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# -*- coding: utf-8 -*-
"""
Exact solvers for the 1D Wasserstein distance using cvxopt
"""
# Author: Remi Flamary <remi.flamary@unice.fr>
# Author: Nicolas Courty <ncourty@irisa.fr>
#
# License: MIT License
import numpy as np
import warnings
from .emd_wrap import emd_1d_sorted
from ..backend import get_backend
from ..utils import list_to_array
def quantile_function(qs, cws, xs):
r""" Computes the quantile function of an empirical distribution
Parameters
----------
qs: array-like, shape (n,)
Quantiles at which the quantile function is evaluated
cws: array-like, shape (m, ...)
cumulative weights of the 1D empirical distribution, if batched, must be similar to xs
xs: array-like, shape (n, ...)
locations of the 1D empirical distribution, batched against the `xs.ndim - 1` first dimensions
Returns
-------
q: array-like, shape (..., n)
The quantiles of the distribution
"""
nx = get_backend(qs, cws)
n = xs.shape[0]
if nx.__name__ == 'torch':
# this is to ensure the best performance for torch searchsorted
# and avoid a warninng related to non-contiguous arrays
cws = cws.T.contiguous()
qs = qs.T.contiguous()
else:
cws = cws.T
qs = qs.T
idx = nx.searchsorted(cws, qs).T
return nx.take_along_axis(xs, nx.clip(idx, 0, n - 1), axis=0)
def wasserstein_1d(u_values, v_values, u_weights=None, v_weights=None, p=1, require_sort=True):
r"""
Computes the 1 dimensional OT loss [15] between two (batched) empirical
distributions
.. math:
OT_{loss} = \int_0^1 |cdf_u^{-1}(q) cdf_v^{-1}(q)|^p dq
It is formally the p-Wasserstein distance raised to the power p.
We do so in a vectorized way by first building the individual quantile functions then integrating them.
This function should be preferred to `emd_1d` whenever the backend is
different to numpy, and when gradients over
either sample positions or weights are required.
Parameters
----------
u_values: array-like, shape (n, ...)
locations of the first empirical distribution
v_values: array-like, shape (m, ...)
locations of the second empirical distribution
u_weights: array-like, shape (n, ...), optional
weights of the first empirical distribution, if None then uniform weights are used
v_weights: array-like, shape (m, ...), optional
weights of the second empirical distribution, if None then uniform weights are used
p: int, optional
order of the ground metric used, should be at least 1 (see [2, Chap. 2], default is 1
require_sort: bool, optional
sort the distributions atoms locations, if False we will consider they have been sorted prior to being passed to
the function, default is True
Returns
-------
cost: float/array-like, shape (...)
the batched EMD
References
----------
.. [15] Peyré, G., & Cuturi, M. (2018). Computational Optimal Transport.
"""
assert p >= 1, "The OT loss is only valid for p>=1, {p} was given".format(p=p)
if u_weights is not None and v_weights is not None:
nx = get_backend(u_values, v_values, u_weights, v_weights)
else:
nx = get_backend(u_values, v_values)
n = u_values.shape[0]
m = v_values.shape[0]
if u_weights is None:
u_weights = nx.full(u_values.shape, 1. / n, type_as=u_values)
elif u_weights.ndim != u_values.ndim:
u_weights = nx.repeat(u_weights[..., None], u_values.shape[-1], -1)
if v_weights is None:
v_weights = nx.full(v_values.shape, 1. / m, type_as=v_values)
elif v_weights.ndim != v_values.ndim:
v_weights = nx.repeat(v_weights[..., None], v_values.shape[-1], -1)
if require_sort:
u_sorter = nx.argsort(u_values, 0)
u_values = nx.take_along_axis(u_values, u_sorter, 0)
v_sorter = nx.argsort(v_values, 0)
v_values = nx.take_along_axis(v_values, v_sorter, 0)
u_weights = nx.take_along_axis(u_weights, u_sorter, 0)
v_weights = nx.take_along_axis(v_weights, v_sorter, 0)
u_cumweights = nx.cumsum(u_weights, 0)
v_cumweights = nx.cumsum(v_weights, 0)
qs = nx.sort(nx.concatenate((u_cumweights, v_cumweights), 0), 0)
u_quantiles = quantile_function(qs, u_cumweights, u_values)
v_quantiles = quantile_function(qs, v_cumweights, v_values)
qs = nx.zero_pad(qs, pad_width=[(1, 0)] + (qs.ndim - 1) * [(0, 0)])
delta = qs[1:, ...] - qs[:-1, ...]
