code: # -*- coding: utf-8 -*-
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  """
  This module defines the plugins required for Ensemble Copula Coupling.
  
  """
  import warnings
  from typing import List, Optional, Tuple
  
  import iris
  import numpy as np
  from iris.cube import Cube
  from iris.exceptions import CoordinateNotFoundError, InvalidCubeError
  from numpy import ndarray
  from scipy import stats
  
  import improver.ensemble_copula_coupling._scipy_continuous_distns as scipy_cont_distns
  from improver import BasePlugin
  from improver.calibration.utilities import convert_cube_data_to_2d
  from improver.ensemble_copula_coupling.utilities import (
      choose_set_of_percentiles,
      concatenate_2d_array_with_2d_array_endpoints,
      create_cube_with_percentiles,
      get_bounds_of_distribution,
      insert_lower_and_upper_endpoint_to_1d_array,
      interpolate_multiple_rows_same_x,
      interpolate_multiple_rows_same_y,
      restore_non_percentile_dimensions,
  )
  from improver.metadata.probabilistic import (
      find_percentile_coordinate,
      find_threshold_coordinate,
      format_cell_methods_for_diagnostic,
      get_diagnostic_cube_name_from_probability_name,
      get_threshold_coord_name_from_probability_name,
      probability_is_above_or_below,
  )
  from improver.utilities.cube_checker import (
      check_cube_coordinates,
      check_for_x_and_y_axes,
  )
  from improver.utilities.cube_manipulation import (
      MergeCubes,
      enforce_coordinate_ordering,
      get_dim_coord_names,
  )
  from improver.utilities.indexing_operations import choose
  
  
  class RebadgePercentilesAsRealizations(BasePlugin):
      """
      Class to rebadge percentiles as ensemble realizations.
      This will allow the quantisation to percentiles to be completed, without
      a subsequent EnsembleReordering step to restore spatial correlations,
      if required.
      """
  
      @staticmethod
      def process(
          cube: Cube, ensemble_realization_numbers: Optional[ndarray] = None
      ) -> Cube:
          """
          Rebadge percentiles as ensemble realizations. The ensemble
          realization numbering will depend upon the number of percentiles in
          the input cube i.e. 0, 1, 2, 3, ..., n-1, if there are n percentiles.
  
          Args:
              cube:
                  Cube containing a percentile coordinate, which will be
                  rebadged as ensemble realization.
              ensemble_realization_numbers:
                  An array containing the ensemble numbers required in the output
                  realization coordinate. Default is None, meaning the
                  realization coordinate will be numbered 0, 1, 2 ... n-1 for n
                  percentiles on the input cube.
  
          Returns:
              Processed cube
  
          Raises:
              InvalidCubeError:
                  If the realization coordinate already exists on the cube.
          """
          percentile_coord_name = find_percentile_coordinate(cube).name()
  
          if ensemble_realization_numbers is None:
              ensemble_realization_numbers = np.arange(
                  len(cube.coord(percentile_coord_name).points), dtype=np.int32
              )
  
          cube.coord(percentile_coord_name).points = ensemble_realization_numbers
  
          # we can't rebadge if the realization coordinate already exists:
          try:
              realization_coord = cube.coord("realization")
          except CoordinateNotFoundError:
              realization_coord = None
  
          if realization_coord:
              raise InvalidCubeError(
                  "Cannot rebadge percentile coordinate to realization "
                  "coordinate because a realization coordinate already exists."
              )
  
          cube.coord(percentile_coord_name).rename("realization")
          cube.coord("realization").units = "1"
          cube.coord("realization").points = cube.coord("realization").points.astype(
              np.int32
          )
  
          return cube
  
  
  class ResamplePercentiles(BasePlugin):
      """
      Class for resampling percentiles from an existing set of percentiles.
      In combination with the Ensemble Reordering plugin, this is a variant of
      Ensemble Copula Coupling.
  
      This class includes the ability to linearly interpolate from an
      input set of percentiles to a different output set of percentiles.
  
      """
  
      def __init__(self, ecc_bounds_warning: bool = False) -> None:
          """
          Initialise the class.
  
          Args:
              ecc_bounds_warning:
                  If true and ECC bounds are exceeded by the percentile values,
                  a warning will be generated rather than an exception.
                  Default value is FALSE.
          """
          self.ecc_bounds_warning = ecc_bounds_warning
  
      def _add_bounds_to_percentiles_and_forecast_at_percentiles(
          self,
          percentiles: ndarray,
          forecast_at_percentiles: ndarray,
          bounds_pairing: Tuple[int, int],
      ) -> Tuple[ndarray, ndarray]:
          """
          Padding of the lower and upper bounds of the percentiles for a
          given phenomenon, and padding of forecast values using the
          constant lower and upper bounds.
  
          Args:
              percentiles:
                  Array of percentiles from a Cumulative Distribution Function.
              forecast_at_percentiles:
                  Array containing the underlying forecast values at each
                  percentile.
              bounds_pairing:
                  Lower and upper bound to be used as the ends of the
                  cumulative distribution function.
  
          Returns:
              - Percentiles
              - Forecast at percentiles with endpoints
  
          Raises:
              ValueError: If the percentile points are outside the ECC bounds
                  and self.ecc_bounds_warning is False.
              ValueError: If the percentiles are not in ascending order.
  
          Warns:
              Warning:  If the percentile points are outside the ECC bounds
                  and self.ecc_bounds_warning is True.
          """
          lower_bound, upper_bound = bounds_pairing
          percentiles = insert_lower_and_upper_endpoint_to_1d_array(percentiles, 0, 100)
          forecast = concatenate_2d_array_with_2d_array_endpoints(
              forecast_at_percentiles, lower_bound, upper_bound
          )
  
          if np.any(np.diff(forecast) < 0):
              out_of_bounds_vals = forecast[np.where(np.diff(forecast) < 0)]
              msg = (
                  "Forecast values exist that fall outside the expected extrema "
                  "values that are defined as bounds in "
                  "ensemble_copula_coupling/constants.py. "
                  "Applying the extrema values as end points to the distribution "
                  "would result in non-monotonically increasing values. "
                  "The defined extremes are {}, whilst the following forecast "
                  "values exist outside this range: {}.".format(
                      bounds_pairing, out_of_bounds_vals
                  )
              )
  
