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def get_unicodes(codepoint): """ Return list of unicodes for <scanning-codepoints> """ result = re.sub('\s', '', codepoint.text) return Extension.convert_to_list_of_unicodes(result)
def handler(self,): """* get request token if OAuth1 * Get user authorization * Get access token """ if self.oauth_version == 'oauth1': request_token, request_token_secret = self.oauth.get_request_token(params={'oauth_callback': self.callback_uri}) ...
def generate_oauth2_headers(self): """Generates header for oauth2 """ encoded_credentials = base64.b64encode(('{0}:{1}'.format(self.consumer_key,self.consumer_secret)).encode('utf-8')) headers={ 'Authorization':'Basic {0}'.format(encoded_credentials.decode('utf-8')), ...
def oauth2_access_parser(self, raw_access): """Parse oauth2 access """ parsed_access = json.loads(raw_access.content.decode('utf-8')) self.access_token = parsed_access['access_token'] self.token_type = parsed_access['token_type'] self.refresh_token = parsed_access['refres...
def refresh_access_token(self,): """Refresh access token """ logger.debug("REFRESHING TOKEN") self.token_time = time.time() credentials = { 'token_time': self.token_time } if self.oauth_version == 'oauth1': self.access_token, self.access_t...
def token_is_valid(self,): """Check the validity of the token :3600s """ elapsed_time = time.time() - self.token_time logger.debug("ELAPSED TIME : {0}".format(elapsed_time)) if elapsed_time > 3540: # 1 minute before it expires logger.debug("TOKEN HAS EXPIRED") ...
def get_data(filename): """Calls right function according to file extension """ name, ext = get_file_extension(filename) func = json_get_data if ext == '.json' else yaml_get_data return func(filename)
def write_data(data, filename): """Call right func to save data according to file extension """ name, ext = get_file_extension(filename) func = json_write_data if ext == '.json' else yaml_write_data return func(data, filename)
def json_write_data(json_data, filename): """Write json data into a file """ with open(filename, 'w') as fp: json.dump(json_data, fp, indent=4, sort_keys=True, ensure_ascii=False) return True return False
def json_get_data(filename): """Get data from json file """ with open(filename) as fp: json_data = json.load(fp) return json_data return False
def yaml_get_data(filename): """Get data from .yml file """ with open(filename, 'rb') as fd: yaml_data = yaml.load(fd) return yaml_data return False
def yaml_write_data(yaml_data, filename): """Write data into a .yml file """ with open(filename, 'w') as fd: yaml.dump(yaml_data, fd, default_flow_style=False) return True return False
def fit(self, X, y=None): ''' If scale_by_median, find :attr:`median_`; otherwise, do nothing. Parameters ---------- X : array The raw pairwise distances. ''' X = check_array(X) if self.scale_by_median: self.median_ = np.median(X[...
def transform(self, X): ''' Turns distances into RBF values. Parameters ---------- X : array The raw pairwise distances. Returns ------- X_rbf : array of same shape as X The distances in X passed through the RBF kernel. ''...
def fit(self, X, y=None): ''' Learn the linear transformation to clipped eigenvalues. Note that if min_eig isn't zero and any of the original eigenvalues were exactly zero, this will leave those eigenvalues as zero. Parameters ---------- X : array, shape [n, n] ...
def fit(self, X, y=None): ''' Learn the linear transformation to flipped eigenvalues. Parameters ---------- X : array, shape [n, n] The *symmetric* input similarities. If X is asymmetric, it will be treated as if it were symmetric based on its lower-trian...
def transform(self, X): ''' Transforms X according to the linear transformation corresponding to flipping the input eigenvalues. Parameters ---------- X : array, shape [n_test, n] The test similarities to training points. Returns ------- ...
def fit_transform(self, X, y=None): ''' Flips the negative eigenvalues of X. Parameters ---------- X : array, shape [n, n] The *symmetric* input similarities. If X is asymmetric, it will be treated as if it were symmetric based on its lower-triangular par...
def fit(self, X, y=None): ''' Learn the transformation to shifted eigenvalues. Only depends on the input dimension. Parameters ---------- X : array, shape [n, n] The *symmetric* input similarities. ''' n = X.shape[0] if X.shape != (n, ...
