Merge readme with master

Author: rflamary

README.md

@@ -230,4 +230,6 @@ You can also post bug reports and feature requests in Github issues. Make sure t
 
 [20] Cuturi, M. and Doucet, A. (2014) [Fast Computation of Wasserstein Barycenters](http://proceedings.mlr.press/v32/cuturi14.html). International Conference in Machine Learning
 
-[21] J. Altschuler, J.Weed, P. Rigollet, (2017) Near-linear time approximation algorithms for optimal transport via Sinkhorn iteration, Advances in Neural Information Processing Systems (NIPS) 31
+[21] Solomon, J., De Goes, F., Peyré, G., Cuturi, M., Butscher, A., Nguyen, A. & Guibas, L. (2015). [Convolutional wasserstein distances: Efficient optimal transportation on geometric domains](https://dl.acm.org/citation.cfm?id=2766963). ACM Transactions on Graphics (TOG), 34(4), 66.
+
+[21] J. Altschuler, J.Weed, P. Rigollet, (2017) [Near-linear time approximation algorithms for optimal transport via Sinkhorn iteration](https://papers.nips.cc/paper/6792-near-linear-time-approximation-algorithms-for-optimal-transport-via-sinkhorn-iteration.pdf), Advances in Neural Information Processing Systems (NIPS) 31

data/duck.png

@@ -0,0 +1,92 @@
+
+#%%
+# -*- coding: utf-8 -*-
+"""
+============================================
+Convolutional Wasserstein Barycenter example
+============================================
+
+This example is designed to illustrate how the Convolutional Wasserstein Barycenter
+function of POT works.
+"""
+
+# Author: Nicolas Courty <ncourty@irisa.fr>
+#
+# License: MIT License
+
+
+import numpy as np
+import pylab as pl
+import ot
+
+##############################################################################
+# Data preparation
+# ----------------
+#
+# The four distributions are constructed from 4 simple images
+
+
+f1 = 1 - pl.imread('../data/redcross.png')[:, :, 2]
+f2 = 1 - pl.imread('../data/duck.png')[:, :, 2]
+f3 = 1 - pl.imread('../data/heart.png')[:, :, 2]
+f4 = 1 - pl.imread('../data/tooth.png')[:, :, 2]
+
+A = []
+f1 = f1 / np.sum(f1)
+f2 = f2 / np.sum(f2)
+f3 = f3 / np.sum(f3)
+f4 = f4 / np.sum(f4)
+A.append(f1)
+A.append(f2)
+A.append(f3)
+A.append(f4)
+A = np.array(A)
+
+nb_images = 5
+
+# those are the four corners coordinates that will be interpolated by bilinear
+# interpolation
+v1 = np.array((1, 0, 0, 0))
+v2 = np.array((0, 1, 0, 0))
+v3 = np.array((0, 0, 1, 0))
+v4 = np.array((0, 0, 0, 1))
+
+
+##############################################################################
+# Barycenter computation and visualization
+# ----------------------------------------
+#
+
+pl.figure(figsize=(10, 10))
+pl.title('Convolutional Wasserstein Barycenters in POT')
+cm = 'Blues'
+# regularization parameter
+reg = 0.004
+for i in range(nb_images):
+    for j in range(nb_images):
+        pl.subplot(nb_images, nb_images, i * nb_images + j + 1)
+        tx = float(i) / (nb_images - 1)
+        ty = float(j) / (nb_images - 1)
+
+        # weights are constructed by bilinear interpolation
+        tmp1 = (1 - tx) * v1 + tx * v2
+        tmp2 = (1 - tx) * v3 + tx * v4
+        weights = (1 - ty) * tmp1 + ty * tmp2
+
+        if i == 0 and j == 0:
+            pl.imshow(f1, cmap=cm)
+            pl.axis('off')
+        elif i == 0 and j == (nb_images - 1):
+            pl.imshow(f3, cmap=cm)
+            pl.axis('off')
+        elif i == (nb_images - 1) and j == 0:
+            pl.imshow(f2, cmap=cm)
+            pl.axis('off')
+        elif i == (nb_images - 1) and j == (nb_images - 1):
+            pl.imshow(f4, cmap=cm)
+            pl.axis('off')
+        else:
+            # call to barycenter computation
+            pl.imshow(ot.bregman.convolutional_barycenter2d(A, reg, weights), cmap=cm)
+            pl.axis('off')
+pl.show()

data/heart.png

@@ -1070,6 +1070,116 @@ def barycenter(A, M, reg, weights=None, numItermax=1000,
         return geometricBar(weights, UKv)
 
