cimport cython from libc.string cimport memcpy, memset from libc.stdint cimport uint32_t import numpy import numpy.linalg import struct cimport numpy as np import math import six import warnings from ..lexeme cimport Lexeme from ..lexeme cimport EMPTY_LEXEME from ..typedefs cimport attr_t, flags_t from ..attrs cimport attr_id_t from ..attrs cimport ID, ORTH, NORM, LOWER, SHAPE, PREFIX, SUFFIX, LENGTH, CLUSTER from ..attrs cimport POS, LEMMA, TAG, DEP, HEAD, SPACY, ENT_IOB, ENT_TYPE from ..parts_of_speech cimport CONJ, PUNCT, NOUN from ..parts_of_speech cimport univ_pos_t from ..lexeme cimport Lexeme from .span cimport Span from .token cimport Token from ..serialize.bits cimport BitArray from ..util import normalize_slice from ..syntax.iterators import CHUNKERS DEF PADDING = 5 cdef int bounds_check(int i, int length, int padding) except -1: if (i + padding) < 0: raise IndexError if (i - padding) >= length: raise IndexError cdef attr_t get_token_attr(const TokenC* token, attr_id_t feat_name) nogil: if feat_name == LEMMA: return token.lemma elif feat_name == POS: return token.pos elif feat_name == TAG: return token.tag elif feat_name == DEP: return token.dep elif feat_name == HEAD: return token.head elif feat_name == SPACY: return token.spacy elif feat_name == ENT_IOB: return token.ent_iob elif feat_name == ENT_TYPE: return token.ent_type else: return Lexeme.get_struct_attr(token.lex, feat_name) cdef class Doc: """ A sequence of `Token` objects. Access sentences and named entities, export annotations to numpy arrays, losslessly serialize to compressed binary strings. Aside: Internals The `Doc` object holds an array of `TokenC` structs. The Python-level `Token` and `Span` objects are views of this array, i.e. they don't own the data themselves. Code: Construction 1 doc = nlp.tokenizer(u'Some text') Code: Construction 2 doc = Doc(nlp.vocab, orths_and_spaces=[(u'Some', True), (u'text', True)]) """ def __init__(self, Vocab vocab, words=None, spaces=None, orths_and_spaces=None): ''' Create a Doc object. Aside: Implementation This method of constructing a `Doc` object is usually only used for deserialization. Standard usage is to construct the document via a call to the language object. Arguments: vocab: A Vocabulary object, which must match any models you want to use (e.g. tokenizer, parser, entity recognizer). words: A list of unicode strings to add to the document as words. If None, defaults to empty list. spaces: A list of boolean values, of the same length as words. True means that the word is followed by a space, False means it is not. If None, defaults to [True]*len(words) ''' self.vocab = vocab size = 20 self.mem = Pool() # Guarantee self.lex[i-x], for any i >= 0 and x < padding is in bounds # However, we need to remember the true starting places, so that we can # realloc. data_start = self.mem.alloc(size + (PADDING*2), sizeof(TokenC)) cdef int i for i in range(size + (PADDING*2)): data_start[i].lex = &EMPTY_LEXEME data_start[i].l_edge = i data_start[i].r_edge = i self.c = data_start + PADDING self.max_length = size self.length = 0 self.is_tagged = False self.is_parsed = False self.getters_for_tokens = {} self.getters_for_spans = {} self.tensor = numpy.zeros((0,), dtype='float32') self.user_data = {} self._py_tokens = [] self._vector = None self.noun_chunks_iterator = CHUNKERS.get(self.vocab.lang) cdef unicode orth cdef bint has_space if orths_and_spaces is None and words is not None: if spaces is None: spaces = [True] * len(words) elif len(spaces) != len(words): raise ValueError( "Arguments 'words' and 'spaces' should be sequences of the " "same length, or 'spaces' should be left default at None. " "spaces should be a sequence of booleans, with True meaning " "that the word owns a ' ' character following it.") orths_and_spaces = zip(words, spaces) if orths_and_spaces is not None: for orth_space in orths_and_spaces: if isinstance(orth_space, unicode): orth = orth_space has_space = True elif isinstance(orth_space, bytes): raise ValueError( "orths_and_spaces expects either List(unicode) or " "List((unicode, bool)). Got bytes instance: %s" % (str(orth_space))) else: orth, has_space = orth_space # Note that we pass self.mem here --- we have ownership, if LexemeC # must be