Source code for toponetx.classes.simplicial_complex
-------
Set of simplices of dimension n.
"""
- if rank < len(self._simplex_set.faces_dict) and rank >= 0:
+ if rank < len(self._simplex_set.faces_dict):
return sorted(tuple(i) for i in self._simplex_set.faces_dict[rank].keys())
# return list(self._simplex_set.faces_dict[n].keys())
if rank < 0:
@@ -554,15 +545,22 @@
Source code for toponetx.classes.simplicial_complex
def __setitem__(self, simplex, **attr):
"""Set attributes to a simplex."""
- if isinstance(simplex, Simplex):
- if simplex.nodes in self.faces_dict[len(simplex) - 1]:
- self.faces_dict[len(simplex) - 1].update(attr)
- elif isinstance(simplex, Iterable):
- simplex = frozenset(simplex)
- self.faces_dict[len(simplex) - 1].update(attr)
- elif isinstance(simplex, Hashable):
- if frozenset({simplex}) in self:
- self.faces_dict[0].update(attr)
+ if simplex in self._simplex_set:
+
+ if isinstance(simplex, Simplex):
+ if simplex.nodes in self.faces_dict[len(simplex) - 1]:
+ self.faces_dict[len(simplex) - 1].update(attr)
+ elif isinstance(simplex, Iterable):
+ simplex = frozenset(simplex)
+ if simplex in self.faces_dict[len(simplex) - 1]:
+ self.faces_dict[len(simplex) - 1].update(attr)
+ else:
+ raise KeyError(
+ f"simplex {simplex} is not in the simplex dictionary, add simplex using add_simplex."
+ )
+ elif isinstance(simplex, Hashable):
+ if frozenset({simplex}) in self:
+ self.faces_dict[0].update(attr)
def __iter__(self):
"""Iterate over all faces of the simplicial complex.
@@ -660,61 +658,46 @@
Source code for toponetx.classes.simplicial_complex
self._simplex_set.faces_dict[k - 1][simplex_].update(attr)
def _insert_node(self, simplex, **attr):
- """Insert a node.
- Parameters
- ----------
- simplex : Hashable or Simplex
- a Hashable or singlton Simplex representing a node in a simplicial complex.
-
- Returns
- -------
- None.
- """
if isinstance(simplex, Hashable) and not isinstance(simplex, Iterable):
- self.add_simplex(simplex, **attr)
+ self.insert_simplex(simplex, **attr)
return
if isinstance(simplex, Iterable) or isinstance(simplex, Simplex):
- if len(simplex) == 1:
- if not isinstance(simplex, Simplex):
- simplex_ = frozenset(sorted((simplex,)))
-
- else:
- simplex_ = simplex.nodes
- self._update_faces_dict_length(simplex_)
+ if not isinstance(simplex, Simplex):
- if (
- simplex_ in self._simplex_set.faces_dict[0]
- ): # simplex is already in the complex, just update the properties if needed
- self._simplex_set.faces_dict[0][simplex_].update(attr)
- return
+ simplex_ = frozenset(sorted((simplex,)))
- if self._simplex_set.max_dim < len(simplex) - 1:
- self._simplex_set.max_dim = len(simplex) - 1
+ else:
+ simplex_ = simplex.nodes
+ self._update_faces_dict_length(simplex_)
- if simplex_ not in self._simplex_set.faces_dict[0]:
+ if (
+ simplex_ in self._simplex_set.faces_dict[0]
+ ): # simplex is already in the complex, just update the properties if needed
+ self._simplex_set.faces_dict[0][simplex_].update(attr)
+ return
- self._simplex_set.faces_dict[0][simplex_] = {
- "is_maximal": True,
- "membership": set(),
- }
- else:
- self._simplex_set.faces_dict[0][simplex_] = {"is_maximal": False}
+ if self._simplex_set.max_dim < len(simplex) - 1:
+ self._simplex_set.max_dim = len(simplex) - 1
- if isinstance(simplex, Simplex):
+ if simplex_ not in self._simplex_set.faces_dict[0]:
- self._simplex_set.faces_dict[0][simplex_].update(simplex.properties)
- else:
- self._simplex_set.faces_dict[0][simplex_].update(attr)
+ self._simplex_set.faces_dict[0][simplex_] = {
+ "is_maximal": True,
+ "membership": set(),
+ }
else:
- raise ValueError(
- "input simplex is not a singleton, use add_simplex to insert the simplex"
- )
+ self._simplex_set.faces_dict[0][simplex_] = {"is_maximal": False}
+ if isinstance(simplex, Simplex):
+
+ self._simplex_set.faces_dict[0][simplex_].update(simplex.properties)
+ else:
+ self._simplex_set.faces_dict[0][simplex_].update(attr)
else:
- raise TypeError("input type must be iterable, or singleton Simplex")
+ raise TypeError("input type must be iterable, or Simplex")
def _add_simplex(self, simplex, **attr):
diff --git a/toponetx/api/classes.html b/toponetx/api/classes.html
index 220eff1d..4ecf8762 100644
--- a/toponetx/api/classes.html
+++ b/toponetx/api/classes.html
@@ -2982,19 +2982,11 @@ Features
+
Features
+
- Parameters:
-
+
simplices (list, optional, default: None) – list of maximal simplices that define the simplicial complex
name (hashable, optional, default: None) – If None then a placeholder ‘’ will be inserted as name
mode (str, optional, default ‘normal’.) – computational mode, available options are “normal” or “gudhi”.
