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bias_calc.py
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bias_calc.py
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"""Utilities to calculate the bias correction factors for biased data that is
going to be fed into the sup3r downscaling models. This is typically used to
bias correct GCM data vs. some historical record like the WTK or NSRDB."""
import copy
import json
import logging
import os
from abc import abstractmethod
from concurrent.futures import ProcessPoolExecutor, as_completed
from glob import glob
import h5py
import numpy as np
import pandas as pd
import rex
from rex.utilities.fun_utils import get_fun_call_str
from scipy import stats
from scipy.ndimage.filters import gaussian_filter
from scipy.spatial import KDTree
import sup3r.preprocessing.data_handling
from sup3r.preprocessing.data_handling.base import DataHandler
from sup3r.utilities import VERSION_RECORD, ModuleName
from sup3r.utilities.cli import BaseCLI
from sup3r.utilities.utilities import nn_fill_array
logger = logging.getLogger(__name__)
class DataRetrievalBase:
"""Base class to handle data retrieval for the biased data and the
baseline data
"""
def __init__(self,
base_fps,
bias_fps,
base_dset,
bias_feature,
distance_upper_bound=None,
target=None,
shape=None,
base_handler='Resource',
bias_handler='DataHandlerNCforCC',
base_handler_kwargs=None,
bias_handler_kwargs=None,
decimals=None):
"""
Parameters
----------
base_fps : list | str
One or more baseline .h5 filepaths representing non-biased data to
use to correct the biased dataset. This is typically several years
of WTK or NSRDB files.
bias_fps : list | str
One or more biased .nc or .h5 filepaths representing the biased
data to be corrected based on the baseline data. This is typically
several years of GCM .nc files.
base_dset : str
A single dataset from the base_fps to retrieve. In the case of wind
components, this can be U_100m or V_100m which will retrieve
windspeed and winddirection and derive the U/V component.
bias_feature : str
This is the biased feature from bias_fps to retrieve. This should
be a single feature name corresponding to base_dset
distance_upper_bound : float
Upper bound on the nearest neighbor distance in decimal degrees.
This should be the approximate resolution of the low-resolution
bias data. None (default) will calculate this based on the median
distance between points in bias_fps
target : tuple
(lat, lon) lower left corner of raster to retrieve from bias_fps.
If None then the lower left corner of the full domain will be used.
shape : tuple
(rows, cols) grid size to retrieve from bias_fps. If None then the
full domain shape will be used.
base_handler : str
Name of rex resource handler or sup3r.preprocessing.data_handling
class to be retrieved from the rex/sup3r library. If a
sup3r.preprocessing.data_handling class is used, all data will be
loaded in this class' initialization and the subsequent bias
calculation will be done in serial
bias_handler : str
Name of the bias data handler class to be retrieved from the
sup3r.preprocessing.data_handling library.
base_handler_kwargs : dict | None
Optional kwargs to send to the initialization of the base_handler
class
bias_handler_kwargs : dict | None
Optional kwargs to send to the initialization of the bias_handler
class
decimals : int | None
Option to round bias and base data to this number of
decimals, this gets passed to np.around(). If decimals
is negative, it specifies the number of positions to
the left of the decimal point.
"""
logger.info('Initializing DataRetrievalBase for base dset "{}" '
'correcting biased dataset(s): {}'.format(
base_dset, bias_feature))
self.base_fps = base_fps
self.bias_fps = bias_fps
self.base_dset = base_dset
self.bias_feature = bias_feature
self.target = target
self.shape = shape
self.decimals = decimals
self.base_handler_kwargs = base_handler_kwargs or {}
self.bias_handler_kwargs = bias_handler_kwargs or {}
self.bad_bias_gids = []
self._distance_upper_bound = distance_upper_bound
if isinstance(self.base_fps, str):
self.base_fps = sorted(glob(self.base_fps))
if isinstance(self.bias_fps, str):
self.bias_fps = sorted(glob(self.bias_fps))
base_sup3r_handler = getattr(sup3r.preprocessing.data_handling,
base_handler, None)
base_rex_handler = getattr(rex, base_handler, None)
if base_rex_handler is not None:
self.base_handler = base_rex_handler
self.base_dh = self.base_handler(self.base_fps[0],
**self.base_handler_kwargs)
elif base_sup3r_handler is not None:
self.base_handler = base_sup3r_handler
self.base_handler_kwargs['features'] = [self.base_dset]
self.base_dh = self.base_handler(self.base_fps,
**self.base_handler_kwargs)
msg = ('Base data handler opened with a sup3r DataHandler class '
'must load cached data!')
