Add relaxed witness cytonization

Add 2000_random_points_on_3D_Torus.csv for rips_complex_from_file_example.py and witness_complex_from_file_example.py


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@1273 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 80469ca5fb20f21d87fd2816e3f212280ac45caf

6 files changed, 2040 insertions, 25 deletions

diff --git a/src/cython/Makefile b/src/cython/Makefile
index ada1d15b..6727bb3d 100644
--- a/src/cython/Makefile
+++ b/src/cython/Makefile
@@ -13,10 +13,12 @@ example:
 	python example/rips_complex_example.py
 	python example/alpha_complex_example.py
 	python example/random_cubical_complex_example.py 10 10
+	python example/cubical_complex_from_perseus_file_example.py -f ../data/bitmap/CubicalTwoSphere.txt
 	# python example/gudhi_graphical_tools_example.py
 	# python example/rips_persistence_diagram.py
 	# python example/alpha_complex_from_file_example.py data/500_random_points_on_3D_Torus.csv
-	# python example/rips_complex_from_file_example.py data/500_random_points_on_3D_Torus.csv
+	# python example/rips_complex_from_file_example.py data/2000_random_points_on_3D_Torus.csv
+	# python example/witness_complex_from_file_example.py data/2000_random_points_on_3D_Torus.csv
 
 clean:
 	rm -rf build/ *.o *.so *.cpp
diff --git a/src/cython/data/2000_random_points_on_3D_Torus.csv b/src/cython/data/2000_random_points_on_3D_Torus.csv
new file mode 100644
index 00000000..c1fefb9f
--- /dev/null
+++ b/src/cython/data/2000_random_points_on_3D_Torus.csv
@@ -0,0 +1,2000 @@
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diff --git a/src/cython/example/rips_complex_from_file_example.py b/src/cython/example/rips_complex_from_file_example.py
index 9385aba0..fae72443 100755
--- a/src/cython/example/rips_complex_from_file_example.py
+++ b/src/cython/example/rips_complex_from_file_example.py
@@ -37,7 +37,7 @@ parser = argparse.ArgumentParser(description='RipsComplex creation from '
                                  'points read in a file.',
                                  epilog='Example: '
                                  'example/rips_complex_from_file_example.py '
-                                 'data/500_random_points_on_3D_Torus.csv '
+                                 'data/2000_random_points_on_3D_Torus.csv '
                                  '- Constructs a rips complex with the '
                                  'points from the given file. File format '
                                  'is X1, X2, ..., Xn')
@@ -46,13 +46,13 @@ args = parser.parse_args()
 
 points = pandas.read_csv(args.file, header=None)
 
-print("RipsComplex with max_edge_length=1.9")
+print("RipsComplex with max_edge_length=0.7")
 
 rips_complex = gudhi.RipsComplex(points=points.values,
-                                 max_dimension=len(points.values[0]), max_edge_length=1.9)
+                                 max_dimension=len(points.values[0]), max_edge_length=0.7)
 
 rips_complex.initialize_filtration()
-diag = rips_complex.persistence(homology_coeff_field=2, min_persistence=0.1)
+diag = rips_complex.persistence(homology_coeff_field=2, min_persistence=0.3)
 
 print("betti_numbers()=")
 print(rips_complex.betti_numbers())
diff --git a/src/cython/example/witness_complex_from_file_example.py b/src/cython/example/witness_complex_from_file_example.py
index 9d1a940f..d67d1c34 100755
--- a/src/cython/example/witness_complex_from_file_example.py
+++ b/src/cython/example/witness_complex_from_file_example.py
@@ -37,7 +37,7 @@ parser = argparse.ArgumentParser(description='WitnessComplex creation from '
                                  'points read in a file.',
                                  epilog='Example: '
                                  'example/witness_complex_from_file_example.py'
-                                 ' data/500_random_points_on_3D_Torus.csv '
+                                 ' data/2000_random_points_on_3D_Torus.csv '
                                  '- Constructs a witness complex with the '
                                  'points from the given file. File format '
                                  'is X1, X2, ..., Xn')
@@ -46,25 +46,20 @@ args = parser.parse_args()
 
 points = pandas.read_csv(args.file, header=None)
 
-print("WitnessComplex with number_of_landmarks=5")
+print("WitnessComplex with number_of_landmarks=100 alpha=0.7 epsilon_mu=0.001 max_dim=10")
 
 witness_complex = gudhi.WitnessComplex(points=points.values,
-                                     number_of_landmarks=200)
-
-print("filtered_tree=", witness_complex.get_filtered_tree())
+                                       number_of_landmarks=100,
+                                       max_alpha_square=0.7,
+                                       mu_epsilon=0.001,
+                                       dimension_limit=10)
 
 witness_complex.initialize_filtration()
 diag = witness_complex.persistence(homology_coeff_field=2, min_persistence=0.1)
 
