.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "_auto_examples/performances/benchmarks_ot_solvers.py"
.. LINE NUMBERS ARE GIVEN BELOW.
.. only:: html
.. note::
:class: sphx-glr-download-link-note
:ref:`Go to the end <sphx_glr_download__auto_examples_performances_benchmarks_ot_solvers.py>`
to download the full example code
.. rst-class:: sphx-glr-example-title
.. _sphx_glr__auto_examples_performances_benchmarks_ot_solvers.py:
Utility routines for benchmarks on OT solvers
===================================================
.. GENERATED FROM PYTHON SOURCE LINES 6-15
.. code-block:: Python
import time
import torch
import numpy as np
use_cuda = torch.cuda.is_available()
tensor = torch.cuda.FloatTensor if use_cuda else torch.FloatTensor
numpy = lambda x: x.detach().cpu().numpy()
.. GENERATED FROM PYTHON SOURCE LINES 16-20
3D dataset
-------------------------
Reading **.ply** files:
.. GENERATED FROM PYTHON SOURCE LINES 20-53
.. code-block:: Python
from plyfile import PlyData, PlyElement
def load_ply_file(fname, offset=[-0.011, 0.109, -0.008], scale=0.04):
"""Loads a .ply mesh to return a collection of weighted Dirac atoms: one per triangle face."""
# Load the data, and read the connectivity information:
plydata = PlyData.read(fname)
triangles = np.vstack(plydata["face"].data["vertex_indices"])
# Normalize the point cloud, as specified by the user:
points = np.vstack([[x, y, z] for (x, y, z) in plydata["vertex"]])
points -= offset
points /= 2 * scale
# Our mesh is given as a collection of ABC triangles:
A, B, C = points[triangles[:, 0]], points[triangles[:, 1]], points[triangles[:, 2]]
# Locations and weights of our Dirac atoms:
X = (A + B + C) / 3 # centers of the faces
S = np.sqrt(np.sum(np.cross(B - A, C - A) ** 2, 1)) / 2 # areas of the faces
print(
"File loaded, and encoded as the weighted sum of {:,} atoms in 3D.".format(
len(X)
)
)
# We return a (normalized) vector of weights + a "list" of points
return tensor(S / np.sum(S)), tensor(X)
.. GENERATED FROM PYTHON SOURCE LINES 54-55
Synthetic sphere - a typical source measure:
.. GENERATED FROM PYTHON SOURCE LINES 55-72
.. code-block:: Python
def create_sphere(n_samples=1000):
"""Creates a uniform sample on the unit sphere."""
n_samples = int(n_samples)
indices = np.arange(0, n_samples, dtype=float) + 0.5
phi = np.arccos(1 - 2 * indices / n_samples)
theta = np.pi * (1 + 5**0.5) * indices
x, y, z = np.cos(theta) * np.sin(phi), np.sin(theta) * np.sin(phi), np.cos(phi)
points = np.vstack((x, y, z)).T
weights = np.ones(n_samples) / n_samples
return tensor(weights), tensor(points)
.. GENERATED FROM PYTHON SOURCE LINES 73-74
Simple (slow) display routine:
.. GENERATED FROM PYTHON SOURCE LINES 74-90
.. code-block:: Python
def display_cloud(ax, measure, color):
w_i, x_i = numpy(measure[0]), numpy(measure[1])
ax.view_init(elev=110, azim=-90)
# ax.set_aspect('equal')
weights = w_i / w_i.sum()
ax.scatter(x_i[:, 0], x_i[:, 1], x_i[:, 2], s=25 * 500 * weights, c=color)
ax.axes.set_xlim3d(left=-1.4, right=1.4)
ax.axes.set_ylim3d(bottom=-1.4, top=1.4)
ax.axes.set_zlim3d(bottom=-1.4, top=1.4)
.. GENERATED FROM PYTHON SOURCE LINES 91-101
Measuring the error made on the marginal constraints
---------------------------------------------------------
Computing the marginals of the implicit transport plan:
.. math::
\pi ~&=~ \exp \tfrac{1}{\varepsilon}( f\oplus g - \text{C})~\cdot~ \alpha\otimes\beta,\\
\text{i.e.}~~\pi_{x_i \leftrightarrow y_j}~&=~ \exp \tfrac{1}{\varepsilon}( F_i + G_j - \text{C}(x_i,y_j))~\cdot~ \alpha_i \beta_j.