assert self.base_dh.data is not None, msg
else:
msg = f'Could not retrieve "{base_handler}" from sup3r or rex!'
logger.error(msg)
raise RuntimeError(msg)
self.bias_handler = getattr(sup3r.preprocessing.data_handling,
bias_handler)
self.base_meta = self.base_dh.meta
self.bias_dh = self.bias_handler(self.bias_fps, [self.bias_feature],
target=self.target,
shape=self.shape,
val_split=0.0,
**self.bias_handler_kwargs)
lats = self.bias_dh.lat_lon[..., 0].flatten()
self.bias_meta = self.bias_dh.meta
self.bias_ti = self.bias_dh.time_index
raster_shape = self.bias_dh.lat_lon[..., 0].shape
bias_lat_lon = self.bias_meta[['latitude', 'longitude']].values
self.bias_tree = KDTree(bias_lat_lon)
self.bias_gid_raster = np.arange(lats.size)
self.bias_gid_raster = self.bias_gid_raster.reshape(raster_shape)
self.nn_dist, self.nn_ind = self.bias_tree.query(
self.base_meta[['latitude', 'longitude']], k=1,
distance_upper_bound=self.distance_upper_bound)
self.out = None
self._init_out()
logger.info('Finished initializing DataRetrievalBase.')
@abstractmethod
def _init_out(self):
"""Initialize output arrays"""
@property
def meta(self):
"""Get a meta data dictionary on how these bias factors were
calculated"""
meta = {'base_fps': self.base_fps,
'bias_fps': self.bias_fps,
'base_dset': self.base_dset,
'bias_feature': self.bias_feature,
'target': self.target,
'shape': self.shape,
'class': str(self.__class__),
'version_record': VERSION_RECORD}
return meta
@property
def distance_upper_bound(self):
"""Maximum distance (float) to map high-resolution data from exo_source
to the low-resolution file_paths input."""
if self._distance_upper_bound is None:
diff = np.diff(self.bias_meta[['latitude', 'longitude']].values,
axis=0)
diff = np.max(np.median(diff, axis=0))
self._distance_upper_bound = diff
logger.info('Set distance upper bound to {:.4f}'
.format(self._distance_upper_bound))
return self._distance_upper_bound
@staticmethod
def compare_dists(base_data, bias_data, adder=0, scalar=1):
"""Compare two distributions using the two-sample Kolmogorov-Smirnov.
When the output is minimized, the two distributions are similar.
Parameters
----------
base_data : np.ndarray
1D array of base data observations.
bias_data : np.ndarray
1D array of biased data observations.
adder : float
Factor to adjust the biased data before comparing distributions:
bias_data * scalar + adder
scalar : float
Factor to adjust the biased data before comparing distributions:
bias_data * scalar + adder
Returns
-------
out : float
KS test statistic
"""
out = stats.ks_2samp(base_data, bias_data * scalar + adder)
return out.statistic
@classmethod
def get_node_cmd(cls, config):
"""Get a CLI call to call cls.run() on a single node based on an input
config.
Parameters
----------
config : dict
sup3r bias calc config with all necessary args and kwargs to
initialize the class and call run() on a single node.
