diff options
28 files changed, 45 insertions, 307 deletions
@@ -1,3 +1,4 @@ Nicolas Courty <ncourty@irisa.fr> Nicolas Courty <Nico@MacBook-Pro-de-Nicolas.local> Nicolas Courty <ncourty@irisa.fr> ncourty <ncourty@irisa.fr> +Nicolas Courty <ncourty@irisa.fr> Nicolas Courty <Nico@pc-mna-08.univ-ubs.fr> Léo Gautheron <leo_g_autheron@hotmail.fr> Leo gautheron <gautheron@iv-cm-359.creatis.insa-lyon.fr> diff --git a/docs/cache_nbrun b/docs/cache_nbrun index 1510b2b..ed1a660 100644 --- a/docs/cache_nbrun +++ b/docs/cache_nbrun @@ -1 +1 @@ -{"plot_otda_mapping_colors_images.ipynb": "4f0587a00a3c082799a75a0ed36e9ce1", "plot_optim_OTreg.ipynb": "71d3c106b3f395a6b1001078a6ca6f8d", "plot_barycenter_1D.ipynb": "6fd8167f98816dc832fe0c58b1d5527b", "plot_WDA.ipynb": "27f8de4c6d7db46497076523673eedfb", "plot_OT_L1_vs_L2.ipynb": "e15219bf651a7e39e7c5c3934069894c", "plot_otda_color_images.ipynb": "d047d635f4987c81072383241590e21f", "plot_otda_classes.ipynb": "44bb8cd93317b5d342cd62e26d9bbe60", "plot_otda_d2.ipynb": "8ac4fd2ff899df0858ce1e5fead37f33", "plot_otda_mapping.ipynb": "d335a15af828aaa3439a1c67570d79d6", "plot_compute_emd.ipynb": "bd95981189df6adcb113d9b360ead734", "plot_OT_1D.ipynb": "e44c83f6112388ae18657cb0ad76d0e9", "plot_OT_2D_samples.ipynb": "3f125714daa35ff3cfe5dae1f71265c4"}
\ No newline at end of file +{"plot_otda_mapping_colors_images.ipynb": "4f0587a00a3c082799a75a0ed36e9ce1", "plot_optim_OTreg.ipynb": "71d3c106b3f395a6b1001078a6ca6f8d", "plot_otda_color_images.ipynb": "d047d635f4987c81072383241590e21f", "plot_WDA.ipynb": "27f8de4c6d7db46497076523673eedfb", "plot_OT_L1_vs_L2.ipynb": "e15219bf651a7e39e7c5c3934069894c", "plot_barycenter_1D.ipynb": "6fd8167f98816dc832fe0c58b1d5527b", "plot_otda_classes.ipynb": "44bb8cd93317b5d342cd62e26d9bbe60", "plot_otda_d2.ipynb": "8ac4fd2ff899df0858ce1e5fead37f33", "plot_otda_mapping.ipynb": "d335a15af828aaa3439a1c67570d79d6", "plot_gromov.ipynb": "f0c6d6431b270f042274de637bc0cb8c", "plot_compute_emd.ipynb": "bd95981189df6adcb113d9b360ead734", "plot_OT_1D.ipynb": "e44c83f6112388ae18657cb0ad76d0e9", "plot_OT_2D_samples.ipynb": "3f125714daa35ff3cfe5dae1f71265c4"}
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a/docs/source/auto_examples/images/thumb/sphx_glr_plot_barycenter_1D_thumb.png +++ b/docs/source/auto_examples/images/thumb/sphx_glr_plot_barycenter_1D_thumb.png diff --git a/docs/source/auto_examples/images/thumb/sphx_glr_plot_compute_emd_thumb.png b/docs/source/auto_examples/images/thumb/sphx_glr_plot_compute_emd_thumb.png Binary files differindex 898cd72..68cbdf7 100644 --- a/docs/source/auto_examples/images/thumb/sphx_glr_plot_compute_emd_thumb.png +++ b/docs/source/auto_examples/images/thumb/sphx_glr_plot_compute_emd_thumb.png diff --git a/docs/source/auto_examples/index.rst b/docs/source/auto_examples/index.rst index 5d7a53d..e69de29 100644 --- a/docs/source/auto_examples/index.rst +++ b/docs/source/auto_examples/index.rst @@ -1,270 +0,0 @@ -:orphan: - -POT Examples -============ - -This is a gallery of all the POT example files. - - - -.. raw:: html - - <div class="sphx-glr-thumbcontainer" tooltip="This example illustrates the computation of EMD and Sinkhorn transport plans and their visualiz..."