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def read_DICOM_files(lstFilesDCM): """ Reads input DICOM Files. Args: ---- lstFilesDCM (list): List containing the file paths of the DICOM Files. Returns: ------- files (list): List containing the pydicom datasets. ArrayDicom (numpy.array): Image resulting from the stack of...
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def ecdsa_sign(sk, msg, k=None): """Sign ecdsa""" sig = sk.sign(msg, hashfunc=sha3.sha3_256, k=k) signature = util.sigdecode_string(sig, order) return signature
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def central_difference_of_log(f, argnum=0): """ 5th order approximation of derivative of log(f). We take advantage of the fact: d(log(f))/dx = 1/f df/dx So we approximate the second term only. """ new_f = lambda x, *args: f(*args[:argnum], x, *args[argnum:]) def _central_difference(_, *ar...
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def solve_tsp(V, c): """solve_tsp -- solve the traveling salesman problem - start with assignment model - check flow from a source to every other node; - if no flow, a sub-cycle has been found --> add cut - otherwise, the solution is optimal Parameters: - V: set/list of...
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def is_option(string): """Whether that string looks like an option to vim >>> is_option('-p') and is_option('+/sought') True """ end = 'finished' if is_final_option(string): setattr(is_option, end, True) if getattr(is_option, end, False): return False return is_dash_opti...
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def get_sources(dataframe): """ extract sources :param pandas.core.frame.DataFrame dataframe: :rtype: set :return: set of archive.org links """ sources = set() for index, row in dataframe.iterrows(): sources.update(row['incident_sources'].keys()) return sources
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def cleanupCallback(context=None): """Create a cleanup callback to clear context-specific storage for the current context""" def callback(context=contextdata.getContext(context)): """Clean up the context, assumes that the context will *not* render again!""" contextdata.cleanupContext(context) ...
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def rupture_name_to_id(rupture_names: np.ndarray, erf_ffp: str): """Converts the given ruptures names to rupture ids Parameters ---------- rupture_names: numpy array of strings erf_name: str Returns ------- numpy array of strings """ return np.char.add(rupture_names.astype(str)...
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import os def full_path(sub_path): """Turn a path relative to the config base dir into a full path :param str sub_path: Subpath relative to the config base dir """ config_base_dir = os.environ.get('SQL_CONNECTORS_CONFIG_DIR', DEFAULT_CONFIG_DIR) return os.pat...
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import sqlite3 def get_info(db: sqlite3.Connection) -> dict: """ Get all other information from the database, e.g. information about models, decks etc. Args: db: Database (:class:`sqlite3.Connection`) Returns: Nested dictionary. """ return read_info(db, "col")
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import urllib def postForm(url, headers=None, data=None): """ post form数据 :param url: :param headers: :param data: :return: code, headers, data """ if data: data = urllib.urlencode(data) if headers: headers['Content-Type'] = 'application/x-www-form-urlencoded' ...
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from datetime import datetime def set_mediafile_attrs(mediafile, ufile, data, user): """ Copy metadata from uploaded file into Model """ mediafile.name = ufile.name mediafile.original_filename = ufile.name mediafile.filesize = ufile.size mediafile.original_path = data['pathinfo0'] # Da...
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def remove_bias(name='bias_correct'): """ This workflow estimates a single multiplicative bias field from the averaged *b0* image, as suggested in [Jeurissen2014]_. .. admonition:: References .. [Jeurissen2014] Jeurissen B. et al., `Multi-tissue constrained spherical deconvolution for im...
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def filter_dis(js, status): """Converts `json` to `DataFrame` """ data = [] filter_tits = ["Wildfires", "Severe_Storms", "Sea_and_Lake_Ice"] for x in js["events"]: tit = x["categories"][0]["title"].replace(" ","_") if tit not in filter_tits: continue try: ...
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from typing import Dict from typing import Any def _apply_templating_directives( stringified_compose_spec: str, services: Dict[str, Any], spec_services_to_container_name: Dict[str, str], ) -> str: """ Some custom rules are supported for replacing `container_name` with the following syntax `%%c...
