From f51c6ab8c25ee371be23ca1a09cb18aed7732132 Mon Sep 17 00:00:00 2001 From: Rémi Flamary Date: Wed, 29 Aug 2018 14:17:19 +0200 Subject: update exmaple bary 1D for better notebook --- .../source/auto_examples/auto_examples_jupyter.zip | Bin 118510 -> 119618 bytes docs/source/auto_examples/auto_examples_python.zip | Bin 79057 -> 79365 bytes .../images/sphx_glr_plot_barycenter_1D_003.png | Bin 108756 -> 41624 bytes .../images/sphx_glr_plot_barycenter_1D_005.png | Bin 108687 -> 108756 bytes .../images/sphx_glr_plot_barycenter_1D_006.png | Bin 105696 -> 105765 bytes docs/source/auto_examples/index.rst | 16 +-- docs/source/auto_examples/plot_barycenter_1D.ipynb | 74 ++++++++++++- docs/source/auto_examples/plot_barycenter_1D.py | 8 +- docs/source/auto_examples/plot_barycenter_1D.rst | 116 ++++++++++++++------- 9 files changed, 161 insertions(+), 53 deletions(-) (limited to 'docs/source/auto_examples') diff --git a/docs/source/auto_examples/auto_examples_jupyter.zip b/docs/source/auto_examples/auto_examples_jupyter.zip index 2325d59..c6a7e90 100644 Binary files a/docs/source/auto_examples/auto_examples_jupyter.zip and b/docs/source/auto_examples/auto_examples_jupyter.zip differ diff --git a/docs/source/auto_examples/auto_examples_python.zip b/docs/source/auto_examples/auto_examples_python.zip index 694d704..28ff08e 100644 Binary files a/docs/source/auto_examples/auto_examples_python.zip and b/docs/source/auto_examples/auto_examples_python.zip differ diff --git a/docs/source/auto_examples/images/sphx_glr_plot_barycenter_1D_003.png b/docs/source/auto_examples/images/sphx_glr_plot_barycenter_1D_003.png index 81cee52..d8db85e 100644 Binary files a/docs/source/auto_examples/images/sphx_glr_plot_barycenter_1D_003.png and b/docs/source/auto_examples/images/sphx_glr_plot_barycenter_1D_003.png differ diff --git a/docs/source/auto_examples/images/sphx_glr_plot_barycenter_1D_005.png b/docs/source/auto_examples/images/sphx_glr_plot_barycenter_1D_005.png index eac9230..81cee52 100644 Binary files a/docs/source/auto_examples/images/sphx_glr_plot_barycenter_1D_005.png and b/docs/source/auto_examples/images/sphx_glr_plot_barycenter_1D_005.png differ diff --git a/docs/source/auto_examples/images/sphx_glr_plot_barycenter_1D_006.png b/docs/source/auto_examples/images/sphx_glr_plot_barycenter_1D_006.png index 2e29ff9..bfa0873 100644 Binary files a/docs/source/auto_examples/images/sphx_glr_plot_barycenter_1D_006.png and b/docs/source/auto_examples/images/sphx_glr_plot_barycenter_1D_006.png differ diff --git a/docs/source/auto_examples/index.rst b/docs/source/auto_examples/index.rst index 77a46aa..5cbfba6 100644 --- a/docs/source/auto_examples/index.rst +++ b/docs/source/auto_examples/index.rst @@ -229,13 +229,13 @@ This is a gallery of all the POT example files. .. raw:: html -
+
.. only:: html - .. figure:: /auto_examples/images/thumb/sphx_glr_plot_otda_mapping_colors_images_thumb.png + .. figure:: /auto_examples/images/thumb/sphx_glr_plot_barycenter_1D_thumb.png - :ref:`sphx_glr_auto_examples_plot_otda_mapping_colors_images.py` + :ref:`sphx_glr_auto_examples_plot_barycenter_1D.py` .. raw:: html @@ -245,17 +245,17 @@ This is a gallery of all the POT example files. .. toctree:: :hidden: - /auto_examples/plot_otda_mapping_colors_images + /auto_examples/plot_barycenter_1D .. raw:: html -
+
