From 09214d0ad3abd0c81b3a2c8051bf8b370350d6e5 Mon Sep 17 00:00:00 2001 From: Hind-M Date: Tue, 1 Jun 2021 11:20:26 +0200 Subject: Add datasets generators documentation --- src/python/doc/datasets_generators.inc | 14 +++++ src/python/doc/datasets_generators.rst | 97 ++++++++++++++++++++++++++++++++++ src/python/doc/examples.rst | 1 + src/python/doc/index.rst | 5 ++ 4 files changed, 117 insertions(+) create mode 100644 src/python/doc/datasets_generators.inc create mode 100644 src/python/doc/datasets_generators.rst (limited to 'src/python/doc') diff --git a/src/python/doc/datasets_generators.inc b/src/python/doc/datasets_generators.inc new file mode 100644 index 00000000..c88115c3 --- /dev/null +++ b/src/python/doc/datasets_generators.inc @@ -0,0 +1,14 @@ +.. table:: + :widths: 30 40 30 + + +-----------------------------------+--------------------------------------------+--------------------------------------------------------------------------------------+ + | | :math:`(x_1, x_2, \ldots, x_d)` | Datasets generators (points). | :Authors: Hind Montassif | + | | | | + | | | :Since: GUDHI 3.5.0 | + | | | | + | | | :License: MIT (`LGPL v3 `_) | + | | | | + | | | :Requires: `CGAL `_ | + +-----------------------------------+--------------------------------------------+--------------------------------------------------------------------------------------+ + | * :doc:`datasets_generators` | + +-----------------------------------+-----------------------------------------------------------------------------------------------------------------------------------+ diff --git a/src/python/doc/datasets_generators.rst b/src/python/doc/datasets_generators.rst new file mode 100644 index 00000000..ef21c9d2 --- /dev/null +++ b/src/python/doc/datasets_generators.rst @@ -0,0 +1,97 @@ + +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + +=========================== +Datasets generators manual +=========================== + +We provide the generation of different customizable datasets to use as inputs for Gudhi complexes and data structures. + + +Points generators +------------------ + +Points on sphere +^^^^^^^^^^^^^^^^ + +The module **_points** enables the generation of random i.i.d. points uniformly on a (d-1)-sphere in :math:`R^d`. +The user should provide the number of points to be generated on the sphere :code:`n_samples` and the ambient dimension :code:`ambient_dim`. +The :code:`radius` of sphere is optional and is equal to **1** by default. +Only random points generation is currently available. + +The generated points are given as an array of shape :math:`(n\_samples, ambient\_dim)`. + +Example +""""""" + +.. code-block:: python + + from gudhi.datasets.generators import _points + from gudhi import AlphaComplex + + # Generate 50 points on a sphere in R^2 + gen_points = _points.sphere(n_samples = 50, ambient_dim = 2, radius = 1, sample = "random") + + # Create an alpha complex from the generated points + alpha_complex = AlphaComplex(points = gen_points) + +.. autofunction:: gudhi.datasets.generators._points.sphere + +Points on torus +^^^^^^^^^^^^^^^^ + +You can also generate points on a torus. + +Two modules are available and give the same output: the first one depends on **CGAL** and the second does not and consists of full python code. + +On another hand, two sample types are provided : you can either generate i.i.d. points on a d-torus in :math:`R^{2d}` *randomly* or on a *grid*. + +First module : **_points** +"""""""""""""""""""""""""" + +The user should provide the number of points to be generated on the torus :code:`n_samples`, and the dimension :code:`dim` of the torus on which points would be generated in :math:`R^{2dim}`. +The flag :code:`uniform` is optional and is set to **False** by default, meaning that the points will be generated randomly. +In this case, the returned generated points would be an array of shape :math:`(n\_samples, 2*dim)`. +Otherwise, if set to **True**, the points are generated as a grid and would be given as an array of shape : + +.. math:: + + ( [n\_samples^{1 \over {dim}}]^{dim}, 2*dim ) + +Example +""""""" +.. code-block:: python + + from gudhi.datasets.generators import _points + + # Generate 50 points randomly on a torus in R^6 + gen_points = _points.torus(n_samples = 50, dim = 3) + + # Generate 27 points on a torus as a grid in R^6 + gen_points = _points.torus(n_samples = 50, dim = 3, uniform = True) + +.. autofunction:: gudhi.datasets.generators._points.torus + +Second module : **points** +"""""""""""""""""""""""""" + +The user should provide the number of points to be generated on the torus :code:`n_samples` and the dimension :code:`dim` of the torus on which points would be generated in :math:`R^{2dim}`. +The :code:`sample` argument is optional and is set to **'random'** by default. +The other allowed value of sample type is **'grid'** and is equivalent to :code:`uniform = True` in the first module. + +Example +""""""" +.. code-block:: python + + from gudhi.datasets.generators import points + + # Generate 50 points randomly on a torus in R^6 + gen_points = points.torus(n_samples = 50, dim = 3) + + # Generate 27 points on a torus as a grid in R^6 + gen_points = points.torus(n_samples = 50, dim = 3, sample = 'grid') + + +.. autofunction:: gudhi.datasets.generators.points.torus diff --git a/src/python/doc/examples.rst b/src/python/doc/examples.rst index 76e5d4c7..1442f185 100644 --- a/src/python/doc/examples.rst +++ b/src/python/doc/examples.rst @@ -8,6 +8,7 @@ Examples .. only:: builder_html * :download:`alpha_complex_diagram_persistence_from_off_file_example.py <../example/alpha_complex_diagram_persistence_from_off_file_example.py>` + * :download:`alpha_complex_from_generated_points_on_sphere_example.py <../example/alpha_complex_from_generated_points_on_sphere_example.py>` * :download:`alpha_complex_from_points_example.py <../example/alpha_complex_from_points_example.py>` * :download:`alpha_rips_persistence_bottleneck_distance.py <../example/alpha_rips_persistence_bottleneck_distance.py>` * :download:`bottleneck_basic_example.py <../example/bottleneck_basic_example.py>` diff --git a/src/python/doc/index.rst b/src/python/doc/index.rst index 040e57a4..2d7921ae 100644 --- a/src/python/doc/index.rst +++ b/src/python/doc/index.rst @@ -91,3 +91,8 @@ Clustering ********** .. include:: clustering.inc + +Datasets generators +******************* + +.. include:: datasets_generators.inc -- cgit v1.2.3 From b04759faf8f474ff98e9e229c41d85ff3bf009da Mon Sep 17 00:00:00 2001 From: Hind-M Date: Mon, 7 Jun 2021 11:56:48 +0200 Subject: Add a 3d sphere image to doc for datasets_generators --- src/python/doc/datasets_generators.inc | 4 ++-- src/python/doc/img/sphere_3d.png | Bin 0 -> 90550 bytes 2 files changed, 2 insertions(+), 2 deletions(-) create mode 100644 src/python/doc/img/sphere_3d.png (limited to 'src/python/doc') diff --git a/src/python/doc/datasets_generators.inc b/src/python/doc/datasets_generators.inc index c88115c3..8d169275 100644 --- a/src/python/doc/datasets_generators.inc +++ b/src/python/doc/datasets_generators.inc @@ -2,8 +2,8 @@ :widths: 30 40 30 +-----------------------------------+--------------------------------------------+--------------------------------------------------------------------------------------+ - | | :math:`(x_1, x_2, \ldots, x_d)` | Datasets generators (points). | :Authors: Hind Montassif | - | | | | + | .. figure:: | Datasets generators (points). | :Authors: Hind Montassif | + | img/sphere_3d.png | | | | | | :Since: GUDHI 3.5.0 | | | | | | | | :License: MIT (`LGPL v3 `_) | diff --git a/src/python/doc/img/sphere_3d.png b/src/python/doc/img/sphere_3d.png new file mode 100644 index 00000000..7e7f0ab2 Binary files /dev/null and b/src/python/doc/img/sphere_3d.png differ -- cgit v1.2.3 From b9160fb8410bbb999913b0b4e91f1aa1ff58d2cd Mon Sep 17 00:00:00 2001 From: Hind-M Date: Mon, 7 Jun 2021 17:07:55 +0200 Subject: Replace 'uniform' flag of torus generation with 'sample' taking two possible values: 'grid'(i.e uniform==True) or 'random' (i.e uniform==False) --- src/Tangential_complex/benchmark/benchmark_tc.cpp | 2 +- src/common/include/gudhi/random_point_generators.h | 10 +++++----- src/common/utilities/off_file_from_shape_generator.cpp | 2 +- src/python/doc/datasets_generators.rst | 8 ++++---- src/python/gudhi/datasets/generators/_points.cc | 10 +++++----- 5 files