.. GENERATED FROM PYTHON SOURCE LINES 101-126
.. code-block:: Python
from pykeops.torch import LazyTensor
def plan_marginals(blur, a_i, x_i, b_j, y_j, F_i, G_j):
"""Returns the marginals of the transport plan encoded in the dual vectors F_i and G_j."""
x_i = LazyTensor(x_i[:, None, :])
y_j = LazyTensor(y_j[None, :, :])
F_i = LazyTensor(F_i[:, None, None])
G_j = LazyTensor(G_j[None, :, None])
# Cost matrix:
C_ij = ((x_i - y_j) ** 2).sum(-1) / 2
# Scaled kernel matrix:
K_ij = ((F_i + G_j - C_ij) / blur**2).exp()
A_i = a_i * (K_ij @ b_j) # First marginal
B_j = b_j * (K_ij.t() @ a_i) # Second marginal
return A_i, B_j
.. GENERATED FROM PYTHON SOURCE LINES 127-135
Compare the marginals using the relevant kernel norm
.. math::
\|\alpha - \beta\|^2_{k_\varepsilon} ~=~
\langle \alpha - \beta , k_\varepsilon \star (\alpha -\beta) \rangle,
with :math:`k_\varepsilon(x,y) = \exp(-\text{C}(x,y)/\varepsilon)`.
.. GENERATED FROM PYTHON SOURCE LINES 135-152
.. code-block:: Python
def blurred_relative_error(blur, x_i, a_i, A_i):
"""Computes the relative error |A_i-a_i| / |a_i| with respect to the kernel norm k_eps."""
x_j = LazyTensor(x_i[None, :, :])
x_i = LazyTensor(x_i[:, None, :])
C_ij = ((x_i - x_j) ** 2).sum(-1) / 2
K_ij = (-C_ij / blur**2).exp()
squared_error = (A_i - a_i).dot(K_ij @ (A_i - a_i))
squared_norm = a_i.dot(K_ij @ a_i)
return (squared_error / squared_norm).sqrt()
.. GENERATED FROM PYTHON SOURCE LINES 153-154
Simple error routine:
.. GENERATED FROM PYTHON SOURCE LINES 154-175
.. code-block:: Python
def marginal_error(blur, a_i, x_i, b_j, y_j, F_i, G_j, mode="blurred"):
"""Measures how well the transport plan encoded in the dual vectors F_i and G_j satisfies the marginal constraints."""
A_i, B_j = plan_marginals(blur, a_i, x_i, b_j, y_j, F_i, G_j)
if mode == "TV":
# Return the (average) total variation error on the marginal constraints:
return ((A_i - a_i).abs().sum() + (B_j - b_j).abs().sum()) / 2
elif mode == "blurred":
# Use the kernel norm k_eps to measure the discrepancy
norm_x = blurred_relative_error(blur, x_i, a_i, A_i)
norm_y = blurred_relative_error(blur, y_j, b_j, B_j)
return (norm_x + norm_y) / 2
else:
raise NotImplementedError()
.. GENERATED FROM PYTHON SOURCE LINES 176-185
Computing the entropic Wasserstein distance
---------------------------------------------------------
Computing the transport cost, assuming that the dual vectors satisfy
the equations at optimality:
.. math::
\text{OT}_\varepsilon(\alpha,\beta)~=~ \langle \alpha, f^\star\rangle + \langle \beta, g^\star \rangle.
.. GENERATED FROM PYTHON SOURCE LINES 185-192
.. code-block:: Python
def transport_cost(a_i, b_j, F_i, G_j):
"""Returns the entropic transport cost associated to the dual variables F_i and G_j."""
return a_i.dot(F_i) + b_j.dot(G_j)
.. GENERATED FROM PYTHON SOURCE LINES 193-201
Compute the "entropic Wasserstein distance"
.. math::
\text{D}_\varepsilon(\alpha,\beta)~=~ \sqrt{2 \cdot \text{OT}_\varepsilon(\alpha,\beta)},
which is **homogeneous to a distance on the ambient space** and is
associated to the (biased) Sinkhorn cost :math:`\text{OT}_\varepsilon`
with cost :math:`\text{C}(x,y) = \tfrac{1}{2}\|x-y\|^2`.