"""
import_str = 'import time;\n'
import_str += 'from gaps import Status;\n'
import_str += 'from rex import init_logger;\n'
import_str += f'from sup3r.bias.bias_calc import {cls.__name__};\n'
if not hasattr(cls, 'run'):
msg = ('I can only get you a node command for subclasses of '
'DataRetrievalBase with a run() method.')
logger.error(msg)
raise NotImplementedError(msg)
# pylint: disable=E1101
init_str = get_fun_call_str(cls, config)
fun_str = get_fun_call_str(cls.run, config)
fun_str = fun_str.partition('.')[-1]
fun_str = 'bc.' + fun_str
log_file = config.get('log_file', None)
log_level = config.get('log_level', 'INFO')
log_arg_str = f'"sup3r", log_level="{log_level}"'
if log_file is not None:
log_arg_str += f', log_file="{log_file}"'
cmd = (f"python -c \'{import_str}\n"
"t0 = time.time();\n"
f"logger = init_logger({log_arg_str});\n"
f"bc = {init_str};\n"
f"{fun_str};\n"
"t_elap = time.time() - t0;\n")
pipeline_step = config.get('pipeline_step') or ModuleName.BIAS_CALC
cmd = BaseCLI.add_status_cmd(config, pipeline_step, cmd)
cmd += ";\'\n"
return cmd.replace('\\', '/')
def get_bias_gid(self, coord):
"""Get the bias gid from a coordinate.
Parameters
----------
coord : tuple
(lat, lon) to get data for.
Returns
-------
bias_gid : int
gid of the data to retrieve in the bias data source raster data.
The gids for this data source are the enumerated indices of the
flattened coordinate array.
d : float
Distance in decimal degrees from coord to bias gid
"""
d, i = self.bias_tree.query(coord)
bias_gid = self.bias_gid_raster.flatten()[i]
return bias_gid, d
def get_base_gid(self, bias_gid):
"""Get one or more base gid(s) corresponding to a bias gid.
Parameters
----------
bias_gid : int
gid of the data to retrieve in the bias data source raster data.
The gids for this data source are the enumerated indices of the
flattened coordinate array.
Returns
-------
dist : np.ndarray
Array of nearest neighbor distances with length equal to the number
of high-resolution baseline gids that map to the low resolution
bias gid pixel.
base_gid : np.ndarray
Array of base gids that are the nearest neighbors of bias_gid with
length equal to the number of high-resolution baseline gids that
map to the low resolution bias gid pixel.
"""
base_gid = np.where(self.nn_ind == bias_gid)[0]
dist = self.nn_dist[base_gid]
return dist, base_gid
def get_data_pair(self, coord, daily_reduction='avg'):
"""Get base and bias data observations based on a single bias gid.
Parameters
----------
coord : tuple
(lat, lon) to get data for.
daily_reduction : None | str
Option to do a reduction of the hourly+ source base data to daily
data. Can be None (no reduction, keep source time frequency), "avg"
(daily average), "max" (daily max), "min" (daily min),
"sum" (daily sum/total)
Returns
-------
base_data : np.ndarray
1D array of base data spatially averaged across the base_gid input
and possibly daily-averaged or min/max'd as well.
bias_data : np.ndarray
1D array of temporal data at the requested gid.
base_dist : np.ndarray
Array of nearest neighbor distances from coord to the base data
sites with length equal to the number of high-resolution baseline
gids that map to the low resolution bias gid pixel.
bias_dist : Float
Nearest neighbor distance from coord to the bias data site
"""
bias_gid, bias_dist = self.get_bias_gid(coord)
base_dist, base_gid = self.get_base_gid(bias_gid)
bias_data = self.get_bias_data(bias_gid)
base_data = self.get_base_data(self.base_fps,
self.base_dset,
base_gid,
self.base_handler,
daily_reduction=daily_reduction,
decimals=self.decimals)
base_data = base_data[0]
return base_data, bias_data, base_dist, bias_dist
def get_bias_data(self, bias_gid):
"""Get data from the biased data source for a single gid
Parameters
----------
bias_gid : int
gid of the data to retrieve in the bias data source raster data.
The gids for this data source are the enumerated indices of the
flattened coordinate array.
Returns
-------
bias_data : np.ndarray
1D array of temporal data at the requested gid.