changed, 16 insertions(+), 16 deletions(-) (limited to 'src/python/doc') diff --git a/src/Tangential_complex/benchmark/benchmark_tc.cpp b/src/Tangential_complex/benchmark/benchmark_tc.cpp index e3b2a04f..6da1425f 100644 --- a/src/Tangential_complex/benchmark/benchmark_tc.cpp +++ b/src/Tangential_complex/benchmark/benchmark_tc.cpp @@ -704,7 +704,7 @@ int main() { points = Gudhi::generate_points_on_torus_d( num_points, intrinsic_dim, - param1 == "Y", // uniform + (param1 == "Y") ? "grid" : "random", // grid or random sample type std::atof(param2.c_str())); // radius_noise_percentage } else if (input == "generate_klein_bottle_3D") { points = Gudhi::generate_points_on_klein_bottle_3D( diff --git a/src/common/include/gudhi/random_point_generators.h b/src/common/include/gudhi/random_point_generators.h index 33fb182d..07e4f3da 100644 --- a/src/common/include/gudhi/random_point_generators.h +++ b/src/common/include/gudhi/random_point_generators.h @@ -185,7 +185,7 @@ std::vector generate_points_on_torus_3D(std::size_t nu // "Private" function used by generate_points_on_torus_d template -static void generate_uniform_points_on_torus_d(const Kernel &k, int dim, std::size_t num_slices, +static void generate_grid_points_on_torus_d(const Kernel &k, int dim, std::size_t num_slices, OutputIterator out, double radius_noise_percentage = 0., std::vector current_point = @@ -208,14 +208,14 @@ static void generate_uniform_points_on_torus_d(const Kernel &k, int dim, std::si double alpha = two_pi * slice_idx / num_slices; cp2.push_back(radius_noise_ratio * std::cos(alpha)); cp2.push_back(radius_noise_ratio * std::sin(alpha)); - generate_uniform_points_on_torus_d( + generate_grid_points_on_torus_d( k, dim, num_slices, out, radius_noise_percentage, cp2); } } } template -std::vector generate_points_on_torus_d(std::size_t num_points, int dim, bool uniform = false, +std::vector generate_points_on_torus_d(std::size_t num_points, int dim, std::string sample = "random", double radius_noise_percentage = 0.) { using namespace boost::math::double_constants; @@ -226,9 +226,9 @@ std::vector generate_points_on_torus_d(std::size_t num std::vector points; points.reserve(num_points); - if (uniform) { + if (sample == "grid") { std::size_t num_slices = (std::size_t)std::pow(num_points, 1. / dim); - generate_uniform_points_on_torus_d( + generate_grid_points_on_torus_d( k, dim, num_slices, std::back_inserter(points), radius_noise_percentage); } else { for (std::size_t i = 0; i < num_points;) { diff --git a/src/common/utilities/off_file_from_shape_generator.cpp b/src/common/utilities/off_file_from_shape_generator.cpp index 6efef4fc..71ede434 100644 --- a/src/common/utilities/off_file_from_shape_generator.cpp +++ b/src/common/utilities/off_file_from_shape_generator.cpp @@ -135,7 +135,7 @@ int main(int argc, char **argv) { if (dimension == 3) points = Gudhi::generate_points_on_torus_3D(points_number, dimension, radius, radius/2.); else - points = Gudhi::generate_points_on_torus_d(points_number, dimension, true); + points = Gudhi::generate_points_on_torus_d(points_number, dimension, "grid"); break; case Data_shape::klein: switch (dimension) { diff --git a/src/python/doc/datasets_generators.rst b/src/python/doc/datasets_generators.rst index ef21c9d2..2802eccd 100644 --- a/src/python/doc/datasets_generators.rst +++ b/src/python/doc/datasets_generators.rst @@ -52,9 +52,9 @@ First module : **_points** """""""""""""""""""""""""" The user should provide the number of points to be generated on the torus :code:`n_samples`, and the dimension :code:`dim` of the torus on which points would be generated in :math:`R^{2dim}`. -The flag :code:`uniform` is optional and is set to **False** by default, meaning that the points will be generated randomly. +The :code:`sample` argument is optional and is set to **'random'** by default. In this case, the returned generated points would be an array of shape :math:`(n\_samples, 2*dim)`. -Otherwise, if set to **True**, the points are generated as a grid and would be given as an array of shape : +Otherwise, if set to **'grid'**, the points are generated on a grid and would be given as an array of shape : .. math:: @@ -70,7 +70,7 @@ Example gen_points = _points.torus(n_samples = 50, dim = 3) # Generate 27 points on a torus as a grid in R^6 - gen_points = _points.torus(n_samples = 50, dim = 3, uniform = True) + gen_points = _points.torus(n_samples = 50, dim = 3, sample = 'grid') .. autofunction:: gudhi.datasets.generators._points.torus @@ -79,7 +79,7 @@ Second module : **points** The user should provide the number of points to be generated on the torus :code:`n_samples` and the dimension :code:`dim` of the torus on which points would be generated in :math:`R^{2dim}`. The :code:`sample` argument is optional and is set to **'random'** by default. -The other allowed value of sample type is **'grid'** and is equivalent to :code:`uniform = True` in the first module. +The other allowed value of sample type is **'grid'**. Example """"""" diff --git a/src/python/gudhi/datasets/generators/_points.cc b/src/python/gudhi/datasets/generators/_points.cc index 55b21b2b..6bbdf284 100644 --- a/src/python/gudhi/datasets/generators/_points.cc +++ b/src/python/gudhi/datasets/generators/_points.cc @@ -46,13 +46,13 @@ py::array_t generate_points_on_sphere(size_t n_samples, int ambient_dim, return points; } -py::array_t generate_points_on_torus(size_t n_samples, int dim, bool uniform) { +py::array_t generate_points_on_torus(size_t n_samples, int dim, std::string sample) { std::vector points_generated; { py::gil_scoped_release release; - points_generated = Gudhi::generate_points_on_torus_d(n_samples, dim, uniform); + points_generated = Gudhi::generate_points_on_torus_d(n_samples, dim, sample); } size_t npoints = points_generated.size(); @@ -93,7 +93,7 @@ PYBIND11_MODULE(_points, m) { )pbdoc"); m.def("torus", &generate_points_on_torus, - py::arg("n_samples"), py::arg("dim"), py::arg("uniform") = false, + py::arg("n_samples"), py::arg("dim"), py::arg("sample") = "random", R"pbdoc( Generate random i.i.d. points on a d-torus in R^2d @@ -101,8 +101,8 @@ PYBIND11_MODULE(_points, m) { :type n_samples: integer :param dim: The dimension of the torus on which points would be generated in R^2*dim. :type dim: integer - :param uniform: A flag to define if the points generation is uniform (i.e generated as a grid). - :type uniform: bool + :param sample: The sample type. Available values are: `"random"` and `"grid"`. Default value is `"random"`. + :type sample: string :rtype: numpy array of float :returns: the generated points on a torus. )pbdoc"); -- cgit v1.2.3 From 01d62172c54b258a1072a42d25a39fd21a38c284 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Thu, 24 Jun 2021 16:15:02 +0200 Subject: Use python_docs_theme. Dependency added in gudhi-deploy --- src/python/doc/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'src/python/doc') diff --git a/src/python/doc/conf.py b/src/python/doc/conf.py index b06baf9c..46debd87 100755 --- a/src/python/doc/conf.py +++ b/src/python/doc/conf.py @@ -120,7 +120,7 @@ pygments_style = 'sphinx' # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. -html_theme = 'classic' +html_theme = 'python_docs_theme' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the -- cgit v1.2.3 From b32f61a66d52a25be177dd96de469420e5b4a980 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Fri, 25 Jun 2021 07:07:32 +0200 Subject: add sphinx-paramlinks and python-docs-theme in installation guide --- src/python/doc/installation.rst | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'src/python/doc') diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst index 9c16b04e..451ae020 100644 --- a/src/python/doc/installation.rst +++ b/src/python/doc/installation.rst @@ -194,8 +194,10 @@ A complete configuration would be : Documentation ============= -To build the documentation, `sphinx-doc `_ and -`sphinxcontrib-bibtex `_ are +To build the documentation, `sphinx-doc `_, +`sphinxcontrib-bibtex `_, +`sphinxcontrib-paramlinks `_ and +`python-docs-theme `_ are required. As the documentation is auto-tested, `CGAL`_, `Eigen`_, `Matplotlib`_, `NumPy`_, `POT`_, `Scikit-learn`_ and `SciPy`_ are also mandatory to build the documentation. -- cgit v1.2.3 From c0cca8dbd60e3da5147517f6f8f37d9bdeefe511 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Fri, 25 Jun 2021 16:26:55 +0200 Subject: update headers, conf.py for the new theme and bottleneck image to be smaller --- src/Bottleneck_distance/doc/perturb_pd.png | Bin 20864 -> 15532 bytes src/common/doc/header.html | 1 + src/python/doc/_templates/layout.html | 1 + src/python/doc/conf.py | 3 --- 4 files changed, 2 insertions(+), 3 deletions(-) (limited to 'src/python/doc') diff --git a/src/Bottleneck_distance/doc/perturb_pd.png b/src/Bottleneck_distance/doc/perturb_pd.png index be638de0..eabf3c8c 100644 Binary files a/src/Bottleneck_distance/doc/perturb_pd.png and b/src/Bottleneck_distance/doc/perturb_pd.png differ diff --git a/src/common/doc/header.html b/src/common/doc/header.html index 9da20bbc..7c20478b 100644 --- a/src/common/doc/header.html +++ b/src/common/doc/header.html @@ -49,6 +49,7 @@ $extrastylesheet
