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def getChanprofIndex(chanprof, profile, chanList): """ List of indices into the RTTOV chanprof(:) array corresponding to the chanlist. NB This assumes you've checked the chanlist against chanprof already. """ ilo = sum(map(len, chanprof[:profile-1])) ichanprof = [] for c in chanList: ...
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def _get_blob_size_string(blob_key): """Return blob size string.""" blob_size = blobs.get_blob_size(blob_key) if blob_size is None: return None return utils.get_size_string(blob_size)
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def masked_softmax_full(input_layer, n_nodes, batch_size): """ A Lambda layer to compute a lower-triangular version of the full adjacency. Each row must sum up to one. We apply a lower triangular mask of ones and then add an upper triangular mask of a large negative number. After that we return the...
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import collections import socket def match_backends_and_tasks(backends, tasks): """Returns tuples of matching (backend, task) pairs, as matched by IP and port. Each backend will be listed exactly once, and each task will be listed once per port. If a backend does not match with a task, (backend, None) will ...
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def _drop_path(x, keep_prob): """ Drops out a whole example hiddenstate with the specified probability. """ batch_size = tf.shape(x)[0] noise_shape = [batch_size, 1, 1, 1] random_tensor = keep_prob random_tensor += tf.random_uniform(noise_shape, dtype=tf.float32) binary_tensor = tf.f...
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import yaml def read_pipeline_definition(file_path): """Function reads the yaml pipeline definitions. Function reads the yaml pipeline definitions. We also remove the variables key as that was only used for yaml placeholders. Args: file_path (str): Path to the pipeline definition. Returns...
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import io def detect_text(path): """Detects text in the file.""" client = vision.ImageAnnotatorClient() with io.open(path, 'rb') as image_file: content = image_file.read() image = vision.types.Image(content=content) response = client.text_detection(image=image) texts = response.text...
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import bisect def find_dataset_ind(windows_ds, win_ind): """Taken from torch.utils.data.dataset.ConcatDataset. """ return bisect.bisect_right(windows_ds.cumulative_sizes, win_ind)
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def from_moment(w): """Converts a moment representation w to a 3D rotation matrix.""" length = vectorops.norm(w) if length < 1e-7: return identity() return rotation(vectorops.mul(w,1.0/length),length)
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def add_menu(data): """ 新增 :param data: :return: """ i = SysMenu.insert(data).execute() return i
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def compute_distance_matrix(m1: np.ndarray, m2: np.ndarray, dist_func: np.ndarray, row_wise: bool = False) \ -> np.ndarray: """ Function for computing the pair-wise distance matrix between two arrays of vectors. Both matrices must have the same number ...
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from typing import List from typing import Iterator from typing import Any def term_table( strings: List[str], row_wise: bool = False, filler: str = "~" ) -> Iterator[Any]: """ :param strings: :param row_wise: :param filler: :return: """ max_str_len = max(len(str) for str in strings) ...
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def create_pipelines_lingspam(): """Reproduces the pipelines evaluated in the LingSpam paper. I. Androutsopoulos, J. Koutsias, K.V. Chandrinos, George Paliouras, and C.D. Spyropoulos, "An Evaluation of Naive Bayesian Anti-Spam Filtering". In Potamias, G., Moustakis, V. and van Someren, M. (Eds.), ...
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def band_dos_plain_spin_polarized( band_folder, dos_folder, output='band_dos_plain_sp.png', up_color='black', down_color='red', linewidth=1.25, up_linestyle='-', down_linestyle=':', figsize=(6, 3), width_ratios=[7, 3], erange=[-6, 6], kpath=None, custom_kpath=None, ...
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def _unsigned16(data, littleEndian=False): """return a 16-bit unsigned integer with selectable Endian""" assert len(data) >= 2 if littleEndian: b0 = data[1] b1 = data[0] else: b0 = data[0] b1 = data[1] val = (b0 << 8) + b1 return val
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def calculate_term_frequencies(tokens): """Given a series of `tokens`, produces a sorted list of tuples in the format of (term frequency, token). """ frequency_dict = {} for token in tokens: frequency_dict.setdefault(token, 0) frequency_dict[token] += 1 tf = [] for token...