def transform(self, X): ''' Transforms X according to the linear transformation corresponding to shifting the input eigenvalues to all be at least ``self.min_eig``. Parameters ---------- X : array, shape [n_test, n] The test similarities to training points. ...
def fit(self, X, y=None): ''' Picks the elements of the basis to use for the given data. Only depends on the dimension of X. If it's more convenient, you can pass a single integer for X, which is the dimension to use. Parameters ---------- X : an integer, a :cla...
def transform(self, X): ''' Transform a list of bag features into its projection series representation. Parameters ---------- X : :class:`skl_groups.features.Features` or list of bag feature arrays New data to transform. The data should all lie in [0, 1]; ...
def get_version(self): """ Get distribution version. This method is enhanced compared to original distutils implementation. If the version string is set to a special value then instead of using the actual value the real version is obtained by querying versiontools. If ...
def __get_live_version(self): """ Get a live version string using versiontools """ try: import versiontools except ImportError: return None else: return str(versiontools.Version.from_expression(self.name))
def fit(self, X, y=None, **params): ''' Fit the transformer on the stacked points. Parameters ---------- X : :class:`Features` or list of arrays of shape ``[n_samples[i], n_features]`` Training set. If a Features object, it will be stacked. any other keyword...
def transform(self, X, **params): ''' Transform the stacked points. Parameters ---------- X : :class:`Features` or list of bag feature arrays New data to transform. any other keyword argument : Passed on as keyword arguments to the transformer's ...
def fit_transform(self, X, y=None, **params): ''' Fit and transform the stacked points. Parameters ---------- X : :class:`Features` or list of bag feature arrays Data to train on and transform. any other keyword argument : Passed on as keyword ar...
def inverse_transform(self, X, **params): ''' Transform data back to its original space, i.e., return an input X_original whose transform would (maybe approximately) be X. Parameters ---------- X : :class:`Features` or list of bag feature arrays Data to train...
def fit(self, X, y=None): """Compute the minimum and maximum to be used for later scaling. Parameters ---------- X : array-like, shape [n_samples, n_features] The data used to compute the per-feature minimum and maximum used for later scaling along the features a...
def transform(self, X): """Scaling features of X according to feature_range. Parameters ---------- X : array-like with shape [n_samples, n_features] Input data that will be transformed. """ X = check_array(X, copy=self.copy) X *= self.scale_ X...
def inverse_transform(self, X): """Undo the scaling of X according to feature_range. Note that if truncate is true, any truncated points will not be restored exactly. Parameters ---------- X : array-like with shape [n_samples, n_features] Input data that wil...
def fit(self, X, y=None): ''' Choose the codewords based on a training set. Parameters ---------- X : :class:`skl_groups.features.Features` or list of arrays of shape ``[n_samples[i], n_features]`` Training set. If a Features object, it will be stacked. ''' ...
def transform(self, X): ''' Transform a list of bag features into its bag-of-words representation. Parameters ---------- X : :class:`skl_groups.features.Features` or list of bag feature arrays New data to transform. Returns ------- X_new : in...
def fit_transform(self, X): ''' Compute clustering and transform a list of bag features into its bag-of-words representation. Like calling fit(X) and then transform(X), but more efficient. Parameters ---------- X : :class:`skl_groups.features.Features` or list of...
def is_categorical_type(ary): "Checks whether the array is either integral or boolean." ary = np.asanyarray(ary) return is_integer_type(ary) or ary.dtype.kind == 'b'
def as_integer_type(ary): ''' Returns argument as an integer array, converting floats if convertable. Raises ValueError if it's a float array with nonintegral values. ''' ary = np.asanyarray(ary) if is_integer_type(ary): return ary rounded = np.rint(ary) if np.any(rounded != ary)...
def show_progress(name, **kwargs): ''' Sets up a :class:`ProgressBarHandler` to handle progess logs for a given module. Parameters ---------- name : string The module name of the progress logger to use. For example, :class:`skl_groups.divergences.KNNDivergenceEstimator` ...