  • Related projects
  • They are talking about us
  • GUDHI in action
    • +
  • Etymology
  • diff --git a/src/python/doc/_templates/layout.html b/src/python/doc/_templates/layout.html index cd40a51b..e074b6c7 100644 --- a/src/python/doc/_templates/layout.html +++ b/src/python/doc/_templates/layout.html @@ -194,6 +194,7 @@
  • Related projects
  • They are talking about us
  • GUDHI in action
    • +
  • Etymology
  • diff --git a/src/python/doc/conf.py b/src/python/doc/conf.py index 46debd87..e69e2751 100755 --- a/src/python/doc/conf.py +++ b/src/python/doc/conf.py @@ -126,9 +126,6 @@ html_theme = 'python_docs_theme' # further. For a list of options available for each theme, see the # documentation. html_theme_options = { - "sidebarbgcolor": "#A1ADCD", - "sidebartextcolor": "black", - "sidebarlinkcolor": "#334D5C", "body_max_width": "100%", } -- cgit v1.2.3 From a91e3bc16d511ef66bb296da6a990a0723100657 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Thu, 5 Aug 2021 18:00:40 +0200 Subject: mailing lists migration and rephrase contributions in installation guides --- .github/for_maintainers/new_gudhi_version_creation.md | 4 ++-- src/common/doc/installation.h | 8 +++++--- src/python/doc/installation.rst | 9 +++++---- src/python/setup.py.in | 2 +- 4 files changed, 13 insertions(+), 10 deletions(-) (limited to 'src/python/doc') diff --git a/.github/for_maintainers/new_gudhi_version_creation.md b/.github/for_maintainers/new_gudhi_version_creation.md index d6c4cdd3..3e5295c5 100644 --- a/.github/for_maintainers/new_gudhi_version_creation.md +++ b/.github/for_maintainers/new_gudhi_version_creation.md @@ -128,5 +128,5 @@ docker image on docker hub. ## Mail sending Send version mail to the following lists : -* gudhi-devel@lists.gforge.inria.fr -* gudhi-users@lists.gforge.inria.fr (not for release candidate) +* gudhi-devel@inria.fr +* gudhi-users@inria.fr (not for release candidate) diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index 610aa17e..5d40a48e 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -243,10 +243,12 @@ make \endverbatim * Witness_complex/example_nearest_landmark_table.cpp * * \section Contributions Bug reports and contributions - * Please help us improving the quality of the GUDHI library. You may report bugs or suggestions to: - * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim + * Please help us improving the quality of the GUDHI library. + * You may report bugs or + * contact us for any suggestions. * - * GUDHI is open to external contributions. If you want to join our development team, please contact us. + * GUDHI is open to external contributions. If you want to join our development team, please take some time to read our + * contributing guide. * */ diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst index 9c16b04e..56f27b21 100644 --- a/src/python/doc/installation.rst +++ b/src/python/doc/installation.rst @@ -396,8 +396,9 @@ TensorFlow Bug reports and contributions ***************************** -Please help us improving the quality of the GUDHI library. You may report bugs or suggestions to: +Please help us improving the quality of the GUDHI library. +You may `report bugs `_ or +`contact us `_ for any suggestions. - Contact: gudhi-users@lists.gforge.inria.fr - -GUDHI is open to external contributions. If you want to join our development team, please contact us. +GUDHI is open to external contributions. If you want to join our development team, please take some time to read our +`contributing guide `_. diff --git a/src/python/setup.py.in b/src/python/setup.py.in index 759ec8d8..c400b601 100644 --- a/src/python/setup.py.in +++ b/src/python/setup.py.in @@ -71,7 +71,7 @@ setup( name = 'gudhi', packages=find_packages(), # find_namespace_packages(include=["gudhi*"]) author='GUDHI Editorial Board', - author_email='gudhi-contact@lists.gforge.inria.fr', + author_email='gudhi-contact@inria.fr', version='@GUDHI_VERSION@', url='https://gudhi.inria.fr/', project_urls={ -- cgit v1.2.3 From 575beed582f9288d83a403f4f578731f172f7f5f Mon Sep 17 00:00:00 2001 From: Hind-M Date: Wed, 11 Aug 2021 14:35:25 +0200 Subject: Add test for sphere and torus Fix numerical approximations inconsistencies with dim fraction exponent when generating points as grid on torus Add notes in doc regarding the torus versions use cases --- src/common/include/gudhi/random_point_generators.h | 2 +- src/python/CMakeLists.txt | 3 ++ src/python/doc/datasets_generators.rst | 5 +++ src/python/gudhi/datasets/generators/_points.cc | 4 +++ src/python/gudhi/datasets/generators/points.py | 5 +-- src/python/test/test_datasets_generators.py | 40 ++++++++++++++++++++++ 6 files changed, 54 insertions(+), 5 deletions(-) create mode 100755 src/python/test/test_datasets_generators.py (limited to 'src/python/doc') diff --git a/src/common/include/gudhi/random_point_generators.h b/src/common/include/gudhi/random_point_generators.h index 07e4f3da..25a7392d 100644 --- a/src/common/include/gudhi/random_point_generators.h +++ b/src/common/include/gudhi/random_point_generators.h @@ -227,7 +227,7 @@ std::vector generate_points_on_torus_d(std::size_t num std::vector points; points.reserve(num_points); if (sample == "grid") { - std::size_t num_slices = (std::size_t)std::pow(num_points, 1. / dim); + std::size_t num_slices = (std::size_t)std::pow(num_points + .5, 1. / dim); // add .5 to avoid rounding down with numerical approximations generate_grid_points_on_torus_d( k, dim, num_slices, std::back_inserter(points), radius_noise_percentage); } else { diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt index 8c46004a..f30dfe6d 100644 --- a/src/python/CMakeLists.txt +++ b/src/python/CMakeLists.txt @@ -443,6 +443,9 @@ if(PYTHONINTERP_FOUND) # Euclidean witness add_gudhi_py_test(test_euclidean_witness_complex) + # Datasets generators + add_gudhi_py_test(test_datasets_generators) # TODO separate full python datasets generators in another test file independant from CGAL ? + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) # Cubical diff --git a/src/python/doc/datasets_generators.rst b/src/python/doc/datasets_generators.rst index 2802eccd..e63dde82 100644 --- a/src/python/doc/datasets_generators.rst +++ b/src/python/doc/datasets_generators.rst @@ -60,6 +60,9 @@ Otherwise, if set to **'grid'**, the points are generated on a grid and would be ( [n\_samples^{1 \over {dim}}]^{dim}, 2*dim ) + +**Note:** This version is recommended when the user wishes to use **'grid'** as sample type, or **'random'** with a relatively small number of samples (~ less than 150). + Example """"""" .. code-block:: python @@ -81,6 +84,8 @@ The user should provide the number of points to be generated on the torus :code: The :code:`sample` argument is optional and is set to **'random'** by default. The other allowed value of sample type is **'grid'**. +**Note:** This version is recommended when the user wishes to use **'random'** as sample type with a great number of samples and a low dimension. + Example """"""" .. code-block:: python diff --git a/src/python/gudhi/datasets/generators/_points.cc b/src/python/gudhi/datasets/generators/_points.cc index 6bbdf284..3d38ff90 100644 --- a/src/python/gudhi/datasets/generators/_points.cc +++ b/src/python/gudhi/datasets/generators/_points.cc @@ -48,6 +48,10 @@ py::array_t generate_points_on_sphere(size_t n_samples, int ambient_dim, py::array_t generate_points_on_torus(size_t n_samples, int dim, std::string sample) { + if ( (sample != "random") && (sample != "grid")) { + throw pybind11::value_error("This sample type is not