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# Copyright (c) 2013-2018 Python-geotiepoints developers
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
"""Generic interpolation routines."""
from abc import ABC, abstractmethod
from functools import partial
import numpy as np
from scipy.interpolate import RectBivariateSpline, splev, splrep, RegularGridInterpolator
def generic_modis5kmto1km(*data5km):
"""Get 1km data for modis from 5km tiepoints."""
cols5km = np.arange(2, 1354, 5)
cols1km = np.arange(1354)
lines = data5km[0].shape[0] * 5
rows5km = np.arange(2, lines, 5)
rows1km = np.arange(lines)
along_track_order = 1
cross_track_order = 3
satint = Interpolator(list(data5km),
(rows5km, cols5km),
(rows1km, cols1km),
along_track_order,
cross_track_order,
chunk_size=10)
satint.fill_borders("y", "x")
return satint.interpolate()
# NOTE: extrapolate on a sphere ?
def _linear_extrapolate(pos, data, xev):
"""Perform linear extrapolation.
>>> import numpy as np
>>> pos = np.array([1, 2])
>>> data = np.arange(10).reshape((2, 5), order="F")
>>> xev = 5
>>> retv = _linear_extrapolate(pos, data, xev)
>>> print([val for val in retv])
[4.0, 6.0, 8.0, 10.0, 12.0]
>>> xev = 0
>>> retv = _linear_extrapolate(pos, data, xev)
>>> print([val for val in retv])
[-1.0, 1.0, 3.0, 5.0, 7.0]
"""
if len(data) != 2 or len(pos) != 2:
raise ValueError("len(pos) and the number of lines of data"
" must be 2.")
return data[1] + ((xev - pos[1]) / (1.0 * (pos[0] - pos[1])) * (data[0] - data[1]))
class Interpolator:
"""Handles interpolation of data from a grid of tie points.
It is preferable to have tie-points out till the edges if the tiepoint grid,
but a method is provided to extrapolate linearly the tiepoints to the borders of the
grid. The extrapolation is done automatically if it seems necessary.
Uses numpy and scipy.
The constructor takes in the tiepointed data as *data*, the *tiepoint_grid* and the desired *final_grid*. As
optional arguments, one can provide *kx_* and *ky_* as interpolation orders (in x and y directions respectively),
and the *chunksize* if the data has to be handled by pieces along the y axis (this affects how the extrapolator
behaves). If *chunksize* is set, don't forget to adjust the interpolation orders accordingly: the interpolation
is indeed done globaly (not chunkwise).
"""
def __init__(self, data, tiepoint_grid, final_grid,
kx_=1, ky_=1, chunk_size=0):
self.row_indices = tiepoint_grid[0]
self.col_indices = tiepoint_grid[1]
self.hrow_indices = final_grid[0]
self.hcol_indices = final_grid[1]
self.chunk_size = chunk_size
if not isinstance(data, (tuple, list)):
self.tie_data = [data]
else:
self.tie_data = list(data)
self.new_data = [[] for _ in self.tie_data]
self.kx_, self.ky_ = kx_, ky_
def fill_borders(self, *args):
"""Extrapolate tiepoint lons and lats to fill in the border of the chunks."""
to_run = []
cases = {"y": self._fill_row_borders,
"x": self._fill_col_borders}
for dim in args:
try:
to_run.append(cases[dim])
except KeyError:
raise NameError("Unrecognized dimension: " + str(dim))
for fun in to_run:
fun()
def _extrapolate_cols(self, data, first=True, last=True):
"""Extrapolate the column of data, to get the first and last together with the data."""
if first:
pos = self.col_indices[:2]
first_column = _linear_extrapolate(pos,
(data[:, 0], data[:, 1]),
self.hcol_indices[0])
if last:
pos = self.col_indices[-2:]
last_column = _linear_extrapolate(pos,
(data[:, -2], data[:, -1]),
self.hcol_indices[-1])
if first and last:
return np.hstack((np.expand_dims(first_column, 1),
data,
np.expand_dims(last_column, 1)))
elif first:
return np.hstack((np.expand_dims(first_column, 1),
data))
elif last:
return np.hstack((data,
np.expand_dims(last_column, 1)))
else:
return data
def _fill_col_borders(self):
"""Add the first and last column to the data by extrapolation."""