def start(self, total): ''' Signal the start of the process. Parameters ---------- total : int The total number of steps in the process, or None if unknown. ''' self.logger.info(json.dumps(['START', self.name, total]))
def _build_indices(X, flann_args): "Builds FLANN indices for each bag." # TODO: should probably multithread this logger.info("Building indices...") indices = [None] * len(X) for i, bag in enumerate(plog(X, name="index building")): indices[i] = idx = FLANNIndex(**flann_args) idx.build...
def _get_rhos(X, indices, Ks, max_K, save_all_Ks, min_dist): "Gets within-bag distances for each bag." logger.info("Getting within-bag distances...") if max_K >= X.n_pts.min(): msg = "asked for K = {}, but there's a bag with only {} points" raise ValueError(msg.format(max_K, X.n_pts.min()))...
def linear(Ks, dim, num_q, rhos, nus): r''' Estimates the linear inner product \int p q between two distributions, based on kNN distances. ''' return _get_linear(Ks, dim)(num_q, rhos, nus)
def alpha_div(alphas, Ks, dim, num_q, rhos, nus): r''' Estimate the alpha divergence between distributions: \int p^\alpha q^(1-\alpha) based on kNN distances. Used in Renyi, Hellinger, Bhattacharyya, Tsallis divergences. Enforces that estimates are >= 0. Returns divergence estimates w...
def jensen_shannon_core(Ks, dim, num_q, rhos, nus): r''' Estimates 1/2 mean_X( d * log radius of largest ball in X+Y around X_i with no more than M/(n+m-1) weight where X points have weight 1 / (2 n - 1) ...
def bhattacharyya(Ks, dim, required, clamp=True, to_self=False): r''' Estimate the Bhattacharyya coefficient between distributions, based on kNN distances: \int \sqrt{p q} If clamp (the default), enforces 0 <= BC <= 1. Returns an array of shape (num_Ks,). ''' est = required if clamp: ...
def hellinger(Ks, dim, required, clamp=True, to_self=False): r''' Estimate the Hellinger distance between distributions, based on kNN distances: \sqrt{1 - \int \sqrt{p q}} Always enforces 0 <= H, to be able to sqrt; if clamp, also enforces H <= 1. Returns a vector: one element for each K. ...
def renyi(alphas, Ks, dim, required, min_val=np.spacing(1), clamp=True, to_self=False): r''' Estimate the Renyi-alpha divergence between distributions, based on kNN distances: 1/(\alpha-1) \log \int p^alpha q^(1-\alpha) If the inner integral is less than min_val (default ``np.spacing(1)``), ...
def tsallis(alphas, Ks, dim, required, clamp=True, to_self=False): r''' Estimate the Tsallis-alpha divergence between distributions, based on kNN distances: (\int p^alpha q^(1-\alpha) - 1) / (\alpha - 1) If clamp (the default), enforces the estimate is nonnegative. Returns an array of shape (num_...
def l2(Ks, dim, X_rhos, Y_rhos, required, clamp=True, to_self=False): r''' Estimates the L2 distance between distributions, via \int (p - q)^2 = \int p^2 - \int p q - \int q p + \int q^2. \int pq and \int qp are estimated with the linear function (in both directions), while \int p^2 and \int q^...
def quadratic(Ks, dim, rhos, required=None): r''' Estimates \int p^2 based on kNN distances. In here because it's used in the l2 distance, above. Returns array of shape (num_Ks,). ''' # Estimated with alpha=1, beta=0: # B_{k,d,1,0} is the same as B_{k,d,0,1} in linear() # and the ful...
def jensen_shannon(Ks, dim, X_rhos, Y_rhos, required, clamp=True, to_self=False): r''' Estimate the difference between the Shannon entropy of an equally-weighted mixture between X and Y and the mixture of the Shannon entropies: JS(X, Y) = H[ (X + Y) / 2 ] - (H[X] + H[Y]) / 2 ...
def topological_sort(deps): ''' Topologically sort a DAG, represented by a dict of child => set of parents. The dependency dict is destroyed during operation. Uses the Kahn algorithm: http://en.wikipedia.org/wiki/Topological_sorting Not a particularly good implementation, but we're just running it ...