supported"); + } + std::vector points_generated; { diff --git a/src/python/gudhi/datasets/generators/points.py b/src/python/gudhi/datasets/generators/points.py index 3870dea6..daada486 100644 --- a/src/python/gudhi/datasets/generators/points.py +++ b/src/python/gudhi/datasets/generators/points.py @@ -23,7 +23,7 @@ def _generate_random_points_on_torus(n_samples, dim): def _generate_grid_points_on_torus(n_samples, dim): # Generate points on a dim-torus as a grid - n_samples_grid = int(n_samples**(1./dim)) + n_samples_grid = int((n_samples+.5)**(1./dim)) # add .5 to avoid rounding down with numerical approximations alpha = np.linspace(0, 2*np.pi, n_samples_grid, endpoint=False) array_points_inter = np.column_stack([np.cos(alpha), np.sin(alpha)]) @@ -45,12 +45,9 @@ def torus(n_samples, dim, sample='random'): """ if sample == 'random': # Generate points randomly - print("Sample is random") return _generate_random_points_on_torus(n_samples, dim) elif sample == 'grid': # Generate points on a grid - print("Sample is grid") return _generate_grid_points_on_torus(n_samples, dim) else: raise ValueError("Sample type '{}' is not supported".format(sample)) - return diff --git a/src/python/test/test_datasets_generators.py b/src/python/test/test_datasets_generators.py new file mode 100755 index 00000000..656c30ee --- /dev/null +++ b/src/python/test/test_datasets_generators.py @@ -0,0 +1,40 @@ +""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + Author(s): Hind Montassif + + Copyright (C) 2021 Inria + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +from gudhi.datasets.generators import points +from gudhi.datasets.generators import _points + +import pytest + +def test_sphere(): + assert _points.sphere(n_samples = 10, ambient_dim = 2, radius = 1., sample = 'random').shape == (10, 2) + + with pytest.raises(ValueError): + _points.sphere(n_samples = 10, ambient_dim = 2, radius = 1., sample = 'other') + +def test_torus(): + assert _points.torus(n_samples = 64, dim = 3, sample = 'random').shape == (64, 6) + assert _points.torus(n_samples = 64, dim = 3, sample = 'grid').shape == (64, 6) + + assert _points.torus(n_samples = 10, dim = 4, sample = 'random').shape == (10, 8) + assert _points.torus(n_samples = 10, dim = 4, sample = 'grid').shape == (1, 8) + + with pytest.raises(ValueError): + _points.torus(n_samples = 10, dim = 4, sample = 'other') + +def test_torus_full_python(): + assert points.torus(n_samples = 64, dim = 3, sample = 'random').shape == (64, 6) + assert points.torus(n_samples = 64, dim = 3, sample = 'grid').shape == (64, 6) + + assert points.torus(n_samples = 10, dim = 4, sample = 'random').shape == (10, 8) + assert points.torus(n_samples = 10, dim = 4, sample = 'grid').shape == (1, 8) + + with pytest.raises(ValueError): + points.torus(n_samples = 10, dim = 4, sample = 'other') -- cgit v1.2.3 From 4db14bad8006638fc8249cb867a1720f581e044d Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 31 Aug 2021 18:18:51 +0200 Subject: Fix broken links. Add a tool to generate cpp example page --- biblio/bibliography.bib | 1 - scripts/cpp_examples_for_doxygen.py | 16 ++ .../utilities/bottleneckdistance.md | 4 +- src/common/doc/examples.h | 164 ++++++++++++--------- src/common/doc/installation.h | 40 ++--- src/python/doc/installation.rst | 2 +- 6 files changed, 137 insertions(+), 90 deletions(-) create mode 100644 scripts/cpp_examples_for_doxygen.py (limited to 'src/python/doc') diff --git a/biblio/bibliography.bib b/biblio/bibliography.bib index 16fa29d0..eed871be 100644 --- a/biblio/bibliography.bib +++ b/biblio/bibliography.bib @@ -15,7 +15,6 @@ title = {{Statistical analysis and parameter selection for Mapper}}, volume = {19}, year = {2018}, url = {http://jmlr.org/papers/v19/17-291.html}, -doi = {10.5555/3291125.3291137} } @inproceedings{Dey13, diff --git a/scripts/cpp_examples_for_doxygen.py b/scripts/cpp_examples_for_doxygen.py new file mode 100644 index 00000000..5c091c4f --- /dev/null +++ b/scripts/cpp_examples_for_doxygen.py @@ -0,0 +1,16 @@ +import os +import glob + +for gd_mod in glob.glob("src/*/"): + mod_files = [] + for paths in [gd_mod + 'utilities', gd_mod + 'example']: + if os.path.isdir(paths): + for root, dirs, files in os.walk(paths): + for file in files: + if file.endswith(".cpp"): + mod_files.append(str(os.path.join(root, file)).split(paths)[1][1:]) + if len(mod_files) > 0: + mod = str(gd_mod).split('/')[1] + print(' * \section ' + mod + '_example_section ' + mod) + for file in mod_files: + print(' * @example ' + file) diff --git a/src/Bottleneck_distance/utilities/bottleneckdistance.md b/src/Bottleneck_distance/utilities/bottleneckdistance.md index a81426cf..2f5dedc9 100644 --- a/src/Bottleneck_distance/utilities/bottleneckdistance.md +++ b/src/Bottleneck_distance/utilities/bottleneckdistance.md @@ -10,14 +10,14 @@ Leave the lines above as it is required by the web site generator 'Jekyll' {:/comment} -## bottleneck_read_file_example ## +## bottleneck_distance ## This program computes the Bottleneck distance between two persistence diagram files. **Usage** ``` - bottleneck_read_file_example [] + bottleneck_distance [] ``` where diff --git a/src/common/doc/examples.h b/src/common/doc/examples.h index b557727b..a2de4335 100644 --- a/src/common/doc/examples.h +++ b/src/common/doc/examples.h @@ -1,98 +1,130 @@ -// List of GUDHI examples - Doxygen needs at least a file tag to analyse comments -// In user_version, `find . -name "*.cpp"` in example and utilities folders +// List of GUDHI examples and utils - Doxygen needs at least a file tag to analyse comments +// Generated from scripts/cpp_examples_for_doxygen.py /*! @file Examples - * \section Alpha_complex_examples Alpha complex - * @example Alpha_complex_from_off.cpp + * \section Skeleton_blocker_example_section Skeleton_blocker + * @example Skeleton_blocker_iteration.cpp + * @example Skeleton_blocker_from_simplices.cpp + * @example Skeleton_blocker_link.cpp + * \section Alpha_complex_example_section Alpha_complex + * @example alpha_complex_persistence.cpp + * @example alpha_complex_3d_persistence.cpp * @example Alpha_complex_from_points.cpp - * \section bottleneck_examples bottleneck - * @example bottleneck_basic_example.cpp - * @example alpha_rips_persistence_bottleneck_distance.cpp - * @example example_nearest_landmark_table.cpp - * @example example_witness_complex_off.cpp - * @example example_witness_complex_sphere.cpp - * @example example_strong_witness_complex_off.cpp + * @example Alpha_complex_3d_from_points.cpp + * @example Weighted_alpha_complex_3d_from_points.cpp + * @example Fast_alpha_complex_from_off.cpp + * @example Alpha_complex_from_off.cpp + * @example Weighted_alpha_complex_from_points.cpp + * \section Simplex_tree_example_section Simplex_tree + * @example cech_complex_cgal_mini_sphere_3d.cpp * @example mini_simplex_tree.cpp + * @example example_alpha_shapes_3_simplex_tree_from_off_file.cpp * @example graph_expansion_with_blocker.cpp * @example simple_simplex_tree.cpp * @example simplex_tree_from_cliques_of_graph.cpp - * @example example_alpha_shapes_3_simplex_tree_from_off_file.cpp - * @example cech_complex_cgal_mini_sphere_3d.cpp - * @example plain_homology.cpp - * @example persistence_from_file.cpp - * @example rips_persistence_step_by_step.cpp + * \section Collapse_example_section Collapse + * @example point_cloud_edge_collapse_rips_persistence.cpp + * @example distance_matrix_edge_collapse_rips_persistence.cpp + * @example edge_collapse_basic_example.cpp + * @example edge_collapse_conserve_persistence.cpp + * \section Persistent_cohomology_example_section Persistent_cohomology * @example rips_persistence_via_boundary_matrix.cpp + * @example rips_persistence_step_by_step.cpp + * @example plain_homology.cpp * @example custom_persistence_sort.cpp * @example persistence_from_simple_simplex_tree.cpp + * @example persistence_from_file.cpp * @example rips_multifield_persistence.cpp - * @example Skeleton_blocker_from_simplices.cpp - * @example Skeleton_blocker_iteration.cpp - * @example Skeleton_blocker_link.cpp - * @example Garland_heckbert.cpp - * @example Rips_contraction.cpp - * @example Random_bitmap_cubical_complex.cpp - * @example example_CGAL_3D_points_off_reader.cpp - * @example example_vector_double_points_off_reader.cpp - * @example example_CGAL_points_off_reader.cpp - * @example example_one_skeleton_rips_from_distance_matrix.cpp - * @example example_one_skeleton_rips_from_points.cpp - * @example example_rips_complex_from_csv_distance_matrix_file.cpp - * @example example_rips_complex_from_off_file.cpp - * @example persistence_intervals.cpp - * @example persistence_vectors.cpp - * @example persistence_heat_maps.cpp - * @example persistence_landscape_on_grid.cpp - * @example persistence_landscape.cpp - * @example example_basic.cpp - * @example example_with_perturb.cpp - * @example example_custom_distance.cpp - * @example example_choose_n_farthest_points.cpp - * @example example_sparsify_point_set.cpp - * @example example_pick_n_random_points.cpp - * @example CoordGIC.cpp + * \section Nerve_GIC_example_section Nerve_GIC + * @example VoronoiGIC.cpp * @example Nerve.cpp * @example FuncGIC.cpp - * @example VoronoiGIC.cpp - * @example example_spatial_searching.cpp - * @example alpha_complex_3d_persistence.cpp - * @example alpha_complex_persistence.cpp - * @example Weighted_alpha_complex_3d_from_points.cpp - * @example bottleneck_distance.cpp - * @example weak_witness_persistence.cpp - * @example strong_witness_persistence.cpp - * @example cubical_complex_persistence.cpp - * @example periodic_cubical_complex_persistence.cpp - * @example off_file_from_shape_generator.cpp - * @example rips_distance_matrix_persistence.cpp + * @example CoordGIC.cpp + * \section Rips_complex_example_section Rips_complex * @example rips_persistence.cpp + * @example sparse_rips_persistence.cpp + * @example rips_correlation_matrix_persistence.cpp + * @example rips_distance_matrix_persistence.cpp + * @example example_one_skeleton_rips_from_correlation_matrix.cpp + * @example example_rips_complex_from_csv_distance_matrix_file.cpp + * @example example_sparse_rips.cpp + * @example example_one_skeleton_rips_from_distance_matrix.cpp + * @example example_rips_complex_from_off_file.cpp + * @example example_one_skeleton_rips_from_points.cpp + * \section Persistence_representations_example_section Persistence_representations + * @example persistence_landscapes_on_grid/average_landscapes_on_grid.cpp * @example persistence_landscapes_on_grid/create_landscapes_on_grid.cpp + * @example persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp * @example persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp * @example persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp - * @example persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp - * @example persistence_landscapes_on_grid/average_landscapes_on_grid.cpp * @example persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp - * @example persistence_intervals/compute_number_of_dominant_intervals.cpp - * @example persistence_intervals/plot_persistence_Betti_numbers.cpp * @example persistence_intervals/plot_persistence_intervals.cpp * @example persistence_intervals/plot_histogram_of_intervals_lengths.cpp * @example persistence_intervals/compute_bottleneck_distance.cpp - * @example persistence_heat_maps/create_pssk.cpp - * @example persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp + * @example persistence_intervals/plot_persistence_Betti_numbers.cpp + * @example persistence_intervals/compute_number_of_dominant_intervals.cpp + * @example persistence_heat_maps/average_persistence_heat_maps.cpp * @example persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp - * @example persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp - * @example persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp + * @example persistence_heat_maps/create_pssk.cpp * @example persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp - * @example persistence_heat_maps/average_persistence_heat_maps.cpp + * @example persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp + * @example persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp * @example persistence_heat_maps/plot_persistence_heat_map.cpp + * @example persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp * @example persistence_heat_maps/create_persistence_heat_maps.cpp - * @example persistence_vectors/plot_persistence_vectors.cpp - * @example persistence_vectors/compute_distance_of_persistence_vectors.cpp * @example persistence_vectors/average_persistence_vectors.cpp + * @example persistence_vectors/plot_persistence_vectors.cpp * @example persistence_vectors/create_persistence_vectors.cpp * @example persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp - * @example persistence_landscapes/average_landscapes.cpp - * @example persistence_landscapes/compute_scalar_product_of_landscapes.cpp + * @example persistence_vectors/compute_distance_of_persistence_vectors.cpp * @example persistence_landscapes/create_landscapes.cpp + * @example persistence_landscapes/average_landscapes.cpp * @example persistence_landscapes/compute_distance_of_landscapes.cpp * @example persistence_landscapes/plot_landscapes.cpp + * @example persistence_landscapes/compute_scalar_product_of_landscapes.cpp + * @example persistence_heat_maps.cpp + * @example sliced_wasserstein.cpp + * @example persistence_intervals.cpp + * @example persistence_vectors.cpp + * @example persistence_landscape.cpp + * @example persistence_landscape_on_grid.cpp + * \section common_example_section common + * @example off_file_from_shape_generator.cpp + * @example example_CGAL_points_off_reader.cpp + * @example example_vector_double_points_off_reader.cpp + * @example example_CGAL_3D_points_off_reader.cpp + * \section Subsampling_example_section Subsampling + * @example example_pick_n_random_points.cpp + * @example example_choose_n_farthest_points.cpp + * @example example_sparsify_point_set.cpp + * @example example_custom_distance.cpp + * \section Contraction_example_section Contraction + * @example Rips_contraction.cpp + * @example Garland_heckbert.cpp + * \section Bottleneck_distance_example_section Bottleneck_distance + * @example bottleneck_distance.cpp + * @example bottleneck_basic_example.cpp + * @example alpha_rips_persistence_bottleneck_distance.cpp + * \section Tangential_complex_example_section Tangential_complex + * @example example_basic.cpp + * @example example_with_perturb.cpp + * \section Cech_complex_example_section Cech_complex + * @example cech_persistence.cpp + * @example cech_complex_example_from_points.cpp + * @example cech_complex_step_by_step.cpp + * \section Spatial_searching_example_section Spatial_searching + * @example example_spatial_searching.cpp + * \section Bitmap_cubical_complex_example_section Bitmap_cubical_complex + * @example periodic_cubical_complex_persistence.cpp + * @example cubical_complex_persistence.cpp + * @example Random_bitmap_cubical_complex.cpp + * \section Toplex_map_example_section Toplex_map + * @example simple_toplex_map.cpp + * \section Witness_complex_example_section Witness_complex + * @example weak_witness_persistence.cpp + * @example strong_witness_persistence.cpp + * @example example_witness_complex_sphere.cpp + * @example example_strong_witness_complex_off.cpp + * @example example_nearest_landmark_table.cpp + * @example example_witness_complex_off.cpp */ diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index 5d40a48e..609f2f2f 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -88,9 +88,9 @@ make \endverbatim * Witness_complex/example_witness_complex_off.cpp * \li * Witness_complex/example_witness_complex_sphere.cpp - * \li + * \li * Alpha_complex/Alpha_complex_from_off.cpp - * \li + * \li * Alpha_complex/Alpha_complex_from_points.cpp * \li * Alpha_complex/alpha_complex_persistence.cpp @@ -100,15 +100,15 @@ make \endverbatim * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp * \li * Bottleneck_distance/bottleneck_basic_example.cpp - * \li + * \li * Bottleneck_distance/bottleneck_distance.cpp - * \li + * \li * Nerve_GIC/CoordGIC.cpp - * \li + * \li * Nerve_GIC/FuncGIC.cpp - * \li + * \li * Nerve_GIC/Nerve.cpp - * \li + * \li * Nerve_GIC/VoronoiGIC.cpp * \li * Spatial_searching/example_spatial_searching.cpp @@ -122,7 +122,7 @@ make \endverbatim * Tangential_complex/example_basic.cpp * \li * Tangential_complex/example_with_perturb.cpp - * \li + * \li * Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp * \li * Alpha_complex/alpha_complex_3d_persistence.cpp @@ -134,15 +134,15 @@ make \endverbatim * * The following examples/utilities require the Eigen and will not be * built if Eigen is not installed: - * \li + * \li * Alpha_complex/Alpha_complex_from_off.cpp - * \li + * \li * Alpha_complex/Alpha_complex_from_points.cpp * \li * Alpha_complex/alpha_complex_persistence.cpp * \li * Alpha_complex/alpha_complex_3d_persistence.cpp - * \li + * \li * Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp * \li * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp @@ -179,27 +179,27 @@ make \endverbatim * Having Intel® TBB installed is recommended to parallelize and accelerate some GUDHI computations. * * The following examples/utilities are using Intel® TBB if installed: - * \li + * \li * Alpha_complex/Alpha_complex_from_off.cpp - * \li + * \li * Alpha_complex/Alpha_complex_from_points.cpp * \li * Alpha_complex/alpha_complex_3d_persistence.cpp * \li * Alpha_complex/alpha_complex_persistence.cpp - * \li + * \li * Bitmap_cubical_complex/cubical_complex_persistence.cpp - * \li + * \li * Bitmap_cubical_complex/periodic_cubical_complex_persistence.cpp - * \li + * \li * Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp - * \li + * \li * Nerve_GIC/CoordGIC.cpp - * \li + * \li * Nerve_GIC/FuncGIC.cpp - * \li + * \li * Nerve_GIC/Nerve.cpp - * \li + * \li * Nerve_GIC/VoronoiGIC.cpp * \li * Simplex_tree/simple_simplex_tree.cpp diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst index cb7700ce..35c344e3 100644 --- a/src/python/doc/installation.rst +++ b/src/python/doc/installation.rst @@ -359,7 +359,7 @@ Python Optimal Transport ------------------------ The :doc:`Wasserstein distance ` -module requires `POT `_, a library that provides +module requires `POT `_, a library that provides several solvers for optimization problems related to Optimal Transport. PyTorch -- cgit v1.2.3 From c5a12380e0744eaa26b59ae043dd4fa160d9f268 Mon Sep 17 00:00:00 2001 From: VincentRouvreau Date: Mon, 13 Sep 2021 16:34:23 +0200 Subject: make_filtration_non_decreasing no more called in alpha complex dD exact version and exact and safe 3d versions --- src/Alpha_complex/doc/Intro_alpha_complex.h | 2 ++ src/Alpha_complex/include/gudhi/Alpha_complex.h | 6 ++++-- src/Alpha_complex/include/gudhi/Alpha_complex_3d.h | 6 ++++-- src/python/doc/alpha_complex_user.rst | 3 +++ 4 files changed, 13 insertions(+), 4 deletions(-) (limited to 'src/python/doc') diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h index f417ebb2..5ab23720 100644 --- a/src/Alpha_complex/doc/Intro_alpha_complex.h +++ b/src/Alpha_complex/doc/Intro_alpha_complex.h @@ -152,6 +152,8 @@ Table of Contents * not quite define a proper filtration (i.e. non-decreasing with respect to inclusion). * We fix that up by calling `SimplicialComplexForAlpha::make_filtration_non_decreasing()`. * + * \note This is not the case in `exact` version, this is the reason why it is not called in this case. + * * \subsubsection pruneabove Prune above given filtration value * * The simplex tree is pruned from the given maximum \f$ \alpha^2 \f$ value (cf. diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index b315fa99..e03bb161 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -435,8 +435,10 @@ class Alpha_complex { // -------------------------------------------------------------------------------------------- // -------------------------------------------------------------------------------------------- - // As Alpha value is an approximation, we have to make filtration non decreasing while increasing the dimension - complex.make_filtration_non_decreasing(); + if (!exact) + // As Alpha value is an approximation, we have to make filtration non decreasing while increasing the dimension + // Only in not exact version, cf. https://github.com/GUDHI/gudhi-devel/issues/57 + complex.make_filtration_non_decreasing(); // Remove all simplices that have a filtration value greater than max_alpha_square complex.prune_above_filtration(max_alpha_square); // -------------------------------------------------------------------------------------------- diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h index 4e5fc933..ccc3d852 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h @@ -554,8 +554,10 @@ Weighted_alpha_complex_3d::Weighted_point_3 wp0(Weighted_alpha_complex_3d::Bare_ std::clog << "cells \t\t" << count_cells << std::endl; #endif // DEBUG_TRACES // -------------------------------------------------------------------------------------------- - // As Alpha value is an approximation, we have to make filtration non decreasing while increasing the dimension - complex.make_filtration_non_decreasing(); + if (Complexity == complexity::FAST) + // As Alpha value is an approximation, we have to make filtration non decreasing while increasing the dimension + // Only in FAST version, cf. https://github.com/GUDHI/gudhi-devel/issues/57 + complex.make_filtration_non_decreasing(); // Remove all simplices that have a filtration value greater than max_alpha_square complex.prune_above_filtration(max_alpha_square); // -------------------------------------------------------------------------------------------- diff --git a/src/python/doc/alpha_complex_user.rst b/src/python/doc/alpha_complex_user.rst index fffcb3db..ef67a457 100644 --- a/src/python/doc/alpha_complex_user.rst +++ b/src/python/doc/alpha_complex_user.rst @@ -165,6 +165,9 @@ respect to inclusion). We fix that up by calling :func:`~gudhi.SimplexTree.make_filtration_non_decreasing` (cf. `C++ version `_). +.. note:: + This is not the case in `exact` version, this is the reason why it is not called in this case. + Prune above given filtration value ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -- cgit v1.2.3 From 65619d48af98680294bf41c4023e04ee94f2745d Mon Sep 17 00:00:00 2001 From: Hind-M Date: Wed, 22 Sep 2021 09:36:18 +0200 Subject: Replace the doc sphere image plotted with trisurf with another using scattered points --- src/python/doc/img/sphere_3d.png | Bin 90550 -> 529148 bytes 1 file changed, 0 insertions(+), 0 deletions(-) (limited to 'src/python/doc') diff --git a/src/python/doc/img/sphere_3d.png b/src/python/doc/img/sphere_3d.png index 7e7f0ab2..70f3184f 100644 Binary files a/src/python/doc/img/sphere_3d.png and b/src/python/doc/img/sphere_3d.png differ -- cgit v1.2.3 From e23ca84fadcc2c65fd8cf2d141be804bf18b2fd6 Mon Sep 17 00:00:00 2001 From: Hind-M Date: Wed, 22 Sep 2021 15:20:03 +0200 Subject: Rename function of torus cpp version and import it with sphere in points Change documentation accordingly --- src/python/doc/datasets_generators.rst | 28 +++++++++++++------------ src/python/gudhi/datasets/generators/_points.cc | 9 +++++--- src/python/gudhi/datasets/generators/points.py | 3 +++ src/python/test/test_datasets_generators.py | 15 +++++++------ 4 files changed, 31 insertions(+), 24 deletions(-) (limited to 'src/python/doc') diff --git a/src/python/doc/datasets_generators.rst b/src/python/doc/datasets_generators.rst index e63dde82..c0bbb973 100644 --- a/src/python/doc/datasets_generators.rst +++ b/src/python/doc/datasets_generators.rst @@ -13,10 +13,12 @@ We provide the generation of different customizable datasets to use as inputs fo Points generators ------------------ +The module **points** enables the generation of random points on a sphere, random points on a torus and as a grid. + Points on sphere ^^^^^^^^^^^^^^^^ -The module **_points** enables the generation of random i.i.d. points uniformly on a (d-1)-sphere in :math:`R^d`. +The function **sphere** enables the generation of random i.i.d. points uniformly on a (d-1)-sphere in :math:`R^d`. The user should provide the number of points to be generated on the sphere :code:`n_samples` and the ambient dimension :code:`ambient_dim`. The :code:`radius` of sphere is optional and is equal to **1** by default. Only random points generation is currently available. @@ -28,28 +30,28 @@ Example .. code-block:: python - from gudhi.datasets.generators import _points + from gudhi.datasets.generators import points from gudhi import AlphaComplex # Generate 50 points on a sphere in R^2 - gen_points = _points.sphere(n_samples = 50, ambient_dim = 2, radius = 1, sample = "random") + gen_points = points.sphere(n_samples = 50, ambient_dim = 2, radius = 1, sample = "random") # Create an alpha complex from the generated points alpha_complex = AlphaComplex(points = gen_points) -.. autofunction:: gudhi.datasets.generators._points.sphere +.. autofunction:: gudhi.datasets.generators.points.sphere Points on torus ^^^^^^^^^^^^^^^^ You can also