# cython: infer_types=True, cdivision=True, boundscheck=False, binding=True from typing import Generator, List, Tuple cimport cython from cython.operator cimport dereference from libc.stdint cimport int32_t from libcpp.pair cimport pair from libcpp.unordered_map cimport unordered_map from libcpp.unordered_set cimport unordered_set import weakref from murmurhash.mrmr cimport hash64 from .. import Errors from ..strings cimport get_string_id from ..structs cimport EdgeC, GraphC from ..typedefs cimport hash_t from .token import Token @cython.freelist(8) cdef class Edge: cdef readonly Graph graph cdef readonly int i def __init__(self, Graph graph, int i): self.graph = graph self.i = i @property def is_none(self) -> bool: return False @property def doc(self) -> "Doc": return self.graph.doc @property def head(self) -> "Node": return Node(self.graph, self.graph.c.edges[self.i].head) @property def tail(self) -> "Tail": return Node(self.graph, self.graph.c.edges[self.i].tail) @property def label(self) -> int: return self.graph.c.edges[self.i].label @property def weight(self) -> float: return self.graph.c.weights[self.i] @property def label_(self) -> str: return self.doc.vocab.strings[self.label] @cython.freelist(8) cdef class Node: cdef readonly Graph graph cdef readonly int i def __init__(self, Graph graph, int i): """A reference to a node of an annotation graph. Each node is made up of an ordered set of zero or more token indices. Node references are usually created by the Graph object itself, or from the Node or Edge objects. You usually won't need to instantiate this class yourself. """ cdef int length = graph.c.nodes.size() if i >= length or -i >= length: raise IndexError(Errors.E1034.format(i=i, length=length)) if i < 0: i += length self.graph = graph self.i = i def __eq__(self, other): if self.graph is not other.graph: return False else: return self.i == other.i def __iter__(self) -> Generator[int]: for i in self.graph.c.nodes[self.i]: yield i def __getitem__(self, int i) -> int: """Get a token index from the node's set of tokens.""" length = self.graph.c.nodes[self.i].size() if i >= length or -i >= length: raise IndexError(Errors.E1035.format(i=i, length=length)) if i < 0: i += length return self.graph.c.nodes[self.i][i] def __len__(self) -> int: """The number of tokens that make up the node.""" return self.graph.c.nodes[self.i].size() @property def is_none(self) -> bool: """Whether the node is a special value, indicating 'none'. The NoneNode type is returned by the Graph, Edge and Node objects when there is no match to a query. It has the same API as Node, but it always returns NoneNode, NoneEdge or empty lists for its queries. """ return False @property def doc(self) -> "Doc": """The Doc object that the graph refers to.""" return self.graph.doc @property def tokens(self) -> Tuple[Token]: """A tuple of Token objects that make up the node.""" doc = self.doc return tuple([doc[i] for i in self]) def head(self, i=None, label=None) -> "Node": """Get the head of the first matching edge, searching by index, label, both or neither. For instance, `node.head(i=1)` will get the head of the second edge that this node is a tail of. `node.head(i=1, label="ARG0")` will further check that the second edge has the label `"ARG0"`. If no matching node can be found, the graph's NoneNode is returned. """ return self.headed(i=i, label=label) def tail(self, i=None, label=None) -> "Node": """Get the tail of the first matching edge, searching by index, label, both or neither. If no matching node can be found, the graph's NoneNode is returned. """ return self.tailed(i=i, label=label).tail def sibling(self, i=None, label=None): """Get the first matching sibling node. Two nodes are siblings if they are both tails of the same head. If no matching node can be found, the graph's NoneNode is returned. """ if i is None: siblings = self.siblings(label=label) return siblings[0] if siblings else NoneNode(self) else: edges = [] for h in self.headed(): edges.extend([e for e in h.tailed() if e.tail.i != self.i]) if i >= len(edges): return NoneNode(self) elif label is not None and edges[i].label != label: return NoneNode(self) else: return edges[i].tail def heads(self, label=None) -> List["Node"]: """Find all matching heads of this node.""" cdef vector[int] edge_indices self._find_edges(edge_indices, "head", label) return [Node(self.graph, self.graph.c.edges[i].head) for i in edge_indices] def tails(self, label=None) -> List["Node"]: """Find all matching tails of this node.""" cdef vector[int] edge_indices self._find_edges(edge_indices, "tail", label) return [Node(self.graph, self.graph.c.edges[i].tail) for i in edge_indices] def siblings(self, label=None) -> List["Node"]: """Find all maching siblings of this node. Two nodes are siblings if they are tails of the same head. """ edges = [] for h in self.headed(): edges.extend([e for e in h.tailed() if e.tail.i != self.i]) if label is None: return [e.tail for e in edges] else: return [e.tail for e in edges if e.label == label] def headed(self, i=None, label=None) -> Edge: """Find the first matching edge headed by this node. If no matching edge can be found, the graph's NoneEdge is returned. """ start, end = self._find_range(i, self.c.n_head[self.i]) idx = self._find_edge("head", start, end, label) if idx == -1: return NoneEdge(self.graph) else: return Edge(self.graph, idx) def tailed(self, i=None, label=None) -> Edge: """Find the first matching edge tailed by this node. If no matching edge can be found, the graph's NoneEdge is returned. """ start, end = self._find_range(i, self.c.n_tail[self.i]) idx = self._find_edge("tail", start, end, label) if idx == -1: return NoneEdge(self.graph) else: return Edge(self.graph, idx) def headeds(self, label=None) -> List[Edge]: """Find all matching edges headed by this node.""" cdef vector[int] edge_indices self._find_edges(edge_indices, "head", label) return [Edge(self.graph, i) for i in edge_indices] def taileds(self, label=None) -> List["Edge"]: """Find all matching edges headed by this node.""" cdef vector[int] edge_indices self._find_edges(edge_indices, "tail", label) return [Edge(self.graph, i) for i in edge_indices] def walk_heads(self): cdef vector[int] node_indices walk_head_nodes(node_indices, &self.graph.c, self.i) for i in node_indices: yield Node(self.graph, i) def walk_tails(self): cdef vector[int] node_indices walk_tail_nodes(node_indices, &self.graph.c, self.i) for i in node_indices: yield Node(self.graph, i) cdef (int, int) _get_range(self, i, n): if i is None: return (0, n) elif i < n: return (i, i+1) else: return (0, 0) cdef int _find_edge(self, str direction, int start, int end, label) except -2: if direction == "head": get_edges = get_head_edges else: get_edges = get_tail_edges cdef vector[int] edge_indices get_edges(edge_indices, &self.graph.c, self.i) if label is None: return edge_indices[start] for edge_index in edge_indices[start:end]: if self.graph.c.edges[edge_index].label == label: return edge_index else: return -1 cdef int _find_edges(self, vector[int]& edge_indices, str direction, label): if direction == "head": get_edges = get_head_edges else: get_edges = get_tail_edges if label is None: get_edges(edge_indices, &self.graph.c, self.i) return edge_indices.size() cdef vector[int] unfiltered get_edges(unfiltered, &self.graph.c, self.i) for edge_index in unfiltered: if self.graph.c.edges[edge_index].label == label: edge_indices.push_back(edge_index) return edge_indices.size() cdef class NoneEdge(Edge): """An Edge subclass, representing a non-result. The NoneEdge has the same API as other Edge instances, but always returns NoneEdge, NoneNode, or empty lists. """ def __init__(self, graph): self.graph = graph self.i = -1 @property def doc(self) -> "Doc": return self.graph.doc @property def head(self) -> "NoneNode": return NoneNode(self.graph) @property def tail(self) -> "NoneNode": return NoneNode(self.graph) @property def label(self) -> int: return 0 @property def weight(self) -> float: return 0.0 @property def label_(self) -> str: return "" cdef class NoneNode(Node): def __init__(self, graph): self.graph = graph self.i = -1 def __getitem__(self, int i): raise IndexError(Errors.E1036) def __len__(self): return 0 @property def is_none(self): return -1 @property def doc(self): return self.graph.doc @property def tokens(self): return tuple() def head(self, i=None, label=None): return self def tail(self, i=None, label=None): return self def walk_heads(self): yield from [] def walk_tails(self): yield from [] cdef class Graph: """A set of directed labelled relationships between sets of tokens. EXAMPLE: Construction 1 >>> graph = Graph(doc, name="srl") Construction 2 >>> graph = Graph( doc, name="srl", nodes=[(0,), (1, 3), (,)], edges=[(0, 2), (2, 1)] ) Construction 3 >>> graph = Graph( doc, name="srl", nodes=[(0,), (1, 3), (,)], edges=[(2, 0), (0, 1)], labels=["word sense ID 1675", "agent"], weights=[-42.6, -1.7] ) >>> assert graph.has_node((0,)) >>> assert graph.has_edge((0,), (1,3), label="agent") """ def __init__( self, doc, *, name="", nodes=[], edges=[], labels=None, weights=None # no-cython-lint ): """Create a Graph object. doc (Doc): The Doc object the graph will