-default is ‘normal’.
-Note : When ghudi is selected additioanl structure
-obtained from the simplicial tree is stored.
-this creates an additional reduannt storage
-but it can be used for access the simplicial
-tree of the complex.
-
diff --git a/toponetx/notebooks/01_simplicial_complexes.html b/toponetx/notebooks/01_simplicial_complexes.html
index 40556f36..b69e1b01 100644
--- a/toponetx/notebooks/01_simplicial_complexes.html
+++ b/toponetx/notebooks/01_simplicial_complexes.html
@@ -455,7 +455,7 @@ Example 2 of simplicial complex: a graph with facesthe face set \([[2, 3, 4], [2, 4, 5]]\).
Vertices, edges and faces are known as 0-rank, 1-rank and 2-rank cells, respectively.
-
+
In ToponetX, the simplicial complex can be instantiated by specifying its edge set and face set. Notice in the code below that it is not needed to specify the whole edge set; it suffices to provide the edges which do not constitute boundaries of the faces.
In [4]:
diff --git a/toponetx/searchindex.js b/toponetx/searchindex.js
index f2772118..79ce4ba3 100644
--- a/toponetx/searchindex.js
+++ b/toponetx/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["api/algorithms", "api/classes", "api/datasets", "api/index", "api/transform", "contributing/index", "index", "notebooks/01_simplicial_complexes", "notebooks/02_cell_complexes", "notebooks/03_combinatorial_complexes", "tutorials/index"], "filenames": ["api/algorithms.rst", "api/classes.rst", "api/datasets.rst", "api/index.rst", "api/transform.rst", "contributing/index.rst", "index.rst", "notebooks/01_simplicial_complexes.ipynb", "notebooks/02_cell_complexes.ipynb", "notebooks/03_combinatorial_complexes.ipynb", "tutorials/index.rst"], "titles": ["Algorithms", "Classes", "Datasets", "API Reference", "Transform", "Contributing", "\ud83c\udf10 TopoNetX (TNX) \ud83c\udf69", "Introduction to Simplicial Complexes", "Cell Complexes", "Combinatorial Complexes", "Tutorials"], "terms": {"util": [0, 1, 3], "relat": [0, 5, 6, 9], "eigen": 0, "decomposit": 0, "danielegrattarola": 0, "ginr": 0, "toponetx": [0, 1, 2, 3, 4, 5, 7, 8, 9], "eigen_align": 0, 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\ No newline at end of file
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[[1, "toponetx.classes.combinatorial_complex.CombinatorialComplex.singletons"]], "size() (toponetx.classes.cell_complex.cellcomplex method)": [[1, "toponetx.classes.cell_complex.CellComplex.size"]], "size() (toponetx.classes.combinatorial_complex.combinatorialcomplex method)": [[1, "toponetx.classes.combinatorial_complex.CombinatorialComplex.size"]], "skeleton() (toponetx.classes.cell_complex.cellcomplex method)": [[1, "toponetx.classes.cell_complex.CellComplex.skeleton"]], "skeleton() (toponetx.classes.combinatorial_complex.combinatorialcomplex method)": [[1, "toponetx.classes.combinatorial_complex.CombinatorialComplex.skeleton"]], "skeleton() (toponetx.classes.complex.complex method)": [[1, "toponetx.classes.complex.Complex.skeleton"]], "skeleton() (toponetx.classes.simplicial_complex.simplicialcomplex method)": [[1, "toponetx.classes.simplicial_complex.SimplicialComplex.skeleton"]], "to_cell_complex() (toponetx.classes.simplicial_complex.simplicialcomplex method)": [[1, "toponetx.classes.simplicial_complex.SimplicialComplex.to_cell_complex"]], "to_combinatorial_complex() (toponetx.classes.cell_complex.cellcomplex