| """Functions for generating trees. |
| |
| The functions sampling trees at random in this module come |
| in two variants: labeled and unlabeled. The labeled variants |
| sample from every possible tree with the given number of nodes |
| uniformly at random. The unlabeled variants sample from every |
| possible *isomorphism class* of trees with the given number |
| of nodes uniformly at random. |
| |
| To understand the difference, consider the following example. |
| There are two isomorphism classes of trees with four nodes. |
| One is that of the path graph, the other is that of the |
| star graph. The unlabeled variant will return a line graph or |
| a star graph with probability 1/2. |
| |
| The labeled variant will return the line graph |
| with probability 3/4 and the star graph with probability 1/4, |
| because there are more labeled variants of the line graph |
| than of the star graph. More precisely, the line graph has |
| an automorphism group of order 2, whereas the star graph has |
| an automorphism group of order 6, so the line graph has three |
| times as many labeled variants as the star graph, and thus |
| three more chances to be drawn. |
| |
| Additionally, some functions in this module can sample rooted |
| trees and forests uniformly at random. A rooted tree is a tree |
| with a designated root node. A rooted forest is a disjoint union |
| of rooted trees. |
| """ |
|
|
| from collections import Counter, defaultdict |
| from math import comb, factorial |
|
|
| import networkx as nx |
| from networkx.utils import py_random_state |
|
|
| __all__ = [ |
| "prefix_tree", |
| "prefix_tree_recursive", |
| "random_labeled_tree", |
| "random_labeled_rooted_tree", |
| "random_labeled_rooted_forest", |
| "random_unlabeled_tree", |
| "random_unlabeled_rooted_tree", |
| "random_unlabeled_rooted_forest", |
| ] |
|
|
|
|
| @nx._dispatchable(graphs=None, returns_graph=True) |
| def prefix_tree(paths): |
| """Creates a directed prefix tree from a list of paths. |
| |
| Usually the paths are described as strings or lists of integers. |
| |
| A "prefix tree" represents the prefix structure of the strings. |
| Each node represents a prefix of some string. The root represents |
| the empty prefix with children for the single letter prefixes which |
| in turn have children for each double letter prefix starting with |
| the single letter corresponding to the parent node, and so on. |
| |
| More generally the prefixes do not need to be strings. A prefix refers |
| to the start of a sequence. The root has children for each one element |
| prefix and they have children for each two element prefix that starts |
| with the one element sequence of the parent, and so on. |
| |
| Note that this implementation uses integer nodes with an attribute. |
| Each node has an attribute "source" whose value is the original element |
| of the path to which this node corresponds. For example, suppose `paths` |
| consists of one path: "can". Then the nodes `[1, 2, 3]` which represent |
| this path have "source" values "c", "a" and "n". |
| |
| All the descendants of a node have a common prefix in the sequence/path |
| associated with that node. From the returned tree, the prefix for each |
| node can be constructed by traversing the tree up to the root and |
| accumulating the "source" values along the way. |
| |
| The root node is always `0` and has "source" attribute `None`. |
| The root is the only node with in-degree zero. |
| The nil node is always `-1` and has "source" attribute `"NIL"`. |
| The nil node is the only node with out-degree zero. |
| |
| |
| Parameters |
| ---------- |
| paths: iterable of paths |
| An iterable of paths which are themselves sequences. |
| Matching prefixes among these sequences are identified with |
| nodes of the prefix tree. One leaf of the tree is associated |
| with each path. (Identical paths are associated with the same |
| leaf of the tree.) |
| |
| |
| Returns |
| ------- |
| tree: DiGraph |
| A directed graph representing an arborescence consisting of the |
| prefix tree generated by `paths`. Nodes are directed "downward", |
| from parent to child. A special "synthetic" root node is added |
