git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/Nerve_GIC@2579 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 697cb9e3146f0b068c6df4e74d972958e793d94b

9 files changed, 30 insertions, 825 deletions

diff --git a/src/Nerve_GIC/example/GIC.cpp b/src/Nerve_GIC/example/GIC.cpp
index 0f50f712..aba0927d 100644
--- a/src/Nerve_GIC/example/GIC.cpp
+++ b/src/Nerve_GIC/example/GIC.cpp
@@ -32,6 +32,8 @@ void usage(int nbArgs, char * const progName) {
 int main(int argc, char **argv) {
   if ((argc != 6) && (argc != 7)) usage(argc, (argv[0] - 1));
 
+  using Point = std::vector<float>;
+
   std::string off_file_name(argv[1]);
   double threshold = atof(argv[2]);
   int coord = atoi(argv[3]);
@@ -43,8 +45,8 @@ int main(int argc, char **argv) {
   // Init of a graph induced complex from an OFF file
   // ----------------------------------------------------------------------------
 
-  Gudhi::graph_induced_complex::Graph_induced_complex GIC;
-  GIC.set_verbose(verb);
+  Gudhi::graph_induced_complex::Graph_induced_complex<Point> GIC;
+  GIC.set_verbose(verb); GIC.set_mask();
 
   bool check = GIC.read_point_cloud(off_file_name);
 
@@ -54,7 +56,7 @@ int main(int argc, char **argv) {
     GIC.set_color_from_coordinate(coord);
     GIC.set_function_from_coordinate(coord);
 
-    GIC.set_graph_from_rips(threshold);
+    GIC.set_graph_from_rips(threshold, Gudhi::Euclidean_distance());
 
     GIC.set_resolution_double(resolution); GIC.set_gain(gain);
     GIC.set_cover_from_function(1);
@@ -63,7 +65,7 @@ int main(int argc, char **argv) {
 
     GIC.plot_txt();
 
-    Simplex_tree stree; GIC.create_complex(stree);
+    Gudhi::graph_induced_complex::Simplex_tree stree; GIC.create_complex(stree);
 
     std::streambuf* streambufffer = std::cout.rdbuf();
     std::ostream output_stream(streambufffer);
diff --git a/src/Nerve_GIC/example/GIC.txt b/src/Nerve_GIC/example/GIC.txt
deleted file mode 100644
index 79f61e92..00000000
--- a/src/Nerve_GIC/example/GIC.txt
+++ /dev/null
@@ -1,89 +0,0 @@
-Graph induced complex is of dimension 1 - 87 simplices - 44 vertices.
-Iterator on graph induced complex simplices
-0 
-1 
-2 
-2 1 
-3 
-3 0 
-4 
-4 2 
-5 
-5 3 
-6 
-6 5 
-7 
-7 4 
-8 
-8 7 
-9 
-9 6 
-10 
-10 8 
-11 
-11 9 
-12 
-12 11 
-13 
-13 10 
-14 
-14 12 
-15 
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-16 14 
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-17 15 
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-18 16 
-18 17 
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-25 
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-26 
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-27 
-27 22 
-28 
-28 25 
-29 
-29 26 
-30 
-30 27 
-31 
-31 28 
-32 
-32 30 
-33 
-33 29 
-34 
-34 32 
-35 
-35 31 
-36 
-36 33 
-37 
-37 34 
-37 35 
-37 36 
-38 
-38 37 
-39 
-39 38 
-40 
-40 39 
-41 
-41 40 
-42 
-42 41 
-43 
-43 42 
diff --git a/src/Nerve_GIC/example/GICvoronoi.cpp b/src/Nerve_GIC/example/GICvoronoi.cpp
index 8061c42d..013d6290 100644
--- a/src/Nerve_GIC/example/GICvoronoi.cpp
+++ b/src/Nerve_GIC/example/GICvoronoi.cpp
@@ -32,6 +32,8 @@ void usage(int nbArgs, char * const progName) {
 int main(int argc, char **argv) {
   if ((argc != 3) && (argc != 4)) usage(argc, (argv[0] - 1));
 
+  using Point = std::vector<float>;
+
   std::string off_file_name(argv[1]);
   int m = atoi(argv[2]);
   bool verb = 0; if(argc == 4)  verb = 1;
@@ -40,8 +42,8 @@ int main(int argc, char **argv) {
   // Init of a graph induced complex from an OFF file
   // ----------------------------------------------------------------------------
 