method)": [[1, "toponetx.classes.cell_complex.CellComplex.to_combinatorial_complex"]], "to_combinatorial_complex() (toponetx.classes.simplicial_complex.simplicialcomplex method)": [[1, "toponetx.classes.simplicial_complex.SimplicialComplex.to_combinatorial_complex"]], "to_hypergraph() (toponetx.classes.cell_complex.cellcomplex method)": [[1, "toponetx.classes.cell_complex.CellComplex.to_hypergraph"]], "to_hypergraph() (toponetx.classes.combinatorial_complex.combinatorialcomplex method)": [[1, "toponetx.classes.combinatorial_complex.CombinatorialComplex.to_hypergraph"]], "to_hypergraph() (toponetx.classes.simplicial_complex.simplicialcomplex method)": [[1, "toponetx.classes.simplicial_complex.SimplicialComplex.to_hypergraph"]], "to_spharapy() (toponetx.classes.simplicial_complex.simplicialcomplex method)": [[1, "toponetx.classes.simplicial_complex.SimplicialComplex.to_spharapy"]], "to_trimesh() (toponetx.classes.simplicial_complex.simplicialcomplex method)": [[1, "toponetx.classes.simplicial_complex.SimplicialComplex.to_trimesh"]], "toponetx.classes.cell": [[1, "module-toponetx.classes.cell"]], "toponetx.classes.cell_complex": [[1, "module-toponetx.classes.cell_complex"]], "toponetx.classes.combinatorial_complex": [[1, "module-toponetx.classes.combinatorial_complex"]], "toponetx.classes.complex": [[1, "module-toponetx.classes.complex"]], "toponetx.classes.hyperedge": [[1, "module-toponetx.classes.hyperedge"]], "toponetx.classes.simplex": [[1, "module-toponetx.classes.simplex"]], "toponetx.classes.simplicial_complex": [[1, "module-toponetx.classes.simplicial_complex"]], "up_laplacian_matrix() (toponetx.classes.cell_complex.cellcomplex method)": [[1, "toponetx.classes.cell_complex.CellComplex.up_laplacian_matrix"]], "up_laplacian_matrix() (toponetx.classes.simplicial_complex.simplicialcomplex method)": [[1, "toponetx.classes.simplicial_complex.SimplicialComplex.up_laplacian_matrix"]], "load_ppi() (in module toponetx.datasets.utils)": [[2, "toponetx.datasets.utils.load_ppi"]], "toponetx.datasets.utils": [[2, "module-toponetx.datasets.utils"]], "graph_2_clique_complex() (in module toponetx.transform.graph_to_simplicial_complex)": [[4, "toponetx.transform.graph_to_simplicial_complex.graph_2_clique_complex"]], "graph_2_neighbor_complex() (in module toponetx.transform.graph_to_simplicial_complex)": [[4, "toponetx.transform.graph_to_simplicial_complex.graph_2_neighbor_complex"]], "toponetx.transform.graph_to_simplicial_complex": [[4, "module-toponetx.transform.graph_to_simplicial_complex"]]}})
\ No newline at end of file
-
+
simplices (list, optional, default: None) – list of maximal simplices that define the simplicial complex
name (hashable, optional, default: None) – If None then a placeholder ‘’ will be inserted as name
-mode (str, optional, default ‘normal’.) – computational mode, available options are “normal” or “gudhi”. -default is ‘normal’.
-Note : When ghudi is selected additioanl structure -obtained from the simplicial tree is stored. -this creates an additional reduannt storage -but it can be used for access the simplicial -tree of the complex.
-
the face set \([[2, 3, 4], [2, 4, 5]]\).
Vertices, edges and faces are known as 0-rank, 1-rank and 2-rank cells, respectively.
-
In ToponetX, the simplicial complex can be instantiated by specifying its edge set and face set. Notice in the code below that it is not needed to specify the whole edge set; it suffices to provide the edges which do not constitute boundaries of the faces.
