Document utilies in README files using Markdown + move/rename some utilities

Only missing doc for now: Garland_heckbert

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2752 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 7ba0113762b6622130835dc9e372acfae29c2db8

5 files changed, 257 insertions, 91 deletions

diff --git a/src/Witness_complex/utilities/CMakeLists.txt b/src/Witness_complex/utilities/CMakeLists.txt
index 918ab864..125a41ff 100644
--- a/src/Witness_complex/utilities/CMakeLists.txt
+++ b/src/Witness_complex/utilities/CMakeLists.txt
@@ -3,24 +3,26 @@ project(Witness_complex_utilities)
 
 # CGAL and Eigen3 are required for Euclidean version of Witness
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
-  add_executable( Witness_complex_example_strong_off example_strong_witness_complex_off.cpp )
-  target_link_libraries(Witness_complex_example_strong_off)
+  
+  add_executable ( Witness_complex_strong_witness_persistence strong_witness_persistence.cpp )
+  target_link_libraries(Witness_complex_strong_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
 
-  add_executable ( Witness_complex_example_strong_witness_persistence example_strong_witness_persistence.cpp )
-  target_link_libraries(Witness_complex_example_strong_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
+  add_executable ( Witness_complex_weak_witness_persistence weak_witness_persistence.cpp )
+  target_link_libraries(Witness_complex_weak_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
 
   if (TBB_FOUND)
-    target_link_libraries(Witness_complex_example_strong_witness_persistence ${TBB_LIBRARIES})
+    target_link_libraries(Witness_complex_strong_witness_persistence ${TBB_LIBRARIES})
+    target_link_libraries(Witness_complex_weak_witness_persistence ${TBB_LIBRARIES})
   endif()
 
-  add_test(NAME Witness_complex_example_strong_off_test_torus
-      COMMAND $<TARGET_FILE:Witness_complex_example_strong_off>
-      "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "20" "1.0" "3")
-  add_test(NAME Witness_complex_example_strong_test_torus_persistence
-      COMMAND $<TARGET_FILE:Witness_complex_example_strong_witness_persistence>
+  add_test(NAME Witness_complex_strong_test_torus_persistence
+      COMMAND $<TARGET_FILE:Witness_complex_strong_witness_persistence>
+      "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5")
+  add_test(NAME Witness_complex_weak_test_torus_persistence
+      COMMAND $<TARGET_FILE:Witness_complex_weak_witness_persistence>
       "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5")
 
-  install(TARGETS Witness_complex_example_strong_off DESTINATION bin)
-  install(TARGETS Witness_complex_example_strong_witness_persistence DESTINATION bin)
+  install(TARGETS Witness_complex_strong_witness_persistence DESTINATION bin)
+  install(TARGETS Witness_complex_weak_witness_persistence DESTINATION bin)
 
 endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
diff --git a/src/Witness_complex/utilities/README b/src/Witness_complex/utilities/README
new file mode 100644
index 00000000..d8dc9ca7
--- /dev/null
+++ b/src/Witness_complex/utilities/README
@@ -0,0 +1,72 @@
+# Witness_complex #

+

+## `weak_witness_persistence` ##

+This program computes the persistent homology with coefficient field *Z/pZ* of a Weak witness complex defined on a set of input points. The output diagram contains one bar per line, written with the convention:

+

+`p dim b d`

+

+where `dim` is the dimension of the homological feature, `b` and `d` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients.

+

+*Usage*

+`weak_witness_persistence [options] <OFF input file>`

+

+*Allowed options*

+

+* `-h [ --help ]` Produce help message

+* `-l [ --landmarks ]` Number of landmarks to choose from the point cloud.

+* `-o [ --output-file ]` Name of file in which the persistence diagram is written. By default, print in std::cout.

+* `-a [ --max-sq-alpha ]` (default = inf) Maximal squared relaxation parameter.

+* `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology.

+* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.

+* `-d [ --cpx-dimension ]` (default = 2147483647) Maximal dimension of the weak witness complex we want to compute.

+

+*Example*

+`weak_witness_persistence data/points/tore3D_1307.off -l 20 -a 0.5 -m 0.006`

+

+outputs:

+```

+Successfully read 1307 points.

+Ambient dimension is 3.

+The complex contains 732 simplices and has dimension 8 

+11  0 0 inf 

+11  1 0 inf 

+11  2 0.0275251 0.0534586 

+11  1 0 0.0239952 

+```

+

+N.B.: output is random as the 20 landmarks are chosen randomly.

+

+## `strong_witness_persistence` ##

+This program computes the persistent homology with coefficient field *Z/pZ* of a Strong witness complex defined on a set of input points. The output diagram contains one bar per line, written with the convention:

+

+`p dim b d`

+

+where `dim` is the dimension of the homological feature, `b` and `d` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients.