.. GENERATED FROM PYTHON SOURCE LINES 201-208
.. code-block:: Python
def wasserstein_distance(a_i, b_j, F_i, G_j):
"""Returns the entropic Wasserstein "distance" associated to the dual variables F_i and G_j."""
return (2 * transport_cost(a_i, b_j, F_i, G_j)).sqrt()
.. GENERATED FROM PYTHON SOURCE LINES 209-210
Compute all these quantities simultaneously, with a proper clock:
.. GENERATED FROM PYTHON SOURCE LINES 210-237
.. code-block:: Python
def benchmark_solver(OT_solver, blur, source, target):
"""Returns a (timing, relative error on the marginals, wasserstein distance) triplet for OT_solver(source, target)."""
a_i, x_i = source
b_j, y_j = target
a_i, x_i = a_i.contiguous(), x_i.contiguous()
b_j, y_j = b_j.contiguous(), y_j.contiguous()
if x_i.is_cuda:
torch.cuda.synchronize()
start = time.time()
F_i, G_j = OT_solver(a_i, x_i, b_j, y_j)
if x_i.is_cuda:
torch.cuda.synchronize()
end = time.time()
F_i, G_j = F_i.view(-1), G_j.view(-1)
return (
end - start,
marginal_error(blur, a_i, x_i, b_j, y_j, F_i, G_j).item(),
wasserstein_distance(a_i, b_j, F_i, G_j).item(),
)
.. GENERATED FROM PYTHON SOURCE LINES 238-241
Benchmarking a collection of OT solvers
---------------------------------------------------------
.. GENERATED FROM PYTHON SOURCE LINES 241-316
.. code-block:: Python
def benchmark_solvers(
name,
OT_solvers,
source,
target,
ground_truth,
blur=0.01,
display=False,
maxtime=None,
):
timings, errors, costs = [], [], []
break_loop = False
print(
'Benchmarking the "{}" family of OT solvers - ground truth = {:.6f}:'.format(
name, ground_truth
)
)
for i, OT_solver in enumerate(OT_solvers):
try:
timing, error, cost = benchmark_solver(OT_solver, blur, source, target)
timings.append(timing)
errors.append(error)
costs.append(cost)
print(
"{}-th solver : t = {:.4f}, error on the constraints = {:.3f}, cost = {:.6f}".format(
i + 1, timing, error, cost
)
)
except RuntimeError:
print("** Memory overflow ! **")
break_loop = True
timings.append(np.nan)
errors.append(np.nan)
costs.append(np.nan)
if break_loop or (maxtime is not None and timing > maxtime):
not_performed = len(OT_solvers) - (i + 1)
timings += [np.nan] * not_performed
errors += [np.nan] * not_performed
costs += [np.nan] * not_performed
break
print("")
timings, errors, costs = np.array(timings), np.array(errors), np.array(costs)
if display: # Fancy display
fig = plt.figure(figsize=(12, 8))
ax_1 = fig.subplots()
ax_1.set_title(
'Benchmarking "{}"\non a {:,}-by-{:,} entropic OT problem, with a blur radius of {:.3f}'.format(
name, len(source[0]), len(target[0]), blur
)
)
ax_1.set_xlabel("time (s)")
ax_1.plot(timings, errors, color="b")
ax_1.set_ylabel("Relative error on the marginal constraints", color="b")
ax_1.tick_params("y", colors="b")
ax_1.set_yscale("log")
ax_1.set_ylim(bottom=1e-5)
ax_2 = ax_1.twinx()
ax_2.plot(timings, abs(costs - ground_truth) / ground_truth, color="r")
ax_2.set_ylabel("Relative error on the cost value", color="r")
ax_2.tick_params("y", colors="r")
ax_2.set_yscale("log")
ax_2.set_ylim(bottom=1e-5)
return timings, errors, costs
.. _sphx_glr_download__auto_examples_performances_benchmarks_ot_solvers.py:
.. only:: html
.. container:: sphx-glr-footer sphx-glr-footer-example
.. container:: sphx-glr-download sphx-glr-download-jupyter
:download:`Download Jupyter notebook: benchmarks_ot_solvers.ipynb <benchmarks_ot_solvers.ipynb>`
.. container:: sphx-glr-download sphx-glr-download-python
:download:`Download Python source code: benchmarks_ot_solvers.py <benchmarks_ot_solvers.py>`
.. only:: html
.. rst-class:: sphx-glr-signature
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