created. self.push_back( self.vocab.get(self.mem, orth), has_space) def __getitem__(self, object i): ''' doc[i] Get the Token object at position i, where i is an integer. Negative indexing is supported, and follows the usual Python semantics, i.e. doc[-2] is doc[len(doc) - 2]. doc[start : end]] Get a `Span` object, starting at position `start` and ending at position `end`, where `start` and `end` are token indices. For instance, `doc[2:5]` produces a span consisting of tokens 2, 3 and 4. Stepped slices (e.g. `doc[start : end : step]`) are not supported, as `Span` objects must be contiguous (cannot have gaps). You can use negative indices and open-ended ranges, which have their normal Python semantics. ''' if isinstance(i, slice): start, stop = normalize_slice(len(self), i.start, i.stop, i.step) return Span(self, start, stop, label=0) if i < 0: i = self.length + i bounds_check(i, self.length, PADDING) if self._py_tokens[i] is not None: return self._py_tokens[i] else: return Token.cinit(self.vocab, &self.c[i], i, self) def __iter__(self): ''' for token in doc Iterate over `Token` objects, from which the annotations can be easily accessed. This is the main way of accessing Token objects, which are the main way annotations are accessed from Python. If faster-than-Python speeds are required, you can instead access the annotations as a numpy array, or access the underlying C data directly from Cython. ''' cdef int i for i in range(self.length): if self._py_tokens[i] is not None: yield self._py_tokens[i] else: yield Token.cinit(self.vocab, &self.c[i], i, self) def __len__(self): ''' len(doc) The number of tokens in the document. ''' return self.length def __unicode__(self): return u''.join([t.text_with_ws for t in self]) def __bytes__(self): return u''.join([t.text_with_ws for t in self]).encode('utf-8') def __str__(self): if six.PY3: return self.__unicode__() return self.__bytes__() def __repr__(self): return self.__str__() def similarity(self, other): if self.vector_norm == 0 or other.vector_norm == 0: return 0.0 return numpy.dot(self.vector, other.vector) / (self.vector_norm * other.vector_norm) property has_vector: def __get__(self): return any(token.has_vector for token in self) property vector: def __get__(self): if self._vector is None: if len(self): self._vector = sum(t.vector for t in self) / len(self) else: return numpy.zeros((self.vocab.vectors_length,), dtype='float32') return self._vector def __set__(self, value): self._vector = value property vector_norm: def __get__(self): cdef float value if self._vector_norm is None: self._vector_norm = 1e-20 for value in self.vector: self._vector_norm += value * value self._vector_norm = math.sqrt(self._vector_norm) return self._vector_norm def __set__(self, value): self._vector_norm = value @property def string(self): return self.text @property def text_with_ws(self): return self.text @property def text(self): return u''.join(t.text_with_ws for t in self) property ents: ''' Yields named-entity `Span` objects, if the entity recognizer has been applied to the document. Iterate over the span to get individual Token objects, or access the label: Example: from spacy.en import English nlp = English() tokens = nlp(u'Mr. Best flew to New York on Saturday morning.') ents = list(tokens.ents) assert ents[0].label == 346 assert ents[0].label_ == 'PERSON' assert ents[0].orth_ == 'Best' assert ents[0].text == 'Mr. Best' ''' def __get__(self): cdef int i cdef const TokenC* token cdef int start = -1 cdef int label = 0 output = [] for i in range(self.length): token = &self.c[i] if token.ent_iob == 1: assert start != -1 elif token.ent_iob == 2 or token.ent_iob == 0: if start != -1: output.append(Span(self, start, i, label=label)) start = -1 label = 0 elif token.ent_iob == 3: if start != -1: output.append(Span(self, start, i, label=label)) start = i label = token.ent_type if start != -1: output.append(Span(self, start, self.length, label=label)) return tuple(output) def __set__(self, ents): # TODO: # 1. Allow negative matches # 2. Ensure pre-set NERs are not over-written during statistical prediction # 3. Test basic data-driven ORTH gazetteer # 4. Test more nuanced date and currency regex cdef int i for i in range(self.length): self.c[i].ent_type = 0 self.c[i].ent_iob = 0 cdef attr_t ent_type cdef int start, end for ent_info in ents: if isinstance(ent_info, Span): ent_id = ent_info.ent_id ent_type = ent_info.label start = ent_info.start end = ent_info.end elif len(ent_info) == 3: ent_type, start, end = ent_info else: ent_id, ent_type, start, end = ent_info if ent_type is None or ent_type < 0: # Mark as O for i in range(start, end): self.c[i].ent_type = 0 self.c[i].ent_iob = 2 else: # Mark (inside) as I for i in range(start, end): self.c[i].ent_type = ent_type self.c[i].ent_iob = 1 # Set start as B self.c[start].ent_iob = 3 property noun_chunks: ''' Yields base noun-phrase #[code Span] objects, if the document has been syntactically parsed. A base noun phrase, or 'NP chunk', is a noun phrase that does not permit other NPs to be nested within it – so no NP-level coordination, no prepositional phrases, and no relative clauses. For example: ''' def __get__(self): if not self.is_parsed: raise ValueError( "noun_chunks requires the dependency parse, which " "requires data to be installed. If you haven't done so, run: " "\npython -m spacy.%s.download all\n" "to install the data" % self.vocab.lang) # Accumulate the result before beginning to iterate over it. This prevents # the tokenisation from being changed out from under us during the iteration. # The tricky thing here is that Span accepts its tokenisation changing, # so it's okay once we have the Span objects. See Issue #375 spans = [] for start, end, label in self.noun_chunks_iterator(self): spans.append(Span(self, start, end, label=label)) for span in spans: yield span property sents: """ Yields sentence `Span` objects. Sentence spans have no label. To improve accuracy on informal texts, spaCy calculates sentence boundaries from the syntactic dependency parse. If the parser is disabled, `sents` iterator will be unavailable. Example: from spacy.en import English nlp = English() doc = nlp("This is a sentence. Here's another...") assert [s.root.orth_ for s in doc.sents] == ["is", "'s"] """ def __get__(self): if not self.is_parsed: raise ValueError( "sentence boundary detection requires the dependency parse, which " "requires data to be installed. If you haven't done so, run: " "\npython -m spacy.%s.download all\n" "to install the data" % self.vocab.lang) cdef int i start = 0 for i in range(1, self.length): if self.c[i].sent_start: yield Span(self, start, i) start = i if start != self.length: yield Span(self, start, self.length) cdef int push_back(self, LexemeOrToken lex_or_tok, bint has_space) except -1: if self.length == self.max_length: self._realloc(self.length * 2) cdef TokenC* t = &self.c[self.length] if LexemeOrToken is const_TokenC_ptr: t[0] = lex_or_tok[0] else: t.lex = lex_or_tok if self.length == 0: t.idx = 0 else: t.idx = (t-1).idx + (t-1).lex.length + (t-1).spacy t.l_edge = self.length t.r_edge = self.length assert t.lex.orth != 0 t.spacy = has_space self.length += 1 self._py_tokens.append(None) return t.idx + t.lex.length + t.spacy @cython.boundscheck(False) cpdef np.ndarray to_array(self, object py_attr_ids): """ Given a list of M attribute IDs, export the tokens to a numpy `ndarray` of shape (N, M), where `N` is the length of the document. The values will be 32-bit integers. Example: from spacy import attrs doc = nlp(text) # All strings mapped to integers, for easy export to numpy np_array = doc.to_array([attrs.LOWER, attrs.POS, attrs.ENT_TYPE, attrs.IS_ALPHA]) Arguments: attr_ids (list[int]): A list of attribute ID ints. Returns: feat_array (numpy.ndarray[long, ndim=2]): A feature matrix, with one row per word, and one column per attribute indicated in the input attr_ids. """ cdef int i, j cdef attr_id_t feature cdef np.ndarray[attr_t, ndim=2] output # Make an array from the attributes --- otherwise our inner loop is Python # dict iteration. cdef np.ndarray[attr_t, ndim=1] attr_ids = numpy.asarray(py_attr_ids, dtype=numpy.int32) output = numpy.ndarray(shape=(self.length, len(attr_ids)), dtype=numpy.int32) for i in range(self.length): for j, feature in enumerate(attr_ids): output[i, j] = get_token_attr(&self.c[i], feature) return output def count_by(self, attr_id_t attr_id, exclude=None, PreshCounter counts=None): """Produce a dict of {attribute (int): count (ints)} frequencies, keyed by the values of the given attribute ID. Example: from spacy.en import English, attrs nlp = English() tokens = nlp(u'apple apple orange banana') tokens.count_by(attrs.ORTH) # {12800L: 1, 11880L: 2, 7561L: 1} tokens.to_array([attrs.ORTH]) # array([[11880], # [11880], # [ 7561], # [12800]]) Arguments: attr_id int The attribute ID to key the counts. """ cdef int i cdef attr_t attr cdef size_t count if counts is None: counts = PreshCounter() output_dict = True else: output_dict = False # Take this check out of the loop, for a bit of extra speed if exclude is None: for i in range(self.length): counts.inc(get_token_attr(&self.c[i], attr_id), 1) else: for i in range(self.length): if not exclude(self[i]): attr = get_token_attr(&self.c[i], attr_id) counts.inc(attr, 1) if output_dict: return dict(counts) def _realloc(self, new_size): self.max_length = new_size n = new_size + (PADDING * 2) # What we're storing is a "padded" array. We've jumped forward PADDING # places, and are storing the pointer to that. This way, we can access # words out-of-bounds, and get out-of-bounds markers. # Now that we want to realloc, we need the address of the true start, # so we jump the pointer back PADDING places. cdef TokenC* data_start = self.c - PADDING data_start = self.mem.realloc(data_start, n * sizeof(TokenC)) self.c = data_start + PADDING cdef int i for i in range(self.length, self.max_length + PADDING): self.c[i].lex = &EMPTY_LEXEME cdef void set_parse(self, const TokenC* parsed) nogil: # TODO: This method is fairly misleading atm. It's used by Parser # to actually apply the parse calculated. Need to rethink this. # Probably we should use from_array? self.is_parsed = True for i in range(self.length): self.c[i] = parsed[i] def from_array(self, attrs, array): '''Write to a `Doc` object, from an `(M, N)` array of attributes. ''' cdef int i, col cdef attr_id_t attr_id cdef TokenC* tokens = self.c cdef int length = len(array) cdef attr_t[:] values for col, attr_id in enumerate(attrs): values = array[:, col] if attr_id == HEAD: for i in range(length): tokens[i].head = values[i] if values[i] >= 1: tokens[i + values[i]].l_kids += 1 elif values[i] < 0: tokens[i + values[i]].r_kids += 1 elif attr_id == TAG: for i in range(length): if values[i] != 0: self.vocab.morphology.assign_tag(&tokens[i], self.vocab.morphology.reverse_index[values[i]]) elif attr_id == POS: for i in range(length): tokens[i].pos = values[i] elif attr_id == DEP: for i in range(length): tokens[i].dep = values[i] elif attr_id == ENT_IOB: for i in range(length): tokens[i].ent_iob = values[i] elif attr_id == ENT_TYPE: for i in range(length): tokens[i].ent_type = values[i] else: raise ValueError("Unknown attribute ID: %d" % attr_id) set_children_from_heads(self.c, self.length) self.is_parsed = bool(HEAD in attrs or DEP in attrs) self.is_tagged = bool(TAG in attrs or POS in attrs) return self def to_bytes(self): '''Serialize, producing a byte string.''' byte_string = self.vocab.serializer.pack(self) cdef uint32_t length = len(byte_string) return struct.pack('I', length) + byte_string def from_bytes(self, data): '''Deserialize, loading from bytes.''' self.vocab.serializer.unpack_into(data[4:], self) return self @staticmethod def read_bytes(file_): ''' A static method, used to read serialized #[code Doc] objects from a file. For example: Example: from spacy.tokens.doc import Doc loc = 'test_serialize.bin' with open(loc, 'wb') as file_: file_.write(nlp(u'This is a document.').to_bytes()) file_.write(nlp(u'This is another.').to_bytes()) docs = [] with open(loc, 'rb') as file_: for byte_string in Doc.read_bytes(file_): docs.append(Doc(nlp.vocab).from_bytes(byte_string)) assert len(docs) == 2 ''' keep_reading = True while keep_reading: try: n_bytes_str = file_.read(4) if len(n_bytes_str) < 4: break n_bytes = struct.unpack('I', n_bytes_str)[0] data = file_.read(n_bytes) except StopIteration: keep_reading = False yield n_bytes_str + data def merge(self, int start_idx, int end_idx, *args, **attributes): """Merge a multi-word expression into a single token.""" cdef unicode tag, lemma, ent_type if len(args) == 3: # TODO: Warn deprecation tag, lemma, ent_type = args