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def max(*l): """ Element-wise max of each of the input tensors (with Numpy-style broadcasting support). Args: *x (a list of Tensor): List of tensors for max. Returns: Tensor, the output """ return Max()(*l)[0]
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def _edr_peak_trough_mean(ecg: pd.Series, peaks: np.array, troughs: np.array) -> np.array: """Estimate respiration signal from ECG based on `peak-trough-mean` method. The `peak-trough-mean` method is based on computing the mean amplitude between R peaks (`peaks`) and minima before R peaks (`troughs`). ...
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import joblib def feature_stacking(n_splits=CV, random_state=None, use_proba=False, verbose=False, drop_words=0.): """ Args: n_splits: n_splits for KFold random_state: random_state for KFlod use_proba: True to predict probabilities of labels instead of labels verbose: True to ...
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import traceback import json def data(request): """ [メソッド概要] アクション履歴画面の一覧表示 """ logger.logic_log('LOSI00001', 'none', request=request) msg = '' lang = request.user.get_lang_mode() ita_flg = False mail_flg = False servicenow_flg = False filter_info = { 'tblname' : ...
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def get_default(): """Get the configuration from the source code""" return {name: dict(block()._asdict()) for name, _, block in triples}
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def npulses(image_number,passno=0): """How many X-ray bursts to send to the sample as function of image number. image_number is 1-based, passno is 0-based. """ # When using sample translation the exposure may be boken up # into several passes. if passno != None: npulses = npulses_of_pass(image_n...
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import torch from typing import Optional def topk__dynamic(ctx, input: torch.Tensor, k: int, dim: Optional[int] = None, largest: bool = True, sorted: bool = True): """Rewrite `topk` for default backend. Cast k to tensor...
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def GetLocalNodeId() -> int: """Returns the current local node id. If none has been set, a default is set and used.""" global _local_node_id if _local_node_id is None: SetLocalNodeId(DEFAULT_LOCAL_NODE_ID) return _local_node_id
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def get_dlons_from_case(case: dict): """pull list of latitudes from test case""" dlons = [geo[1] for geo in case["destinations"]] return dlons
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def account_info(info): """Extract user information from IdP response""" return dict( user=dict( email=info['User.email'][0], profile=dict( username=info['User.FirstName'][0], full_name=info['User.FirstName'][0])), external_id=info['User.em...
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from typing import Concatenate def MangoYOLO(inputs, num_anchors, num_classes, **kwargs): """Create Tiny YOLO_v3 model CNN body in keras.""" x1 = compose( DarknetConv2D_BN_Leaky(16, (3,3), **kwargs), DarknetConv2D_BN_Leaky(16, (3, 3), strides=2, **kwargs), DarknetConv2D_BN_Leaky(32, (3,3), **kwargs), Darkne...
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def zone_max_matching(plan_a, plan_b): """ Determines the optimal bipartite matching of districts in plan_a to districts in plan_b to maximize the total population overlap. Both plans should have districts indexed from 1 to k, where k is some positive integer. Based on the concept of "...
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def dyn_sim_feedback_discrete_time(A, Bu, Bd, x0, u, d, t_series, K): """ Simulate discrete-time ODE Args: A: discrete-time A Bu: discrete-time B for control Bd: discrete-time B for disturbance x0: Initial condition in numpy array nx*1 u: Control signal in numpy array...
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import logging def get_recordings(mysql, symbol_id): """ Parameters ---------- mysql : dict Connection information symbol_id : int ID of a symbol on write-math.com Returns ------- list : A list of HandwrittenData objects """ connection = pymysql.connect...
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def horiLine(lineLength, lineWidth=None, lineCharacter=None, printOut=None): """Generate a horizontal line. Args: lineLength (int): The length of the line or how many characters the line will have. lineWidth (int, optional): The width of the line or how many lines of text the line will take spa...
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import struct import functools def decrypt(content, salt=None, key=None, private_key=None, dh=None, auth_secret=None, keyid=None, keylabel="P-256", rs=4096, version="aes128gcm"): """ Decrypt a data block :param content: Data to be decrypted :type content: str :...
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import math def _rescale_read_counts_if_necessary(n_ref_reads, n_total_reads, max_allowed_reads): """Ensures that n_total_reads <= max_allowed_reads, rescaling if necessary. This function ensures that n_total_reads <= max_allowed_reads. If n_total_reads is <= max_allowed_r...
