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-rw-r--r--src/Nerve_GIC/doc/COPYRIGHT2
-rw-r--r--src/Nerve_GIC/doc/Intro_graph_induced_complex.h2
-rw-r--r--src/Nerve_GIC/example/CoordGIC.cpp5
-rw-r--r--src/Nerve_GIC/example/FuncGIC.cpp2
-rw-r--r--src/Nerve_GIC/include/gudhi/GIC.h60
-rw-r--r--src/Nerve_GIC/test/test_GIC.cpp2
-rwxr-xr-xsrc/Nerve_GIC/utilities/KeplerMapperVisuFromTxtFile.py4
-rw-r--r--src/Nerve_GIC/utilities/Nerve.cpp2
-rw-r--r--src/Nerve_GIC/utilities/VoronoiGIC.cpp2
-rw-r--r--src/Nerve_GIC/utilities/covercomplex.md3
10 files changed, 40 insertions, 44 deletions
diff --git a/src/Nerve_GIC/doc/COPYRIGHT b/src/Nerve_GIC/doc/COPYRIGHT
index 0c36a526..6b33053e 100644
--- a/src/Nerve_GIC/doc/COPYRIGHT
+++ b/src/Nerve_GIC/doc/COPYRIGHT
@@ -4,7 +4,7 @@ computational topology.
Author(s): Mathieu Carrière
-Copyright (C) 2017 INRIA
+Copyright (C) 2017 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
diff --git a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h
index 2b648425..bc8aecc3 100644
--- a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h
+++ b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h
@@ -4,7 +4,7 @@
*
* Author(s): Mathieu Carriere
*
- * Copyright (C) 2017 INRIA
+ * Copyright (C) 2017 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
diff --git a/src/Nerve_GIC/example/CoordGIC.cpp b/src/Nerve_GIC/example/CoordGIC.cpp
index c92cf235..73edae18 100644
--- a/src/Nerve_GIC/example/CoordGIC.cpp
+++ b/src/Nerve_GIC/example/CoordGIC.cpp
@@ -4,7 +4,7 @@
*
* Author(s): Mathieu Carrière
*
- * Copyright (C) 2017 INRIA
+ * Copyright (C) 2017 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
@@ -66,6 +66,9 @@ int main(int argc, char **argv) {
GIC.find_simplices();
+ GIC.compute_distribution(10);
+ GIC.compute_p_value();
+
GIC.plot_DOT();
Gudhi::Simplex_tree<> stree;
diff --git a/src/Nerve_GIC/example/FuncGIC.cpp b/src/Nerve_GIC/example/FuncGIC.cpp
index cb0f0d63..1f5de999 100644
--- a/src/Nerve_GIC/example/FuncGIC.cpp
+++ b/src/Nerve_GIC/example/FuncGIC.cpp
@@ -4,7 +4,7 @@
*
* Author(s): Mathieu Carrière
*
- * Copyright (C) 2017 INRIA
+ * Copyright (C) 2017 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
diff --git a/src/Nerve_GIC/include/gudhi/GIC.h b/src/Nerve_GIC/include/gudhi/GIC.h
index f5b67be6..aa6478e5 100644
--- a/src/Nerve_GIC/include/gudhi/GIC.h
+++ b/src/Nerve_GIC/include/gudhi/GIC.h
@@ -4,7 +4,7 @@
*
* Author: Mathieu Carriere
*
- * Copyright (C) 2017 INRIA
+ * Copyright (C) 2017 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
@@ -142,18 +142,6 @@ class Cover_complex {
std::string point_cloud_name;
std::string color_name;
- // Point comparator
- struct Less {
- Less(std::vector<double> func) { Fct = func; }
- std::vector<double> Fct;
- bool operator()(int a, int b) {
- if (Fct[a] == Fct[b])
- return a < b;
- else
- return Fct[a] < Fct[b];
- }
- };
-
// Remove all edges of a graph.
