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

6 files changed, 212 insertions, 2 deletions

diff --git a/src/Rips_complex/example/CMakeLists.txt b/src/Rips_complex/example/CMakeLists.txt
index 3962b15e..9ba9d941 100644
--- a/src/Rips_complex/example/CMakeLists.txt
+++ b/src/Rips_complex/example/CMakeLists.txt
@@ -1,27 +1,50 @@
 cmake_minimum_required(VERSION 2.6)
 project(Rips_complex_examples)
 
+# Point cloud
 add_executable ( ripsoffreader example_rips_complex_from_off_file.cpp )
 target_link_libraries(ripsoffreader  ${Boost_SYSTEM_LIBRARY})
 
 add_executable ( oneskeletonripspoints example_one_skeleton_rips_from_points.cpp )
 target_link_libraries(oneskeletonripspoints  ${Boost_SYSTEM_LIBRARY})
 
+# Distance matrix
+add_executable ( oneskeletonripsdistance example_one_skeleton_rips_from_distance_matrix.cpp )
+target_link_libraries(oneskeletonripsdistance  ${Boost_SYSTEM_LIBRARY})
+
+add_executable ( ripscsvdistancereader example_rips_complex_from_csv_distance_matrix_file.cpp )
+target_link_libraries(ripscsvdistancereader  ${Boost_SYSTEM_LIBRARY})
+
 if (TBB_FOUND)
   target_link_libraries(ripsoffreader ${TBB_LIBRARIES})
   target_link_libraries(oneskeletonripspoints ${TBB_LIBRARIES})
+  target_link_libraries(oneskeletonripsdistance ${TBB_LIBRARIES})
+  target_link_libraries(ripscsvdistancereader ${TBB_LIBRARIES})
 endif()
 