+

+*Usage*

+`strong_witness_persistence [options] <OFF input file>`

+

+*Allowed options*

+

+* `-h [ --help ]` Produce help message

+* `-l [ --landmarks ]` Number of landmarks to choose from the point cloud.

+* `-o [ --output-file ]` Name of file in which the persistence diagram is written. By default, print in std::cout.

+* `-a [ --max-sq-alpha ]` (default = inf) Maximal squared relaxation parameter.

+* `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology.

+* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.

+* `-d [ --cpx-dimension ]` (default = 2147483647) Maximal dimension of the weak witness complex we want to compute.

+

+*Example*

+`strong_witness_persistence data/points/tore3D_1307.off -l 20 -a 0.5 -m 0.06`

+

+outputs:

+```

+Successfully read 1307 points.

+Ambient dimension is 3.

+The complex contains 1836 simplices and has dimension 8 

+11  0 0 inf 

+11  1 0.00674748 inf 

+11  2 0.0937751 0.235354 

+```

+

+N.B.: output is random as the 20 landmarks are chosen randomly.

diff --git a/src/Witness_complex/utilities/example_strong_witness_complex_off.cpp b/src/Witness_complex/utilities/example_strong_witness_complex_off.cpp
deleted file mode 100644
index 0ee9ee90..00000000
--- a/src/Witness_complex/utilities/example_strong_witness_complex_off.cpp
+++ /dev/null
@@ -1,79 +0,0 @@
-/*    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):       Siargey Kachanovich
- *
- *    Copyright (C) 2016  INRIA (France)
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#include <gudhi/Simplex_tree.h>
-#include <gudhi/Euclidean_strong_witness_complex.h>
-#include <gudhi/pick_n_random_points.h>
-#include <gudhi/Points_off_io.h>
-
-#include <CGAL/Epick_d.h>
-
-#include <iostream>
-#include <fstream>
-#include <ctime>
-#include <string>
-#include <vector>
-
-using K = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>;
-using Point_d = typename K::Point_d;
-using Witness_complex = Gudhi::witness_complex::Euclidean_strong_witness_complex<K>;
-using Point_vector = std::vector<Point_d>;
-
-int main(int argc, char * const argv[]) {
-  if (argc != 5) {
-    std::cerr << "Usage: " << argv[0]
-        << " path_to_point_file number_of_landmarks max_squared_alpha limit_dimension\n";
-    return 0;
-  }
-
-  std::string file_name = argv[1];
-  int nbL = atoi(argv[2]), lim_dim = atoi(argv[4]);
-  double alpha2 = atof(argv[3]);
-  clock_t start, end;
-  Gudhi::Simplex_tree<> simplex_tree;
-
-  // Read the point file
-  Point_vector point_vector, landmarks;
-  Gudhi::Points_off_reader<Point_d> off_reader(file_name);
-  if (!off_reader.is_valid()) {
-      std::cerr << "Strong witness complex - Unable to read file " << file_name << "\n";
-      exit(-1);  // ----- >>
-    }
-  point_vector = Point_vector(off_reader.get_point_cloud());
-
-  std::cout << "Successfully read " << point_vector.size() << " points.\n";
-  std::cout << "Ambient dimension is " << point_vector[0].dimension() << ".\n";
-
-  // Choose landmarks
-  Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks));
-
-  // Compute witness complex
-  start = clock();
-  Witness_complex witness_complex(landmarks,
-                                  point_vector);
-
-  witness_complex.create_complex(simplex_tree, alpha2, lim_dim);
-  end = clock();
-  std::cout << "Strong witness complex took "
-      << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n";
-  std::cout << "Number of simplices is: " << simplex_tree.num_simplices() << "\n";
-}
diff --git a/src/Witness_complex/utilities/example_strong_witness_persistence.cpp b/src/Witness_complex/utilities/strong_witness_persistence.cpp
index f786fe7b..f786fe7b 100644
--- a/src/Witness_complex/utilities/example_strong_witness_persistence.cpp
+++ b/src/Witness_complex/utilities/strong_witness_persistence.cpp
diff --git a/src/Witness_complex/utilities/weak_witness_persistence.cpp b/src/Witness_complex/utilities/weak_witness_persistence.cpp
new file mode 100644
index 00000000..a1146922
--- /dev/null
+++ b/src/Witness_complex/utilities/weak_witness_persistence.cpp
@@ -0,0 +1,171 @@
+/*    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):       Siargey Kachanovich
+ *
+ *    Copyright (C) 2016  INRIA (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Euclidean_witness_complex.h>
+#include <gudhi/Persistent_cohomology.h>
+#include <gudhi/Points_off_io.h>
+#include <gudhi/pick_n_random_points.h>
+
+#include <boost/program_options.hpp>
+
+#include <CGAL/Epick_d.h>
+
+#include <string>
+#include <vector>
+#include <limits>  // infinity
+
+using K = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>;
+using Point_d = K::Point_d;
+
+using Point_vector = std::vector<Point_d>;
+using Witness_complex = Gudhi::witness_complex::Euclidean_witness_complex<K>;
+using SimplexTree = Gudhi::Simplex_tree<>;