void remove_edges(Graph& G) {
boost::graph_traits<Graph>::edge_iterator ei, ei_end;
@@ -280,7 +268,7 @@ class Cover_complex {
point_cloud.emplace_back(point.begin(), point.begin() + data_dimension);
boost::add_vertex(one_skeleton_OFF);
vertices.push_back(boost::add_vertex(one_skeleton));
- std::vector<int> dummy; dummy.clear(); cover.push_back(dummy);
+ cover.emplace_back();
i++;
}
}
@@ -671,7 +659,7 @@ class Cover_complex {
// Sort points according to function values
std::vector<int> points(n);
for (int i = 0; i < n; i++) points[i] = i;
- std::sort(points.begin(), points.end(), Less(this->func));
+ std::sort(points.begin(), points.end(), [=](const int & p1, const int & p2){return (this->func[p1] < this->func[p2]);});
int id = 0;
int pos = 0;
@@ -1158,22 +1146,25 @@ class Cover_complex {
* @param[in] N number of bootstrap iterations.
*
*/
- template <typename SimplicialComplex>
- void compute_distribution(int N = 100) {
- if (distribution.size() >= N) {
+ void compute_distribution(unsigned int N = 100) {
+ unsigned int sz = distribution.size();
+ if (sz >= N) {
std::cout << "Already done!" << std::endl;
} else {
- for (int i = 0; i < N - distribution.size(); i++) {
- Cover_complex Cboot;
- Cboot.n = this->n;
+ for (unsigned int i = 0; i < N - sz; i++) {
+ if (verbose) std::cout << "Computing " << i << "th bootstrap, bottleneck distance = ";
+
+ Cover_complex Cboot; Cboot.n = this->n; Cboot.data_dimension = this->data_dimension; Cboot.type = this->type; Cboot.functional_cover = true;
+
std::vector<int> boot(this->n);
for (int j = 0; j < this->n; j++) {
double u = GetUniform();
- int id = std::floor(u * (this->n));
- boot[j] = id;
- Cboot.point_cloud[j] = this->point_cloud[id];
- Cboot.func.emplace(j, this->func[id]);
+ int id = std::floor(u * (this->n)); boot[j] = id;
+ Cboot.point_cloud.push_back(this->point_cloud[id]); Cboot.cover.emplace_back(); Cboot.func.push_back(this->func[id]);
+ boost::add_vertex(Cboot.one_skeleton_OFF); Cboot.vertices.push_back(boost::add_vertex(Cboot.one_skeleton));
}
+ Cboot.set_color_from_vector(Cboot.func);
+
for (int j = 0; j < n; j++) {
std::vector<double> dist(n);
for (int k = 0; k < n; k++) dist[k] = distances[boot[j]][boot[k]];
@@ -1186,8 +1177,9 @@ class Cover_complex {
Cboot.set_cover_from_function();
Cboot.find_simplices();
Cboot.compute_PD();
-
- distribution.push_back(Gudhi::persistence_diagram::bottleneck_distance(this->PD, Cboot.PD));
+ double db = Gudhi::persistence_diagram::bottleneck_distance(this->PD, Cboot.PD);
+ if (verbose) std::cout << db << std::endl;
+ distribution.push_back(db);
}
std::sort(distribution.begin(), distribution.end());
@@ -1201,7 +1193,7 @@ class Cover_complex {
*
*/
double compute_distance_from_confidence_level(double alpha) {
- int N = distribution.size();
+ unsigned int N = distribution.size();
return distribution[std::floor(alpha * N)];
}
@@ -1212,9 +1204,11 @@ class Cover_complex {
*
*/
double compute_confidence_level_from_distance(double d) {
- int N = distribution.size();
- for (int i = 0; i < N; i++)
- if (distribution[i] > d) return i * 1.0 / N;
