diff options
| -rwxr-xr-x | scripts/generate_version.sh | 4 | ||||
| -rw-r--r-- | src/cython/gudhi.pyx | 105 | ||||
| -rwxr-xr-x | src/cython/main.py | 8 |
3 files changed, 107 insertions, 10 deletions
diff --git a/scripts/generate_version.sh b/scripts/generate_version.sh index 323396dc..8395723e 100755 --- a/scripts/generate_version.sh +++ b/scripts/generate_version.sh @@ -76,6 +76,10 @@ do then # SPECIFIC FOR GUDHI USER INTERFACE cp -R $ROOT_DIR/src/$package $VERSION_DIR + elif [ "$package" == "cython" ] + then + # SPECIFIC FOR CYTHON INTERFACE + cp -R $ROOT_DIR/src/$package $VERSION_DIR else # PACKAGE COPY if [ -d "$ROOT_DIR/src/$package$PACKAGE_INC_DIR" ] diff --git a/src/cython/gudhi.pyx b/src/cython/gudhi.pyx index ae9669f4..dd87f4bb 100644 --- a/src/cython/gudhi.pyx +++ b/src/cython/gudhi.pyx @@ -4,6 +4,7 @@ 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 @@ -37,17 +38,57 @@ cdef class SimplexTree: complex.push_back(i) return self.thisptr.find_simplex(complex) def insert(self, simplex, filtration = 0.0): - return self.thisptr.insert_simplex(simplex, <double>filtration) + 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): - return self.thisptr.insert_simplex_and_subfaces(simplex, <double>filtration) + 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): - return self.thisptr.get_filtered_tree() + 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): - return self.thisptr.get_skeleton_tree(<int>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): - return self.thisptr.get_star_tree(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): - return self.thisptr.get_coface_tree(simplex, <int>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: @@ -70,3 +111,55 @@ cdef class MiniSimplexTree: 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 diff --git a/src/cython/main.py b/src/cython/main.py index a36b4fa8..a4fc87ba 100755 --- a/src/cython/main.py +++ b/src/cython/main.py @@ -52,13 +52,13 @@ print("MiniSimplexTree creation from insertion") triangle012 = [0, 1, 2] edge03 = [0, 3] mini_st = gudhi.MiniSimplexTree() -mini_st.insert_simplex_and_subfaces(triangle012) -mini_st.insert_simplex_and_subfaces(edge03) +mini_st.insert_with_subfaces(triangle012) +mini_st.insert_with_subfaces(edge03) # FIXME: Remove this line mini_st.set_dimension(2); edge02 = [0, 2] -if st.st.find(edge02): +if mini_st.find(edge02): # Only coface is 012 - print("coface(edge02,1)=", st_from_graph_expansion.get_coface_tree(edge02, 1)) + print("coface(edge02,1)=", mini_st.get_coface_tree(edge02, 1)) |