| to be the parent of the first node in each path. A special |
| "synthetic" leaf node, the "nil" node `-1`, is added to be the child |
| of all nodes representing the last element in a path. (The |
| addition of this nil node technically makes this not an |
| arborescence but a directed acyclic graph; removing the nil node |
| makes it an arborescence.) |
| |
| |
| Notes |
| ----- |
| The prefix tree is also known as a *trie*. |
| |
| |
| Examples |
| -------- |
| Create a prefix tree from a list of strings with common prefixes:: |
| |
| >>> paths = ["ab", "abs", "ad"] |
| >>> T = nx.prefix_tree(paths) |
| >>> list(T.edges) |
| [(0, 1), (1, 2), (1, 4), (2, -1), (2, 3), (3, -1), (4, -1)] |
| |
| The leaf nodes can be obtained as predecessors of the nil node:: |
| |
| >>> root, NIL = 0, -1 |
| >>> list(T.predecessors(NIL)) |
| [2, 3, 4] |
| |
| To recover the original paths that generated the prefix tree, |
| traverse up the tree from the node `-1` to the node `0`:: |
| |
| >>> recovered = [] |
| >>> for v in T.predecessors(NIL): |
| ... prefix = "" |
| ... while v != root: |
| ... prefix = str(T.nodes[v]["source"]) + prefix |
| ... v = next(T.predecessors(v)) # only one predecessor |
| ... recovered.append(prefix) |
| >>> sorted(recovered) |
| ['ab', 'abs', 'ad'] |
| """ |
|
|
| def get_children(parent, paths): |
| children = defaultdict(list) |
| |
| |
| for path in paths: |
| |
| if not path: |
| tree.add_edge(parent, NIL) |
| continue |
| child, *rest = path |
| |
| children[child].append(rest) |
| return children |
|
|
| |
| tree = nx.DiGraph() |
| root = 0 |
| tree.add_node(root, source=None) |
| NIL = -1 |
| tree.add_node(NIL, source="NIL") |
| children = get_children(root, paths) |
| stack = [(root, iter(children.items()))] |
| while stack: |
| parent, remaining_children = stack[-1] |
| try: |
| child, remaining_paths = next(remaining_children) |
| |
| except StopIteration: |
| stack.pop() |
| continue |
| |
| new_name = len(tree) - 1 |
| |
| tree.add_node(new_name, source=child) |
| tree.add_edge(parent, new_name) |
| children = get_children(new_name, remaining_paths) |
| stack.append((new_name, iter(children.items()))) |
|
|
| return tree |
|
|
|
|
| @nx._dispatchable(graphs=None, returns_graph=True) |
| def prefix_tree_recursive(paths): |
| """Recursively creates a directed prefix tree from a list of paths. |
| |
| The original recursive version of prefix_tree for comparison. It is |
| the same algorithm but the recursion is unrolled onto a stack. |
| |
| Usually the paths are described as strings or lists of integers. |
| |
| A "prefix tree" represents the prefix structure of the strings. |
| Each node represents a prefix of some string. The root represents |
| the empty prefix with children for the single letter prefixes which |
| in turn have children for each double letter prefix starting with |
| the single letter corresponding to the parent node, and so on. |
| |
| More generally the prefixes do not need to be strings. A prefix refers |
| to the start of a sequence. The root has children for each one element |
| prefix and they have children for each two element prefix that starts |
| with the one element sequence of the parent, and so on. |
| |
| Note that this implementation uses integer nodes with an attribute. |
| Each node has an attribute "source" whose value is the original element |
| of the path to which this node corresponds. For example, suppose `paths` |
| consists of one path: "can". Then the nodes `[1, 2, 3]` which represent |
| this path have "source" values "c", "a" and "n". |
| |
| All the descendants of a node have a common prefix in the sequence/path |
| associated with that node. From the returned tree, ehe prefix for each |
| node can be constructed by traversing the tree up to the root and |
| accumulating the "source" values along the way. |
| |
| The root node is always `0` and has "source" attribute `None`. |
| The root is the only node with in-degree zero. |
| The nil node is always `-1` and has "source" attribute `"NIL"`. |
| The nil node is the only node with out-degree zero. |
| |
| |
| Parameters |
| ---------- |
| paths: iterable of paths |
| An iterable of paths which are themselves sequences. |