-  Gudhi::graph_induced_complex::Graph_induced_complex GIC;
-  GIC.set_verbose(verb);
+  Gudhi::graph_induced_complex::Graph_induced_complex<Point> GIC;
+  GIC.set_verbose(verb); GIC.set_mask();
 
   bool check = GIC.read_point_cloud(off_file_name);
 
@@ -52,13 +54,13 @@ int main(int argc, char **argv) {
 
     GIC.set_graph_from_OFF(off_file_name);
 
-    GIC.set_cover_from_Voronoi(m);
+    GIC.set_cover_from_Voronoi(Gudhi::Euclidean_distance(),m);
 
     GIC.find_GIC_simplices();
 
     GIC.plot_OFF();
 
-    Simplex_tree stree; GIC.create_complex(stree);
+    Gudhi::graph_induced_complex::Simplex_tree stree; GIC.create_complex(stree);
 
     std::streambuf* streambufffer = std::cout.rdbuf();
     std::ostream output_stream(streambufffer);
diff --git a/src/Nerve_GIC/example/GICvoronoi.txt b/src/Nerve_GIC/example/GICvoronoi.txt
deleted file mode 100644
index 34517933..00000000
--- a/src/Nerve_GIC/example/GICvoronoi.txt
+++ /dev/null
@@ -1,563 +0,0 @@
-Graph induced complex is of dimension 2 - 561 simplices - 100 vertices.
-Iterator on graph induced complex simplices
-0 
-1 
-2 
-3 
-3 0 
-4 
-4 1 
-5 
-6 
-7 
-8 
-9 
-9 1 
-10 
-11 
-11 1 
-11 9 
-11 9 1 
-12 
-12 1 
-12 11 
-12 11 1 
-13 
-13 2 
-14 
-14 11 
-15 
-15 4 
-16 
-16 2 
-16 15 
-17 
-17 3 
-18 
-19 
-19 8 
-20 
-20 11 
-20 12 
-20 12 11 
-21 
-22 
-22 12 
-23 
-23 22 
-24 
-24 19 
-25 
-25 0 
-25 3 
-25 18 
-26 
-26 1 
-26 4 
-26 4 1 
-27 
-27 26 
-28 
-28 27 
-29 
-30 
-31 
-31 30 
-32 
-32 30 
-32 31 
-32 31 30 
-33 
-33 1 
-33 4 
-33 4 1 
-33 24 
-33 29 
-34 
-34 5 
-34 21 
-35 
-35 2 
-35 16 
-35 16 2 
-36 
-36 17 
-37 
-37 24 
-37 29 
-38 
-38 3 
-38 25 
-38 25 3 
-39 
-39 8 
-39 25 
-39 38 
-39 38 25 
-40 
-40 7 
-40 19 
-40 24 
-40 24 19 
-40 37 
-40 37 24 
-40 39 
-41 
-41 5 
-41 34 
-41 34 5 
-42 
-42 21 
-42 41 
-43 
-43 5 
-43 41 
-43 41 5 
-43 42 
-43 42 41 
-44 
-44 14 
-44 27 
-45 
-45 21 
-46 
-46 8 
-46 19 
-46 19 8 
-46 39 
-46 39 8 
-47 
-47 0 
-47 3 
-47 3 0 
-47 19 
-47 38 
-47 38 3 
-47 39 
-47 39 38 
-47 40 
-47 40 19 
-47 40 39 
-47 46 
-47 46 19 
-47 46 39 
-48 
-48 37 
-48 45 
-49 
-49 10 
-49 37 
-49 48 
-49 48 37 
-50 
-50 10 
-50 37 
-50 45 
-50 49 
-50 49 10 
-50 49 37 
-51 
-51 45 
-51 48 
-51 48 45 
-51 50 
-51 50 45 
-52 
-52 27 
-52 30 
-52 31 
-52 31 30 
-53 
-53 10 
-53 45 
-53 48 
-53 48 45 
-53 50 
-53 50 10 
-54 
-54 6 
-55 
-55 54 
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-56 44 
-57 
-57 13 
-58 
-58 24 
-58 29 
-58 33 
-58 33 24 
-58 33 29 
-58 37 
-58 37 24 
-58 37 29 
-59 
-59 7 
-59 29 
-60 
-60 1 
-60 12 
-60 12 1 
-60 22 
-60 22 12 
-60 26 
-60 26 1 
-60 27 
-60 27 26 
-60 44 
-60 44 27 
-60 56 
-60 56 44 
-61 
-61 5 
-61 21 
-61 34 
-61 34 5 
-61 34 21 
-61 42 
-61 42 21 
-61 43 
-61 43 5 
-61 43 42 
-62 
-62 6 
-62 54 
-62 54 6 
-62 55 
-62 55 54 
-63 
-63 6 
-63 62 
-63 62 6 
-64 
-64 10 
-64 48 
-64 49 
-64 49 10 
-64 49 48 
-64 53 
-64 53 10 
-64 53 48 
-65 
-65 21 
-65 45 
-65 45 21 
-65 50 
-65 50 45 
-65 53 
-65 53 50 
-66 
-66 14 
-66 44 
-66 44 14 
-66 56 
-66 56 44 
-67 
-67 13 