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import torch def norm(x): """Compute RMS norm.""" if torch.is_tensor(x): return x.norm() / (x.numel()**0.5) else: return torch.sqrt(sum(x_.norm()**2 for x_ in x) / sum(x_.numel() for x_ in x))
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def assume_role(credentials, account, role): """Use FAWS provided credentials to assume defined role.""" sts = boto3.client( 'sts', aws_access_key_id=credentials['accessKeyId'], aws_secret_access_key=credentials['secretAccessKey'], aws_session_token=credentials['sessionToken'], ...
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import ipaddress def is_valid_ipv6_address(ip): """Return True if valid ipv6 address """ try: ipaddress.IPv6Address(ip) return True except ipaddress.AddressValueError: return False
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def create_nested_grid_samples(order, dim=1): """ Create samples from a nested grid. Args: order (int): The order of the grid. Defines the number of samples. dim (int): The number of dimensions in the grid Returns (numpy.ndarray): Regular grid with ``sha...
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from typing import Union from typing import Sequence def validate_string_encoding(value: StringEncodingArgument) -> StringEncoding: """Validates and coerces a value to a StringEncoding. Parameters ---------- value : StringEncodingArgument The value to validate and coerce. If this is a...
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from typing import Optional def get_link(prefix: str, identifier: str, use_bioregistry_io: bool = True) -> Optional[str]: """Get the best link for the CURIE, if possible.""" providers = get_providers(prefix, identifier) for key in LINK_PRIORITY: if not use_bioregistry_io and key == "bioregistry": ...
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import argparse def parse_args(): """Parses arguments.""" parser = argparse.ArgumentParser( description='Train semantic boundary with given latent codes and ' 'attribute scores.') parser.add_argument('-o', '--output_dir', type=str, required=True, help='Directory to ...
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def calc_case_peaks_and_indices_fd(forces, disps): """ Calculates the cumulative change stored energy for an oscillating system at the peaks Note: This quantity is double the area of the triangles in a full cycle, since positive and negative triangles are counted. >>> disp = np.array([0, 4, 0, -2,...
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def _smooth_spm(con, vcon, msk, sigma): """ Given a contrast image `con` and the corresponding variance image `vcon`, both assumed to be estimated from non-smoothed first-level data, compute what `con` and `vcon` would have been had the data been smoothed with a Gaussian kernel. """ scon = _...
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from typing import Iterator import os import json import tqdm def get_statistics(samples: Iterator): """ Input: samples: [{ "text": "label": }] Output: dict: "label":n_samples usage: you can test it with following code: ...
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import torch def to_tensor(data: FeatureDataType) -> torch.Tensor: """ Convert data to tensor :param data which is either numpy or Tensor :return torch.Tensor """ if isinstance(data, torch.Tensor): return data elif isinstance(data, np.ndarray): return torch.from_numpy(data)...
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import inspect def case(pattern: str): """ Use `case` as a decorator for functions, with full unpacking of the argument(s). ``` @case("[x @ int|float, *y]") def foo(x, y): ... ``` Guards are not supported at the moment. """ def decorate(f): name = f.__code__.co_nam...
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import os from multiprocessing import Manager, Process import logging import tqdm def get_all_distances_rounded( station_locations: np.ndarray, grid_points: np.ndarray, settings: dict ) -> np.ndarray: """ Computes the distances between all station locations and grid_points. Rounds them to settings["de...
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import random def generate_chars(charset: tuple[int, int], count: int) -> str: """Character generation routine for execution in a process pool.""" characters = "".join(chr(random.randint(charset[0], charset[1])) for i in range(count)) return discord.utils.escape_markdown(characters)
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from typing import Union def get_simple_graph_from_multigraph(multigraph: Union[nx.MultiGraph, nx.MultiDiGraph]) -> nx.Graph: """Convert undirected graph from multigraph.""" graph = Graph() for u, v, data in multigraph.edges(data=True): u = get_label_node(u) v = get_label_node(v) ...
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def get_list_view_name(model): """ Return list view name for model. """ return '{}-list'.format( model._meta.object_name.lower() )
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import warnings import copy from re import T def PCA_latentFeatures( spark, idf, list_of_cols="all", drop_cols=[], explained_variance_cutoff=0.95, pre_existing_model=False, model_path="NA", standardization=True, standardization_configs={"pre_existing_model": False, "model_path": "N...
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import os def execute(file_names, timeout): """Execute problem with OPTIC""" domain_file_name = os.path.join(files_manager.TEMP_FOLDER, file_names[0]) problem_file_name = os.path.join(files_manager.TEMP_FOLDER, file_names[1]) try: output = check_output([ "timeout", "{}s".format(timeout), OPTI...