| Matching prefixes among these sequences are identified with |
| nodes of the prefix tree. One leaf of the tree is associated |
| with each path. (Identical paths are associated with the same |
| leaf of the tree.) |
| |
| |
| Returns |
| ------- |
| tree: DiGraph |
| A directed graph representing an arborescence consisting of the |
| prefix tree generated by `paths`. Nodes are directed "downward", |
| from parent to child. A special "synthetic" root node is added |
| to be the parent of the first node in each path. A special |
| "synthetic" leaf node, the "nil" node `-1`, is added to be the child |
| of all nodes representing the last element in a path. (The |
| addition of this nil node technically makes this not an |
| arborescence but a directed acyclic graph; removing the nil node |
| makes it an arborescence.) |
| |
| |
| Notes |
| ----- |
| The prefix tree is also known as a *trie*. |
| |
| |
| Examples |
| -------- |
| Create a prefix tree from a list of strings with common prefixes:: |
| |
| >>> paths = ["ab", "abs", "ad"] |
| >>> T = nx.prefix_tree(paths) |
| >>> list(T.edges) |
| [(0, 1), (1, 2), (1, 4), (2, -1), (2, 3), (3, -1), (4, -1)] |
| |
| The leaf nodes can be obtained as predecessors of the nil node. |
| |
| >>> root, NIL = 0, -1 |
| >>> list(T.predecessors(NIL)) |
| [2, 3, 4] |
| |
| To recover the original paths that generated the prefix tree, |
| traverse up the tree from the node `-1` to the node `0`:: |
| |
| >>> recovered = [] |
| >>> for v in T.predecessors(NIL): |
| ... prefix = "" |
| ... while v != root: |
| ... prefix = str(T.nodes[v]["source"]) + prefix |
| ... v = next(T.predecessors(v)) # only one predecessor |
| ... recovered.append(prefix) |
| >>> sorted(recovered) |
| ['ab', 'abs', 'ad'] |
| """ |
|
|
| def _helper(paths, root, tree): |
| """Recursively create a trie from the given list of paths. |
| |
| `paths` is a list of paths, each of which is itself a list of |
| nodes, relative to the given `root` (but not including it). This |
| list of paths will be interpreted as a tree-like structure, in |
| which two paths that share a prefix represent two branches of |
| the tree with the same initial segment. |
| |
| `root` is the parent of the node at index 0 in each path. |
| |
| `tree` is the "accumulator", the :class:`networkx.DiGraph` |
| representing the branching to which the new nodes and edges will |
| be added. |
| |
| """ |
| |
| |
| children = defaultdict(list) |
| for path in paths: |
| |
| if not path: |
| tree.add_edge(root, NIL) |
| continue |
| child, *rest = path |
| |
| children[child].append(rest) |
| |
| for child, remaining_paths in children.items(): |
| |
| new_name = len(tree) - 1 |
| |
| tree.add_node(new_name, source=child) |
| tree.add_edge(root, new_name) |
| _helper(remaining_paths, new_name, tree) |
|
|
| |
| tree = nx.DiGraph() |
| root = 0 |
| tree.add_node(root, source=None) |
| NIL = -1 |
| tree.add_node(NIL, source="NIL") |
| |
| _helper(paths, root, tree) |
| return tree |
|
|
|
|
| @py_random_state("seed") |
| @nx._dispatchable(graphs=None, returns_graph=True) |
| def random_labeled_tree(n, *, seed=None): |
| """Returns a labeled tree on `n` nodes chosen uniformly at random. |
| |
| Generating uniformly distributed random Prüfer sequences and |
| converting them into the corresponding trees is a straightforward |
| method of generating uniformly distributed random labeled trees. |
| This function implements this method. |
| |
| Parameters |
| ---------- |
| n : int |
| The number of nodes, greater than zero. |
| seed : random_state |
| Indicator of random number generation state. |
| See :ref:`Randomness<randomness>` |
| |
| Returns |
| ------- |
| :class:`networkx.Graph` |
| A `networkx.Graph` with nodes in the set {0, …, *n* - 1}. |
| |
| Raises |
| ------ |
| NetworkXPointlessConcept |
| If `n` is zero (because the null graph is not a tree). |
| |
| Examples |
| -------- |
| >>> G = nx.random_labeled_tree(5, seed=42) |
| >>> nx.is_tree(G) |
| True |
| >>> G.edges |
| EdgeView([(0, 1), (0, 3), (0, 2), (2, 4)]) |
| |
| A tree with *arbitrarily directed* edges can be created by assigning |
| generated edges to a ``DiGraph``: |
| |
| >>> DG = nx.DiGraph() |
| >>> DG.add_edges_from(G.edges) |