> - -.. only:: html - - .. figure:: /auto_examples/images/thumb/sphx_glr_plot_OT_1D_thumb.png - - :ref:`sphx_glr_auto_examples_plot_OT_1D.py` - -.. raw:: html - - </div> - - -.. toctree:: - :hidden: - - /auto_examples/plot_OT_1D - -.. raw:: html - - <div class="sphx-glr-thumbcontainer" tooltip="Illustrates the use of the generic solver for regularized OT with user-designed regularization ..."> - -.. only:: html - - .. figure:: /auto_examples/images/thumb/sphx_glr_plot_optim_OTreg_thumb.png - - :ref:`sphx_glr_auto_examples_plot_optim_OTreg.py` - -.. raw:: html - - </div> - - -.. toctree:: - :hidden: - - /auto_examples/plot_optim_OTreg - -.. raw:: html - - <div class="sphx-glr-thumbcontainer" tooltip="Illustration of 2D optimal transport between discributions that are weighted sum of diracs. The..."> - -.. only:: html - - .. figure:: /auto_examples/images/thumb/sphx_glr_plot_OT_2D_samples_thumb.png - - :ref:`sphx_glr_auto_examples_plot_OT_2D_samples.py` - -.. raw:: html - - </div> - - -.. toctree:: - :hidden: - - /auto_examples/plot_OT_2D_samples - -.. raw:: html - - <div class="sphx-glr-thumbcontainer" tooltip="Shows how to compute multiple EMD and Sinkhorn with two differnt ground metrics and plot their ..."> - -.. only:: html - - .. figure:: /auto_examples/images/thumb/sphx_glr_plot_compute_emd_thumb.png - - :ref:`sphx_glr_auto_examples_plot_compute_emd.py` - -.. raw:: html - - </div> - - -.. toctree:: - :hidden: - - /auto_examples/plot_compute_emd - -.. raw:: html - - <div class="sphx-glr-thumbcontainer" tooltip="This example illustrate the use of WDA as proposed in [11]."> - -.. only:: html - - .. figure:: /auto_examples/images/thumb/sphx_glr_plot_WDA_thumb.png - - :ref:`sphx_glr_auto_examples_plot_WDA.py` - -.. raw:: html - - </div> - - -.. toctree:: - :hidden: - - /auto_examples/plot_WDA - -.. raw:: html - - <div class="sphx-glr-thumbcontainer" tooltip="This example presents a way of transferring colors between two image with Optimal Transport as ..."> - -.. only:: html - - .. figure:: /auto_examples/images/thumb/sphx_glr_plot_otda_color_images_thumb.png - - :ref:`sphx_glr_auto_examples_plot_otda_color_images.py` - -.. raw:: html - - </div> - - -.. toctree:: - :hidden: - - /auto_examples/plot_otda_color_images - -.. raw:: html - - <div class="sphx-glr-thumbcontainer" tooltip="This example illustrates the computation of regularized Wassersyein Barycenter as proposed in [..."> - -.. only:: html - - .. figure:: /auto_examples/images/thumb/sphx_glr_plot_barycenter_1D_thumb.png - - :ref:`sphx_glr_auto_examples_plot_barycenter_1D.py` - -.. raw:: html - - </div> - - -.. toctree:: - :hidden: - - /auto_examples/plot_barycenter_1D - -.. raw:: html - - <div class="sphx-glr-thumbcontainer" tooltip="OT for domain adaptation with image color adaptation [6] with mapping estimation [8]."> - -.. only:: html - - .. figure:: /auto_examples/images/thumb/sphx_glr_plot_otda_mapping_colors_images_thumb.png - - :ref:`sphx_glr_auto_examples_plot_otda_mapping_colors_images.py` - -.. raw:: html - - </div> - - -.. toctree:: - :hidden: - - /auto_examples/plot_otda_mapping_colors_images - -.. raw:: html - - <div class="sphx-glr-thumbcontainer" tooltip="This example presents how to use MappingTransport to estimate at the same time both the couplin..."> - -.. only:: html - - .. figure:: /auto_examples/images/thumb/sphx_glr_plot_otda_mapping_thumb.png - - :ref:`sphx_glr_auto_examples_plot_otda_mapping.py` - -.. raw:: html - - </div> - - -.. toctree:: - :hidden: - - /auto_examples/plot_otda_mapping - -.. raw:: html - - <div class="sphx-glr-thumbcontainer" tooltip="This example introduces a domain adaptation in a 2D setting and the 4 OTDA approaches currently..."