              if self.ecc_bounds_warning:
                  warn_msg = msg + (
                      " The percentile values that have "
                      "exceeded the existing bounds will be used "
                      "as new bounds."
                  )
                  warnings.warn(warn_msg)
                  if upper_bound < forecast.max():
                      upper_bound = forecast.max()
                  if lower_bound > forecast.min():
                      lower_bound = forecast.min()
                  forecast = concatenate_2d_array_with_2d_array_endpoints(
                      forecast_at_percentiles, lower_bound, upper_bound
                  )
              else:
                  raise ValueError(msg)
          if np.any(np.diff(percentiles) < 0):
              msg = (
                  "The percentiles must be in ascending order."
                  "The input percentiles were {}".format(percentiles)
              )
              raise ValueError(msg)
          return percentiles, forecast
  
      def _interpolate_percentiles(
          self,
          forecast_at_percentiles: Cube,
          desired_percentiles: ndarray,
          bounds_pairing: Tuple[int, int],
          percentile_coord_name: str,
      ) -> Cube:
          """
          Interpolation of forecast for a set of percentiles from an initial
          set of percentiles to a new set of percentiles. This is constructed
          by linearly interpolating between the original set of percentiles
          to a new set of percentiles.
  
          Args:
              forecast_at_percentiles:
                  Cube containing a percentile coordinate.
              desired_percentiles:
                  Array of the desired percentiles.
              bounds_pairing:
                  Lower and upper bound to be used as the ends of the
                  cumulative distribution function.
              percentile_coord_name:
                  Name of required percentile coordinate.
  
          Returns:
              Cube containing values for the required diagnostic e.g.
              air_temperature at the required percentiles.
          """
          original_percentiles = forecast_at_percentiles.coord(
              percentile_coord_name
          ).points
  
          original_mask = None
          if np.ma.is_masked(forecast_at_percentiles.data):
              original_mask = forecast_at_percentiles.data.mask[0]
  
          # Ensure that the percentile dimension is first, so that the
          # conversion to a 2d array produces data in the desired order.
          enforce_coordinate_ordering(forecast_at_percentiles, percentile_coord_name)
          forecast_at_reshaped_percentiles = convert_cube_data_to_2d(
              forecast_at_percentiles, coord=percentile_coord_name
          )
  
          (
              original_percentiles,
              forecast_at_reshaped_percentiles,
          ) = self._add_bounds_to_percentiles_and_forecast_at_percentiles(
              original_percentiles, forecast_at_reshaped_percentiles, bounds_pairing
          )
  
          forecast_at_interpolated_percentiles = interpolate_multiple_rows_same_x(
              np.array(desired_percentiles, dtype=np.float64),
              original_percentiles.astype(np.float64),
              forecast_at_reshaped_percentiles.astype(np.float64),
          )
          forecast_at_interpolated_percentiles = np.transpose(
              forecast_at_interpolated_percentiles
          )
  
          # Reshape forecast_at_percentiles, so the percentiles dimension is
          # first, and any other dimension coordinates follow.
          forecast_at_percentiles_data = restore_non_percentile_dimensions(
              forecast_at_interpolated_percentiles,
              next(forecast_at_percentiles.slices_over(percentile_coord_name)),
              len(desired_percentiles),
          )
  
          template_cube = next(forecast_at_percentiles.slices_over(percentile_coord_name))
          template_cube.remove_coord(percentile_coord_name)
          percentile_cube = create_cube_with_percentiles(
              desired_percentiles, template_cube, forecast_at_percentiles_data,
          )
          if original_mask is not None:
              original_mask = np.broadcast_to(original_mask, percentile_cube.shape)
              percentile_cube.data = np.ma.MaskedArray(
                  percentile_cube.data, mask=original_mask
              )
          return percentile_cube
  
      def process(
          self,
          forecast_at_percentiles: Cube,
          no_of_percentiles: Optional[int] = None,
          sampling: Optional[str] = "quantile",
          percentiles: Optional[List] = None,
      ) -> Cube:
          """
          1. Creates a list of percentiles, if not provided.
          2. Accesses the lower and upper bound pair of the forecast values,
             in order to specify lower and upper bounds for the percentiles.
          3. Interpolate the percentile coordinate into an alternative
             set of percentiles using linear interpolation.
  
          Args:
              forecast_at_percentiles:
                  Cube expected to contain a percentile coordinate.
              no_of_percentiles:
                  Number of percentiles
                  If None, the number of percentiles within the input
                  forecast_at_percentiles cube is used as the
                  number of percentiles.
              sampling:
                  Type of sampling of the distribution to produce a set of
                  percentiles e.g. quantile or random.
  
                  Accepted options for sampling are:
  
                  * Quantile: A regular set of equally-spaced percentiles aimed
                       at dividing a Cumulative Distribution Function into
                       blocks of equal probability.
                  * Random: A random set of ordered percentiles.
              percentiles:
                  List of the desired output percentiles.
  
          Returns:
              Cube with forecast values at the desired set of percentiles.
              The percentile coordinate is always the zeroth dimension.
  
          Raises:
              ValueError: The percentiles supplied must be between 0 and 100.
          """
          percentile_coord = find_percentile_coordinate(forecast_at_percentiles)
  
          if percentiles:
              if any(p < 0 or p > 100 for p in percentiles):
                  msg = (
                      "The percentiles supplied must be between 0 and 100. "
                      f"Percentiles supplied: {percentiles}"
                  )
                  raise ValueError(msg)
          else:
              if no_of_percentiles is None:
                  no_of_percentiles = len(
                      forecast_at_percentiles.coord(percentile_coord).points
                  )
              percentiles = choose_set_of_percentiles(
                  no_of_percentiles, sampling=sampling
              )
  
          cube_units = forecast_at_percentiles.units
          bounds_pairing = get_bounds_of_distribution(
              forecast_at_percentiles.name(), cube_units
          )
  
          forecast_at_percentiles = self._interpolate_percentiles(
              forecast_at_percentiles,
              percentiles,
              bounds_pairing,
              percentile_coord.name(),
          )
          return forecast_at_percentiles
  
  
  class ConvertProbabilitiesToPercentiles(BasePlugin):
      """
      Class for generating percentiles from probabilities.
      In combination with the Ensemble Reordering plugin, this is a variant
      Ensemble Copula Coupling.
  