.. only:: html - .. figure:: /auto_examples/images/thumb/sphx_glr_plot_barycenter_1D_thumb.png + .. figure:: /auto_examples/images/thumb/sphx_glr_plot_otda_mapping_colors_images_thumb.png - :ref:`sphx_glr_auto_examples_plot_barycenter_1D.py` + :ref:`sphx_glr_auto_examples_plot_otda_mapping_colors_images.py` .. raw:: html @@ -265,7 +265,7 @@ This is a gallery of all the POT example files. .. toctree:: :hidden: - /auto_examples/plot_barycenter_1D + /auto_examples/plot_otda_mapping_colors_images .. raw:: html diff --git a/docs/source/auto_examples/plot_barycenter_1D.ipynb b/docs/source/auto_examples/plot_barycenter_1D.ipynb index 5866088..fc60e1f 100644 --- a/docs/source/auto_examples/plot_barycenter_1D.ipynb +++ b/docs/source/auto_examples/plot_barycenter_1D.ipynb @@ -26,7 +26,79 @@ }, "outputs": [], "source": [ - "# Author: Remi Flamary \n#\n# License: MIT License\n\nimport numpy as np\nimport matplotlib.pylab as pl\nimport ot\n# necessary for 3d plot even if not used\nfrom mpl_toolkits.mplot3d import Axes3D # noqa\nfrom matplotlib.collections import PolyCollection\n\n#\n# Generate data\n# -------------\n\n#%% parameters\n\nn = 100 # nb bins\n\n# bin positions\nx = np.arange(n, dtype=np.float64)\n\n# Gaussian distributions\na1 = ot.datasets.make_1D_gauss(n, m=20, s=5) # m= mean, s= std\na2 = ot.datasets.make_1D_gauss(n, m=60, s=8)\n\n# creating matrix A containing all distributions\nA = np.vstack((a1, a2)).T\nn_distributions = A.shape[1]\n\n# loss matrix + normalization\nM = ot.utils.dist0(n)\nM /= M.max()\n\n#\n# Plot data\n# ---------\n\n#%% plot the distributions\n\npl.figure(1, figsize=(6.4, 3))\nfor i in range(n_distributions):\n pl.plot(x, A[:, i])\npl.title('Distributions')\npl.tight_layout()\n\n#\n# Barycenter computation\n# ----------------------\n\n#%% barycenter computation\n\nalpha = 0.2 # 0<=alpha<=1\nweights = np.array([1 - alpha, alpha])\n\n# l2bary\nbary_l2 = A.dot(weights)\n\n# wasserstein\nreg = 1e-3\nbary_wass = ot.bregman.barycenter(A, M, reg, weights)\n\npl.figure(2)\npl.clf()\npl.subplot(2, 1, 1)\nfor i in range(n_distributions):\n pl.plot(x, A[:, i])\npl.title('Distributions')\n\npl.subplot(2, 1, 2)\npl.plot(x, bary_l2, 'r', label='l2')\npl.plot(x, bary_wass, 'g', label='Wasserstein')\npl.legend()\npl.title('Barycenters')\npl.tight_layout()\n\n#\n# Barycentric interpolation\n# -------------------------\n\n#%% barycenter interpolation\n\nn_alpha = 11\nalpha_list = np.linspace(0, 1, n_alpha)\n\n\nB_l2 = np.zeros((n, n_alpha))\n\nB_wass = np.copy(B_l2)\n\nfor i in range(0, n_alpha):\n alpha = alpha_list[i]\n weights = np.array([1 - alpha, alpha])\n B_l2[:, i] = A.dot(weights)\n B_wass[:, i] = ot.bregman.barycenter(A, M, reg, weights)\n\n#%% plot interpolation\n\npl.figure(3)\n\ncmap = pl.cm.get_cmap('viridis')\nverts = []\nzs = alpha_list\nfor i, z in enumerate(zs):\n ys = B_l2[:, i]\n verts.append(list(zip(x, ys)))\n\nax = pl.gcf().gca(projection='3d')\n\npoly = PolyCollection(verts, facecolors=[cmap(a) for a in alpha_list])\npoly.set_alpha(0.7)\nax.add_collection3d(poly, zs=zs, zdir='y')\nax.set_xlabel('x')\nax.set_xlim3d(0, n)\nax.set_ylabel('$\\\\alpha$')\nax.set_ylim3d(0, 1)\nax.set_zlabel('')\nax.set_zlim3d(0, B_l2.max() * 1.01)\npl.title('Barycenter interpolation with l2')\npl.tight_layout()\n\npl.figure(4)\ncmap = pl.cm.get_cmap('viridis')\nverts = []\nzs = alpha_list\nfor i, z in enumerate(zs):\n ys = B_wass[:, i]\n verts.append(list(zip(x, ys)))\n\nax = pl.gcf().gca(projection='3d')\n\npoly = PolyCollection(verts, facecolors=[cmap(a) for a in alpha_list])\npoly.set_alpha(0.7)\nax.add_collection3d(poly, zs=zs, zdir='y')\nax.set_xlabel('x')\nax.set_xlim3d(0, n)\nax.set_ylabel('$\\\\alpha$')\nax.set_ylim3d(0, 1)\nax.set_zlabel('')\nax.set_zlim3d(0, B_l2.max() * 