diff_quantiles = nx.abs(u_quantiles - v_quantiles)
if p == 1:
return nx.sum(delta * nx.abs(diff_quantiles), axis=0)
return nx.sum(delta * nx.power(diff_quantiles, p), axis=0)
def emd_1d(x_a, x_b, a=None, b=None, metric='sqeuclidean', p=1., dense=True,
log=False):
r"""Solves the Earth Movers distance problem between 1d measures and returns
the OT matrix
.. math::
\gamma = arg\min_\gamma \sum_i \sum_j \gamma_{ij} d(x_a[i], x_b[j])
s.t. \gamma 1 = a,
\gamma^T 1= b,
\gamma\geq 0
where :
- d is the metric
- x_a and x_b are the samples
- a and b are the sample weights
When 'minkowski' is used as a metric, :math:`d(x, y) = |x - y|^p`.
Uses the algorithm detailed in [1]_
Parameters
----------
x_a : (ns,) or (ns, 1) ndarray, float64
Source dirac locations (on the real line)
x_b : (nt,) or (ns, 1) ndarray, float64
Target dirac locations (on the real line)
a : (ns,) ndarray, float64, optional
Source histogram (default is uniform weight)
b : (nt,) ndarray, float64, optional
Target histogram (default is uniform weight)
metric: str, optional (default='sqeuclidean')
Metric to be used. Only strings listed in :func:`ot.dist` are accepted.
Due to implementation details, this function runs faster when
`'sqeuclidean'`, `'cityblock'`, or `'euclidean'` metrics are used.
p: float, optional (default=1.0)
The p-norm to apply for if metric='minkowski'
dense: boolean, optional (default=True)
If True, returns math:`\gamma` as a dense ndarray of shape (ns, nt).
Otherwise returns a sparse representation using scipy's `coo_matrix`
format. Due to implementation details, this function runs faster when
`'sqeuclidean'`, `'minkowski'`, `'cityblock'`, or `'euclidean'` metrics
are used.
log: boolean, optional (default=False)
If True, returns a dictionary containing the cost.
Otherwise returns only the optimal transportation matrix.
Returns
-------
gamma: (ns, nt) ndarray
Optimal transportation matrix for the given parameters
log: dict
If input log is True, a dictionary containing the cost
Examples
--------
Simple example with obvious solution. The function emd_1d accepts lists and
performs automatic conversion to numpy arrays
>>> import ot
>>> a=[.5, .5]
>>> b=[.5, .5]
>>> x_a = [2., 0.]
>>> x_b = [0., 3.]
>>> ot.emd_1d(x_a, x_b, a, b)
array([[0. , 0.5],
[0.5, 0. ]])
>>> ot.emd_1d(x_a, x_b)
array([[0. , 0.5],
[0.5, 0. ]])
References
----------
.. [1] Peyré, G., & Cuturi, M. (2017). "Computational Optimal
Transport", 2018.
