From 0c47b28201093851140ab499331017ef42312ce7 Mon Sep 17 00:00:00 2001 From: yuichi-ike Date: Thu, 21 May 2020 11:02:00 +0900 Subject: DTM Rips added (straightforward way) --- src/python/CMakeLists.txt | 10 ++++- src/python/doc/rips_complex_ref.rst | 13 ++++++ src/python/doc/rips_complex_sum.inc | 3 ++ src/python/doc/rips_complex_user.rst | 20 +++++++++ src/python/gudhi/dtm_rips_complex.py | 46 +++++++++++++++++++ src/python/test/test_dtm_rips_complex.py | 40 +++++++++++++++++ src/python/test/test_weighted_rips.py | 63 --------------------------- src/python/test/test_weighted_rips_complex.py | 63 +++++++++++++++++++++++++++ 8 files changed, 194 insertions(+), 64 deletions(-) create mode 100644 src/python/gudhi/dtm_rips_complex.py create mode 100644 src/python/test/test_dtm_rips_complex.py delete mode 100644 src/python/test/test_weighted_rips.py create mode 100644 src/python/test/test_weighted_rips_complex.py (limited to 'src/python') diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt index ab08cd6d..96dd3f6f 100644 --- a/src/python/CMakeLists.txt +++ b/src/python/CMakeLists.txt @@ -58,6 +58,7 @@ if(PYTHONINTERP_FOUND) set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'wasserstein', ") set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'point_cloud', ") set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'weighted_rips_complex', ") + set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'dtm_rips_complex', ") add_gudhi_debug_info("Python version ${PYTHON_VERSION_STRING}") add_gudhi_debug_info("Cython version ${CYTHON_VERSION}") @@ -234,6 +235,7 @@ if(PYTHONINTERP_FOUND) file(COPY "gudhi/wasserstein" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi") file(COPY "gudhi/point_cloud" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi") file(COPY "gudhi/weighted_rips_complex.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi") + file(COPY "gudhi/dtm_rips_complex.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi") add_custom_command( OUTPUT gudhi.so @@ -492,9 +494,15 @@ if(PYTHONINTERP_FOUND) # Weighted Rips if(SCIPY_FOUND) - add_gudhi_py_test(test_weighted_rips) + add_gudhi_py_test(test_weighted_rips_complex) endif() + # DTM Rips + if(SCIPY_FOUND) + add_gudhi_py_test(test_dtm_rips_complex) + endif() + + # Set missing or not modules set(GUDHI_MODULES ${GUDHI_MODULES} "python" CACHE INTERNAL "GUDHI_MODULES") else(CYTHON_FOUND) diff --git a/src/python/doc/rips_complex_ref.rst b/src/python/doc/rips_complex_ref.rst index 5f3e46c1..f781fd92 100644 --- a/src/python/doc/rips_complex_ref.rst +++ b/src/python/doc/rips_complex_ref.rst @@ -25,3 +25,16 @@ Weighted Rips complex reference manual :show-inheritance: .. automethod:: gudhi.weighted_rips_complex.WeightedRipsComplex.__init__ + +.. _dtm-rips-complex-reference-manual: + +================================= +DTM Rips complex reference manual +================================= + +.. autoclass:: gudhi.dtm_rips_complex.DtmRipsComplex + :members: + :undoc-members: + :show-inheritance: + + .. automethod:: gudhi.dtm_rips_complex.DtmRipsComplex.__init__ \ No newline at end of file diff --git a/src/python/doc/rips_complex_sum.inc b/src/python/doc/rips_complex_sum.inc index f7580714..9cd8074b 100644 --- a/src/python/doc/rips_complex_sum.inc +++ b/src/python/doc/rips_complex_sum.inc @@ -14,6 +14,9 @@ | | | | | | Weighted Rips complex constructs a simplicial complex from a distance | | | | matrix and weights on vertices. | | + | | | | + | | DTM Rips complex builds a simplicial complex from a point set or | | + | | a distance matrix. | | +----------------------------------------------------------------+------------------------------------------------------------------------+----------------------------------------------------------------------+ | * :doc:`rips_complex_user` | * :doc:`rips_complex_ref` | +----------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------+ diff --git a/src/python/doc/rips_complex_user.rst b/src/python/doc/rips_complex_user.rst index 819568be..eb2657df 100644 --- a/src/python/doc/rips_complex_user.rst +++ b/src/python/doc/rips_complex_user.rst @@ -398,3 +398,23 @@ The output is: .. testoutput:: [(0, (3.1622776601683795, inf)), (0, (3.1622776601683795, 