1.01)\npl.title('Barycenter interpolation with Wasserstein')\npl.tight_layout()\n\npl.show()" + "# Author: Remi Flamary \n#\n# License: MIT License\n\nimport numpy as np\nimport matplotlib.pylab as pl\nimport ot\n# necessary for 3d plot even if not used\nfrom mpl_toolkits.mplot3d import Axes3D # noqa\nfrom matplotlib.collections import PolyCollection" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Generate data\n-------------\n\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "#%% parameters\n\nn = 100 # nb bins\n\n# bin positions\nx = np.arange(n, dtype=np.float64)\n\n# Gaussian distributions\na1 = ot.datasets.make_1D_gauss(n, m=20, s=5) # m= mean, s= std\na2 = ot.datasets.make_1D_gauss(n, m=60, s=8)\n\n# creating matrix A containing all distributions\nA = np.vstack((a1, a2)).T\nn_distributions = A.shape[1]\n\n# loss matrix + normalization\nM = ot.utils.dist0(n)\nM /= M.max()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Plot data\n---------\n\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "#%% plot the distributions\n\npl.figure(1, figsize=(6.4, 3))\nfor i in range(n_distributions):\n pl.plot(x, A[:, i])\npl.title('Distributions')\npl.tight_layout()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Barycenter computation\n----------------------\n\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "#%% barycenter computation\n\nalpha = 0.2 # 0<=alpha<=1\nweights = np.array([1 - alpha, alpha])\n\n# l2bary\nbary_l2 = A.dot(weights)\n\n# wasserstein\nreg = 1e-3\nbary_wass = ot.bregman.barycenter(A, M, reg, weights)\n\npl.figure(2)\npl.clf()\npl.subplot(2, 1, 1)\nfor i in range(n_distributions):\n pl.plot(x, A[:, i])\npl.title('Distributions')\n\npl.subplot(2, 1, 2)\npl.plot(x, bary_l2, 'r', label='l2')\npl.plot(x, bary_wass, 'g', label='Wasserstein')\npl.legend()\npl.title('Barycenters')\npl.tight_layout()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Barycentric interpolation\n-------------------------\n\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "#%% barycenter interpolation\n\nn_alpha = 11\nalpha_list = np.linspace(0, 1, n_alpha)\n\n\nB_l2 = np.zeros((n, n_alpha))\n\nB_wass = np.copy(B_l2)\n\nfor i in range(0, n_alpha):\n alpha = alpha_list[i]\n weights = np.array([1 - alpha, alpha])\n B_l2[:, i] = A.dot(weights)\n B_wass[:, i] = ot.bregman.barycenter(A, M, reg, weights)\n\n#%% plot interpolation\n\npl.figure(3)\n\ncmap = pl.cm.get_cmap('viridis')\nverts = []\nzs = alpha_list\nfor i, z in enumerate(zs):\n ys = B_l2[:, i]\n verts.append(list(zip(x, ys)))\n\nax = pl.gcf().gca(projection='3d')\n\npoly = PolyCollection(verts, facecolors=[cmap(a) for a in alpha_list])\npoly.set_alpha(0.7)\nax.add_collection3d(poly, zs=zs, zdir='y')\nax.set_xlabel('x')\nax.set_xlim3d(0, n)\nax.set_ylabel('$\\\\alpha$')\nax.set_ylim3d(0, 1)\nax.set_zlabel('')\nax.set_zlim3d(0, B_l2.max() * 1.01)\npl.title('Barycenter interpolation with l2')\npl.tight_layout()\n\npl.figure(4)\ncmap = pl.cm.get_cmap('viridis')\nverts = []\nzs = alpha_list\nfor i, z in enumerate(zs):\n ys = B_wass[:, i]\n verts.append(list(zip(x, ys)))\n\nax = pl.gcf().gca(projection='3d')\n\npoly = PolyCollection(verts, facecolors=[cmap(a) for a in alpha_list])\npoly.set_alpha(0.7)\nax.add_collection3d(poly, zs=zs, zdir='y')\nax.set_xlabel('x')\nax.set_xlim3d(0, n)\nax.set_ylabel('$\\\\alpha$')\nax.set_ylim3d(0, 1)\nax.set_zlabel('')\nax.set_zlim3d(0, B_l2.max() * 1.01)\npl.title('Barycenter interpolation with Wasserstein')\npl.tight_layout()\n\npl.show()" ] } ], diff --git