-67 57 
-67 57 13 
-68 
-68 2 
-68 13 
-68 13 2 
-68 35 
-68 35 2 
-69 
-69 21 
-69 34 
-69 34 21 
-69 41 
-69 41 34 
-69 42 
-69 42 21 
-69 42 41 
-69 65 
-69 65 21 
-70 
-70 11 
-70 14 
-70 14 11 
-70 20 
-70 20 11 
-70 56 
-70 66 
-70 66 14 
-70 66 56 
-71 
-71 6 
-71 54 
-71 54 6 
-71 55 
-71 55 54 
-71 62 
-71 62 55 
-71 63 
-71 63 6 
-71 63 62 
-72 
-72 37 
-72 48 
-72 48 37 
-72 51 
-72 51 48 
-73 
-73 3 
-73 17 
-73 17 3 
-73 36 
-73 36 17 
-74 
-74 7 
-74 8 
-74 39 
-74 39 8 
-74 40 
-74 40 7 
-74 40 39 
-74 52 
-74 59 
-74 59 7 
-75 
-75 4 
-75 15 
-75 15 4 
-76 
-76 15 
-76 75 
-76 75 15 
-77 
-77 4 
-77 75 
-77 75 4 
-78 
-78 4 
-78 26 
-78 26 4 
-78 27 
-78 27 26 
-78 28 
-78 28 27 
-78 75 
-78 77 
-78 77 4 
-78 77 75 
-79 
-79 9 
-79 11 
-79 11 9 
-79 14 
-79 14 11 
-79 27 
-79 30 
-79 32 
-79 32 30 
-79 44 
-79 44 14 
-79 44 27 
-79 52 
-79 52 27 
-79 52 30 
-80 
-80 0 
-80 25 
-80 25 0 
-80 39 
-80 39 25 
-80 47 
-80 47 0 
-80 47 39 
-81 
-81 2 
-81 4 
-81 15 
-81 15 4 
-81 16 
-81 16 2 
-81 16 15 
-81 27 
-81 29 
-81 33 
-81 33 4 
-81 33 29 
-81 52 
-81 52 27 
-81 59 
-81 59 29 
-81 74 
-81 74 52 
-81 74 59 
-81 75 
-81 78 
-81 78 27 
-81 78 75 
-82 
-82 2 
-82 75 
-82 81 
-82 81 2 
-82 81 75 
-83 
-83 0 
-83 3 
-83 3 0 
-83 25 
-83 25 0 
-83 73 
-83 73 3 
-84 
-84 1 
-84 8 
-84 19 
-84 19 8 
-84 24 
-84 24 19 
-84 33 
-84 33 1 
-84 33 24 
-84 74 
-84 74 8 
-85 
-85 17 
-85 36 
-85 36 17 
-85 73 
-85 73 36 
-86 
-86 6 
-86 63 
-86 63 6 
-87 
-87 3 
-87 17 
-87 17 3 
-87 18 
-87 25 
-87 25 3 
-87 25 18 
-88 
-88 17 
-88 18 
-88 85 
-88 85 17 
-88 87 
-88 87 17 
-88 87 18 
-89 
-89 63 
-89 86 
-89 86 63 
-90 
-90 7 
-90 37 
-90 40 
-90 40 7 
-90 40 37 
-90 59 
-90 59 7 
-91 
-91 21 
-91 45 
-91 45 21 
-91 53 
-91 53 45 
-91 65 
-91 65 21 
-91 65 53 
-92 
-92 9 
-92 55 
-92 71 
-92 71 55 
-93 
-93 2 
-93 15 
-93 16 
-93 16 15 
-93 35 
-93 35 2 
-93 35 16 
-93 75 
-93 76 
-93 76 15 
-93 76 75 
-93 82 
-93 82 2 
-93 82 75 
-94 
-94 1 
-94 9 
-94 9 1 
-94 31 
-94 32 
-94 32 31 
-94 52 
-94 52 31 
-94 55 
-94 74 
-94 74 52 
-94 79 
-94 79 9 
-94 79 32 
-94 84 
-94 84 1 
-94 84 74 
-94 92 
-94 92 9 
-94 92 55 
-95 
-95 18 
-95 25 
-95 25 18 
-95 83 
-95 83 25 
-95 85 
-95 88 
-95 88 18 
-95 88 85 
-96 
-96 63 
-96 86 
-96 86 63 
-96 89 
-96 89 63 
-96 89 86 
-97 
-97 73 
-97 83 
-97 83 73 
-97 85 
-97 85 73 
-97 95 
-97 95 83 
-97 95 85 
-98 
-98 12 
-98 20 
-98 20 12 
-98 22 
-98 22 12 
-98 23 
-98 23 22 
-98 56 
-98 60 
-98 60 22 
-98 60 56 
-98 70 
-98 70 20 
-98 70 56 
-99 
-99 29 
-99 37 
-99 37 29 
-99 50 
-99 50 37 
-99 51 
-99 51 50 
-99 59 
-99 59 29 
-99 72 
-99 72 37 
-99 72 51 
-99 90 
-99 90 37 
-99 90 59 
diff --git a/src/Nerve_GIC/example/MapperDeltaCoord.cpp b/src/Nerve_GIC/example/MapperDeltaCoord.cpp
index 84a25bad..9927f762 100644
--- a/src/Nerve_GIC/example/MapperDeltaCoord.cpp
+++ b/src/Nerve_GIC/example/MapperDeltaCoord.cpp
@@ -32,6 +32,8 @@ void usage(int nbArgs, char * const progName) {
 int main(int argc, char **argv) {
   if ((argc != 3) && (argc != 4)) usage(argc, (argv[0] - 1));
 