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def encode_log_entry_to_json(logEntry): """ Transform the log entry to jason format dict to store into MongoDB """ if logEntry.action == "Query_Success" or "Commit_Success": # Common fileds for query and commit log entry json_dict= {"date": logEntry.utcTimestamp, ...
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def run_backward_rnn(sess, test_idx, test_feat, num_lstm_units): """ Run backward RNN given a query.""" res_set = [] lstm_state = np.zeros([1, 2 * num_lstm_units]) for test_id in reversed(test_idx): input_feed = np.reshape(test_feat[test_id], [1, -1]) [lstm_state, lstm_output] = rnn_one_step( ...
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import functools def preprocess_xarray(func): """Decorate a function to convert all DataArray arguments to pint.Quantities. This uses the metpy xarray accessors to do the actual conversion. """ @functools.wraps(func) def wrapper(*args, **kwargs): args = tuple(a.metpy.unit_array if isinsta...
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def _get_verticalalignment(angle, location, side, is_vertical, is_flipped_x, is_flipped_y): """Return vertical alignment along the y axis. Parameters ---------- angle : {0, 90, -90} location : {'first', 'last', 'inner', 'outer'} side : {'first', 'last'} is_vertica...
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def load_dict(path): """ Load a dictionary and a corresponding reverse dictionary from the given file where line number (0-indexed) is key and line string is value. """ retdict = list() rev_retdict = dict() with open(path) as fin: for idx, line in enumerate(fin): text = line.stri...
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import numpy def hsplit(ary, indices_or_sections): """ Split an array into multiple sub-arrays horizontally (column-wise). Please refer to the `split` documentation. `hsplit` is equivalent to `split` with ``axis=1``, the array is always split along the second axis regardless of the array dimensi...
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def is_valid_ipv6_addr(input=""): """Check if this is a valid IPv6 string. Returns ------- bool A boolean indicating whether this is a valid IPv6 string """ assert input != "" if _RGX_IPV6ADDR.search(input): return True return False
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def calc_TEC( maindir, window=4096, incoh_int=100, sfactor=4, offset=0.0, timewin=[0, 0], snrmin=0.0, ): """ Estimation of phase curve using coherent and incoherent integration. Args: maindir (:obj:`str`): Path for data. window (:obj:'int'): Window length in samp...
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def solve(A, b): """solve a sparse system Ax = b Args: A (torch.sparse.Tensor[b, m, m]): the sparse matrix defining the system. b (torch.Tensor[b, m, n]): the target matrix b Returns: x (torch.Tensor[b, m, n]): the initially unknown matrix x Note: 'A' should be 'dense'...
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def smiles_to_fp(smiles): """ Convert smiles to Daylight FP and MACCSkeys. Parameters ---------- smiles : str, smiles representation of a molecule Returns ------- fp : np.ndarray zero and one representation of the fingerprints """ try: mol = Chem.MolFromSmiles(smiles) ...
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import re def _networkinfo(interface): """Given an interface name, returns dict containing network and broadcast address as IPv4Interface objects If an interface has no IP, returns None """ ipcmds = "ip -o -4 address show dev {}".format(interface).split() out = check_output(ipcmds).decode('ut...
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def score_decorator(f): """Decorator for sklearn's _score function. Special `hack` for sklearn.model_selection._validation._score in order to score pipelines that drop samples during transforming. """ def wrapper(*args, **kwargs): args = list(args) # Convert to list for item assignment ...
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def trait(name, notify=True, optional=False): """ Create a new expression for observing a trait with the exact name given. Events emitted (if any) will be instances of :class:`~traits.observation.events.TraitChangeEvent`. Parameters ---------- name : str Name of the trait to match....
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def get_splits(space, data, props, max_specs=None, seed=None, fp_type="morgan"): """ Get representations and values of the data given a certain set of Morgan hyperparameters. Args: space (dict): hyperopt` space of hyperpara...
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def amortized_loan(principal, apr, periods, m=12): """ """ return principal / pvifa(apr, periods, m)
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from typing import Optional from typing import Iterable def horizontal_legend( fig: Figure, handles: Optional[Iterable[Artist]] = None, labels: Optional[Iterable[str]] = None, *, ncol: int = 1, **kwargs, ) -> Legend: """ Place a legend on the figure, with the items arranged to read right to left rathe...