      This class includes the ability to interpolate between probabilities
      specified using multiple thresholds in order to generate the percentiles,
      see Figure 1 from Flowerdew, 2014.
  
      Scientific Reference:
      Flowerdew, J., 2014.
      Calibrated ensemble reliability whilst preserving spatial structure.
      Tellus Series A, Dynamic Meteorology and Oceanography, 66, 22662.
  
      """
  
      def __init__(self, ecc_bounds_warning: bool = False) -> None:
          """
          Initialise the class.
  
          Args:
              ecc_bounds_warning:
                  If true and ECC bounds are exceeded by the percentile values,
                  a warning will be generated rather than an exception.
                  Default value is FALSE.
          """
          self.ecc_bounds_warning = ecc_bounds_warning
  
      def _add_bounds_to_thresholds_and_probabilities(
          self,
          threshold_points: ndarray,
          probabilities_for_cdf: ndarray,
          bounds_pairing: Tuple[int, int],
      ) -> Tuple[ndarray, ndarray]:
          """
          Padding of the lower and upper bounds of the distribution for a
          given phenomenon for the threshold_points, and padding of
          probabilities of 0 and 1 to the forecast probabilities.
  
          Args:
              threshold_points:
                  Array of threshold values used to calculate the probabilities.
              probabilities_for_cdf:
                  Array containing the probabilities used for constructing an
                  cumulative distribution function i.e. probabilities
                  below threshold.
              bounds_pairing:
                  Lower and upper bound to be used as the ends of the
                  cumulative distribution function.
  
          Returns:
              - Array of threshold values padded with the lower and upper
                bound of the distribution.
              - Array containing the probabilities padded with 0 and 1 at
                each end.
  
          Raises:
              ValueError: If the thresholds exceed the ECC bounds for
                  the diagnostic and self.ecc_bounds_warning is False.
  
          Warns:
              Warning: If the thresholds exceed the ECC bounds for
                  the diagnostic and self.ecc_bounds_warning is True.
          """
          lower_bound, upper_bound = bounds_pairing
          threshold_points_with_endpoints = insert_lower_and_upper_endpoint_to_1d_array(
              threshold_points, lower_bound, upper_bound
          )
          probabilities_for_cdf = concatenate_2d_array_with_2d_array_endpoints(
              probabilities_for_cdf, 0, 1
          )
  
          if np.any(np.diff(threshold_points_with_endpoints) < 0):
              msg = (
                  "The calculated threshold values {} are not in ascending "
                  "order as required for the cumulative distribution "
                  "function (CDF). This is due to the threshold values "
                  "exceeding the range given by the ECC bounds {}.".format(
                      threshold_points_with_endpoints, bounds_pairing
                  )
              )
              # If ecc_bounds_warning has been set, generate a warning message
              # rather than raising an exception so that subsequent processing
              # can continue. Then apply the new bounds as necessary to
              # ensure the threshold values and endpoints are in ascending
              # order and avoid problems further along the processing chain.
              if self.ecc_bounds_warning:
                  warn_msg = msg + (
                      " The threshold points that have "
                      "exceeded the existing bounds will be used "
                      "as new bounds."
                  )
                  warnings.warn(warn_msg)
                  if upper_bound < max(threshold_points_with_endpoints):
                      upper_bound = max(threshold_points_with_endpoints)
                  if lower_bound > min(threshold_points_with_endpoints):
                      lower_bound = min(threshold_points_with_endpoints)
                  threshold_points_with_endpoints = insert_lower_and_upper_endpoint_to_1d_array(
                      threshold_points, lower_bound, upper_bound
                  )
              else:
                  raise ValueError(msg)
          return threshold_points_with_endpoints, probabilities_for_cdf
  
      def _probabilities_to_percentiles(
          self,
          forecast_probabilities: Cube,
          percentiles: ndarray,
          bounds_pairing: Tuple[int, int],
      ) -> Cube:
          """
          Conversion of probabilities to percentiles through the construction
          of an cumulative distribution function. This is effectively
          constructed by linear interpolation from the probabilities associated
          with each threshold to a set of percentiles.
  
          Args:
              forecast_probabilities:
                  Cube with a threshold coordinate.
              percentiles:
                  Array of percentiles, at which the corresponding values will be
                  calculated.
              bounds_pairing:
                  Lower and upper bound to be used as the ends of the
                  cumulative distribution function.
  
          Returns:
              Cube containing values for the required diagnostic e.g.
              air_temperature at the required percentiles.
  
          Raises:
              NotImplementedError: If the threshold coordinate has an
                  spp__relative_to_threshold attribute that is not either
                  "above" or "below".
  
          Warns:
              Warning: If the probability values are not ascending, so the
                  resulting cdf is not monotonically increasing.
          """
          threshold_coord = find_threshold_coordinate(forecast_probabilities)
          threshold_unit = threshold_coord.units
          threshold_points = threshold_coord.points
  
          original_mask = None
          if np.ma.is_masked(forecast_probabilities.data):
              original_mask = forecast_probabilities.data.mask[0]
  
          # Ensure that the percentile dimension is first, so that the
          # conversion to a 2d array produces data in the desired order.
          enforce_coordinate_ordering(forecast_probabilities, threshold_coord.name())
          prob_slices = convert_cube_data_to_2d(
              forecast_probabilities, coord=threshold_coord.name()
          )
  
          # The requirement below for a monotonically changing probability
          # across thresholds can be thwarted by precision errors of order 1E-10,
          # as such, here we round to a precision of 9 decimal places.
          prob_slices = np.around(prob_slices, 9)
  
          # Invert probabilities for data thresholded above thresholds.
          relation = probability_is_above_or_below(forecast_probabilities)
          if relation == "above":
              probabilities_for_cdf = 1 - prob_slices
          elif relation == "below":
              probabilities_for_cdf = prob_slices
          else:
              msg = (
                  "Probabilities to percentiles only implemented for "
                  "thresholds above or below a given value."
                  "The relation to threshold is given as {}".format(relation)
              )
              raise NotImplementedError(msg)
  
