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diff --git a/docs/source/auto_examples/plot_gromov_barycenter.ipynb b/docs/source/auto_examples/plot_gromov_barycenter.ipynb deleted file mode 100644 index 4c2f28f..0000000 --- a/docs/source/auto_examples/plot_gromov_barycenter.ipynb +++ /dev/null @@ -1,126 +0,0 @@ -{ - "cells": [ - { - "execution_count": null, - "metadata": { - "collapsed": false - }, - "outputs": [], - "source": [ - "%matplotlib inline" - ], - "cell_type": "code" - }, - { - "metadata": {}, - "source": [ - "\n# Gromov-Wasserstein Barycenter example\n\n\nThis example is designed to show how to use the Gromov-Wasserstein distance\ncomputation in POT.\n\n" - ], - "cell_type": "markdown" - }, - { - "execution_count": null, - "metadata": { - "collapsed": false - }, - "outputs": [], - "source": [ - "# Author: Erwan Vautier <erwan.vautier@gmail.com>\n# Nicolas Courty <ncourty@irisa.fr>\n#\n# License: MIT License\n\n\nimport numpy as np\nimport scipy as sp\n\nimport scipy.ndimage as spi\nimport matplotlib.pylab as pl\nfrom sklearn import manifold\nfrom sklearn.decomposition import PCA\n\nimport ot" - ], - "cell_type": "code" - }, - { - "metadata": {}, - "source": [ - "Smacof MDS\n----------\n\nThis function allows to find an embedding of points given a dissimilarity matrix\nthat will be given by the output of the algorithm\n\n" - ], - "cell_type": "markdown" - }, - { - "execution_count": null, - "metadata": { - "collapsed": false - }, - "outputs": [], - "source": [ - "def smacof_mds(C, dim, max_iter=3000, eps=1e-9):\n \"\"\"\n Returns an interpolated point cloud following the dissimilarity matrix C\n using SMACOF multidimensional scaling (MDS) in specific dimensionned\n target space\n\n Parameters\n ----------\n C : ndarray, shape (ns, ns)\n dissimilarity matrix\n dim : int\n dimension of the targeted space\n max_iter : int\n Maximum number of iterations of the SMACOF algorithm for a single run\n eps : float\n relative tolerance w.r.t stress to declare converge\n\n Returns\n -------\n npos : ndarray, shape (R, dim)\n Embedded coordinates of the interpolated point cloud (defined with\n one isometry)\n \"\"\"\n\n rng = np.random.RandomState(seed=3)\n\n mds = manifold.MDS(\n dim,\n max_iter=max_iter,\n eps=1e-9,\n dissimilarity='precomputed',\n n_init=1)\n pos = mds.fit(C).embedding_\n\n nmds = manifold.MDS(\n 2,\n max_iter=max_iter,\n eps=1e-9,\n dissimilarity=\"precomputed\",\n random_state=rng,\n n_init=1)\n npos = nmds.fit_transform(C, init=pos)\n\n return npos" - ], - "cell_type": "code" - }, - { - "metadata": {}, - "source": [ - "Data preparation\n----------------\n\nThe four distributions are constructed from 4 simple images\n\n" - ], - "cell_type": "markdown" - }, - { - "execution_count": null, - "metadata": { - "collapsed": false - }, - "outputs": [], - "source": [ - "def im2mat(I):\n \"\"\"Converts and image to matrix (one pixel per line)\"\"\"\n return I.reshape((I.shape[0] * I.shape[1], I.shape[2]))\n\n\nsquare = spi.imread('../data/square.png').astype(np.float64)[:, :, 2] / 256\ncross = spi.imread('../data/cross.png').astype(np.float64)[:, :, 2] / 256\ntriangle = spi.imread('../data/triangle.png').astype(np.float64)[:, :, 2] / 256\nstar = spi.imread('../data/star.png').astype(np.float64)[:, :, 2] / 256\n\nshapes = [square, cross, triangle, star]\n\nS = 4\nxs = [[] for i in range(S)]\n\n\nfor nb in range(4):\n for i in range(8):\n for j in range(8):\n if shapes[nb][i, j] < 0.95:\n xs[nb].append([j, 8 - i])\n\nxs = np.array([np.array(xs[0]), np.array(xs[1]),\n np.array(xs[2]), np.array(xs[3])])" - ], - "cell_type": "code" - }, - { - "metadata": {}, - "source": [ - "Barycenter computation\n----------------------\n\n" - ], - "cell_type": "markdown" - }, - { - "execution_count": null, - "metadata": { - "collapsed": false - }, - "outputs": [], - "source": [ - "ns = [len(xs[s]) for s in range(S)]\nn_samples = 30\n\n\"\"\"Compute all distances matrices for the four shapes\"\"\"\nCs = [sp.spatial.distance.cdist(xs[s], xs[s]) for s in range(S)]\nCs = [cs / cs.max() for cs in