diff options
| author | tlacombe <lacombe1993@gmail.com> | 2020-03-31 12:53:42 +0200 |
|---|---|---|
| committer | tlacombe <lacombe1993@gmail.com> | 2020-03-31 12:53:42 +0200 |
| commit | e6c21aa957bbf66854f31824cd4313c61f7ea9fc (patch) | |
| tree | 091c246f585e5836a2b1868414227d3d12938eaa /src/python | |
| parent | dae83f0907a5bd94cb483ad0f54755da2d49fb75 (diff) | |
| parent | 2f46606b406aafc69e37a68dca33e1858ab7b817 (diff) | |
merged master
Diffstat (limited to 'src/python')
36 files changed, 355 insertions, 121 deletions
diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt index 9fa7b129..b7d43bea 100644 --- a/src/python/CMakeLists.txt +++ b/src/python/CMakeLists.txt @@ -129,16 +129,6 @@ if(PYTHONINTERP_FOUND) endif () if(CGAL_FOUND) - can_cgal_use_cxx11_thread_local() - if (NOT CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT) - if(CMAKE_BUILD_TYPE MATCHES Debug) - add_GUDHI_PYTHON_lib("${Boost_THREAD_LIBRARY_DEBUG}") - else() - add_GUDHI_PYTHON_lib("${Boost_THREAD_LIBRARY_RELEASE}") - endif() - message("** Add Boost ${Boost_LIBRARY_DIRS}") - set(GUDHI_PYTHON_LIBRARY_DIRS "${GUDHI_PYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ") - endif() # Add CGAL compilation args if(CGAL_HEADER_ONLY) add_gudhi_debug_info("CGAL header only version ${CGAL_VERSION}") diff --git a/src/python/doc/alpha_complex_sum.inc b/src/python/doc/alpha_complex_sum.inc index b5af0d27..9e6414d0 100644 --- a/src/python/doc/alpha_complex_sum.inc +++ b/src/python/doc/alpha_complex_sum.inc @@ -1,12 +1,12 @@ .. table:: - :widths: 30 50 20 + :widths: 30 40 30 +----------------------------------------------------------------+------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------+ | .. figure:: | Alpha complex is a simplicial complex constructed from the finite | :Author: Vincent Rouvreau | | ../../doc/Alpha_complex/alpha_complex_representation.png | cells of a Delaunay Triangulation. | | - | :alt: Alpha complex representation | | :Introduced in: GUDHI 2.0.0 | + | :alt: Alpha complex representation | | :Since: GUDHI 2.0.0 | | :figclass: align-center | The filtration value of each simplex is computed as the **square** of | | - | | the circumradius of the simplex if the circumsphere is empty (the | :Copyright: MIT (`GPL v3 </licensing/>`_) | + | | the circumradius of the simplex if the circumsphere is empty (the | :License: MIT (`GPL v3 </licensing/>`_) | | | simplex is then said to be Gabriel), and as the minimum of the | | | | filtration values of the codimension 1 cofaces that make it not | :Requires: `Eigen <installation.html#eigen>`__ :math:`\geq` 3.1.0 and `CGAL <installation.html#cgal>`__ :math:`\geq` 4.11.0 | | | Gabriel otherwise. | | diff --git a/src/python/doc/bottleneck_distance_sum.inc b/src/python/doc/bottleneck_distance_sum.inc index 6eb0ac19..0de4625c 100644 --- a/src/python/doc/bottleneck_distance_sum.inc +++ b/src/python/doc/bottleneck_distance_sum.inc @@ -1,12 +1,12 @@ .. table:: - :widths: 30 50 20 + :widths: 30 40 30 +-----------------------------------------------------------------+----------------------------------------------------------------------+------------------------------------------------------------------+ | .. figure:: | Bottleneck distance measures the similarity between two persistence | :Author: François Godi | | ../../doc/Bottleneck_distance/perturb_pd.png | diagrams. It's the shortest distance b for which there exists a | | - | :figclass: align-center | perfect matching between the points of the two diagrams (+ all the | :Introduced in: GUDHI 2.0.0 | + | :figclass: align-center | perfect matching between the points of the two diagrams (+ all the | :Since: GUDHI 2.0.0 | | | diagonal points) such that any couple of matched points are at | | - | Bottleneck distance is the length of | distance at most b, where the distance between points is the sup | :Copyright: MIT (`GPL v3 </licensing/>`_) | + | Bottleneck distance is the length of | distance at most b, where the distance between points is the sup | :License: MIT (`GPL v3 </licensing/>`_) | | the longest edge | norm in :math:`\mathbb{R}^2`. | | | | | :Requires: `CGAL <installation.html#cgal>`__ :math:`\geq` 4.11.0 | +-----------------------------------------------------------------+----------------------------------------------------------------------+------------------------------------------------------------------+ diff --git a/src/python/doc/cubical_complex_sum.inc b/src/python/doc/cubical_complex_sum.inc index f200e695..28bf8e94 100644 --- a/src/python/doc/cubical_complex_sum.inc +++ b/src/python/doc/cubical_complex_sum.inc @@ -1,12 +1,12 @@ .. table:: - :widths: 30 50 20 + :widths: 30 40 30 +--------------------------------------------------------------------------+----------------------------------------------------------------------+-----------------------------+ | .. figure:: | The cubical complex is an example of a structured complex useful in | :Author: Pawel Dlotko | | ../../doc/Bitmap_cubical_complex/Cubical_complex_representation.png | computational mathematics (specially rigorous numerics) and image | | - | :alt: Cubical complex representation | analysis. | :Introduced in: GUDHI 2.0.0 | + | :alt: Cubical complex representation | analysis. | :Since: GUDHI 2.0.0 | | :figclass: align-center | | | - | | | :Copyright: MIT | + | | | :License: MIT | | | | | +--------------------------------------------------------------------------+----------------------------------------------------------------------+-----------------------------+ | * :doc:`cubical_complex_user` | * :doc:`cubical_complex_ref` | diff --git a/src/python/doc/cubical_complex_user.rst b/src/python/doc/cubical_complex_user.rst index 56cf0170..93ca6b24 100644 --- a/src/python/doc/cubical_complex_user.rst +++ b/src/python/doc/cubical_complex_user.rst @@ -8,7 +8,7 @@ Definition ---------- ===================================== ===================================== ===================================== -:Author: Pawel Dlotko :Introduced in: GUDHI PYTHON 2.0.0 :Copyright: GPL v3 +:Author: Pawel Dlotko :Since: GUDHI PYTHON 2.0.0 :License: GPL v3 ===================================== ===================================== ===================================== +---------------------------------------------+----------------------------------------------------------------------+ diff --git a/src/python/doc/nerve_gic_complex_sum.inc b/src/python/doc/nerve_gic_complex_sum.inc index d633c4ff..7fe55aff 100644 --- a/src/python/doc/nerve_gic_complex_sum.inc +++ b/src/python/doc/nerve_gic_complex_sum.inc @@ -1,12 +1,12 @@ .. table:: - :widths: 30 50 20 + :widths: 30 40 30 +----------------------------------------------------------------+------------------------------------------------------------------------+------------------------------------------------------------------+ | .. figure:: | Nerves and Graph Induced Complexes are cover complexes, i.e. | :Author: Mathieu Carrière | | ../../doc/Nerve_GIC/gicvisu.jpg | simplicial complexes that provably contain topological information | | - | :alt: Graph Induced Complex of a point cloud. | about the input data. They can be computed with a cover of the data, | :Introduced in: GUDHI 2.3.0 | + | :alt: Graph Induced Complex of a point cloud. | about the input data. They can be computed with a cover of the data, | :Since: GUDHI 2.3.0 | | :figclass: align-center | that comes i.e. from the preimage of a family of intervals covering | | - | | the image of a scalar-valued function defined on the data. | :Copyright: MIT (`GPL v3 </licensing/>`_) | + | | the image of a scalar-valued function defined on the data. | :License: MIT (`GPL v3 </licensing/>`_) | | | | | | | | :Requires: `CGAL <installation.html#cgal>`__ :math:`\geq` 4.11.0 | | | | | diff --git a/src/python/doc/persistence_graphical_tools_sum.inc b/src/python/doc/persistence_graphical_tools_sum.inc index ef376802..b68d3d7e 100644 --- a/src/python/doc/persistence_graphical_tools_sum.inc +++ b/src/python/doc/persistence_graphical_tools_sum.inc @@ -1,12 +1,12 @@ .. table:: - :widths: 30 50 20 + :widths: 30 40 30 +-----------------------------------------------------------------+-----------------------------------------------------------------------+-----------------------------------------------+ | .. figure:: | These graphical tools comes on top of persistence results and allows | :Author: Vincent Rouvreau, Theo Lacombe | | img/graphical_tools_representation.png | the user to display easily persistence barcode, diagram or density. | | - | | | :Introduced in: GUDHI 2.0.0 | + | | | :Since: GUDHI 2.0.0 | | | Note that these functions return the matplotlib axis, allowing | | - | | for further modifications (title, aspect, etc.) | :Copyright: MIT | + | | for further modifications (title, aspect, etc.) | :License: MIT | | | | | | | | :Requires: matplotlib, numpy and scipy | +-----------------------------------------------------------------+-----------------------------------------------------------------------+-----------------------------------------------+ diff --git a/src/python/doc/persistent_cohomology_sum.inc b/src/python/doc/persistent_cohomology_sum.inc index 4d7b077e..0effb50f 100644 --- a/src/python/doc/persistent_cohomology_sum.inc +++ b/src/python/doc/persistent_cohomology_sum.inc @@ -1,12 +1,12 @@ .. table:: - :widths: 30 50 20 + :widths: 30 40 30 +-----------------------------------------------------------------+-----------------------------------------------------------------------+-----------------------------------------------+ | .. figure:: | The theory of homology consists in attaching to a topological space | :Author: Clément Maria | | ../../doc/Persistent_cohomology/3DTorus_poch.png | a sequence of (homology) groups, capturing global topological | | - | :figclass: align-center | features like connected components, holes, cavities, etc. Persistent | :Introduced in: GUDHI 2.0.0 | + | :figclass: align-center | features like connected components, holes, cavities, etc. Persistent | :Since: GUDHI 2.0.0 | | | homology studies the evolution -- birth, life and death -- of these | | - | Rips Persistent Cohomology on a 3D | features when the topological space is changing. Consequently, the | :Copyright: MIT | + | Rips Persistent Cohomology on a 3D | features when the topological space is changing. Consequently, the | :License: MIT | | Torus | theory is essentially composed of three elements: topological spaces, | | | | their homology groups and an evolution scheme. | | | | | | diff --git a/src/python/doc/persistent_cohomology_user.rst b/src/python/doc/persistent_cohomology_user.rst index de83cda1..5f931b3a 100644 --- a/src/python/doc/persistent_cohomology_user.rst +++ b/src/python/doc/persistent_cohomology_user.rst @@ -7,7 +7,7 @@ Persistent cohomology user manual Definition ---------- ===================================== ===================================== ===================================== -:Author: Clément Maria :Introduced in: GUDHI PYTHON 2.0.0 :Copyright: GPL v3 +:Author: Clément Maria :Since: GUDHI PYTHON 2.0.0 :License: GPL v3 ===================================== ===================================== ===================================== +-----------------------------------------------------------------+-----------------------------------------------------------------------+ diff --git a/src/python/doc/point_cloud_sum.inc b/src/python/doc/point_cloud_sum.inc index 85d52de7..0a159680 100644 --- a/src/python/doc/point_cloud_sum.inc +++ b/src/python/doc/point_cloud_sum.inc @@ -1,12 +1,12 @@ .. table:: - :widths: 30 50 20 + :widths: 30 40 30 +----------------------------------------------------------------+------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------+ | | :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 | + | | | :Since: GUDHI 2.0.0 | | | | | - | | | :Copyright: MIT (`GPL v3 </licensing/>`_) | + | | | :License: 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 | | | | | diff --git a/src/python/doc/representations_sum.inc b/src/python/doc/representations_sum.inc