          (
              threshold_points,
              probabilities_for_cdf,
          ) = self._add_bounds_to_thresholds_and_probabilities(
              threshold_points, probabilities_for_cdf, bounds_pairing
          )
  
          if np.any(np.diff(probabilities_for_cdf) < 0):
              msg = (
                  "The probability values used to construct the "
                  "Cumulative Distribution Function (CDF) "
                  "must be ascending i.e. in order to yield "
                  "a monotonically increasing CDF."
                  "The probabilities are {}".format(probabilities_for_cdf)
              )
              warnings.warn(msg)
  
          # Convert percentiles into fractions.
          percentiles_as_fractions = np.array(
              [x / 100.0 for x in percentiles], dtype=np.float32
          )
  
          forecast_at_percentiles = interpolate_multiple_rows_same_y(
              percentiles_as_fractions.astype(np.float64),
              probabilities_for_cdf.astype(np.float64),
              threshold_points.astype(np.float64),
          )
          forecast_at_percentiles = forecast_at_percentiles.transpose()
  
          # Reshape forecast_at_percentiles, so the percentiles dimension is
          # first, and any other dimension coordinates follow.
          forecast_at_percentiles = restore_non_percentile_dimensions(
              forecast_at_percentiles,
              next(forecast_probabilities.slices_over(threshold_coord)),
              len(percentiles),
          )
  
          template_cube = next(forecast_probabilities.slices_over(threshold_coord.name()))
          template_cube.rename(
              get_diagnostic_cube_name_from_probability_name(template_cube.name())
          )
          template_cube.remove_coord(threshold_coord.name())
  
          percentile_cube = create_cube_with_percentiles(
              percentiles,
              template_cube,
              forecast_at_percentiles,
              cube_unit=threshold_unit,
          )
  
          if original_mask is not None:
              original_mask = np.broadcast_to(original_mask, percentile_cube.shape)
              percentile_cube.data = np.ma.MaskedArray(
                  percentile_cube.data, mask=original_mask
              )
          return percentile_cube
  
      def process(
          self,
          forecast_probabilities: Cube,
          no_of_percentiles: Optional[int] = None,
          percentiles: Optional[List[float]] = None,
          sampling: str = "quantile",
      ) -> Cube:
          """
          1. Concatenates cubes with a threshold coordinate.
          2. Creates a list of percentiles.
          3. Accesses the lower and upper bound pair to find the ends of the
             cumulative distribution function.
          4. Convert the threshold coordinate into
             values at a set of percentiles using linear interpolation,
             see Figure 1 from Flowerdew, 2014.
  
          Args:
              forecast_probabilities:
                  Cube containing a threshold coordinate.
              no_of_percentiles:
                  Number of percentiles. If None and percentiles is not set,
                  the number of thresholds within the input
                  forecast_probabilities cube is used as the number of
                  percentiles. This argument is mutually exclusive with
                  percentiles.
              percentiles:
                  The desired percentile values in the interval [0, 100].
                  This argument is mutually exclusive with no_of_percentiles.
              sampling:
                  Type of sampling of the distribution to produce a set of
                  percentiles e.g. quantile or random.
  
                  Accepted options for sampling are:
  
                  * Quantile: A regular set of equally-spaced percentiles aimed
                            at dividing a Cumulative Distribution Function into
                            blocks of equal probability.
                  * Random: A random set of ordered percentiles.
  
          Returns:
              Cube with forecast values at the desired set of percentiles.
              The threshold coordinate is always the zeroth dimension.
  
          Raises:
              ValueError: If both no_of_percentiles and percentiles are provided
          """
          if no_of_percentiles is not None and percentiles is not None:
              raise ValueError(
                  "Cannot specify both no_of_percentiles and percentiles to "
                  "{}".format(self.__class__.__name__)
              )
  
          threshold_coord = find_threshold_coordinate(forecast_probabilities)
          phenom_name = get_threshold_coord_name_from_probability_name(
              forecast_probabilities.name()
          )
  
          if no_of_percentiles is None:
              no_of_percentiles = len(
                  forecast_probabilities.coord(threshold_coord.name()).points
              )
  
          if percentiles is None:
              percentiles = choose_set_of_percentiles(
                  no_of_percentiles, sampling=sampling
              )
          elif not isinstance(percentiles, (tuple, list)):
              percentiles = [percentiles]
          percentiles = np.array(percentiles, dtype=np.float32)
  
          cube_units = forecast_probabilities.coord(threshold_coord.name()).units
          bounds_pairing = get_bounds_of_distribution(phenom_name, cube_units)
  
          # If a cube still has multiple realizations, slice over these to reduce
          # the memory requirements into manageable chunks.
          try:
              slices_over_realization = forecast_probabilities.slices_over("realization")
          except CoordinateNotFoundError:
              slices_over_realization = [forecast_probabilities]
  
          cubelist = iris.cube.CubeList([])
          for cube_realization in slices_over_realization:
              cubelist.append(
                  self._probabilities_to_percentiles(
                      cube_realization, percentiles, bounds_pairing
                  )
              )
          forecast_at_percentiles = cubelist.merge_cube()
  
          # Update cell methods on final cube
          if forecast_at_percentiles.cell_methods:
              format_cell_methods_for_diagnostic(forecast_at_percentiles)
  
          return forecast_at_percentiles
  
  
  class ConvertLocationAndScaleParameters:
      """
      Base Class to support the plugins that compute percentiles and
      probabilities from the location and scale parameters.
      """
  
      def __init__(
          self, distribution: str = "norm", shape_parameters: Optional[ndarray] = None,
      ) -> None:
          """
          Initialise the class.
  
          In order to construct percentiles or probabilities from the location
          or scale parameter, the distribution for the resulting output needs
          to be selected. For use with the outputs from EMOS, where it has been
          assumed that the outputs from minimising the CRPS follow a particular
          distribution, then the same distribution should be selected, as used
          for the CRPS minimisation. The conversion to percentiles and
          probabilities from the location and scale parameter relies upon
          functionality within scipy.stats.
  
          Args:
              distribution:
                  Name of a distribution supported by scipy.stats.
              shape_parameters:
                  For use with distributions in scipy.stats (e.g. truncnorm) that
                  require the specification of shape parameters to be able to
                  define the shape of the distribution. For the truncated normal
                  distribution, the shape parameters should be appropriate for
                  the distribution constructed from the location and scale
                  parameters provided.
                  Please note that for use with
                  :meth:`~improver.calibration.\
  ensemble_calibration.ContinuousRankedProbabilityScoreMinimisers.\
  calculate_truncated_normal_crps`,
                  the shape parameters for a truncated normal distribution with
                  a lower bound of zero should be [0, np.inf].
  