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def google_maps(maiden: str, center: bool = False) -> str: """ generate Google Maps URL from Maidenhead grid Parameters ---------- maiden : str Maidenhead grid center : bool If true, return the center of provided maidenhead grid square, instead of default south-west corner ...
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def make_prompt(title, context=''): """ input: a twee title ie :: titlename output: a twee title surounded by GPT-3 readable start/end tokens <begin tokens>:: titlename<end tokens> """ if context: context = context.strip() + ENDCONTEXT return BEGIN + context + title + ENDPROMPT
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from typing import Callable def warm_up_polynomial_schedule( base_learning_rate: float, end_learning_rate: float, decay_steps: int, warmup_steps: int, decay_power: float, ) -> Callable: """Please see uncertainty_baselines.schedules.WarmUpPolynomialSchedule. """ poly_schedule = optax.polynomi...
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import copy def render_plugins(plugins, context, placeholder, processors=None): """ Renders a collection of plugins with the given context, using the appropriate processors for a given placeholder name, and returns a list containing a "rendered content" string for each plugin. This is the mai...
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def getkey(value, key): """ Return a dictionary item specified by key """ return value[key]
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import scipy def direct_2d2(x, x_s, dx, dt, c, f): """Use the 2D Green's function to determine the wavefield at a given location and time due to the given source. """ r = np.linalg.norm(x - x_s) nt = len(f) def func(tp, t): return f[int(tp / dt)] / np.sqrt(c**2 * (t - tp)**2 - r**2) ...
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def spring1s(ep,ed): """ Compute element force in spring element (spring1e). :param float ep: spring stiffness or analog quantity :param list ed: element displacements [d0, d1] :return float es: element force [N] """ k = ep return k*(ed[1]-ed[0]);
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def add_comment(msg, user_id): """Add a comment to our comments list.""" # Create comment entity in datastore and add comment fields to it ds_comment = ds_create_comment(user_id) ds_comment['commenter'] = msg.commenter ds_comment['text'] = msg.text ds_comment['time'] = msg.time try: ...
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import requests def capture_payment(order_id, access_token, transaction_amount=0, transaction_text="Capture"): """ Captures the reserved payment for the provided order id. :param order_id: ID for the transaction. :param access_token: A token for authorizing the request to Vipps. :param transactio...
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import os def generate_payload(provider, generator, filtering, verify_name=True, verify_size=True): """ Payload formatter to format results the way Elementum expects them Args: provider (str): Provider ID generator (function): Generator method, can be either ``extract_torrents`` or ``...
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from typing import List from typing import NamedTuple def get_user_models(creds: PostgresCredentials, uid: str) -> List[NamedTuple]: """DB function used to retrieve models for a given user Args: uid (str): [ Returns: List[NamedTuple]: [description] """ with get_cursor(creds)...
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def distance(x_1, x_2, method='euclidean'): """Pairwise distance metric between two vectors. The vectors are assumed to be rows. Parameters ---------- x_1 : array-like One of two vectors to compute distance between. x_2 : array-like One of two vectors to compute distance between...
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import copy import re def ip_match_replace(request, injectionstring): """ Simple match and replace of string within request """ newrequest = copy.deepcopy(request) rawrequest = request.get_raw_request() for r in INJECT_MATCH_REPLACE: regex = re.compile(r) if regex.search(rawreq...
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import subprocess def run_cmd(cmd): """Run console command. Return stdout print stderr.""" process = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) stdout, stderr = process.communicate() if process.returncode > 0: print("The com...
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def _putheader_wrapper(func, instance, args, kwargs): """ This is the wrapper of the function that called after that the http request was sent. Note that we don't examine the response data because it may change the original behaviour (ret_val.peek()). """ kwargs["headers"]["X-Amzn-Trace-Id"] = Spans...
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def _validate_workflow_var_format(value: str) -> str: """Validate workflow vars Arguments: value {str} -- A '.' seperated string to be checked for workflow variable formatting. Returns: str -- A string with validation error messages """ add_info = '' parts = value.s...
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from typing import Literal async def authenticate( username: str, password: str ) -> Result[Literal[False], account_dao.Account]: """認証 """ got_account = await account_dao.find(username=username) if got_account is None or not verify_password( plain_password=password, hashed_password=got_ac...