+ unsigned int N = distribution.size();
+ double level = 1;
+ for (unsigned int i = 0; i < N; i++)
+ if (distribution[i] > d){ level = i * 1.0 / N; break; }
+ return level;
}
public:
@@ -1226,7 +1220,9 @@ class Cover_complex {
double distancemin = -std::numeric_limits<double>::lowest();
int N = PD.size();
for (int i = 0; i < N; i++) distancemin = std::min(distancemin, 0.5 * (PD[i].second - PD[i].first));
- return 1 - compute_confidence_level_from_distance(distancemin);
+ double p_value = 1 - compute_confidence_level_from_distance(distancemin);
+ if (verbose) std::cout << "p value = " << p_value << std::endl;
+ return p_value;
}
// *******************************************************************************************************************
diff --git a/src/Nerve_GIC/test/test_GIC.cpp b/src/Nerve_GIC/test/test_GIC.cpp
index e3067d35..0db2cce2 100644
--- a/src/Nerve_GIC/test/test_GIC.cpp
+++ b/src/Nerve_GIC/test/test_GIC.cpp
@@ -4,7 +4,7 @@
*
* Author(s): Mathieu Carrière
*
- * Copyright (C) 2017 INRIA
+ * Copyright (C) 2017 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
diff --git a/src/Nerve_GIC/utilities/KeplerMapperVisuFromTxtFile.py b/src/Nerve_GIC/utilities/KeplerMapperVisuFromTxtFile.py
index c811f610..701e7a52 100755
--- a/src/Nerve_GIC/utilities/KeplerMapperVisuFromTxtFile.py
+++ b/src/Nerve_GIC/utilities/KeplerMapperVisuFromTxtFile.py
@@ -11,7 +11,7 @@ import argparse
Author(s): Mathieu Carriere
- Copyright (C) 2017 INRIA
+ Copyright (C) 2017 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
@@ -28,7 +28,7 @@ import argparse
"""
__author__ = "Mathieu Carriere"
-__copyright__ = "Copyright (C) 2017 INRIA"
+__copyright__ = "Copyright (C) 2017 Inria"
__license__ = "GPL v3"
parser = argparse.ArgumentParser(description='Creates an html Keppler Mapper '
diff --git a/src/Nerve_GIC/utilities/Nerve.cpp b/src/Nerve_GIC/utilities/Nerve.cpp
index aefc3874..667129e0 100644
--- a/src/Nerve_GIC/utilities/Nerve.cpp
+++ b/src/Nerve_GIC/utilities/Nerve.cpp
@@ -4,7 +4,7 @@
*
* Author(s): Mathieu Carrière
*
- * Copyright (C) 2017 INRIA
+ * Copyright (C) 2017 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
diff --git a/src/Nerve_GIC/utilities/VoronoiGIC.cpp b/src/Nerve_GIC/utilities/VoronoiGIC.cpp
index 54bb871e..33deca40 100644
--- a/src/Nerve_GIC/utilities/VoronoiGIC.cpp
+++ b/src/Nerve_GIC/utilities/VoronoiGIC.cpp
@@ -4,7 +4,7 @@
*
* Author(s): Mathieu Carrière
*
- * Copyright (C) 2017 INRIA
+ * Copyright (C) 2017 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
diff --git a/src/Nerve_GIC/utilities/covercomplex.md b/src/Nerve_GIC/utilities/covercomplex.md
index 6d16d16f..683c1b75 100644
--- a/src/Nerve_GIC/utilities/covercomplex.md
+++ b/src/Nerve_GIC/utilities/covercomplex.md
@@ -10,9 +10,6 @@ Leave the lines above as it is required by the web site generator 'Jekyll'
{:/comment}
-# Cover complex #
-
-
## Nerve ##
This program builds the Nerve of a point cloud sampled on an OFF file.
The cover C comes from the preimages of intervals covering a coordinate function,
generated by cgit v1.2.3 (git 2.39.1) at 2024-07-03 09:10:43 +0000