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def bool_tag(name, value): """Create a DMAP tag with boolean data.""" return name.encode('utf-8') + \ b'\x00\x00\x00\x01' + \ (b'\x01' if value else b'\x00')
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def _concat(*lists): """Concatenates the items in `lists`, ignoring `None` arguments.""" concatenated = [] for list in lists: if list: concatenated += list return concatenated
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def get_least_squares_size(modelform, r, m=0, affines=None): """Calculate the number of columns in the operator matrix O in the Operator Inference least-squares problem. Parameters --------- modelform : str containing 'c', 'A', 'H', 'G', and/or 'B' The structure of the desired reduced-order model. Each character indicates the presence of a different term in the model: 'c' : Constant term c 'A' : Linear state term Ax. 'H' : Quadratic state term H(x⊗x). 'G' : Cubic state term G(x⊗x⊗x). 'B' : Input term Bu. For example, modelform=="AB" means f(x,u) = Ax + Bu. r : int The dimension of the reduced order model. m : int The dimension of the inputs of the model. Must be zero unless 'B' is in `modelform`. affines : dict(str -> list(callables)) Functions that define the structures of the affine operators. Keys must match the modelform: * 'c': Constant term c(µ). * 'A': Linear state matrix A(µ). * 'H': Quadratic state matrix H(µ). * 'G': Cubic state matrix G(µ). * 'B': linear Input matrix B(µ). For example, if the constant term has the affine structure c(µ) = θ1(µ)c1 + θ2(µ)c2 + θ3(µ)c3, then 'c' -> [θ1, θ2, θ3]. Returns ------- ncols : int The number of columns in the Operator Inference least-squares problem. """ has_inputs = 'B' in modelform if has_inputs and m == 0: raise ValueError(f"argument m > 0 required since 'B' in modelform") if not has_inputs and m != 0: raise ValueError(f"argument m={m} invalid since 'B' in modelform") if affines is None: affines = {} qc = len(affines['c']) if 'c' in affines else 1 if 'c' in modelform else 0 qA = len(affines['A']) if 'A' in affines else 1 if 'A' in modelform else 0 qH = len(affines['H']) if 'H' in affines else 1 if 'H' in modelform else 0 qG = len(affines['G']) if 'G' in affines else 1 if 'G' in modelform else 0 qB = len(affines['B']) if 'B' in affines else 1 if 'B' in modelform else 0 return qc + qA*r + qH*r*(r+1)//2 + qG*r*(r+1)*(r+2)//6 + qB*m
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def read(rows): """Reads the list of rows and returns the sudoku dict. The sudoku dict maps an index to a known value. Unknown values are not written. Indices go from 0 to 80. """ sudoku = {} i = 0 for rn, row in enumerate(rows): if rn in (3, 7): continue j = 0 for cn, c in enumerate(row.rstrip()): if cn in (3, 7): continue if c != ".": sudoku[i * 9 + j] = int(c) j += 1 i += 1 return sudoku
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def uniquify(iterable): """Remove duplicates in given iterable, preserving order.""" uniq = set() return (x for x in iterable if x not in uniq and (uniq.add(x) or True))
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def badFormatting(s, charSet): """Tells if a character from charSet appears in a string s.""" for c in charSet: if c in s: return True return False
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def column_to_width(df_in, column, width): """Pad the column header and the values in the column with whitespace to a specific width. """ df = df_in.copy() df[column] = df[column].apply(lambda x: ('{:>' + str(width) + '}').format(x)) df = df.rename(columns={column: ('{:>' + str(width) + '}').format(column)}) return df
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def use_netrc(netrc, urls, patterns): """compute an auth dict from a parsed netrc file and a list of URLs Args: netrc: a netrc file already parsed to a dict, e.g., as obtained from read_netrc urls: a list of URLs. patterns: optional dict of url to authorization patterns Returns: dict suitable as auth argument for ctx.download; more precisely, the dict will map all URLs where the netrc file provides login and password to a dict containing the corresponding login, password and optional authorization pattern, as well as the mapping of "type" to "basic" or "pattern". """ auth = {} for url in urls: schemerest = url.split("://", 1) if len(schemerest) < 2: continue if not (schemerest[0] in ["http", "https"]): # For other protocols, bazel currently does not support # authentication. So ignore them. continue host = schemerest[1].split("/")[0].split(":")[0] if not host in netrc: continue authforhost = netrc[host] if host in patterns: auth_dict = { "type": "pattern", "pattern": patterns[host], } if "login" in authforhost: auth_dict["login"] = authforhost["login"] if "password" in authforhost: auth_dict["password"] = authforhost["password"] auth[url] = auth_dict elif "login" in authforhost and "password" in authforhost: auth[url] = { "type": "basic", "login": authforhost["login"], "password": authforhost["password"], } return auth
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def str_cutoff(string: str, max_length: int, cut_tail: bool = False) -> str: """ Abbreviate a string to a given length. The resulting string will carry an indicator if it's abbreviated, like ``stri#``. Parameters ---------- string : str String which is to be cut. max_length : int Max resulting string length. cut_tail : bool ``False`` for string abbreviation from the front, else ``True``. Returns ------- str Resulting string """ if max_length < 1: raise ValueError("max_length < 1 not allowed") if len(string) > max_length: pos = max_length - 1 return string[:pos] + "#" if cut_tail else "#" + string[-pos:] return string