> - -.. only:: html - - .. figure:: /auto_examples/images/thumb/sphx_glr_plot_otda_classes_thumb.png - - :ref:`sphx_glr_auto_examples_plot_otda_classes.py` - -.. raw:: html - - </div> - - -.. toctree:: - :hidden: - - /auto_examples/plot_otda_classes - -.. raw:: html - - <div class="sphx-glr-thumbcontainer" tooltip="This example introduces a domain adaptation in a 2D setting. It explicits the problem of domain..."> - -.. only:: html - - .. figure:: /auto_examples/images/thumb/sphx_glr_plot_otda_d2_thumb.png - - :ref:`sphx_glr_auto_examples_plot_otda_d2.py` - -.. raw:: html - - </div> - - -.. toctree:: - :hidden: - - /auto_examples/plot_otda_d2 - -.. raw:: html - - <div class="sphx-glr-thumbcontainer" tooltip="2D OT on empirical distributio with different gound metric."> - -.. only:: html - - .. figure:: /auto_examples/images/thumb/sphx_glr_plot_OT_L1_vs_L2_thumb.png - - :ref:`sphx_glr_auto_examples_plot_OT_L1_vs_L2.py` - -.. raw:: html - - </div> - - -.. toctree:: - :hidden: - - /auto_examples/plot_OT_L1_vs_L2 -.. raw:: html - - <div style='clear:both'></div> - - - -.. container:: sphx-glr-footer - - - .. container:: sphx-glr-download - - :download:`Download all examples in Python source code: auto_examples_python.zip <//home/rflamary/PYTHON/POT/docs/source/auto_examples/auto_examples_python.zip>` - - - - .. container:: sphx-glr-download - - :download:`Download all examples in Jupyter notebooks: auto_examples_jupyter.zip <//home/rflamary/PYTHON/POT/docs/source/auto_examples/auto_examples_jupyter.zip>` - -.. rst-class:: sphx-glr-signature - - `Generated by Sphinx-Gallery <https://sphinx-gallery.readthedocs.io>`_ diff --git a/docs/source/auto_examples/plot_OT_1D.rst b/docs/source/auto_examples/plot_OT_1D.rst index b91916e..975a923 100644 --- a/docs/source/auto_examples/plot_OT_1D.rst +++ b/docs/source/auto_examples/plot_OT_1D.rst @@ -171,7 +171,7 @@ Solve Sinkhorn 110|1.527180e-10| -**Total running time of the script:** ( 0 minutes 0.748 seconds) +**Total running time of the script:** ( 0 minutes 1.198 seconds) @@ -190,4 +190,4 @@ Solve Sinkhorn .. rst-class:: sphx-glr-signature - `Generated by Sphinx-Gallery <https://sphinx-gallery.readthedocs.io>`_ + `Generated by Sphinx-Gallery <http://sphinx-gallery.readthedocs.io>`_ diff --git a/docs/source/auto_examples/plot_OT_2D_samples.rst b/docs/source/auto_examples/plot_OT_2D_samples.rst index 0ad9cf0..5565c54 100644 --- a/docs/source/auto_examples/plot_OT_2D_samples.rst +++ b/docs/source/auto_examples/plot_OT_2D_samples.rst @@ -191,7 +191,7 @@ Compute Sinkhorn -**Total running time of the script:** ( 0 minutes 1.743 seconds) +**Total running time of the script:** ( 0 minutes 3.380 seconds) @@ -210,4 +210,4 @@ Compute Sinkhorn .. rst-class:: sphx-glr-signature - `Generated by Sphinx-Gallery <https://sphinx-gallery.readthedocs.io>`_ + `Generated by Sphinx-Gallery <http://sphinx-gallery.readthedocs.io>`_ diff --git a/docs/source/auto_examples/plot_OT_L1_vs_L2.rst b/docs/source/auto_examples/plot_OT_L1_vs_L2.rst index f97b373..a569b50 100644 --- a/docs/source/auto_examples/plot_OT_L1_vs_L2.rst +++ b/docs/source/auto_examples/plot_OT_L1_vs_L2.rst @@ -290,7 +290,7 @@ Dataset 2 : Plot OT Matrices -**Total running time of the script:** ( 0 minutes 