diff options
Diffstat (limited to 'src/python')
46 files changed, 321 insertions, 226 deletions
diff --git a/src/python/doc/alpha_complex_sum.inc b/src/python/doc/alpha_complex_sum.inc index c5ba9dc7..a1184663 100644 --- a/src/python/doc/alpha_complex_sum.inc +++ b/src/python/doc/alpha_complex_sum.inc @@ -9,9 +9,9 @@ | | circumradius of the simplex if the circumsphere is empty (the simplex | :Copyright: MIT (`GPL v3 </licensing/>`_) | | | is then said to be Gabriel), and as the minimum of the filtration | | | | values of the codimension 1 cofaces that make it not Gabriel | :Requires: `Eigen <installation.html#eigen>`__ :math:`\geq` 3.1.0 and `CGAL <installation.html#cgal>`__ :math:`\geq` 4.11.0 | - | | otherwise. All simplices that have a filtration value strictly | | - | | greater than a given alpha squared value are not inserted into the | | - | | complex. | | + | | otherwise. All simplices that have a filtration value | | + | | :math:`> \alpha^2` are removed from the Delaunay complex | | + | | when creating the simplicial complex if it is specified. | | | | | | | | This package requires having CGAL version 4.7 or higher (4.8.1 is | | | | advised for better performance). | | diff --git a/src/python/doc/alpha_complex_user.rst b/src/python/doc/alpha_complex_user.rst index b7e69e12..60319e84 100644 --- a/src/python/doc/alpha_complex_user.rst +++ b/src/python/doc/alpha_complex_user.rst @@ -16,7 +16,8 @@ Definition Remarks ^^^^^^^ -When an :math:`\alpha`-complex is constructed with an infinite value of :math:`\alpha`, the complex is a Delaunay complex (with special filtration values). +When an :math:`\alpha`-complex is constructed with an infinite value of :math:`\alpha^2`, +the complex is a Delaunay complex (with special filtration values). Example from points ------------------- @@ -137,19 +138,20 @@ sets the filtration value (0 in case of a vertex - propagation will have no effe Non decreasing filtration values ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -As the squared radii computed by CGAL are an approximation, it might happen that these alpha squared values do not -quite define a proper filtration (i.e. non-decreasing with respect to inclusion). +As the squared radii computed by CGAL are an approximation, it might happen that these +: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 <http://gudhi.gforge.inria.fr/doc/latest/index.html>`_). Prune above given filtration value ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -The simplex tree is pruned from the given maximum alpha squared value (cf. +The simplex tree is pruned from the given maximum :math:`\alpha^2` value (cf. :func:`~gudhi.SimplexTree.prune_above_filtration`). Note that this does not provide any kind of speed-up, since we always first build the full filtered complex, so it is recommended not to use :paramref:`~gudhi.AlphaComplex.create_simplex_tree.max_alpha_square`. -In the following example, a threshold of 59 is used. +In the following example, a threshold of :math:`\alpha^2 = 32.0` is used. Example from OFF file @@ -166,7 +168,7 @@ Then, it is asked to display information about the alpha complex: import gudhi alpha_complex = gudhi.AlphaComplex(off_file=gudhi.__root_source_dir__ + \ '/data/points/alphacomplexdoc.off') - simplex_tree = alpha_complex.create_simplex_tree(max_alpha_square=59.0) + simplex_tree = alpha_complex.create_simplex_tree(max_alpha_square=32.0) result_str = 'Alpha complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \ repr(simplex_tree.num_simplices()) + ' simplices - ' + \ repr(simplex_tree.num_vertices()) + ' vertices.' @@ -179,7 +181,7 @@ the program output is: .. testoutput:: - Alpha complex is of dimension 2 - 23 simplices - 7 vertices. + Alpha complex is of dimension 2 - 20 simplices - 7 vertices. [0] -> 0.00 [1] -> 0.00 [2] -> 0.00 @@ -200,9 +202,6 @@ the program output is: [4, 6] -> 22.74 [4, 5, 6] -> 22.74 [3, 6] -> 30.25 - [2, 6] -> 36.50 - [2, 3, 6] -> 36.50 - [2, 4, 6] -> 37.24 CGAL citations ============== diff --git a/src/python/doc/cubical_complex_user.rst b/src/python/doc/cubical_complex_user.rst index b13b500e..56cf0170 100644 --- a/src/python/doc/cubical_complex_user.rst +++ b/src/python/doc/cubical_complex_user.rst @@ -142,8 +142,7 @@ Or it can be defined as follows: .. testcode:: from gudhi import PeriodicCubicalComplex as pcc - periodic_cc = pcc(dimensions=[3,3], - top_dimensional_cells= [0, 0, 0, 0, 1, 0, 0, 0, 0], + periodic_cc = pcc(top_dimensional_cells = [[0, 0, 0], [0, 1, 0], [0, 0, 0]], periodic_dimensions=[True, False]) result_str = 'Periodic cubical complex is of dimension ' + repr(periodic_cc.dimension()) + ' - ' + \ repr(periodic_cc.num_simplices()) + ' simplices.' diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst index 50a697c7..40f3f44b 100644 --- a/src/python/doc/installation.rst +++ b/src/python/doc/installation.rst @@ -257,6 +257,13 @@ The :doc:`Wasserstein distance </wasserstein_distance_user>` module requires `POT <https://pot.readthedocs.io/>`_, a library that provides several solvers for optimization problems related to Optimal Transport. +Scikit-learn +============ + +The :doc:`persistence representations </representations>` module require +`scikit-learn <https://scikit-learn.org/>`_, a Python-based ecosystem of +open-source software for machine learning. + SciPy ===== diff --git a/src/python/doc/persistence_graphical_tools_user.rst b/src/python/doc/persistence_graphical_tools_user.rst index f41a926b..80002db6 100644 --- a/src/python/doc/persistence_graphical_tools_user.rst +++ b/src/python/doc/persistence_graphical_tools_user.rst @@ -24,7 +24,7 @@ This function can display the persistence result as a barcode: import gudhi off_file = gudhi.