f"sampling='{self.sampling}', target_dim='{self.target_dim}', target_var='{self.target_var}', " \
f"time_dim='{self.time_dim}', window_history_size={self.window_history_size}, " \
f"window_lead_time={self.window_lead_time}, interpolation_limit={self.interpolation_limit}, " \
- f"interpolation_method='{self.interpolation_method}', overwrite_local_data={self.overwrite_local_data}, " \
- f"transformation={self._print_transformation_as_string})"
-
- @property
- def _print_transformation_as_string(self):
- str_name = ''
- if self.transformation is None:
- str_name = f'{None}'
- else:
- for k, v in self.transformation.items():
- if v is not None:
- try:
- v_pr = f"xr.DataArray.from_dict({v.to_dict()})"
- except AttributeError:
- v_pr = f"'{v}'"
- str_name += f"'{k}':{v_pr}, "
- str_name = f"{{{str_name}}}"
- return str_name
+ f"interpolation_method='{self.interpolation_method}', overwrite_local_data={self.overwrite_local_data})"
def get_transposed_history(self) -> xr.DataArray:
"""Return history.
@@ -153,18 +131,10 @@ class DataHandlerSingleStation(AbstractDataHandler):
return coords.rename(index={"station_lon": "lon", "station_lat": "lat"}).to_dict()[str(self)]
def call_transform(self, inverse=False):
- self.transform(dim=self.time_dim, method=self.transformation["method"],
- mean=self.transformation['mean'], std=self.transformation["std"],
- min_val=self.transformation["min"], max_val=self.transformation["max"],
- inverse=inverse
- )
-
- def set_transformation(self, transformation: dict):
- if self._transform_method is not None:
- self.call_transform(inverse=True)
- self.transformation = self.setup_transformation(transformation)
- self.call_transform()
- self.make_samples()
+ kwargs = helpers.remove_items(self.input_data.as_dict(), ["data"])
+ self.transform(self.input_data, dim=self.time_dim, inverse=inverse, **kwargs)
+ kwargs = helpers.remove_items(self.target_data.as_dict(), ["data"])
+ self.transform(self.target_data, dim=self.time_dim, inverse=inverse, **kwargs)
@TimeTrackingWrapper
def setup_samples(self):
@@ -173,10 +143,17 @@ class DataHandlerSingleStation(AbstractDataHandler):
"""
self.load_data()
self.interpolate(dim=self.time_dim, method=self.interpolation_method, limit=self.interpolation_limit)
- if self.transformation is not None:
+ self.set_inputs_and_targets()
+ if self.do_transformation:
self.call_transform()
self.make_samples()
+ def set_inputs_and_targets(self):
+ inputs = self._data.sel({self.target_dim: helpers.to_list(self.variables)})
+ targets = self._data.sel({self.target_dim: self.target_var})
+ self.input_data.data = inputs
+ self.target_data.data = targets
+
def make_samples(self):
self.make_history_window(self.target_dim, self.window_history_size, self.time_dim)
self.make_labels(self.target_dim, self.target_var, self.time_dim, self.window_lead_time)
@@ -217,7 +194,7 @@ class DataHandlerSingleStation(AbstractDataHandler):
logging.debug("loading finished")