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def mock_command_checker(mocker: MockerFixture) -> MockerFixture: """Fixture for mocking CommandChecker.check.""" return mocker.patch("git_portfolio.use_cases.command_checker.CommandChecker.check")
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import imghdr from datetime import datetime def write_id3v2_header( data, fields ): """Add an ID3v2 header to the data assuming none already present""" body = bytes() if 'title' in fields: title_bytes = b'\x03' + fields['title'].encode( 'utf_8' ) body += b'TIT2' + len( title_bytes ).to_bytes( 4, 'big' ) + b'\...
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def _calspec_file_parse_name_(stdname): """ """ return stdname.replace("+","_").lower()
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def getmodel(name: str) -> ba.Model: """getmodel(name: str) -> ba.Model Return a model, loading it if necessary. Category: Asset Functions Note that this function returns immediately even if the media has yet to be loaded. To avoid hitches, instantiate your media objects in advance of when yo...
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def calculate_jaccard(tp_fp_fn_dict: dict) -> np.array: """Calculate list of Jaccard indices. Args: tp_fp_fn_dict: {"true_positives": true_positives, "false_positives": false_positives, "false_negatives": false_negatives} Returns: """ epsilo...
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def make_reg_ex(seq): """Make regular expression for ambiguous DNA.""" return "".join(ambiguous_dna_re[letter] for letter in seq)
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def init_decorrelated_plsa( dataset, modalities_to_use, main_modality, num_topics, model_params: dict = None ): """ Creates simple artm model with standard scores. Parameters ---------- dataset : Dataset modalities_to_use : list of str main_modality :...
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from datetime import datetime def today_recurrence(recurrence: dict, now_date=datetime.date.today()) -> bool: """ Checks the recurrence to know if today is a recurrence day. :param recurrence: list Recurrence information :param now_date: date Today date :return: bool True if today is a day of the ...
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import re def remove_comments(codelines): """ Removes all comments from codelines. """ lines_removed = [] for l in codelines: # remove comments lines_removed.append(re.sub("#.*", "", l)) return lines_removed
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import pandas def raw_difference_frame(raw_model,mean_frame,**options): """Creates a difference pandas.DataFrame given a raw NIST model and a mean pandas.DataFrame""" defaults={"column_names":mean_frame.columns.tolist()} difference_options={} for key,value in defaults.items(): difference_optio...
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def sdm_25d_point(omega, x0, n0, xs, xref=[0, 0, 0], c=None): """Point source by 2.5-dimensional SDM. The secondary sources have to be located on the x-axis (y0=0). Driving funcnction from :cite:`Spors2010`, Eq.(24):: D(x0,k) = """ x0 = util.asarray_of_rows(x0) n0 = util.asarray_of_ro...
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def predict(): """Receives a url photo, process it and make a prediction using SVC model. Args: url (str): url containing the image. """ form = URLRequisition() # Process the url to get and embedding representation of the face. if form.validate_on_submit(): url = f...
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def build_game_using_payoff_matrices( lambda_2, lambda_1_1, lambda_1_2, mu_1, mu_2, num_of_servers_1, num_of_servers_2, system_capacity_1, system_capacity_2, buffer_capacity_1, buffer_capacity_2, target, payoff_matrix_A=None, payoff_matrix_B=None, alternative_...
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from unittest.mock import patch from typing import List def with_mock_subp(func): """Decorator that sets up a Popen mock. Any function that uses this decorator should take a function as an argument. When called wtih a series of return codes, that function will mock out subprocess.Popen, and set it to...
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def diff_2nd_xx(fp, f0, fm, eps): """Evaluates an on-diagonal 2nd derivative term""" return (fp - 2.0*f0 + fm)/eps**2
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def valid_client_request_body(initialize_db): """ A fixture for creating a valid client model. Args: initialize_db (None): initializes the database and drops tables when test function finishes. """ return {'username': 'Leroy Jenkins', 'avatar_url': ''}
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def invert_map(variables): """Converts a dict(OS, dict(deptype, list(dependencies)) to a flattened view. Returns a tuple of: 1. dict(deptype, dict(dependency, set(OSes)) for easier processing. 2. All the OSes found as a set. """ KEYS = ( KEY_TOUCHED, KEY_TRACKED, KEY_UNTRACKED, 'command...