refer to. name (str): A string name to help identify the graph. Defaults to "". nodes (List[Tuple[int]]): A list of token-index tuples to add to the graph as nodes. Defaults to []. edges (List[Tuple[int, int]]): A list of edges between the provided nodes. Each edge should be a (head, tail) tuple, where `head` and `tail` are integers pointing into the `nodes` list. Defaults to []. labels (Optional[List[str]]): A list of labels for the provided edges. If None, all of the edges specified by the edges argument will have be labelled with the empty string (""). If `labels` is not `None`, it must have the same length as the `edges` argument. weights (Optional[List[float]]): A list of weights for the provided edges. If None, all of the edges specified by the edges argument will have the weight 0.0. If `weights` is not `None`, it must have the same length as the `edges` argument. """ if weights is not None: assert len(weights) == len(edges) else: weights = [0.0] * len(edges) if labels is not None: assert len(labels) == len(edges) else: labels = [""] * len(edges) self.c.node_map = new unordered_map[hash_t, int]() self.c.edge_map = new unordered_map[hash_t, int]() self.c.roots = new unordered_set[int]() self.name = name self.doc_ref = weakref.ref(doc) for node in nodes: self.add_node(node) for (head, tail), label, weight in zip(edges, labels, weights): self.add_edge( Node(self, head), Node(self, tail), label=label, weight=weight ) def __dealloc__(self): del self.c.node_map del self.c.edge_map del self.c.roots @property def doc(self) -> "Doc": """The Doc object the graph refers to.""" return self.doc_ref() @property def edges(self) -> Generator[Edge]: """Iterate over the edges in the graph.""" for i in range(self.c.edges.size()): yield Edge(self, i) @property def nodes(self) -> Generator[Node]: """Iterate over the nodes in the graph.""" for i in range(self.c.nodes.size()): yield Node(self, i) def add_edge(self, head, tail, *, label="", weight=None) -> Edge: """Add an edge to the graph, connecting two groups of tokens. If there is already an edge for the (head, tail, label) triple, it will be returned, and no new edge will be created. The weight of the edge will be updated if a weight is specified. """ edge_index = add_edge( &self.c, EdgeC( head=self.add_node(head).i, tail=self.add_node(tail).i, label=self.doc.vocab.strings.as_int(label), ), weight=weight if weight is not None else 0.0 ) return Edge(self, edge_index) def get_edge(self, head, tail, *, label="") -> Edge: """Look up an edge in the graph. If the graph has no matching edge, the NoneEdge object is returned. """ head_node = self.get_node(head) if head_node.is_none: return NoneEdge(self) tail_node = self.get_node(tail) if tail_node.is_none: return NoneEdge(self) edge_index = get_edge( &self.c, EdgeC(head=head_node.i, tail=tail_node.i, label=get_string_id(label)) ) if edge_index < 0: return NoneEdge(self) else: return Edge(self, edge_index) def has_edge(self, head, tail, label) -> bool: """Check whether a (head, tail, label) triple is an edge in the graph.""" return not self.get_edge(head, tail, label=label).is_none def add_node(self, indices) -> Node: """Add a node to the graph and return it. Nodes refer to ordered sets of token indices. This method is idempotent: if there is already a node for the given indices, it is returned without a new node being created. """ if isinstance(indices, Node): return indices cdef vector[int32_t] node node.reserve(len(indices)) for idx in indices: node.push_back(idx) i = add_node(&self.c, node) return Node(self, i) def get_node(self, indices) -> Node: """Get a node from the graph, or the NoneNode if there is no node for the given indices. """ if isinstance(indices, Node): return indices cdef vector[int32_t] node node.reserve(len(indices)) for idx in indices: node.push_back(idx) node_index = get_node(&self.c, node) if node_index < 0: return NoneNode(self) else: return Node(self, node_index) def has_node(self, tuple indices) -> bool: """Check whether the graph has a node for the given indices.""" return not self.get_node(indices).is_none cdef int add_edge(GraphC* graph, EdgeC edge, float weight) nogil: key = hash64(&edge, sizeof(edge), 0) it = graph.edge_map.find(key) if it != graph.edge_map.end(): edge_index = dereference(it).second graph.weights[edge_index] = weight return edge_index else: edge_index = graph.edges.size() graph.edge_map.insert(pair[hash_t, int](key, edge_index)) graph.edges.push_back(edge) if graph.n_tails[edge.head] == 0: graph.first_tail[edge.head] = edge_index if graph.n_heads[edge.tail] == 0: graph.first_head[edge.tail] = edge_index