          """
          if distribution == "truncnorm":
              # Use scipy v1.3.3 truncnorm
              self.distribution = scipy_cont_distns.truncnorm
          else:
              try:
                  self.distribution = getattr(stats, distribution)
              except AttributeError as err:
                  msg = (
                      "The distribution requested {} is not a valid distribution "
                      "in scipy.stats. {}".format(distribution, err)
                  )
                  raise AttributeError(msg)
  
          if shape_parameters is None:
              if self.distribution.name == "truncnorm":
                  raise ValueError(
                      "For the truncated normal distribution, "
                      "shape parameters must be specified."
                  )
              shape_parameters = []
          self.shape_parameters = shape_parameters
  
      def __repr__(self) -> str:
          """Represent the configured plugin instance as a string."""
          result = (
              "<ConvertLocationAndScaleParameters: distribution: {}; "
              "shape_parameters: {}>"
          )
          return result.format(self.distribution.name, self.shape_parameters)
  
      def _rescale_shape_parameters(
          self, location_parameter: ndarray, scale_parameter: ndarray
      ) -> None:
          """
          Rescale the shape parameters for the desired location and scale
          parameters for the truncated normal distribution. The shape parameters
          for any other distribution will remain unchanged.
  
          For the truncated normal distribution, if the shape parameters are not
          rescaled, then :data:`scipy.stats.truncnorm` will assume that the shape
          parameters are appropriate for a standard normal distribution. As the
          aim is to construct a distribution using specific values for the
          location and scale parameters, the assumption of a standard normal
          distribution is not appropriate. Therefore the shape parameters are
          rescaled using the equations:
  
          .. math::
            a\\_rescaled = (a - location\\_parameter)/scale\\_parameter
  
            b\\_rescaled = (b - location\\_parameter)/scale\\_parameter
  
          Please see :data:`scipy.stats.truncnorm` for some further information.
  
          Args:
              location_parameter:
                  Location parameter to be used to scale the shape parameters.
              scale_parameter:
                  Scale parameter to be used to scale the shape parameters.
          """
          if self.distribution.name == "truncnorm":
              rescaled_values = []
              for value in self.shape_parameters:
                  rescaled_values.append((value - location_parameter) / scale_parameter)
              self.shape_parameters = rescaled_values
  
  
  class ConvertLocationAndScaleParametersToPercentiles(
      BasePlugin, ConvertLocationAndScaleParameters
  ):
      """
      Plugin focusing on generating percentiles from location and scale
      parameters. In combination with the EnsembleReordering plugin, this is
      Ensemble Copula Coupling.
      """
  
      def __repr__(self) -> str:
          """Represent the configured plugin instance as a string."""
          result = (
              "<ConvertLocationAndScaleParametersToPercentiles: "
              "distribution: {}; shape_parameters: {}>"
          )
          return result.format(self.distribution.name, self.shape_parameters)
  
      def _location_and_scale_parameters_to_percentiles(
          self,
          location_parameter: Cube,
          scale_parameter: Cube,
          template_cube: Cube,
          percentiles: List[float],
      ) -> Cube:
          """
          Function returning percentiles based on the supplied location and
          scale parameters.
  
          Args:
              location_parameter:
                  Location parameter of calibrated distribution.
              scale_parameter:
                  Scale parameter of the calibrated distribution.
              template_cube:
                  Template cube containing either a percentile or realization
                  coordinate. All coordinates apart from the percentile or
                  realization coordinate will be copied from the template cube.
                  Metadata will also be copied from this cube.
              percentiles:
                  Percentiles at which to calculate the value of the phenomenon
                  at.
  
          Returns:
              Cube containing the values for the phenomenon at each of the
              percentiles requested.
  
          Raises:
              ValueError: If any of the resulting percentile values are
                  nans and these nans are not caused by a scale parameter of
                  zero.
          """
          # Remove any mask that may be applied to location and scale parameters
          # and replace with ones
          location_data = np.ma.filled(location_parameter.data, 1).flatten()
          scale_data = np.ma.filled(scale_parameter.data, 1).flatten()
  
          # Convert percentiles into fractions.
          percentiles_as_fractions = np.array(
              [x / 100.0 for x in percentiles], dtype=np.float32
          )
  
          result = np.zeros(
              (len(percentiles_as_fractions), location_data.shape[0]), dtype=np.float32
          )
  
          self._rescale_shape_parameters(location_data, scale_data)
  
          percentile_method = self.distribution(
              *self.shape_parameters, loc=location_data, scale=scale_data
          )
  
          # Loop over percentiles, and use the distribution as the
          # "percentile_method" with the location and scale parameter to
          # calculate the values at each percentile.
          for index, percentile in enumerate(percentiles_as_fractions):
              percentile_list = np.repeat(percentile, len(location_data))
              result[index, :] = percentile_method.ppf(percentile_list)
              # If percent point function (PPF) returns NaNs, fill in
              # mean instead of NaN values. NaN will only be generated if the
              # scale parameter (standard deviation) is zero. Therefore, if the
              # scale parameter (standard deviation) is zero, the mean value is
              # used for all gridpoints with a NaN.
              if np.any(scale_data == 0):
                  nan_index = np.argwhere(np.isnan(result[index, :]))
                  result[index, nan_index] = location_data[nan_index]
              if np.any(np.isnan(result)):
                  msg = (
                      "NaNs are present within the result for the {} "
                      "percentile. Unable to calculate the percent point "
                      "function."
                  )
                  raise ValueError(msg)
  
          # Reshape forecast_at_percentiles, so the percentiles dimension is
          # first, and any other dimension coordinates follow.
          result = result.reshape((len(percentiles),) + location_parameter.data.shape)
  
          for prob_coord_name in ["realization", "percentile"]:
              if template_cube.coords(prob_coord_name, dim_coords=True):
                  prob_coord = template_cube.coord(prob_coord_name)
                  template_slice = next(template_cube.slices_over(prob_coord))
                  template_slice.remove_coord(prob_coord)
              elif template_cube.coords(prob_coord_name, dim_coords=False):
                  template_slice = template_cube
  
          percentile_cube = create_cube_with_percentiles(
              percentiles, template_slice, result
          )
          # Define a mask to be reapplied later
          mask = np.logical_or(
              np.ma.getmaskarray(location_parameter.data),
              np.ma.getmaskarray(scale_parameter.data),
          )
          # Make the mask defined above fit the data size and then apply to the
          # percentile cube.
          mask_array = np.stack([mask] * len(percentiles))
          percentile_cube.data = np.ma.masked_where(mask_array, percentile_cube.data)
          # Remove cell methods associated with finding the ensemble mean
          percentile_cube.cell_methods = {}
          return percentile_cube
  
      def process(
          self,
          location_parameter: Cube,
          scale_parameter: Cube,
          template_cube: Cube,
          no_of_percentiles: Optional[int] = None,
          percentiles: Optional[List[float]] = None,
      ) -> Cube:
          """
          Generate ensemble percentiles from the location and scale parameters.
  