index 700828f1..eac89b9d 100644 --- a/src/python/doc/representations_sum.inc +++ b/src/python/doc/representations_sum.inc @@ -1,12 +1,12 @@ .. table:: - :widths: 30 50 20 + :widths: 30 40 30 +------------------------------------------------------------------+----------------------------------------------------------------+-----------------------------------------------+ | .. figure:: | Vectorizations, distances and kernels that work on persistence | :Author: Mathieu Carrière | | img/sklearn-tda.png | diagrams, compatible with scikit-learn. | | - | | | :Introduced in: GUDHI 3.1.0 | + | | | :Since: GUDHI 3.1.0 | | | | | - | | | :Copyright: MIT | + | | | :License: MIT | | | | | | | | :Requires: scikit-learn | +------------------------------------------------------------------+----------------------------------------------------------------+-----------------------------------------------+ diff --git a/src/python/doc/rips_complex_sum.inc b/src/python/doc/rips_complex_sum.inc index 857c6893..6feb74cd 100644 --- a/src/python/doc/rips_complex_sum.inc +++ b/src/python/doc/rips_complex_sum.inc @@ -1,12 +1,12 @@ .. table:: - :widths: 30 50 20 + :widths: 30 40 30 +----------------------------------------------------------------+------------------------------------------------------------------------+----------------------------------------------------------------------+ | .. figure:: | Rips complex is a simplicial complex constructed from a one skeleton | :Authors: Clément Maria, Pawel Dlotko, Vincent Rouvreau, Marc Glisse | | ../../doc/Rips_complex/rips_complex_representation.png | graph. | | - | :figclass: align-center | | :Introduced in: GUDHI 2.0.0 | + | :figclass: align-center | | :Since: GUDHI 2.0.0 | | | The filtration value of each edge is computed from a user-given | | - | | distance function and is inserted until a user-given threshold | :Copyright: MIT | + | | distance function and is inserted until a user-given threshold | :License: MIT | | | value. | | | | | | | | This complex can be built from a point cloud and a distance function, | | diff --git a/src/python/doc/rips_complex_user.rst b/src/python/doc/rips_complex_user.rst index a27573e8..8efb12e6 100644 --- a/src/python/doc/rips_complex_user.rst +++ b/src/python/doc/rips_complex_user.rst @@ -8,7 +8,7 @@ Definition ---------- ==================================================================== ================================ ====================== -:Authors: Clément Maria, Pawel Dlotko, Vincent Rouvreau, Marc Glisse :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 +:Authors: Clément Maria, Pawel Dlotko, Vincent Rouvreau, Marc Glisse :Since: GUDHI 2.0.0 :License: GPL v3 ==================================================================== ================================ ====================== +-------------------------------------------+----------------------------------------------------------------------+ diff --git a/src/python/doc/simplex_tree_sum.inc b/src/python/doc/simplex_tree_sum.inc index 5ba58d2b..a8858f16 100644 --- a/src/python/doc/simplex_tree_sum.inc +++ b/src/python/doc/simplex_tree_sum.inc @@ -1,12 +1,12 @@ .. table:: - :widths: 30 50 20 + :widths: 30 40 30 +----------------------------------------------------------------+------------------------------------------------------------------------+-----------------------------+ | .. figure:: | The simplex tree is an efficient and flexible data structure for | :Author: Clément Maria | | ../../doc/Simplex_tree/Simplex_tree_representation.png | representing general (filtered) simplicial complexes. | | - | :alt: Simplex tree representation | | :Introduced in: GUDHI 2.0.0 | + | :alt: Simplex tree representation | | :Since: GUDHI 2.0.0 | | :figclass: align-center | The data structure is described in | | - | | :cite:`boissonnatmariasimplextreealgorithmica` | :Copyright: MIT | + | | :cite:`boissonnatmariasimplextreealgorithmica` | :License: MIT | | | | | +----------------------------------------------------------------+------------------------------------------------------------------------+-----------------------------+ | * :doc:`simplex_tree_user` | * :doc:`simplex_tree_ref` | diff --git a/src/python/doc/tangential_complex_sum.inc b/src/python/doc/tangential_complex_sum.inc index d84aa433..45ce2a66 100644 --- a/src/python/doc/tangential_complex_sum.inc +++ b/src/python/doc/tangential_complex_sum.inc @@ -1,12 +1,12 @@ .. table:: - :widths: 30 50 20 + :widths: 30 40 30 +----------------------------------------------------------------+------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------+ | .. figure:: | A Tangential Delaunay complex is a simplicial complex designed to | :Author: Clément Jamin | | ../../doc/Tangential_complex/tc_examples.png | reconstruct a :math:`k`-dimensional manifold embedded in :math:`d`- | | - | :figclass: align-center | dimensional Euclidean space. The input is a point sample coming from | :Introduced in: GUDHI 2.0.0 | + | :figclass: align-center | dimensional Euclidean space. The input is a point sample coming from | :Since: GUDHI 2.0.0 | | | an unknown manifold. The running time depends only linearly on the | | - | | extrinsic dimension :math:`d` and exponentially on the intrinsic | :Copyright: MIT (`GPL v3 </licensing/>`_) | + | | extrinsic dimension :math:`d` and exponentially on the intrinsic | :License: MIT (`GPL v3 </licensing/>`_) | | | dimension :math:`k`. | | | | | :Requires: `Eigen <installation.html#eigen>`__ :math:`\geq` 3.1.0 and `CGAL <installation.html#cgal>`__ :math:`\geq` 4.11.0 | +----------------------------------------------------------------+------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------+ diff --git a/src/python/doc/wasserstein_distance_sum.inc b/src/python/doc/wasserstein_distance_sum.inc index 09424de2..f10472bc 100644 --- a/src/python/doc/wasserstein_distance_sum.inc +++ b/src/python/doc/wasserstein_distance_sum.inc @@ -1,5 +1,5 @@ .. table:: - :widths: 30 50 20 + :widths: 30 40 30 +-----------------------------------------------------------------+----------------------------------------------------------------------+------------------------------------------------------------------+ | .. figure:: | The q-Wasserstein distance measures the similarity between two | :Author: Theo Lacombe | diff --git a/src/python/doc/witness_complex_sum.inc b/src/python/doc/witness_complex_sum.inc index 71b65a71..34d4df4a 100644 --- a/src/python/doc/witness_complex_sum.inc +++ b/src/python/doc/witness_complex_sum.inc @@ -1,12 +1,12 @@ .. table:: - :widths: 30 50 20 + :widths: 30 40 30 +-------------------------------------------------------------------+----------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------+ | .. figure:: | Witness complex :math:`Wit(W,L)` is a simplicial complex defined on | :Author: Siargey Kachanovich | | ../../doc/Witness_complex/Witness_complex_representation.png | two sets of points in :math:`\mathbb{R}^D`. | | - | :alt: Witness complex representation | | :Introduced in: GUDHI 2.0.0 | + | :alt: Witness complex representation | | :Since: GUDHI 2.0.0 | | :figclass: align-center | The data structure is described in | | - | | :cite:`boissonnatmariasimplextreealgorithmica`. | :Copyright: MIT (`GPL v3 </licensing/>`_ for Euclidean versions only) | + | | :cite:`boissonnatmariasimplextreealgorithmica`. | :License: MIT (`GPL v3 </licensing/>`_ for Euclidean versions only) | | | | | | | | :Requires: `Eigen <installation.html#eigen>`__ :math:`\geq` 3.1.0 and `CGAL <installation.html#cgal>`__ :math:`\geq` 4.11.0 for Euclidean versions only | +-------------------------------------------------------------------+----------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------+ diff --git a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py index 4079a469..727af4fa 100755 --- a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py @@ -1,11 +1,15 @@ #!/usr/bin/env python import argparse +import errno +import os import matplotlib.pyplot as plot 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. +""" 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 @@ -41,7 +45,7 @@ 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"): - print("#####################################################################") + print("##############################################################") print("AlphaComplex creation from points read in a OFF file") message = "AlphaComplex with max_edge_length=" + repr(args.max_alpha_square) @@ -64,6 +68,7 @@ with open(args.file, "r") as f: gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: - print(args.file, "is not a valid OFF file") + raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), + args.file) f.close() diff --git a/src/python/example/alpha_rips_persistence_bottleneck_distance.py b/src/python/example/alpha_rips_persistence_bottleneck_distance.py index d5c33ec8..f156826d 100755 --- a/src/python/example/alpha_rips_persistence_bottleneck_distance.py +++ b/src/python/example/alpha_rips_persistence_bottleneck_distance.py @@ -3,9 +3,13 @@ import gudhi import argparse import math +import errno +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. +""" 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 @@ -36,7 +40,7 @@ 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_points_from_off_file(off_file=args.file) - print("#####################################################################") + print("##############################################################") print("RipsComplex creation from points read in a OFF file") message = "RipsComplex with max_edge_length=" + repr(args.threshold) @@ -46,14 +50,15 @@ with open(args.file, "r") as f: points=point_cloud, max_edge_length=args.threshold ) - rips_stree = rips_complex.create_simplex_tree(max_dimension=args.max_dimension) + rips_stree = rips_complex.create_simplex_tree( + max_dimension=args.max_dimension) message = "Number of simplices=" + repr(rips_stree.num_simplices()) print(message) rips_diag = rips_stree.persistence() - print("#####################################################################") + print("##############################################################") print("AlphaComplex creation from points read in a OFF file") message = "AlphaComplex with max_edge_length=" + repr(args.threshold) @@ -93,13 +98,13 @@ with open(args.file, "r") as f: print(message) max_b_distance = max(bottleneck_distance, max_b_distance) - print( - "================================================================================" - ) + print("==============================================================") message = "Bottleneck distance is " + repr(max_b_distance) print(message) else: - print(args.file, "is not a valid OFF file") + raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), + args.file) + f.close() 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 4903667e..e1e572df 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 @@ -1,11 +1,15 @@ #!/usr/bin/env python import argparse +import errno +import os import matplotlib.pyplot as plot 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. +""" 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 @@ -44,8 +48,9 @@ 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"): - print("#####################################################################") - print("EuclideanStrongWitnessComplex creation from points read in a OFF file") + print("##############################################################") + print("EuclideanStrongWitnessComplex creation from points read "\ + "in a OFF file") witnesses = gudhi.read_points_from_off_file(off_file=args.file) landmarks = gudhi.pick_n_random_points( @@ -64,7 +69,8 @@ with open(args.file, "r") as f: witnesses=witnesses, landmarks=landmarks ) simplex_tree = witness_complex.create_simplex_tree( - max_alpha_square=args.max_alpha_square, limit_dimension=args.limit_dimension + max_alpha_square=args.max_alpha_square, + limit_dimension=args.limit_dimension ) message = "Number of simplices=" + repr(simplex_tree.num_simplices()) @@ -79,6 +85,7 @@ with open(args.file, "r") as f: gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: - print(args.file, "is not a valid OFF file") + raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), + args.file) f.close() 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 339a8577..58cb2bb5 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 @@ -1,11 +1,15 @@ #!