1.134 seconds) +**Total running time of the script:** ( 0 minutes 1.976 seconds) @@ -309,4 +309,4 @@ Dataset 2 : Plot OT Matrices .. rst-class:: sphx-glr-signature - `Generated by Sphinx-Gallery <https://sphinx-gallery.readthedocs.io>`_ + `Generated by Sphinx-Gallery <http://sphinx-gallery.readthedocs.io>`_ diff --git a/docs/source/auto_examples/plot_WDA.rst b/docs/source/auto_examples/plot_WDA.rst index 64ddb47..2d83123 100644 --- a/docs/source/auto_examples/plot_WDA.rst +++ b/docs/source/auto_examples/plot_WDA.rst @@ -150,21 +150,27 @@ Compute Wasserstein Discriminant Analysis Compiling cost function... Computing gradient of cost function... iter cost val grad. norm - 1 +5.4993226050368416e-01 5.18285173e-01 - 2 +3.4883000507542844e-01 1.96795818e-01 - 3 +2.9841234004693890e-01 2.33029475e-01 - 4 +2.3976476757548179e-01 1.38593951e-01 - 5 +2.3614468346177828e-01 1.19615394e-01 - 6 +2.2586536502789240e-01 4.82430685e-02 - 7 +2.2451030967794622e-01 2.56564039e-02 - 8 +2.2421446331083625e-01 1.47932578e-02 - 9 +2.2407441444450052e-01 1.12040327e-03 - 10 +2.2407365923337522e-01 3.78899763e-04 - 11 +2.2407356874011675e-01 1.79740810e-05 - 12 +2.2407356862959993e-01 1.25643005e-05 - 13 +2.2407356853043561e-01 1.40415001e-06 - 14 +2.2407356852925220e-01 3.41183585e-07 - Terminated - min grad norm reached after 14 iterations, 6.78 seconds. + 1 +9.0167295050534191e-01 2.28422652e-01 + 2 +4.8324990550878105e-01 4.89362707e-01 + 3 +3.4613154515357075e-01 2.84117562e-01 + 4 +2.5277108387195002e-01 1.24888750e-01 + 5 +2.4113858393736629e-01 8.07491482e-02 + 6 +2.3642108593032782e-01 1.67612140e-02 + 7 +2.3625721372202199e-01 7.68640008e-03 + 8 +2.3625461994913738e-01 7.42200784e-03 + 9 +2.3624493441436939e-01 6.43534105e-03 + 10 +2.3621901383686217e-01 2.17960585e-03 + 11 +2.3621854258326572e-01 2.03306749e-03 + 12 +2.3621696458678049e-01 1.37118721e-03 + 13 +2.3621569489873540e-01 2.76368907e-04 + 14 +2.3621565599232983e-01 1.41898134e-04 + 15 +2.3621564465487518e-01 5.96602069e-05 + 16 +2.3621564232556647e-01 1.08709521e-05 + 17 +2.3621564230277003e-01 9.17855656e-06 + 18 +2.3621564224857586e-01 1.73728345e-06 + 19 +2.3621564224748123e-01 1.17770019e-06 + 20 +2.3621564224658587e-01 2.16179383e-07 + Terminated - min grad norm reached after 20 iterations, 9.20 seconds. Plot 2D projections @@ -216,7 +222,7 @@ Plot 2D projections -**Total running time of the script:** ( 0 minutes 7.637 seconds) +**Total running time of the script:** ( 0 minutes 16.182 seconds) @@ -235,4 +241,4 @@ Plot 2D projections .. rst-class:: sphx-glr-signature - `Generated by Sphinx-Gallery <https://sphinx-gallery.readthedocs.io>`_ + `Generated by Sphinx-Gallery <http://sphinx-gallery.readthedocs.io>`_ diff --git a/docs/source/auto_examples/plot_barycenter_1D.rst b/docs/source/auto_examples/plot_barycenter_1D.rst index 413fae3..f17f2c2 100644 --- a/docs/source/auto_examples/plot_barycenter_1D.rst +++ b/docs/source/auto_examples/plot_barycenter_1D.rst @@ -230,7 +230,7 @@ Barycentric interpolation -**Total running time of the script:** ( 0 minutes 0.431 seconds) +**Total running time of the script:** ( 0 minutes 0.814 seconds) @@ -249,4 +249,4 @@ Barycentric interpolation .. rst-class:: sphx-glr-signature - `Generated by Sphinx-Gallery <https://sphinx-gallery.readthedocs.io>`_ + `Generated by Sphinx-Gallery <http://sphinx-gallery.readthedocs.io>`_ diff --git