# create slices and check for negative concentration.
data = self._slice_prep(data)
- self.data = self.check_for_negative_concentrations(data)
+ self._data = self.check_for_negative_concentrations(data)
def download_data_from_join(self, file_name: str, meta_file: str) -> [xr.DataArray, pd.DataFrame]:
"""
@@ -372,8 +349,8 @@ class DataHandlerSingleStation(AbstractDataHandler):
:return: xarray.DataArray
"""
- self.data = self.data.interpolate_na(dim=dim, method=method, limit=limit, use_coordinate=use_coordinate,
- **kwargs)
+ self._data = self._data.interpolate_na(dim=dim, method=method, limit=limit, use_coordinate=use_coordinate,
+ **kwargs)
def make_history_window(self, dim_name_of_inputs: str, window: int, dim_name_of_shift: str) -> None:
"""
@@ -390,7 +367,7 @@ class DataHandlerSingleStation(AbstractDataHandler):
:param dim_name_of_shift: Dimension along shift will be applied
"""
window = -abs(window)
- data = self.data.sel({dim_name_of_inputs: self.variables})
+ data = self.input_data.data
self.history = self.shift(data, dim_name_of_shift, window)
def make_labels(self, dim_name_of_target: str, target_var: str_or_list, dim_name_of_shift: str,
@@ -407,7 +384,7 @@ class DataHandlerSingleStation(AbstractDataHandler):
:param window: lead time of label
"""
window = abs(window)
- data = self.data.sel({dim_name_of_target: target_var})
+ data = self.target_data.data
self.label = self.shift(data, dim_name_of_shift, window)
def make_observation(self, dim_name_of_target: str, target_var: str_or_list, dim_name_of_shift: str) -> None:
@@ -420,7 +397,7 @@ class DataHandlerSingleStation(AbstractDataHandler):
:param target_var: Name of observation variable(s) in 'dimension'
:param dim_name_of_shift: Name of dimension on which xarray.DataArray.shift will be applied
"""
- data = self.data.sel({dim_name_of_target: target_var})
+ data = self.target_data.data
self.observation = self.shift(data, dim_name_of_shift, 0)
def remove_nan(self, dim: str) -> None:
@@ -495,7 +472,7 @@ class DataHandlerSingleStation(AbstractDataHandler):
return data
@staticmethod
- def setup_transformation(transformation: Dict):
+ def setup_transformation(transformation: statistics.TransformationClass):
"""
Set up transformation by extracting all relevant information.
@@ -561,23 +538,13 @@ class DataHandlerSingleStation(AbstractDataHandler):
"""
if transformation is None:
- return
- elif not isinstance(transformation, dict):
- raise TypeError(f"`transformation' must be either `None' or dict like e.g. `{{'method': 'standardise'}},"
- f" but transformation is of type {type(transformation)}.")
- transformation = transformation.copy()
- method = transformation.get("method", None)
- mean = transformation.get("mean", None)
- std = transformation.get("std", None)
- max_val = transformation.get("max", None)
- min_val = transformation.get("min", None)
-
- transformation["method"] = method
- transformation["mean"] = mean
- transformation["std"] = std
- transformation["max"] = max_val
- transformation["min"] = min_val
- return transformation
+ return statistics.DataClass(), statistics.DataClass()
+ elif isinstance(transformation, statistics.DataClass):
+ return transformation, transformation
+ elif isinstance(transformation, statistics.TransformationClass):
+ return copy.deepcopy(transformation.inputs), copy.deepcopy(transformation.targets)
+ else:
+ raise NotImplementedError("Cannot handle this.")
def load_data(self):
try:
@@ -586,8 +553,9 @@ class DataHandlerSingleStation(AbstractDataHandler):
self.download_data()
self.load_data()
- def transform(self, dim: Union[str, int] = 0, method: str = 'standardise', inverse: bool = False, mean=None,
- std=None, min_val=None, max_val=None) -> None:
+ def transform(self, data_class, dim: Union[str, int] = 0, transform_method: str = 'standardise',
+ inverse: bool = False, mean=None,
+ std=None, min=None, max=None) -> None:
"""
Transform data according to given transformation settings.
@@ -607,9 +575,9 @@ class DataHandlerSingleStation(AbstractDataHandler):
calculated over the data in this class instance.
:param std: Used for transformation (if required by 'method') based on external data. If 'None' the std is
calculated over the data in this class instance.
- :param min_val: Used for transformation (if required by 'method') based on external data. If 'None' min_val is
+ :param min: Used for transformation (if required by 'method') based on external data. If 'None' min_val is
extracted from the data in this class instance.
- :param max_val: Used for transformation (if required by 'method') based on external data. If 'None' max_val is
+ :param max: Used for transformation (if required by 'method') based on external data. If 'None' max_val is
extracted from the data in this class instance.