"""
idx = np.where(self.bias_gid_raster == bias_gid)
if self.bias_dh.data is None:
self.bias_dh.load_cached_data()
bias_data = self.bias_dh.data[idx][0]
if bias_data.shape[-1] == 1:
bias_data = bias_data[:, 0]
else:
msg = ('Found a weird number of feature channels for the bias '
'data retrieval: {}. Need just one channel'.format(
bias_data.shape))
logger.error(msg)
raise RuntimeError(msg)
if self.decimals is not None:
bias_data = np.around(bias_data, decimals=self.decimals)
return bias_data
@classmethod
def get_base_data(cls,
base_fps,
base_dset,
base_gid,
base_handler,
base_handler_kwargs=None,
daily_reduction='avg',
decimals=None,
base_dh_inst=None):
"""Get data from the baseline data source, possibly for many high-res
base gids corresponding to a single coarse low-res bias gid.
Parameters
----------
base_fps : list | str
One or more baseline .h5 filepaths representing non-biased data to
use to correct the biased dataset. This is typically several years
of WTK or NSRDB files.
base_dset : str
A single dataset from the base_fps to retrieve.
base_gid : int | np.ndarray
One or more spatial gids to retrieve from base_fps. The data will
be spatially averaged across all of these sites.
base_handler : rex.Resource
A rex data handler similar to rex.Resource or sup3r.DataHandler
classes (if using the latter, must also input base_dh_inst)
base_handler_kwargs : dict | None
Optional kwargs to send to the initialization of the base_handler
class
daily_reduction : None | str
Option to do a reduction of the hourly+ source base data to daily
data. Can be None (no reduction, keep source time frequency), "avg"
(daily average), "max" (daily max), "min" (daily min),
"sum" (daily sum/total)
decimals : int | None
Option to round bias and base data to this number of
decimals, this gets passed to np.around(). If decimals
is negative, it specifies the number of positions to
the left of the decimal point.
base_dh_inst : sup3r.DataHandler
Instantiated DataHandler class that has already loaded the base
data (required if base files are .nc and are not being opened by a
rex Resource handler).
Returns
-------
out_data : np.ndarray
1D array of base data spatially averaged across the base_gid input
and possibly daily-averaged or min/max'd as well.
out_ti : pd.DatetimeIndex
DatetimeIndex object of datetimes corresponding to the
output data.
"""
out_data = []
out_ti = []
all_cs_ghi = []
base_handler_kwargs = base_handler_kwargs or {}
if issubclass(base_handler, DataHandler) and base_dh_inst is None:
msg = ('The method `get_base_data()` is only to be used with '
'`base_handler` as a `sup3r.DataHandler` subclass if '
'`base_dh_inst` is also provided!')
logger.error(msg)
raise RuntimeError(msg)
if issubclass(base_handler, DataHandler) and base_dh_inst is not None:
out_ti = base_dh_inst.time_index
out_data = cls._read_base_sup3r_data(base_dh_inst, base_dset,
base_gid)
all_cs_ghi = np.ones(len(out_data), dtype=np.float32) * np.nan
else:
for fp in base_fps:
with base_handler(fp, **base_handler_kwargs) as res:
base_ti = res.time_index
temp_out = cls._read_base_rex_data(res, base_dset,
base_gid)
base_data, base_cs_ghi = temp_out
out_data.append(base_data)
out_ti.append(base_ti)
all_cs_ghi.append(base_cs_ghi)
out_data = np.hstack(out_data)
out_ti = pd.DatetimeIndex(np.hstack(out_ti))
all_cs_ghi = np.hstack(all_cs_ghi)
if daily_reduction is not None:
out_data, out_ti = cls._reduce_base_data(out_ti,
out_data,
all_cs_ghi,
base_dset,
daily_reduction)
if decimals is not None:
out_data = np.around(out_data, decimals=decimals)
return out_data, out_ti
@staticmethod
def _read_base_sup3r_data(dh, base_dset, base_gid):
"""Read baseline data from a sup3r DataHandler
Parameters
----------
dh : sup3r.DataHandler
sup3r DataHandler that is an open file handler of the base file(s)
base_dset : str
A single dataset from the base_fps to retrieve.
base_gid : int | np.ndarray
One or more spatial gids to retrieve from base_fps. The data will
be spatially averaged across all of these sites.
Returns
-------
base_data : np.ndarray
1D array of base data spatially averaged across the base_gid input
"""
idf = dh.features.index(base_dset)
gid_raster = np.arange(len(dh.meta))
gid_raster = gid_raster.reshape(dh.shape[:2])
idy, idx = np.where(np.isin(gid_raster, base_gid))
base_data = dh.data[idy, idx, :, idf]
assert base_data.shape[0] == len(base_gid)
assert base_data.shape[1] == len(dh.time_index)
return base_data.mean(axis=0)
@staticmethod
def _read_base_rex_data(res, base_dset, base_gid):
"""Read baseline data from a rex resource handler with extra logic for
special datasets (e.g. u/v wind components or clearsky_ratio)
Parameters
----------
res : rex.Resource
rex Resource handler that is an open file handler of the base
file(s)
base_dset : str
A single dataset from the base_fps to retrieve.
base_gid : int | np.ndarray
One or more spatial gids to retrieve from base_fps. The data will
be spatially averaged across all of these sites.
Returns
-------
base_data : np.ndarray
1D array of base data spatially averaged across the base_gid input
base_cs_ghi : np.ndarray
If base_dset == "clearsky_ratio", the base_data array is GHI and
this base_cs_ghi is clearsky GHI. Otherwise this is an array with
same length as base_data but full of np.nan
"""
msg = '`res` input must not be a `DataHandler` subclass!'
assert not issubclass(res.__class__, DataHandler), msg
base_cs_ghi = None
if base_dset.startswith(('U_', 'V_')):
dset_ws = base_dset.replace('U_', 'windspeed_')
dset_ws = dset_ws.replace('V_', 'windspeed_')
dset_wd = dset_ws.replace('speed', 'direction')
base_ws = res[dset_ws, :, base_gid]
base_wd = res[dset_wd, :, base_gid]
if base_dset.startswith('U_'):
base_data = -base_ws * np.sin(np.radians(base_wd))
else:
base_data = -base_ws * np.cos(np.radians(base_wd))
elif base_dset == 'clearsky_ratio':
base_data = res['ghi', :, base_gid]
base_cs_ghi = res['clearsky_ghi', :, base_gid]
else:
base_data = res[base_dset, :, base_gid]
if len(base_data.shape) == 2:
base_data = np.nanmean(base_data, axis=1)
if base_cs_ghi is not None:
base_cs_ghi = np.nanmean(base_cs_ghi, axis=1)
if base_cs_ghi is None:
base_cs_ghi = np.ones(len(base_data), dtype=np.float32) * np.nan
return base_data, base_cs_ghi
@staticmethod
def _reduce_base_data(base_ti, base_data, base_cs_ghi, base_dset,
daily_reduction):
"""Reduce the base timeseries data using some sort of daily reduction
function.
Parameters
----------
base_ti : pd.DatetimeIndex
Time index associated with base_data
base_data : np.ndarray
1D array of base data spatially averaged across the base_gid input
base_cs_ghi : np.ndarray
If base_dset == "clearsky_ratio", the base_data array is GHI and
this base_cs_ghi is clearsky GHI. Otherwise this is an array with
same length as base_data but full of np.nan
base_dset : str
A single dataset from the base_fps to retrieve.
daily_reduction : str
Option to do a reduction of the hourly+ source base data to daily
data. Can be None (no reduction, keep source time frequency), "avg"
(daily average), "max" (daily max), "min" (daily min),
"sum" (daily sum/total)
Returns
-------
base_data : np.ndarray
1D array of base data spatially averaged across the base_gid input
and possibly daily-averaged or min/max'd as well.
daily_ti : pd.DatetimeIndex
Daily DatetimeIndex corresponding to the daily base_data
"""
if daily_reduction is None:
return base_data
daily_ti = pd.DatetimeIndex(sorted(set(base_ti.date)))
df = pd.DataFrame({'date': base_ti.date,
'base_data': base_data,
'base_cs_ghi': base_cs_ghi})
cs_ratio = (daily_reduction.lower() in ('avg', 'average', 'mean')
and base_dset == 'clearsky_ratio')
if cs_ratio:
daily_ghi = df.groupby('date').sum()['base_data'].values
daily_cs_ghi = df.groupby('date').sum()['base_cs_ghi'].values
base_data = daily_ghi / daily_cs_ghi
msg = ('Could not calculate daily average "clearsky_ratio" with '
'base_data and base_cs_ghi inputs: \n{}, \n{}'
.format(base_data, base_cs_ghi))
assert not np.isnan(base_data).any(), msg
elif daily_reduction.lower() in ('avg', 'average', 'mean'):
base_data = df.groupby('date').mean()['base_data'].values
elif daily_reduction.lower() in ('max', 'maximum'):
base_data = df.groupby('date').max()['base_data'].values
elif daily_reduction.lower() in ('min', 'minimum'):
base_data = df.groupby('date').min()['base_data'].values
elif daily_reduction.lower() in ('sum', 'total'):
base_data = df.groupby('date').sum()['base_data'].values
msg = (f'Daily reduced base data shape {base_data.shape} does not '
f'match daily time index shape {daily_ti.shape}, '
'something went wrong!')
assert len(base_data.shape) == 1, msg
assert base_data.shape == daily_ti.shape, msg
return base_data, daily_ti
class LinearCorrection(DataRetrievalBase):
"""Calculate linear correction *scalar +adder factors to bias correct data
This calculation operates on single bias sites for the full time series of
available data (no season bias correction)
"""
NT = 1
"""size of the time dimension, 1 is no time-based bias correction"""
def _init_out(self):
"""Initialize output arrays"""
keys = [f'{self.bias_feature}_scalar',
f'{self.bias_feature}_adder',
f'bias_{self.bias_feature}_mean',
f'bias_{self.bias_feature}_std',
f'base_{self.base_dset}_mean',
f'base_{self.base_dset}_std',
]
self.out = {k: np.full((*self.bias_gid_raster.shape, self.NT),
np.nan, np.float32)
for k in keys}
@staticmethod
def get_linear_correction(bias_data, base_data, bias_feature, base_dset):
"""Get the linear correction factors based on 1D bias and base datasets
Parameters
----------
bias_data : np.ndarray
1D array of biased data observations.
base_data : np.ndarray
1D array of base data observations.
bias_feature : str
This is the biased feature from bias_fps to retrieve. This should
be a single feature name corresponding to base_dset
base_dset : str
A single dataset from the base_fps to retrieve. In the case of wind
components, this can be U_100m or V_100m which will retrieve
windspeed and winddirection and derive the U/V component.
Returns
-------
out : dict
Dictionary of values defining the mean/std of the bias + base
data and the scalar + adder factors to correct the biased data
like: bias_data * scalar + adder
"""
bias_std = np.nanstd(bias_data)
if bias_std == 0:
bias_std = np.nanstd(base_data)
scalar = np.nanstd(base_data) / bias_std
adder = np.nanmean(base_data) - np.nanmean(bias_data) * scalar
out = {
f'bias_{bias_feature}_mean': np.nanmean(bias_data),
f'bias_{bias_feature}_std': bias_std,
f'base_{base_dset}_mean': np.nanmean(base_data),
f'base_{base_dset}_std': np.nanstd(base_data),
f'{bias_feature}_scalar': scalar,
f'{bias_feature}_adder': adder,
}
return out
# pylint: disable=W0613
@classmethod
def _run_single(cls,
bias_data,
base_fps,
bias_feature,
base_dset,
base_gid,
base_handler,
daily_reduction,
bias_ti,
decimals,
base_dh_inst=None):
"""Find the nominal scalar + adder combination to bias correct data
at a single site"""
base_data, _ = cls.get_base_data(base_fps,
base_dset,
base_gid,
base_handler,
daily_reduction=daily_reduction,
decimals=decimals,
base_dh_inst=base_dh_inst)
out = cls.get_linear_correction(bias_data, base_data, bias_feature,
base_dset)
return out
def fill_and_smooth(self,
out,
fill_extend=True,
smooth_extend=0,
smooth_interior=0):
"""Fill data extending beyond the base meta data extent by doing a
nearest neighbor gap fill. Smooth interior and extended region with
given smoothing values.
