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-rw-r--r--src/cython/CMakeLists.txt2
-rw-r--r--src/cython/cython/alpha_complex.pyx2
-rw-r--r--src/cython/cython/subsampling.pyx40
-rw-r--r--src/cython/include/Subsampling_interface.h22
-rwxr-xr-xsrc/cython/test/test_subsampling.py94
5 files changed, 155 insertions, 5 deletions
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index c2026682..998908e7 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -47,7 +47,7 @@ if(PYTHON_PATH AND CYTHON_PATH)
file(COPY include DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
file(COPY cython DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
file(COPY test DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
-
+
if (CGAL_FOUND)
if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
# If CGAL_VERSION >= 4.8.1, include subsampling
diff --git a/src/cython/cython/alpha_complex.pyx b/src/cython/cython/alpha_complex.pyx
index 56cf925c..6b27594a 100644
--- a/src/cython/cython/alpha_complex.pyx
+++ b/src/cython/cython/alpha_complex.pyx
@@ -62,7 +62,7 @@ cdef class AlphaComplex:
cdef Alpha_complex_interface * thisptr
# Fake constructor that does nothing but documenting the constructor
- def __init__(self, points=None, off_file=''):
+ def __init__(self, points=[], off_file=''):
"""AlphaComplex constructor.
:param points: A list of points in d-Dimension.
diff --git a/src/cython/cython/subsampling.pyx b/src/cython/cython/subsampling.pyx
index e59e0c6a..5ca38099 100644
--- a/src/cython/cython/subsampling.pyx
+++ b/src/cython/cython/subsampling.pyx
@@ -32,6 +32,42 @@ __license__ = "GPL v3"
cdef extern from "Subsampling_interface.h" namespace "Gudhi::subsampling":
vector[vector[double]] subsampling_n_farthest_points(vector[vector[double]] points, unsigned nb_points)
+ vector[vector[double]] subsampling_n_farthest_points(vector[vector[double]] points, unsigned nb_points, unsigned starting_point)
+ vector[vector[double]] subsampling_n_farthest_points_from_file(string off_file, unsigned nb_points)
+ vector[vector[double]] subsampling_n_farthest_points_from_file(string off_file, unsigned nb_points, unsigned starting_point)
-def choose_n_farthest_points(points, nb_points):
- subsampling_n_farthest_points(points, nb_points)
+def choose_n_farthest_points(points=[], off_file='', nb_points=0, starting_point = ''):
+ """Subsample by a greedy strategy of iteratively adding the farthest point
+ from the current chosen point set to the subsampling.
+ The iteration starts with the landmark `starting point`.
+
+ :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 nb_points: Number of points of the subsample.
+ :type nb_points: unsigned.
+ :param starting_point: The iteration starts with the landmark `starting \
+ 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.
+ :rtype: vector[vector[double]]
+ """
+ if off_file is not '':
+ if os.path.isfile(off_file):
+ if starting_point is '':
+ return subsampling_n_farthest_points_from_file(off_file, nb_points)
+ else:
+ return subsampling_n_farthest_points_from_file(off_file, nb_points, starting_point)
+ else:
+ print("file " + off_file + " not found.")
+ else:
+ if starting_point is '':
+ return subsampling_n_farthest_points(points, nb_points)
+ else:
+ return subsampling_n_farthest_points(points, nb_points, starting_point)
diff --git a/src/cython/include/Subsampling_interface.h b/src/cython/include/Subsampling_interface.h
index bd37a015..12c48012 100644
--- a/src/cython/include/Subsampling_interface.h
+++ b/src/cython/include/Subsampling_interface.h
@@ -45,12 +45,32 @@ std::vector<std::vector<double>> subsampling_n_farthest_points(std::vector<std::
std::vector<std::vector<double>> landmarks;
Subsampling_dynamic_kernel k;
choose_n_farthest_points(k, points, nb_points, std::back_inserter(landmarks));
- std::cout << "output " << landmarks.size() << std::endl;
+ return landmarks;
+}
+
+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));
return landmarks;
}
+std::vector<std::vector<double>> subsampling_n_farthest_points_from_file(std::string& off_file, unsigned nb_points) {
+ Gudhi::Points_off_reader<std::vector<double>> off_reader(off_file);
+ std::vector<std::vector<double>> points = off_reader.get_point_cloud();
+ return subsampling_n_farthest_points(points, nb_points);
+}
+
+std::vector<std::vector<double>> subsampling_n_farthest_points_from_file(std::string& off_file, unsigned nb_points, unsigned starting_point) {
+ Gudhi::Points_off_reader<std::vector<double>> off_reader(off_file);
+ std::vector<std::vector<double>> points = off_reader.get_point_cloud();
+ return subsampling_n_farthest_points(points, nb_points, starting_point);
+}
} // namespace subsampling
} // namespace Gudhi
diff --git a/src/cython/test/test_subsampling.py b/src/cython/test/test_subsampling.py
new file mode 100755
index 00000000..e5f2d70a
--- /dev/null
+++ b/src/cython/test/test_subsampling.py
@@ -0,0 +1,94 @@
+import gudhi
+import os
+
+"""This file is part of the Gudhi Library. The Gudhi library
+ (Geometric Understanding in Higher Dimensions) is a generic C++
+ library for computational topology.
+
+ Author(s): Vincent Rouvreau
+
+ Copyright (C) 2016 INRIA
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+
+def test_write_off_file_for_tests():
+ file = open("n_farthest.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()
+
+def test_simple_choose_n_farthest_points_with_a_starting_point():
+ point_set = [[0,1], [0,0], [1,0], [1,1]]
+ 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)
+ 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)
+ assert sub_set[1] == point_set[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)
+ assert sub_set[1] == point_set[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) == []
+
+ print(os.getcwd())
+ # From off file test
+ for i in range (0, 7):
+ assert len(gudhi.choose_n_farthest_points(off_file = 'n_farthest.off', nb_points = i, starting_point = i)) == i
+
+def test_simple_choose_n_farthest_points_randomed():
+ point_set = [[0,1], [0,0], [1,0], [1,1]]
+
+ # Test the limits
+ assert gudhi.choose_n_farthest_points(points = [], nb_points = 0) == []
+ assert gudhi.choose_n_farthest_points(points = [], nb_points = 1) == []
+ assert gudhi.choose_n_farthest_points(points = point_set, nb_points = 0) == []
+ # Go furter than point set on purpose
+ for iter in range(1,10):
+ sub_set = gudhi.choose_n_farthest_points(points = point_set, nb_points = iter)
+ for sub in sub_set:
+ found = False
+ for point in point_set:
+ if point == sub:
+ found = True
+ assert found == True
+
+ print(os.getcwd())
+ # From off file test
+ for i in range (0, 7):
+ assert len(gudhi.choose_n_farthest_points(off_file = 'n_farthest.off', nb_points = i)) == i
generated by cgit v1.2.3 (git 2.39.1) at 2024-05-23 04:59:21 +0000