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def wireless(card, mode=None, apn=None): """Retrieve wireless modem info or customize modem behavior. Args: card (Notecard): The current Notecard object. mode (string): The wireless module mode to set. apn (string): Access Point Name (APN) when using an external SIM. Returns: string: The result of the Notecard request. """ req = {"req": "card.wireless"} if mode: req["mode"] = mode if apn: req["apn"] = apn return card.Transaction(req)
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def filter_none(x): """ Recursively removes key, value pairs or items that is None. """ if isinstance(x, dict): return {k: filter_none(v) for k, v in x.items() if v is not None} elif isinstance(x, list): return [filter_none(i) for i in x if x is not None] else: return x
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def _dmet_orb_list(mol, atom_list): """Rearrange the orbital label Args: mol (pyscf.gto.Mole): The molecule to simulate. atom_list (list): Atom list for IAO assignment (int). Returns: newlist (list): The orbital list in new order (int). """ newlist = [] for i in range(mol.natm): for j in range(mol.nao_nr()): if (atom_list[j] == i): newlist.append(j) return newlist
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def _post_processing(metric_map: dict[str, float]) -> dict[str, float]: """ unit conversion etc... time: taskTime, executorDeserializeTime, executorRunTime, jvmGcTime are milliseconds executorDeserializeCpuTime, executorCpuTime are nanoseconds """ metric_map["executorDeserializeCpuTime"] = metric_map[ "executorDeserializeCpuTime"] * 1e-6 metric_map["executorCpuTime"] = metric_map["executorCpuTime"] * 1e-6 return metric_map
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from bs4 import BeautifulSoup import requests def get_soup(url: str) -> BeautifulSoup: """Get an instance of BeautifulSoup for a specific url""" response = requests.get(url) if response.status_code != requests.codes.ok: print(f"url request error: response.status_code is {response.status_code}") raise requests.ConnectionError html = response.text soup: BeautifulSoup = BeautifulSoup(html, "html.parser") return soup
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def intersect(hrect, r2, centroid): """ checks if the hyperrectangle hrect intersects with the hypersphere defined by centroid and r2 """ maxval = hrect[1, :] minval = hrect[0, :] p = centroid.copy() idx = p < minval p[idx] = minval[idx] idx = p > maxval p[idx] = maxval[idx] return ((p - centroid) ** 2).sum() < r2
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def is_method_of(method, obj): """Return True if *method* is a method of *obj*. *method* should be a method on a class instance; *obj* should be an instance of a class. """ # Check for both 'im_self' (Python < 3.0) and '__self__' (Python >= 3.0). cls = obj.__class__ mainObj = getattr(method, "im_self", getattr(method, "__self__", None)) return isinstance(mainObj, cls)
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from typing import Counter def number_of_pairs(gloves): """ Given an array describing the color of each glove, return the number of pairs you can constitute, assuming that only gloves of the same color can form pairs. Examples: input = ["red", "green", "red", "blue", "blue"] result = 2 (1 red pair + 1 blue pair) """ count = 0 gloves = Counter(gloves) for x in gloves.values(): count += x // 2 return count
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def Rmax_Q11(Vmax): """ Estimation of the radius of maximum wind according to the formula proposed by Quiring et al. (2011); Vmax and Rmax are in nautical miles. Expression herein converted in km""" Vm= Vmax * 0.5399568 Rmax = ((49.67 - 0.24 * Vm)) * 1.852 return Rmax
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def get_option_value(elem): """ Get the value attribute, or if it doesn't exist the text content. <option value="foo">bar</option> => "foo" <option>bar</option> => "bar" :param elem: a soup element """ value = elem.get("value") if value is None: value = elem.text.strip() if value is None or value == "": msg = u"Error parsing value from {}.".format(elem) raise ValueError(msg) return value
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def EI(sections, normal=None): # {{{ """Calculate the bending stiffnes of a cross-section. The cross-section is composed out of rectangular nonoverlapping sections that can have different Young's moduli. Each section is represented by a 4-tuple (width, height, offset, E). The offset is the distance from the top of the section to the top of the highest section. This should always be a positive value. E is the Young's modulus of the material of this section. Arguments: sections: Iterable of section properties. normal: The Young's modulus to which the total cross-section will be normalized. (Not used anymore, retained for compatibility.) Returns: Tuple of EI, top and bottom. Top and bottom are with respect to the neutral line. Examples: >>> E = 210000 >>> B = 100 >>> H = 20 >>> sections = ((B, H, 0, E),) >>> EI(sections) (14000000000.0, 10.0, -10.0) >>> B = 100 >>> h = 18 >>> t = 1 >>> H = h + 2 * t >>> E = 210000 >>> sections = ((B, t, 0, E), (B, t, h+t, E)) >>> EI(sections) (3794000000.0, 10.0, -10.0) >>> E1, E2 = 200000, 71000 >>> t1, t2 = 1.5, 2.5 >>> H = 31 >>> B = 100 >>> sections = ((B, t1, 0, E1), (B, t2, H-t2, E2)) >>> EI(sections) (9393560891.143106, 11.530104712041885, -19.469895287958117) """ normal = sections[0][-1] normalized = tuple((w * E / normal, h, offs) for w, h, offs, E in sections) A = sum(w * h for w, h, _ in normalized) S = sum(w * h * (offs + h / 2) for w, h, offs in normalized) yn = S / A # Find any geometry that straddles yn. to_split = tuple(g for g in sections if g[2] < yn and g[1] + g[2] > yn) geom = tuple(g for g in sections if g not in to_split) # split that geometry. # The new tuple has the format (width, height, top, bottom) new_geom = [] for w, h, offs, E in to_split: h1 = yn - offs h2 = h - h1 new_geom.append((w, h1, h1, 0, E)) new_geom.append((w, h2, 0, -h2, E)) # Convert the remaining geometry to reference yn. for w, h, offs, E in geom: new_geom.append((w, h, yn - offs, yn - offs - h, E)) EI = sum(E * w * (top ** 3 - bot ** 3) / 3 for w, h, top, bot, E in new_geom) top = max(g[-3] for g in new_geom) bot = min(g[-2] for g in new_geom) return EI, top, bot