Interior smoothing can reduce the affect of extreme values
within aggregations over large number of pixels.
The interior is assumed to be defined by the region without nan values.
The extended region is assumed to be the region with nan values.
Parameters
----------
out : dict
Dictionary of values defining the mean/std of the bias + base
data and the scalar + adder factors to correct the biased data
like: bias_data * scalar + adder. Each value is of shape
(lat, lon, time).
fill_extend : bool
Whether to fill data extending beyond the base meta data with
nearest neighbor values.
smooth_extend : float
Option to smooth the scalar/adder data outside of the spatial
domain set by the threshold input. This alleviates the weird seams
far from the domain of interest. This value is the standard
deviation for the gaussian_filter kernel
smooth_interior : float
Value to use to smooth the scalar/adder data inside of the spatial
domain set by the threshold input. This can reduce the effect of
extreme values within aggregations over large number of pixels.
This value is the standard deviation for the gaussian_filter
kernel.
Returns
-------
out : dict
Dictionary of values defining the mean/std of the bias + base
data and the scalar + adder factors to correct the biased data
like: bias_data * scalar + adder. Each value is of shape
(lat, lon, time).
"""
if len(self.bad_bias_gids) > 0:
logger.info('Found {} bias gids that are out of bounds: {}'
.format(len(self.bad_bias_gids), self.bad_bias_gids))
for key, arr in out.items():
nan_mask = np.isnan(arr[..., 0])
for idt in range(arr.shape[-1]):
arr_smooth = arr[..., idt]
needs_fill = (np.isnan(arr_smooth).any()
and fill_extend) or smooth_interior > 0
if needs_fill:
logger.info('Filling NaN values outside of valid spatial '
'extent for dataset "{}" for timestep {}'
.format(key, idt))
arr_smooth = nn_fill_array(arr_smooth)
arr_smooth_int = arr_smooth_ext = arr_smooth
if smooth_extend > 0:
arr_smooth_ext = gaussian_filter(arr_smooth_ext,
smooth_extend,
mode='nearest')
if smooth_interior > 0:
arr_smooth_int = gaussian_filter(arr_smooth_int,
smooth_interior,
mode='nearest')
out[key][nan_mask, idt] = arr_smooth_ext[nan_mask]
out[key][~nan_mask, idt] = arr_smooth_int[~nan_mask]
return out
def write_outputs(self, fp_out, out):
"""Write outputs to an .h5 file.
Parameters
----------
fp_out : str | None
Optional .h5 output file to write scalar and adder arrays.
out : dict
Dictionary of values defining the mean/std of the bias + base
data and the scalar + adder factors to correct the biased data
like: bias_data * scalar + adder. Each value is of shape
(lat, lon, time).
"""
if fp_out is not None:
if not os.path.exists(os.path.dirname(fp_out)):
os.makedirs(os.path.dirname(fp_out), exist_ok=True)
with h5py.File(fp_out, 'w') as f:
# pylint: disable=E1136
lat = self.bias_dh.lat_lon[..., 0]
lon = self.bias_dh.lat_lon[..., 1]
f.create_dataset('latitude', data=lat)
f.create_dataset('longitude', data=lon)
for dset, data in out.items():
f.create_dataset(dset, data=data)
for k, v in self.meta.items():
f.attrs[k] = json.dumps(v)
logger.info(
'Wrote scalar adder factors to file: {}'.format(fp_out))
def run(self,
fp_out=None,
max_workers=None,
daily_reduction='avg',
fill_extend=True,
smooth_extend=0,
smooth_interior=0):
"""Run linear correction factor calculations for every site in the bias
dataset
Parameters
----------
fp_out : str | None
Optional .h5 output file to write scalar and adder arrays.