a/docs/source/auto_examples/plot_compute_emd.rst b/docs/source/auto_examples/plot_compute_emd.rst index ce79e20..cdbc620 100644 --- a/docs/source/auto_examples/plot_compute_emd.rst +++ b/docs/source/auto_examples/plot_compute_emd.rst @@ -162,7 +162,7 @@ Compute Sinkhorn for the different losses -**Total running time of the script:** ( 0 minutes 0.441 seconds) +**Total running time of the script:** ( 0 minutes 0.697 seconds) @@ -181,4 +181,4 @@ Compute Sinkhorn for the different losses .. rst-class:: sphx-glr-signature - `Generated by Sphinx-Gallery <https://sphinx-gallery.readthedocs.io>`_ + `Generated by Sphinx-Gallery <http://sphinx-gallery.readthedocs.io>`_ diff --git a/docs/source/conf.py b/docs/source/conf.py index 4105d87..7bf392c 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -33,7 +33,7 @@ class Mock(MagicMock): return MagicMock() MOCK_MODULES = ['ot.lp.emd_wrap','autograd','pymanopt','cudamat','autograd.numpy','pymanopt.manifolds','pymanopt.solvers'] # 'autograd.numpy','pymanopt.manifolds','pymanopt.solvers', -sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES) +#sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES) # !!!! # If extensions (or modules to document with autodoc) are in another directory, @@ -62,7 +62,7 @@ extensions = [ 'sphinx.ext.ifconfig', 'sphinx.ext.viewcode', 'sphinx.ext.napoleon', - #'sphinx_gallery.gen_gallery', + 'sphinx_gallery.gen_gallery', ] # Add any paths that contain templates here, relative to this directory. diff --git a/examples/plot_gromov.py b/examples/plot_gromov.py index dce66c4..5132024 100644 --- a/examples/plot_gromov.py +++ b/examples/plot_gromov.py @@ -3,6 +3,7 @@ ==========================
Gromov-Wasserstein example
==========================
+
This example is designed to show how to use the Gromov-Wassertsein distance
computation in POT.
"""
@@ -15,7 +16,7 @@ computation in POT. import scipy as sp
import numpy as np
import matplotlib.pylab as pl
-
+from mpl_toolkits.mplot3d import Axes3D # noqa
import ot
diff --git a/examples/plot_gromov_barycenter.py b/examples/plot_gromov_barycenter.py index 52f4966..93533c0 100755 --- a/examples/plot_gromov_barycenter.py +++ b/examples/plot_gromov_barycenter.py @@ -3,6 +3,7 @@ =====================================
Gromov-Wasserstein Barycenter example
=====================================
+
This example is designed to show how to use the Gromov-Wasserstein distance
computation in POT.
"""
@@ -24,7 +25,6 @@ from sklearn.decomposition import PCA import ot
"""
-
Smacof MDS
==========
This function allows to find an embedding of points given a dissimilarity matrix
@@ -134,28 +134,28 @@ 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, stopThr=1e-3)
+ 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, stopThr=1e-3)
+ 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, stopThr=1e-3)
+ 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, stopThr=1e-3)
+ max_iter=100, tol=1e-3)
"""
Visualization
diff --git a/ot/__init__.py b/ot/__init__.py index a295e1b..c9bb8c0 100644 --- a/ot/__init__.py +++ b/ot/__init__.py @@ -29,7 +29,7 @@ from .gromov import gromov_wasserstein, gromov_wasserstein2 # utils functions from .utils import dist, unif, tic, toc, toq -__version__ = "0.3.1" +__version__ = "0.4.0b" __all__ = ["emd", "emd2", "sinkhorn", "sinkhorn2", "utils", 'datasets', 'bregman', 'lp', 'plot', 'tic', 'toc', 'toq', |