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def _create_lock_inventory(session, rp_uuid, inventories): """Return a function that will lock inventory for this rp.""" def _lock_inventory(): rp_url = '/resource_providers/%s' % rp_uuid inv_url = rp_url + '/' + 'inventories' resp = session.get(rp_url) if resp: data ...
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def strip(string, p=" \t\n\r"): """ strip(string, p=" \t\n\r") """ return string.strip(p)
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def correlation_matrix_plot( df, function=pearsonr, significance_level=0.05, cbar_levels=8, figsize=(6, 6) ): """Plot corrmat considering p-vals.""" corr, pvals = correlation_matrix(df, function=function) # create triangular mask for heatmap mask = np.zeros_like(corr) mask[np.triu_indices_from(...
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def _unvec(vecA, m=None): """inverse of _vec() operator""" N = vecA.shape[0] if m is None: m = np.sqrt(vecA.shape[1] + 0.25).astype(np.int64) return vecA.reshape((N, m, -1), order='F')
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import logging def one_hot_encode(sequences): """One hot encoding of a list of DNA sequences Args: sequences (list):: python list of strings of equal length Returns: numpy.ndarray: 3-dimension numpy array with shape (len(sequences), len(list_i...
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def binary_cross_entropy(labels, logits, linear_input=True, eps=1.e-5, name='binary_cross_entropy_loss'): """ Same as cross_entropy_loss for the binary classification problem. the model should have a one dimensional output, the targets should be given in form of a matrix of dimensions batch_size x 1 with va...
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def get_number_from_user(): """ None -> (int) Get a symbol by index from the user's input. """ movers = ApiWrapper.get_movers() while True: print("To choose a company, enter a responding integer from the list below") print_movers(movers) y = input("Enter the number of compan...
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def read_refseqscan_results(fn): """Read RefSeqScan output file""" ret = dict() for line in open(fn): line = line.strip() if line == '' or line.startswith('#'): continue cols = line.split() ret[cols[0]] = cols[2] return ret
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import array def discretize_categories(iterable): """ :param iterable: :return: """ uniques = sorted(set(iterable)) discretize = False for v in uniques: if isinstance(v, str): discretize = True if discretize: # Discretize and return an array str_to_int_...
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def multhist(hists, asone=1): """Takes a set of histograms and combines them. If asone is true, then returns one histogram of key->[val1, val2, ...]. Otherwise, returns one histogram per input""" ret = {} num = len(hists) for i, h in enumerate(hists): for k in sorted(h): if k...
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def to_dict(obj, table=None, scrub=None, fields=None): """ Takes a single or list of sqlalchemy objects and serializes to JSON-compatible base python objects. If scrub is set to True, then this function will also remove all keys that match the specified list """ data = None serialize_obj = ...
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import torch def CWLoss(output, target, confidence=0): """ CW loss (Marging loss). """ num_classes = output.shape[-1] target = target.data target_onehot = torch.zeros(target.size() + (num_classes,)) target_onehot = target_onehot.cuda() target_onehot.scatter_(1, target.unsqueeze(1), 1.)...
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def get_square(array, size, y, x, position=False, force=False, verbose=True): """ Return an square subframe from a 2d array or image. Parameters ---------- array : 2d array_like Input frame. size : int Size of the subframe. y : int Y coordinate of the center of the s...
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def iou_with_anchors(anchors_min, anchors_max, box_min, box_max): """Compute jaccard score between a box and the anchors. """ len_anchors = anchors_max - anchors_min int_xmin = np.maximum(anchors_min, box_min) int_xmax = np.minimum(anchors_max, box_max) inter_len = np.maximum(int_xmax - int_xmi...
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def load_from_np(filename, arr_idx_der): """ arr_idx_der 1 for rho and 2 for p """ # load npy data of 3D tube arr = np.load(filename) arr_t = arr[:, 0] arr_der = arr[:, arr_idx_der] return arr_t, arr_der
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def rxzero_vel_amp_eval(parm, t_idx): """ siglognormal velocity amplitude evaluation """ if len(parm) == 6: D, t0, mu, sigma, theta_s, theta_e = parm elif len(parm) == 4: D, t0, mu, sigma = parm else: print 'Invalid length of parm...' return None #argument for...