/usr/bin/env python import argparse +import errno +import os import matplotlib.pyplot as plot 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. +""" 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 @@ -78,6 +82,7 @@ with open(args.file, "r") as f: gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: - print(args.file, "is not a valid OFF file") + raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), + args.file) f.close() diff --git a/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py b/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py index c692e66f..499171df 100755 --- a/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py +++ b/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py @@ -2,10 +2,14 @@ import argparse import matplotlib.pyplot as plot +import errno +import os 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. +""" 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 @@ -57,9 +61,10 @@ parser.add_argument( args = parser.parse_args() if is_file_perseus(args.file): - print("#####################################################################") + print("##################################################################") print("PeriodicCubicalComplex creation") - periodic_cubical_complex = gudhi.PeriodicCubicalComplex(perseus_file=args.file) + periodic_cubical_complex = gudhi.PeriodicCubicalComplex( + perseus_file=args.file) print("persistence(homology_coeff_field=3, min_persistence=0)=") diag = periodic_cubical_complex.persistence( @@ -73,4 +78,5 @@ if is_file_perseus(args.file): gudhi.plot_persistence_barcode(diag) plot.show() else: - print(args.file, "is not a valid perseus style file") + raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), + args.file) 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 c757aca7..6f992508 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 @@ -1,11 +1,15 @@ #!/usr/bin/env python import argparse +import errno +import os import matplotlib.pyplot as plot 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. +""" 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 @@ -42,10 +46,11 @@ 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"): - print("#####################################################################") + print("##############################################################") print("RipsComplex creation from points read in a OFF file") - message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length) + message = "RipsComplex with max_edge_length=" + \ + repr(args.max_edge_length) print(message) point_cloud = gudhi.read_points_from_off_file(off_file=args.file) @@ -68,6 +73,7 @@ with open(args.file, "r") as f: gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: - print(args.file, "is not a valid OFF file") + raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), + args.file) f.close() diff --git a/src/python/example/tangential_complex_plain_homology_from_off_file_example.py b/src/python/example/tangential_complex_plain_homology_from_off_file_example.py index f0df2189..85bade4a 100755 --- a/src/python/example/tangential_complex_plain_homology_from_off_file_example.py +++ b/src/python/example/tangential_complex_plain_homology_from_off_file_example.py @@ -1,11 +1,15 @@ #!/usr/bin/env python import argparse +import errno +import os import matplotlib.pyplot as plot 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. +""" 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 @@ -19,7 +23,7 @@ __copyright__ = "Copyright (C) 2016 Inria" __license__ = "MIT" parser = argparse.ArgumentParser( - description="TangentialComplex creation from " "points read in a OFF file.", + description="TangentialComplex creation from points read in a OFF file.", epilog="Example: " "example/tangential_complex_plain_homology_from_off_file_example.py " "-f ../data/points/tore3D_300.off -i 3" @@ -41,10 +45,11 @@ 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"): - print("#####################################################################") + print("##############################################################") print("TangentialComplex creation from points read in a OFF file") - tc = gudhi.TangentialComplex(intrisic_dim=args.intrisic_dim, off_file=args.file) + tc = gudhi.TangentialComplex(intrisic_dim=args.intrisic_dim, + off_file=args.file) tc.compute_tangential_complex() st = tc.create_simplex_tree() @@ -60,6 +65,7 @@ with open(args.file, "r") as f: gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: - print(args.file, "is not a valid OFF file") + raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), + args.file) f.close() diff --git a/src/python/gudhi/alpha_complex.pyx b/src/python/gudhi/alpha_complex.pyx index fff3e920..e04dc652 100644 --- a/src/python/gudhi/alpha_complex.pyx +++ b/src/python/gudhi/alpha_complex.pyx @@ -1,5 +1,7 @@ -# 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. +# 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 @@ -7,6 +9,7 @@ # Modification(s): # - YYYY/MM Author: Description of the modification +from __future__ import print_function from cython cimport numeric from libcpp.vector cimport vector from libcpp.utility cimport pair @@ -69,7 +72,8 @@ cdef class AlphaComplex: def __cinit__(self, points = None, off_file = ''): if off_file: if os.path.isfile(off_file): - self.thisptr = new Alpha_complex_interface(off_file.encode('utf-8'), True) + self.thisptr = new Alpha_complex_interface( + off_file.encode('utf-8'), True) else: print("file " + off_file + " not found.") else: diff --git a/src/python/gudhi/cubical_complex.pyx b/src/python/gudhi/cubical_complex.pyx index cbeda014..d5ad1266 100644 --- a/src/python/gudhi/cubical_complex.pyx +++ b/src/python/gudhi/cubical_complex.pyx @@ -1,5 +1,7 @@ -# 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. +# 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 @@ -7,12 +9,15 @@ # Modification(s): # - YYYY/MM Author: Description of the modification +from __future__ import print_function from cython cimport numeric from libcpp.vector cimport vector from libcpp.utility cimport pair from libcpp.string cimport string from libcpp cimport bool +import errno import os +import sys import numpy as np @@ -87,10 +92,12 @@ cdef class CubicalComplex: if os.path.isfile(perseus_file): self.thisptr = new Bitmap_cubical_complex_base_interface(perseus_file.encode('utf-8')) else: - print("file " + perseus_file + " not found.") + raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), + perseus_file) else: print("CubicalComplex can be constructed from dimensions and " - "top_dimensional_cells or from a Perseus-style file name.") + "top_dimensional_cells or from a Perseus-style file name.", + file=sys.stderr) def __dealloc__(self): if self.thisptr != NULL: @@ -199,5 +206,5 @@ cdef class CubicalComplex: intervals_result = self.pcohptr.intervals_in_dimension(dimension) else: print("intervals_in_dim function requires persistence function" - " to be launched first.") + " to be launched first.", file=sys.stderr) return np.array(intervals_result) diff --git a/src/python/gudhi/nerve_gic.pyx b/src/python/gudhi/nerve_gic.pyx index 45cc8eba..9c89b239 100644 --- a/src/python/gudhi/nerve_gic.pyx +++ b/src/python/gudhi/nerve_gic.pyx @@ -1,5 +1,7 @@ -# 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. +# 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 @@ -7,11 +9,13 @@ # Modification(s): # - YYYY/MM Author: Description of the modification +from __future__ import print_function from cython cimport numeric from libcpp.vector cimport vector from libcpp.utility cimport pair from libcpp.string cimport string from libcpp cimport bool +import errno import os from libc.stdint cimport intptr_t @@ -96,7 +100,8 @@ cdef class CoverComplex: return self.thisptr != NULL def set_point_cloud_from_range(self, cloud): - """ Reads and stores the input point cloud from a vector stored in memory. + """ Reads and stores the input point cloud from a vector stored in + memory. :param cloud: Input vector containing the point cloud. :type cloud: vector[vector[double]] @@ -104,7 +109,8 @@ cdef class CoverComplex: return self.thisptr.set_point_cloud_from_range(cloud) def set_distances_from_range(self, distance_matrix): - """ Reads and stores the input distance matrix from a vector stored in memory. + """ Reads and stores the input distance matrix from a vector stored in + memory. :param distance_matrix: Input vector containing the distance matrix. :type distance_matrix: vector[vector[double]] @@ -163,7 +169,8 @@ cdef class CoverComplex: """ stree = SimplexTree() cdef intptr_t stree_int_ptr=stree.thisptr - self.thisptr.create_simplex_tree(<Simplex_tree_interface_full_featured*>stree_int_ptr) + self.thisptr.create_simplex_tree( + <Simplex_tree_interface_full_featured*>stree_int_ptr) return stree def find_simplices(self): @@ -182,8 +189,8 @@ cdef class CoverComplex: if os.path.isfile(off_file): return self.thisptr.read_point_cloud(off_file.encode('utf-8')) else: - print("file " + off_file + " not found.") - return False + raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), + off_file) def set_automatic_resolution(self): """Computes the optimal length of intervals (i.e. the smallest interval @@ -214,7 +221,8 @@ cdef class CoverComplex: if os.path.isfile(color_file_name): self.thisptr.set_color_from_file(color_file_name.encode('utf-8')) else: - print("file " + color_file_name + " not found.") + raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), + color_file_name) def set_color_from_range(self, color): """Computes the function used to color the nodes of the simplicial @@ -235,7 +243,8 @@ cdef class CoverComplex: if os.path.isfile(cover_file_name): self.thisptr.set_cover_from_file(cover_file_name.encode('utf-8')) else: - print("file " + cover_file_name + " not found.") + raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), + cover_file_name) def set_cover_from_function(self): """Creates a cover C from the preimages of the function f. @@ -268,7 +277,8 @@ cdef class CoverComplex: if os.path.isfile(func_file_name): self.thisptr.set_function_from_file(func_file_name.encode('utf-8')) else: - print("file " + func_file_name + " not found.") + raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), + func_file_name) def set_function_from_range(self, function): """Creates the function f from a vector stored in memory. @@ -302,14 +312,15 @@ cdef class CoverComplex: """Creates a graph G from a file containing the edges. :param graph_file_name: Name of the input graph file. The graph file - contains one edge per line, each edge being represented by the IDs of - its two nodes. + contains one edge per line, each edge being represented by the IDs + of its two nodes. :type graph_file_name: string """ if os.path.isfile(graph_file_name): self.thisptr.set_graph_from_file(graph_file_name.encode('utf-8')) else: - print("file " + graph_file_name + " not found.") + raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), + graph_file_name) def set_graph_from_OFF(self): """Creates a graph G from the triangulation given by the input OFF diff --git a/src/python/gudhi/off_reader.pyx b/src/python/gudhi/off_reader.pyx index 7e6d9d80..a3200704 100644 --- a/src/python/gudhi/off_reader.pyx +++ b/src/python/gudhi/off_reader.pyx @@ -1,5 +1,7 @@ -# 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. +# 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 @@ -7,9 +9,11 @@ # Modification(s): # - YYYY/MM Author: Description of the modification +from __future__ import print_function from cython cimport numeric from libcpp.vector cimport vector from libcpp.string cimport string +import errno import os __author__ = "Vincent Rouvreau" @@ -32,6 +36,6 @@ def