def _parse_specs(specs, Ks): ''' Set up the different functions we need to call. Returns: - a dict mapping base estimator functions to _FuncInfo objects. If the function needs_alpha, then the alphas attribute is an array of alpha values and pos is a corresponding array of indice...
def _get_Ks(self): "Ks as an array and type-checked." Ks = as_integer_type(self.Ks) if Ks.ndim != 1: raise TypeError("Ks should be 1-dim, got shape {}".format(Ks.shape)) if Ks.min() < 1: raise ValueError("Ks should be positive; got {}".format(Ks.min())) re...
def _flann_args(self, X=None): "The dictionary of arguments to give to FLANN." args = {'cores': self._n_jobs} if self.flann_algorithm == 'auto': if X is None or X.dim > 5: args['algorithm'] = 'linear' else: args['algorithm'] = 'kdtree_singl...
def fit(self, X, y=None, get_rhos=False): ''' Sets up for divergence estimation "from" new data "to" X. Builds FLANN indices for each bag, and maybe gets within-bag distances. Parameters ---------- X : list of arrays or :class:`skl_groups.features.Features` T...
def transform(self, X): r''' Computes the divergences from X to :attr:`features_`. Parameters ---------- X : list of bag feature arrays or :class:`skl_groups.features.Features` The bags to search "from". Returns ------- divs : array of shape ...
def as_features(X, stack=False, bare=False): ''' Returns a version of X as a :class:`Features` object. Parameters ---------- stack : boolean, default False Make a stacked version of X. Note that if X is a features object, this will stack it in-place, since that's usually what you wa...
def make_stacked(self): "If unstacked, convert to stacked. If stacked, do nothing." if self.stacked: return self._boundaries = bounds = np.r_[0, np.cumsum(self.n_pts)] self.stacked_features = stacked = np.vstack(self.features) self.features = np.array( [s...
def copy(self, stack=False, copy_meta=False, memo=None): ''' Copies the Feature object. Makes a copy of the features array. Parameters ---------- stack : boolean, optional, default False Whether to stack the copy if this one is unstacked. copy_meta : boolean...
def bare(self): "Make a Features object with no metadata; points to the same features." if not self.meta: return self elif self.stacked: return Features(self.stacked_features, self.n_pts, copy=False) else: return Features(self.features, copy=False)
def kl(Ks, dim, num_q, rhos, nus, clamp=True): r''' Estimate the KL divergence between distributions: \int p(x) \log (p(x) / q(x)) using the kNN-based estimator (5) of Qing Wang, Sanjeev R Kulkarni, and Sergio Verdu (2009). Divergence Estimation for Multidimensional Densities Via ...
def fit(self, X, y=None): ''' Specify the data to which kernel values should be computed. Parameters ---------- X : list of arrays or :class:`skl_groups.features.Features` The bags to compute "to". ''' self.features_ = as_features(X, stack=True, bare=...
def transform(self, X): ''' Compute kernels from X to :attr:`features_`. Parameters ---------- X : list of arrays or :class:`skl_groups.features.Features` The bags to compute "from". Must have same dimension as :attr:`features_`. Returns ...
def transform(self, X): ''' Transform a list of bag features into a matrix of its mean features. Parameters ---------- X : :class:`skl_groups.features.Features` or list of bag feature arrays Data to transform. Returns ------- X_new : array, s...
def from_shypo(cls, xml, encoding='utf-8'): """Constructor from xml element *SHYPO* :param xml.etree.ElementTree xml: the xml *SHYPO* element :param string encoding: encoding of the xml """ score = float(xml.get('SCORE')) words = [Word.from_whypo(w_xml, encoding) for w_...
def from_whypo(cls, xml, encoding='utf-8'): """Constructor from xml element *WHYPO* :param xml.etree.ElementTree xml: the xml *WHYPO* element :param string encoding: encoding of the xml """ word = unicode(xml.get('WORD'), encoding) confidence = float(xml.get('CM')) ...