graph.n_tails[edge.head] += 1 graph.n_heads[edge.tail] += 1 graph.weights.push_back(weight) # If we had the tail marked as a root, remove it. tail_root_index = graph.roots.find(edge.tail) if tail_root_index != graph.roots.end(): graph.roots.erase(tail_root_index) return edge_index cdef int get_edge(const GraphC* graph, EdgeC edge) nogil: key = hash64(&edge, sizeof(edge), 0) it = graph.edge_map.find(key) if it == graph.edge_map.end(): return -1 else: return dereference(it).second cdef int has_edge(const GraphC* graph, EdgeC edge) nogil: return get_edge(graph, edge) >= 0 cdef int add_node(GraphC* graph, vector[int32_t]& node) nogil: key = hash64(&node[0], node.size() * sizeof(node[0]), 0) it = graph.node_map.find(key) if it != graph.node_map.end(): # Item found. Convert the iterator to an index value. return dereference(it).second else: index = graph.nodes.size() graph.nodes.push_back(node) graph.n_heads.push_back(0) graph.n_tails.push_back(0) graph.first_head.push_back(0) graph.first_tail.push_back(0) graph.roots.insert(index) graph.node_map.insert(pair[hash_t, int](key, index)) return index cdef int get_node(const GraphC* graph, vector[int32_t] node) nogil: key = hash64(&node[0], node.size() * sizeof(node[0]), 0) it = graph.node_map.find(key) if it == graph.node_map.end(): return -1 else: return dereference(it).second cdef int has_node(const GraphC* graph, vector[int32_t] node) nogil: return get_node(graph, node) >= 0 cdef int get_head_nodes(vector[int]& output, const GraphC* graph, int node) nogil: todo = graph.n_heads[node] if todo == 0: return 0 output.reserve(output.size() + todo) start = graph.first_head[node] end = graph.edges.size() for i in range(start, end): if todo <= 0: break elif graph.edges[i].tail == node: output.push_back(graph.edges[i].head) todo -= 1 return todo cdef int get_tail_nodes(vector[int]& output, const GraphC* graph, int node) nogil: todo = graph.n_tails[node] if todo == 0: return 0 output.reserve(output.size() + todo) start = graph.first_tail[node] end = graph.edges.size() for i in range(start, end): if todo <= 0: break elif graph.edges[i].head == node: output.push_back(graph.edges[i].tail) todo -= 1 return todo cdef int get_sibling_nodes(vector[int]& output, const GraphC* graph, int node) nogil: cdef vector[int] heads cdef vector[int] tails get_head_nodes(heads, graph, node) for i in range(heads.size()): get_tail_nodes(tails, graph, heads[i]) for j in range(tails.size()): if tails[j] != node: output.push_back(tails[j]) tails.clear() return output.size() cdef int get_head_edges(vector[int]& output, const GraphC* graph, int node) nogil: todo = graph.n_heads[node] if todo == 0: return 0 output.reserve(output.size() + todo) start = graph.first_head[node] end = graph.edges.size() for i in range(start, end): if todo <= 0: break elif graph.edges[i].tail == node: output.push_back(i) todo -= 1 return todo cdef int get_tail_edges(vector[int]& output, const GraphC* graph, int node) nogil: todo = graph.n_tails[node] if todo == 0: return 0 output.reserve(output.size() + todo) start = graph.first_tail[node] end = graph.edges.size() for i in range(start, end): if todo <= 0: break elif graph.edges[i].head == node: output.push_back(i) todo -= 1 return todo cdef int walk_head_nodes(vector[int]& output, const GraphC* graph, int node) nogil: cdef unordered_set[int] seen = unordered_set[int]() get_head_nodes(output, graph, node) seen.insert(node) i = 0 while i < output.size(): if seen.find(output[i]) == seen.end(): seen.insert(output[i]) get_head_nodes(output, graph, output[i]) i += 1 return i cdef int walk_tail_nodes(vector[int]& output, const GraphC* graph, int node) nogil: cdef unordered_set[int] seen = unordered_set[int]() get_tail_nodes(output, graph, node) seen.insert(node) i = 0 while i < output.size(): if seen.find(output[i]) == seen.end(): seen.insert(output[i]) get_tail_nodes(output, graph, output[i]) i += 1 return i cdef int walk_head_edges(vector[int]& output, const GraphC* graph, int node) nogil: cdef unordered_set[int] seen = unordered_set[int]() get_head_edges(output, graph, node) seen.insert(node) i = 0 while i < output.size(): if seen.find(output[i]) == seen.end(): seen.insert(output[i]) get_head_edges(output, graph, output[i]) i += 1 return i cdef int walk_tail_edges(vector[int]& output, const GraphC* graph, int node) nogil: cdef unordered_set[int] seen = unordered_set[int]() get_tail_edges(output, graph, node) seen.insert(node) i = 0 while i < output.size(): if seen.find(output[i]) == seen.end(): seen.insert(output[i]) get_tail_edges(output, graph, output[i]) i += 1 return i