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def filter_labels_by_class(obj_labels, classes): """Filters object labels by classes. Args: obj_labels: List of object labels classes: List of classes to keep, e.g. ['Car', 'Pedestrian', 'Cyclist'] Returns: obj_labels: List of filtered labels class_mask: Mask of labels to keep """ class_mask = [(obj.type in classes) for obj in obj_labels] return obj_labels[class_mask], class_mask
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def probably_reconstruction(file) -> bool: """Decide if a path may be a reconstruction file.""" return file.endswith("json") and "reconstruction" in file
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from typing import Counter def check_author_count(counter: Counter) -> bool: """ Takes a set of documents and counts the number of authors. If less than 2, returns False otherwise True. :param counter: a Counter object for author counts. :return: a boolean indicating whether or not the document set can be analyzed (True for yes, no for False). """ if len(counter) == 1: return False return True
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def default_destinations(iata_code_original_destination): """Get three default destinations different from original destination of query.""" # Paris, London, Rome, New York defaults = ['CDG', 'LHR', 'FCO', 'JFK'] if iata_code_original_destination in defaults: defaults.remove(iata_code_original_destination) else: defaults.remove('JFK') return defaults
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import json def get_boxnote_text(filepath): """Convert a boxnote to plain text. Parameters: filepath (str): the path to the boxfile Returns: the text of the boxfile as a string """ f = open(filepath, encoding="utf8") text = json.loads(f.read())["atext"]["text"] f.close() return text
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from typing import Dict def filter_val_not_none(d: Dict) -> Dict: """ Return a new dictionary composed of all key-value pairs (k, v) in d where v is not None. :param d: original dictionary :return: d, without key-value pairs where value is None >>> filter_val_not_none({"a": 5, "b": 10, "c": None}) == {"a": 5, "b": 10} True """ return {k: v for k, v in d.items() if v is not None}
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def get_card_ids(db) -> list: """ Gets a list of all card IDs in the datase. :return: List of card IDs. """ return db['cards'].distinct('_id')
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import time def datetime_to_integer(datetime): """Convert datetime object to integer value. 'datetime' is the datetime object""" return time.mktime(datetime.timetuple())
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def crop_to_ratio(im, desired_ratio=4 / 3): """ Crop (either) the rows or columns of an image to match (as best as possible) the desired ratio. Arguments: im (np.array): Image to be processed. desired_ratio (float): The desired ratio of the output image expressed as width/height so 3:2 (= 3/2) or 16:9 ( = 16/9). Returns: An image (np.array) with the desired ratio. """ height = im.shape[0] width = im.shape[1] if width / height < desired_ratio: # Crop rows desired_height = int(round(width / desired_ratio)) to_crop = height - desired_height top_crop = to_crop // 2 bottom_crop = to_crop - top_crop cropped_image = im[top_crop:height - bottom_crop, :] else: # Crop columns desired_width = int(round(height * desired_ratio)) to_crop = width - desired_width left_crop = to_crop // 2 right_crop = to_crop - left_crop cropped_image = im[:, left_crop:width - right_crop] return cropped_image
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def grompp_npt(job): """Run GROMACS grompp for the npt step.""" npt_mdp_path = "npt.mdp" msg = f"gmx grompp -f {npt_mdp_path} -o npt.tpr -c em.gro -p init.top --maxwarn 1" return msg
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def uri_leaf(uri): """ Get the "leaf" - fragment id or last segment - of a URI. Useful e.g. for getting a term from a "namespace like" URI. >>> uri_leaf("http://purl.org/dc/terms/title") == 'title' True >>> uri_leaf("http://www.w3.org/2004/02/skos/core#Concept") == 'Concept' True >>> uri_leaf("http://www.w3.org/2004/02/skos/core#") # returns None """ for char in ('#', '/', ':'): if uri.endswith(char): break if char in uri: sep = char leaf = uri.rsplit(char)[-1] else: sep = '' leaf = uri if sep and leaf: return leaf
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import yaml def load_yaml_config(filename): """Load a YAML configuration file.""" with open(filename, "rt", encoding='utf-8') as file: config_dict = yaml.safe_load(file) return config_dict
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import uuid def build_request_body(method, params): """Build a JSON-RPC request body based on the parameters given.""" data = { "jsonrpc": "2.0", "method": method, "params": params, "id": str(uuid.uuid4()) } return data
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def part1(input_data): """ >>> part1(["939","7,13,x,x,59,x,31,19"]) 295 """ timestamp = int(input_data[0]) bus_ids = input_data[1].split(',') # Ignore bus_ids with 'x' bus_ids = map(int, filter(lambda bus_id: bus_id != 'x', bus_ids)) # (id, time_to_wait) # last_busstop = timestamp % id # time_to_wait = id - last_busstop bus_ids = [(bus_id, bus_id - (timestamp % bus_id)) for bus_id in bus_ids] bus_ids.sort(key=lambda x: x[1]) next_bus_id, next_bus_time_to_wait = bus_ids[0] return next_bus_id * next_bus_time_to_wait