| >>> nx.is_tree(DG) |
| True |
| >>> DG.edges |
| OutEdgeView([(0, 1), (0, 3), (0, 2), (2, 4)]) |
| """ |
| |
| if n == 0: |
| raise nx.NetworkXPointlessConcept("the null graph is not a tree") |
| if n == 1: |
| return nx.empty_graph(1) |
| return nx.from_prufer_sequence([seed.choice(range(n)) for i in range(n - 2)]) |
|
|
|
|
| @py_random_state("seed") |
| @nx._dispatchable(graphs=None, returns_graph=True) |
| def random_labeled_rooted_tree(n, *, seed=None): |
| """Returns a labeled rooted tree with `n` nodes. |
| |
| The returned tree is chosen uniformly at random from all labeled rooted trees. |
| |
| Parameters |
| ---------- |
| n : int |
| The number of nodes |
| seed : integer, random_state, or None (default) |
| Indicator of random number generation state. |
| See :ref:`Randomness<randomness>`. |
| |
| Returns |
| ------- |
| :class:`networkx.Graph` |
| A `networkx.Graph` with integer nodes 0 <= node <= `n` - 1. |
| The root of the tree is selected uniformly from the nodes. |
| The "root" graph attribute identifies the root of the tree. |
| |
| Notes |
| ----- |
| This function returns the result of :func:`random_labeled_tree` |
| with a randomly selected root. |
| |
| Raises |
| ------ |
| NetworkXPointlessConcept |
| If `n` is zero (because the null graph is not a tree). |
| """ |
| t = random_labeled_tree(n, seed=seed) |
| t.graph["root"] = seed.randint(0, n - 1) |
| return t |
|
|
|
|
| @py_random_state("seed") |
| @nx._dispatchable(graphs=None, returns_graph=True) |
| def random_labeled_rooted_forest(n, *, seed=None): |
| """Returns a labeled rooted forest with `n` nodes. |
| |
| The returned forest is chosen uniformly at random using a |
| generalization of Prüfer sequences [1]_ in the form described in [2]_. |
| |
| Parameters |
| ---------- |
| n : int |
| The number of nodes. |
| seed : random_state |
| See :ref:`Randomness<randomness>`. |
| |
| Returns |
| ------- |
| :class:`networkx.Graph` |
| A `networkx.Graph` with integer nodes 0 <= node <= `n` - 1. |
| The "roots" graph attribute is a set of integers containing the roots. |
| |
| References |
| ---------- |
| .. [1] Knuth, Donald E. "Another Enumeration of Trees." |
| Canadian Journal of Mathematics, 20 (1968): 1077-1086. |
| https://doi.org/10.4153/CJM-1968-104-8 |
| .. [2] Rubey, Martin. "Counting Spanning Trees". Diplomarbeit |
| zur Erlangung des akademischen Grades Magister der |
| Naturwissenschaften an der Formal- und Naturwissenschaftlichen |
| Fakultät der Universität Wien. Wien, May 2000. |
| """ |
|
|
| |
| |
| def _select_k(n, seed): |
| r = seed.randint(0, (n + 1) ** (n - 1) - 1) |
| cum_sum = 0 |
| for k in range(1, n): |
| cum_sum += (factorial(n - 1) * n ** (n - k)) // ( |
| factorial(k - 1) * factorial(n - k) |
| ) |
| if r < cum_sum: |
| return k |
|
|
| return n |
|
|
| F = nx.empty_graph(n) |
| if n == 0: |
| F.graph["roots"] = {} |
| return F |
| |
| k = _select_k(n, seed) |
| if k == n: |
| F.graph["roots"] = set(range(n)) |
| return F |
| |
| roots = seed.sample(range(n), k) |
| |
| p = set(range(n)).difference(roots) |
| |
| N = [seed.randint(0, n - 1) for i in range(n - k - 1)] |
| |
| degree = Counter([x for x in N if x in p]) |
| |
| iterator = iter(x for x in p if degree[x] == 0) |
| u = last = next(iterator) |
| |
| |
| for v in N: |
| F.add_edge(u, v) |
| degree[v] -= 1 |
| if v < last and degree[v] == 0: |
| u = v |
| else: |
| last = u = next(iterator) |
|
|
| F.add_edge(u, roots[0]) |
| F.graph["roots"] = set(roots) |
| return F |
|
|
|
|
| |
|
|
|
|
| def _to_nx(edges, n_nodes, root=None, roots=None): |
| """ |
| Converts the (edges, n_nodes) input to a :class:`networkx.Graph`. |
| The (edges, n_nodes) input is a list of even length, where each pair |
| of consecutive integers represents an edge, and an integer `n_nodes`. |
| Integers in the list are elements of `range(n_nodes)`. |
| |
| Parameters |
| ---------- |
| edges : list of ints |
| The flattened list of edges of the graph. |
| n_nodes : int |
| The number of nodes of the graph. |
| root: int (default=None) |
| If not None, the "root" attribute of the graph will be set to this value. |
| roots: collection of ints (default=None) |