In [4]:
diff --git a/toponetx/searchindex.js b/toponetx/searchindex.js
index f2772118..79ce4ba3 100644
--- a/toponetx/searchindex.js
+++ b/toponetx/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["api/algorithms", "api/classes", "api/datasets", "api/index", "api/transform", "contributing/index", "index", "notebooks/01_simplicial_complexes", "notebooks/02_cell_complexes", "notebooks/03_combinatorial_complexes", "tutorials/index"], "filenames": ["api/algorithms.rst", "api/classes.rst", "api/datasets.rst", "api/index.rst", "api/transform.rst", "contributing/index.rst", "index.rst", "notebooks/01_simplicial_complexes.ipynb", "notebooks/02_cell_complexes.ipynb", "notebooks/03_combinatorial_complexes.ipynb", "tutorials/index.rst"], "titles": ["Algorithms", "Classes", "Datasets", "API Reference", "Transform", "Contributing", "\ud83c\udf10 TopoNetX (TNX) \ud83c\udf69", "Introduction to Simplicial Complexes", "Cell Complexes", "Combinatorial Complexes", "Tutorials"], "terms": {"util": [0, 1, 3], "relat": [0, 5, 6, 9], "eigen": 0, "decomposit": 0, "danielegrattarola": 0, "ginr": 0, "toponetx": [0, 1, 2, 3, 4, 5, 7, 8, 9], "eigen_align": 0, 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\ No newline at end of file
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[[1, "toponetx.classes.combinatorial_complex.CombinatorialComplex.singletons"]], "size() (toponetx.classes.cell_complex.cellcomplex method)": [[1, "toponetx.classes.cell_complex.CellComplex.size"]], "size() (toponetx.classes.combinatorial_complex.combinatorialcomplex method)": [[1, "toponetx.classes.combinatorial_complex.CombinatorialComplex.size"]], "skeleton() (toponetx.classes.cell_complex.cellcomplex method)": [[1, "toponetx.classes.cell_complex.CellComplex.skeleton"]], "skeleton() (toponetx.classes.combinatorial_complex.combinatorialcomplex method)": [[1, "toponetx.classes.combinatorial_complex.CombinatorialComplex.skeleton"]], "skeleton() (toponetx.classes.complex.complex method)": [[1, "toponetx.classes.complex.Complex.skeleton"]], "skeleton() (toponetx.classes.simplicial_complex.simplicialcomplex method)": [[1, "toponetx.classes.simplicial_complex.SimplicialComplex.skeleton"]], "to_cell_complex() (toponetx.classes.simplicial_complex.simplicialcomplex method)": [[1, "toponetx.classes.simplicial_complex.SimplicialComplex.to_cell_complex"]], "to_combinatorial_complex() (toponetx.classes.cell_complex.cellcomplex method)": [[1, "toponetx.classes.cell_complex.CellComplex.to_combinatorial_complex"]], "to_combinatorial_complex() (toponetx.classes.simplicial_complex.simplicialcomplex method)": [[1, "toponetx.classes.simplicial_complex.SimplicialComplex.to_combinatorial_complex"]], "to_hypergraph() (toponetx.classes.cell_complex.cellcomplex method)": [[1, "toponetx.classes.cell_complex.CellComplex.to_hypergraph"]], "to_hypergraph() (toponetx.classes.combinatorial_complex.combinatorialcomplex method)": [[1, "toponetx.classes.combinatorial_complex.CombinatorialComplex.to_hypergraph"]], "to_hypergraph() (toponetx.classes.simplicial_complex.simplicialcomplex method)": [[1, "toponetx.classes.simplicial_complex.SimplicialComplex.to_hypergraph"]], "to_spharapy() (toponetx.classes.simplicial_complex.simplicialcomplex method)": [[1, "toponetx.classes.simplicial_complex.SimplicialComplex.to_spharapy"]], "to_trimesh() (toponetx.classes.simplicial_complex.simplicialcomplex method)": [[1, "toponetx.classes.simplicial_complex.SimplicialComplex.to_trimesh"]], "toponetx.classes.cell": [[1, "module-toponetx.classes.cell"]], "toponetx.classes.cell_complex": [[1, "module-toponetx.classes.cell_complex"]], "toponetx.classes.combinatorial_complex": [[1, "module-toponetx.classes.combinatorial_complex"]], "toponetx.classes.complex": [[1, "module-toponetx.classes.complex"]], "toponetx.classes.hyperedge": [[1, "module-toponetx.classes.hyperedge"]], "toponetx.classes.simplex": [[1, "module-toponetx.classes.simplex"]], "toponetx.classes.simplicial_complex": [[1, "module-toponetx.classes.simplicial_complex"]], "up_laplacian_matrix() (toponetx.classes.cell_complex.cellcomplex method)": [[1, "toponetx.classes.cell_complex.CellComplex.up_laplacian_matrix"]], "up_laplacian_matrix() (toponetx.classes.simplicial_complex.simplicialcomplex method)": [[1, "toponetx.classes.simplicial_complex.SimplicialComplex.up_laplacian_matrix"]], "load_ppi() (in module toponetx.datasets.utils)": [[2, "toponetx.datasets.utils.load_ppi"]], "toponetx.datasets.utils": [[2, "module-toponetx.datasets.utils"]], "graph_2_clique_complex() (in module toponetx.transform.graph_to_simplicial_complex)": [[4, "toponetx.transform.graph_to_simplicial_complex.graph_2_clique_complex"]], "graph_2_neighbor_complex() (in module toponetx.transform.graph_to_simplicial_complex)": [[4, "toponetx.transform.graph_to_simplicial_complex.graph_2_neighbor_complex"]], "toponetx.transform.graph_to_simplicial_complex": [[4, "module-toponetx.transform.graph_to_simplicial_complex"]]}})
\ No newline at end of file