diff options
-rw-r--r-- | next_release.md | 26 | ||||
-rw-r--r-- | src/python/doc/diagram_readers_ref.rst (renamed from src/python/doc/reader_utils_ref.rst) | 10 | ||||
-rw-r--r-- | src/python/doc/index.rst | 44 | ||||
-rw-r--r-- | src/python/doc/point_cloud.rst | 22 | ||||
-rw-r--r-- | src/python/doc/point_cloud_sum.inc | 15 | ||||
-rwxr-xr-x | src/python/example/alpha_complex_from_points_example.py | 7 | ||||
-rw-r--r-- | src/python/gudhi/alpha_complex.pyx | 11 | ||||
-rw-r--r-- | src/python/gudhi/euclidean_strong_witness_complex.pyx | 4 | ||||
-rw-r--r-- | src/python/gudhi/euclidean_witness_complex.pyx | 4 | ||||
-rw-r--r-- | src/python/gudhi/off_reader.pyx | 2 | ||||
-rw-r--r-- | src/python/gudhi/reader_utils.pyx | 8 | ||||
-rw-r--r-- | src/python/gudhi/rips_complex.pyx | 2 | ||||
-rw-r--r-- | src/python/gudhi/simplex_tree.pxd | 2 | ||||
-rw-r--r-- | src/python/gudhi/strong_witness_complex.pyx | 4 | ||||
-rw-r--r-- | src/python/gudhi/subsampling.pyx | 18 | ||||
-rw-r--r-- | src/python/gudhi/witness_complex.pyx | 4 | ||||
-rw-r--r-- | src/python/include/Alpha_complex_interface.h | 10 | ||||
-rwxr-xr-x | src/python/test/test_alpha_complex.py | 28 |
18 files changed, 135 insertions, 86 deletions
diff --git a/next_release.md b/next_release.md index 08b736b1..26d4fca5 100644 --- a/next_release.md +++ b/next_release.md @@ -1,27 +1,19 @@ -We are pleased to announce the release 3.1.0 of the GUDHI library. +We are pleased to announce the release 3.X.X of the GUDHI library. -As a major new feature, the GUDHI library now offers 2 new Python modules: Persistence representations and Wasserstein distance. +As a major new feature, the GUDHI library now offers ... -We are now using GitHub to develop the GUDHI library, do not hesitate to [fork the GUDHI project on GitHub](https://github.com/GUDHI/gudhi-devel). From a user point of view, we recommend to download GUDHI user version (gudhi.3.1.0.rc1.tar.gz). +We are now using GitHub to develop the GUDHI library, do not hesitate to [fork the GUDHI project on GitHub](https://github.com/GUDHI/gudhi-devel). From a user point of view, we recommend to download GUDHI user version (gudhi.3.X.X.tar.gz). -Below is a list of changes made since Gudhi 3.0.0: +Below is a list of changes made since Gudhi 3.1.0: -- [Persistence representations](https://gudhi.inria.fr/python/3.1.0.rc1/representations.html) (new Python module) - - Vectorizations, distances and kernels that work on persistence diagrams, compatible with scikit-learn. This module was originally available at https://github.com/MathieuCarriere/sklearn-tda and named sklearn_tda. +- [Module](link) + - ... -- [Wasserstein distance](https://gudhi.inria.fr/python/3.1.0.rc1/wasserstein_distance_user.html) (new Python module) - - The q-Wasserstein distance measures the similarity between two persistence diagrams. - -- [Alpha complex](https://gudhi.inria.fr/doc/3.1.0.rc1/group__alpha__complex.html) (new C++ interface) - - Thanks to [CGAL 5.0 Epeck_d](https://doc.cgal.org/latest/Kernel_d/structCGAL_1_1Epeck__d.html) kernel, an exact computation version of Alpha complex dD is available and the default one (even in Python). - -- [Persistence graphical tools](https://gudhi.inria.fr/python/3.1.0.rc1/persistence_graphical_tools_user.html) (new Python interface) - - Axes as a parameter allows the user to subplot graphics. - - Use matplotlib default palette (can be user defined). +- [Module](link) + - ... - Miscellaneous - - Python `read_off` function has been renamed `read_points_from_off_file` as it only reads points from OFF files. - - See the list of [bug fixes](https://github.com/GUDHI/gudhi-devel/issues?utf8=%E2%9C%93&q=is%3Aissue+label%3A3.1.0+). + - See the list of [bug fixes](https://github.com/GUDHI/gudhi-devel/issues?utf8=%E2%9C%93&q=is%3Aissue+label%3A3.X.X+). All modules are distributed under the terms of the MIT license. diff --git a/src/python/doc/reader_utils_ref.rst b/src/python/doc/diagram_readers_ref.rst index b8977a5a..c79daf9c 100644 --- a/src/python/doc/reader_utils_ref.rst +++ b/src/python/doc/diagram_readers_ref.rst @@ -2,13 +2,9 @@ .. To get rid of