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import torch def fetch_optimizer(lr, wdecay, epsilon, num_steps, params): """ Create the optimizer and learning rate scheduler """ optimizer = torch.optim.AdamW(params, lr=lr, weight_decay=wdecay, eps=epsilon) scheduler = torch.optim.lr_scheduler.OneCycleLR(optimizer, lr, num_steps+100, pct_start=0.05, cycle_momentum=False, anneal_strategy='linear') return optimizer, scheduler
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import re def to_num(string): """Convert string to number (or None) if possible""" if type(string) != str: return string if string == "None": return None if re.match("\d+\.\d*$", string): return float(string) elif re.match("\d+$", string): return int(string) else: return string
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def get_tidy_invocation(f, clang_tidy_binary, checks, build_path, quiet, config): """Gets a command line for clang-tidy.""" start = [clang_tidy_binary] # Show warnings in all in-project headers by default. start.append('-header-filter=src/') if checks: start.append('-checks=' + checks) start.append('-p=' + build_path) if quiet: start.append('-quiet') if config: start.append('-config=' + config) start.append(f) return start
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def dataset_pre_0_3(client): """Return paths of dataset metadata for pre 0.3.4.""" project_is_pre_0_3 = int(client.project.version) < 2 if project_is_pre_0_3: return (client.path / 'data').rglob(client.METADATA) return []
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import copy def sanitize_slicing(slice_across, slice_relative_position): """ Return standardized format for `slice_across` and `slice_relative_position`: - either `slice_across` and `slice_relative_position` are both `None` (no slicing) - or `slice_across` and `slice_relative_position` are both lists, with the same number of elements Parameters ---------- slice_relative_position : float, or list of float, or None slice_across : str, or list of str, or None Direction(s) across which the data should be sliced """ # Skip None and empty lists if slice_across is None or slice_across == []: return None, None # Convert to lists if not isinstance(slice_across, list): slice_across = [slice_across] if slice_relative_position is None: slice_relative_position = [0]*len(slice_across) if not isinstance(slice_relative_position, list): slice_relative_position = [slice_relative_position] # Check that the length are matching if len(slice_across) != len(slice_relative_position): raise ValueError( 'The argument `slice_relative_position` is erroneous: \nIt should have' 'the same number of elements as `slice_across`.') # Return a copy. This is because the rest of the `openPMD-viewer` code # sometimes modifies the objects returned by `sanitize_slicing`. # Using a copy avoids directly modifying objects that the user may pass # to this function (and live outside of openPMD-viewer, e.g. directly in # a user's notebook) return copy.copy(slice_across), copy.copy(slice_relative_position)
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def get_traitset_map(pop): """ Utility method which returns a map of culture ID's (hashes) and the trait set corresponding to a random individual of that culture (actually, the first one we encounter). """ traitsets = {} graph = pop.agentgraph for nodename in graph.nodes(): traits = graph.node[nodename]['traits'] culture = pop.get_traits_packed(traits) if culture not in traitsets: traitsets[culture] = traits return traitsets
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def prefix(txt, pref): """ Place a prefix in front of the text. """ return str(pref) + str(txt)
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def isinstance_all(iterable, class_or_tuple): """ Check if all items of an iterable are instance of a class ou tuple of classes >>> isinstance_all(['Hello', 'World'], str) True >>> isinstance_all([1, 'Hello'], (str, int)) True >>> isinstance_all([True, 'Hello', 5], int) False """ return all( isinstance(obj, class_or_tuple) for obj in iterable )
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import tarfile import pathlib def _strip_paths(tarinfo: tarfile.TarInfo) -> tarfile.TarInfo: """Ensure source filesystem absolute paths are not reflected in tar file.""" original_path = pathlib.Path(tarinfo.name) tarinfo.name = f"{original_path.name}" return tarinfo
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import re def re_cap(*regexes): """ Capture first of the supplied regex :param regexes: list or regex strings :return: captured string | None """ def go(string): for reg in regexes: matches = re.search(reg, string) if matches: return matches.group(1) return None return go
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def set_crs(gdf, crs): """ Set CRS in GeoDataFrame when current projection is not defined. Parameters ---------- gdf : geopandas.GeoDataFrame the geodataframe to set the projection Returns ------- gdf : geopandas.GeoDataFrame the geodataframe with the projection defined """ gdf = gdf.set_crs(crs) return gdf