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import json def read_json(json_file): """ Read input JSON file and return the dict. """ json_data = None with open(json_file, 'rt') as json_fh: json_data = json.load(json_fh) return json_data
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def mixnet_xl(pretrained=False, num_classes=1000, in_chans=3, **kwargs): """Creates a MixNet Extra-Large model. Not a paper spec, experimental def by RW w/ depth scaling. """ default_cfg = default_cfgs['mixnet_xl'] #kwargs['drop_connect_rate'] = 0.2 model = _gen_mixnet_m( channel_multipl...
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def accuracy(results): """ Evaluate the accuracy of results, considering victories and defeats. Args: results: List of 2 elements representing the number of victories and defeats Returns: results accuracy """ return results[1] / (results[0] + results[1]) * 100
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def sub_sellos_agregar(): """ Agregar nuevo registro a 'sub_sellos' """ form = SQLFORM(db.sub_sellos, submit_button='Aceptar') if form.accepts(request.vars, session): response.flash = 'Registro ingresado' return dict(form=form)
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async def ensure_valid_path(current_path: str) -> bool: """ ensures the path is configured to allow auto refresh """ paths_to_check = settings.NO_AUTO_REFRESH for path in paths_to_check: if path in current_path: return False return True
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from typing import List def part_1_original_approach(lines: List[str]) -> int: """ This was my original approach. I missed a few critical details that really bit me in the ass. 1. Operator precedence for modulo. """ ans = 0 seq = [[int(c) for c in x] for x in lines] for _ in range(10...
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def get_distances(username,location,dist): """ The purpose of this function is the calculation of distances between user and created rooms """ distances=[] keys = ['_id','dist'] base=list(nego.find({},{'location':0})) ## Retrieves every user in the base except location for d in base: ...
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import pickle def AcProgEgrep(context, grep, selection=None): """Corresponds to AC_PROG_EGREP_ autoconf macro :Parameters: context SCons configuration context. grep Path to ``grep`` program as found by `AcProgGrep`. selection If ``None`` (default), ...
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def is_number(s): """Is string a number.""" try: float(s) return True except ValueError: return False
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import numpy def calc_motif_dist(motifList): """Given a list of motifs, returns a dictionary of the distances for each motif pair, e.g. {Motif1:Motif2:(dist, offset, sense/antisense)} """ ret = {} for m1 in motifList: for m2 in motifList: if m1.id != m2.id: #che...
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def step(name=None): """ Decorates functions that will register a step. """ def decorator(func): add_step(get_name(name, func), func) return func return decorator
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def prepare_subimg(image5d, size, offset): """Extracts a subimage from a larger image. Args: image5d: Image array as a 5D array (t, z, y, x, c), or 4D if no separate channel dimension exists as with most one channel images. size: Size of the region of interest as ...
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def filter_plants_by_region_id(region_id, year, host='switch-db2.erg.berkeley.edu', area=0.5): """ Filters generation plant data by NERC Region, according to the provided id. Generation plants w/o Region get assigned to the NERC Region with which more than a certain percentage of its County area interse...
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def _get_image_blob(roidb, scale_ind): """Builds an input blob from the images in the roidb at the specified scales. """ num_images = len(roidb) processed_ims = [] # processed_ims_depth = [] # processed_ims_normal = [] im_scales = [] for i in xrange(num_images): # rgba ...
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def translate_month(month): """ Translates the month string into an integer value Args: month (unicode): month string parsed from the website listings. Returns: int: month index starting from 1 Examples: >>> translate_month('jan') 1 """ for key, values ...
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def gencpppxd(desc, exception_type='+'): """Generates a cpp_*.pxd Cython header file for exposing C/C++ data from to other Cython wrappers based off of a dictionary description. Parameters ---------- desc : dict Class description dictonary. exception_type : str, optional Cython...
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def no_results_to_show(): """Produce an error message when there are no results to show.""" return format_html('<p class="expenses-empty">{}</p>', _("No results to show."))
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def enhance_shadows(Shw, method, **kwargs): """ Given a specific method, employ shadow transform Parameters ---------- Shw : np.array, size=(m,n), dtype={float,integer} array with intensities of shading and shadowing method : {‘mean’,’kuwahara’,’median’,’otsu’,'anistropic'} method n...