WARNING: document isn't included in any toctree -============================= -Reader utils reference manual -============================= - -.. autofunction:: gudhi.read_points_from_off_file - -.. autofunction:: gudhi.read_lower_triangular_matrix_from_csv_file +================================ +Diagram readers reference manual +================================ .. autofunction:: gudhi.read_persistence_intervals_grouped_by_dimension diff --git a/src/python/doc/index.rst b/src/python/doc/index.rst index c36a578f..3387a64f 100644 --- a/src/python/doc/index.rst +++ b/src/python/doc/index.rst @@ -6,8 +6,8 @@ GUDHI Python modules documentation :alt: Gudhi banner :figclass: align-center -Complexes -********* +Data structures for cell complexes +********************************** Cubical complexes ================= @@ -17,18 +17,26 @@ Cubical complexes Simplicial complexes ==================== +Simplex tree +------------ + +.. include:: simplex_tree_sum.inc + +Filtrations and reconstructions +******************************* + Alpha complex -------------- +============= .. include:: alpha_complex_sum.inc Rips complex ------------- +============ .. include:: rips_complex_sum.inc Witness complex ---------------- +=============== .. include:: witness_complex_sum.inc @@ -37,16 +45,10 @@ Cover complexes .. include:: nerve_gic_complex_sum.inc -Data structures and basic operations -************************************ - -Data structures -=============== - -Simplex tree ------------- +Tangential complex +================== -.. include:: simplex_tree_sum.inc +.. include:: tangential_complex_sum.inc Topological descriptors computation *********************************** @@ -56,15 +58,6 @@ Persistence cohomology .. include:: persistent_cohomology_sum.inc -Manifold reconstruction -*********************** - -Tangential complex -================== - -.. include:: tangential_complex_sum.inc - - Topological descriptors tools ***************************** @@ -88,6 +81,11 @@ Persistence graphical tools .. include:: persistence_graphical_tools_sum.inc +Point cloud utilities +********************* + +.. include:: point_cloud_sum.inc + Bibliography ************ diff --git a/src/python/doc/point_cloud.rst b/src/python/doc/point_cloud.rst new file mode 100644 index 00000000..d668428a --- /dev/null +++ b/src/python/doc/point_cloud.rst @@ -0,0 +1,22 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + +============================ +Point cloud utilities manual +============================ + +File Readers +------------ + +.. autofunction:: gudhi.read_points_from_off_file + +.. autofunction:: gudhi.read_lower_triangular_matrix_from_csv_file + +Subsampling +----------- + +.. automodule:: gudhi.subsampling + :members: + :special-members: + :show-inheritance: diff --git a/src/python/doc/point_cloud_sum.inc b/src/python/doc/point_cloud_sum.inc new file mode 100644 index 00000000..85d52de7 --- /dev/null +++ b/src/python/doc/point_cloud_sum.inc @@ -0,0 +1,15 @@ +.. table:: + :widths: 30 50 20 + + +----------------------------------------------------------------+------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------+ + | | :math:`(x_1, x_2, \ldots, x_d)` | Utilities to process point clouds: read from file, subsample, etc. | :Author: Vincent Rouvreau | + | | :math:`(y_1, y_2, \ldots, y_d)` | | | + | | | :Introduced in: GUDHI 2.0.0 | + | | | | + | | | :Copyright: MIT (`GPL v3 </licensing/>`_) | + | | Parts of this package require CGAL. | | + | | | :Requires: `Eigen <installation.html#eigen>`__ :math:`\geq` 3.1.0 and `CGAL <installation.html#cgal>`__ :math:`\geq` 4.11.0 | + | | | | + +----------------------------------------------------------------+------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------+ + | * :doc:`point_cloud` | + +----------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ diff --git a/src/python/example/alpha_complex_from_points_example.py b/src/python/example/alpha_complex_from_points_example.py index a746998c..844d7a82 100755 --- a/src/python/example/alpha_complex_from_points_example.py +++ b/src/python/example/alpha_complex_from_points_example.py @@ -52,4 +52,9 @@ print("star([0])=", simplex_tree.get_star([0])) print("coface([0], 1)=", simplex_tree.get_cofaces([0], 1)) print("point[0]=", alpha_complex.get_point(0)) -print("point[5]=", alpha_complex.get_point(5)) +try: + print("point[5]=", alpha_complex.get_point(5)) +except IndexError: + pass +else: + assert False diff --git a/src/python/gudhi/alpha_complex.pyx b/src/python/gudhi/alpha_complex.pyx index f3ca3dd5..fff3e920 100644 --- a/src/python/gudhi/alpha_complex.pyx +++ b/src/python/gudhi/alpha_complex.pyx @@ -24,11 +24,11 @@ __license__ = "GPL v3" cdef extern from "Alpha_complex_interface.h" namespace "Gudhi": cdef cppclass Alpha_complex_interface "Gudhi::alpha_complex::Alpha_complex_interface": - Alpha_complex_interface(vector[vector[double]] points) + Alpha_complex_interface(vector[vector[double]] points) except + # bool from_file is a workaround for cython to find the correct signature - Alpha_complex_interface(string off_file, bool from_file) - vector[double] get_point(int vertex) - void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) + Alpha_complex_interface(string off_file, bool from_file) except + + vector[double] get_point(int vertex) except + + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) except + # AlphaComplex python interface cdef class AlphaComplex: @@ -96,8 +96,7 @@ cdef class AlphaComplex: :rtype: list of float :returns: the point. """ - cdef vector[double] point = self.thisptr.get_point(vertex) - return point + return self.thisptr.get_point(vertex) def create_simplex_tree(self, max_alpha_square = float('inf')): """ diff --git a/src/python/gudhi/euclidean_strong_witness_complex.pyx b/src/python/gudhi/euclidean_strong_witness_complex.pyx index 9889f92c..aca6084e 100644 --- a/src/python/gudhi/euclidean_strong_witness_complex.pyx +++ b/src/python/gudhi/euclidean_strong_witness_complex.pyx @@ -22,9 +22,9 @@ __license__ = "GPL v3" cdef extern from "Euclidean_strong_witness_complex_interface.h" namespace "Gudhi": cdef cppclass Euclidean_strong_witness_complex_interface "Gudhi::witness_complex::Euclidean_strong_witness_complex_interface": Euclidean_strong_witness_complex_interface(vector[vector[double]] landmarks, vector[vector[double]] witnesses) - void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) except + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square, - unsigned limit_dimension) + unsigned limit_dimension) except + vector[double] get_point(unsigned vertex) # EuclideanStrongWitnessComplex python interface diff --git a/src/python/gudhi/euclidean_witness_complex.pyx b/src/python/gudhi/euclidean_witness_complex.pyx index e3ce0e82..fb0c2201 100644 --- a/src/python/gudhi/euclidean_witness_complex.pyx +++ b/src/python/gudhi/euclidean_witness_complex.pyx @@ -22,9 +22,9 @@ __license__ = "GPL v3" cdef extern from "Euclidean_witness_complex_interface.h" namespace "Gudhi": cdef cppclass Euclidean_witness_complex_interface "Gudhi::witness_complex::Euclidean_witness_complex_interface": Euclidean_witness_complex_interface(vector[vector[double]] landmarks, vector[vector[double]] witnesses) - void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) except + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square, - unsigned limit_dimension) + unsigned limit_dimension) except + vector[double] get_point(unsigned vertex) # EuclideanWitnessComplex python interface diff --git a/src/python/gudhi/off_reader.pyx b/src/python/gudhi/off_reader.pyx index a0d5bf25..7e6d9d80 100644 --- a/src/python/gudhi/off_reader.pyx +++ b/src/python/gudhi/off_reader.pyx @@ -26,7 +26,7 @@ def read_points_from_off_file(off_file=''): :type off_file: string :returns: The point set. - :rtype: vector[vector[double]] + :rtype: List[List[float]] """ if off_file: if os.path.isfile(off_file): diff --git a/src/python/gudhi/reader_utils.pyx b/src/python/gudhi/reader_utils.pyx index d6033b86..fe1c3a2e 100644 --- a/src/python/gudhi/reader_utils.pyx +++ b/src/python/gudhi/reader_utils.pyx @@ -34,7 +34,7 @@ def read_lower_triangular_matrix_from_csv_file(csv_file='', separator=';'): :type separator: char :returns: The lower triangular matrix. - :rtype: vector[vector[double]] + :rtype: List[List[float]] """ if csv_file: if path.isfile(csv_file): @@ -45,15 +45,15 @@ def read_lower_triangular_matrix_from_csv_file(csv_file='', separator=';'): def read_persistence_intervals_grouped_by_dimension(persistence_file=''): """Reads a file containing persistence intervals. Each line might contain 2, 3 or 4 values: [[field] dimension] birth death - The return value is an `map[dim, vector[pair[birth, death]]]` - where `dim` is an `int`, `birth` a `double`, and `death` a `double`. + The return value is a `dict(dim, list(tuple(birth, death)))` + where `dim` is an `int`, `birth` a `float`, and `death` a `float`. Note: the function does not check that birth <= death. :param persistence_file: A persistence file style name. :type persistence_file: string :returns: The persistence pairs grouped by dimension. - :rtype: map[int, vector[pair[double, double]]] + :rtype: Dict[int, List[Tuple[float, float]]] """ if persistence_file: if path.isfile(persistence_file): diff --git a/src/python/gudhi/rips_complex.pyx b/src/python/gudhi/rips_complex.pyx index 722cdcdc..deb8057a 100644 --- a/src/python/gudhi/rips_complex.pyx +++ b/src/python/gudhi/rips_complex.pyx @@ -28,7 +28,7 @@ cdef extern from "Rips_complex_interface.h" namespace "Gudhi": void init_matrix(vector[vector[double]] values, double threshold) void init_points_sparse(vector[vector[double]] values, double threshold, double sparse) void init_matrix_sparse(vector[vector[double]] values, double threshold, double sparse) - void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, int dim_max) + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, int dim_max) except + # RipsComplex python interface cdef class RipsComplex: diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd index 1066d44b..96d14079 100644 --- a/src/python/gudhi/simplex_tree.pxd +++ b/src/python/gudhi/simplex_tree.pxd @@ -39,7 +39,7 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": vector[pair[vector[int], double]] get_star(vector[int] simplex) vector[pair[vector[int], double]] get_cofaces(vector[int] simplex, int dimension) - void expansion(int max_dim) + void expansion(int max_dim) except + void remove_maximal_simplex(vector[int] simplex) bool prune_above_filtration(double filtration) bool make_filtration_non_decreasing() diff --git a/src/python/gudhi/strong_witness_complex.pyx b/src/python/gudhi/strong_witness_complex.pyx index 2c33c3f2..9f89d3ae 100644 --- a/src/python/gudhi/strong_witness_complex.pyx +++ b/src/python/gudhi/strong_witness_complex.pyx @@ -22,9 +22,9 @@ __license__ = "MIT" cdef extern from "Strong_witness_complex_interface.h" namespace "Gudhi": cdef cppclass Strong_witness_complex_interface "Gudhi::witness_complex::Strong_witness_complex_interface": Strong_witness_complex_interface(vector[vector[pair[size_t, double]]] nearest_landmark_table) - void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) except + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square, - unsigned limit_dimension) + unsigned limit_dimension) except + # StrongWitnessComplex python interface cdef class StrongWitnessComplex: diff --git a/src/python/gudhi/subsampling.pyx b/src/python/gudhi/subsampling.pyx index c501d16b..f77c6f75 100644 --- a/src/python/gudhi/subsampling.pyx +++ b/src/python/gudhi/subsampling.pyx @@ -33,13 +33,15 @@ def choose_n_farthest_points(points=None, off_file='', nb_points=0, starting_poi The iteration starts with the landmark `starting point`. :param points: The input point set. - :type points: vector[vector[double]]. + :type points: Iterable[Iterable[float]]. Or :param off_file: An OFF file style name. :type off_file: string + And in both cases + :param nb_points: Number of points of the subsample. :type nb_points: unsigned. :param starting_point: The iteration starts with the landmark `starting \ @@ -47,7 +49,7 @@ def choose_n_farthest_points(points=None, off_file='', nb_points=0, starting_poi index is chosen randomly. :type starting_point: unsigned. :returns: The subsample point set. - :rtype: vector[vector[double]] + :rtype: List[List[float]]. """ if off_file: if os.path.isfile(off_file): @@ -74,17 +76,19 @@ def pick_n_random_points(points=None, off_file='', nb_points=0): """Subsample a point set by picking random vertices. :param points: The input point set. - :type points: vector[vector[double]]. + :type points: Iterable[Iterable[float]]. Or :param off_file: An OFF file style name. :type off_file: string + And in both cases + :param nb_points: Number of points of the subsample. :type nb_points: unsigned. :returns: The subsample point set. - :rtype: vector[vector[double]] + :rtype: List[List[float]] """ if off_file: if os.path.isfile(off_file): @@ -103,18 +107,20 @@ def sparsify_point_set(points=None, off_file='', min_squared_dist=0.0): between any two points is greater than or equal to min_squared_dist. :param points: The input point set. - :type points: vector[vector[double]]. + :type points: Iterable[Iterable[float]]. Or :param off_file: An OFF file style name. :type off_file: string + And in both cases + :param min_squared_dist: Minimum squared distance separating the output \ points. :type min_squared_dist: float. :returns: The subsample point set. - :rtype: vector[vector[double]] + :rtype: List[List[float]] """ if off_file: if os.path.isfile(off_file): diff --git a/src/python/gudhi/witness_complex.pyx b/src/python/gudhi/witness_complex.pyx index b032a5a1..e589d006 100644 --- a/src/python/gudhi/witness_complex.pyx +++ b/src/python/gudhi/witness_complex.pyx @@ -22,9 +22,9 @@ __license__ = "MIT" cdef extern from "Witness_complex_interface.h" namespace "Gudhi": cdef cppclass Witness_complex_interface "Gudhi::witness_complex::Witness_complex_interface": Witness_complex_interface(vector[vector[pair[size_t, double]]] nearest_landmark_table) - void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) except + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square, - unsigned limit_dimension) + unsigned limit_dimension) except + # WitnessComplex python interface cdef class WitnessComplex: diff --git a/src/python/include/Alpha_complex_interface.h b/src/python/include/Alpha_complex_interface.h index e9bbadb0..8614eee3 100644 --- a/src/python/include/Alpha_complex_interface.h +++ b/src/python/include/Alpha_complex_interface.h @@ -50,13 +50,9 @@ class Alpha_complex_interface { std::vector<double> get_point(int vh) { std::vector<double> vd; - try { - Point_d const& ph = alpha_complex_->get_point(vh); - for (auto coord = ph.cartesian_begin(); coord != ph.cartesian_end(); coord++) - vd.push_back(CGAL::to_double(*coord)); - } catch (std::out_of_range const&) { - // std::out_of_range is thrown in case not found. Other exceptions must be re-thrown - } + Point_d const& ph = alpha_complex_->get_point(vh); + for (auto coord = ph.cartesian_begin(); coord != ph.cartesian_end(); coord++) + vd.push_back(CGAL::to_double(*coord)); return vd; } diff --git a/src/python/test/test_alpha_complex.py b/src/python/test/test_alpha_complex.py index 0d9e9e45..3761fe16 100755 --- a/src/python/test/test_alpha_complex.py +++ b/src/python/test/test_alpha_complex.py @@ -65,8 +65,18 @@ def test_infinite_alpha(): assert point_list[1] == alpha_complex.get_point(1) assert point_list[2] == alpha_complex.get_point(2) assert point_list[3] == alpha_complex.get_point(3) - assert alpha_complex.get_point(4) == [] - assert alpha_complex.get_point(125) == [] + try: + alpha_complex.get_point(4) == [] + except IndexError: + pass + else: + assert False + try: + alpha_complex.get_point(125) == [] + except IndexError: + pass + else: + assert False def test_filtered_alpha(): @@ -82,8 +92,18 @@ def test_filtered_alpha(): assert point_list[1] == filtered_alpha.get_point(1) assert point_list[2] == filtered_alpha.get_point(2) assert point_list[3] == filtered_alpha.get_point(3) - assert filtered_alpha.get_point(4) == [] - assert filtered_alpha.get_point(125) == [] + try: + filtered_alpha.get_point(4) == [] + except IndexError: + pass + else: + assert False + try: + filtered_alpha.get_point(125) == [] + except IndexError: + pass + else: + assert False assert simplex_tree.get_filtration() == [ ([0], 0.0), |