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def GetDistinguishableNames(keys, delimiter, prefixes_to_remove): """Reduce keys to a concise and distinguishable form. Example: GetDistinguishableNames(['Day.NewYork.BigApple', 'Night.NewYork.BigMelon'], '.', ['Big']) results in {'Day.NewYork.BigApple': 'Day.Apple', 'Night.NewYork.BigMelon': 'Night.Melon'}. If a key has all parts commonly shared with others, then include the last shared part in the names. E.g., GetDistinguishableNames(['Day.NewYork', 'Day.NewYork.BigMelon'], '.', ['Big']) results in {'Day.NewYork.BigApple': 'NewYork', 'Night.NewYork.BigMelon': 'NewYork.Melon'}. Args: keys: The list of strings, each is delimited by parts. delimiter: The delimiter to separate parts of each string. prefixes_to_remove: The list of prefix strings to be removed from the parts. Returns: short_names: A dictionary of shortened keys. """ def RemovePrefix(part, prefixes_to_remove): for prefix in prefixes_to_remove: if part.startswith(prefix): return part[len(prefix):] return part key_part_lists = [key.split(delimiter) for key in keys] shortest_length = min(len(part_list) for part_list in key_part_lists) # common_part[i] = True if all parts at position i are the same across keys. common_part = [True] * shortest_length for part_list in key_part_lists[1:]: for i in range(shortest_length): if part_list[i] != key_part_lists[0][i]: common_part[i] = False # The prefix list to add if one of the key happens to be the concatenation of # all common parts. prefix_list = ([key_part_lists[0][shortest_length - 1]] if all(common_part) else []) short_names = {} for key, part_list in zip(keys, key_part_lists): short_names[key] = delimiter.join(prefix_list + [ RemovePrefix(part, prefixes_to_remove) for n, part in enumerate(part_list) if n >= shortest_length or not common_part[n]]) return short_names
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import binascii import re def humanhexlify(data, n=-1): """Hexlify given data with 1 space char btw hex values for easier reading for humans :param data: binary data to hexlify :param n: If n is a positive integer then shorten the output of this function to n hexlified bytes. Input like 'ab\x04ce' becomes '61 62 04 63 65' With n=3 input like data='ab\x04ce', n=3 becomes '61 62 04 ...' """ tail = b' ...' if 0 < n < len(data) else b'' if tail: data = data[:n] hx = binascii.hexlify(data) return b' '.join(re.findall(b'..', hx)) + tail
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def make_arc_consistent(Xj, Xk, csp): """Make arc between parent (Xj) and child (Xk) consistent under the csp's constraints, by removing the possible values of Xj that cause inconsistencies.""" # csp.curr_domains[Xj] = [] for val1 in csp.domains[Xj]: keep = False # Keep or remove val1 for val2 in csp.domains[Xk]: if csp.constraints(Xj, val1, Xk, val2): # Found a consistent assignment for val1, keep it keep = True break if not keep: # Remove val1 csp.prune(Xj, val1, None) return csp.curr_domains[Xj]
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def get_reference_data(p): """Summarise the bibliographic data of an article from an ADS query Returns dict of 'author' (list of strings), 'title' (string), and 'ref' (string giving journal, first page, and year). """ data = {} try: data['author'] = p.author except: data['author'] = 'Anon' try: data['title'] = p.title except: data['title'] = 'Untitled' try: refstring = p.pub except: refstring = 'Unknown' try: refstring += f' {p.volume}, {p.page[0]}' except: pass try: refstring += f' ({p.year})' except: pass data['ref'] = refstring return data
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def _parse_config_args(args): """ Parse stub configuration arguments, which are strings of the form "KEY=VAL". `args` is a list of arguments from the command line. Any argument that does not match the "KEY=VAL" format will be logged and skipped. Returns a dictionary with the configuration keys and values. """ config_dict = dict() for config_str in args: try: components = config_str.split('=') if len(components) >= 2: config_dict[components[0]] = "=".join(components[1:]) except: # lint-amnesty, pylint: disable=bare-except print(f"Warning: could not interpret config value '{config_str}'") return config_dict
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def add_pylivetrader_imports(code: str) -> str: """ add all imports from the pylivetrader api """ imports = """ from pylivetrader.api import * \r\n """ return imports + code
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import re def what_lang(filename): """ Judge what language the file is written by from filename extention. """ langs=[('c|cc|cpp|h', 'c/c++'), ('java', 'java'), ('sh', 'sh'), ('pl', 'perl'), ('rb', 'ruby'), ('py', 'python'), ('xml', 'xml'), ('txt|md', 'txt')] for lang in langs: reg = r'.+\.(' + lang[0] + r')$' if re.match(reg, filename): return lang[1] return 'default'
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def get_text(xml, tag): """Return the text from a given tag and XML element. """ elem = xml.find(tag) if elem is not None: return elem.text.strip()
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from typing import Dict from typing import Any from typing import Iterable from typing import Hashable def get_in( dictionary: Dict[Any, Any], keys: Iterable[Hashable], default: Any = None, ) -> Any: """Traverses a set of nested dictionaries using the keys in kws, and returns the value assigned to the final keyword in the innermost dictionary. Calling get_in(d, [X, Y]) is equivalent to calling d.get(X).get(Y), with the difference that any missing keys causes the default value to be returned. Behavior on non-dictgionaries is undefined.""" keys = list(keys) for key in keys[:-1]: try: dictionary = dictionary[key] except KeyError: return default return dictionary.get(keys[-1], default)
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def _unique_in_order(seq): """ Utility to preserver order while making a set of unique elements. Copied from Markus Jarderot's answer at https://stackoverflow.com/questions/480214/how-do-you-remove-duplicates-from-a-list-in-whilst-preserving-order Args: seq : sequence Returns: unique_list : list List of unique elements in their original order """ seen = set() seen_add = seen.add return [x for x in seq if not (x in seen or seen_add(x))]
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def extra_node_ids(a, b): """ Return list of nodes in a which aren't in b by id attribute. :param etree.ElementTree a: ElementTree representing first SVG document. :param etree.ElementTree a: ElementTree representing second SVG document. """ ids_a = set([ el.attrib['id'] for el in a.iter() ]) ids_b = set([ el.attrib['id'] for el in b.iter() ]) return ids_a - ids_b
