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Diffstat (limited to 'docs/source/auto_examples/plot_barycenter_fgw.rst')
| -rw-r--r-- | docs/source/auto_examples/plot_barycenter_fgw.rst | 110 |
1 files changed, 81 insertions, 29 deletions
diff --git a/docs/source/auto_examples/plot_barycenter_fgw.rst b/docs/source/auto_examples/plot_barycenter_fgw.rst index 2c44a65..ad4c275 100644 --- a/docs/source/auto_examples/plot_barycenter_fgw.rst +++ b/docs/source/auto_examples/plot_barycenter_fgw.rst @@ -1,6 +1,12 @@ +.. only:: html + + .. note:: + :class: sphx-glr-download-link-note + Click :ref:`here <sphx_glr_download_auto_examples_plot_barycenter_fgw.py>` to download the full example code + .. rst-class:: sphx-glr-example-title -.. _sphx_glr_auto_examples_plot_barycenter_fgw.py: + .. _sphx_glr_auto_examples_plot_barycenter_fgw.py: ================================= @@ -18,15 +24,23 @@ Requires networkx >=2 - -.. code-block:: python +.. code-block:: default # Author: Titouan Vayer <titouan.vayer@irisa.fr> # # License: MIT License - #%% load libraries + + + + + + + + +.. code-block:: default + import numpy as np import matplotlib.pyplot as plt import networkx as nx @@ -35,7 +49,16 @@ Requires networkx >=2 import matplotlib.colors as mcol from matplotlib import cm from ot.gromov import fgw_barycenters - #%% Graph functions + + + + + + + + +.. code-block:: default + def find_thresh(C, inf=0.5, sup=3, step=10): @@ -138,17 +161,16 @@ Requires networkx >=2 + Generate data ------------- +We build a dataset of noisy circular graphs. +Noise is added on the structures by random connections and on the features by gaussian noise. -.. code-block:: python - +.. code-block:: default - #%% circular dataset - # We build a dataset of noisy circular graphs. - # Noise is added on the structures by random connections and on the features by gaussian noise. np.random.seed(30) @@ -162,15 +184,13 @@ Generate data + Plot data --------- +.. code-block:: default -.. code-block:: python - - - #%% Plot graphs plt.figure(figsize=(8, 10)) for i in range(len(X0)): @@ -185,7 +205,17 @@ Plot data .. image:: /auto_examples/images/sphx_glr_plot_barycenter_fgw_001.png - :align: center + :class: sphx-glr-single-img + + +.. rst-class:: sphx-glr-script-out + + Out: + + .. code-block:: none + + /home/rflamary/PYTHON/POT/examples/plot_barycenter_fgw.py:155: UserWarning: Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure. + plt.show() @@ -193,13 +223,11 @@ Plot data Barycenter computation ---------------------- +Features distances are the euclidean distances -.. code-block:: python +.. code-block:: default - - #%% We compute the barycenter using FGW. Structure matrices are computed using the shortest_path distance in the graph - # Features distances are the euclidean distances Cs = [shortest_path(nx.adjacency_matrix(x)) for x in X0] ps = [np.ones(len(x.nodes())) / len(x.nodes()) for x in X0] Ys = [np.array([v for (k, v) in nx.get_node_attributes(x, 'attr_name').items()]).reshape(-1, 1) for x in X0] @@ -214,20 +242,27 @@ Barycenter computation + Plot Barycenter ------------------------- +.. code-block:: default -.. code-block:: python - - - #%% Create the barycenter bary = nx.from_numpy_matrix(sp_to_adjency(C, threshinf=0, threshsup=find_thresh(C, sup=100, step=100)[0])) for i, v in enumerate(A.ravel()): bary.add_node(i, attr_name=v) - #%% + + + + + + + + +.. code-block:: default + pos = nx.kamada_kawai_layout(bary) nx.draw(bary, pos=pos, node_color=graph_colors(bary, vmin=-1, vmax=1), with_labels=False) plt.suptitle('Barycenter', fontsize=20) @@ -236,27 +271,44 @@ Plot Barycenter .. image:: /auto_examples/images/sphx_glr_plot_barycenter_fgw_002.png - :align: center + :class: sphx-glr-single-img + + +.. rst-class:: sphx-glr-script-out + + Out: + .. code-block:: none + /home/rflamary/PYTHON/POT/examples/plot_barycenter_fgw.py:184: UserWarning: Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure. + plt.show() -**Total running time of the script:** ( 0 minutes 2.065 seconds) +.. rst-class:: sphx-glr-timing + + **Total running time of the script:** ( 0 minutes 1.949 seconds) + + +.. _sphx_glr_download_auto_examples_plot_barycenter_fgw.py: + + .. only :: html .. container:: sphx-glr-footer + :class: sphx-glr-footer-example + - .. container:: sphx-glr-download + .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plot_barycenter_fgw.py <plot_barycenter_fgw.py>` - .. container:: sphx-glr-download + .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: plot_barycenter_fgw.ipynb <plot_barycenter_fgw.ipynb>` @@ -265,4 +317,4 @@ Plot Barycenter .. rst-class:: sphx-glr-signature - `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.readthedocs.io>`_ + `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_ |