diff options
author | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2016-12-03 14:46:37 +0000 |
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committer | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2016-12-03 14:46:37 +0000 |
commit | 0c85e54d44a95aa7aff3f6d51a587287ce4a88d6 (patch) | |
tree | f0f5e815ba819f710757551765a8fce95d286bb8 /src | |
parent | 9a3373a0db722c75994826d44b4cfbe1b7b5aeb0 (diff) |
sparsify point set cythonization
unitary tested
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@1816 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: 170f14ffcf009ebe1169df90a4e088441eaad13f
Diffstat (limited to 'src')
-rw-r--r-- | src/cython/cython/subsampling.pyx | 30 | ||||
-rw-r--r-- | src/cython/include/Subsampling_interface.h | 31 | ||||
-rwxr-xr-x | src/cython/test/test_subsampling.py | 22 |
3 files changed, 72 insertions, 11 deletions
diff --git a/src/cython/cython/subsampling.pyx b/src/cython/cython/subsampling.pyx index c71f5810..05c0232f 100644 --- a/src/cython/cython/subsampling.pyx +++ b/src/cython/cython/subsampling.pyx @@ -37,6 +37,8 @@ cdef extern from "Subsampling_interface.h" namespace "Gudhi::subsampling": vector[vector[double]] subsampling_n_farthest_points_from_file(string off_file, unsigned nb_points, unsigned starting_point) vector[vector[double]] subsampling_n_random_points(vector[vector[double]] points, unsigned nb_points) vector[vector[double]] subsampling_n_random_points_from_file(string off_file, unsigned nb_points) + vector[vector[double]] subsampling_sparsify_points(vector[vector[double]] points, double min_squared_dist) + vector[vector[double]] subsampling_sparsify_points_from_file(string off_file, double min_squared_dist) def choose_n_farthest_points(points=[], off_file='', nb_points=0, starting_point = ''): """Subsample by a greedy strategy of iteratively adding the farthest point @@ -57,7 +59,7 @@ def choose_n_farthest_points(points=[], off_file='', nb_points=0, starting_point point`,which is the index of the poit to start with. If not set, this \ index is choosen randomly. :type starting_point: unsigned. - :returns: The subsamplepoint set. + :returns: The subsample point set. :rtype: vector[vector[double]] """ if off_file is not '': @@ -87,7 +89,7 @@ def pick_n_random_points(points=[], off_file='', nb_points=0): :param nb_points: Number of points of the subsample. :type nb_points: unsigned. - :returns: The subsamplepoint set. + :returns: The subsample point set. :rtype: vector[vector[double]] """ if off_file is not '': @@ -97,3 +99,27 @@ def pick_n_random_points(points=[], off_file='', nb_points=0): print("file " + off_file + " not found.") else: return subsampling_n_random_points(points, nb_points) + +def sparsify_point_set(points=[], off_file='', min_squared_dist=0.0): + """Subsample a point set by picking random vertices. + + :param points: The input point set. + :type points: vector[vector[double]]. + + Or + + :param off_file: An OFF file style name. + :type off_file: string + + :param min_squared_dist: Number of points of the subsample. + :type min_squared_dist: unsigned. + :returns: The subsample point set. + :rtype: vector[vector[double]] + """ + if off_file is not '': + if os.path.isfile(off_file): + return subsampling_sparsify_points_from_file(off_file, min_squared_dist) + else: + print("file " + off_file + " not found.") + else: + return subsampling_sparsify_points(points, min_squared_dist) diff --git a/src/cython/include/Subsampling_interface.h b/src/cython/include/Subsampling_interface.h index 8ef4fea1..9340cd86 100644 --- a/src/cython/include/Subsampling_interface.h +++ b/src/cython/include/Subsampling_interface.h @@ -24,6 +24,8 @@ #define SUBSAMPLING_INTERFACE_H #include <gudhi/choose_n_farthest_points.h> +#include <gudhi/pick_n_random_points.h> +#include <gudhi/sparsify_point_set.h> #include <gudhi/Points_off_io.h> #include <CGAL/Epick_d.h> @@ -40,9 +42,6 @@ using Subsampling_ft = Subsampling_dynamic_kernel::FT; // ------ choose_n_farthest_points ------ std::vector<std::vector<double>> subsampling_n_farthest_points(std::vector<std::vector<double>>& points, unsigned nb_points) { - std::vector<Subsampling_point_d> input, output; - for (auto point : points) - input.push_back(Subsampling_point_d(point.size(), point.begin(), point.end())); std::vector<std::vector<double>> landmarks; Subsampling_dynamic_kernel k; choose_n_farthest_points(k, points, nb_points, std::back_inserter(landmarks)); @@ -51,9 +50,6 @@ std::vector<std::vector<double>> subsampling_n_farthest_points(std::vector<std:: } std::vector<std::vector<double>> subsampling_n_farthest_points(std::vector<std::vector<double>>& points, unsigned nb_points, unsigned starting_point) { - std::vector<Subsampling_point_d> input, output; - for (auto point : points) - input.push_back(Subsampling_point_d(point.size(), point.begin(), point.end())); std::vector<std::vector<double>> landmarks; Subsampling_dynamic_kernel k; choose_n_farthest_points(k, points, nb_points, starting_point, std::back_inserter(landmarks)); @@ -75,9 +71,6 @@ std::vector<std::vector<double>> subsampling_n_farthest_points_from_file(std::st // ------ pick_n_random_points ------ std::vector<std::vector<double>> subsampling_n_random_points(std::vector<std::vector<double>>& points, unsigned nb_points) { - std::vector<Subsampling_point_d> input, output; - for (auto point : points) - input.push_back(Subsampling_point_d(point.size(), point.begin(), point.end())); std::vector<std::vector<double>> landmarks; pick_n_random_points(points, nb_points, std::back_inserter(landmarks)); @@ -90,6 +83,26 @@ std::vector<std::vector<double>> subsampling_n_random_points_from_file(std::stri return subsampling_n_random_points(points, nb_points); } +// ------ sparsify_point_set ------ +std::vector<std::vector<double>> subsampling_sparsify_points(std::vector<std::vector<double>>& points, double min_squared_dist) { + std::vector<Subsampling_point_d> input, output; + for (auto point : points) + input.push_back(Subsampling_point_d(point.size(), point.begin(), point.end())); + Subsampling_dynamic_kernel k; + sparsify_point_set(k, input, min_squared_dist, std::back_inserter(output)); + + std::vector<std::vector<double>> landmarks; + for (auto point : output) + landmarks.push_back(std::vector<double>(point.cartesian_begin(), point.cartesian_end())); + return landmarks; +} + +std::vector<std::vector<double>> subsampling_sparsify_points_from_file(std::string& off_file, double min_squared_dist) { + Gudhi::Points_off_reader<std::vector<double>> off_reader(off_file); + std::vector<std::vector<double>> points = off_reader.get_point_cloud(); + return subsampling_sparsify_points(points, min_squared_dist); +} + } // namespace subsampling diff --git a/src/cython/test/test_subsampling.py b/src/cython/test/test_subsampling.py index 2dc12a89..2caf4ddb 100755 --- a/src/cython/test/test_subsampling.py +++ b/src/cython/test/test_subsampling.py @@ -109,3 +109,25 @@ def test_simple_pick_n_random_points(): found = True # Check each sub set point is existing in the point set assert found == True + + # 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 + +def test_simple_sparsify_points(): + point_set = [[0,1], [0,0], [1,0], [1,1]] + # Test the limits + # assert gudhi.sparsify_point_set(points = [], min_squared_dist = 0.0) == [] + # assert gudhi.sparsify_point_set(points = [], min_squared_dist = 10.0) == [] + assert gudhi.sparsify_point_set(points = point_set, min_squared_dist = 0.0) == point_set + assert gudhi.sparsify_point_set(points = point_set, min_squared_dist = 1.0) == point_set + assert gudhi.sparsify_point_set(points = point_set, min_squared_dist = 2.0) == [[0,1], [1,0]] + assert gudhi.sparsify_point_set(points = point_set, min_squared_dist = 2.01) == [[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 = 40.0)) == 4 + assert len(gudhi.sparsify_point_set(off_file = 'subsample.off', min_squared_dist = 90.0)) == 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 = 325.0)) == 2 + assert len(gudhi.sparsify_point_set(off_file = 'subsample.off', min_squared_dist = 325.01)) == 1 |