+
+using Filtration_value = SimplexTree::Filtration_value;
+
+using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
+using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<SimplexTree, Field_Zp>;
+
+void program_options(int argc, char * argv[]
+                     , int & nbL
+                     , std::string & file_name
+                     , std::string & filediag
+                     , Filtration_value & max_squared_alpha
+                     , int & p
+                     , int & dim_max
+                     , Filtration_value & min_persistence);
+
+int main(int argc, char * argv[]) {
+  std::string file_name;
+  std::string filediag;
+  Filtration_value max_squared_alpha;
+  int p, nbL, lim_d;
+  Filtration_value min_persistence;
+  SimplexTree simplex_tree;
+
+  program_options(argc, argv, nbL, file_name, filediag, max_squared_alpha, p, lim_d, min_persistence);
+
+  // Extract the points from the file file_name
+  Point_vector witnesses, landmarks;
+  Gudhi::Points_off_reader<Point_d> off_reader(file_name);
+  if (!off_reader.is_valid()) {
+      std::cerr << "Witness complex - Unable to read file " << file_name << "\n";
+      exit(-1);  // ----- >>
+  }
+  witnesses = Point_vector(off_reader.get_point_cloud());
+  std::cout << "Successfully read " << witnesses.size() << " points.\n";
+  std::cout << "Ambient dimension is " << witnesses[0].dimension() << ".\n";
+
+  // Choose landmarks from witnesses
+  Gudhi::subsampling::pick_n_random_points(witnesses, nbL, std::back_inserter(landmarks));
+
+  // Compute witness complex
+  Witness_complex witness_complex(landmarks,
+                                  witnesses);
+
+  witness_complex.create_complex(simplex_tree, max_squared_alpha, lim_d);
+
+  std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n";
+  std::cout << "   and has dimension " << simplex_tree.dimension() << " \n";
+
+  // Sort the simplices in the order of the filtration
+  simplex_tree.initialize_filtration();
+
+  // Compute the persistence diagram of the complex
+  Persistent_cohomology pcoh(simplex_tree);
+  // initializes the coefficient field for homology
+  pcoh.init_coefficients(p);
+
+  pcoh.compute_persistent_cohomology(min_persistence);
+
+  // Output the diagram in filediag
+  if (filediag.empty()) {
+    pcoh.output_diagram();
+  } else {
+    std::ofstream out(filediag);
+    pcoh.output_diagram(out);
+    out.close();
+  }
+
+  return 0;
+}
+
+
+void program_options(int argc, char * argv[]
+                     , int & nbL
+                     , std::string & file_name
+                     , std::string & filediag
+                     , Filtration_value & max_squared_alpha
+                     , int & p
+                     , int & dim_max
+                     , Filtration_value & min_persistence) {
+  namespace po = boost::program_options;
+
+  po::options_description hidden("Hidden options");
+  hidden.add_options()
+      ("input-file", po::value<std::string>(&file_name),
+      "Name of file containing a point set in off format.");
+
+  Filtration_value default_alpha = std::numeric_limits<Filtration_value>::infinity();
+  po::options_description visible("Allowed options", 100);
+  visible.add_options()
+      ("help,h", "produce help message")
+      ("landmarks,l", po::value<int>(&nbL),
+       "Number of landmarks to choose from the point cloud.")
+      ("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-sq-alpha,a", po::value<Filtration_value>(&max_squared_alpha)->default_value(default_alpha),
+       "Maximal squared relaxation parameter.")
+      ("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)->default_value(0),
+       "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals")
+      ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(std::numeric_limits<int>::max()),
+       "Maximal dimension of the weak witness complex we want to compute.");
+
+  po::positional_options_description pos;
+  pos.add("input-file", 1);
+
+  po::options_description all;
+  all.add(visible).add(hidden);
+  po::variables_map 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")) {
+    std::cout << std::endl;
+    std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
+    std::cout << "of a Weak witness complex defined on a set of input points.\n \n";
+    std::cout << "The output diagram contains one bar per line, written with the convention: \n";
+    std::cout << "   p   dim b d \n";
+    std::cout << "where dim is the dimension of the homological feature,\n";
+    std::cout << "b and d are respectively the birth and death of the feature and \n";
+    std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
+
+    std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
+    std::cout << visible << std::endl;
+    std::abort();
+  }
+}