def run(self): """Start listening to the server""" logger.info(u'Started listening') while not self._stop: xml = self._readxml() # Exit on invalid XML if xml is None: break # Raw xml only if not self.modelize: ...
def connect(self): """Connect to the server :raise ConnectionError: If socket cannot establish a connection """ try: logger.info(u'Connecting %s:%d' % (self.host, self.port)) self.sock.connect((self.host, self.port)) except socket.error: rais...
def disconnect(self): """Disconnect from the server""" logger.info(u'Disconnecting') self.sock.shutdown(socket.SHUT_RDWR) self.sock.close() self.state = DISCONNECTED
def send(self, command, timeout=5): """Send a command to the server :param string command: command to send """ logger.info(u'Sending %s' % command) _, writable, __ = select.select([], [self.sock], [], timeout) if not writable: raise SendTimeoutError() ...
def _readline(self): """Read a line from the server. Data is read from the socket until a character ``\n`` is found :return: the read line :rtype: string """ line = '' while 1: readable, _, __ = select.select([self.sock], [], [], 0.5) if self._st...
def _readblock(self): """Read a block from the server. Lines are read until a character ``.`` is found :return: the read block :rtype: string """ block = '' while not self._stop: line = self._readline() if line == '.': break ...
def _readxml(self): """Read a block and return the result as XML :return: block as xml :rtype: xml.etree.ElementTree """ block = re.sub(r'<(/?)s>', r'&lt;\1s&gt;', self._readblock()) try: xml = XML(block) except ParseError: xml = None ...
def cli(id): """Analyse an OpenStreetMap changeset.""" ch = Analyse(id) ch.full_analysis() click.echo( 'Created: %s. Modified: %s. Deleted: %s' % (ch.create, ch.modify, ch.delete) ) if ch.is_suspect: click.echo('The changeset {} is suspect! Reasons: {}'.format( id...
def get_user_details(user_id): """Get information about number of changesets, blocks and mapping days of a user, using both the OSM API and the Mapbox comments APIself. """ reasons = [] try: url = OSM_USERS_API.format(user_id=requests.compat.quote(user_id)) user_request = requests.ge...
def changeset_info(changeset): """Return a dictionary with id, user, user_id, bounds, date of creation and all the tags of the changeset. Args: changeset: the XML string of the changeset. """ keys = [tag.attrib.get('k') for tag in changeset.getchildren()] keys += ['id', 'user', 'uid', '...
def get_changeset(changeset): """Get the changeset using the OSM API and return the content as a XML ElementTree. Args: changeset: the id of the changeset. """ url = 'https://www.openstreetmap.org/api/0.6/changeset/{}/download'.format( changeset ) return ET.fromstring(re...
def get_metadata(changeset): """Get the metadata of a changeset using the OSM API and return it as a XML ElementTree. Args: changeset: the id of the changeset. """ url = 'https://www.openstreetmap.org/api/0.6/changeset/{}'.format(changeset) return ET.fromstring(requests.get(url).content...
def get_bounds(changeset): """Get the bounds of the changeset and return it as a Polygon object. If the changeset has not coordinates (case of the changesets that deal only with relations), it returns an empty Polygon. Args: changeset: the XML string of the changeset. """ try: r...
def find_words(text, suspect_words, excluded_words=[]): """Check if a text has some of the suspect words (or words that starts with one of the suspect words). You can set some words to be excluded of the search, so you can remove false positives like 'important' be detected when you search by 'import'. ...
def read_file(self, changeset_file): """Download the replication changeset file or read it directly from the filesystem (to test purposes). """ if isfile(changeset_file): self.filename = changeset_file else: self.path = mkdtemp() self.filename ...
def get_area(self, geojson): """Read the first feature from the geojson and return it as a Polygon object. """ geojson = json.load(open(geojson, 'r')) self.area = Polygon(geojson['features'][0]['geometry']['coordinates'][0])
def filter(self): """Filter the changesets that intersects with the geojson geometry.""" self.content = [ ch for ch in self.xml.getchildren() if get_bounds(ch).intersects(self.area) ]
def set_fields(self, changeset): """Set the fields of this class with the metadata of the analysed changeset. """ self.id = int(changeset.get('id')) self.user = changeset.get('user') self.uid = changeset.get('uid') self.editor = changeset.get('created_by', None) ...