+  using Point = std::vector<float>;
+
   std::string off_file_name(argv[1]);
   int coord = atoi(argv[2]);
   bool verb = 0; if(argc == 4)  verb = 1;
@@ -40,8 +42,8 @@ int main(int argc, char **argv) {
   // Init of a Mapper Delta from an OFF file
   // ---------------------------------------
 
-  Gudhi::graph_induced_complex::Graph_induced_complex GIC;
-  GIC.set_verbose(verb);
+  Gudhi::graph_induced_complex::Graph_induced_complex<Point> GIC;
+  GIC.set_verbose(verb); GIC.set_mask(); GIC.set_subsampling();
 
   bool check = GIC.read_point_cloud(off_file_name);
 
@@ -51,16 +53,16 @@ int main(int argc, char **argv) {
     GIC.set_color_from_coordinate(coord);
     GIC.set_function_from_coordinate(coord);
 
-    GIC.set_graph_from_automatic_rips();
+    GIC.set_graph_from_automatic_rips(Gudhi::Euclidean_distance());
 
     GIC.set_automatic_resolution_for_GICMAP(); GIC.set_gain();
     GIC.set_cover_from_function(1);
 
     GIC.find_GICMAP_simplices_with_functional_minimal_cover();
 
-    GIC.plot_txt();
+    GIC.plot_pdf();
 
-    Simplex_tree stree; GIC.create_complex(stree);
+    Gudhi::graph_induced_complex::Simplex_tree stree; GIC.create_complex(stree);
 
     std::streambuf* streambufffer = std::cout.rdbuf();
     std::ostream output_stream(streambufffer);
diff --git a/src/Nerve_GIC/example/MapperDeltaCoord.txt b/src/Nerve_GIC/example/MapperDeltaCoord.txt
deleted file mode 100644
index faf832c7..00000000
--- a/src/Nerve_GIC/example/MapperDeltaCoord.txt
+++ /dev/null
@@ -1,143 +0,0 @@
-Mapper Delta is of dimension 1 - 141 simplices - 71 vertices.
-Iterator on Mapper Delta simplices
-0 
-1 
-2 
-2 1 
-3 
-3 0 
-4 
-4 2 
-5 
-5 3 
-6 
-6 4 
-7 
-7 5 
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-55 52 
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-60 
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-61 
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-62 
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-65 
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-66 
-66 65 
-67 
-67 66 
-68 
-68 67 
-69 
-69 68 
-70 
-70 69 
diff --git a/src/Nerve_GIC/example/MapperDeltaFunc.cpp b/src/Nerve_GIC/example/MapperDeltaFunc.cpp
index fa95ca58..f3d57d2f 100644
--- a/src/Nerve_GIC/example/MapperDeltaFunc.cpp
+++ b/src/Nerve_GIC/example/MapperDeltaFunc.cpp
@@ -32,6 +32,8 @@ void usage(int nbArgs, char * const progName) {
 int main(int argc, char **argv) {
   if ((argc != 3) && (argc != 4)) usage(argc, (argv[0] - 1));
 