generate points on a torus. -Two modules are available and give the same output: the first one depends on **CGAL** and the second does not and consists of full python code. +Two functions are available and give the same output: the first one depends on **CGAL** and the second does not and consists of full python code. On another hand, two sample types are provided : you can either generate i.i.d. points on a d-torus in :math:`R^{2d}` *randomly* or on a *grid*. -First module : **_points** -"""""""""""""""""""""""""" +First function : **ctorus** +""""""""""""""""""""""""""" The user should provide the number of points to be generated on the torus :code:`n_samples`, and the dimension :code:`dim` of the torus on which points would be generated in :math:`R^{2dim}`. The :code:`sample` argument is optional and is set to **'random'** by default. @@ -67,18 +69,18 @@ Example """"""" .. code-block:: python - from gudhi.datasets.generators import _points + from gudhi.datasets.generators import points # Generate 50 points randomly on a torus in R^6 - gen_points = _points.torus(n_samples = 50, dim = 3) + gen_points = points.ctorus(n_samples = 50, dim = 3) # Generate 27 points on a torus as a grid in R^6 - gen_points = _points.torus(n_samples = 50, dim = 3, sample = 'grid') + gen_points = points.ctorus(n_samples = 50, dim = 3, sample = 'grid') -.. autofunction:: gudhi.datasets.generators._points.torus +.. autofunction:: gudhi.datasets.generators.points.ctorus -Second module : **points** -"""""""""""""""""""""""""" +Second function : **torus** +""""""""""""""""""""""""""" The user should provide the number of points to be generated on the torus :code:`n_samples` and the dimension :code:`dim` of the torus on which points would be generated in :math:`R^{2dim}`. The :code:`sample` argument is optional and is set to **'random'** by default. diff --git a/src/python/gudhi/datasets/generators/_points.cc b/src/python/gudhi/datasets/generators/_points.cc index 3d38ff90..536fa949 100644 --- a/src/python/gudhi/datasets/generators/_points.cc +++ b/src/python/gudhi/datasets/generators/_points.cc @@ -96,10 +96,10 @@ PYBIND11_MODULE(_points, m) { :returns: the generated points on a sphere. )pbdoc"); - m.def("torus", &generate_points_on_torus, + m.def("ctorus", &generate_points_on_torus, py::arg("n_samples"), py::arg("dim"), py::arg("sample") = "random", R"pbdoc( - Generate random i.i.d. points on a d-torus in R^2d + Generate random i.i.d. points on a d-torus in R^2d or as a grid :param n_samples: The number of points to be generated. :type n_samples: integer @@ -107,7 +107,10 @@ PYBIND11_MODULE(_points, m) { :type dim: integer :param sample: The sample type. Available values are: `"random"` and `"grid"`. Default value is `"random"`. :type sample: string - :rtype: numpy array of float + :rtype: numpy array of float. + The shape of returned numpy array is : + if sample is 'random' : (n_samples, 2*dim). + if sample is 'grid' : ([n_samples**(1./dim)]**dim, 2*dim). :returns: the generated points on a torus. )pbdoc"); } diff --git a/src/python/gudhi/datasets/generators/points.py b/src/python/gudhi/datasets/generators/points.py index daada486..1995f769 100644 --- a/src/python/gudhi/datasets/generators/points.py +++ b/src/python/gudhi/datasets/generators/points.py @@ -10,6 +10,9 @@ import numpy as np import itertools +from ._points import ctorus +from ._points import sphere + def _generate_random_points_on_torus(n_samples, dim): # Generate random angles of size n_samples*dim diff --git a/src/python/test/test_datasets_generators.py b/src/python/test/test_datasets_generators.py index 656c30ee..4c087c57 100755 --- a/src/python/test/test_datasets_generators.py +++ b/src/python/test/test_datasets_generators.py @@ -9,25 +9,24 @@ """ from gudhi.datasets.generators import points -from gudhi.datasets.generators import _points import pytest def test_sphere(): - assert _points.sphere(n_samples = 10, ambient_dim = 2, radius = 1., sample = 'random').shape == (10, 2) + assert points.sphere(n_samples = 10, ambient_dim = 2, radius = 1., sample = 'random').shape == (10, 2) with pytest.raises(ValueError): - _points.sphere(n_samples = 10, ambient_dim = 2, radius = 1., sample = 'other') + points.sphere(n_samples = 10, ambient_dim = 2, radius = 1., sample = 'other') def test_torus(): - assert _points.torus(n_samples = 64, dim = 3, sample = 'random').shape == (64, 6) - assert _points.torus(n_samples = 64, dim = 3, sample = 'grid').shape == (64, 6) + assert points.ctorus(n_samples = 64, dim = 3, sample = 'random').shape == (64, 6) + assert points.ctorus(n_samples = 64, dim = 3, sample = 'grid').shape == (64, 6) - assert _points.torus(n_samples = 10, dim = 4, sample = 'random').shape == (10, 8) - assert _points.torus(n_samples = 10, dim = 4, sample = 'grid').shape == (1, 8) + assert points.ctorus(n_samples = 10, dim = 4, sample = 'random').shape == (10, 8) + assert points.ctorus(n_samples = 10, dim = 4, sample = 'grid').shape == (1, 8) with pytest.raises(ValueError): - _points.torus(n_samples = 10, dim = 4, sample = 'other') + points.ctorus(n_samples = 10, dim = 4, sample = 'other') def test_torus_full_python(): assert points.torus(n_samples = 64, dim = 3, sample = 'random').shape == (64, 6) -- cgit v1.2.3 From bb8c4994b89fb6bfdd80b76912acadf6197f93cc Mon Sep 17 00:00:00 2001 From: Hind-M Date: Tue, 26 Oct 2021 13:59:44 +0200 Subject: Add comments and some minor changes following code review --- src/python/doc/datasets_generators.rst | 13 +++++++------ src/python/gudhi/datasets/generators/_points.cc | 2 +- src/python/gudhi/datasets/generators/points.py | 6 +++--- src/python/test/test_datasets_generators.py | 2 ++ 4 files changed, 13 insertions(+), 10 deletions(-) (limited to 'src/python/doc') diff --git a/src/python/doc/datasets_generators.rst b/src/python/doc/datasets_generators.rst index c0bbb973..3700b8a2 100644 --- a/src/python/doc/datasets_generators.rst +++ b/src/python/doc/datasets_generators.rst @@ -48,22 +48,23 @@ You can also generate points on a torus. Two functions are available and give the same output: the first one depends on **CGAL** and the second does not and consists of full python code. -On another hand, two sample types are provided : you can either generate i.i.d. points on a d-torus in :math:`R^{2d}` *randomly* or on a *grid*. +On another hand, two sample types are provided: you can either generate i.i.d. points on a d-torus in :math:`R^{2d}` *randomly* or on a *grid*. -First function : **ctorus** +First function: **ctorus** """"""""""""""""""""""""""" The user should provide the number of points to be generated on the torus :code:`n_samples`, and the dimension :code:`dim` of the torus on which points would be generated in :math:`R^{2dim}`. The :code:`sample` argument is optional and is set to **'random'** by default. In this case, the returned generated points would be an array of shape :math:`(n\_samples, 2*dim)`. -Otherwise, if set to **'grid'**, the points are generated on a grid and would be given as an array of shape : +Otherwise, if set to **'grid'**, the points are generated on a grid and would be given as an array of shape: .. math:: - ( [n\_samples^{1 \over {dim}}]^{dim}, 2*dim ) + ( ⌊n\_samples^{1 \over {dim}}⌋^{dim}, 2*dim ) +**Note 1:** The output array first shape is rounded down to the closest perfect :math:`dim^{th}` power. -**Note:** This version is recommended when the user wishes to use **'grid'** as sample type, or **'random'** with a relatively small number of samples (~ less than 150). +**Note 2:** This version is recommended when the user wishes to use **'grid'** as sample type, or **'random'** with a relatively small number of samples (~ less than 150). Example """"""" @@ -79,7 +80,7 @@ Example .. autofunction:: gudhi.datasets.generators.points.ctorus -Second function : **torus** +Second function: **torus** """"""""""""""""""""""""""" The user should provide the number of points to be generated on the torus :code:`n_samples` and the dimension :code:`dim` of the torus on which points would be generated in :math:`R^{2dim}`. diff --git a/src/python/gudhi/datasets/generators/_points.cc b/src/python/gudhi/datasets/generators/_points.cc index 536fa949..5d675930 100644 --- a/src/python/gudhi/datasets/generators/_points.cc +++ b/src/python/gudhi/datasets/generators/_points.cc @@ -110,7 +110,7 @@ PYBIND11_MODULE(_points, m) { :rtype: numpy array of float. The shape of returned numpy array is : if sample is 'random' : (n_samples, 2*dim). - if sample is 'grid' : ([n_samples**(1./dim)]**dim, 2*dim). + if sample is 'grid' : (⌊n_samples**(1./dim)⌋**dim, 2*dim), where shape[0] is rounded down to the closest perfect 'dim'th power. :returns: the generated points on a torus. )pbdoc"); } diff --git a/src/python/gudhi/datasets/generators/points.py b/src/python/gudhi/datasets/generators/points.py index 1995f769..7f4667af 100644 --- a/src/python/gudhi/datasets/generators/points.py +++ b/src/python/gudhi/datasets/generators/points.py @@ -36,15 +36,15 @@ def _generate_grid_points_on_torus(n_samples, dim): def torus(n_samples, dim, sample='random'): """ - Generate points on a dim-torus in R^2dim either randomly or on a grid + Generate points on a flat dim-torus in R^2dim either randomly or on a grid :param n_samples: The number of points to be generated. :param dim: The dimension of the torus on which points would be generated in R^2*dim. :param sample: The sample type of the generated points. Can be 'random' or 'grid'. :returns: numpy array containing the generated points on a torus. - The shape of returned numpy array is : + The shape of returned numpy array is: if sample is 'random' : (n_samples, 2*dim). - if sample is 'grid' : ([n_samples**(1./dim)]**dim, 2*dim). + if sample is 'grid' : (⌊n_samples**(1./dim)⌋**dim, 2*dim), where shape[0] is rounded down to the closest perfect 'dim'th power. """ if sample == 'random': # Generate points randomly diff --git a/src/python/test/test_datasets_generators.py b/src/python/test/test_datasets_generators.py index e2d300e0..933a763e 100755 --- a/src/python/test/test_datasets_generators.py +++ b/src/python/test/test_datasets_generators.py @@ -23,6 +23,8 @@ def _basic_torus(impl): assert impl(n_samples = 64, dim = 3, sample = 'grid').shape == (64, 6) assert impl(n_samples = 10, dim = 4, sample = 'random').shape == (10, 8) + + # Here 1**dim < n_samples < 2**dim, the output shape is therefore (1, 2*dim) = (1, 8), where shape[0] is rounded down to the closest perfect 'dim'th power assert impl(n_samples = 10, dim = 4, sample = 'grid').shape == (1, 8) with pytest.raises(ValueError): -- cgit v1.2.3 From 6bbd3c0c62d02ac5641ba77a33f7c5d100320ce0 Mon Sep 17 00:00:00 2001 From: Vincent Rouvreau <10407034+VincentRouvreau@users.noreply.github.com> Date: Tue, 2 Nov 2021 14:38:01 +0100 Subject: Precise the torus is flat Co-authored-by: Marc Glisse --- src/python/doc/datasets_generators.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'src/python/doc') diff --git a/src/python/doc/datasets_generators.rst b/src/python/doc/datasets_generators.rst index 3700b8a2..6f36bce1 100644 --- a/src/python/doc/datasets_generators.rst +++ b/src/python/doc/datasets_generators.rst @@ -41,7 +41,7 @@ Example .. autofunction:: gudhi.datasets.generators.points.sphere -Points on torus +Points on a flat torus ^^^^^^^^^^^^^^^^ You can also generate points on a torus. -- cgit v1.2.3 From 79e6a20ce026ff4c86b1632bb3f1ed16ae5c92a1 Mon Sep 17 00:00:00 2001 From: Vincent Rouvreau Date: Tue, 2 Nov 2021 17:27:25 +0100 Subject: No more gforge references --- .../for_maintainers/new_gudhi_version_creation.md | 22 ++++---- scripts/create_gudhi_version.sh | 66 ---------------------- src/python/doc/alpha_complex_user.rst | 2 +- 3 files changed, 11 insertions(+), 79 deletions(-) delete mode 100755 scripts/create_gudhi_version.sh (limited to 'src/python/doc') diff --git a/.github/for_maintainers/new_gudhi_version_creation.md b/.github/for_maintainers/new_gudhi_version_creation.md index 3e5295c5..812758e3 100644 --- a/.github/for_maintainers/new_gudhi_version_creation.md +++ b/.github/for_maintainers/new_gudhi_version_creation.md @@ -68,20 +68,18 @@ make -j 4 all && ctest -j 4 --output-on-failure ## Upload the documentation -Upload by ftp the content of the directory gudhi.doc.@GUDHI_VERSION@/cpp in a new directory on ForgeLogin@scm.gforge.inria.fr:/home/groups/gudhi/htdocs/doc/@GUDHI_VERSION@ +[GUDHI GitHub pages](https://gudhi.github.io/) is only used as a _"qualification"_ web hosting service. +The _"production"_ web hosting service is https://files.inria.fr (cf. [this doc](https://doc-si.inria.fr/display/SU/Espace+web) +or [this one](https://www.nextinpact.com/article/30325/109058-se-connecter-a-serveur-webdav-sous-linux-macos-ou-windows)). -Upload by ftp the content of the directory gudhi.doc.@GUDHI_VERSION@/python in a new directory on ForgeLogin@scm.gforge.inria.fr:/home/groups/gudhi/htdocs/python/@GUDHI_VERSION@ +Upload the content of the directory gudhi.doc.@GUDHI_VERSION@/cpp in a new directory on gudhi WebDAV in doc/@GUDHI_VERSION@ +Delete the directory doc/latest on gudhi WebDAV. +Copy gudhi WebDAV doc/@GUDHI_VERSION@ as doc/latest (no symbolic link with WebDAV). + +Upload the content of the directory gudhi.doc.@GUDHI_VERSION@/python in a new directory on gudhi WebDAV in python/@GUDHI_VERSION@ +Delete the directory python/latest on gudhi WebDAV. +Copy gudhi WebDAV python/@GUDHI_VERSION@ as python/latest (no symbolic link with WebDAV). -Through ssh, make the **latest** link to your new version of the documentation: -```bash -ssh ForgeLogin@scm.gforge.inria.fr -cd /home/groups/gudhi/htdocs/doc -rm latest -ln -s @GUDHI_VERSION@ latest -cd /home/groups/gudhi/htdocs/python -rm latest -ln -s @GUDHI_VERSION@ latest -``` ## Put a version label on files diff --git a/scripts/create_gudhi_version.sh b/scripts/create_gudhi_version.sh deleted file mode 100755 index f2a9233f..00000000 --- a/scripts/create_gudhi_version.sh +++ /dev/null @@ -1,66 +0,0 @@ -#!/bin/bash - -login="vrouvrea" -version="2.3.0" -cgaldir="/home/vincent/workspace/CGAL-4.11-HO/build" -cpucount=7 - - -# We start from scripts dir in the dev branch -cd .. -RELATIVEURL=`svn info . |grep -F "Relative URL:" | awk '{print $NF}'` - -if [ "$RELATIVEURL" != "^/trunk" ] -then -echo "Script must be launched in trunk and not in $RELATIVEURL" -exit -fi - -rm -rf build; mkdir build; cd build; cmake -DCMAKE_BUILD_TYPE=Debug -DDEBUG_TRACES=ON -DCGAL_DIR=${cgaldir} -DWITH_GUDHI_EXAMPLE=ON -DWITH_GUDHI_BENCHMARK=ON -DPython_ADDITIONAL_VERSIONS=3 .. -cmake -DCMAKE_BUILD_TYPE=Debug . - -CURRENTDIRECTORY=`pwd` -export PYTHONPATH=$CURRENTDIRECTORY/src/cython:$PYTHONPATH - -make -j ${cpucount} all test - -cd .. -svn st | grep -v GUDHIVersion.cmake | grep "^\?" | awk "{print \$2}" | xargs rm -rf - -svn copy svn+ssh://${login}@scm.gforge.inria.fr/svnroot/gudhi/trunk svn+ssh://${login}@scm.gforge.inria.fr/svnroot/gudhi/tags/gudhi-release-${version} \ - -m "Creating a tag of Gudhi release version ${version}." - -cd build -make user_version - -userversiondir=`find . -type d -name "*_GUDHI_${version}" | sed 's/\.\///g'` -echo "User version directory = ${userversiondir}" - -tar -czvf ${userversiondir}.tar.gz ${userversiondir} - -userdocdir=${userversiondir/GUDHI/GUDHI_DOC} -echo "User documentation directory = ${userdocdir}" -mkdir ${userdocdir} -make doxygen - -cp -R ${userversiondir}/doc/html ${userdocdir}/cpp -cd ${userversiondir} -rm -rf build; mkdir build; cd build; cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=./installed -DCGAL_DIR=${cgaldir} -DWITH_GUDHI_EXAMPLE=ON -DPython_ADDITIONAL_VERSIONS=3 .. - -CURRENTDIRECTORY=`pwd` -export PYTHONPATH=$CURRENTDIRECTORY/cython:$PYTHONPATH - -make sphinx - -cp -R cython/sphinx ../../${userdocdir}/python -cd ../.. -tar -czvf ${userdocdir}.tar.gz ${userdocdir} - -cd ${userversiondir}/build -make -j ${cpucount} all test install - -cd ../.. -actualdir=`pwd` -echo "Library is available at ${actualdir}/${userversiondir}.tar.gz" -sha256sum ${userversiondir}.tar.gz -echo "Documentation is available at ${actualdir}/${userdocdir}.tar.gz" diff --git a/src/python/doc/alpha_complex_user.rst b/src/python/doc/alpha_complex_user.rst index fffcb3db..3de94bb8 100644 --- a/src/python/doc/alpha_complex_user.rst +++ b/src/python/doc/alpha_complex_user.rst @@ -163,7 +163,7 @@ As the squared radii computed by CGAL are an approximation, it might happen that :math:`\alpha^2` values do not quite define a proper filtration (i.e. non-decreasing with respect to inclusion). We fix that up by calling :func:`~gudhi.SimplexTree.make_filtration_non_decreasing` (cf. -`C++ version `_). +`C++ version `_). Prune above given filtration value ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -- cgit v1.2.3