read_points_from_off_file(off_file=''): if os.path.isfile(off_file): return read_points_from_OFF_file(off_file.encode('utf-8')) else: - print("file " + off_file + " not found.") - return [] + raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), + off_file) diff --git a/src/python/gudhi/periodic_cubical_complex.pyx b/src/python/gudhi/periodic_cubical_complex.pyx index 37f76201..fd08b976 100644 --- a/src/python/gudhi/periodic_cubical_complex.pyx +++ b/src/python/gudhi/periodic_cubical_complex.pyx @@ -7,11 +7,13 @@ # Modification(s): # - YYYY/MM Author: Description of the modification +from __future__ import print_function from cython cimport numeric from libcpp.vector cimport vector from libcpp.utility cimport pair from libcpp.string cimport string from libcpp cimport bool +import sys import os import numpy as np @@ -95,12 +97,12 @@ cdef class PeriodicCubicalComplex: if os.path.isfile(perseus_file): self.thisptr = new Periodic_cubical_complex_base_interface(perseus_file.encode('utf-8')) else: - print("file " + perseus_file + " not found.") + print("file " + perseus_file + " not found.", file=sys.stderr) else: 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.") + "a Perseus-style file name.", file=sys.stderr) def __dealloc__(self): if self.thisptr != NULL: @@ -209,5 +211,5 @@ cdef class PeriodicCubicalComplex: intervals_result = self.pcohptr.intervals_in_dimension(dimension) else: print("intervals_in_dim function requires persistence function" - " to be launched first.") + " to be launched first.", file=sys.stderr) return np.array(intervals_result) diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd index 82f155de..595f22bb 100644 --- a/src/python/gudhi/simplex_tree.pxd +++ b/src/python/gudhi/simplex_tree.pxd @@ -57,6 +57,8 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": void remove_maximal_simplex(vector[int] simplex) bool prune_above_filtration(double filtration) bool make_filtration_non_decreasing() + void compute_extended_filtration() + vector[vector[pair[int, pair[double, double]]]] compute_extended_persistence_subdiagrams(vector[pair[int, pair[double, double]]] dgm, double min_persistence) # Iterators over Simplex tree pair[vector[int], double] get_simplex_and_filtration(Simplex_tree_simplex_handle f_simplex) Simplex_tree_simplices_iterator get_simplices_iterator_begin() diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx index c01cc905..cc3753e1 100644 --- a/src/python/gudhi/simplex_tree.pyx +++ b/src/python/gudhi/simplex_tree.pyx @@ -396,6 +396,57 @@ cdef class SimplexTree: """ return self.get_ptr().make_filtration_non_decreasing() + def extend_filtration(self): + """ Extend filtration for computing extended persistence. This function only uses the + filtration values at the 0-dimensional simplices, and computes the extended persistence + diagram induced by the lower-star filtration computed with these values. + + .. note:: + + Note that after calling this function, the filtration + values are actually modified within the Simplex_tree. + The function :func:`extended_persistence()<gudhi.SimplexTree.extended_persistence>` + retrieves the original values. + + .. note:: + + Note that this code creates an extra vertex internally, so you should make sure that + the Simplex_tree does not contain a vertex with the largest possible value (i.e., 4294967295). + """ + return self.get_ptr().compute_extended_filtration() + + def extended_persistence(self, homology_coeff_field=11, min_persistence=0): + """This function retrieves good values for extended persistence, and separate the diagrams + into the Ordinary, Relative, Extended+ and Extended- subdiagrams. + + :param homology_coeff_field: The homology coefficient field. Must be a + prime number. Default value is 11. + :type homology_coeff_field: int. + :param min_persistence: The minimum persistence value (i.e., the absolute value of the difference between the persistence diagram point coordinates) to take into + account (strictly greater than min_persistence). Default value is + 0.0. + Sets min_persistence to -1.0 to see all values. + :type min_persistence: float. + :returns: A list of four persistence diagrams in the format described in :func:`persistence()<gudhi.SimplexTree.persistence>`. The first one is Ordinary, the second one is Relative, the third one is Extended+ and the fourth one is Extended-. See https://link.springer.com/article/10.1007/s10208-008-9027-z and/or section 2.2 in https://link.springer.com/article/10.1007/s10208-017-9370-z for a description of these subtypes. + + .. note:: + + This function should be called only if :func:`extend_filtration()<gudhi.SimplexTree.extend_filtration>` has been called first! + + .. note:: + + The coordinates of the persistence diagram points might be a little different than the + original filtration values due to the internal transformation (scaling to [-2,-1]) that is + performed on these values during the computation of extended persistence. + """ + cdef vector[pair[int, pair[double, double]]] persistence_result + if self.pcohptr != NULL: + del self.pcohptr + self.pcohptr = new Simplex_tree_persistence_interface(self.get_ptr(), False) + persistence_result = self.pcohptr.get_persistence(homology_coeff_field, -1.) + return self.get_ptr().compute_extended_persistence_subdiagrams(persistence_result, min_persistence) + + def persistence(self, homology_coeff_field=11, min_persistence=0, persistence_dim_max = False): """This function returns the persistence of the simplicial complex. diff --git a/src/python/include/Simplex_tree_interface.h b/src/python/include/Simplex_tree_interface.h index 4a7062d6..1a18aed6 100644 --- a/src/python/include/Simplex_tree_interface.h +++ b/src/python/include/Simplex_tree_interface.h @@ -37,8 +37,12 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> { using Filtered_simplices = std::vector<Simplex_and_filtration>; using Skeleton_simplex_iterator = typename Base::Skeleton_simplex_iterator; using Complex_simplex_iterator = typename Base::Complex_simplex_iterator; + using Extended_filtration_data = typename Base::Extended_filtration_data; public: + + Extended_filtration_data efd; + bool find_simplex(const Simplex& vh) { return (Base::find(vh) != Base::null_simplex()); } @@ -117,6 +121,42 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> { return cofaces; } + void compute_extended_filtration() { + this->efd = this->extend_filtration(); + this->initialize_filtration(); + return; + } + + std::vector<std::vector<std::pair<int, std::pair<Filtration_value, Filtration_value>>>> compute_extended_persistence_subdiagrams(const std::vector<std::pair<int, std::pair<Filtration_value, Filtration_value>>>& dgm, Filtration_value min_persistence){ + std::vector<std::vector<std::pair<int, std::pair<Filtration_value, Filtration_value>>>> new_dgm(4); + for (unsigned int i = 0; i < dgm.size(); i++){ + std::pair<Filtration_value, Extended_simplex_type> px = this->decode_extended_filtration(dgm[i].second.first, this->efd); + std::pair<Filtration_value, Extended_simplex_type> py = this->decode_extended_filtration(dgm[i].second.second, this->efd); + std::pair<int, std::pair<Filtration_value, Filtration_value>> pd_point = std::make_pair(dgm[i].first, std::make_pair(px.first, py.first)); + if(std::abs(px.first - py.first) > min_persistence){ + //Ordinary + if (px.second == Extended_simplex_type::UP && py.second == Extended_simplex_type::UP){ + new_dgm[0].push_back(pd_point); + } + // Relative + else if (px.second == Extended_simplex_type::DOWN && py.second == Extended_simplex_type::DOWN){ + new_dgm[1].push_back(pd_point); + } + else{ + // Extended+ + if (px.first < py.first){ + new_dgm[2].push_back(pd_point); + } + //Extended- + else{ + new_dgm[3].push_back(pd_point); + } + } + } + } + return new_dgm; + } + void create_persistence(Gudhi::Persistent_cohomology_interface<Base>* pcoh) { Base::initialize_filtration(); pcoh = new Gudhi::Persistent_cohomology_interface<Base>(*this); diff --git a/src/python/test/test_cover_complex.py b/src/python/test/test_cover_complex.py index 32bc5a26..260f6a5c 100755 --- a/src/python/test/test_cover_complex.py +++ b/src/python/test/test_cover_complex.py @@ -9,6 +9,7 @@ """ from gudhi import CoverComplex +import pytest __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2018 Inria" @@ -24,7 +25,8 @@ def test_empty_constructor(): def test_non_existing_file_read(): # Try to open a non existing file cover = CoverComplex() - assert cover.read_point_cloud("pouetpouettralala.toubiloubabdou") == False + with pytest.raises(FileNotFoundError): + cover.read_point_cloud("pouetpouettralala.toubiloubabdou") def test_files_creation(): diff --git a/src/python/test/test_cubical_complex.py b/src/python/test/test_cubical_complex.py index 8c1b2600..fce4875c 100755 --- a/src/python/test/test_cubical_complex.py +++ b/src/python/test/test_cubical_complex.py @@ -10,6 +10,7 @@ from gudhi import CubicalComplex, PeriodicCubicalComplex import numpy as np +import pytest __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" @@ -25,9 +26,8 @@ def test_empty_constructor(): def test_non_existing_perseus_file_constructor(): # Try to open a non existing file - cub = CubicalComplex(perseus_file="pouetpouettralala.toubiloubabdou") - assert cub.__is_defined() == False - assert cub.__is_persistence_defined() == False + with pytest.raises(FileNotFoundError): + cub = CubicalComplex(perseus_file="pouetpouettralala.toubiloubabdou") def test_dimension_or_perseus_file_constructor(): diff --git a/src/python/test/test_simplex_tree.py b/src/python/test/test_simplex_tree.py index f7848379..70b26e97 100755 --- a/src/python/test/test_simplex_tree.py +++ b/src/python/test/test_simplex_tree.py @@ -9,6 +9,7 @@ """ from gudhi import SimplexTree +import pytest __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" @@ -250,6 +251,87 @@ def test_make_filtration_non_decreasing(): assert st.filtration([3, 4]) == 2.0 assert st.filtration([4, 5]) == 2.0 +def test_extend_filtration(): + + # Inserted simplex: + # 5 4 + # o o + # / \ / + # o o + # /2\ /3 + # o o + # 1 0 + + st = SimplexTree() + st.insert([0,2]) + st.insert([1,2]) + st.insert([0,3]) + st.insert([2,5]) + st.insert([3,4]) + st.insert([3,5]) + st.assign_filtration([0], 1.) + st.assign_filtration([1], 2.) + st.assign_filtration([2], 3.) + st.assign_filtration([3], 4.) + st.assign_filtration([4], 5.) + st.assign_filtration([5], 6.) + + assert list(st.get_filtration()) == [ + ([0, 2], 0.0), + ([1, 2], 0.0), + ([0, 3], 0.0), + ([3, 4], 0.0), + ([2, 5], 0.0), + ([3, 5], 0.0), + ([0], 1.0), + ([1], 2.0), + ([2], 3.0), + ([3], 4.0), + ([4], 5.0), + ([5], 6.0) + ] + + st.extend_filtration() + + assert list(st.get_filtration()) == [ + ([6], -3.0), + ([0], -2.0), + ([1], -1.8), + ([2], -1.6), + ([0, 2], -1.6), + ([1, 2], -1.6), + ([3], -1.4), + ([0, 3], -1.4), + ([4], -1.2), + ([3, 4], -1.2), + ([5], -1.0), + ([2, 5], -1.0), + ([3, 5], -1.0), + ([5, 6], 1.0), + ([4, 6], 1.2), + ([3, 6], 1.4), + ([3, 4, 6], 1.4), + ([3, 5, 6], 1.4), + ([2, 6], 1.6), + ([2, 5, 6], 1.6), + ([1, 6], 1.8), + ([1, 2, 6], 1.8), + ([0, 6], 2.0), + ([0, 2, 6], 2.0), + ([0, 3, 6], 2.0) + ] + + dgms = st.extended_persistence(min_persistence=-1.) + + assert dgms[0][0][1][0] == pytest.approx(2.) + assert dgms[0][0][1][1] == pytest.approx(3.) + assert dgms[1][0][1][0] == pytest.approx(5.) + assert dgms[1][0][1][1] == pytest.approx(4.) + assert dgms[2][0][1][0] == pytest.approx(1.) + assert dgms[2][0][1][1] == pytest.approx(6.) + assert dgms[3][0][1][0] == pytest.approx(6.) + assert dgms[3][0][1][1] == pytest.approx(1.) + def test_simplices_iterator(): st = SimplexTree() diff --git a/src/python/test/test_subsampling.py b/src/python/test/test_subsampling.py index fe0985fa..31f64e32 100755 --- a/src/python/test/test_subsampling.py +++ b/src/python/test/test_subsampling.py @@ -120,7 +120,6 @@ def test_simple_pick_n_random_points(): # Go furter than point set on purpose for iter in range(1, 10): sub_set = gudhi.pick_n_random_points(points=point_set, nb_points=iter) - print(5) for sub in sub_set: found = False for point in point_set: |