a/docs/source/auto_examples/plot_barycenter_1D.py b/docs/source/auto_examples/plot_barycenter_1D.py index 5ed9f3f..6864301 100644 --- a/docs/source/auto_examples/plot_barycenter_1D.py +++ b/docs/source/auto_examples/plot_barycenter_1D.py @@ -25,7 +25,7 @@ import ot from mpl_toolkits.mplot3d import Axes3D # noqa from matplotlib.collections import PolyCollection -# +############################################################################## # Generate data # ------------- @@ -48,7 +48,7 @@ n_distributions = A.shape[1] M = ot.utils.dist0(n) M /= M.max() -# +############################################################################## # Plot data # --------- @@ -60,7 +60,7 @@ for i in range(n_distributions): pl.title('Distributions') pl.tight_layout() -# +############################################################################## # Barycenter computation # ---------------------- @@ -90,7 +90,7 @@ pl.legend() pl.title('Barycenters') pl.tight_layout() -# +############################################################################## # Barycentric interpolation # ------------------------- diff --git a/docs/source/auto_examples/plot_barycenter_1D.rst b/docs/source/auto_examples/plot_barycenter_1D.rst index b314dc1..66ac042 100644 --- a/docs/source/auto_examples/plot_barycenter_1D.rst +++ b/docs/source/auto_examples/plot_barycenter_1D.rst @@ -18,52 +18,34 @@ SIAM Journal on Scientific Computing, 37(2), A1111-A1138. +.. code-block:: python -.. rst-class:: sphx-glr-horizontal - - - * - .. image:: /auto_examples/images/sphx_glr_plot_barycenter_1D_001.png - :scale: 47 + # 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 - .. image:: /auto_examples/images/sphx_glr_plot_barycenter_1D_002.png - :scale: 47 - * - .. image:: /auto_examples/images/sphx_glr_plot_barycenter_1D_003.png - :scale: 47 - * - .. image:: /auto_examples/images/sphx_glr_plot_barycenter_1D_004.png - :scale: 47 +Generate data +------------- .. code-block:: python - # 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 - # ------------- - #%% parameters n = 100 # nb bins @@ -83,9 +65,19 @@ SIAM Journal on Scientific Computing, 37(2), A1111-A1138. M = ot.utils.dist0(n) M /= M.max() - # - # Plot data - # --------- + + + + + + +Plot data +--------- + + + +.. code-block:: python + #%% plot the distributions @@ -95,9 +87,22 @@ SIAM Journal on Scientific Computing, 37(2), A1111-A1138. pl.title('Distributions') pl.tight_layout() - # - # Barycenter computation - # ---------------------- + + + +.. image:: /auto_examples/images/sphx_glr_plot_barycenter_1D_001.png + :align: center + + + + +Barycenter computation +---------------------- + + + +.. code-block:: python + #%% barycenter computation @@ -125,9 +130,22 @@ SIAM Journal on Scientific Computing, 37(2), A1111-A1138. pl.title('Barycenters') pl.tight_layout() - # - # Barycentric interpolation - # ------------------------- + + + +.. image:: /auto_examples/images/sphx_glr_plot_barycenter_1D_003.png + :align: center + + + + +Barycentric interpolation +------------------------- + + + +.. code-block:: python + #%% barycenter interpolation @@ -194,7 +212,25 @@ SIAM Journal on Scientific Computing, 37(2), A1111-A1138. pl.show() -**Total running time of the script:** ( 0 minutes 0.363 seconds) + + +.. rst-class:: sphx-glr-horizontal + + + * + + .. image:: /auto_examples/images/sphx_glr_plot_barycenter_1D_005.png + :scale: 47 + + * + + .. image:: /auto_examples/images/sphx_glr_plot_barycenter_1D_006.png + :scale: 47 + + + + +**Total running time of the script:** ( 0 minutes 0.413 seconds) -- cgit v1.2.3