 
+def convolutional_barycenter2d(A, reg, weights=None, numItermax=10000, stopThr=1e-9, stabThr=1e-30, verbose=False, log=False):
+    """Compute the entropic regularized wasserstein barycenter of distributions A
+    where A is a collection of 2D images.
+
+     The function solves the following optimization problem:
+
+    .. math::
+       \mathbf{a} = arg\min_\mathbf{a} \sum_i W_{reg}(\mathbf{a},\mathbf{a}_i)
+
+    where :
+
+    - :math:`W_{reg}(\cdot,\cdot)` is the entropic regularized Wasserstein distance (see ot.bregman.sinkhorn)
+    - :math:`\mathbf{a}_i` are training distributions (2D images) in the mast two dimensions of matrix :math:`\mathbf{A}`
+    - reg is the regularization strength scalar value
+
+    The algorithm used for solving the problem is the Sinkhorn-Knopp matrix scaling algorithm as proposed in [21]_
+
+    Parameters
+    ----------
+    A : np.ndarray (n,w,h)
+        n distributions (2D images) of size w x h
+    reg : float
+        Regularization term >0
+    weights : np.ndarray (n,)
+        Weights of each image on the simplex (barycentric coodinates)
+    numItermax : int, optional
+        Max number of iterations
+    stopThr : float, optional
+        Stop threshol on error (>0)
+    stabThr : float, optional
+        Stabilization threshold to avoid numerical precision issue
+    verbose : bool, optional
+        Print information along iterations
+    log : bool, optional
+        record log if True
+
+
+    Returns
+    -------
+    a : (w,h) ndarray
+        2D Wasserstein barycenter
+    log : dict
+        log dictionary return only if log==True in parameters
+
+
+    References
+    ----------
+
+    .. [21] Solomon, J., De Goes, F., Peyré, G., Cuturi, M., Butscher, A., Nguyen, A. & Guibas, L. (2015).
+    Convolutional wasserstein distances: Efficient optimal transportation on geometric domains
+    ACM Transactions on Graphics (TOG), 34(4), 66
+
+
+    """
+
+    if weights is None:
+        weights = np.ones(A.shape[0]) / A.shape[0]
+    else:
+        assert(len(weights) == A.shape[0])
+
+    if log:
+        log = {'err': []}
+
+    b = np.zeros_like(A[0, :, :])
+    U = np.ones_like(A)
+    KV = np.ones_like(A)
+
+    cpt = 0
+    err = 1
+
+    # build the convolution operator
+    t = np.linspace(0, 1, A.shape[1])
+    [Y, X] = np.meshgrid(t, t)
+    xi1 = np.exp(-(X - Y)**2 / reg)
+
+    def K(x):
+        return np.dot(np.dot(xi1, x), xi1)
+
+    while (err > stopThr and cpt < numItermax):
+
+        bold = b
+        cpt = cpt + 1
+
+        b = np.zeros_like(A[0, :, :])
+        for r in range(A.shape[0]):
+            KV[r, :, :] = K(A[r, :, :] / np.maximum(stabThr, K(U[r, :, :])))
+            b += weights[r] * np.log(np.maximum(stabThr, U[r, :, :] * KV[r, :, :]))
+        b = np.exp(b)
+        for r in range(A.shape[0]):
+            U[r, :, :] = b / np.maximum(stabThr, KV[r, :, :])
+
+        if cpt % 10 == 1:
+            err = np.sum(np.abs(bold - b))
+            # log and verbose print
+            if log:
+                log['err'].append(err)
+
+            if verbose:
+                if cpt % 200 == 0:
+                    print('{:5s}|{:12s}'.format('It.', 'Err') + '\n' + '-' * 19)
+                print('{:5d}|{:8e}|'.format(cpt, err))
+
+    if log:
+        log['niter'] = cpt
+        log['U'] = U
+        return b, log
+    else:
+        return b
+
+
 def unmix(a, D, M, M0, h0, reg, reg0, alpha, numItermax=1000,
           stopThr=1e-3, verbose=False, log=False):
     """

data/redcross.png

@@ -108,6 +108,30 @@ def test_bary():
     ot.bregman.barycenter(A, M, reg, log=True, verbose=True)
 
 
+def test_wassersteinbary():
+
+    size = 100  # size of a square image
+    a1 = np.random.randn(size, size)
+    a1 += a1.min()
+    a1 = a1 / np.sum(a1)
+    a2 = np.random.randn(size, size)
+    a2 += a2.min()
+    a2 = a2 / np.sum(a2)
+    # creating matrix A containing all distributions
+    A = np.zeros((2, 100, 100))
+    A[0, :, :] = a1
+    A[1, :, :] = a2
+
+    # wasserstein
+    reg = 1e-3
+    bary_wass = ot.bregman.convolutional_barycenter2d(A, reg)
+
+    np.testing.assert_allclose(1, np.sum(bary_wass))
+
+    # help in checking if log and verbose do not bug the function
+    ot.bregman.convolutional_barycenter2d(A, reg, log=True, verbose=True)
+
+
 def test_unmix():
 
     n_bins = 50  # nb bins

data/tooth.png

@@ -32,7 +32,7 @@ def test_stochastic_sag():
     # test sag
     n = 15
     reg = 1
-    numItermax = 300000
+    numItermax = 30000
     rng = np.random.RandomState(0)
 
     x = rng.randn(n, 2)
@@ -62,7 +62,7 @@ def test_stochastic_asgd():
     # test asgd
     n = 15
     reg = 1
-    numItermax = 300000
+    numItermax = 100000
     rng = np.random.RandomState(0)
 
     x = rng.randn(n, 2)
@@ -92,7 +92,7 @@ def test_sag_asgd_sinkhorn():
     # test all algorithms
     n = 15
     reg = 1
-    nb_iter = 300000
+    nb_iter = 100000
     rng = np.random.RandomState(0)
 
     x = rng.randn(n, 2)
@@ -167,7 +167,7 @@ def test_dual_sgd_sinkhorn():
     # test all dual algorithms
     n = 10
     reg = 1
-    nb_iter = 150000
+    nb_iter = 15000
     batch_size = 10
     rng = np.random.RandomState(0)