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from typing import Iterable def get_score(bits: Iterable[int]) -> int: """Get the score. For each "1" add 1 for each "0" takeaway 1 """ return sum(-1 if bit == 0 else 1 for bit in bits)
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def get_cli_fname(lon, lat, scenario=0): """Get the climate file name for the given lon, lat, and scenario""" # The trouble here is relying on rounding is problematic, so we just # truncate lon = round(lon, 2) lat = round(lat, 2) return "/i/%s/cli/%03ix%03i/%06.2fx%06.2f.cli" % ( scenario, 0 - lon, lat, 0 - lon, lat, )
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def conv_repoids_to_list(repo_ids): """ Convert repo ids seperated by "\n" to list. """ if not repo_ids: return [] repoid_list = [] for repo_id in repo_ids.split("\n"): if repo_id == '': continue repoid_list.append(repo_id) return repoid_list
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def rename(term): """ Re-format feature terms after they've been formated by the vectorizer. Parameters: ---------- term : str Mutilated term in string format. Returns ------- str The normalised term. """ term = term.upper() if 'IPR' in term: return term elif 'PF' in term: return term elif 'GO' in term: return term.replace("GO", 'GO:').replace('::', ':') else: return term
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def bpstr(ts, accum): """Make a string representation of this breakpoint and accumulation""" return "%02i.%02i %6.2f" % (ts.hour, ts.minute / 60.0 * 100.0, accum)
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def find_direction(start, end): """ Find direction from start to end """ if start[0] == end[0]: if start[1] < end[1]: return 5 else: return 1 elif start[1] == end[1]: if start[0] < end[0]: return 3 else: return 7 elif start[0] < end[0]: if start[1] < end[1]: return 4 else: return 2 elif start[0] > end[0]: if start[1] < end[1]: return 6 else: return 8
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def _pad_digits(text: str) -> str: """A str method with hacks to support better lexicographic ordering. The output strings are not intended to be human readable. The returned string will have digit-runs zero-padded up to at least 8 digits. That way, instead of 'a10' coming before 'a2', 'a000010' will come after 'a000002'. Also, the original length of each digit-run is appended after the zero-padded run. This is so that 'a0' continues to come before 'a00'. """ was_on_digits = False last_transition = 0 chunks = [] def handle_transition_at(k): chunk = text[last_transition:k] if was_on_digits: chunk = chunk.rjust(8, '0') + ':' + str(len(chunk)) chunks.append(chunk) for i in range(len(text)): on_digits = text[i].isdigit() if was_on_digits != on_digits: handle_transition_at(i) was_on_digits = on_digits last_transition = i handle_transition_at(len(text)) return ''.join(chunks)
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from typing import List def get_missing_settings(settings_class) -> List[str]: """Used to validate required settings. Verifies that all attributes which don't start with ``_`` and aren't named in ``_optional_settings`` are not set to None. Args: settings_class: The global settings class to validate settings on. Returns: List of setting names that should not be ``None``. If the list is empty then all required settings are defined. """ missing_settings = [] for attr in vars(settings_class): if attr.startswith("_") or \ attr in getattr(settings_class, "_optional_settings", ()): continue if getattr(settings_class, attr) is None: missing_settings.append(attr) return missing_settings
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def _check_equal_list(iterator): """ Check that all elements in list are equal """ return len(set(iterator)) <= 1
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def find_layer(model, layer_class): """ Find all layers in model that are instances of layer_class """ layers = [] for layer in model.layers: if isinstance(layer, layer_class): layers.append(layer) elif hasattr(layer, "layers"): # search in nested layers layers += find_layer(layer, layer_class) return layers
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def in_region(pos, regions): """Find whether a position is included in a region. Parameters ---------- pos : int DNA base position. regions : list of tuples List of (start, end) position integers. Returns ------- bool True if the position is within an of the regions, False otherwise. Examples -------- # Empty list >>> in_region(1, []) False # In list >>> in_region(10, [(3, 5), (9, 12)]) True # Not in list >>> in_region(10, [(3, 5), (11, 12)]) False """ for region in regions: if (pos >= region[0]) and (pos <= region[1]): return True return False
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import six def zero_lpad(number, length): """ Fill 0 on the left of number :param number: number to be padded :param length: length of result string :return: """ if six.PY3: return str(number).ljust(length, '0') return '{number:0>{length}}'.format(number=number, length=length)
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def line0(x,a): """ Straight line through origin: a*x Parameters ---------- x : float or array_like of floats independent variable a : float first parameter Returns ------- float function value(s) """ return a*x
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import json def to_json(msg): """Pretty-print a dict as a JSON string Use Unicode and 2-space indents. """ return json.dumps(msg, ensure_ascii=False, indent=2)
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import inspect def _filter_module_all(path, root, children): """Filters module children based on the "__all__" arrtibute. Args: path: API to this symbol root: The object children: A list of (name, object) pairs. Returns: `children` filtered to respect __all__ """ del path if not (inspect.ismodule(root) and hasattr(root, '__all__')): return children module_all = set(root.__all__) children = [(name, value) for (name, value) in children if name in module_all] return children