:return: xarray.DataArrays or pandas.DataFrames:
@@ -619,36 +587,37 @@ class DataHandlerSingleStation(AbstractDataHandler):
"""
def f(data):
- if method == 'standardise':
+ if transform_method == 'standardise':
return statistics.standardise(data, dim)
- elif method == 'centre':
+ elif transform_method == 'centre':
return statistics.centre(data, dim)
- elif method == 'normalise':
+ elif transform_method == 'normalise':
# use min/max of data or given min/max
raise NotImplementedError
else:
raise NotImplementedError
def f_apply(data):
- if method == "standardise":
+ if transform_method == "standardise":
return mean, std, statistics.standardise_apply(data, mean, std)
- elif method == "centre":
+ elif transform_method == "centre":
return mean, None, statistics.centre_apply(data, mean)
else:
raise NotImplementedError
if not inverse:
- if self._transform_method is not None:
- raise AssertionError(f"Transform method is already set. Therefore, data was already transformed with "
- f"{self._transform_method}. Please perform inverse transformation of data first.")
+ if data_class._method is not None:
+ raise AssertionError(f"Internal _method is already set. Therefore, data was already transformed with "
+ f"{data_class._method}. Please perform inverse transformation of data first.")
# apply transformation on local data instance (f) if mean is None, else apply by using mean (and std) from
# external data.
- self.mean, self.std, self.data = locals()["f" if mean is None else "f_apply"](self.data)
+ data_class.mean, data_class.std, data_class.data = locals()["f" if mean is None else "f_apply"](
+ data_class.data)
# set transform method to find correct method for inverse transformation.
- self._transform_method = method
+ data_class._method = transform_method
else:
- self.inverse_transform()
+ self.inverse_transform(data_class)
@staticmethod
def check_inverse_transform_params(mean: data_or_none, std: data_or_none, method: str) -> None:
@@ -670,7 +639,7 @@ class DataHandlerSingleStation(AbstractDataHandler):
if len(msg) > 0:
raise AttributeError(f"Inverse transform {method} can not be executed because following is None: {msg}")
- def inverse_transform(self) -> None:
+ def inverse_transform(self, data_class) -> None:
"""
Perform inverse transformation.
@@ -690,36 +659,26 @@ class DataHandlerSingleStation(AbstractDataHandler):
else:
raise NotImplementedError
- if self._transform_method is None:
+ if data_class.transform_method is None:
raise AssertionError("Inverse transformation method is not set. Data cannot be inverse transformed.")
- self.check_inverse_transform_params(self.mean, self.std, self._transform_method)
- self.data, self.mean, self.std = f_inverse(self.data, self.mean, self.std, self._transform_method)
- self._transform_method = None
+ self.check_inverse_transform_params(data_class.mean, data_class.std, data_class._method)
+ data_class.data, data_class.mean, data_class.std = f_inverse(data_class.data, data_class.mean, data_class.std,
+ data_class._method)
+ data_class.transform_method = None
# update X and Y
self.make_samples()
- def get_transformation_information(self, variable: str = None) -> Tuple[data_or_none, data_or_none, str]:
+ def get_transformation_targets(self) -> Tuple[data_or_none, data_or_none, str]:
"""
Extract transformation statistics and method.
- Get mean and standard deviation for given variable and the transformation method if set. If a transformation
+ Get mean and standard deviation for target values and the transformation method if set. If a transformation
depends only on particular statistics (e.g. only mean is required for centering), the remaining statistics are
returned with None as fill value.
- :param variable: Variable for which the information on transformation is requested.
