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diff --git a/docs/source/auto_examples/plot_gromov_barycenter.rst b/docs/source/auto_examples/plot_gromov_barycenter.rst deleted file mode 100644 index 531ee22..0000000 --- a/docs/source/auto_examples/plot_gromov_barycenter.rst +++ /dev/null @@ -1,329 +0,0 @@ - - -.. _sphx_glr_auto_examples_plot_gromov_barycenter.py: - - -===================================== -Gromov-Wasserstein Barycenter example -===================================== - -This example is designed to show how to use the Gromov-Wasserstein distance -computation in POT. - - - -.. code-block:: python - - - # Author: Erwan Vautier <erwan.vautier@gmail.com> - # Nicolas Courty <ncourty@irisa.fr> - # - # License: MIT License - - - import numpy as np - import scipy as sp - - import scipy.ndimage as spi - import matplotlib.pylab as pl - from sklearn import manifold - from sklearn.decomposition import PCA - - import ot - - - - - - - -Smacof MDS ----------- - -This function allows to find an embedding of points given a dissimilarity matrix -that will be given by the output of the algorithm - - - -.. code-block:: python - - - - def smacof_mds(C, dim, max_iter=3000, eps=1e-9): - """ - Returns an interpolated point cloud following the dissimilarity matrix C - using SMACOF multidimensional scaling (MDS) in specific dimensionned - target space - - Parameters - ---------- - C : ndarray, shape (ns, ns) - dissimilarity matrix - dim : int - dimension of the targeted space - max_iter : int - Maximum number of iterations of the SMACOF algorithm for a single run - eps : float - relative tolerance w.r.t stress to declare converge - - Returns - ------- - npos : ndarray, shape (R, dim) - Embedded coordinates of the interpolated point cloud (defined with - one isometry) - """ - - rng = np.random.RandomState(seed=3) - - mds = manifold.MDS( - dim, - max_iter=max_iter, - eps=1e-9, - dissimilarity='precomputed', - n_init=1) - pos = mds.fit(C).embedding_ - - nmds = manifold.MDS( - 2, - max_iter=max_iter, - eps=1e-9, - dissimilarity="precomputed", - random_state=rng, - n_init=1) - npos = nmds.fit_transform(C, init=pos) - - return npos - - - - - - - - -Data preparation ----------------- - -The four distributions are constructed from 4 simple images - - - -.. code-block:: python - - - - def im2mat(I): - """Converts and image to matrix (one pixel per line)""" - return I.reshape((I.shape[0] * I.shape[1], I.shape[2])) - - - square = spi.imread('../data/square.png').astype(np.float64)[:, :, 2] / 256 - cross = spi.imread('../data/cross.png').astype(np.float64)[:, :, 2] / 256 - triangle = spi.imread('../data/triangle.png').astype(np.float64)[:, :, 2] / 256 - star = spi.imread('../data/star.png').astype(np.float64)[:, :, 2] / 256 - - shapes = [square, cross, triangle, star] - - S = 4 - xs = [[] for i in range(S)] - - - for nb in range(4): - for i in range(8): - for j in range(8): - if shapes[nb][i, j] < 0.95: - xs[nb].append([j, 8 - i]) - - xs = np.array([np.array(xs[0]), np.array(xs[1]), - np.array(xs[2]), np.array(xs[3])]) - - - - - - - -Barycenter computation ----------------------- - - - -.. code-block:: python - - - - ns = [len(xs[s]) for s in range(S)] - n_samples = 30 - - """Compute all distances matrices for the four shapes""" - Cs = [sp.spatial.distance.cdist(xs[s], xs[s]) for s in range(S)] - Cs = [cs / cs.max() for cs in Cs] - - ps = [ot.unif(ns[s]) for s in range(S)] - p = ot.unif(n_samples) - - - lambdast = [[float(i) / 3, float(3 - i) / 3] for i in [1, 2]] - - Ct01 = [0 for i in range(2)] - for i in range(2): - Ct01[i] = ot.gromov.gromov_barycenters(n_samples, [Cs[0], Cs[1]], - [ps[0], ps[1] - ], p, lambdast[i], 'square_loss', # 5e-4, - max_iter=100, tol=1e-3) - - Ct02 = [0 for i in