5.39834563766817)), (0, (3.1622776601683795, 5.39834563766817))] + +DTM Rips Complex +---------------- + +`DtmdRipsComplex `_ builds a simplicial complex from a point set or a full distence matrix (in the form of ndarray), as described in the above example. + +.. testcode:: + + import numpy as np + from dtm_rips_complex import DtmRipsComplex + pts = np.array([[2.0, 2.0], [0.0, 1.0], [3.0, 4.0]]) + dtm_rips = DtmRipsComplex(points=pts, k=2) + st = dtm_rips.create_simplex_tree(max_dimension=2) + print(st.persistence()) + +The output is: + +.. testoutput:: + + [(0, (3.1622776601683795, inf)), (0, (3.1622776601683795, 5.39834563766817)), (0, (3.1622776601683795, 5.39834563766817))] diff --git a/src/python/gudhi/dtm_rips_complex.py b/src/python/gudhi/dtm_rips_complex.py new file mode 100644 index 00000000..6d2f9f31 --- /dev/null +++ b/src/python/gudhi/dtm_rips_complex.py @@ -0,0 +1,46 @@ +# 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): Yuichi Ike, Raphaël Tinarrage +# +# Copyright (C) 2020 Inria, Copyright (C) 2020 FUjitsu Laboratories Ltd. +# +# Modification(s): +# - YYYY/MM Author: Description of the modification + + +from gudhi.weighted_rips_complex import WeightedRipsComplex +from gudhi.point_cloud.dtm import DistanceToMeasure +from scipy.spatial.distance import cdist + +class DtmRipsComplex(WeightedRipsComplex): + """ + Class to generate a DTM Rips complex from a distance matrix or a point set, + in the way described in :cite:`dtmfiltrations`. + Remark that all the filtration values are doubled compared to the definition in the paper + for the consistency with RipsComplex. + """ + def __init__(self, + points=None, + distance_matrix=None, + k=1, + q=2, + max_filtration=float('inf')): + """ + Args: + points (Sequence[Sequence[float]]): list of points. + distance_matrix (ndarray): full distance matrix. + k (int): number of neighbors for the computation of DTM. Defaults to 1, which is equivalent to the usual Rips complex. + q (float): order used to compute the distance to measure. Defaults to 2. + max_filtration (float): specifies the maximal filtration value to be considered. + """ + if distance_matrix is None: + if points is None: + # Empty Rips construction + points=[] + distance_matrix = cdist(points,points) + self.distance_matrix = distance_matrix + dtm = DistanceToMeasure(k, q=q, metric="precomputed") + # TODO: address the error when k is too large + self.weights = dtm.fit_transform(distance_matrix) + self.max_filtration = max_filtration + diff --git a/src/python/test/test_dtm_rips_complex.py b/src/python/test/test_dtm_rips_complex.py new file mode 100644 index 00000000..bc6e5a59 --- /dev/null +++ b/src/python/test/test_dtm_rips_complex.py @@ -0,0 +1,40 @@ +""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + Author(s): Yuichi Ike + + Copyright (C) 2020 Inria, Copyright (C) 2020 FUjitsu Laboratories Ltd. + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +from gudhi.dtm_rips_complex import DtmRipsComplex +import numpy as np +from math import sqrt +import pytest + +def test_dtm_rips_complex(): + pts = np.array([[2.0, 2.0], [0.0, 1.0], [3.0, 4.0]]) + dtm_rips = DtmRipsComplex(points=pts, k=2) + st = dtm_rips.create_simplex_tree(max_dimension=2) + st.persistence() + persistence_intervals0 = st.persistence_intervals_in_dimension(0) + assert persistence_intervals0 == pytest.approx(np.array([[3.16227766, 5.39834564],[3.16227766, 5.39834564], [3.16227766, float("inf")]])) + +def test_compatibility_with_rips(): + distance_matrix = np.array([[0, 1, 1, sqrt(2)], [1, 0, sqrt(2), 1], [1, sqrt(2), 0, 1], [sqrt(2), 1, 1, 0]]) + dtm_rips = DtmRipsComplex(distance_matrix=distance_matrix, max_filtration=42) + st = dtm_rips.create_simplex_tree(max_dimension=1) + assert list(st.get_filtration()) == [ + ([0], 0.0), + ([1], 0.0), + ([2], 0.0), + ([3], 0.0), + ([0, 1], 1.0), + ([0, 2], 1.0), + ([1, 3], 1.0), + ([2, 3], 1.0), + ([1, 2], sqrt(2)), + ([0, 3], sqrt(2)), + ] + diff --git a/src/python/test/test_weighted_rips.py b/src/python/test/test_weighted_rips.py deleted file mode 100644 index 7ef48333..00000000 --- a/src/python/test/test_weighted_rips.py +++ /dev/null @@ -1,63 +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): Yuichi Ike and Masatoshi Takenouchi - - Copyright (C) 2020 