first = True
last = True
if self.col_indices[0] == self.hcol_indices[0]:
first = False
if self.col_indices[-1] == self.hcol_indices[-1]:
last = False
for num, data in enumerate(self.tie_data):
self.tie_data[num] = self._extrapolate_cols(data, first, last)
if first and last:
self.col_indices = np.concatenate((np.array([self.hcol_indices[0]]),
self.col_indices,
np.array([self.hcol_indices[-1]])))
elif first:
self.col_indices = np.concatenate((np.array([self.hcol_indices[0]]),
self.col_indices))
elif last:
self.col_indices = np.concatenate((self.col_indices,
np.array([self.hcol_indices[-1]])))
def _extrapolate_rows(self, data, row_indices, first_index, last_index):
"""Extrapolate the rows of data, to get the first and last together with the data."""
pos = row_indices[:2]
first_row = _linear_extrapolate(pos,
(data[0, :], data[1, :]),
first_index)
pos = row_indices[-2:]
last_row = _linear_extrapolate(pos,
(data[-2, :], data[-1, :]),
last_index)
return np.vstack((np.expand_dims(first_row, 0),
data,
np.expand_dims(last_row, 0)))
def _fill_row_borders(self):
"""Add the first and last rows to the data by extrapolation."""
lines = len(self.hrow_indices)
chunk_size = self.chunk_size or lines
factor = len(self.hrow_indices) / len(self.row_indices)
tmp_data = []
for _num in range(len(self.tie_data)):
tmp_data.append([])
row_indices = []
for index in range(0, lines, chunk_size):
indices = np.logical_and(self.row_indices >= index / factor,
self.row_indices < (index + chunk_size) / factor)
ties = np.argwhere(indices).squeeze()
tiepos = self.row_indices[indices].squeeze()
for num, data in enumerate(self.tie_data):
to_extrapolate = data[ties, :]
if len(to_extrapolate) > 0:
extrapolated = self._extrapolate_rows(to_extrapolate,
tiepos,
self.hrow_indices[
index],
self.hrow_indices[index + chunk_size - 1])
tmp_data[num].append(extrapolated)
row_indices.append(np.array([self.hrow_indices[index]]))
row_indices.append(tiepos)
row_indices.append(np.array([self.hrow_indices[index + chunk_size - 1]]))
for num in range(len(self.tie_data)):
self.tie_data[num] = np.vstack(tmp_data[num])
self.row_indices = np.concatenate(row_indices)
def _interp(self):
"""Interpolate the cartesian coordinates."""
if np.array_equal(self.hrow_indices, self.row_indices):
return self._interp1d()
for num, data in enumerate(self.tie_data):
spl = RectBivariateSpline(self.row_indices,
self.col_indices,
data,
s=0,
kx=self.kx_,
ky=self.ky_)
self.new_data[num] = spl(self.hrow_indices, self.hcol_indices, grid=True)
def _interp1d(self):
"""Interpolate in one dimension."""
lines = len(self.hrow_indices)
for num, data in enumerate(self.tie_data):
self.new_data[num] = np.empty((len(self.hrow_indices),
len(self.hcol_indices)),
data.dtype)
for cnt in range(lines):
tck = splrep(self.col_indices, data[cnt, :], k=self.ky_, s=0)
self.new_data[num][cnt, :] = splev(
self.hcol_indices, tck, der=0)
def interpolate(self):
"""Do the interpolation, and return resulting longitudes and latitudes."""
self._interp()
return self.new_data
class AbstractSingleInterpolator(ABC):
"""An abstract interpolator for a single 2d data array."""
def __init__(self, points, values, scipy_interpolator, **interpolator_init_kwargs):
"""Set up the interpolator.
*kwargs* are passed to the underlying scipy interpolator instance.
So for example, to allow extrapolation, the kwargs can be `bounds_error=False, fill_value=None`.
"""
self.interpolator = scipy_interpolator(points, values, **interpolator_init_kwargs)
self.points = points
self.values = values
def interpolate(self, fine_points, chunks=None, **interpolator_call_kwargs):
"""Interpolate the value points to the *fine_points* grid.
Args:
fine_points: the points on the target grid to use, as one dimensional vectors for each dimension.
chunks: If not None, a lazy (dask-based) interpolation will be performed using the chunk sizes specified.
The result will be a dask array in this case. Defaults to None.
interpolator_kwargs: The keyword arguments to pass to the underlying scipy interpolator.