+  using Point = std::vector<float>;
+
   std::string off_file_name(argv[1]);
   std::string func_file_name = argv[2];
   bool verb = 0; if(argc == 4)  verb = 1;
@@ -40,8 +42,8 @@ int main(int argc, char **argv) {
   // Init of a Mapper Delta from an OFF file
   // ---------------------------------------
 
-  Gudhi::graph_induced_complex::Graph_induced_complex GIC;
-  GIC.set_verbose(verb);
+  Gudhi::graph_induced_complex::Graph_induced_complex<Point> GIC;
+  GIC.set_verbose(verb); GIC.set_mask(); GIC.set_subsampling();
 
   bool check = GIC.read_point_cloud(off_file_name);
 
@@ -51,7 +53,7 @@ int main(int argc, char **argv) {
     GIC.set_color_from_file(func_file_name);
     GIC.set_function_from_file(func_file_name);
 
-    GIC.set_graph_from_automatic_rips();
+    GIC.set_graph_from_automatic_rips(Gudhi::Euclidean_distance());
 
     GIC.set_automatic_resolution_for_GICMAP(); GIC.set_gain();
     GIC.set_cover_from_function(1);
@@ -60,7 +62,7 @@ int main(int argc, char **argv) {
 
     GIC.plot_pdf();
 
-    Simplex_tree stree; GIC.create_complex(stree);
+    Gudhi::graph_induced_complex::Simplex_tree stree; GIC.create_complex(stree);
 
     std::streambuf* streambufffer = std::cout.rdbuf();
     std::ostream output_stream(streambufffer);
diff --git a/src/Nerve_GIC/example/MapperDeltaFunc.dot b/src/Nerve_GIC/example/MapperDeltaFunc.dot
deleted file mode 100644
index beafa7f1..00000000
--- a/src/Nerve_GIC/example/MapperDeltaFunc.dot
+++ /dev/null
@@ -1,10 +0,0 @@
-graph Mapper {
-0[shape=circle fontcolor=black color=black label="0:26" style=filled fillcolor="0, 1, 1"]
-1[shape=circle fontcolor=black color=black label="1:4" style=filled fillcolor="0.240095, 1, 1"]
-2[shape=circle fontcolor=black color=black label="2:11" style=filled fillcolor="0.209621, 1, 1"]
-3[shape=circle fontcolor=black color=black label="3:42" style=filled fillcolor="0.6, 1, 1"]
-  0 -- 1 [weight=15];
-  0 -- 2 [weight=15];
-  1 -- 3 [weight=15];
-  2 -- 3 [weight=15];
-}
\ No newline at end of file
diff --git a/src/Nerve_GIC/example/Nerve.cpp b/src/Nerve_GIC/example/Nerve.cpp
index 8f8037d4..10c5ba3b 100644
--- a/src/Nerve_GIC/example/Nerve.cpp
+++ b/src/Nerve_GIC/example/Nerve.cpp
@@ -32,6 +32,8 @@ void usage(int nbArgs, char * const progName) {
 int main(int argc, char **argv) {
   if ((argc != 5) && (argc != 6)) usage(argc, (argv[0] - 1));
 
+  using Point = std::vector<float>;
+
   std::string off_file_name(argv[1]);
   int coord = atoi(argv[2]);
   int resolution = atoi(argv[3]);
@@ -42,8 +44,8 @@ int main(int argc, char **argv) {
   // Init of a Nerve from an OFF file
   // --------------------------------
 
-  Gudhi::graph_induced_complex::Graph_induced_complex GIC;
-  GIC.set_verbose(verb);
+  Gudhi::graph_induced_complex::Graph_induced_complex<Point> GIC;
+  GIC.set_verbose(verb); GIC.set_mask();
 
   bool check = GIC.read_point_cloud(off_file_name);
 
@@ -62,7 +64,7 @@ int main(int argc, char **argv) {
 
     GIC.plot_txt();
 
-    Simplex_tree stree; GIC.create_complex(stree);
+    Gudhi::graph_induced_complex::Simplex_tree stree; GIC.create_complex(stree);
 
     std::streambuf* streambufffer = std::cout.rdbuf();
     std::ostream output_stream(streambufffer);