From 1a728400187d89db914e865a979c85c7260b0b02 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Mon, 21 Nov 2016 16:24:15 +0000
Subject: Add distance matrix rips construction (doc, code, test)

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/distance_matrix_in_rips_module@1766 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 6b9bdecbaf0aca12facb023e66bdea71e8e8cd38
---
 ..._rips_complex_from_csv_distance_matrix_file.cpp | 72 ++++++++++++++++++++++
 1 file changed, 72 insertions(+)
 create mode 100644 src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp

(limited to 'src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp')

diff --git a/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp b/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp
new file mode 100644
index 00000000..cfada84a
--- /dev/null
+++ b/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp
@@ -0,0 +1,72 @@
+#include <gudhi/Rips_complex.h>
+// to construct Rips_complex from a OFF file of points
+#include <gudhi/reader_utils.h>
+// to construct a simplex_tree from rips complex
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/distance_functions.h>
+
+#include <iostream>
+#include <string>
+
+void usage(int nbArgs, char * const progName) {
+  std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n";
+  std::cerr << "Usage: " << progName << " filename.csv threshold dim_max [ouput_file.txt]\n";
+  std::cerr << "       i.e.: " << progName << " ../../data/distance_matrix/full_square_distance_matrix.csv 1.0 3\n";
+  exit(-1);  // ----- >>
+}
+
+int main(int argc, char **argv) {
+  if ((argc != 4) && (argc != 5)) usage(argc, (argv[0] - 1));
+
+  std::string csv_file_name(argv[1]);
+  double threshold = atof(argv[2]);
+  int dim_max = atoi(argv[3]);
+
+  // Type definitions
+  using Simplex_tree = Gudhi::Simplex_tree<>;
+  using Filtration_value = Simplex_tree::Filtration_value;
+  using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
+  using Distance_matrix = std::vector<std::vector<Filtration_value>>;
+
+  // ----------------------------------------------------------------------------
+  // Init of a rips complex from a distance matrix in a csv file
+  // Default separator is ';'
+  // ----------------------------------------------------------------------------
+  Distance_matrix distances = read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_file_name);
+  Rips_complex rips_complex_from_file(distances, threshold);
+
+  std::streambuf* streambufffer;
+  std::ofstream ouput_file_stream;
+
+  if (argc == 5) {
+    ouput_file_stream.open(std::string(argv[4]));
+    streambufffer = ouput_file_stream.rdbuf();
+  } else {
+    streambufffer = std::cout.rdbuf();
+  }
+
+  Simplex_tree simplex;
+  if (rips_complex_from_file.create_complex(simplex, dim_max)) {
+    std::ostream output_stream(streambufffer);
+
+    // ----------------------------------------------------------------------------
+    // Display information about the rips complex
+    // ----------------------------------------------------------------------------
+    output_stream << "Rips complex is of dimension " << simplex.dimension() <<
+        " - " << simplex.num_simplices() << " simplices - " <<
+        simplex.num_vertices() << " vertices." << std::endl;
+
+    output_stream << "Iterator on rips complex simplices in the filtration order, with [filtration value]:" <<
+        std::endl;
+    for (auto f_simplex : simplex.filtration_simplex_range()) {
+      output_stream << "   ( ";
+      for (auto vertex : simplex.simplex_vertex_range(f_simplex)) {
+        output_stream << vertex << " ";
+      }
+      output_stream << ") -> " << "[" << simplex.filtration(f_simplex) << "] ";
+      output_stream << std::endl;
+    }
+  }
+  ouput_file_stream.close();
+  return 0;
+}
-- 
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