From 8804aa1580c500ed927d65c25e8b78700725338e Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Tue, 8 Nov 2022 22:26:36 +0100 Subject: Clarify doc of RipsComplex.__init__ --- src/python/gudhi/rips_complex.pyx | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) (limited to 'src') diff --git a/src/python/gudhi/rips_complex.pyx b/src/python/gudhi/rips_complex.pyx index c3470292..a0924cd6 100644 --- a/src/python/gudhi/rips_complex.pyx +++ b/src/python/gudhi/rips_complex.pyx @@ -45,20 +45,19 @@ cdef class RipsComplex: max_edge_length=float('inf'), sparse=None): """RipsComplex constructor. - :param max_edge_length: Rips value. - :type max_edge_length: float - :param points: A list of points in d-Dimension. - :type points: list of list of float + :type points: List[List[float]] Or :param distance_matrix: A distance matrix (full square or lower triangular). - :type points: list of list of float + :type distance_matrix: List[List[float]] And in both cases + :param max_edge_length: Rips value. + :type max_edge_length: float :param sparse: If this is not None, it switches to building a sparse Rips and represents the approximation parameter epsilon. :type sparse: float -- cgit v1.2.3 From 7c17408897a95a1f74626e8ff0ec8101ac4f92fd Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Tue, 8 Nov 2022 22:36:16 +0100 Subject: Reject positional arguments in RipsComplex.__init__ --- .github/next_release.md | 3 +++ src/python/gudhi/rips_complex.pyx | 4 ++-- src/python/test/test_simplex_generators.py | 2 +- 3 files changed, 6 insertions(+), 3 deletions(-) (limited to 'src') diff --git a/.github/next_release.md b/.github/next_release.md index 81599b2c..d5fcef1c 100644 --- a/.github/next_release.md +++ b/.github/next_release.md @@ -9,6 +9,9 @@ Below is a list of changes made since GUDHI 3.6.0: - [Module](link) - ... +- [Rips complex](https://gudhi.inria.fr/python/latest/rips_complex_user.html) + - Construction now rejects positional arguments, you need to specify `points=X`. + - Installation - c++17 is the new minimal standard to compile the library. This implies Visual Studio minimal version is now 2017. diff --git a/src/python/gudhi/rips_complex.pyx b/src/python/gudhi/rips_complex.pyx index a0924cd6..d748f91e 100644 --- a/src/python/gudhi/rips_complex.pyx +++ b/src/python/gudhi/rips_complex.pyx @@ -41,7 +41,7 @@ cdef class RipsComplex: cdef Rips_complex_interface thisref # Fake constructor that does nothing but documenting the constructor - def __init__(self, points=None, distance_matrix=None, + def __init__(self, *, points=None, distance_matrix=None, max_edge_length=float('inf'), sparse=None): """RipsComplex constructor. @@ -64,7 +64,7 @@ cdef class RipsComplex: """ # The real cython constructor - def __cinit__(self, points=None, distance_matrix=None, + def __cinit__(self, *, points=None, distance_matrix=None, max_edge_length=float('inf'), sparse=None): if sparse is not None: if distance_matrix is not None: diff --git a/src/python/test/test_simplex_generators.py b/src/python/test/test_simplex_generators.py index 8a9b4844..c567d4c1 100755 --- a/src/python/test/test_simplex_generators.py +++ b/src/python/test/test_simplex_generators.py @@ -14,7 +14,7 @@ import numpy as np def test_flag_generators(): pts = np.array([[0, 0], [0, 1.01], [1, 0], [1.02, 1.03], [100, 0], [100, 3.01], [103, 0], [103.02, 3.03]]) - r = gudhi.RipsComplex(pts, max_edge_length=4) + r = gudhi.RipsComplex(points=pts, max_edge_length=4) st = r.create_simplex_tree(max_dimension=50) st.persistence() g = st.flag_persistence_generators() -- cgit v1.2.3 From ad1123c3c7cfddc1c15e9933b96af08ef3398b3c Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Wed, 9 Nov 2022 17:46:39 +0100 Subject: New write_points_to_off_file --- src/python/CMakeLists.txt | 4 +- src/python/doc/installation.rst | 4 +- src/python/doc/point_cloud.rst | 5 ++ src/python/gudhi/off_reader.pyx | 41 -------------- src/python/gudhi/off_utils.pyx | 57 ++++++++++++++++++++ src/python/test/test_subsampling.py | 103 ++++++++---------------------------- 6 files changed, 88 insertions(+), 126 deletions(-) delete mode 100644 src/python/gudhi/off_reader.pyx create mode 100644 src/python/gudhi/off_utils.pyx (limited to 'src') diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt index 8f8df138..35ddb778 100644 --- a/src/python/CMakeLists.txt +++ b/src/python/CMakeLists.txt @@ -53,7 +53,7 @@ if(PYTHONINTERP_FOUND) set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'datasets', ") # Cython modules - set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'off_reader', ") + set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'off_utils', ") set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'simplex_tree', ") set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'rips_complex', ") set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'cubical_complex', ") @@ -152,7 +152,7 @@ if(PYTHONINTERP_FOUND) set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ") endif (EIGEN3_FOUND) - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'off_reader', ") + set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'off_utils', ") set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'simplex_tree', ") set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'rips_complex', ") set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'cubical_complex', ") diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst index 276ac4e2..5491542f 100644 --- a/src/python/doc/installation.rst +++ b/src/python/doc/installation.rst @@ -150,7 +150,7 @@ You shall have something like: Cython version 0.29.25 Numpy version 1.21.4 Boost version 1.77.0 - + Installed modules are: off_reader;simplex_tree;rips_complex;cubical_complex;periodic_cubical_complex; + + Installed modules are: off_utils;simplex_tree;rips_complex;cubical_complex;periodic_cubical_complex; persistence_graphical_tools;reader_utils;witness_complex;strong_witness_complex; + Missing modules are: bottleneck;nerve_gic;subsampling;tangential_complex;alpha_complex;euclidean_witness_complex; euclidean_strong_witness_complex; @@ -188,7 +188,7 @@ A complete configuration would be : GMPXX_LIBRARIES = /usr/lib/x86_64-linux-gnu/libgmpxx.so MPFR_LIBRARIES = /usr/lib/x86_64-linux-gnu/libmpfr.so TBB version 9107 found and used - + Installed modules are: bottleneck;off_reader;simplex_tree;rips_complex;cubical_complex;periodic_cubical_complex; + + Installed modules are: bottleneck;off_utils;simplex_tree;rips_complex;cubical_complex;periodic_cubical_complex; persistence_graphical_tools;reader_utils;witness_complex;strong_witness_complex;nerve_gic;subsampling; tangential_complex;alpha_complex;euclidean_witness_complex;euclidean_strong_witness_complex; + Missing modules are: diff --git a/src/python/doc/point_cloud.rst b/src/python/doc/point_cloud.rst index ffd8f85b..473b303f 100644 --- a/src/python/doc/point_cloud.rst +++ b/src/python/doc/point_cloud.rst @@ -13,6 +13,11 @@ File Readers .. autofunction:: gudhi.read_lower_triangular_matrix_from_csv_file +File Writers +------------ + +.. autofunction:: gudhi.write_points_to_off_file + Subsampling ----------- diff --git a/src/python/gudhi/off_reader.pyx b/src/python/gudhi/off_reader.pyx deleted file mode 100644 index a3200704..00000000 --- a/src/python/gudhi/off_reader.pyx +++ /dev/null @@ -1,41 +0,0 @@ -# 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 __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" -__copyright__ = "Copyright (C) 2016 Inria" -__license__ = "MIT" - -cdef extern from "Off_reader_interface.h" namespace "Gudhi": - vector[vector[double]] read_points_from_OFF_file(string off_file) - -def read_points_from_off_file(off_file=''): - """Read points from OFF file. - - :param off_file: An OFF file style name. - :type off_file: string - - :returns: The point set. - :rtype: List[List[float]] - """ - if off_file: - if os.path.isfile(off_file): - return read_points_from_OFF_file(off_file.encode('utf-8')) - else: - raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), - off_file) - diff --git a/src/python/gudhi/off_utils.pyx b/src/python/gudhi/off_utils.pyx new file mode 100644 index 00000000..155575d5 --- /dev/null +++ b/src/python/gudhi/off_utils.pyx @@ -0,0 +1,57 @@ +# 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 __future__ import print_function +from cython cimport numeric +from libcpp.vector cimport vector +from libcpp.string cimport string +cimport cython +import errno +import os +import numpy as np + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 Inria" +__license__ = "MIT" + +cdef extern from "Off_reader_interface.h" namespace "Gudhi": + vector[vector[double]] read_points_from_OFF_file(string off_file) + +def read_points_from_off_file(off_file=''): + """Read points from OFF file. + + :param off_file: An OFF file style name. + :type off_file: string + + :returns: The point set. + :rtype: List[List[float]] + """ + if off_file: + if os.path.isfile(off_file): + return read_points_from_OFF_file(off_file.encode('utf-8')) + else: + raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), + off_file) + +@cython.embedsignature(True) +def write_points_to_off_file(fname, points): + """Write points to an OFF file. + + A simple wrapper for `numpy.savetxt`. + + :param fname: Name of the OFF file. + :type fname: str or file handle + :param points: Point coordinates. + :type points: numpy array of shape (n, dim) + """ + points = np.array(points, copy=False) + assert len(points.shape) == 2 + np.savetxt(fname, points, header='nOFF\n{} {} 0 0'.format(points.shape[1], points.shape[0]), comments='') diff --git a/src/python/test/test_subsampling.py b/src/python/test/test_subsampling.py index 3431f372..c1cb4e3f 100755 --- a/src/python/test/test_subsampling.py +++ b/src/python/test/test_subsampling.py @@ -16,17 +16,9 @@ __license__ = "MIT" def test_write_off_file_for_tests(): - file = open("subsample.off", "w") - file.write("nOFF\n") - file.write("2 7 0 0\n") - file.write("1.0 1.0\n") - file.write("7.0 0.0\n") - file.write("4.0 6.0\n") - file.write("9.0 6.0\n") - file.write("0.0 14.0\n") - file.write("2.0 19.0\n") - file.write("9.0 17.0\n") - file.close() + gudhi.write_points_to_off_file( + "subsample.off", [[1.0, 1.0], [7.0, 0.0], [4.0, 6.0], [9.0, 6.0], [0.0, 14.0], [2.0, 19.0], [9.0, 17.0]] + ) def test_simple_choose_n_farthest_points_with_a_starting_point(): @@ -34,54 +26,29 @@ def test_simple_choose_n_farthest_points_with_a_starting_point(): i = 0 for point in point_set: # The iteration starts with the given starting point - sub_set = gudhi.choose_n_farthest_points( - points=point_set, nb_points=1, starting_point=i - ) + sub_set = gudhi.choose_n_farthest_points(points=point_set, nb_points=1, starting_point=i) assert sub_set[0] == point_set[i] i = i + 1 # The iteration finds then the farthest - sub_set = gudhi.choose_n_farthest_points( - points=point_set, nb_points=2, starting_point=1 - ) + sub_set = gudhi.choose_n_farthest_points(points=point_set, nb_points=2, starting_point=1) assert sub_set[1] == point_set[3] - sub_set = gudhi.choose_n_farthest_points( - points=point_set, nb_points=2, starting_point=3 - ) + sub_set = gudhi.choose_n_farthest_points(points=point_set, nb_points=2, starting_point=3) assert sub_set[1] == point_set[1] - sub_set = gudhi.choose_n_farthest_points( - points=point_set, nb_points=2, starting_point=0 - ) + sub_set = gudhi.choose_n_farthest_points(points=point_set, nb_points=2, starting_point=0) assert sub_set[1] == point_set[2] - sub_set = gudhi.choose_n_farthest_points( - points=point_set, nb_points=2, starting_point=2 - ) + sub_set = gudhi.choose_n_farthest_points(points=point_set, nb_points=2, starting_point=2) assert sub_set[1] == point_set[0] # Test the limits - assert ( - gudhi.choose_n_farthest_points(points=[], nb_points=0, starting_point=0) == [] - ) - assert ( - gudhi.choose_n_farthest_points(points=[], nb_points=1, starting_point=0) == [] - ) - assert ( - gudhi.choose_n_farthest_points(points=[], nb_points=0, starting_point=1) == [] - ) - assert ( - gudhi.choose_n_farthest_points(points=[], nb_points=1, starting_point=1) == [] - ) + assert gudhi.choose_n_farthest_points(points=[], nb_points=0, starting_point=0) == [] + assert gudhi.choose_n_farthest_points(points=[], nb_points=1, starting_point=0) == [] + assert gudhi.choose_n_farthest_points(points=[], nb_points=0, starting_point=1) == [] + assert gudhi.choose_n_farthest_points(points=[], nb_points=1, starting_point=1) == [] # From off file test for i in range(0, 7): - assert ( - len( - gudhi.choose_n_farthest_points( - off_file="subsample.off", nb_points=i, starting_point=i - ) - ) - == i - ) + assert len(gudhi.choose_n_farthest_points(off_file="subsample.off", nb_points=i, starting_point=i)) == i def test_simple_choose_n_farthest_points_randomed(): @@ -104,10 +71,7 @@ def test_simple_choose_n_farthest_points_randomed(): # From off file test for i in range(0, 7): - assert ( - len(gudhi.choose_n_farthest_points(off_file="subsample.off", nb_points=i)) - == i - ) + assert len(gudhi.choose_n_farthest_points(off_file="subsample.off", nb_points=i)) == i def test_simple_pick_n_random_points(): @@ -130,9 +94,7 @@ def test_simple_pick_n_random_points(): # From off file test for i in range(0, 7): - assert ( - len(gudhi.pick_n_random_points(off_file="subsample.off", nb_points=i)) == i - ) + assert len(gudhi.pick_n_random_points(off_file="subsample.off", nb_points=i)) == i def test_simple_sparsify_points(): @@ -152,31 +114,10 @@ def test_simple_sparsify_points(): ] assert gudhi.sparsify_point_set(points=point_set, min_squared_dist=2.001) == [[0, 1]] - assert ( - len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=0.0)) - == 7 - ) - assert ( - len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=30.0)) - == 5 - ) - assert ( - len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=40.1)) - == 4 - ) - assert ( - len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=89.9)) - == 3 - ) - assert ( - len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=100.0)) - == 2 - ) - assert ( - len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=324.9)) - == 2 - ) - assert ( - len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=325.01)) - == 1 - ) + assert len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=0.0)) == 7 + assert len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=30.0)) == 5 + assert len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=40.1)) == 4 + assert len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=89.9)) == 3 + assert len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=100.0)) == 2 + assert len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=324.9)) == 2 + assert len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=325.01)) == 1 -- cgit v1.2.3 From 4118bcb622c624130e768d9116a7e147a5e45c68 Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Fri, 11 Nov 2022 18:00:42 +0100 Subject: Link to OFF format --- src/python/gudhi/off_utils.pyx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'src') diff --git a/src/python/gudhi/off_utils.pyx b/src/python/gudhi/off_utils.pyx index 155575d5..a8142791 100644 --- a/src/python/gudhi/off_utils.pyx +++ b/src/python/gudhi/off_utils.pyx @@ -26,7 +26,7 @@ cdef extern from "Off_reader_interface.h" namespace "Gudhi": vector[vector[double]] read_points_from_OFF_file(string off_file) def read_points_from_off_file(off_file=''): - """Read points from OFF file. + """Read points from an `OFF file `_. :param off_file: An OFF file style name. :type off_file: string @@ -43,7 +43,7 @@ def read_points_from_off_file(off_file=''): @cython.embedsignature(True) def write_points_to_off_file(fname, points): - """Write points to an OFF file. + """Write points to an `OFF file `_. A simple wrapper for `numpy.savetxt`. -- cgit v1.2.3 From 2d5039b7eeb16116ab859076aa0a93f092250d88 Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Fri, 11 Nov 2022 18:59:42 +0100 Subject: Special case for writing 3d OFF --- src/python/CMakeLists.txt | 1 + src/python/gudhi/off_utils.pyx | 7 ++++++- src/python/test/test_off.py | 21 +++++++++++++++++++++ 3 files changed, 28 insertions(+), 1 deletion(-) create mode 100644 src/python/test/test_off.py (limited to 'src') diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt index 35ddb778..32ec13bd 100644 --- a/src/python/CMakeLists.txt +++ b/src/python/CMakeLists.txt @@ -546,6 +546,7 @@ if(PYTHONINTERP_FOUND) # Reader utils add_gudhi_py_test(test_reader_utils) + add_gudhi_py_test(test_off) # Wasserstein if(OT_FOUND) diff --git a/src/python/gudhi/off_utils.pyx b/src/python/gudhi/off_utils.pyx index a8142791..9276c7b0 100644 --- a/src/python/gudhi/off_utils.pyx +++ b/src/python/gudhi/off_utils.pyx @@ -54,4 +54,9 @@ def write_points_to_off_file(fname, points): """ points = np.array(points, copy=False) assert len(points.shape) == 2 - np.savetxt(fname, points, header='nOFF\n{} {} 0 0'.format(points.shape[1], points.shape[0]), comments='') + dim = points.shape[1] + if dim == 3: + head = 'OFF\n{} 0 0'.format(points.shape[0]) + else: + head = 'nOFF\n{} {} 0 0'.format(dim, points.shape[0]) + np.savetxt(fname, points, header=head, comments='') diff --git a/src/python/test/test_off.py b/src/python/test/test_off.py new file mode 100644 index 00000000..69bfa1f9 --- /dev/null +++ b/src/python/test/test_off.py @@ -0,0 +1,21 @@ +""" 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): Marc Glisse + + Copyright (C) 2022 Inria + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +import gudhi as gd +import numpy as np +import pytest + + +def test_off_rw(): + for dim in range(2, 6): + X = np.random.rand(123, dim) + gd.write_points_to_off_file('rand.off', X) + Y = gd.read_points_from_off_file('rand.off') + assert Y == pytest.approx(X) -- cgit v1.2.3 From f4f930169fbf2db2707d69b334cfe5b941c64350 Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Fri, 11 Nov 2022 19:03:54 +0100 Subject: black --- src/python/test/test_off.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'src') diff --git a/src/python/test/test_off.py b/src/python/test/test_off.py index 69bfa1f9..aea1941b 100644 --- a/src/python/test/test_off.py +++ b/src/python/test/test_off.py @@ -16,6 +16,6 @@ import pytest def test_off_rw(): for dim in range(2, 6): X = np.random.rand(123, dim) - gd.write_points_to_off_file('rand.off', X) - Y = gd.read_points_from_off_file('rand.off') + gd.write_points_to_off_file("rand.off", X) + Y = gd.read_points_from_off_file("rand.off") assert Y == pytest.approx(X) -- cgit v1.2.3