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def contains_pattern(input: str, pattern: str) -> bool: """Check if the `input` contains all signals of the given `pattern`""" assert len(input) >= len(pattern) return all([p in input for p in pattern])
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def nbest_oracle_eval(nbest, n=None): """Return the evaluation object of the best sentence in the nbest list.""" return nbest.oracle_hyp(n=n).eval_
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def reaction_class_from_data(class_typ, class_spin, class_radrad, class_isc): """ Build a full-class description including the following useful descriptors of the reaction class: typ: type of reaction (e.g., abstraction, addition, migration) spin: whether the reaction occurs on a low- or high-spin state radrad: whether the reactants or products are two-or-more radicals :param class_typ: reaction type designation :type class_typ: str :param class_spin: spin type designation :type class_spin: str :param class_radrad: radical-radical type designation :type class_radrad: bool :param class_isc: intersystem-crossing designation :type class_isc: bool :rtype: (str, str, bool, bool) """ return (class_typ, class_spin, class_radrad, class_isc)
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import pickle def get_one_hot_encodings(filepath='../data/one-hot.pkl'): """ Gets the one_hot encodings of the verses of the Quran, along with mappings of characters to ints :param filepath: the filepath to the one_hot encoding pickled file :return: """ with open(filepath, 'rb') as one_hot_quran_pickle_file: one_hot_obj = pickle.load(one_hot_quran_pickle_file) return one_hot_obj
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def flatten(lst): """Flatten a nested list lst""" return [i for subl in lst for i in subl]
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import random def extract_words(text, word_count): """ Extract a list of words from a text in sequential order. :param text: source text, tokenized :param word_count: number of words to return :return: list list of words """ text_length = len(text) if word_count > text_length: raise RuntimeError('Cannot extract {} words from a text of {} words.'.format(word_count, text_length)) # Determine start index max_range = text_length - word_count start_range = random.randrange(max_range) return text[start_range:start_range + word_count]
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def rgb_to_hex(color): """Helper function for converting RGB color to hex code Args: color (list): List of R,G,B value Returns: str: Hex code for the RGB value """ r,g,b = color #print('%02x%02x%02x' % (r,g,b)) return '#%02x%02x%02x' % (r,g,b)
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def sort_queryset(queryset, request, allowed_sorts, default=None): """ Sorts the queryset by one of allowed_sorts based on parameters 'sort' and 'dir' from request """ sort = request.GET.get('sort', None) if sort in allowed_sorts: direction = request.GET.get('dir', 'asc') sort = ('-' if direction == 'desc' else '') + sort queryset = queryset.order_by(sort) elif default: queryset = queryset.order_by(default) return queryset
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def extract_path_from_filepath(file_path): """ ex: 'folder/to/file.txt' returns 'folder/to/' :param file_path: :return: """ st_ind=file_path.rfind('/') foldern = file_path[0:st_ind]+'/' return foldern
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def fname_to_string(fname): """Return given file as sring Parameters ---------- fname : str absolute path to file. """ with open(fname) as fid: string = fid.read() return string
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def global_color_table(color_depth, palette): """ Return a valid global color table. The global color table of a GIF image is a 1-d bytearray of the form [r1, g1, b1, r2, g2, b2, ...] with length equals to 2**n where n is the color depth of the image. ---------- Parameters color_depth: color depth of the GIF. palette: a list of rgb colors of the format [r1, g1, b1, r2, g2, b2, ...]. The number of colors must be greater than or equal to 2**n where n is the color depth. Redundant colors will be discarded. """ try: palette = bytearray(palette) except: raise ValueError('Cannot convert palette to bytearray.') valid_length = 3 * (1 << color_depth) if len(palette) < valid_length: raise ValueError('Invalid palette length.') if len(palette) > valid_length: palette = palette[:valid_length] return palette
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import math def arclen(angle, radius, rad=False): """Calculates the size of an arc of a circle""" if rad: angle = math.degrees(angle) return (angle / 360) * (2 * math.pi * radius)
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import hashlib def hash_seqs(sequences): """ Generates hexdigest of Sha1 hash for each sequence in a list of sequences. This function is useful for generating sequence specific identifiers that allow for easier comparison of features from multiple sequencing runs or sequence processing runs. """ new_sequences = list() for seq in sequences: # get sequence string and encode using UTF-8 for consistency seq = seq.encode('UTF-8') # get sha1 hash of sequence hash_ = hashlib.sha1() hash_.update(seq) hash_hex = hash_.hexdigest() new_sequences.append(hash_hex) return new_sequences
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def get_paths(link, nb): """ Generate a list containing all URLs Args: link [str]: Base HTML link nb [int]: Number of pages usingHTML link Returns: url [str]: [List containing all URLs] """ url = [] for si in range(2000, 2020): for ti in range(1, nb+1): result = link + str(si) + "-" + str(si+1) + "&teamId=" + str(ti) url.append(result) return url