__root_source_dir__ + '/data/points/tore3D_300.off' - point_cloud = gudhi.read_off(off_file=off_file) + point_cloud = gudhi.read_points_from_off_file(off_file=off_file) rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.7) simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) diff --git a/src/python/doc/reader_utils_ref.rst b/src/python/doc/reader_utils_ref.rst index f3ecebad..b8977a5a 100644 --- a/src/python/doc/reader_utils_ref.rst +++ b/src/python/doc/reader_utils_ref.rst @@ -6,7 +6,7 @@ Reader utils reference manual ============================= -.. autofunction:: gudhi.read_off +.. autofunction:: gudhi.read_points_from_off_file .. autofunction:: gudhi.read_lower_triangular_matrix_from_csv_file diff --git a/src/python/doc/rips_complex_user.rst b/src/python/doc/rips_complex_user.rst index a8659542..a27573e8 100644 --- a/src/python/doc/rips_complex_user.rst +++ b/src/python/doc/rips_complex_user.rst @@ -136,7 +136,8 @@ Finally, it is asked to display information about the Rips complex. .. testcode:: import gudhi - point_cloud = gudhi.read_off(off_file=gudhi.__root_source_dir__ + '/data/points/alphacomplexdoc.off') + off_file = gudhi.__root_source_dir__ + '/data/points/alphacomplexdoc.off' + point_cloud = gudhi.read_points_from_off_file(off_file = off_file) rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=12.0) simplex_tree = rips_complex.create_simplex_tree(max_dimension=1) result_str = 'Rips complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \ diff --git a/src/python/doc/witness_complex_user.rst b/src/python/doc/witness_complex_user.rst index 45ba5b3b..7087fa98 100644 --- a/src/python/doc/witness_complex_user.rst +++ b/src/python/doc/witness_complex_user.rst @@ -101,7 +101,7 @@ Let's start with a simple example, which reads an off point file and computes a print("#####################################################################") print("EuclideanWitnessComplex creation from points read in a OFF file") - witnesses = gudhi.read_off(off_file=args.file) + witnesses = gudhi.read_points_from_off_file(off_file=args.file) landmarks = gudhi.pick_n_random_points(points=witnesses, nb_points=args.number_of_landmarks) message = "EuclideanWitnessComplex with max_edge_length=" + repr(args.max_alpha_square) + \ diff --git a/src/python/example/alpha_rips_persistence_bottleneck_distance.py b/src/python/example/alpha_rips_persistence_bottleneck_distance.py index 086307ee..d5c33ec8 100755 --- a/src/python/example/alpha_rips_persistence_bottleneck_distance.py +++ b/src/python/example/alpha_rips_persistence_bottleneck_distance.py @@ -35,7 +35,7 @@ args = parser.parse_args() with open(args.file, "r") as f: first_line = f.readline() if (first_line == "OFF\n") or (first_line == "nOFF\n"): - point_cloud = gudhi.read_off(off_file=args.file) + point_cloud = gudhi.read_points_from_off_file(off_file=args.file) print("#####################################################################") print("RipsComplex creation from points read in a OFF file") diff --git a/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py index 0eedd140..4903667e 100755 --- a/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py @@ -47,7 +47,7 @@ with open(args.file, "r") as f: print("#####################################################################") print("EuclideanStrongWitnessComplex creation from points read in a OFF file") - witnesses = gudhi.read_off(off_file=args.file) + witnesses = gudhi.read_points_from_off_file(off_file=args.file) landmarks = gudhi.pick_n_random_points( points=witnesses, nb_points=args.number_of_landmarks ) diff --git a/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py index 1fe55737..339a8577 100755 --- a/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py @@ -46,7 +46,7 @@ with open(args.file, "r") as f: print("#####################################################################") print("EuclideanWitnessComplex creation from points read in a OFF file") - witnesses = gudhi.read_off(off_file=args.file) + witnesses = gudhi.read_points_from_off_file(off_file=args.file) landmarks = gudhi.pick_n_random_points( points=witnesses, nb_points=args.number_of_landmarks ) diff --git a/src/python/example/plot_rips_complex.py b/src/python/example/plot_rips_complex.py index 1c878db1..214a3c0a 100755 --- a/src/python/example/plot_rips_complex.py +++ b/src/python/example/plot_rips_complex.py @@ -2,7 +2,7 @@ import numpy as np import gudhi -points = np.array(gudhi.read_off('../../data/points/Kl.off')) +points = np.array(gudhi.read_points_from_off_file('../../data/points/Kl.off')) rc = gudhi.RipsComplex(points=points, max_edge_length=.2) st = rc.create_simplex_tree(max_dimension=2) # We are only going to plot the triangles diff --git a/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py index b9074cf9..c757aca7 100755 --- a/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py @@ -48,7 +48,7 @@ with open(args.file, "r") as f: message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length) print(message) - point_cloud = gudhi.read_off(off_file=args.file) + point_cloud = gudhi.read_points_from_off_file(off_file=args.file) rips_complex = gudhi.RipsComplex( points=point_cloud, max_edge_length=args.max_edge_length ) diff --git a/src/python/gudhi/__init__.py.in b/src/python/gudhi/__init__.py.in index 0c462b02..79e12fbc 100644 --- a/src/python/gudhi/__init__.py.in +++ b/src/python/gudhi/__init__.py.in @@ -1,5 +1,3 @@ -from importlib import import_module - # 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): Vincent Rouvreau @@ -9,6 +7,9 @@ from importlib import import_module # Modification(s): # - YYYY/MM Author: Description of the modification +from importlib import import_module +from sys import exc_info + __author__ = "GUDHI Editorial Board" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "https://gudhi.inria.fr/licensing/" @@ -17,9 +18,6 @@ __version__ = "@GUDHI_VERSION@" __root_source_dir__ = "@CMAKE_SOURCE_DIR@" __debug_info__ = @GUDHI_PYTHON_DEBUG_INFO@ -from sys import exc_info -from importlib import import_module - __all__ = [@GUDHI_PYTHON_MODULES@ @GUDHI_PYTHON_MODULES_EXTRA@] __available_modules = '' diff --git a/src/python/gudhi/alpha_complex.pyx b/src/python/gudhi/alpha_complex.pyx index 24e36bea..db11416c 100644 --- a/src/python/gudhi/alpha_complex.pyx +++ b/src/python/gudhi/alpha_complex.pyx @@ -1,3 +1,12 @@ +# 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): Vincent Rouvreau +# +# Copyright (C) 2016 Inria +# +# Modification(s): +# - YYYY/MM Author: Description of the modification + from cython cimport numeric from libcpp.vector cimport vector from libcpp.utility cimport pair @@ -9,15 +18,6 @@ import os from gudhi.simplex_tree cimport * from gudhi.simplex_tree import SimplexTree -# 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): Vincent Rouvreau -# -# Copyright (C) 2016 Inria -# -# Modification(s): -# - YYYY/MM Author: Description of the modification - __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" diff --git a/src/python/gudhi/bottleneck.pyx b/src/python/gudhi/bottleneck.pyx index c2361024..af011e88 100644 --- a/src/python/gudhi/bottleneck.pyx +++ b/src/python/gudhi/bottleneck.pyx @@ -1,8 +1,3 @@ -from cython cimport numeric -from libcpp.vector cimport vector -from libcpp.utility cimport pair -import os - # 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): Vincent Rouvreau @@ -12,6 +7,11 @@ import os # Modification(s): # - YYYY/MM Author: Description of the modification +from cython cimport numeric +from libcpp.vector cimport vector +from libcpp.utility cimport pair +import os + __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" diff --git a/src/python/gudhi/cubical_complex.pyx b/src/python/gudhi/cubical_complex.pyx index 011c407c..92ff6411 100644 --- a/src/python/gudhi/cubical_complex.pyx +++ b/src/python/gudhi/cubical_complex.pyx @@ -1,12 +1,3 @@ -from cython cimport numeric -from libcpp.vector cimport vector -from libcpp.utility cimport pair -from libcpp.string cimport string -from libcpp cimport bool -import os - -from numpy import array as np_array - # 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): Vincent Rouvreau @@ -16,6 +7,15 @@ from numpy import array as np_array # Modification(s): # - YYYY/MM Author: Description of the modification +from cython cimport numeric +from libcpp.vector cimport vector +from libcpp.utility cimport pair +from libcpp.string cimport string +from libcpp cimport bool +import os + +import numpy as np + __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "MIT" @@ -47,7 +47,7 @@ cdef class CubicalComplex: # Fake constructor that does nothing but documenting the constructor def __init__(self, dimensions=None, top_dimensional_cells=None, - perseus_file=''): + perseus_file=''): """CubicalComplex constructor from dimensions and top_dimensional_cells or from a Perseus-style file name. @@ -58,6 +58,12 @@ cdef class CubicalComplex: Or + :param top_dimensional_cells: A multidimensional array of cells + filtration values. + :type top_dimensional_cells: anything convertible to a numpy ndarray + + Or + :param perseus_file: A Perseus-style file name. :type perseus_file: string """ @@ -65,9 +71,19 @@ cdef class CubicalComplex: # The real cython constructor def __cinit__(self, dimensions=None, top_dimensional_cells=None, perseus_file=''): - if (dimensions is not None) and (top_dimensional_cells is not None) and (perseus_file == ''): + if ((dimensions is not None) and (top_dimensional_cells is not None) + and (perseus_file == '')): + self.thisptr = new Bitmap_cubical_complex_base_interface(dimensions, top_dimensional_cells) + elif ((dimensions is None) and (top_dimensional_cells is not None) + and (perseus_file == '')): + top_dimensional_cells = np.array(top_dimensional_cells, + copy = False, + order = 'F') + dimensions = top_dimensional_cells.shape + top_dimensional_cells = top_dimensional_cells.ravel(order='F') self.thisptr = new Bitmap_cubical_complex_base_interface(dimensions, top_dimensional_cells) - elif (dimensions is None) and (top_dimensional_cells is None) and (perseus_file != ''): + elif ((dimensions is None) and (top_dimensional_cells is None) + and (perseus_file != '')): if os.path.isfile(perseus_file): self.thisptr = new Bitmap_cubical_complex_base_interface(str.encode(perseus_file)) else: @@ -184,4 +200,4 @@ cdef class CubicalComplex: else: print("intervals_in_dim function requires persistence function" " to be launched first.") - return np_array(intervals_result) + return np.array(intervals_result) diff --git a/src/python/gudhi/euclidean_strong_witness_complex.pyx b/src/python/gudhi/euclidean_strong_witness_complex.pyx index e3f451f0..9889f92c 100644 --- a/src/python/gudhi/euclidean_strong_witness_complex.pyx +++ b/src/python/gudhi/euclidean_strong_witness_complex.pyx @@ -1,11 +1,3 @@ -from cython cimport numeric -from libcpp.vector cimport vector -from libcpp.utility cimport pair -from libc.stdint cimport intptr_t - -from gudhi.simplex_tree cimport * -from gudhi.simplex_tree import SimplexTree - # 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): Vincent Rouvreau @@ -15,6 +7,14 @@ from gudhi.simplex_tree import SimplexTree # Modification(s): # - YYYY/MM Author: Description of the modification +from cython cimport numeric +from libcpp.vector cimport vector +from libcpp.utility cimport pair +from libc.stdint cimport intptr_t + +from gudhi.simplex_tree cimport * +from gudhi.simplex_tree import SimplexTree + __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" diff --git a/src/python/gudhi/euclidean_witness_complex.pyx b/src/python/gudhi/euclidean_witness_complex.pyx index 84a8ea1a..e3ce0e82 100644 --- a/src/python/gudhi/euclidean_witness_complex.pyx +++ b/src/python/gudhi/euclidean_witness_complex.pyx @@ -1,11 +1,3 @@ -from cython cimport numeric -from libcpp.vector cimport vector -from libcpp.utility cimport pair -from libc.stdint cimport intptr_t - -from gudhi.simplex_tree cimport * -from gudhi.simplex_tree import SimplexTree - # 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): Vincent Rouvreau @@ -15,6 +7,14 @@ from gudhi.simplex_tree import SimplexTree # Modification(s): # - YYYY/MM Author: Description of the modification +from cython cimport numeric +from libcpp.vector cimport vector +from libcpp.utility cimport pair +from libc.stdint cimport intptr_t + +from gudhi.simplex_tree cimport * +from gudhi.simplex_tree import SimplexTree + __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" diff --git a/src/python/gudhi/nerve_gic.pyx b/src/python/gudhi/nerve_gic.pyx index acb78564..68c06432 100644 --- a/src/python/gudhi/nerve_gic.pyx +++ b/src/python/gudhi/nerve_gic.pyx @@ -1,3 +1,12 @@ +# 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): Vincent Rouvreau +# +# Copyright (C) 2018 Inria +# +# Modification(s): +# - YYYY/MM Author: Description of the modification + from cython cimport numeric from libcpp.vector cimport vector from libcpp.utility cimport pair @@ -9,15 +18,6 @@ from libc.stdint cimport intptr_t from gudhi.simplex_tree cimport * from gudhi.simplex_tree import SimplexTree -# 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): Vincent Rouvreau -# -# Copyright (C) 2018 Inria -# -# Modification(s): -# - YYYY/MM Author: Description of the modification - __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2018 Inria" __license__ = "GPL v3" diff --git a/src/python/gudhi/off_reader.pyx b/src/python/gudhi/off_reader.pyx index 225e981c..58f05db8 100644 --- a/src/python/gudhi/off_reader.pyx +++ b/src/python/gudhi/off_reader.pyx @@ -1,8 +1,3 @@ -from cython cimport numeric -from libcpp.vector cimport vector -from libcpp.string cimport string -import os - # 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): Vincent Rouvreau @@ -12,6 +7,11 @@ import os # Modification(s): # - YYYY/MM Author: Description of the modification +from cython cimport numeric +from libcpp.vector cimport vector +from libcpp.string cimport string +import os + __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "MIT" @@ -19,7 +19,7 @@ __license__ = "MIT" cdef extern from "Off_reader_interface.h" namespace "Gudhi": vector[vector[double]] read_points_from_OFF_file(string off_file) -def read_off(off_file=''): +def read_points_from_off_file(off_file=''): """Read points from OFF file. :param off_file: An OFF file style name. diff --git a/src/python/gudhi/periodic_cubical_complex.pyx b/src/python/gudhi/periodic_cubical_complex.pyx index c89055db..b5dece10 100644 --- a/src/python/gudhi/periodic_cubical_complex.pyx +++ b/src/python/gudhi/periodic_cubical_complex.pyx @@ -1,12 +1,3 @@ -from cython cimport numeric -from libcpp.vector cimport vector -from libcpp.utility cimport pair -from libcpp.string cimport string -from libcpp cimport bool -import os - -from numpy import array as np_array - # 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): Vincent Rouvreau @@ -16,6 +7,15 @@ from numpy import array as np_array # Modification(s): # - YYYY/MM Author: Description of the modification +from cython cimport numeric +from libcpp.vector cimport vector +from libcpp.utility cimport pair +from libcpp.string cimport string +from libcpp cimport bool +import os + +import numpy as np + __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "MIT" @@ -47,7 +47,7 @@ cdef class PeriodicCubicalComplex: # Fake constructor that does nothing but documenting the constructor def __init__(self, dimensions=None, top_dimensional_cells=None, - periodic_dimensions=None, perseus_file=''): + periodic_dimensions=None, perseus_file=''): """PeriodicCubicalComplex constructor from dimensions and top_dimensional_cells or from a Perseus-style file name. @@ -60,6 +60,14 @@ cdef class PeriodicCubicalComplex: Or + :param top_dimensional_cells: A multidimensional array of cells + filtration values. + :type top_dimensional_cells: anything convertible to a numpy ndarray + :param periodic_dimensions: A list of top dimensional cells periodicity value. + :type periodic_dimensions: list of boolean + + Or + :param perseus_file: A Perseus-style file name. :type perseus_file: string """ @@ -67,16 +75,32 @@ cdef class PeriodicCubicalComplex: # The real cython constructor def __cinit__(self, dimensions=None, top_dimensional_cells=None, periodic_dimensions=None, perseus_file=''): - if (dimensions is not None) and (top_dimensional_cells is not None) and (periodic_dimensions is not None) and (perseus_file == ''): - self.thisptr = new Periodic_cubical_complex_base_interface(dimensions, top_dimensional_cells, periodic_dimensions) - elif (dimensions is None) and (top_dimensional_cells is None) and (periodic_dimensions is None) and (perseus_file != ''): + if ((dimensions is not None) and (top_dimensional_cells is not None) + and (periodic_dimensions is not None) and (perseus_file == '')): + self.thisptr = new Periodic_cubical_complex_base_interface(dimensions, + top_dimensional_cells, + periodic_dimensions) + elif ((dimensions is None) and (top_dimensional_cells is not None) + and (periodic_dimensions is not None) and (perseus_file == '')): + top_dimensional_cells = np.array(top_dimensional_cells, + copy = False, + order = 'F') + dimensions = top_dimensional_cells.shape + top_dimensional_cells = top_dimensional_cells.ravel(order='F') + self.thisptr = new Periodic_cubical_complex_base_interface(dimensions, + top_dimensional_cells, + periodic_dimensions) + elif ((dimensions is None) and (top_dimensional_cells is None) + and (periodic_dimensions is None) and (perseus_file != '')): if os.path.isfile(perseus_file): self.thisptr = new Periodic_cubical_complex_base_interface(str.encode(perseus_file)) else: print("file " + perseus_file + " not found.") else: - print("CubicalComplex can be constructed from dimensions and " - "top_dimensional_cells or from a Perseus-style file name.") + print("CubicalComplex can be constructed from dimensions, " + "top_dimensional_cells and periodic_dimensions, or from " + "top_dimensional_cells and periodic_dimensions or from " + "a Perseus-style file name.") def __dealloc__(self): if self.thisptr != NULL: @@ -186,4 +210,4 @@ cdef class PeriodicCubicalComplex: else: print("intervals_in_dim function requires persistence function" " to be launched first.") - return np_array(intervals_result) + return np.array(intervals_result) diff --git a/src/python/gudhi/persistence_graphical_tools.py b/src/python/gudhi/persistence_graphical_tools.py index 7d232c85..246280de 100644 --- a/src/python/gudhi/persistence_graphical_tools.py +++ b/src/python/gudhi/persistence_graphical_tools.py @@ -1,10 +1,3 @@ -from os import path -from math import isfinite -import numpy as np - -from gudhi.reader_utils import read_persistence_intervals_in_dimension -from gudhi.reader_utils import read_persistence_intervals_grouped_by_dimension - # 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): Vincent Rouvreau, Bertrand Michel @@ -14,6 +7,13 @@ from gudhi.reader_utils import read_persistence_intervals_grouped_by_dimension # Modification(s): # - YYYY/MM Author: Description of the modification +from os import path +from math import isfinite +import numpy as np + +from gudhi.reader_utils import read_persistence_intervals_in_dimension +from gudhi.reader_utils import read_persistence_intervals_grouped_by_dimension + __author__ = "Vincent Rouvreau, Bertrand Michel" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "MIT" diff --git a/src/python/gudhi/reader_utils.pyx b/src/python/gudhi/reader_utils.pyx index 6994c4f9..345c92f8 100644 --- a/src/python/gudhi/reader_utils.pyx +++ b/src/python/gudhi/reader_utils.pyx @@ -1,12 +1,3 @@ -from cython cimport numeric -from libcpp.vector cimport vector -from libcpp.string cimport string -from libcpp.map cimport map -from libcpp.pair cimport pair - -from os import path -from numpy import array as np_array - # 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): Vincent Rouvreau @@ -16,6 +7,15 @@ from numpy import array as np_array # Modification(s): # - YYYY/MM Author: Description of the modification +from cython cimport numeric +from libcpp.vector cimport vector +from libcpp.string cimport string +from libcpp.map cimport map +from libcpp.pair cimport pair + +from os import path +from numpy import array as np_array + __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2017 Inria" __license__ = "MIT" diff --git a/src/python/gudhi/rips_complex.pyx b/src/python/gudhi/rips_complex.pyx index cbbbab0d..722cdcdc 100644 --- a/src/python/gudhi/rips_complex.pyx +++ b/src/python/gudhi/rips_complex.pyx @@ -1,3 +1,12 @@ +# 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): Vincent Rouvreau +# +# Copyright (C) 2016 Inria +# +# Modification(s): +# - YYYY/MM Author: Description of the modification + from cython cimport numeric from libcpp.vector cimport vector from libcpp.utility cimport pair @@ -8,15 +17,6 @@ from libc.stdint cimport intptr_t from gudhi.simplex_tree cimport * from gudhi.simplex_tree import SimplexTree -# 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): Vincent Rouvreau -# -# Copyright (C) 2016 Inria -# -# Modification(s): -# - YYYY/MM Author: Description of the modification - __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "MIT" diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd index 5f86cfe2..1066d44b 100644 --- a/src/python/gudhi/simplex_tree.pxd +++ b/src/python/gudhi/simplex_tree.pxd @@ -1,19 +1,18 @@ +# 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): Vincent Rouvreau +# +# Copyright (C) 2016 Inria +# +# Modification(s): +# - YYYY/MM Author: Description of the modification + from cython cimport numeric from libcpp.vector cimport vector from libcpp.utility cimport pair from libcpp cimport bool from libcpp.string cimport string -""" 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): Vincent Rouvreau - - Copyright (C) 2016 Inria - - Modification(s): - - YYYY/MM Author: Description of the modification -""" - __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "MIT" diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx index 4a3cd9bc..85d25492 100644 --- a/src/python/gudhi/simplex_tree.pyx +++ b/src/python/gudhi/simplex_tree.pyx @@ -1,7 +1,3 @@ -from libc.stdint cimport intptr_t -from numpy import array as np_array -cimport simplex_tree - # 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): Vincent Rouvreau @@ -11,6 +7,10 @@ cimport simplex_tree # Modification(s): # - YYYY/MM Author: Description of the modification +from libc.stdint cimport intptr_t +from numpy import array as np_array +cimport simplex_tree + __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "MIT" diff --git a/src/python/gudhi/strong_witness_complex.pyx b/src/python/gudhi/strong_witness_complex.pyx index 66d49b49..2c33c3f2 100644 --- a/src/python/gudhi/strong_witness_complex.pyx +++ b/src/python/gudhi/strong_witness_complex.pyx @@ -1,11 +1,3 @@ -from cython cimport numeric -from libcpp.vector cimport vector -from libcpp.utility cimport pair -from libc.stdint cimport intptr_t - -from gudhi.simplex_tree cimport * -from gudhi.simplex_tree import SimplexTree - # 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): Vincent Rouvreau @@ -15,6 +7,14 @@ from gudhi.simplex_tree import SimplexTree # Modification(s): # - YYYY/MM Author: Description of the modification +from cython cimport numeric +from libcpp.vector cimport vector +from libcpp.utility cimport pair +from libc.stdint cimport intptr_t + +from gudhi.simplex_tree cimport * +from gudhi.simplex_tree import SimplexTree + __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "MIT" diff --git a/src/python/gudhi/subsampling.pyx b/src/python/gudhi/subsampling.pyx index e0cd1348..b1812087 100644 --- a/src/python/gudhi/subsampling.pyx +++ b/src/python/gudhi/subsampling.pyx @@ -1,9 +1,3 @@ -from cython cimport numeric -from libcpp.vector cimport vector -from libcpp.string cimport string -from libcpp cimport bool -import os - # 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): Vincent Rouvreau @@ -13,6 +7,12 @@ import os # Modification(s): # - YYYY/MM Author: Description of the modification +from cython cimport numeric +from libcpp.vector cimport vector +from libcpp.string cimport string +from libcpp cimport bool +import os + __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" diff --git a/src/python/gudhi/tangential_complex.pyx b/src/python/gudhi/tangential_complex.pyx index f4c8b079..0083033c 100644 --- a/src/python/gudhi/tangential_complex.pyx +++ b/src/python/gudhi/tangential_complex.pyx @@ -1,3 +1,12 @@ +# 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): Vincent Rouvreau +# +# Copyright (C) 2016 Inria +# +# Modification(s): +# - YYYY/MM Author: Description of the modification + from cython cimport numeric from libcpp.vector cimport vector from libcpp.utility cimport pair @@ -9,15 +18,6 @@ import os from gudhi.simplex_tree cimport * from gudhi.simplex_tree import SimplexTree -# 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): Vincent Rouvreau -# -# Copyright (C) 2016 Inria -# -# Modification(s): -# - YYYY/MM Author: Description of the modification - __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" diff --git a/src/python/gudhi/wasserstein.py b/src/python/gudhi/wasserstein.py index 3eb7faef..db5ddff2 100644 --- a/src/python/gudhi/wasserstein.py +++ b/src/python/gudhi/wasserstein.py @@ -1,10 +1,3 @@ -import numpy as np -import scipy.spatial.distance as sc -try: - import ot -except ImportError: - print("POT (Python Optimal Transport) package is not installed. Try to run $ conda install -c conda-forge pot ; or $ pip install POT") - # 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): Theo Lacombe @@ -14,6 +7,13 @@ except ImportError: # Modification(s): # - YYYY/MM Author: Description of the modification +import numpy as np +import scipy.spatial.distance as sc +try: + import ot +except ImportError: + print("POT (Python Optimal Transport) package is not installed. Try to run $ conda install -c conda-forge pot ; or $ pip install POT") + def _proj_on_diag(X): ''' :param X: (n x 2) array encoding the points of a persistent diagram. diff --git a/src/python/gudhi/witness_complex.pyx b/src/python/gudhi/witness_complex.pyx index 153fc615..b032a5a1 100644 --- a/src/python/gudhi/witness_complex.pyx +++ b/src/python/gudhi/witness_complex.pyx @@ -1,11 +1,3 @@ -from cython cimport numeric -from libcpp.vector cimport vector -from libcpp.utility cimport pair -from libc.stdint cimport intptr_t - -from gudhi.simplex_tree cimport * -from gudhi.simplex_tree import SimplexTree - # 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): Vincent Rouvreau @@ -15,6 +7,14 @@ from gudhi.simplex_tree import SimplexTree # Modification(s): # - YYYY/MM Author: Description of the modification +from cython cimport numeric +from libcpp.vector cimport vector +from libcpp.utility cimport pair +from libc.stdint cimport intptr_t + +from gudhi.simplex_tree cimport * +from gudhi.simplex_tree import SimplexTree + __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "MIT" diff --git a/src/python/setup.py.in b/src/python/setup.py.in index 3f1d4424..24d05025 100644 --- a/src/python/setup.py.in +++ b/src/python/setup.py.in @@ -1,7 +1,3 @@ -from setuptools import setup, Extension -from Cython.Build import cythonize -from numpy import get_include as numpy_get_include - """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): Vincent Rouvreau @@ -12,6 +8,10 @@ from numpy import get_include as numpy_get_include - YYYY/MM Author: Description of the