| If not None, he "roots" attribute of the graph will be set to this value. |
| |
| Returns |
| ------- |
| :class:`networkx.Graph` |
| The graph with `n_nodes` nodes and edges given by `edges`. |
| """ |
| G = nx.empty_graph(n_nodes) |
| G.add_edges_from(edges) |
| if root is not None: |
| G.graph["root"] = root |
| if roots is not None: |
| G.graph["roots"] = roots |
| return G |
|
|
|
|
| def _num_rooted_trees(n, cache_trees): |
| """Returns the number of unlabeled rooted trees with `n` nodes. |
| |
| See also https://oeis.org/A000081. |
| |
| Parameters |
| ---------- |
| n : int |
| The number of nodes |
| cache_trees : list of ints |
| The $i$-th element is the number of unlabeled rooted trees with $i$ nodes, |
| which is used as a cache (and is extended to length $n+1$ if needed) |
| |
| Returns |
| ------- |
| int |
| The number of unlabeled rooted trees with `n` nodes. |
| """ |
| for n_i in range(len(cache_trees), n + 1): |
| cache_trees.append( |
| sum( |
| [ |
| d * cache_trees[n_i - j * d] * cache_trees[d] |
| for d in range(1, n_i) |
| for j in range(1, (n_i - 1) // d + 1) |
| ] |
| ) |
| // (n_i - 1) |
| ) |
| return cache_trees[n] |
|
|
|
|
| def _select_jd_trees(n, cache_trees, seed): |
| """Returns a pair $(j,d)$ with a specific probability |
| |
| Given $n$, returns a pair of positive integers $(j,d)$ with the probability |
| specified in formula (5) of Chapter 29 of [1]_. |
| |
| Parameters |
| ---------- |
| n : int |
| The number of nodes |
| cache_trees : list of ints |
| Cache for :func:`_num_rooted_trees`. |
| seed : random_state |
| See :ref:`Randomness<randomness>`. |
| |
| Returns |
| ------- |
| (int, int) |
| A pair of positive integers $(j,d)$ satisfying formula (5) of |
| Chapter 29 of [1]_. |
| |
| References |
| ---------- |
| .. [1] Nijenhuis, Albert, and Wilf, Herbert S. |
| "Combinatorial algorithms: for computers and calculators." |
| Academic Press, 1978. |
| https://doi.org/10.1016/C2013-0-11243-3 |
| """ |
| p = seed.randint(0, _num_rooted_trees(n, cache_trees) * (n - 1) - 1) |
| cumsum = 0 |
| for d in range(n - 1, 0, -1): |
| for j in range(1, (n - 1) // d + 1): |
| cumsum += ( |
| d |
| * _num_rooted_trees(n - j * d, cache_trees) |
| * _num_rooted_trees(d, cache_trees) |
| ) |
| if p < cumsum: |
| return (j, d) |
|
|
|
|
| def _random_unlabeled_rooted_tree(n, cache_trees, seed): |
| """Returns an unlabeled rooted tree with `n` nodes. |
| |
| Returns an unlabeled rooted tree with `n` nodes chosen uniformly |
| at random using the "RANRUT" algorithm from [1]_. |
| The tree is returned in the form: (list_of_edges, number_of_nodes) |
| |
| Parameters |
| ---------- |
| n : int |
| The number of nodes, greater than zero. |
| cache_trees : list ints |
| Cache for :func:`_num_rooted_trees`. |
| seed : random_state |
| See :ref:`Randomness<randomness>`. |
| |
| Returns |
| ------- |
| (list_of_edges, number_of_nodes) : list, int |
| A random unlabeled rooted tree with `n` nodes as a 2-tuple |
| ``(list_of_edges, number_of_nodes)``. |
| The root is node 0. |
| |
| References |
| ---------- |
| .. [1] Nijenhuis, Albert, and Wilf, Herbert S. |
| "Combinatorial algorithms: for computers and calculators." |
| Academic Press, 1978. |
| https://doi.org/10.1016/C2013-0-11243-3 |
| """ |
| if n == 1: |
| edges, n_nodes = [], 1 |
| return edges, n_nodes |
| if n == 2: |
| edges, n_nodes = [(0, 1)], 2 |
| return edges, n_nodes |
|
|
| j, d = _select_jd_trees(n, cache_trees, seed) |
| t1, t1_nodes = _random_unlabeled_rooted_tree(n - j * d, cache_trees, seed) |
| t2, t2_nodes = _random_unlabeled_rooted_tree(d, cache_trees, seed) |
| t12 = [(0, t2_nodes * i + t1_nodes) for i in range(j)] |
| t1.extend(t12) |
| for _ in range(j): |
| t1.extend((n1 + t1_nodes, n2 + t1_nodes) for n1, n2 in t2) |
| t1_nodes += t2_nodes |
|
|
| return t1, t1_nodes |
|
|
|
|
| @py_random_state("seed") |
| @nx._dispatchable(graphs=None, returns_graph=True) |
| def random_unlabeled_rooted_tree(n, *, number_of_trees=None, seed=None): |
| """Returns a number of unlabeled rooted trees uniformly at random |
| |
| Returns one or more (depending on `number_of_trees`) |
| unlabeled rooted trees with `n` nodes drawn uniformly |
| at random. |
| |
| Parameters |
| ---------- |
| n : int |