max_workers : int
Number of workers to run in parallel. 1 is serial and None is all
available.
daily_reduction : None | str
Option to do a reduction of the hourly+ source base data to daily
data. Can be None (no reduction, keep source time frequency), "avg"
(daily average), "max" (daily max), "min" (daily min),
"sum" (daily sum/total)
fill_extend : bool
Flag to fill data past distance_upper_bound using spatial nearest
neighbor. If False, the extended domain will be left as NaN.
smooth_extend : float
Option to smooth the scalar/adder data outside of the spatial
domain set by the distance_upper_bound input. This alleviates the
weird seams far from the domain of interest. This value is the
standard deviation for the gaussian_filter kernel
smooth_interior : float
Option to smooth the scalar/adder data within the valid spatial
domain. This can reduce the affect of extreme values within
aggregations over large number of pixels.
Returns
-------
out : dict
Dictionary of values defining the mean/std of the bias + base
data and the scalar + adder factors to correct the biased data
like: bias_data * scalar + adder. Each value is of shape
(lat, lon, time).
"""
logger.debug('Starting linear correction calculation...')
logger.info('Initialized scalar / adder with shape: {}'
.format(self.bias_gid_raster.shape))
self.bad_bias_gids = []
# sup3r DataHandler opening base files will load all data in parallel
# during the init and should not be passed in parallel to workers
if isinstance(self.base_dh, DataHandler):
max_workers = 1
if max_workers == 1:
logger.debug('Running serial calculation.')
for i, bias_gid in enumerate(self.bias_meta.index):
raster_loc = np.where(self.bias_gid_raster == bias_gid)
_, base_gid = self.get_base_gid(bias_gid)
if not base_gid.any():
self.bad_bias_gids.append(bias_gid)
else:
bias_data = self.get_bias_data(bias_gid)
single_out = self._run_single(
bias_data,
self.base_fps,
self.bias_feature,
self.base_dset,
base_gid,
self.base_handler,
daily_reduction,
self.bias_ti,
self.decimals,
base_dh_inst=self.base_dh,
)
for key, arr in single_out.items():
self.out[key][raster_loc] = arr
logger.info('Completed bias calculations for {} out of {} '
'sites'.format(i + 1, len(self.bias_meta)))
else:
logger.debug(
'Running parallel calculation with {} workers.'.format(
max_workers))
with ProcessPoolExecutor(max_workers=max_workers) as exe:
futures = {}
for bias_gid in self.bias_meta.index:
raster_loc = np.where(self.bias_gid_raster == bias_gid)
_, base_gid = self.get_base_gid(bias_gid)
if not base_gid.any():
self.bad_bias_gids.append(bias_gid)
else:
bias_data = self.get_bias_data(bias_gid)
future = exe.submit(
self._run_single,
bias_data,
self.base_fps,
self.bias_feature,
self.base_dset,
base_gid,
self.base_handler,
daily_reduction,
self.bias_ti,
self.decimals,
)
futures[future] = raster_loc
logger.debug('Finished launching futures.')
for i, future in enumerate(as_completed(futures)):
raster_loc = futures[future]
single_out = future.result()
for key, arr in single_out.items():
self.out[key][raster_loc] = arr
logger.info('Completed bias calculations for {} out of {} '
'sites'.format(i + 1, len(futures)))
logger.info('Finished calculating bias correction factors.')
self.out = self.fill_and_smooth(self.out, fill_extend, smooth_extend,
smooth_interior)
self.write_outputs(fp_out, self.out)
return copy.deepcopy(self.out)
class MonthlyLinearCorrection(LinearCorrection):
"""Calculate linear correction *scalar +adder factors to bias correct data
This calculation operates on single bias sites on a montly basis
"""
NT = 12
"""size of the time dimension, 12 is monthly bias correction"""
@classmethod
def _run_single(cls,
bias_data,