range(2)] - for i in range(2): - Ct02[i] = ot.gromov.gromov_barycenters(n_samples, [Cs[0], Cs[2]], - [ps[0], ps[2] - ], p, lambdast[i], 'square_loss', # 5e-4, - max_iter=100, tol=1e-3) - - Ct13 = [0 for i in range(2)] - for i in range(2): - Ct13[i] = ot.gromov.gromov_barycenters(n_samples, [Cs[1], Cs[3]], - [ps[1], ps[3] - ], p, lambdast[i], 'square_loss', # 5e-4, - max_iter=100, tol=1e-3) - - Ct23 = [0 for i in range(2)] - for i in range(2): - Ct23[i] = ot.gromov.gromov_barycenters(n_samples, [Cs[2], Cs[3]], - [ps[2], ps[3] - ], p, lambdast[i], 'square_loss', # 5e-4, - max_iter=100, tol=1e-3) - - - - - - - - -Visualization -------------- - -The PCA helps in getting consistency between the rotations - - - -.. code-block:: python - - - - clf = PCA(n_components=2) - npos = [0, 0, 0, 0] - npos = [smacof_mds(Cs[s], 2) for s in range(S)] - - npost01 = [0, 0] - npost01 = [smacof_mds(Ct01[s], 2) for s in range(2)] - npost01 = [clf.fit_transform(npost01[s]) for s in range(2)] - - npost02 = [0, 0] - npost02 = [smacof_mds(Ct02[s], 2) for s in range(2)] - npost02 = [clf.fit_transform(npost02[s]) for s in range(2)] - - npost13 = [0, 0] - npost13 = [smacof_mds(Ct13[s], 2) for s in range(2)] - npost13 = [clf.fit_transform(npost13[s]) for s in range(2)] - - npost23 = [0, 0] - npost23 = [smacof_mds(Ct23[s], 2) for s in range(2)] - npost23 = [clf.fit_transform(npost23[s]) for s in range(2)] - - - fig = pl.figure(figsize=(10, 10)) - - ax1 = pl.subplot2grid((4, 4), (0, 0)) - pl.xlim((-1, 1)) - pl.ylim((-1, 1)) - ax1.scatter(npos[0][:, 0], npos[0][:, 1], color='r') - - ax2 = pl.subplot2grid((4, 4), (0, 1)) - pl.xlim((-1, 1)) - pl.ylim((-1, 1)) - ax2.scatter(npost01[1][:, 0], npost01[1][:, 1], color='b') - - ax3 = pl.subplot2grid((4, 4), (0, 2)) - pl.xlim((-1, 1)) - pl.ylim((-1, 1)) - ax3.scatter(npost01[0][:, 0], npost01[0][:, 1], color='b') - - ax4 = pl.subplot2grid((4, 4), (0, 3)) - pl.xlim((-1, 1)) - pl.ylim((-1, 1)) - ax4.scatter(npos[1][:, 0], npos[1][:, 1], color='r') - - ax5 = pl.subplot2grid((4, 4), (1, 0)) - pl.xlim((-1, 1)) - pl.ylim((-1, 1)) - ax5.scatter(npost02[1][:, 0], npost02[1][:, 1], color='b') - - ax6 = pl.subplot2grid((4, 4), (1, 3)) - pl.xlim((-1, 1)) - pl.ylim((-1, 1)) - ax6.scatter(npost13[1][:, 0], npost13[1][:, 1], color='b') - - ax7 = pl.subplot2grid((4, 4), (2, 0)) - pl.xlim((-1, 1)) - pl.ylim((-1, 1)) - ax7.scatter(npost02[0][:, 0], npost02[0][:, 1], color='b') - - ax8 = pl.subplot2grid((4, 4), (2, 3)) - pl.xlim((-1, 1)) - pl.ylim((-1, 1)) - ax8.scatter(npost13[0][:, 0], npost13[0][:, 1], color='b') - - ax9 = pl.subplot2grid((4, 4), (3, 0)) - pl.xlim((-1, 1)) - pl.ylim((-1, 1)) - ax9.scatter(npos[2][:, 0], npos[2][:, 1], color='r') - - ax10 = pl.subplot2grid((4, 4), (3, 1)) - pl.xlim((-1, 1)) - pl.ylim((-1, 1)) - ax10.scatter(npost23[1][:, 0], npost23[1][:, 1], color='b') - - ax11 = pl.subplot2grid((4, 4), (3, 2)) - pl.xlim((-1, 1)) - pl.ylim((-1, 1)) - ax11.scatter(npost23[0][:, 0], npost23[0][:, 1], color='b') - - ax12 = pl.subplot2grid((4, 4), (3, 3)) - pl.xlim((-1, 1)) - pl.ylim((-1, 1)) - ax12.scatter(npos[3][:, 0], npos[3][:, 1], color='r') - - - -.. image:: /auto_examples/images/sphx_glr_plot_gromov_barycenter_001.png - :align: center - - - - -**Total running time of the script:** ( 0 minutes 5.906 seconds) - - - -.. only :: html - - .. container:: sphx-glr-footer - - - .. container:: sphx-glr-download - - :download:`Download Python source code: plot_gromov_barycenter.py <plot_gromov_barycenter.py>` - - - - .. container:: sphx-glr-download - - :download:`Download Jupyter notebook: plot_gromov_barycenter.ipynb <plot_gromov_barycenter.ipynb>` - - -.. only:: html - - .. rst-class:: sphx-glr-signature - - `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.readthedocs.io>`_ |