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def yolo_loss(args, anchors, num_classes, ignore_thresh=.5): """Return yolo_loss tensor Parameters ---------- yolo_outputs: list of tensor, the output of yolo_body or tiny_yolo_body y_true: list of array, the output of preprocess_true_boxes anchors: array, shape=(N, 2), wh num_classes: inte...
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def HexToRGB(hex_str): """Returns a list of red/green/blue values from a hex string. @param hex_str: hex string to convert to rgb """ hexval = hex_str if hexval[0] == u"#": hexval = hexval[1:] ldiff = 6 - len(hexval) hexval += ldiff * u"0" # Convert hex values to integer ...
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def data_context_path_computation_context_path_comp_serviceuuid_end_pointlocal_id_capacity_bandwidth_profile_peak_information_rate_get(uuid, local_id): # noqa: E501 """data_context_path_computation_context_path_comp_serviceuuid_end_pointlocal_id_capacity_bandwidth_profile_peak_information_rate_get returns tap...
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import requests def check_parent_login(username, dob): """ Checks if user input for their credentials is correct. Parameters: username -- student's PID (format: XXXNameXXXX) where X - integers dob -- student's date of birth (required to log into parent's portal) """ ...
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from typing import Optional from typing import Sequence from typing import Tuple def isel( axis: Optional[int], chunks: Sequence[zarr.Array], key: Optional[Sequence[slice]], tensor_domain: Optional[Sequence[slice]], ) -> Tuple[Sequence[zarr.Array], Sequence[slice]]: """Select a subset of the chunk...
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def MakeSavedQuery( query_id, name, base_query_id, query, subscription_mode=None, executes_in_project_ids=None): """Make SavedQuery PB for the given info.""" saved_query = tracker_pb2.SavedQuery( name=name, base_query_id=base_query_id, query=query) if query_id is not None: saved_query.query_id =...
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def evaluate_nbests(nbests): """Return a single evaluation of list of n-best lists.""" evals = list(map(evaluate_nbest, nbests)) return sum_evals(evals)
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from typing import Union from pathlib import Path from typing import Optional def check_for_project(path: Union[Path, str] = ".") -> Optional[Path]: """Checks for a Brownie project.""" path = Path(path).resolve() for folder in [path] + list(path.parents): structure_config = _load_project_structur...
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def _get_W(k, M, epsilon=2e-2): """ Evaluates the auxiliary function at particular value of the independent variable. Parameters ---------- k: float Indepentent variable. M: int Number of revolutions epsilon: float Tolerance parameter. Default value as in the ori...
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import requests def return_figures(states=states_default): """Creates a plotly visualization using the COVID tracking API (http://covidtracking.com/data/api) # Example of the COVID API endpoint: # https://api.covidtracking.com/v1/states/{state}/daily.json by state Args: state_...
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def append_dict_key_value( in_dict, keys, value, delimiter=DEFAULT_TARGET_DELIM, ordered_dict=False ): """ Ensures that in_dict contains the series of recursive keys defined in keys. Also appends `value` to the list that is at the end of `in_dict` traversed with `keys`. :param dict in_dict: The...
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def index(page): """Exibe todos os socios cadastrados.""" try: atualizao_status_socio() perpage = 12 startat = ( page - 1 ) * perpage perpage *= page totalsocio = db.query_bd('select * from socio') totalpages = int(len(totalsocio) / 12) + 1 if request.met...
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import sys def getScopeId (scope, serverName, nodeName, clusterName): """useful when scope is a required parameter for a function""" if scope == "cell": try: result = getCellId() except: my_sep(sys.exc_info()) # end except elif scope == "node": if no...
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def get_scheduler(params, optimizer, num_epochs=0): """Get scheduler. Args: params (dict): scheduler parameters, see `PyTorch documentation <https://pytorch.org/docs/stable/optim.html>`__ optimizer (torch optim): num_epochs (int): number of epochs. Returns: torch.optim, boo...
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def generate_pv_limits(): """Get the control limits and precision values from the live machine for all normal PVS. """ data = [("pv", "upper", "lower", "precision")] lattice = atip.utils.loader() for element in lattice: for field in element.get_fields()[pytac.SIM]: pv = eleme...
