From 470ee54e1bdb0ff074db9213412766476ccf51fb Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Thu, 10 Oct 2019 10:03:21 +0200
Subject: Add maximal edge length parameter for sparse rips persistence utility

---
 src/Rips_complex/utilities/ripscomplex.md              |  1 +
 src/Rips_complex/utilities/sparse_rips_persistence.cpp | 15 +++++++++++----
 2 files changed, 12 insertions(+), 4 deletions(-)

(limited to 'src/Rips_complex')

diff --git a/src/Rips_complex/utilities/ripscomplex.md b/src/Rips_complex/utilities/ripscomplex.md
index 03838085..61f31e3c 100644
--- a/src/Rips_complex/utilities/ripscomplex.md
+++ b/src/Rips_complex/utilities/ripscomplex.md
@@ -99,6 +99,7 @@ where `dim` is the dimension of the homological feature, `birth` and `death` are
 
 * `-h [ --help ]` Produce help message
 * `-o [ --output-file ]` Name of file in which the persistence diagram is written. Default print in standard output.
+* `-r [ --max-edge-length ]` (default = inf) Maximal length of an edge for the Rips complex construction.
 * `-e [ --approximation ]` (default = .5) Epsilon, where the sparse Rips complex is a (1+epsilon)/(1-epsilon)-approximation of the Rips complex.
 * `-d [ --cpx-dimension ]` (default = INT_MAX) Maximal dimension of the Rips complex we want to compute.
 * `-p [ --field-charac ]` (default = 11)     Characteristic p of the coefficient field Z/pZ for computing homology.
diff --git a/src/Rips_complex/utilities/sparse_rips_persistence.cpp b/src/Rips_complex/utilities/sparse_rips_persistence.cpp
index 1a86eafe..cefd8a67 100644
--- a/src/Rips_complex/utilities/sparse_rips_persistence.cpp
+++ b/src/Rips_complex/utilities/sparse_rips_persistence.cpp
@@ -28,21 +28,24 @@ using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomolog
 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, double& epsilon,
+void program_options(int argc, char* argv[], std::string& off_file_points, std::string& filediag,
+                     Filtration_value& threshold, double& epsilon,
                      int& dim_max, int& p, Filtration_value& min_persistence);
 
 int main(int argc, char* argv[]) {
   std::string off_file_points;
   std::string filediag;
+  Filtration_value threshold;
   double epsilon;
   int dim_max;
   int p;
   Filtration_value min_persistence;
 
-  program_options(argc, argv, off_file_points, filediag, epsilon, dim_max, p, min_persistence);
+  program_options(argc, argv, off_file_points, filediag, threshold, epsilon, dim_max, p, min_persistence);
 
   Points_off_reader off_reader(off_file_points);
-  Sparse_rips sparse_rips(off_reader.get_point_cloud(), Gudhi::Euclidean_distance(), epsilon);
+  Sparse_rips sparse_rips(off_reader.get_point_cloud(), Gudhi::Euclidean_distance(), epsilon,
+                          -std::numeric_limits<Filtration_value>::infinity(), threshold);
 
   // Construct the Rips complex in a Simplex Tree
   Simplex_tree simplex_tree;
@@ -73,7 +76,8 @@ int main(int argc, char* argv[]) {
   return 0;
 }
 
-void program_options(int argc, char* argv[], std::string& off_file_points, std::string& filediag, double& epsilon,
+void program_options(int argc, char* argv[], std::string& off_file_points, std::string& filediag,
+                     Filtration_value& threshold, double& epsilon,
                      int& dim_max, int& p, Filtration_value& min_persistence) {
   namespace po = boost::program_options;
   po::options_description hidden("Hidden options");
@@ -84,6 +88,9 @@ void program_options(int argc, char* argv[], std::string& off_file_points, std::
   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.")(
       "approximation,e", po::value<double>(&epsilon)->default_value(.5),
       "Epsilon, where the sparse Rips complex is a (1+epsilon)-approximation of the Rips complex.")(
       "cpx-dimension,d", po::value<int>(&dim_max)->default_value(std::numeric_limits<int>::max()),
-- 
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