From a303cc6b483d3cd958c399621e22e40574bcbbc8 Mon Sep 17 00:00:00 2001 From: Rémi Flamary Date: Tue, 21 Apr 2020 17:48:37 +0200 Subject: [MRG] Actually run sphinx-gallery (#146) * generate gallery * remove mock * add sklearn to requirermnt?txt for example * remove latex from fgw example * add networks for graph example * remove all * add requirement.txt rtd * rtd debug * update readme * eradthedoc with redirection * add conf rtd --- docs/source/auto_examples/plot_barycenter_1D.rst | 280 ----------------------- 1 file changed, 280 deletions(-) delete mode 100644 docs/source/auto_examples/plot_barycenter_1D.rst (limited to 'docs/source/auto_examples/plot_barycenter_1D.rst') diff --git a/docs/source/auto_examples/plot_barycenter_1D.rst b/docs/source/auto_examples/plot_barycenter_1D.rst deleted file mode 100644 index a65ac3d..0000000 --- a/docs/source/auto_examples/plot_barycenter_1D.rst +++ /dev/null @@ -1,280 +0,0 @@ -.. only:: html - - .. note:: - :class: sphx-glr-download-link-note - - Click :ref:`here ` to download the full example code - .. rst-class:: sphx-glr-example-title - - .. _sphx_glr_auto_examples_plot_barycenter_1D.py: - - -============================== -1D Wasserstein barycenter demo -============================== - -This example illustrates the computation of regularized Wassersyein Barycenter -as proposed in [3]. - - -[3] Benamou, J. D., Carlier, G., Cuturi, M., Nenna, L., & Peyré, G. (2015). -Iterative Bregman projections for regularized transportation problems -SIAM Journal on Scientific Computing, 37(2), A1111-A1138. - - - -.. code-block:: default - - - # Author: Remi Flamary - # - # License: MIT License - - import numpy as np - import matplotlib.pylab as pl - import ot - # necessary for 3d plot even if not used - from mpl_toolkits.mplot3d import Axes3D # noqa - from matplotlib.collections import PolyCollection - - - - - - - - -Generate data -------------- - - -.. code-block:: default - - - n = 100 # nb bins - - # bin positions - x = np.arange(n, dtype=np.float64) - - # Gaussian distributions - a1 = ot.datasets.make_1D_gauss(n, m=20, s=5) # m= mean, s= std - a2 = ot.datasets.make_1D_gauss(n, m=60, s=8) - - # creating matrix A containing all distributions - A = np.vstack((a1, a2)).T - n_distributions = A.shape[1] - - # loss matrix + normalization - M = ot.utils.dist0(n) - M /= M.max() - - - - - - - - -Plot data ---------- - - -.. code-block:: default - - - pl.figure(1, figsize=(6.4, 3)) - for i in range(n_distributions): - pl.plot(x, A[:, i]) - pl.title('Distributions') - pl.tight_layout() - - - - -.. image:: /auto_examples/images/sphx_glr_plot_barycenter_1D_001.png - :class: sphx-glr-single-img - - - - - -Barycenter computation ----------------------- - - -.. code-block:: default - - - alpha = 0.2 # 0<=alpha<=1 - weights = np.array([1 - alpha, alpha]) - - # l2bary - bary_l2 = A.dot(weights) - - # wasserstein - reg = 1e-3 - bary_wass = ot.bregman.barycenter(A, M, reg, weights) - - pl.figure(2) - pl.clf() - pl.subplot(2, 1, 1) - for i in range(n_distributions): - pl.plot(x, A[:, i]) - pl.title('Distributions') - - pl.subplot(2, 1, 2) - pl.plot(x, bary_l2, 'r', label='l2') - pl.plot(x, bary_wass, 'g', label='Wasserstein') - pl.legend() - pl.title('Barycenters') - pl.tight_layout() - - - - -.. image:: /auto_examples/images/sphx_glr_plot_barycenter_1D_002.png - :class: sphx-glr-single-img - - - - - -Barycentric interpolation -------------------------- - - -.. code-block:: default - - - n_alpha = 11 - alpha_list = np.linspace(0, 1, n_alpha) - - - B_l2 = np.zeros((n, n_alpha)) - - B_wass = np.copy(B_l2) - - for i in range(0, n_alpha): - alpha = alpha_list[i] - weights = np.array([1 - alpha, alpha]) - B_l2[:, i] = A.dot(weights) - B_wass[:, i] = ot.bregman.barycenter(A, M, reg, weights) - - - - - - - - - -.. code-block:: default - - - pl.figure(3) - - cmap = pl.cm.get_cmap('viridis') - verts = [] - zs = alpha_list - for i, z in enumerate(zs): - ys = B_l2[:, i] - verts.append(list(zip(x, ys))) - - ax = pl.gcf().gca(projection='3d') - - poly = PolyCollection(verts, facecolors=[cmap(a) for a in alpha_list]) - poly.set_alpha(0.7) - ax.add_collection3d(poly, zs=zs, zdir='y') - ax.set_xlabel('x') - ax.set_xlim3d(0, n) - ax.set_ylabel('$\\alpha$') - ax.set_ylim3d(0, 1) - ax.set_zlabel('') - ax.set_zlim3d(0, B_l2.max() * 1.01) - pl.title('Barycenter interpolation with l2') - pl.tight_layout() - - pl.figure(4) - cmap = pl.cm.get_cmap('viridis') - verts = [] - zs = alpha_list - for i, z in enumerate(zs): - ys = B_wass[:, i] - verts.append(list(zip(x, ys))) - - ax = pl.gcf().gca(projection='3d') - - poly = PolyCollection(verts, facecolors=[cmap(a) for a in alpha_list]) - poly.set_alpha(0.7) - ax.add_collection3d(poly, zs=zs, zdir='y') - ax.set_xlabel('x') - ax.set_xlim3d(0, n) - ax.set_ylabel('$\\alpha$') - ax.set_ylim3d(0, 1) - ax.set_zlabel('') - ax.set_zlim3d(0, B_l2.max() * 1.01) - pl.title('Barycenter interpolation with Wasserstein') - pl.tight_layout() - - pl.show() - - - -.. rst-class:: sphx-glr-horizontal - - - * - - .. image:: /auto_examples/images/sphx_glr_plot_barycenter_1D_003.png - :class: sphx-glr-multi-img - - * - - .. image:: /auto_examples/images/sphx_glr_plot_barycenter_1D_004.png - :class: sphx-glr-multi-img - - -.. rst-class:: sphx-glr-script-out - - Out: - - .. code-block:: none - - /home/rflamary/PYTHON/POT/examples/plot_barycenter_1D.py:160: UserWarning: Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure. - pl.show() - - - - - -.. rst-class:: sphx-glr-timing - - **Total running time of the script:** ( 0 minutes 0.769 seconds) - - -.. _sphx_glr_download_auto_examples_plot_barycenter_1D.py: - - -.. only :: html - - .. container:: sphx-glr-footer - :class: sphx-glr-footer-example - - - - .. container:: sphx-glr-download sphx-glr-download-python - - :download:`Download Python source code: plot_barycenter_1D.py ` - - - - .. container:: sphx-glr-download sphx-glr-download-jupyter - - :download:`Download Jupyter notebook: plot_barycenter_1D.ipynb ` - - -.. only:: html - - .. rst-class:: sphx-glr-signature - - `Gallery generated by Sphinx-Gallery `_ -- cgit v1.2.3