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import subprocess def is_file_tracked(file, git="git", cwd=None): """ Args: file: relative path to file within a git repository cwd: optional path to change before executing the command Returns: true if the given file is tracked by a git repository, false otherwise """ ret...
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def T2(a): """Rotation matrix about third axis Assumptions: N/A Source: N/A Inputs: a [radians] angle of rotation Outputs: T [-] rotation matrix Properties Used: N/A """ # T = np.array([[cos ,sin,0], # [-sin,cos,0],...
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def train_step(data_iterator, model, optimizer, lr_scheduler, args, timers,tokenizer): """Single training step.""" # Forward model for one step. timers('forward').start() lm_loss = forward_step(data_iterator, model, args, timers,tokenizer) timers('forward').stop() #print_rank_0(...
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def getBoardStr(board): """Return a text-representation of the board.""" return ''' {}|{}|{} 1 2 3 -+-+- {}|{}|{} 4 5 6 -+-+- {}|{}|{} 7 8 9'''.format(board['1'], board['2'], board['3'], board['4'], board['5'], board['6'], board['7'], board['8'], board['9'])
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import gzip import bz2 import sys import re def store_pathways(verbose): """ Store the uniref ids from the pathways file """ uniref_pathways={} for file in PATHWAYS_DATABASES: try: if file.endswith(".gz"): file_handle = gzip.open(file, "rt") ...
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import random def get_random_account(): """Get data from random account""" return random.choice(data)
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import os def interesting(conditionArgs, prefix): """ This function check if the file is interesting to reduce """ global buggy_line global debug project_dir = conditionArgs[0] testcase = conditionArgs[1] expected = conditionArgs[2] source_file = conditionArgs[3] file_basename = ...
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def main(binary, axes=None): """Find and retunrs the coordinates of the 4 points of interest Arguments --------- binary : 2D array Binarized and and cropped version of the butterfly ax : obj If any is provided, POI, smoothed wings boundaries and binary will be plotted on it ...
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def kirsch_operator(img_to_kirsch: np.ndarray) -> np.ndarray: """Runs the Kirsch Operator algorithm Reference: AlNouri, M., al Saei, J., Younis, M., Bouri, F., al Habash, M. A., Shah, M. H., & al Dosari, M. (2015). Comparison of Edge Detection Algorithms for Automated Radiographic Measurement of the Ca...
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import os import yaml def load_spectrometers(spectometers_path, splib07a_dir): """ Load all spectrometer data contained in specified directory. Parameters ---------- spectrometers_dir: str path to directory containing spectrometer metadata splib07a_dir: str path to top-level ...
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def UnitVec3_getAs(p): """ UnitVec3_getAs(double const * p) -> UnitVec3 Parameters ---------- p: double const * """ return _simbody.UnitVec3_getAs(p)
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def seed_from_str(s: str) -> int: """ Obtains an integer seed from a string using the hash function """ return hash(s) % (2 ** 32)
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def get_rend_as_mean(image_file_path: str) -> float: """Read image from given path and return mean of the pixels.""" array = get_rend_as_ndarray_wl(image_file_path) return np.mean(array)
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def download_puppy_texture(load=True): # pragma: no cover """Download puppy texture. Parameters ---------- load : bool, optional Load the dataset after downloading it when ``True``. Set this to ``False`` and only the filename will be returned. Returns ------- pyvista.Data...
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def compute_pca(image_set): """Calculates and returns PCA of a set of images Args: image_set: List of images read with cv2.imread in np.uint8 format Returns: PCA for the set of images """ # Check for valid input assert(image_set[0].dtype == np.uint8) # Reshape data into s...
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import re def cleanse_sentences(tweet_list: list) -> list: """ Runs checks for the tweets so that most special characters, emojis, links and retweet tags are removed. :param tweet_list: List containing tweets :return: Cleansed list of strings. """ result = [] for tweet in tweet_list: ...
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import os def os_path_expanduser(path): """wrap os.path.expanduser""" path = toUnicodeFileEncoding(path) result = os.path.normpath(os.path.expanduser(path)) return result
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import torch def reflect_conj_concat(kern, dim): """Reflects and conjugates kern before concatenating along dim. Args: kern (tensor): One half of a full, Hermitian-symmetric kernel. dim (int): The integer across which to apply Hermitian symmetry. Returns: tensor: The full FFT ker...
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