 add_test(oneskeletonripspoints ${CMAKE_CURRENT_BINARY_DIR}/oneskeletonripspoints 12.0)
+
+add_test(oneskeletonripsdistance ${CMAKE_CURRENT_BINARY_DIR}/oneskeletonripspoints 1.0)
+
 # Do not forget to copy test files in current binary dir
 file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 add_test(ripsoffreader_doc_12_1 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader alphacomplexdoc.off 12.0 1 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_1.txt)
 add_test(ripsoffreader_doc_12_3 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader alphacomplexdoc.off 12.0 3 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_3.txt)
+
+file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+add_test(ripscsvdistancereader_doc_1_1 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvdistancereader full_square_distance_matrix.csv 1.0 1 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_1_1.txt)
+add_test(ripscsvdistancereader_doc_1_3 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvdistancereader full_square_distance_matrix.csv 1.0 3 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_1_3.txt)
+
+
 if (DIFF_PATH)
   # Do not forget to copy test results files in current binary dir
   file(COPY "one_skeleton_rips_points_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
   file(COPY "full_skeleton_rips_points_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+  file(COPY "one_skeleton_rips_distance_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+  file(COPY "full_skeleton_rips_distance_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 
   add_test(ripsoffreader_doc_12_1_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_1.txt ${CMAKE_CURRENT_BINARY_DIR}/one_skeleton_rips_points_for_doc.txt)
   add_test(ripsoffreader_doc_12_3_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_3.txt ${CMAKE_CURRENT_BINARY_DIR}/full_skeleton_rips_points_for_doc.txt)
+  add_test(ripscsvreader_doc_1_1_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_1_1.txt ${CMAKE_CURRENT_BINARY_DIR}/one_skeleton_rips_distance_for_doc.txt)
+  add_test(ripscsvreader_doc_1_3_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_1_3.txt ${CMAKE_CURRENT_BINARY_DIR}/full_skeleton_rips_distance_for_doc.txt)
 endif()
diff --git a/src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp b/src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp
new file mode 100644
index 00000000..54fa3aa1
--- /dev/null
+++ b/src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp
@@ -0,0 +1,68 @@
+#include <gudhi/Rips_complex.h>
+// to construct a simplex_tree from rips complex
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/distance_functions.h>
+
+#include <iostream>
+#include <string>
+#include <limits>  // for std::numeric_limits
+
+void usage(int nbArgs, char * const progName) {
+  std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n";
+  std::cerr << "Usage: " << progName << " threshold\n";
+  std::cerr << "       i.e.: " << progName << " 12.0\n";
+  exit(-1);  // ----- >>
+}
+
+int main(int argc, char **argv) {
+  if (argc != 2) usage(argc, argv[0]);
+
+  double threshold = atof(argv[1]);
+
+  // Type definitions
+  using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
+  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>>;
+
+  // User defined distance matrix is:
+  // | 0    0.94 0.77 0.99 0.11  |
+  // | 0.94 0    0.26 0.99 0.39  |
+  // | 0.77 0.26 0    0.28 0.97  |
+  // | 0.99 0.99 0.28 0    0.30  |
+  // | 0.11 0.39 0.97 0.30 0     |
+
+  Distance_matrix distances;
+  distances.push_back({});
+  distances.push_back({0.94});
+  distances.push_back({0.77, 0.26});
+  distances.push_back({0.99, 0.99, 0.28});
+  distances.push_back({0.11, 0.39, 0.97, 0.30});
+  
+  // ----------------------------------------------------------------------------
+  // Init of a rips complex from points
+  // ----------------------------------------------------------------------------
+  Rips_complex rips_complex_from_points(distances, threshold);
+
+  Simplex_tree simplex;
+  if (rips_complex_from_points.create_complex(simplex, 1)) {
+    // ----------------------------------------------------------------------------
+    // Display information about the one skeleton rips complex
+    // ----------------------------------------------------------------------------
+    std::cout << "Rips complex is of dimension " << simplex.dimension() <<
+        " - " << simplex.num_simplices() << " simplices - " <<
+        simplex.num_vertices() << " vertices." << std::endl;
+
+    std::cout << "Iterator on rips complex simplices in the filtration order, with [filtration value]:" <<
+        std::endl;
+    for (auto f_simplex : simplex.filtration_simplex_range()) {
+      std::cout << "   ( ";
+      for (auto vertex : simplex.simplex_vertex_range(f_simplex)) {
+        std::cout << vertex << " ";
+      }
+      std::cout << ") -> " << "[" << simplex.filtration(f_simplex) << "] ";
+      std::cout << std::endl;
+    }
+  }
+  return 0;
+}
diff --git a/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp b/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp
index 2e63d9a6..26517876 100644
--- a/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp
+++ b/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp
@@ -1,6 +1,4 @@
 #include <gudhi/Rips_complex.h>
-// to construct Rips_complex from a OFF file of points
-#include <gudhi/Points_off_io.h>
 // to construct a simplex_tree from rips complex
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/distance_functions.h>
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;
+}
diff --git a/src/Rips_complex/example/full_skeleton_rips_distance_for_doc.txt b/src/Rips_complex/example/full_skeleton_rips_distance_for_doc.txt
new file mode 100644
index 00000000..6744532d
--- /dev/null
+++ b/src/Rips_complex/example/full_skeleton_rips_distance_for_doc.txt
@@ -0,0 +1,32 @@
+Rips complex is of dimension 3 - 30 simplices - 5 vertices.
+Iterator on rips complex simplices in the filtration order, with [filtration value]:
+   ( 0 ) -> [0] 
+   ( 1 ) -> [0] 
+   ( 2 ) -> [0] 
+   ( 3 ) -> [0] 
+   ( 4 ) -> [0] 
+   ( 4 0 ) -> [0.11] 
+   ( 2 1 ) -> [0.26] 
+   ( 3 2 ) -> [0.28] 
+   ( 4 3 ) -> [0.3] 
+   ( 4 1 ) -> [0.39] 
+   ( 2 0 ) -> [0.77] 
+   ( 1 0 ) -> [0.94] 
+   ( 2 1 0 ) -> [0.94] 
+   ( 4 1 0 ) -> [0.94] 
+   ( 4 2 ) -> [0.97] 
+   ( 4 2 0 ) -> [0.97] 
+   ( 4 2 1 ) -> [0.97] 
+   ( 4 2 1 0 ) -> [0.97] 
+   ( 4 3 2 ) -> [0.97] 
+   ( 3 0 ) -> [0.99] 
+   ( 3 1 ) -> [0.99] 
+   ( 3 1 0 ) -> [0.99] 
+   ( 3 2 0 ) -> [0.99] 
+   ( 3 2 1 ) -> [0.99] 
+   ( 3 2 1 0 ) -> [0.99] 
+   ( 4 3 0 ) -> [0.99] 
+   ( 4 3 1 ) -> [0.99] 
+   ( 4 3 1 0 ) -> [0.99] 
+   ( 4 3 2 0 ) -> [0.99] 
+   ( 4 3 2 1 ) -> [0.99] 
diff --git a/src/Rips_complex/example/one_skeleton_rips_distance_for_doc.txt b/src/Rips_complex/example/one_skeleton_rips_distance_for_doc.txt
new file mode 100644
index 00000000..9bb1a7ab
--- /dev/null
+++ b/src/Rips_complex/example/one_skeleton_rips_distance_for_doc.txt
@@ -0,0 +1,17 @@
+Rips complex is of dimension 1 - 15 simplices - 5 vertices.
+Iterator on rips complex simplices in the filtration order, with [filtration value]:
+   ( 0 ) -> [0] 
+   ( 1 ) -> [0] 
+   ( 2 ) -> [0] 
+   ( 3 ) -> [0] 
+   ( 4 ) -> [0] 
+   ( 4 0 ) -> [0.11] 
+   ( 2 1 ) -> [0.26] 
+   ( 3 2 ) -> [0.28] 
+   ( 4 3 ) -> [0.3] 
+   ( 4 1 ) -> [0.39] 
+   ( 2 0 ) -> [0.77] 
+   ( 1 0 ) -> [0.94] 
+   ( 4 2 ) -> [0.97] 
+   ( 3 0 ) -> [0.99] 
+   ( 3 1 ) -> [0.99]