def label_suspicious(self, reason): """Add suspicion reason and set the suspicious flag.""" self.suspicion_reasons.append(reason) self.is_suspect = True
def full_analysis(self): """Execute the count and verify_words methods.""" self.count() self.verify_words() self.verify_user() if self.review_requested == 'yes': self.label_suspicious('Review requested')
def verify_user(self): """Verify if the changeset was made by a inexperienced mapper (anyone with less than 5 edits) or by a user that was blocked more than once. """ user_reasons = get_user_details(self.uid) [self.label_suspicious(reason) for reason in user_reasons]
def verify_words(self): """Verify the fields source, imagery_used and comment of the changeset for some suspect words. """ if self.comment: if find_words(self.comment, self.suspect_words, self.excluded_words): self.label_suspicious('suspect_word') if ...
def verify_editor(self): """Verify if the software used in the changeset is a powerfull_editor. """ powerful_editors = [ 'josm', 'level0', 'merkaartor', 'qgis', 'arcgis', 'upload.py', 'osmapi', 'Services_OpenStreetMap' ] if self.editor is not None: ...
def count(self): """Count the number of elements created, modified and deleted by the changeset and analyses if it is a possible import, mass modification or a mass deletion. """ xml = get_changeset(self.id) actions = [action.tag for action in xml.getchildren()] s...
def _unwrap_stream(uri, timeout, scanner, requests_session): """ Get a stream URI from a playlist URI, ``uri``. Unwraps nested playlists until something that's not a playlist is found or the ``timeout`` is reached. """ original_uri = uri seen_uris = set() deadline = time.time() + timeou...
def serve(self, sock, request_handler, error_handler, debug=False, request_timeout=60, ssl=None, request_max_size=None, reuse_port=False, loop=None, protocol=HttpProtocol, backlog=100, **kwargs): """Start asynchronous HTTP Server on an individual process. :para...
def spawn(self, generations): """Grow this Pantheon by multiplying Gods.""" egg_donors = [god for god in self.gods.values() if god.chromosomes == 'XX'] sperm_donors = [god for god in self.gods.values() if god.chromosomes == 'XY'] for i in range(generations): print("\nGENERAT...
def breed(self, egg_donor, sperm_donor): """Get it on.""" offspring = [] try: num_children = npchoice([1,2], 1, p=[0.8, 0.2])[0] # 20% chance of twins for _ in range(num_children): child = God(egg_donor, sperm_donor) offspring.append(child)...
def get_matches(word, tokens, limit, offset=0): """Return words from <tokens> that are most closely related to <word>.""" return closest(tokens, word_vec(word), limit, offset)
def cosine(vec1, vec2): """Compare vectors. Borrowed from A. Parish.""" if norm(vec1) > 0 and norm(vec2) > 0: return dot(vec1, vec2) / (norm(vec1) * norm(vec2)) else: return 0.0
def closest(tokens, search_vec, limit, offset=0): """Return the <limit> words from <tokens> whose vectors most closely resemble the search_vec. Skip the first <offset> results. """ return sorted(tokens, key=lambda x: cosine(search_vec, word_vec(x)), reverse=True)[offs...
def tokenize_texts(): """Generate a json file for each txt file in the /data/corpora directory.""" text_files = [fname for fname in os.listdir(corpora_dir) \ if fname.split('.')[1] == 'txt'] for text_fname in text_files: json_fname = text_fname.split('.')[0] + '.json' if os.path.isf...
def make_tokens_dir(dir_, sources): """Create a new directory named <dir_>. Create a new file within it called sources.json. The input <sources> is a list of names of tokenized texts. Write <sources> into sources.json. """ os.mkdir(tokens_dir + dir_) for source in sources: if not os.path...
def make_tokens_list(dir_, filters): """Find sources.json in <dir_>. It contains a list of tokenized texts. For each tokenized text listed in sources.json, read its tokens, filter them, and add them to an aggregated list. Write the aggregated list to disk using a filename based on the <filters> given. ...