1 files changed, 165 insertions, 0 deletions
diff --git a/src/cython/gudhi.pyx b/src/cython/gudhi.pyx
new file mode 100644
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+++ b/src/cython/gudhi.pyx
@@ -0,0 +1,165 @@
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.utility cimport pair
+
+cimport cgudhi
+
+
+# SimplexTree python interface
+cdef class SimplexTree:
+    cdef cgudhi.Simplex_tree_interface[cgudhi.Simplex_tree_options_full_featured] *thisptr
+    def __cinit__(self, points=None, max_dimension=3, max_edge_length=float('inf')):
+        self.thisptr = new cgudhi.Simplex_tree_interface[cgudhi.Simplex_tree_options_full_featured]()
+        # Constructor from graph expansion
+        if points is not None:
+            self.thisptr.graph_expansion(points,max_dimension,max_edge_length)
+    def __dealloc__(self):
+        if self.thisptr != NULL:
+            del self.thisptr
+    def get_filtration(self):
+        return self.thisptr.filtration()
+    def filtration(self, simplex):
+        return self.thisptr.simplex_filtration(simplex)
+    def set_filtration(self, filtration):
+        self.thisptr.set_filtration(<double>filtration)
+    def initialize_filtration(self):
+        self.thisptr.initialize_filtration()
+    def num_vertices(self):
+        return self.thisptr.num_vertices()
+    def num_simplices(self):
+        return self.thisptr.num_simplices()
+    def dimension(self):
+        return self.thisptr.dimension()
+    def set_dimension(self, dim):
+        self.thisptr.set_dimension(<int>dim)
+    def find(self, simplex):
+        cdef vector[int] complex
+        for i in simplex:
+          complex.push_back(i)
+        return self.thisptr.find_simplex(complex)
+    def insert(self, simplex, filtration = 0.0):
+        cdef vector[int] complex
+        for i in simplex:
+          complex.push_back(i)
+        return self.thisptr.insert_simplex(complex, <double>filtration)
+    def insert_with_subfaces(self, simplex, filtration = 0.0):
+        cdef vector[int] complex
+        for i in simplex:
+          complex.push_back(i)
+        return self.thisptr.insert_simplex_and_subfaces(complex, <double>filtration)
+    def get_filtered_tree(self):
+        cdef vector[pair[vector[int], double]] coface_tree = self.thisptr.get_filtered_tree()
+        ct = []
+        for filtered_complex in coface_tree:
+            v = []
+            for vertex in filtered_complex.first:
+                v.append(vertex)
+            ct.append((v,filtered_complex.second))
+        return ct
+    def get_skeleton_tree(self, dim):
+        cdef vector[pair[vector[int], double]] coface_tree = self.thisptr.get_skeleton_tree(<int>dim)
+        ct = []
+        for filtered_complex in coface_tree:
+            v = []
+            for vertex in filtered_complex.first:
+                v.append(vertex)
+            ct.append((v,filtered_complex.second))
+        return ct
+    def get_star_tree(self, simplex):
+        cdef vector[int] complex
+        for i in simplex:
+          complex.push_back(i)
+        cdef vector[pair[vector[int], double]] coface_tree = self.thisptr.get_star_tree(complex)
+        ct = []
+        for filtered_complex in coface_tree:
+            v = []
+            for vertex in filtered_complex.first:
+                v.append(vertex)
+            ct.append((v,filtered_complex.second))
+        return ct
+    def get_coface_tree(self, simplex, dim):
+        cdef vector[int] complex
+        for i in simplex:
+          complex.push_back(i)
+        cdef vector[pair[vector[int], double]] coface_tree = self.thisptr.get_coface_tree(complex, <int>dim)
+        ct = []
+        for filtered_complex in coface_tree:
+            v = []
+            for vertex in filtered_complex.first:
+                v.append(vertex)
+            ct.append((v,filtered_complex.second))
+        return ct
+
+
+cdef class MiniSimplexTree:
+    cdef cgudhi.Simplex_tree_interface[cgudhi.Simplex_tree_options_mini] *thisptr
+    def __cinit__(self):
+        self.thisptr = new cgudhi.Simplex_tree_interface[cgudhi.Simplex_tree_options_mini]()
+    def __dealloc__(self):
+        if self.thisptr != NULL:
+            del self.thisptr
+    def num_vertices(self):
+        return self.thisptr.num_vertices()
+    def num_simplices(self):
+        return self.thisptr.num_simplices()
+    def dimension(self):
+        return self.thisptr.dimension()
+    def set_dimension(self, dim):
+        self.thisptr.set_dimension(<int>dim)
+    def find(self, simplex):
+        cdef vector[int] complex
+        for i in simplex:
+          complex.push_back(i)
+        return self.thisptr.find_simplex(complex)
+    def insert(self, simplex):
+        cdef vector[int] complex
+        for i in simplex:
+          complex.push_back(i)
+        return self.thisptr.insert_simplex(complex, 0.0)
+    def insert_with_subfaces(self, simplex, filtration = 0.0):
+        cdef vector[int] complex
+        for i in simplex:
+          complex.push_back(i)
+        return self.thisptr.insert_simplex_and_subfaces(complex, <double>filtration)
+    def get_filtered_tree(self):
+        cdef vector[pair[vector[int], double]] coface_tree = self.thisptr.get_filtered_tree()
+        ct = []
+        for filtered_complex in coface_tree:
+            v = []
+            for vertex in filtered_complex.first:
+                v.append(vertex)
+            ct.append((v,filtered_complex.second))
+        return ct
+    def get_skeleton_tree(self, dim):
+        cdef vector[pair[vector[int], double]] coface_tree = self.thisptr.get_skeleton_tree(<int>dim)
+        ct = []
+        for filtered_complex in coface_tree:
+            v = []
+            for vertex in filtered_complex.first:
+                v.append(vertex)
+            ct.append((v,filtered_complex.second))
+        return ct
+    def get_star_tree(self, simplex):
+        cdef vector[int] complex
+        for i in simplex:
+          complex.push_back(i)
+        cdef vector[pair[vector[int], double]] coface_tree = self.thisptr.get_star_tree(complex)
+        ct = []
+        for filtered_complex in coface_tree:
+            v = []
+            for vertex in filtered_complex.first:
+                v.append(vertex)
+            ct.append((v,filtered_complex.second))
+        return ct
+    def get_coface_tree(self, simplex, dim):
+        cdef vector[int] complex
+        for i in simplex:
+          complex.push_back(i)
+        cdef vector[pair[vector[int], double]] coface_tree = self.thisptr.get_coface_tree(complex, <int>dim)
+        ct = []
+        for filtered_complex in coface_tree:
+            v = []
+            for vertex in filtered_complex.first:
+                v.append(vertex)
+            ct.append((v,filtered_complex.second))
+        return ct