| The number of nodes |
| number_of_trees : int or None (default) |
| If not None, this number of trees is generated and returned. |
| seed : integer, random_state, or None (default) |
| Indicator of random number generation state. |
| See :ref:`Randomness<randomness>`. |
| |
| Returns |
| ------- |
| :class:`networkx.Graph` or list of :class:`networkx.Graph` |
| A single `networkx.Graph` (or a list thereof, if `number_of_trees` |
| is specified) with nodes in the set {0, …, *n* - 1}. |
| The "root" graph attribute identifies the root of the tree. |
| |
| Notes |
| ----- |
| The trees are generated using the "RANRUT" algorithm from [1]_. |
| The algorithm needs to compute some counting functions |
| that are relatively expensive: in case several trees are needed, |
| it is advisable to use the `number_of_trees` optional argument |
| to reuse the counting functions. |
| |
| Raises |
| ------ |
| NetworkXPointlessConcept |
| If `n` is zero (because the null graph is not a tree). |
| |
| References |
| ---------- |
| .. [1] Nijenhuis, Albert, and Wilf, Herbert S. |
| "Combinatorial algorithms: for computers and calculators." |
| Academic Press, 1978. |
| https://doi.org/10.1016/C2013-0-11243-3 |
| """ |
| if n == 0: |
| raise nx.NetworkXPointlessConcept("the null graph is not a tree") |
| cache_trees = [0, 1] |
| if number_of_trees is None: |
| return _to_nx(*_random_unlabeled_rooted_tree(n, cache_trees, seed), root=0) |
| return [ |
| _to_nx(*_random_unlabeled_rooted_tree(n, cache_trees, seed), root=0) |
| for i in range(number_of_trees) |
| ] |
|
|
|
|
| def _num_rooted_forests(n, q, cache_forests): |
| """Returns the number of unlabeled rooted forests with `n` nodes, and with |
| no more than `q` nodes per tree. A recursive formula for this is (2) in |
| [1]_. This function is implemented using dynamic programming instead of |
| recursion. |
| |
| Parameters |
| ---------- |
| n : int |
| The number of nodes. |
| q : int |
| The maximum number of nodes for each tree of the forest. |
| cache_forests : list of ints |
| The $i$-th element is the number of unlabeled rooted forests with |
| $i$ nodes, and with no more than `q` nodes per tree; this is used |
| as a cache (and is extended to length `n` + 1 if needed). |
| |
| Returns |
| ------- |
| int |
| The number of unlabeled rooted forests with `n` nodes with no more than |
| `q` nodes per tree. |
| |
| References |
| ---------- |
| .. [1] Wilf, Herbert S. "The uniform selection of free trees." |
| Journal of Algorithms 2.2 (1981): 204-207. |
| https://doi.org/10.1016/0196-6774(81)90021-3 |
| """ |
| for n_i in range(len(cache_forests), n + 1): |
| q_i = min(n_i, q) |
| cache_forests.append( |
| sum( |
| [ |
| d * cache_forests[n_i - j * d] * cache_forests[d - 1] |
| for d in range(1, q_i + 1) |
| for j in range(1, n_i // d + 1) |
| ] |
| ) |
| // n_i |
| ) |
|
|
| return cache_forests[n] |
|
|
|
|
| def _select_jd_forests(n, q, cache_forests, seed): |
| """Given `n` and `q`, returns a pair of positive integers $(j,d)$ |
| such that $j\\leq d$, with probability satisfying (F1) of [1]_. |
| |
| Parameters |
| ---------- |
| n : int |
| The number of nodes. |
| q : int |
| The maximum number of nodes for each tree of the forest. |
| cache_forests : list of ints |
| Cache for :func:`_num_rooted_forests`. |
| seed : random_state |
| See :ref:`Randomness<randomness>`. |
| |
| Returns |
| ------- |
| (int, int) |
| A pair of positive integers $(j,d)$ |
| |
| References |
| ---------- |
| .. [1] Wilf, Herbert S. "The uniform selection of free trees." |
| Journal of Algorithms 2.2 (1981): 204-207. |
| https://doi.org/10.1016/0196-6774(81)90021-3 |
| """ |
| p = seed.randint(0, _num_rooted_forests(n, q, cache_forests) * n - 1) |
| cumsum = 0 |
| for d in range(q, 0, -1): |
| for j in range(1, n // d + 1): |
| cumsum += ( |
| d |
| * _num_rooted_forests(n - j * d, q, cache_forests) |
| * _num_rooted_forests(d - 1, q, cache_forests) |
| ) |
| if p < cumsum: |
| return (j, d) |
|
|
|
|
| def _random_unlabeled_rooted_forest(n, q, cache_trees, cache_forests, seed): |
| """Returns an unlabeled rooted forest with `n` nodes, and with no more |
| than `q` nodes per tree, drawn uniformly at random. It is an implementation |