Cs]\n\nps = [ot.unif(ns[s]) for s in range(S)]\np = ot.unif(n_samples)\n\n\nlambdast = [[float(i) / 3, float(3 - i) / 3] for i in [1, 2]]\n\nCt01 = [0 for i in range(2)]\nfor i in range(2):\n Ct01[i] = ot.gromov.gromov_barycenters(n_samples, [Cs[0], Cs[1]],\n [ps[0], ps[1]\n ], p, lambdast[i], 'square_loss', # 5e-4,\n max_iter=100, tol=1e-3)\n\nCt02 = [0 for i in range(2)]\nfor i in range(2):\n Ct02[i] = ot.gromov.gromov_barycenters(n_samples, [Cs[0], Cs[2]],\n [ps[0], ps[2]\n ], p, lambdast[i], 'square_loss', # 5e-4,\n max_iter=100, tol=1e-3)\n\nCt13 = [0 for i in range(2)]\nfor i in range(2):\n Ct13[i] = ot.gromov.gromov_barycenters(n_samples, [Cs[1], Cs[3]],\n [ps[1], ps[3]\n ], p, lambdast[i], 'square_loss', # 5e-4,\n max_iter=100, tol=1e-3)\n\nCt23 = [0 for i in range(2)]\nfor i in range(2):\n Ct23[i] = ot.gromov.gromov_barycenters(n_samples, [Cs[2], Cs[3]],\n [ps[2], ps[3]\n ], p, lambdast[i], 'square_loss', # 5e-4,\n max_iter=100, tol=1e-3)" - ], - "cell_type": "code" - }, - { - "metadata": {}, - "source": [ - "Visualization\n-------------\n\nThe PCA helps in getting consistency between the rotations\n\n" - ], - "cell_type": "markdown" - }, - { - "execution_count": null, - "metadata": { - "collapsed": false - }, - "outputs": [], - "source": [ - "clf = PCA(n_components=2)\nnpos = [0, 0, 0, 0]\nnpos = [smacof_mds(Cs[s], 2) for s in range(S)]\n\nnpost01 = [0, 0]\nnpost01 = [smacof_mds(Ct01[s], 2) for s in range(2)]\nnpost01 = [clf.fit_transform(npost01[s]) for s in range(2)]\n\nnpost02 = [0, 0]\nnpost02 = [smacof_mds(Ct02[s], 2) for s in range(2)]\nnpost02 = [clf.fit_transform(npost02[s]) for s in range(2)]\n\nnpost13 = [0, 0]\nnpost13 = [smacof_mds(Ct13[s], 2) for s in range(2)]\nnpost13 = [clf.fit_transform(npost13[s]) for s in range(2)]\n\nnpost23 = [0, 0]\nnpost23 = [smacof_mds(Ct23[s], 2) for s in range(2)]\nnpost23 = [clf.fit_transform(npost23[s]) for s in range(2)]\n\n\nfig = pl.figure(figsize=(10, 10))\n\nax1 = pl.subplot2grid((4, 4), (0, 0))\npl.xlim((-1, 1))\npl.ylim((-1, 1))\nax1.scatter(npos[0][:, 0], npos[0][:, 1], color='r')\n\nax2 = pl.subplot2grid((4, 4), (0, 1))\npl.xlim((-1, 1))\npl.ylim((-1, 1))\nax2.scatter(npost01[1][:, 0], npost01[1][:, 1], color='b')\n\nax3 = pl.subplot2grid((4, 4), (0, 2))\npl.xlim((-1, 1))\npl.ylim((-1, 1))\nax3.scatter(npost01[0][:, 0], npost01[0][:, 1], color='b')\n\nax4 = pl.subplot2grid((4, 4), (0, 3))\npl.xlim((-1, 1))\npl.ylim((-1, 1))\nax4.scatter(npos[1][:, 0], npos[1][:, 1], color='r')\n\nax5 = pl.subplot2grid((4, 4), (1, 0))\npl.xlim((-1, 1))\npl.ylim((-1, 1))\nax5.scatter(npost02[1][:, 0], npost02[1][:, 1], color='b')\n\nax6 = pl.subplot2grid((4, 4), (1, 3))\npl.xlim((-1, 1))\npl.ylim((-1, 1))\nax6.scatter(npost13[1][:, 0], npost13[1][:, 1], color='b')\n\nax7 = pl.subplot2grid((4, 4), (2, 0))\npl.xlim((-1, 1))\npl.ylim((-1, 1))\nax7.scatter(npost02[0][:, 0], npost02[0][:, 1], color='b')\n\nax8 = pl.subplot2grid((4, 4), (2, 3))\npl.xlim((-1, 1))\npl.ylim((-1, 1))\nax8.scatter(npost13[0][:, 0], npost13[0][:, 1], color='b')\n\nax9 = pl.subplot2grid((4, 4), (3, 0))\npl.xlim((-1, 1))\npl.ylim((-1, 1))\nax9.scatter(npos[2][:, 0], npos[2][:, 1], color='r')\n\nax10 = pl.subplot2grid((4, 4), (3, 1))\npl.xlim((-1, 1))\npl.ylim((-1, 1))\nax10.scatter(npost23[1][:, 0], npost23[1][:, 1], color='b')\n\nax11 = pl.subplot2grid((4, 4), (3, 2))\npl.xlim((-1, 1))\npl.ylim((-1, 1))\nax11.scatter(npost23[0][:, 0], npost23[0][:, 1], color='b')\n\nax12 = pl.subplot2grid((4, 4), (3, 3))\npl.xlim((-1, 1))\npl.ylim((-1, 1))\nax12.scatter(npos[3][:, 0], npos[3][:, 1], color='r')" - ], - "cell_type": "code" - } - ], - "metadata": { - "language_info": { - "name": "python", - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "nbconvert_exporter": "python", - "version": "3.5.2", - "pygments_lexer": "ipython3", - "file_extension": ".py", - "mimetype": "text/x-python" - }, - "kernelspec": { - "display_name": "Python 3", - "name": "python3", - "language": "python" - } - }, - "nbformat_minor": 0, - "nbformat": 4 -}
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