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from typing import Optional from typing import Set import collections def _to_real_set( number_or_sequence: Optional[ScalarOrSequence] ) -> Set[chex.Scalar]: """Converts the optional number or sequence to a set.""" if number_or_sequence is None: return set() elif isinstance(number_or_sequence, (float, i...
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def alt_or_ref(record, samples: list): """ takes in a single record in a vcf file and returns the sample names divided into two lists: ones that have the reference snp state and ones that have the alternative snp state Parameters ---------- record the record supplied by the vcf reader ...
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def plot_loss(ctx, tests, rulers=[], sfx="", **kwargs): """Loss plot (1 row per test, val on left, train on right).""" vh = len(tests) fig, axs = plt.subplots(vh, 2, figsize=(16, 4 * vh)) for base, row in zip(tests, axs.reshape(vh, 2)): ctx.plot_loss( base, row[0], baselines=["adam"]...
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def mpi_rank(): """ Returns the rank of the calling process. """ comm = mpi4py.MPI.COMM_WORLD rank = comm.Get_rank() return rank
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def db(app): """ Setup our database, this only gets executed once per session. :param app: Pytest fixture :return: SQLAlchemy database session """ _db.drop_all() _db.create_all() # Create a single user because a lot of tests do not mutate this user. # It will result in faster tests...
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def is_const_component(record_component): """Determines whether a group or dataset in the HDF5 file is constant. Parameters ---------- record_component : h5py.Group or h5py.Dataset Returns ------- bool True if constant, False otherwise References ---------- .. https://...
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def centernet_resnet101b_voc(pretrained_backbone=False, classes=20, **kwargs): """ CenterNet model on the base of ResNet-101b for VOC Detection from 'Objects as Points,' https://arxiv.org/abs/1904.07850. Parameters: ---------- pretrained_backbone : bool, default False Whether to load th...
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import pytz def isodate(dt): """Formats a datetime to ISO format.""" tz = pytz.timezone('Europe/Zagreb') return dt.astimezone(tz).isoformat()
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def _ncells_after_subdiv(ms_inf, divisor): """Calculates total number of vtu cells in partition after subdivision :param ms_inf: Mesh/solninformation. ('ele_type', [npts, nele, ndims]) :type ms_inf: tuple: (str, list) :rtype: integer """ # Catch all for cases where cell subdivision is not perf...
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def match_santa_pairs(participants: list): """ This function returns a list of tuples of (Santa, Target) pairings """ shuffle(participants) return list(make_circular_pairs(participants))
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def conv_relu_forward(x, w, b, conv_param): """ A convenience layer that performs a convolution followed by a ReLU. Inputs: - x: Input to the convolutional layer - w, b, conv_param: Weights and parameters for the convolutional layer Returns a tuple of: - out: Output from the ReLU - cache: Object to give to t...
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def top_rank(df, target, n=None, ascending=False, method='spearman'): """ Calculate first / last N correlation with target This method is measuring single-feature relevance importance and works well for independent features But suffers in the presence of codependent features. pearson : standard corr...
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def sample_points_on_sphere(center, distance_from_center, hemisphere=False): """just use the polar coordinates to do this, this can be sped up do that """ EPS = 1e-6 thetas = np.linspace(0+EPS, 2*np.pi, 64) phis = np.linspace(0+EPS, np.pi/2, 64) if hemisphere else np.linspace(0+EPS, np.pi, 64) p...
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from pathlib import Path def get_package_path() -> Path: """ Get local install path of the package. """ return to_path(__file__).parent.absolute()
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import inspect import types def parameterized_class(cls): """A class decorator for running parameterized test cases. Mark your class with @parameterized_class. Mark your test cases with @parameterized. """ test_functions = inspect.getmembers(cls, predicate=inspect.ismethod) for (name, f) in t...
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def isStringLike(s): """ Returns True if s acts "like" a string, i.e. is str or unicode. Args: s (string): instance to inspect Returns: True if s acts like a string """ try: s + '' except: return False else: return True
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def velocity_to_wavelength(velocities, input_units, center_wavelength=None, center_wavelength_units=None, wavelength_units='meters', convention='optical'): """ Conventions defined here: http://www.gb.nrao.edu/~fghigo/gbtdoc/doppler.html * Radio V = c (c/l0 - c/l)/(c/l0) f(V) = (c/l0)...
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