| of the algorithm "Forest" of [1]_. |
| |
| Parameters |
| ---------- |
| n : int |
| The number of nodes. |
| q : int |
| The maximum number of nodes per tree. |
| cache_trees : |
| Cache for :func:`_num_rooted_trees`. |
| cache_forests : |
| Cache for :func:`_num_rooted_forests`. |
| seed : random_state |
| See :ref:`Randomness<randomness>`. |
| |
| Returns |
| ------- |
| (edges, n, r) : (list, int, list) |
| The forest (edges, n) and a list r of root nodes. |
| |
| References |
| ---------- |
| .. [1] Wilf, Herbert S. "The uniform selection of free trees." |
| Journal of Algorithms 2.2 (1981): 204-207. |
| https://doi.org/10.1016/0196-6774(81)90021-3 |
| """ |
| if n == 0: |
| return ([], 0, []) |
|
|
| j, d = _select_jd_forests(n, q, cache_forests, seed) |
| t1, t1_nodes, r1 = _random_unlabeled_rooted_forest( |
| n - j * d, q, cache_trees, cache_forests, seed |
| ) |
| t2, t2_nodes = _random_unlabeled_rooted_tree(d, cache_trees, seed) |
| for _ in range(j): |
| r1.append(t1_nodes) |
| t1.extend((n1 + t1_nodes, n2 + t1_nodes) for n1, n2 in t2) |
| t1_nodes += t2_nodes |
| return t1, t1_nodes, r1 |
|
|
|
|
| @py_random_state("seed") |
| @nx._dispatchable(graphs=None, returns_graph=True) |
| def random_unlabeled_rooted_forest(n, *, q=None, number_of_forests=None, seed=None): |
| """Returns a forest or list of forests selected at random. |
| |
| Returns one or more (depending on `number_of_forests`) |
| unlabeled rooted forests with `n` nodes, and with no more than |
| `q` nodes per tree, drawn uniformly at random. |
| The "roots" graph attribute identifies the roots of the forest. |
| |
| Parameters |
| ---------- |
| n : int |
| The number of nodes |
| q : int or None (default) |
| The maximum number of nodes per tree. |
| number_of_forests : int or None (default) |
| If not None, this number of forests is generated and returned. |
| seed : integer, random_state, or None (default) |
| Indicator of random number generation state. |
| See :ref:`Randomness<randomness>`. |
| |
| Returns |
| ------- |
| :class:`networkx.Graph` or list of :class:`networkx.Graph` |
| A single `networkx.Graph` (or a list thereof, if `number_of_forests` |
| is specified) with nodes in the set {0, …, *n* - 1}. |
| The "roots" graph attribute is a set containing the roots |
| of the trees in the forest. |
| |
| Notes |
| ----- |
| This function implements the algorithm "Forest" of [1]_. |
| The algorithm needs to compute some counting functions |
| that are relatively expensive: in case several trees are needed, |
| it is advisable to use the `number_of_forests` optional argument |
| to reuse the counting functions. |
| |
| Raises |
| ------ |
| ValueError |
| If `n` is non-zero but `q` is zero. |
| |
| References |
| ---------- |
| .. [1] Wilf, Herbert S. "The uniform selection of free trees." |
| Journal of Algorithms 2.2 (1981): 204-207. |
| https://doi.org/10.1016/0196-6774(81)90021-3 |
| """ |
| if q is None: |
| q = n |
| if q == 0 and n != 0: |
| raise ValueError("q must be a positive integer if n is positive.") |
|
|
| cache_trees = [0, 1] |
| cache_forests = [1] |
|
|
| if number_of_forests is None: |
| g, nodes, rs = _random_unlabeled_rooted_forest( |
| n, q, cache_trees, cache_forests, seed |
| ) |
| return _to_nx(g, nodes, roots=set(rs)) |
|
|
| res = [] |
| for i in range(number_of_forests): |
| g, nodes, rs = _random_unlabeled_rooted_forest( |
| n, q, cache_trees, cache_forests, seed |
| ) |
| res.append(_to_nx(g, nodes, roots=set(rs))) |
| return res |
|
|
|
|
| def _num_trees(n, cache_trees): |
| """Returns the number of unlabeled trees with `n` nodes. |
| |
| See also https://oeis.org/A000055. |
| |
| Parameters |
| ---------- |
| n : int |
| The number of nodes. |
| cache_trees : list of ints |
| Cache for :func:`_num_rooted_trees`. |
| |
| Returns |
| ------- |
| int |
| The number of unlabeled trees with `n` nodes. |
| """ |
| r = _num_rooted_trees(n, cache_trees) - sum( |
| [ |
| _num_rooted_trees(j, cache_trees) * _num_rooted_trees(n - j, cache_trees) |
| for j in range(1, n // 2 + 1) |
| ] |
| ) |
| if n % 2 == 0: |
| r += comb(_num_rooted_trees(n // 2, cache_trees) + 1, 2) |
| return r |
|
|
|
|
| def _bicenter(n, cache, seed): |