          Args:
              location_parameter:
                  Cube containing the location parameters.
              scale_parameter:
                  Cube containing the scale parameters.
              template_cube:
                  Template cube containing either a percentile or realization
                  coordinate. All coordinates apart from the percentile or
                  realization coordinate will be copied from the template cube.
                  Metadata will also be copied from this cube.
              no_of_percentiles:
                  Integer defining the number of percentiles that will be
                  calculated from the location and scale parameters.
              percentiles:
                  List of percentiles that will be generated from the location
                  and scale parameters provided.
  
          Returns:
              Cube for calibrated percentiles.
              The percentile coordinate is always the zeroth dimension.
  
          Raises:
              ValueError: Ensure that it is not possible to supply
                  "no_of_percentiles" and "percentiles" simultaneously
                  as keyword arguments.
          """
          if no_of_percentiles and percentiles:
              msg = (
                  "Please specify either the number of percentiles or "
                  "provide a list of percentiles. The number of percentiles "
                  "provided was {} and the list of percentiles "
                  "provided was {}".format(no_of_percentiles, percentiles)
              )
              raise ValueError(msg)
  
          if no_of_percentiles:
              percentiles = choose_set_of_percentiles(no_of_percentiles)
          calibrated_forecast_percentiles = self._location_and_scale_parameters_to_percentiles(
              location_parameter, scale_parameter, template_cube, percentiles
          )
  
          return calibrated_forecast_percentiles
  
  
  class ConvertLocationAndScaleParametersToProbabilities(
      BasePlugin, ConvertLocationAndScaleParameters
  ):
      """
      Plugin to generate probabilities relative to given thresholds from the
      location and scale parameters of a distribution.
      """
  
      def __repr__(self) -> str:
          """Represent the configured plugin instance as a string."""
          result = (
              "<ConvertLocationAndScaleParametersToProbabilities: "
              "distribution: {}; shape_parameters: {}>"
          )
          return result.format(self.distribution.name, self.shape_parameters)
  
      def _check_template_cube(self, cube: Cube) -> None:
          """
          The template cube is expected to contain a leading threshold dimension
          followed by spatial (y/x) dimensions for a gridded cube. For a spot
          template cube, the spatial dimensions are not expected to be dimension
          coordinates. If the cube contains the expected dimensions,
          a threshold leading order is enforced.
  
          Args:
              cube:
                  A cube whose dimensions are checked to ensure they match what
                  is expected.
  
          Raises:
              ValueError: If cube is not of the expected dimensions.
          """
          require_dim_coords = False if cube.coords("wmo_id") else True
          check_for_x_and_y_axes(cube, require_dim_coords=require_dim_coords)
          dim_coords = get_dim_coord_names(cube)
          msg = (
              "{} expects a cube with only a leading threshold dimension, "
              "followed by spatial (y/x) dimensions. "
              "Got dimensions: {}".format(self.__class__.__name__, dim_coords)
          )
  
          try:
              threshold_coord = find_threshold_coordinate(cube)
          except CoordinateNotFoundError:
              raise ValueError(msg)
  
          if len(dim_coords) < 4:
              enforce_coordinate_ordering(cube, threshold_coord.name())
              return
  
          raise ValueError(msg)
  
      @staticmethod
      def _check_unit_compatibility(
          location_parameter: Cube, scale_parameter: Cube, probability_cube_template: Cube
      ) -> None:
          """
          The location parameter, scale parameters, and threshold values come
          from three different cubes. This is a sanity check to ensure the units
          are as expected, converting units of the location parameter and
          scale parameter if possible.
  
          Args:
              location_parameter:
                  Cube of location parameter values.
              scale_parameter:
                  Cube of scale parameter values.
              probability_cube_template:
                  Cube containing threshold values.
  
          Raises:
              ValueError: If units of input cubes are not compatible.
          """
          threshold_units = find_threshold_coordinate(probability_cube_template).units
  
          try:
              location_parameter.convert_units(threshold_units)
              scale_parameter.convert_units(threshold_units)
          except ValueError as err:
              msg = (
                  "Error: {} This is likely because the location parameter, "
                  "scale parameter and template cube threshold units are "
                  "not equivalent/compatible.".format(err)
              )
              raise ValueError(msg)
  
      def _location_and_scale_parameters_to_probabilities(
          self,
          location_parameter: Cube,
          scale_parameter: Cube,
          probability_cube_template: Cube,
      ) -> Cube:
          """
          Function returning probabilities relative to provided thresholds based
          on the supplied location and scale parameters.
  
          Args:
              location_parameter:
                  Predictor for the calibrated forecast location parameter.
              scale_parameter:
                  Scale parameter for the calibrated forecast.
              probability_cube_template:
                  A probability cube that has a threshold coordinate, where the
                  probabilities are defined as above or below the threshold by
                  the spp__relative_to_threshold attribute. This cube matches
                  the desired output cube format.
  