"""
if chunks is not None:
res = self.interpolate_dask(fine_points, chunks=chunks, **interpolator_call_kwargs)
else:
res = self.interpolate_numpy(fine_points, **interpolator_call_kwargs)
return res
def interpolate_dask(self, fine_points, chunks, **interpolator_call_kwargs):
"""Interpolate (lazily) to a dask array."""
from dask.base import tokenize
import dask.array as da
from dask.array.core import normalize_chunks
v_fine_points, h_fine_points = fine_points
shape = len(v_fine_points), len(h_fine_points)
chunks = normalize_chunks(chunks, shape, dtype=self.values.dtype)
token = tokenize(chunks, self.points, self.values, fine_points, interpolator_call_kwargs)
name = 'interpolate-' + token
interpolate_slices = partial(self.interpolate_slices, **interpolator_call_kwargs)
dskx = {(name, ) + position: (interpolate_slices,
slices)
for position, slices in _enumerate_chunk_slices(chunks)}
res = da.Array(dskx, name, shape=list(shape),
chunks=chunks,
dtype=self.values.dtype)
return res
@abstractmethod
def interpolate_numpy(self, fine_points, **interpolator_call_kwargs):
"""Interpolate to a numpy array."""
raise NotImplementedError
def interpolate_slices(self, fine_points, **interpolator_call_kwargs):
"""Interpolate using slices.
*fine_points* are a tuple of slices for the y and x dimensions
"""
slice_y, slice_x = fine_points
points_y = np.arange(slice_y.start, slice_y.stop)
points_x = np.arange(slice_x.start, slice_x.stop)
fine_points = points_y, points_x
return self.interpolate_numpy(fine_points, **interpolator_call_kwargs)
def _enumerate_chunk_slices(chunks):
"""Enumerate chunks with slices."""
for position in np.ndindex(tuple(map(len, (chunks)))):
slices = []
for pos, chunk in zip(position, chunks):
chunk_size = chunk[pos]
offset = sum(chunk[:pos])
slices.append(slice(offset, offset + chunk_size))
yield (position, slices)
class SingleGridInterpolator(AbstractSingleInterpolator):
"""A regular grid interpolator for a single 2d data array."""
def __init__(self, *args, **interpolator_init_kwargs):
"""Set up the grid interpolator."""
super().__init__(*args, scipy_interpolator=RegularGridInterpolator, **interpolator_init_kwargs)
def interpolate_numpy(self, fine_points, **interpolator_call_kwargs):
"""Interpolate to a numpy array."""
fine_x, fine_y = np.meshgrid(*fine_points, indexing='ij')
return self.interpolator((fine_x, fine_y), **interpolator_call_kwargs).astype(self.values.dtype)
class SingleSplineInterpolator(AbstractSingleInterpolator):
"""An spline interpolator for a single 2d data array."""
def __init__(self, points, values, **interpolator_init_kwargs):
"""Set up the spline interpolator."""
self.interpolator = RectBivariateSpline(*points, values, **interpolator_init_kwargs)
self.points = points
self.values = values
def interpolate_numpy(self, fine_points, **interpolator_call_kwargs):
"""Interpolate to a numpy array."""
return self.interpolator(*fine_points, **interpolator_call_kwargs).astype(self.values.dtype)
class AbstractMultipleInterpolator(ABC): # noqa: B024
"""Abstract interpolator that works on mulitple arrays."""
def __init__(self, interpolator, tie_points, *data, **interpolator_init_kwargs):
"""Set up the interpolator from the multiple `data` arrays."""
self.interpolators = []
for values in data:
self.interpolators.append(interpolator(tie_points, values, **interpolator_init_kwargs))
def interpolate(self, fine_points, **kwargs):
"""Interpolate the data.
The keyword arguments will be passed on to SingleGridInterpolator's interpolate function.
"""
return (interpolator.interpolate(fine_points, **kwargs) for interpolator in self.interpolators)
def interpolate_to_shape(self, shape, **interpolator_call_kwargs):
"""Interpolate to a given *shape*."""
fine_points = [np.arange(size) for size in shape]
return self.interpolate(fine_points, **interpolator_call_kwargs)
class MultipleGridInterpolator(AbstractMultipleInterpolator):
"""Grid interpolator that works on multiple data arrays."""
def __init__(self, tie_points, *data, **interpolator_init_kwargs):
"""Set up the interpolator from the multiple `data` arrays."""
super().__init__(SingleGridInterpolator, tie_points, *data, **interpolator_init_kwargs)
class MultipleSplineInterpolator(AbstractMultipleInterpolator):
"""Spline interpolator that works on multiple data arrays."""
def __init__(self, tie_points, *data, **interpolator_init_kwargs):
"""Set up the interpolator from the multiple `data` arrays."""
super().__init__(SingleSplineInterpolator, tie_points, *data, **interpolator_init_kwargs)
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