attributes[TAG] = self.vocab.strings[tag] attributes[LEMMA] = self.vocab.strings[lemma] attributes[ENT_TYPE] = self.vocab.strings[ent_type] elif args: raise ValueError( "Doc.merge received %d non-keyword arguments. " "Expected either 3 arguments (deprecated), or 0 (use keyword arguments). " "Arguments supplied:\n%s\n" "Keyword arguments:%s\n" % (len(args), repr(args), repr(attributes))) cdef int start = token_by_start(self.c, self.length, start_idx) if start == -1: return None cdef int end = token_by_end(self.c, self.length, end_idx) if end == -1: return None # Currently we have the token index, we want the range-end index end += 1 cdef Span span = self[start:end] tag = self.vocab.strings[attributes.get(TAG, span.root.tag)] lemma = self.vocab.strings[attributes.get(LEMMA, span.root.lemma)] ent_type = self.vocab.strings[attributes.get(ENT_TYPE, span.root.ent_type)] # Get LexemeC for newly merged token new_orth = ''.join([t.text_with_ws for t in span]) if span[-1].whitespace_: new_orth = new_orth[:-len(span[-1].whitespace_)] cdef const LexemeC* lex = self.vocab.get(self.mem, new_orth) # House the new merged token where it starts cdef TokenC* token = &self.c[start] token.spacy = self.c[end-1].spacy if tag in self.vocab.morphology.tag_map: self.vocab.morphology.assign_tag(token, tag) else: token.tag = self.vocab.strings[tag] token.lemma = self.vocab.strings[lemma] if ent_type == 'O': token.ent_iob = 2 token.ent_type = 0 else: token.ent_iob = 3 token.ent_type = self.vocab.strings[ent_type] # Begin by setting all the head indices to absolute token positions # This is easier to work with for now than the offsets # Before thinking of something simpler, beware the case where a dependency # bridges over the entity. Here the alignment of the tokens changes. span_root = span.root.i token.dep = span.root.dep # We update token.lex after keeping span root and dep, since # setting token.lex will change span.start and span.end properties # as it modifies the character offsets in the doc token.lex = lex for i in range(self.length): self.c[i].head += i # Set the head of the merged token, and its dep relation, from the Span token.head = self.c[span_root].head # Adjust deps before shrinking tokens # Tokens which point into the merged token should now point to it # Subtract the offset from all tokens which point to >= end offset = (end - start) - 1 for i in range(self.length): head_idx = self.c[i].head if start <= head_idx < end: self.c[i].head = start elif head_idx >= end: self.c[i].head -= offset # Now compress the token array for i in range(end, self.length): self.c[i - offset] = self.c[i] for i in range(self.length - offset, self.length): memset(&self.c[i], 0, sizeof(TokenC)) self.c[i].lex = &EMPTY_LEXEME self.length -= offset for i in range(self.length): # ...And, set heads back to a relative position self.c[i].head -= i # Set the left/right children, left/right edges set_children_from_heads(self.c, self.length) # Clear the cached Python objects self._py_tokens = [None] * self.length # Return the merged Python object return self[start] cdef int token_by_start(const TokenC* tokens, int length, int start_char) except -2: cdef int i for i in range(length): if tokens[i].idx == start_char: return i else: return -1 cdef int token_by_end(const TokenC* tokens, int length, int end_char) except -2: cdef int i for i in range(length): if tokens[i].idx + tokens[i].lex.length == end_char: return i else: return -1 cdef int set_children_from_heads(TokenC* tokens, int length) except -1: cdef TokenC* head cdef TokenC* child cdef int i # Set number of left/right children to 0. We'll increment it in the loops. for i in range(length): tokens[i].l_kids = 0 tokens[i].r_kids = 0 tokens[i].l_edge = i tokens[i].r_edge = i # Set left edges for i in range(length): child = &tokens[i] head = &tokens[i + child.head] if child < head: if child.l_edge < head.l_edge: head.l_edge = child.l_edge head.l_kids += 1 # Set right edges --- same as above, but iterate in reverse for i in range(length-1, -1, -1): child = &tokens[i] head = &tokens[i + child.head] if child > head: if child.r_edge > head.r_edge: head.r_edge = child.r_edge head.r_kids += 1 # Set sentence starts for i in range(length): if tokens[i].head == 0 and tokens[i].dep != 0: tokens[tokens[i].l_edge].sent_start = True