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def heaviside(x, bias=0): """ Heaviside function Theta(x - bias) returns 1 if x >= bias else 0 :param x: :param bias: :return: """ indicator = 1 if x >= bias else 0 return indicator
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def biggest_differences_words(prunedTable): """ Finds the words that are most different from their most frequent alternative across each semantic dimension Parameters ---------- prunedTable : a data frame The data frame representing arousal, valence, and dominance ratings for words and their most frequent alternatives across time within a paragraph Returns ------- a dictionary mapping from a semantic dimension to row indexing information about the word with the greatest difference for that dimension """ prunedTable = prunedTable.assign(absADiff = (prunedTable['WordA'] - prunedTable['AltA']).abs(), absVDiff = (prunedTable['WordV'] - prunedTable['AltV']).abs(), absDDiff = (prunedTable['WordD'] - prunedTable['AltD']).abs()) biggestDifferencesWords = {'Arousal': prunedTable.loc[prunedTable['absADiff'].idxmax()], 'Valence': prunedTable.loc[prunedTable['absVDiff'].idxmax()], 'Dominance': prunedTable.loc[prunedTable['absDDiff'].idxmax()]} return biggestDifferencesWords
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def build_help_text(command_class): """Generate help text from a command class.""" command = command_class() parser = command.create_parser({}) return parser.format_help()
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import io def read_names(f): """Read names, specified one per line, from a file.""" return (line.strip() for line in io.open(f, 'r', encoding='utf-8'))
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def format_cols_2digit(df, skip_last_col=True): """Formats a dataframes columns so that numbers are always two-digits (padded with 0) Parameters ---------- df : pandas DataFrame Input DataFrame. skip_last_col : bool A special case, where the very last column contains text, rather than a number, and should be excluded. Returns ------- reformatted_cols : list The DataFrame columns, reformatted with padded 0 to make 2 digits. """ if skip_last_col: # reformat the columns to be padded stringnumbers. (exclude the last "Contains_Data") reformatted_cols = ["%02d" % col for col in df.columns[:-1]] # add last column back to list reformatted_cols.append(df.columns[-1]) else: # reformat the columns to be padded stringnumbers. (exclude the last "Contains_Data") reformatted_cols = ["%02d" % col for col in df.columns] return reformatted_cols
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def reverse_complement_no_loops(seq): """Return WC complement of a base without loops""" # Initialize rev_seq to a lowercase seq rev_seq = seq.lower() # Substitute bases rev_seq = rev_seq.replace('t','A') rev_seq = rev_seq.replace('a','T') rev_seq = rev_seq.replace('g','C') rev_seq = rev_seq.replace('c','G') return rev_seq[::-1]
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from collections import OrderedDict def update(data_df, cal_dict, param, bound, start, end): """Update calibration times for give parameter and boundary""" if param not in cal_dict["parameters"]: cal_dict["parameters"][param] = OrderedDict() if bound not in cal_dict["parameters"][param]: cal_dict["parameters"][param][bound] = OrderedDict() cal_dict["parameters"][param][bound]["start"] = start cal_dict["parameters"][param][bound]["end"] = end return cal_dict
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def viaCombusta(obj): """ Returns if an object is in the Via Combusta. """ return 195 < obj.lon < 225
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def copresence(acc, w1, w2): """Results 1 if a pair of figures is on stage at the same time, and 0 otherwise.""" return int(acc + w1 + w2 > 0)
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def gen_bool_parse(val): """Convert a string, as a human might type it, to a boolean. Unrecognized values raise an exception. """ val = val.strip() if not val: return False try: return bool(int(val)) except: pass ch = val[0] if ch in {'t', 'T', 'y', 'Y'}: return True if ch in {'f', 'F', 'n', 'N'}: return False raise ValueError('"%s" does not look like a boolean' % (val,))
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import glob def _expand_glob_path(file_roots): """ Applies shell globbing to a set of directories and returns the expanded paths """ unglobbed_path = [] for path in file_roots: try: if glob.has_magic(path): unglobbed_path.extend(glob.glob(path)) else: unglobbed_path.append(path) except Exception: unglobbed_path.append(path) return unglobbed_path
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def nth_triangle_number(n): """ Compute the nth triangle number """ return n * (n + 1) // 2
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import re def check_ignore(item, ignores=[]): """ take a string (item) and see if any of the strings in ignores list are in the item if so ignore it. """ ignore = False for i in ignores: if i and re.search(i, str(item)): # print "ignoring item: %s for ignore: %s" % (item, i) ignore = True return ignore
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def all_segments(N): """ Return (start, end) pairs of indexes that orm segments of tour of length N """ return [(start, start + length) for length in range(N, 2-1, -1) for start in range(N - length + 1)]
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import torch def epe(input_flow, target_flow): """ End-point-Error computation Args: input_flow: estimated flow [BxHxWx2] target_flow: ground-truth flow [BxHxWx2] Output: Averaged end-point-error (value) """ return torch.norm(target_flow - input_flow, p=2, dim=1).mean()
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