-print("diag=", diag)
-
-gudhi.diagram_persistence(diag)
-
-"""
 print("betti_numbers()=")
 print(witness_complex.betti_numbers())
 
 gudhi.diagram_persistence(diag)
 
 gudhi.barcode_persistence(diag)
-"""
\ No newline at end of file
diff --git a/src/cython/src/cpp/Witness_complex_interface.h b/src/cython/src/cpp/Witness_complex_interface.h
index bdfea91f..2b3aa4bf 100644
--- a/src/cython/src/cpp/Witness_complex_interface.h
+++ b/src/cython/src/cpp/Witness_complex_interface.h
@@ -24,8 +24,9 @@
 #define	WITNESS_COMPLEX_INTERFACE_H
 
 #include <gudhi/Simplex_tree.h>
-#include <gudhi/Witness_complex.h>
-#include <gudhi/Landmark_choice_by_furthest_point.h>
+#include <gudhi/Relaxed_witness_complex.h>
+#include <gudhi/Landmark_choice_sparsification.h>
+#include <gudhi/A0_complex.h>
 
 #include "Persistent_cohomology_interface.h"
 
@@ -45,13 +46,22 @@ class Witness_complex_interface {
   using Complex_tree = std::vector<Filtered_complex>;
 
  public:
-  Witness_complex_interface(std::vector<std::vector<double>>&points, int number_of_landmarks)
+  Witness_complex_interface(std::vector<std::vector<double>>&points, int number_of_landmarks, double max_alpha_square,
+                            double mu_epsilon, int dimension_limit)
   : pcoh_(nullptr) {
     std::vector<std::vector< int > > knn;
+    std::vector<std::vector< FT > > distances;
+    std::vector< Point_d > landmarks;
+    std::vector<Point_d> point_vector;
+    for (auto point : points) {
+      point_vector.push_back(Point_d(point.size(), point.begin(), point.end()));
+    }
+    Gudhi::witness_complex::landmark_choice_by_sparsification(point_vector, number_of_landmarks, mu_epsilon, landmarks);
+    Gudhi::witness_complex::build_distance_matrix(point_vector, landmarks, max_alpha_square, dimension_limit, knn,
+                                                  distances);
 
-    Gudhi::witness_complex::landmark_choice_by_furthest_point(points, number_of_landmarks, knn);
-    Gudhi::witness_complex::witness_complex(knn, number_of_landmarks, points[0].size(), simplex_tree_);
-
+    A0_complex< Simplex_tree<> > rw(distances, knn, simplex_tree_, number_of_landmarks, max_alpha_square,
+                                    dimension_limit);
   }
 
   bool find_simplex(const Simplex& vh) {
diff --git a/src/cython/src/cython/witness_complex.pyx b/src/cython/src/cython/witness_complex.pyx
index b9f354d5..1f99bd8c 100644
--- a/src/cython/src/cython/witness_complex.pyx
+++ b/src/cython/src/cython/witness_complex.pyx
@@ -30,7 +30,7 @@ __license__ = "GPL v3"
 
 cdef extern from "Witness_complex_interface.h" namespace "Gudhi":
     cdef cppclass Witness_complex_interface "Gudhi::witness_complex::Witness_complex_interface":
-        Witness_complex_interface(vector[vector[double]] points, int number_of_landmarks)
+        Witness_complex_interface(vector[vector[double]] points, int number_of_landmarks, double max_alpha_square, double mu_epsilon, int dimension_limit)
         double filtration()
         double simplex_filtration(vector[int] simplex)
         void set_filtration(double filtration)
@@ -63,17 +63,25 @@ cdef class WitnessComplex:
 
     #cdef Witness_complex_persistence_interface * pcohptr
 
-    def __cinit__(self, points=None, number_of_landmarks=5):
+    def __cinit__(self, points, number_of_landmarks, max_alpha_square,
+                  mu_epsilon, dimension_limit):
         """WitnessComplex constructor.
 
         Args:
            points (list): A list of points in d-Dimension.
            number_of_landmarks (int): Number of landmarks to build the
            WitnessComplex.
+           max_alpha_square (float): Maximum alpha square value to build the
+           distance matrix.
+           mu_epsilon (float): Mu epsilon value for sparsification.
+           dimension_limit (int): Dimension limit of the simplicial complex.
         """
         if points is not None:
             self.thisptr = new Witness_complex_interface(points,
-                                                         number_of_landmarks)
+                                                         number_of_landmarks,
+                                                         max_alpha_square,
+                                                         mu_epsilon,
+                                                         dimension_limit)
 
     def __dealloc__(self):
         if self.thisptr != NULL: