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-rw-r--r--src/Rips_complex/doc/Intro_rips_complex.h2
-rw-r--r--src/Rips_complex/test/test_rips_complex.cpp25
-rw-r--r--src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp61
-rw-r--r--src/Rips_complex/utilities/rips_persistence.cpp60
-rw-r--r--src/Rips_complex/utilities/ripscomplex.md (renamed from src/Rips_complex/utilities/README)55
5 files changed, 75 insertions, 128 deletions
diff --git a/src/Rips_complex/doc/Intro_rips_complex.h b/src/Rips_complex/doc/Intro_rips_complex.h
index 124dfec9..8c517516 100644
--- a/src/Rips_complex/doc/Intro_rips_complex.h
+++ b/src/Rips_complex/doc/Intro_rips_complex.h
@@ -146,8 +146,6 @@ namespace rips_complex {
*
* \include Rips_complex/full_skeleton_rips_for_doc.txt
*
- * \copyright GNU General Public License v3.
- * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
*/
/** @} */ // end defgroup rips_complex
diff --git a/src/Rips_complex/test/test_rips_complex.cpp b/src/Rips_complex/test/test_rips_complex.cpp
index fc83f5f7..89afbc25 100644
--- a/src/Rips_complex/test/test_rips_complex.cpp
+++ b/src/Rips_complex/test/test_rips_complex.cpp
@@ -36,6 +36,7 @@
#include <gudhi/Simplex_tree.h>
#include <gudhi/distance_functions.h>
#include <gudhi/reader_utils.h>
+#include <gudhi/Unitary_tests_utils.h>
// Type definitions
using Point = std::vector<double>;
@@ -44,10 +45,6 @@ using Filtration_value = Simplex_tree::Filtration_value;
using Rips_complex = Gudhi::rips_complex::Rips_complex<Simplex_tree::Filtration_value>;
using Distance_matrix = std::vector<std::vector<Filtration_value>>;
-bool are_almost_the_same(float a, float b) {
- return std::fabs(a - b) < std::numeric_limits<float>::epsilon();
-}
-
BOOST_AUTO_TEST_CASE(RIPS_DOC_OFF_file) {
// ----------------------------------------------------------------------------
//
@@ -92,7 +89,7 @@ BOOST_AUTO_TEST_CASE(RIPS_DOC_OFF_file) {
std::cout << ") - distance =" << Gudhi::Euclidean_distance()(vp.at(0), vp.at(1)) <<
" - filtration =" << st.filtration(f_simplex) << std::endl;
BOOST_CHECK(vp.size() == 2);
- BOOST_CHECK(are_almost_the_same(st.filtration(f_simplex), Gudhi::Euclidean_distance()(vp.at(0), vp.at(1))));
+ GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), Gudhi::Euclidean_distance()(vp.at(0), vp.at(1)));
}
}
@@ -113,14 +110,14 @@ BOOST_AUTO_TEST_CASE(RIPS_DOC_OFF_file) {
Simplex_tree::Filtration_value f12 = st2.filtration(st2.find({1, 2}));
Simplex_tree::Filtration_value f012 = st2.filtration(st2.find({0, 1, 2}));
std::cout << "f012= " << f012 << " | f01= " << f01 << " - f02= " << f02 << " - f12= " << f12 << std::endl;
- BOOST_CHECK(are_almost_the_same(f012, std::max(f01, std::max(f02,f12))));
+ GUDHI_TEST_FLOAT_EQUALITY_CHECK(f012, std::max(f01, std::max(f02,f12)));
Simplex_tree::Filtration_value f45 = st2.filtration(st2.find({4, 5}));
Simplex_tree::Filtration_value f56 = st2.filtration(st2.find({5, 6}));
Simplex_tree::Filtration_value f46 = st2.filtration(st2.find({4, 6}));
Simplex_tree::Filtration_value f456 = st2.filtration(st2.find({4, 5, 6}));
std::cout << "f456= " << f456 << " | f45= " << f45 << " - f56= " << f56 << " - f46= " << f46 << std::endl;
- BOOST_CHECK(are_almost_the_same(f456, std::max(f45, std::max(f56,f46))));
+ GUDHI_TEST_FLOAT_EQUALITY_CHECK(f456, std::max(f45, std::max(f56,f46)));
const int DIMENSION_3 = 3;
Simplex_tree st3;
@@ -140,7 +137,7 @@ BOOST_AUTO_TEST_CASE(RIPS_DOC_OFF_file) {
Simplex_tree::Filtration_value f0123 = st3.filtration(st3.find({0, 1, 2, 3}));
std::cout << "f0123= " << f0123 << " | f012= " << f012 << " - f123= " << f123 << " - f013= " << f013 <<
" - f023= " << f023 << std::endl;
- BOOST_CHECK(are_almost_the_same(f0123, std::max(f012, std::max(f123, std::max(f013, f023)))));
+ GUDHI_TEST_FLOAT_EQUALITY_CHECK(f0123, std::max(f012, std::max(f123, std::max(f013, f023))));
}
@@ -219,12 +216,12 @@ BOOST_AUTO_TEST_CASE(Rips_complex_from_points) {
std::cout << "dimension(" << st.dimension(f_simplex) << ") - f = " << st.filtration(f_simplex) << std::endl;
switch (st.dimension(f_simplex)) {
case 0:
- BOOST_CHECK(are_almost_the_same(st.filtration(f_simplex), 0.0));
+ GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), 0.0);
break;
case 1:
case 2:
case 3:
- BOOST_CHECK(are_almost_the_same(st.filtration(f_simplex), 2.0));
+ GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), 2.0);
break;
default:
BOOST_CHECK(false); // Shall not happen
@@ -276,7 +273,7 @@ BOOST_AUTO_TEST_CASE(Rips_doc_csv_file) {
}
std::cout << ") - filtration =" << st.filtration(f_simplex) << std::endl;
BOOST_CHECK(vvh.size() == 2);
- BOOST_CHECK(are_almost_the_same(st.filtration(f_simplex), distances[vvh.at(0)][vvh.at(1)]));
+ GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), distances[vvh.at(0)][vvh.at(1)]);
}
}
@@ -297,14 +294,14 @@ BOOST_AUTO_TEST_CASE(Rips_doc_csv_file) {
Simplex_tree::Filtration_value f12 = st2.filtration(st2.find({1, 2}));
Simplex_tree::Filtration_value f012 = st2.filtration(st2.find({0, 1, 2}));
std::cout << "f012= " << f012 << " | f01= " << f01 << " - f02= " << f02 << " - f12= " << f12 << std::endl;
- BOOST_CHECK(are_almost_the_same(f012, std::max(f01, std::max(f02,f12))));
+ GUDHI_TEST_FLOAT_EQUALITY_CHECK(f012, std::max(f01, std::max(f02,f12)));
Simplex_tree::Filtration_value f45 = st2.filtration(st2.find({4, 5}));
Simplex_tree::Filtration_value f56 = st2.filtration(st2.find({5, 6}));
Simplex_tree::Filtration_value f46 = st2.filtration(st2.find({4, 6}));
Simplex_tree::Filtration_value f456 = st2.filtration(st2.find({4, 5, 6}));
std::cout << "f456= " << f456 << " | f45= " << f45 << " - f56= " << f56 << " - f46= " << f46 << std::endl;
- BOOST_CHECK(are_almost_the_same(f456, std::max(f45, std::max(f56,f46))));
+ GUDHI_TEST_FLOAT_EQUALITY_CHECK(f456, std::max(f45, std::max(f56,f46)));
const int DIMENSION_3 = 3;
Simplex_tree st3;
@@ -324,7 +321,7 @@ BOOST_AUTO_TEST_CASE(Rips_doc_csv_file) {
Simplex_tree::Filtration_value f0123 = st3.filtration(st3.find({0, 1, 2, 3}));
std::cout << "f0123= " << f0123 << " | f012= " << f012 << " - f123= " << f123 << " - f013= " << f013 <<
" - f023= " << f023 << std::endl;
- BOOST_CHECK(are_almost_the_same(f0123, std::max(f012, std::max(f123, std::max(f013, f023)))));
+ GUDHI_TEST_FLOAT_EQUALITY_CHECK(f0123, std::max(f012, std::max(f123, std::max(f013, f023))));
}
diff --git a/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp b/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp
index d38808c7..ca3c0327 100644
--- a/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp
+++ b/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp
@@ -1,5 +1,5 @@
-/* This file is part of the Gudhi Library. The Gudhi library
- * (Geometric Understanding in Higher Dimensions) is a generic C++
+/* 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): Pawel Dlotko, Vincent Rouvreau
@@ -36,18 +36,13 @@ using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persis
using Filtration_value = Simplex_tree::Filtration_value;
using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
-using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp >;
+using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp>;
using Distance_matrix = std::vector<std::vector<Filtration_value>>;
-void program_options(int argc, char * argv[]
- , std::string & csv_matrix_file
- , std::string & filediag
- , Filtration_value & threshold
- , int & dim_max
- , int & p
- , Filtration_value & min_persistence);
+void program_options(int argc, char* argv[], std::string& csv_matrix_file, std::string& filediag,
+ Filtration_value& threshold, int& dim_max, int& p, Filtration_value& min_persistence);
-int main(int argc, char * argv[]) {
+int main(int argc, char* argv[]) {
std::string csv_matrix_file;
std::string filediag;
Filtration_value threshold;
@@ -88,33 +83,28 @@ int main(int argc, char * argv[]) {
return 0;
}
-void program_options(int argc, char * argv[]
- , std::string & csv_matrix_file
- , std::string & filediag
- , Filtration_value & threshold
- , int & dim_max
- , int & p
- , Filtration_value & min_persistence) {
+void program_options(int argc, char* argv[], std::string& csv_matrix_file, std::string& filediag,
+ Filtration_value& threshold, int& dim_max, int& p, Filtration_value& min_persistence) {
namespace po = boost::program_options;
po::options_description hidden("Hidden options");
- hidden.add_options()
- ("input-file", po::value<std::string>(&csv_matrix_file),
- "Name of file containing a distance matrix. Can be square or lower triangular matrix. Separator is ';'.");
+ hidden.add_options()(
+ "input-file", po::value<std::string>(&csv_matrix_file),
+ "Name of file containing a distance matrix. Can be square or lower triangular matrix. Separator is ';'.");
po::options_description visible("Allowed options", 100);
- visible.add_options()
- ("help,h", "produce help message")
- ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
- "Name of file in which the persistence diagram is written. Default print in std::cout")
- ("max-edge-length,r",
- po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()),
- "Maximal length of an edge for the Rips complex construction.")
- ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
- "Maximal dimension of the Rips complex we want to compute.")
- ("field-charac,p", po::value<int>(&p)->default_value(11),
- "Characteristic p of the coefficient field Z/pZ for computing homology.")
- ("min-persistence,m", po::value<Filtration_value>(&min_persistence),
- "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals");
+ visible.add_options()("help,h", "produce help message")(
+ "output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
+ "Name of file in which the persistence diagram is written. Default print in std::cout")(
+ "max-edge-length,r",
+ po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()),
+ "Maximal length of an edge for the Rips complex construction.")(
+ "cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
+ "Maximal dimension of the Rips complex we want to compute.")(
+ "field-charac,p", po::value<int>(&p)->default_value(11),
+ "Characteristic p of the coefficient field Z/pZ for computing homology.")(
+ "min-persistence,m", po::value<Filtration_value>(&min_persistence),
+ "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length "
+ "intervals");
po::positional_options_description pos;
pos.add("input-file", 1);
@@ -123,8 +113,7 @@ void program_options(int argc, char * argv[]
all.add(visible).add(hidden);
po::variables_map vm;
- po::store(po::command_line_parser(argc, argv).
- options(all).positional(pos).run(), vm);
+ po::store(po::command_line_parser(argc, argv).options(all).positional(pos).run(), vm);
po::notify(vm);
if (vm.count("help") || !vm.count("input-file")) {
diff --git a/src/Rips_complex/utilities/rips_persistence.cpp b/src/Rips_complex/utilities/rips_persistence.cpp
index d504798b..8405c014 100644
--- a/src/Rips_complex/utilities/rips_persistence.cpp
+++ b/src/Rips_complex/utilities/rips_persistence.cpp
@@ -1,5 +1,5 @@
-/* This file is part of the Gudhi Library. The Gudhi library
- * (Geometric Understanding in Higher Dimensions) is a generic C++
+/* 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): Clément Maria
@@ -37,19 +37,14 @@ using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persis
using Filtration_value = Simplex_tree::Filtration_value;
using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
-using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp >;
+using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp>;
using Point = std::vector<double>;
using Points_off_reader = Gudhi::Points_off_reader<Point>;
-void program_options(int argc, char * argv[]
- , std::string & off_file_points
- , std::string & filediag
- , Filtration_value & threshold
- , int & dim_max
- , int & p
- , Filtration_value & min_persistence);
+void program_options(int argc, char* argv[], std::string& off_file_points, std::string& filediag,
+ Filtration_value& threshold, int& dim_max, int& p, Filtration_value& min_persistence);
-int main(int argc, char * argv[]) {
+int main(int argc, char* argv[]) {
std::string off_file_points;
std::string filediag;
Filtration_value threshold;
@@ -91,33 +86,27 @@ int main(int argc, char * argv[]) {
return 0;
}
-void program_options(int argc, char * argv[]
- , std::string & off_file_points
- , std::string & filediag
- , Filtration_value & threshold
- , int & dim_max
- , int & p
- , Filtration_value & min_persistence) {
+void program_options(int argc, char* argv[], std::string& off_file_points, std::string& filediag,
+ Filtration_value& threshold, int& dim_max, int& p, Filtration_value& min_persistence) {
namespace po = boost::program_options;
po::options_description hidden("Hidden options");
- hidden.add_options()
- ("input-file", po::value<std::string>(&off_file_points),
- "Name of an OFF file containing a point set.\n");
+ hidden.add_options()("input-file", po::value<std::string>(&off_file_points),
+ "Name of an OFF file containing a point set.\n");
po::options_description visible("Allowed options", 100);
- visible.add_options()
- ("help,h", "produce help message")
- ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
- "Name of file in which the persistence diagram is written. Default print in std::cout")
- ("max-edge-length,r",
- po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()),
- "Maximal length of an edge for the Rips complex construction.")
- ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
- "Maximal dimension of the Rips complex we want to compute.")
- ("field-charac,p", po::value<int>(&p)->default_value(11),
- "Characteristic p of the coefficient field Z/pZ for computing homology.")
- ("min-persistence,m", po::value<Filtration_value>(&min_persistence),
- "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals");
+ visible.add_options()("help,h", "produce help message")(
+ "output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
+ "Name of file in which the persistence diagram is written. Default print in std::cout")(
+ "max-edge-length,r",
+ po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()),
+ "Maximal length of an edge for the Rips complex construction.")(
+ "cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
+ "Maximal dimension of the Rips complex we want to compute.")(
+ "field-charac,p", po::value<int>(&p)->default_value(11),
+ "Characteristic p of the coefficient field Z/pZ for computing homology.")(
+ "min-persistence,m", po::value<Filtration_value>(&min_persistence),
+ "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length "
+ "intervals");
po::positional_options_description pos;
pos.add("input-file", 1);
@@ -126,8 +115,7 @@ void program_options(int argc, char * argv[]
all.add(visible).add(hidden);
po::variables_map vm;
- po::store(po::command_line_parser(argc, argv).
- options(all).positional(pos).run(), vm);
+ po::store(po::command_line_parser(argc, argv).options(all).positional(pos).run(), vm);
po::notify(vm);
if (vm.count("help") || !vm.count("input-file")) {
diff --git a/src/Rips_complex/utilities/README b/src/Rips_complex/utilities/ripscomplex.md
index 4d20c806..4291fae7 100644
--- a/src/Rips_complex/utilities/README
+++ b/src/Rips_complex/utilities/ripscomplex.md
@@ -1,13 +1,16 @@
-# Rips_complex #
-## `rips_persistence` ##
-This program computes the persistent homology with coefficient field *Z/pZ* of a Rips complex defined on a set of input points. The output diagram contains one bar per line, written with the convention:
+
+# Rips complex #
+
+## rips_persistence ##
+This program computes the persistent homology with coefficient field *Z/pZ* of a Rips complex defined on a set of input points, using Euclidean distance. The output diagram contains one bar per line, written with the convention:
`p dim birth death`
where `dim` is the dimension of the homological feature, `birth` and `death` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p` must be a prime number).
**Usage**
+
`rips_persistence [options] <OFF input file>`
**Allowed options**
@@ -22,53 +25,25 @@ where `dim` is the dimension of the homological feature, `birth` and `death` are
Beware: this program may use a lot of RAM and take a lot of time if `max-edge-length` is set to a large value.
**Example 1 with Z/2Z coefficients**
-`rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2`
-outputs:
-```
-2 0 0 inf
-2 1 0.0983494 inf
-2 1 0.104347 inf
-2 2 0.138335 inf
-```
+`rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2`
**Example 2 with Z/3Z coefficients**
-rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3
+`rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3`
-outputs:
-```
-3 0 0 inf
-3 1 0.0983494 inf
-3 1 0.104347 inf
-3 2 0.138335 inf
-```
+## rips_distance_matrix_persistence ##
+Same as `rips_persistence` but taking a distance matrix as input.
-
-## `rips_distance_matrix_persistence` ##
-Same as `rips_persistence` but taking a distance matrix as input.
-
**Usage**
-`rips_persistence [options] <CSV input file>`
-where
+
+`rips_persistence [options] <CSV input file>`
+
+where
`<CSV input file>` is the path to the file containing a distance matrix. Can be square or lower triangular matrix. Separator is ';'.
**Example**
-`rips_distance_matrix_persistence data/distance_matrix/full_square_distance_matrix.csv -r 15 -d 3 -p 3 -m 0`
-outputs:
-```
-The complex contains 46 simplices
- and has dimension 3
-3 0 0 inf
-3 0 0 8.94427
-3 0 0 7.28011
-3 0 0 6.08276
-3 0 0 5.83095
-3 0 0 5.38516
-3 0 0 5
-3 1 11 12.0416
-3 1 6.32456 6.7082
-```
+`rips_distance_matrix_persistence data/distance_matrix/full_square_distance_matrix.csv -r 15 -d 3 -p 3 -m 0`
generated by cgit v1.2.3 (git 2.39.1) at 2024-07-07 08:17:49 +0000