See Also
--------
ot.lp.emd : EMD for multidimensional distributions
ot.lp.emd2_1d : EMD for 1d distributions (returns cost instead of the
transportation matrix)
"""
a, b, x_a, x_b = list_to_array(a, b, x_a, x_b)
nx = get_backend(x_a, x_b)
assert (x_a.ndim == 1 or x_a.ndim == 2 and x_a.shape[1] == 1), \
"emd_1d should only be used with monodimensional data"
assert (x_b.ndim == 1 or x_b.ndim == 2 and x_b.shape[1] == 1), \
"emd_1d should only be used with monodimensional data"
# if empty array given then use uniform distributions
if a is None or a.ndim == 0 or len(a) == 0:
a = nx.ones((x_a.shape[0],), type_as=x_a) / x_a.shape[0]
if b is None or b.ndim == 0 or len(b) == 0:
b = nx.ones((x_b.shape[0],), type_as=x_b) / x_b.shape[0]
# ensure that same mass
np.testing.assert_almost_equal(
nx.to_numpy(nx.sum(a, axis=0)),
nx.to_numpy(nx.sum(b, axis=0)),
err_msg='a and b vector must have the same sum'
)
b = b * nx.sum(a) / nx.sum(b)
x_a_1d = nx.reshape(x_a, (-1,))
x_b_1d = nx.reshape(x_b, (-1,))
perm_a = nx.argsort(x_a_1d)
perm_b = nx.argsort(x_b_1d)
G_sorted, indices, cost = emd_1d_sorted(
nx.to_numpy(a[perm_a]).astype(np.float64),
nx.to_numpy(b[perm_b]).astype(np.float64),
nx.to_numpy(x_a_1d[perm_a]).astype(np.float64),
nx.to_numpy(x_b_1d[perm_b]).astype(np.float64),
metric=metric, p=p
)
G = nx.coo_matrix(
G_sorted,
perm_a[indices[:, 0]],
perm_b[indices[:, 1]],
shape=(a.shape[0], b.shape[0]),
type_as=x_a
)
if dense:
G = nx.todense(G)
elif str(nx) == "jax":
warnings.warn("JAX does not support sparse matrices, converting to dense")
if log:
log = {'cost': nx.from_numpy(cost, type_as=x_a)}
return G, log
return G
def emd2_1d(x_a, x_b, a=None, b=None, metric='sqeuclidean', p=1., dense=True,
log=False):
r"""Solves the Earth Movers distance problem between 1d measures and returns
the loss
.. math::
\gamma = arg\min_\gamma \sum_i \sum_j \gamma_{ij} d(x_a[i], x_b[j])
s.t. \gamma 1 = a,
\gamma^T 1= b,
\gamma\geq 0
where :
- d is the metric
- x_a and x_b are the samples
- a and b are the sample weights
When 'minkowski' is used as a metric, :math:`d(x, y) = |x - y|^p`.
Uses the algorithm detailed in [1]_
Parameters
----------
x_a : (ns,) or (ns, 1) ndarray, float64
Source dirac locations (on the real line)
x_b : (nt,) or (ns, 1) ndarray, float64
Target dirac locations (on the real line)
a : (ns,) ndarray, float64, optional
Source histogram (default is uniform weight)
b : (nt,) ndarray, float64, optional
Target histogram (default is uniform weight)
metric: str, optional (default='sqeuclidean')
Metric to be used. Only strings listed in :func:`ot.dist` are accepted.
Due to implementation details, this function runs faster when
`'sqeuclidean'`, `'minkowski'`, `'cityblock'`, or `'euclidean'` metrics
are used.
p: float, optional (default=1.0)
The p-norm to apply for if metric='minkowski'
dense: boolean, optional (default=True)
If True, returns math:`\gamma` as a dense ndarray of shape (ns, nt).
Otherwise returns a sparse representation using scipy's `coo_matrix`
format. Only used if log is set to True. Due to implementation details,
this function runs faster when dense is set to False.
log: boolean, optional (default=False)
If True, returns a dictionary containing the transportation matrix.
Otherwise returns only the loss.
Returns
-------
loss: float
Cost associated to the optimal transportation
log: dict
If input log is True, a dictionary containing the Optimal transportation
matrix for the given parameters
Examples
--------
Simple example with obvious solution. The function emd2_1d accepts lists and
performs automatic conversion to numpy arrays
>>> import ot
>>> a=[.5, .5]
>>> b=[.5, .5]
>>> x_a = [2., 0.]
>>> x_b = [0., 3.]
>>> ot.emd2_1d(x_a, x_b, a, b)
0.5
>>> ot.emd2_1d(x_a, x_b)
0.5
References
----------
.. [1] Peyré, G., & Cuturi, M. (2017). "Computational Optimal
Transport", 2018.
See Also
--------
ot.lp.emd2 : EMD for multidimensional distributions
ot.lp.emd_1d : EMD for 1d distributions (returns the transportation matrix
instead of the cost)
"""
# If we do not return G (log==False), then we should not to cast it to dense
# (useless overhead)
G, log_emd = emd_1d(x_a=x_a, x_b=x_b, a=a, b=b, metric=metric, p=p,
dense=dense and log, log=True)
cost = log_emd['cost']
if log:
log_emd = {'G': G}
return cost, log_emd
return cost
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