          Returns:
              Cube containing the data expressed as probabilities relative to
              the provided thresholds in the way described by
              spp__relative_to_threshold.
          """
          # Define a mask to be reapplied later
          loc_mask = np.ma.getmaskarray(location_parameter.data)
          scale_mask = np.ma.getmaskarray(scale_parameter.data)
          mask = np.logical_or(loc_mask, scale_mask)
          # Remove any mask that may be applied to location and scale parameters
          # and replace with ones
          location_parameter.data = np.ma.filled(location_parameter.data, 1)
          scale_parameter.data = np.ma.filled(scale_parameter.data, 1)
          thresholds = find_threshold_coordinate(probability_cube_template).points
          relative_to_threshold = probability_is_above_or_below(probability_cube_template)
  
          self._rescale_shape_parameters(
              location_parameter.data.flatten(), scale_parameter.data.flatten()
          )
  
          # Loop over thresholds, and use the specified distribution with the
          # location and scale parameter to calculate the probabilities relative
          # to each threshold.
          probabilities = np.empty_like(probability_cube_template.data)
  
          distribution = self.distribution(
              *self.shape_parameters,
              loc=location_parameter.data.flatten(),
              scale=scale_parameter.data.flatten(),
          )
  
          probability_method = distribution.cdf
          if relative_to_threshold == "above":
              probability_method = distribution.sf
  
          for index, threshold in enumerate(thresholds):
              probabilities[index, ...] = np.reshape(
                  probability_method(threshold), probabilities.shape[1:]
              )
  
          probability_cube = probability_cube_template.copy(data=probabilities)
          # Make the mask defined above fit the data size and then apply to the
          # probability cube.
          mask_array = np.array([mask] * len(probabilities))
          probability_cube.data = np.ma.masked_where(mask_array, probability_cube.data)
          return probability_cube
  
      def process(
          self,
          location_parameter: Cube,
          scale_parameter: Cube,
          probability_cube_template: Cube,
      ) -> Cube:
          """
          Generate probabilities from the location and scale parameters of the
          distribution.
  
          Args:
              location_parameter:
                  Cube containing the location parameters.
              scale_parameter:
                  Cube containing the scale parameters.
              probability_cube_template:
                  A probability cube that has a threshold coordinate, where the
                  probabilities are defined as above or below the threshold by
                  the spp__relative_to_threshold attribute. This cube matches
                  the desired output cube format.
  
          Returns:
              A cube of diagnostic data expressed as probabilities relative
              to the thresholds found in the probability_cube_template.
          """
          self._check_template_cube(probability_cube_template)
          self._check_unit_compatibility(
              location_parameter, scale_parameter, probability_cube_template
          )
  
          probability_cube = self._location_and_scale_parameters_to_probabilities(
              location_parameter, scale_parameter, probability_cube_template
          )
  
          return probability_cube
  
  
  class EnsembleReordering(BasePlugin):
      """
      Plugin for applying the reordering step of Ensemble Copula Coupling,
      in order to generate ensemble realizations with multivariate structure
      from percentiles. The percentiles are assumed to be in ascending order.
  
      Reference:
      Schefzik, R., Thorarinsdottir, T.L. & Gneiting, T., 2013.
      Uncertainty Quantification in Complex Simulation Models Using Ensemble
      Copula Coupling.
      Statistical Science, 28(4), pp.616-640.
  
      """
  
      @staticmethod
      def _recycle_raw_ensemble_realizations(
          post_processed_forecast_percentiles: Cube,
          raw_forecast_realizations: Cube,
          percentile_coord_name: str,
      ) -> Cube:
          """
          Function to determine whether there is a mismatch between the number
          of percentiles and the number of raw forecast realizations. If more
          percentiles are requested than ensemble realizations, then the ensemble
          realizations are recycled. This assumes that the identity of the
          ensemble realizations within the raw ensemble forecast is random, such
          that the raw ensemble realizations are exchangeable. If fewer
          percentiles are requested than ensemble realizations, then only the
          first n ensemble realizations are used.
  
          Args:
              post_processed_forecast_percentiles :
                  Cube for post-processed percentiles.
                  The percentiles are assumed
                  to be in ascending order.
              raw_forecast_realizations:
                  Cube containing the raw (not post-processed) forecasts.
              percentile_coord_name:
                  Name of required percentile coordinate.
  
          Returns:
              Cube for the raw ensemble forecast, where the raw ensemble
              realizations have either been recycled or constrained,
              depending upon the number of percentiles present
              in the post-processed forecast cube.
          """
          plen = len(
              post_processed_forecast_percentiles.coord(percentile_coord_name).points
          )
          mlen = len(raw_forecast_realizations.coord("realization").points)
          if plen == mlen:
              pass
          else:
              raw_forecast_realizations_extended = iris.cube.CubeList()
              realization_list = []
              mpoints = raw_forecast_realizations.coord("realization").points
              # Loop over the number of percentiles and finding the
              # corresponding ensemble realization number. The ensemble
              # realization numbers are recycled e.g. 1, 2, 3, 1, 2, 3, etc.
              for index in range(plen):
                  realization_list.append(mpoints[index % len(mpoints)])
  
              # Assume that the ensemble realizations are ascending linearly.
              new_realization_numbers = realization_list[0] + list(range(plen))
  
              # Extract the realizations required in the realization_list from
              # the raw_forecast_realizations. Edit the realization number as
              # appropriate and append to a cubelist containing rebadged
              # raw ensemble realizations.
              for realization, index in zip(realization_list, new_realization_numbers):
                  constr = iris.Constraint(realization=realization)
                  raw_forecast_realization = raw_forecast_realizations.extract(constr)
                  raw_forecast_realization.coord("realization").points = index
                  raw_forecast_realizations_extended.append(raw_forecast_realization)
              raw_forecast_realizations = MergeCubes()(
                  raw_forecast_realizations_extended, slice_over_realization=True
              )
          return raw_forecast_realizations
  
      @staticmethod
      def rank_ecc(
          post_processed_forecast_percentiles: Cube,
          raw_forecast_realizations: Cube,
          random_ordering: bool = False,
          random_seed: Optional[int] = None,
      ) -> Cube:
          """
          Function to apply Ensemble Copula Coupling. This ranks the
          post-processed forecast realizations based on a ranking determined from
          the raw forecast realizations.
  
          Args:
              post_processed_forecast_percentiles:
                  Cube for post-processed percentiles. The percentiles are
                  assumed to be in ascending order.
              raw_forecast_realizations:
                  Cube containing the raw (not post-processed) forecasts.
                  The probabilistic dimension is assumed to be the zeroth
                  dimension.
              random_ordering:
                  If random_ordering is True, the post-processed forecasts are
                  reordered randomly, rather than using the ordering of the
                  raw ensemble.
              random_seed:
                  If random_seed is an integer, the integer value is used for
                  the random seed.
                  If random_seed is None, no random seed is set, so the random
                  values generated are not reproducible.
  
          Returns:
              Cube for post-processed realizations where at a particular grid
              point, the ranking of the values within the ensemble matches
              the ranking from the raw ensemble.
          """
          results = iris.cube.CubeList([])
          for rawfc, calfc in zip(
              raw_forecast_realizations.slices_over("time"),
              post_processed_forecast_percentiles.slices_over("time"),
          ):
              if random_seed is not None:
                  random_seed = int(random_seed)
              random_seed = np.random.RandomState(random_seed)
              random_data = random_seed.rand(*rawfc.data.shape)
              if random_ordering:
                  # Returns the indices that would sort the array.
                  # As these indices are from a random dataset, only an argsort
                  # is used.
                  ranking = np.argsort(random_data, axis=0)
              else:
                  # Lexsort returns the indices sorted firstly by the
                  # primary key, the raw forecast data (unless random_ordering
                  # is enabled), and secondly by the secondary key, an array of
                  # random data, in order to split tied values randomly.
                  sorting_index = np.lexsort((random_data, rawfc.data), axis=0)
                  # Returns the indices that would sort the array.
                  ranking = np.argsort(sorting_index, axis=0)
              # Index the post-processed forecast data using the ranking array.
              # The following uses a custom choose function that reproduces the
              # required elements of the np.choose method without the limitation
              # of having < 32 arrays or a leading dimension < 32 in the
              # input data array. This function allows indexing of a 3d array
              # using a 3d array.
              mask = np.ma.getmask(calfc.data)
              calfc.data = choose(ranking, calfc.data)
              if mask is not np.ma.nomask:
                  calfc.data = np.ma.MaskedArray(calfc.data, mask, dtype=np.float32)
              results.append(calfc)
          # Ensure we haven't lost any dimensional coordinates with only one
          # value in.
          results = results.merge_cube()
          results = check_cube_coordinates(post_processed_forecast_percentiles, results)
          return results
  
      @staticmethod
      def _check_input_cube_masks(post_processed_forecast, raw_forecast):
          """
          Checks that if the raw_forecast is masked the post_processed_forecast
          is also masked. The code supports the post_processed_forecast being
          masked even if the raw_forecast isn't masked, but not vice versa.
  
          If both post_processed_forecast and raw_forecast are masked checks
          that both input cubes have the same mask applied to each
          x-y slice.
  
          Args:
              post_processed_forecast:
                  The cube containing the post-processed
                  forecast realizations.
              raw_forecast:
                  The cube containing the raw (not post-processed)
                  forecast.
  
          Raises:
              ValueError:
                  If only the raw_forecast is masked
              ValueError:
                  If the post_processed_forecast does not have same mask on all
                  x-y slices
              ValueError:
                  If the raw_forecast x-y slices do not all have the same mask
                  as the post_processed_forecast.
          """
          if np.ma.is_masked(post_processed_forecast.data) and np.ma.is_masked(
              raw_forecast.data
          ):
              for aslice in post_processed_forecast.data.mask[1:, ...]:
                  if np.any(aslice != post_processed_forecast.data.mask[0]):
  
                      message = (
                          "The post_processed_forecast does not have same"
                          " mask on all x-y slices"
                      )
                      raise (ValueError(message))
              for aslice in raw_forecast.data.mask[0:, ...]:
                  if np.any(aslice != post_processed_forecast.data.mask[0]):
                      message = (
                          "The raw_forecast x-y slices do not all have the"
                          " same mask as the post_processed_forecast."
                      )
                      raise (ValueError(message))
          if np.ma.is_masked(raw_forecast.data) and not np.ma.is_masked(
              post_processed_forecast.data
          ):
              message = (
                  "The raw_forecast provided has a mask, but the "
                  "post_processed_forecast isn't masked. The "
                  "post_processed_forecast and the raw_forecast should "
                  "have the same mask applied to them."
              )
              raise (ValueError(message))
  
      def process(
          self,
          post_processed_forecast: Cube,
          raw_forecast: Cube,
          random_ordering: bool = False,
          random_seed: Optional[int] = None,
      ) -> Cube:
          """
          Reorder post-processed forecast using the ordering of the
          raw ensemble.
  
          Args:
              post_processed_forecast:
                  The cube containing the post-processed
                  forecast realizations.
              raw_forecast:
                  The cube containing the raw (not post-processed)
                  forecast.
              random_ordering:
                  If random_ordering is True, the post-processed forecasts are
                  reordered randomly, rather than using the ordering of the
                  raw ensemble.
              random_seed:
                  If random_seed is an integer, the integer value is used for
                  the random seed.
                  If random_seed is None, no random seed is set, so the random
                  values generated are not reproducible.
  
          Returns:
              Cube containing the new ensemble realizations where all points
              within the dataset have been reordered in comparison to the
              input percentiles. This cube contains the same ensemble
              realization numbers as the raw forecast.
          """
          percentile_coord_name = find_percentile_coordinate(
              post_processed_forecast
          ).name()
  
          enforce_coordinate_ordering(post_processed_forecast, percentile_coord_name)
          enforce_coordinate_ordering(raw_forecast, "realization")
  
          self._check_input_cube_masks(post_processed_forecast, raw_forecast)
  
          raw_forecast = self._recycle_raw_ensemble_realizations(
              post_processed_forecast, raw_forecast, percentile_coord_name
          )
          post_processed_forecast_realizations = self.rank_ecc(
              post_processed_forecast,
              raw_forecast,
              random_ordering=random_ordering,
              random_seed=random_seed,
          )
          plugin = RebadgePercentilesAsRealizations()
          post_processed_forecast_realizations = plugin(
              post_processed_forecast_realizations,
              ensemble_realization_numbers=raw_forecast.coord("realization").points,
          )
  
          enforce_coordinate_ordering(post_processed_forecast_realizations, "realization")
          return post_processed_forecast_realizations
  
apis: numpy.logical_or numpy.ma.is_masked numpy.transpose numpy.ma.masked_where numpy.diff numpy.ma.getmask numpy.any numpy.argsort numpy.ma.filled numpy.empty_like numpy.random.RandomState numpy.lexsort numpy.ma.MaskedArray numpy.broadcast_to numpy.array numpy.around numpy.ma.getmaskarray numpy.isnan