modification """ +from setuptools import setup, Extension +from Cython.Build import cythonize +from numpy import get_include as numpy_get_include + __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "MIT" diff --git a/src/python/test/test_alpha_complex.py b/src/python/test/test_alpha_complex.py index 9b27fff2..712a50b6 100755 --- a/src/python/test/test_alpha_complex.py +++ b/src/python/test/test_alpha_complex.py @@ -1,9 +1,3 @@ -from gudhi import AlphaComplex, SimplexTree -import math -import numpy as np -import itertools -import pytest - """ 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): Vincent Rouvreau @@ -14,6 +8,12 @@ import pytest - YYYY/MM Author: Description of the modification """ +from gudhi import AlphaComplex, SimplexTree +import math +import numpy as np +import itertools +import pytest + __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "MIT" diff --git a/src/python/test/test_bottleneck_distance.py b/src/python/test/test_bottleneck_distance.py index f5f019b9..70b2abad 100755 --- a/src/python/test/test_bottleneck_distance.py +++ b/src/python/test/test_bottleneck_distance.py @@ -1,5 +1,3 @@ -import gudhi - """ 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): Vincent Rouvreau @@ -10,6 +8,8 @@ import gudhi - YYYY/MM Author: Description of the modification """ +import gudhi + __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "MIT" diff --git a/src/python/test/test_cover_complex.py b/src/python/test/test_cover_complex.py index 8cd12272..32bc5a26 100755 --- a/src/python/test/test_cover_complex.py +++ b/src/python/test/test_cover_complex.py @@ -1,5 +1,3 @@ -from gudhi import CoverComplex - """ 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): Vincent Rouvreau @@ -10,6 +8,8 @@ from gudhi import CoverComplex - YYYY/MM Author: Description of the modification """ +from gudhi import CoverComplex + __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2018 Inria" __license__ = "MIT" diff --git a/src/python/test/test_cubical_complex.py b/src/python/test/test_cubical_complex.py index 68f54fbe..8c1b2600 100755 --- a/src/python/test/test_cubical_complex.py +++ b/src/python/test/test_cubical_complex.py @@ -1,5 +1,3 @@ -from gudhi import CubicalComplex - """ 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): Vincent Rouvreau @@ -10,6 +8,9 @@ from gudhi import CubicalComplex - YYYY/MM Author: Description of the modification """ +from gudhi import CubicalComplex, PeriodicCubicalComplex +import numpy as np + __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "MIT" @@ -56,7 +57,7 @@ def test_dimension_or_perseus_file_constructor(): assert cub.__is_persistence_defined() == False -def test_dimension_simple_constructor(): +def simple_constructor(cub): cub = CubicalComplex( dimensions=[3, 3], top_dimensional_cells=[1, 2, 3, 4, 5, 6, 7, 8, 9] ) @@ -67,12 +68,22 @@ def test_dimension_simple_constructor(): assert cub.betti_numbers() == [1, 0, 0] assert cub.persistent_betti_numbers(0, 1000) == [0, 0, 0] - -def test_user_case_simple_constructor(): +def test_simple_constructor_from_top_cells(): cub = CubicalComplex( dimensions=[3, 3], - top_dimensional_cells=[float("inf"), 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0], + top_dimensional_cells=[1, 2, 3, 4, 5, 6, 7, 8, 9], ) + simple_constructor(cub) + +def test_simple_constructor_from_numpy_array(): + cub = CubicalComplex( + top_dimensional_cells=np.array([[1, 2, 3], + [4, 5, 6], + [7, 8, 9]]) + ) + simple_constructor(cub) + +def user_case_simple_constructor(cub): assert cub.__is_defined() == True assert cub.__is_persistence_defined() == False assert cub.persistence() == [(1, (0.0, 1.0)), (0, (0.0, float("inf")))] @@ -83,6 +94,20 @@ def test_user_case_simple_constructor(): ) assert other_cub.persistence() == [(1, (0.0, 1.0)), (0, (0.0, float("inf")))] +def test_user_case_simple_constructor_from_top_cells(): + cub = CubicalComplex( + dimensions=[3, 3], + top_dimensional_cells=[float("inf"), 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0], + ) + user_case_simple_constructor(cub) + +def test_user_case_simple_constructor_from_numpy_array(): + cub = CubicalComplex( + top_dimensional_cells=np.array([[float("inf"), 0.0, 0.0], + [0.0, 1.0, 0.0], + [0.0, 0.0, 0.0]]) + ) + user_case_simple_constructor(cub) def test_dimension_file_constructor(): # Create test file @@ -96,3 +121,29 @@ def test_dimension_file_constructor(): assert cub.__is_persistence_defined() == True assert cub.betti_numbers() == [1, 0, 0] assert cub.persistent_betti_numbers(0, 1000) == [1, 0, 0] + +def test_connected_sublevel_sets(): + array_cells = np.array([[3, 3], [2, 2], [4, 4]]) + linear_cells = [3, 3, 2, 2, 4, 4] + dimensions = [2, 3] + periodic_dimensions = [False, False] + # with a numpy array version + cub = CubicalComplex(top_dimensional_cells = array_cells) + assert cub.persistence() == [(0, (2.0, float("inf")))] + assert cub.betti_numbers() == [1, 0, 0] + # with vector of dimensions + cub = CubicalComplex(dimensions = dimensions, + top_dimensional_cells = linear_cells) + assert cub.persistence() == [(0, (2.0, float("inf")))] + assert cub.betti_numbers() == [1, 0, 0] + # periodic with a numpy array version + cub = PeriodicCubicalComplex(top_dimensional_cells = array_cells, + periodic_dimensions = periodic_dimensions) + assert cub.persistence() == [(0, (2.0, float("inf")))] + assert cub.betti_numbers() == [1, 0, 0] + # periodic with vector of dimensions + cub = PeriodicCubicalComplex(dimensions = dimensions, + top_dimensional_cells = linear_cells, + periodic_dimensions = periodic_dimensions) + assert cub.persistence() == [(0, (2.0, float("inf")))] + assert cub.betti_numbers() == [1, 0, 0] diff --git a/src/python/test/test_euclidean_witness_complex.py b/src/python/test/test_euclidean_witness_complex.py index f5eae5fa..c18d2484 100755 --- a/src/python/test/test_euclidean_witness_complex.py +++ b/src/python/test/test_euclidean_witness_complex.py @@ -1,5 +1,3 @@ -import gudhi - """ 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): Vincent Rouvreau @@ -10,6 +8,8 @@ import gudhi - YYYY/MM Author: Description of the modification """ +import gudhi + __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "MIT" diff --git a/src/python/test/test_reader_utils.py b/src/python/test/test_reader_utils.py index 4c7b32c2..90da6651 100755 --- a/src/python/test/test_reader_utils.py +++ b/src/python/test/test_reader_utils.py @@ -1,6 +1,3 @@ -import gudhi -import numpy as np - """ 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): Vincent Rouvreau @@ -11,6 +8,9 @@ import numpy as np - YYYY/MM Author: Description of the modification """ +import gudhi +import numpy as np + __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2017 Inria" __license__ = "MIT" diff --git a/src/python/test/test_representations.py b/src/python/test/test_representations.py index 4ff65f98..dba7f952 100755 --- a/src/python/test/test_representations.py +++ b/src/python/test/test_representations.py @@ -1,11 +1,12 @@ import os import sys import matplotlib.pyplot as plt -# Disable graphics for testing purposes -plt.show = lambda:None -here = os.path.dirname(os.path.realpath(__file__)) -sys.path.append(here + "/../example") -import diagram_vectorizations_distances_kernels -# pytest is unhappy if there are 0 tests -def test_nothing(): + +def test_representations_examples(): + # Disable graphics for testing purposes + plt.show = lambda:None + here = os.path.dirname(os.path.realpath(__file__)) + sys.path.append(here + "/../example") + import diagram_vectorizations_distances_kernels + return None diff --git a/src/python/test/test_rips_complex.py b/src/python/test/test_rips_complex.py index d55ae22f..b02a68e1 100755 --- a/src/python/test/test_rips_complex.py +++ b/src/python/test/test_rips_complex.py @@ -1,6 +1,3 @@ -from gudhi import RipsComplex -from math import sqrt - """ 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): Vincent Rouvreau @@ -11,6 +8,9 @@ from math import sqrt - YYYY/MM Author: Description of the modification """ +from gudhi import RipsComplex +from math import sqrt + __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "MIT" diff --git a/src/python/test/test_simplex_tree.py b/src/python/test/test_simplex_tree.py index 8d8971c1..1822c43b 100755 --- a/src/python/test/test_simplex_tree.py +++ b/src/python/test/test_simplex_tree.py @@ -1,5 +1,3 @@ -from gudhi import SimplexTree - """ 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): Vincent Rouvreau @@ -10,6 +8,8 @@ from gudhi import SimplexTree - YYYY/MM Author: Description of the modification """ +from gudhi import SimplexTree + __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "MIT" diff --git a/src/python/test/test_subsampling.py b/src/python/test/test_subsampling.py index c816e203..fe0985fa 100755 --- a/src/python/test/test_subsampling.py +++ b/src/python/test/test_subsampling.py @@ -1,5 +1,3 @@ -import gudhi - """ 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): Vincent Rouvreau @@ -10,6 +8,8 @@ import gudhi - YYYY/MM Author: Description of the modification """ +import gudhi + __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "MIT" diff --git a/src/python/test/test_tangential_complex.py b/src/python/test/test_tangential_complex.py index 0f828d8e..e650e99c 100755 --- a/src/python/test/test_tangential_complex.py +++ b/src/python/test/test_tangential_complex.py @@ -1,5 +1,3 @@ -from gudhi import TangentialComplex, SimplexTree - """ 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): Vincent Rouvreau @@ -10,6 +8,8 @@ from gudhi import TangentialComplex, SimplexTree - YYYY/MM Author: Description of the modification """ +from gudhi import TangentialComplex, SimplexTree + __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "MIT" diff --git a/src/python/test/test_wasserstein_distance.py b/src/python/test/test_wasserstein_distance.py index 602e4bf1..43dda77e 100755 --- a/src/python/test/test_wasserstein_distance.py +++ b/src/python/test/test_wasserstein_distance.py @@ -1,6 +1,3 @@ -from gudhi.wasserstein import wasserstein_distance -import numpy as np - """ 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): Theo Lacombe @@ -11,6 +8,9 @@ import numpy as np - YYYY/MM Author: Description of the modification """ +from gudhi.wasserstein import wasserstein_distance +import numpy as np + __author__ = "Theo Lacombe" __copyright__ = "Copyright (C) 2019 Inria" __license__ = "MIT" diff --git a/src/python/test/test_witness_complex.py b/src/python/test/test_witness_complex.py index 36ced635..7baf18c9 100755 --- a/src/python/test/test_witness_complex.py +++ b/src/python/test/test_witness_complex.py @@ -1,5 +1,3 @@ -from gudhi import WitnessComplex, StrongWitnessComplex, SimplexTree - """ 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): Vincent Rouvreau @@ -10,6 +8,8 @@ from gudhi import WitnessComplex, StrongWitnessComplex, SimplexTree - YYYY/MM Author: Description of the modification """ +from gudhi import WitnessComplex, StrongWitnessComplex, SimplexTree + __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "MIT" |