-
:return: mean, standard deviation and transformation method
"""
- variable = self.target_var if variable is None else variable
- try:
- mean = self.mean.sel({'variables': variable}).values
- except AttributeError:
- mean = None
- try:
- std = self.std.sel({'variables': variable}).values
- except AttributeError:
- std = None
- return mean, std, self._transform_method
+ return self.target_data.mean, self.target_data.std, self.target_data.transform_method
if __name__ == "__main__":
@@ -732,7 +691,6 @@ if __name__ == "__main__":
time_dim='datetime', window_history_size=7, window_lead_time=3,
interpolation_limit=0
) # transformation={'method': 'standardise'})
- # sp.set_transformation({'method': 'standardise', 'mean': sp.mean+2, 'std': sp.std+1})
sp2 = DataHandlerSingleStation(data_path='/home/felix/PycharmProjects/mlt_new/data/', station='DEBY122',
statistics_per_var=statistics_per_var, station_type='background',
network='UBA', sampling='daily', target_dim='variables', target_var='o3',
diff --git a/mlair/data_handler/default_data_handler.py b/mlair/data_handler/default_data_handler.py
index 8ed4f8743d90b313d074a3be15cc49fd9ffa07c0..4dedceb0a942ffbbf0abba530798898b40281ed4 100644
--- a/mlair/data_handler/default_data_handler.py
+++ b/mlair/data_handler/default_data_handler.py
@@ -145,7 +145,7 @@ class DefaultDataHandler(AbstractDataHandler):
return self.id_class.observation.copy().squeeze()
def get_transformation_Y(self):
- return self.id_class.get_transformation_information()
+ return self.id_class.get_transformation_targets()
def multiply_extremes(self, extreme_values: num_or_list = 1., extremes_on_right_tail_only: bool = False,
timedelta: Tuple[int, str] = (1, 'm'), dim="datetime"):
@@ -218,26 +218,30 @@ class DefaultDataHandler(AbstractDataHandler):
@classmethod
def transformation(cls, set_stations, **kwargs):
sp_keys = {k: copy.deepcopy(kwargs[k]) for k in cls._requirements if k in kwargs}
- transformation_dict = sp_keys.pop("transformation")
- if transformation_dict is None:
+ transformation_class = sp_keys.get("transformation", None)
+ if transformation_class is None:
return
- scope = transformation_dict.pop("scope")
- method = transformation_dict.pop("method")
- if transformation_dict.pop("mean", None) is not None:
+
+ transformation_inputs = transformation_class.inputs
+ if transformation_inputs.mean is not None:
return
- mean, std = None, None
+ means = [None, None]
+ stds = [None, None]
for station in set_stations:
try:
- sp = cls.data_handler_transformation(station, transformation={"method": method}, **sp_keys)
- mean = sp.mean.copy(deep=True) if mean is None else mean.combine_first(sp.mean)
- std = sp.std.copy(deep=True) if std is None else std.combine_first(sp.std)
+ sp = cls.data_handler_transformation(station, **sp_keys)
+ for i, data in enumerate([sp.input_data, sp.target_data]):
+ means[i] = data.mean.copy(deep=True) if means[i] is None else means[i].combine_first(data.mean)
+ stds[i] = data.std.copy(deep=True) if stds[i] is None else stds[i].combine_first(data.std)
except (AttributeError, EmptyQueryResult):
continue
- if mean is None:
+ if means[0] is None:
return None
- mean_estimated = mean.mean("Stations")
- std_estimated = std.mean("Stations")
- return {"scope": scope, "method": method, "mean": mean_estimated, "std": std_estimated}
+ transformation_class.inputs.mean = means[0].mean("Stations")
+ transformation_class.inputs.std = stds[0].mean("Stations")
+ transformation_class.targets.mean = means[1].mean("Stations")
+ transformation_class.targets.std = stds[1].mean("Stations")
+ return transformation_class
def get_coordinates(self):
return self.id_class.get_coordinates()
\ No newline at end of file
diff --git a/mlair/helpers/statistics.py b/mlair/helpers/statistics.py
index 4d51b1915ea4c027ff88a2106de29e572af069a0..3db6618a5e8ebd575d61bc261144ff47ccaf9b53 100644
--- a/mlair/helpers/statistics.py
+++ b/mlair/helpers/statistics.py
@@ -11,11 +11,34 @@ import pandas as pd
from typing import Union, Tuple, Dict
from matplotlib import pyplot as plt
-from mlair.helpers import to_list
+from mlair.helpers import to_list, remove_items
Data = Union[xr.DataArray, pd.DataFrame]
+class DataClass:
+
+ def __init__(self, data=None, mean=None, std=None, max=None, min=None, transform_method=None):
+ self.data = data
+ self.mean = mean
+ self.std = std
+ self.max = max
+ self.min = min
+ self.transform_method = transform_method
+ self._method = None
+
+ def as_dict(self):
+ return remove_items(self.__dict__, "_method")
+
+
+class TransformationClass:
+
+ def __init__(self, inputs_mean=None, inputs_std=None, inputs_method=None, targets_mean=None, targets_std=None,
+ targets_method=None):
+ self.inputs = DataClass(mean=inputs_mean, std=inputs_std, transform_method=inputs_method)
+ self.targets = DataClass(mean=targets_mean, std=targets_std, transform_method=targets_method)
+
+
def apply_inverse_transformation(data: Data, mean: Data, std: Data = None, method: str = "standardise") -> Data:
"""
Apply inverse transformation for given statistics.