| """Returns a bi-centroidal tree on `n` nodes drawn uniformly at random. |
| |
| This function implements the algorithm Bicenter of [1]_. |
| |
| Parameters |
| ---------- |
| n : int |
| The number of nodes (must be even). |
| cache : list of ints. |
| Cache for :func:`_num_rooted_trees`. |
| seed : random_state |
| See :ref:`Randomness<randomness>` |
| |
| Returns |
| ------- |
| (edges, n) |
| The tree as a list of edges and number of nodes. |
| |
| References |
| ---------- |
| .. [1] Wilf, Herbert S. "The uniform selection of free trees." |
| Journal of Algorithms 2.2 (1981): 204-207. |
| https://doi.org/10.1016/0196-6774(81)90021-3 |
| """ |
| t, t_nodes = _random_unlabeled_rooted_tree(n // 2, cache, seed) |
| if seed.randint(0, _num_rooted_trees(n // 2, cache)) == 0: |
| t2, t2_nodes = t, t_nodes |
| else: |
| t2, t2_nodes = _random_unlabeled_rooted_tree(n // 2, cache, seed) |
| t.extend([(n1 + (n // 2), n2 + (n // 2)) for n1, n2 in t2]) |
| t.append((0, n // 2)) |
| return t, t_nodes + t2_nodes |
|
|
|
|
| def _random_unlabeled_tree(n, cache_trees, cache_forests, seed): |
| """Returns a tree on `n` nodes drawn uniformly at random. |
| It implements the Wilf's algorithm "Free" of [1]_. |
| |
| Parameters |
| ---------- |
| n : int |
| The number of nodes, greater than zero. |
| cache_trees : list of ints |
| Cache for :func:`_num_rooted_trees`. |
| cache_forests : list of ints |
| Cache for :func:`_num_rooted_forests`. |
| seed : random_state |
| Indicator of random number generation state. |
| See :ref:`Randomness<randomness>` |
| |
| Returns |
| ------- |
| (edges, n) |
| The tree as a list of edges and number of nodes. |
| |
| References |
| ---------- |
| .. [1] Wilf, Herbert S. "The uniform selection of free trees." |
| Journal of Algorithms 2.2 (1981): 204-207. |
| https://doi.org/10.1016/0196-6774(81)90021-3 |
| """ |
| if n % 2 == 1: |
| p = 0 |
| else: |
| p = comb(_num_rooted_trees(n // 2, cache_trees) + 1, 2) |
| if seed.randint(0, _num_trees(n, cache_trees) - 1) < p: |
| return _bicenter(n, cache_trees, seed) |
| else: |
| f, n_f, r = _random_unlabeled_rooted_forest( |
| n - 1, (n - 1) // 2, cache_trees, cache_forests, seed |
| ) |
| for i in r: |
| f.append((i, n_f)) |
| return f, n_f + 1 |
|
|
|
|
| @py_random_state("seed") |
| @nx._dispatchable(graphs=None, returns_graph=True) |
| def random_unlabeled_tree(n, *, number_of_trees=None, seed=None): |
| """Returns a tree or list of trees chosen randomly. |
| |
| Returns one or more (depending on `number_of_trees`) |
| unlabeled trees with `n` nodes drawn uniformly at random. |
| |
| Parameters |
| ---------- |
| n : int |
| The number of nodes |
| number_of_trees : int or None (default) |
| If not None, this number of trees is generated and returned. |
| seed : integer, random_state, or None (default) |
| Indicator of random number generation state. |
| See :ref:`Randomness<randomness>`. |
| |
| Returns |
| ------- |
| :class:`networkx.Graph` or list of :class:`networkx.Graph` |
| A single `networkx.Graph` (or a list thereof, if |
| `number_of_trees` is specified) with nodes in the set {0, …, *n* - 1}. |
| |
| Raises |
| ------ |
| NetworkXPointlessConcept |
| If `n` is zero (because the null graph is not a tree). |
| |
| Notes |
| ----- |
| This function generates an unlabeled tree uniformly at random using |
| Wilf's algorithm "Free" of [1]_. The algorithm needs to |
| compute some counting functions that are relatively expensive: |
| in case several trees are needed, it is advisable to use the |
| `number_of_trees` optional argument to reuse the counting |
| functions. |
| |
| References |
| ---------- |
| .. [1] Wilf, Herbert S. "The uniform selection of free trees." |
| Journal of Algorithms 2.2 (1981): 204-207. |
| https://doi.org/10.1016/0196-6774(81)90021-3 |
| """ |
| if n == 0: |
| raise nx.NetworkXPointlessConcept("the null graph is not a tree") |
|
|
| cache_trees = [0, 1] |
| cache_forests = [1] |
| if number_of_trees is None: |
| return _to_nx(*_random_unlabeled_tree(n, cache_trees, cache_forests, seed)) |
| else: |
| return [ |
| _to_nx(*_random_unlabeled_tree(n, cache_trees, cache_forests, seed)) |
| for i in range(number_of_trees) |
| ] |
|
|