Inria - - Modification(s): - - YYYY/MM Author: Description of the modification -""" - -from gudhi.weighted_rips_complex import WeightedRipsComplex -from gudhi.point_cloud.dtm import DistanceToMeasure -import numpy as np -from math import sqrt -from scipy.spatial.distance import cdist -import pytest - -def test_non_dtm_rips_complex(): - dist = [[], [1]] - weights = [1, 100] - w_rips = WeightedRipsComplex(distance_matrix=dist, weights=weights) - st = w_rips.create_simplex_tree(max_dimension=2) - assert st.filtration([0,1]) == pytest.approx(200.0) - -def test_compatibility_with_rips(): - distance_matrix = [[0], [1, 0], [1, sqrt(2), 0], [sqrt(2), 1, 1, 0]] - w_rips = WeightedRipsComplex(distance_matrix=distance_matrix,max_filtration=42) - st = w_rips.create_simplex_tree(max_dimension=1) - assert list(st.get_filtration()) == [ - ([0], 0.0), - ([1], 0.0), - ([2], 0.0), - ([3], 0.0), - ([0, 1], 1.0), - ([0, 2], 1.0), - ([1, 3], 1.0), - ([2, 3], 1.0), - ([1, 2], sqrt(2)), - ([0, 3], sqrt(2)), - ] - -def test_compatibility_with_filtered_rips(): - distance_matrix = [[0], [1, 0], [1, sqrt(2), 0], [sqrt(2), 1, 1, 0]] - w_rips = WeightedRipsComplex(distance_matrix=distance_matrix,max_filtration=1.0) - st = w_rips.create_simplex_tree(max_dimension=1) - - assert st.__is_defined() == True - assert st.__is_persistence_defined() == False - - assert st.num_simplices() == 8 - assert st.num_vertices() == 4 - -def test_dtm_rips_complex(): - pts = np.array([[2.0, 2.0], [0.0, 1.0], [3.0, 4.0]]) - dist = cdist(pts,pts) - dtm = DistanceToMeasure(2, q=2, metric="precomputed") - r = dtm.fit_transform(dist) - w_rips = WeightedRipsComplex(distance_matrix=dist, weights=r) - st = w_rips.create_simplex_tree(max_dimension=2) - st.persistence() - persistence_intervals0 = st.persistence_intervals_in_dimension(0) - assert persistence_intervals0 == pytest.approx(np.array([[3.16227766, 5.39834564],[3.16227766, 5.39834564], [3.16227766, float("inf")]])) - diff --git a/src/python/test/test_weighted_rips_complex.py b/src/python/test/test_weighted_rips_complex.py new file mode 100644 index 00000000..7ef48333 --- /dev/null +++ b/src/python/test/test_weighted_rips_complex.py @@ -0,0 +1,63 @@ +""" 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): Yuichi Ike and Masatoshi Takenouchi + + Copyright (C) 2020 Inria + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +from gudhi.weighted_rips_complex import WeightedRipsComplex +from gudhi.point_cloud.dtm import DistanceToMeasure +import numpy as np +from math import sqrt +from scipy.spatial.distance import cdist +import pytest + +def test_non_dtm_rips_complex(): + dist = [[], [1]] + weights = [1, 100] + w_rips = WeightedRipsComplex(distance_matrix=dist, weights=weights) + st = w_rips.create_simplex_tree(max_dimension=2) + assert st.filtration([0,1]) == pytest.approx(200.0) + +def test_compatibility_with_rips(): + distance_matrix = [[0], [1, 0], [1, sqrt(2), 0], [sqrt(2), 1, 1, 0]] + w_rips = WeightedRipsComplex(distance_matrix=distance_matrix,max_filtration=42) + st = w_rips.create_simplex_tree(max_dimension=1) + assert list(st.get_filtration()) == [ + ([0], 0.0), + ([1], 0.0), + ([2], 0.0), + ([3], 0.0), + ([0, 1], 1.0), + ([0, 2], 1.0), + ([1, 3], 1.0), + ([2, 3], 1.0), + ([1, 2], sqrt(2)), + ([0, 3], sqrt(2)), + ] + +def test_compatibility_with_filtered_rips(): + distance_matrix = [[0], [1, 0], [1, sqrt(2), 0], [sqrt(2), 1, 1, 0]] + w_rips = WeightedRipsComplex(distance_matrix=distance_matrix,max_filtration=1.0) + st = w_rips.create_simplex_tree(max_dimension=1) + + assert st.__is_defined() == True + assert st.__is_persistence_defined() == False + + assert st.num_simplices() == 8 + assert st.num_vertices() == 4 + +def test_dtm_rips_complex(): + pts = np.array([[2.0, 2.0], [0.0, 1.0], [3.0, 4.0]]) + dist = cdist(pts,pts) + dtm = DistanceToMeasure(2, q=2, metric="precomputed") + r = dtm.fit_transform(dist) + w_rips = WeightedRipsComplex(distance_matrix=dist, weights=r) + st = w_rips.create_simplex_tree(max_dimension=2) + st.persistence() + persistence_intervals0 = st.persistence_intervals_in_dimension(0) + assert persistence_intervals0 == pytest.approx(np.array([[3.16227766, 5.39834564],[3.16227766, 5.39834564], [3.16227766, float("inf")]])) + -- cgit v1.2.3