diff --git a/mlair/plotting/postprocessing_plotting.py b/mlair/plotting/postprocessing_plotting.py
index 327dc40de1aa6986c9763186a68a0138be61bb5a..c8682374e0d4c0d724d83a5e36977543ac3a50f8 100644
--- a/mlair/plotting/postprocessing_plotting.py
+++ b/mlair/plotting/postprocessing_plotting.py
@@ -137,15 +137,16 @@ class PlotMonthlySummary(AbstractPlotClass):
data_cnn = data.sel(type="CNN").squeeze()
if len(data_cnn.shape) > 1:
- data_cnn.coords["ahead"].values = [f"{days}d" for days in data_cnn.coords["ahead"].values]
+ data_cnn = data_cnn.assign_coords(ahead=[f"{days}d" for days in data_cnn.coords["ahead"].values])
data_obs = data.sel(type="obs", ahead=1).squeeze()
data_obs.coords["ahead"] = "obs"
data_concat = xr.concat([data_obs, data_cnn], dim="ahead")
- data_concat = data_concat.drop("type")
+ data_concat = data_concat.drop_vars("type")
- data_concat.index.values = data_concat.index.values.astype("datetime64[M]").astype(int) % 12 + 1
+ new_index = data_concat.index.values.astype("datetime64[M]").astype(int) % 12 + 1
+ data_concat = data_concat.assign_coords(index=new_index)
data_concat = data_concat.clip(min=0)
forecasts = xr.concat([forecasts, data_concat], 'index') if forecasts is not None else data_concat
diff --git a/mlair/run_modules/post_processing.py b/mlair/run_modules/post_processing.py
index 7b1d145541d694b7f7145e42778f91d0716579ba..571d3a07d15873af1c1ccedc59e0cc462e07820f 100644
--- a/mlair/run_modules/post_processing.py
+++ b/mlair/run_modules/post_processing.py
@@ -399,10 +399,10 @@ class PostProcessing(RunEnvironment):
:return: filled data array with ols predictions
"""
tmp_ols = self.ols_model.predict(input_data)
- if not normalised:
- tmp_ols = statistics.apply_inverse_transformation(tmp_ols, mean, std, transformation_method)
target_shape = ols_prediction.values.shape
ols_prediction.values = np.swapaxes(tmp_ols, 2, 0) if target_shape != tmp_ols.shape else tmp_ols
+ if not normalised:
+ ols_prediction = statistics.apply_inverse_transformation(ols_prediction, mean, std, transformation_method)
return ols_prediction
def _create_persistence_forecast(self, data, persistence_prediction: xr.DataArray, mean: xr.DataArray,
@@ -423,9 +423,10 @@ class PostProcessing(RunEnvironment):
:return: filled data array with persistence predictions
"""
tmp_persi = data.copy()
- if not normalised:
- tmp_persi = statistics.apply_inverse_transformation(tmp_persi, mean, std, transformation_method)
persistence_prediction.values = np.tile(tmp_persi, (self.window_lead_time, 1)).T
+ if not normalised:
+ persistence_prediction = statistics.apply_inverse_transformation(persistence_prediction, mean, std,
+ transformation_method)
return persistence_prediction
def _create_nn_forecast(self, input_data: xr.DataArray, nn_prediction: xr.DataArray, mean: xr.DataArray,
@@ -447,8 +448,6 @@ class PostProcessing(RunEnvironment):
:return: filled data array with nn predictions
"""
tmp_nn = self.model.predict(input_data)
- if not normalised:
- tmp_nn = statistics.apply_inverse_transformation(tmp_nn, mean, std, transformation_method)
if isinstance(tmp_nn, list):
nn_prediction.values = tmp_nn[-1]
elif tmp_nn.ndim == 3:
@@ -457,6 +456,8 @@ class PostProcessing(RunEnvironment):
nn_prediction.values = tmp_nn
else:
raise NotImplementedError(f"Number of dimension of model output must be 2 or 3, but not {tmp_nn.dims}.")
+ if not normalised:
+ nn_prediction = statistics.apply_inverse_transformation(nn_prediction, mean, std, transformation_method)
return nn_prediction
@staticmethod