sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
381e7453c4fcec984261327188f3a37ab1d2fad46ef90ca5e15a98e858636c18 | Python | 8,394 | 193 | # Copyright (c) ONNX Project Contributors
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import onnx.shape_inference
from onnx import ModelProto, TensorProto, TensorShapeProto, ValueInfoProto, helper
from onnx.helper import make_model, make_tensor_value_info
class TestSymbolicShape:
de... |
63835a868b44c7ef7661022d11a067e2d6cf6e2a55933a2f6de374e98c7fa7a6 | Python | 8,397 | 222 | # SPDX-License-Identifier: LGPL-3.0-or-later
"""Import released Uni-Mol v1 checkpoints into deepmd.
The released files (``mol_pre_all_h_220816.pt`` and ``mol_pre_no_h_220816.pt``,
MIT licensed, from the Uni-Mol repository and its Hugging Face mirror) hold a
single ``model`` entry with 211 float32 tensors and no traini... |
ec097281cf83f53f3250201af3c7cf85325886e87701735f1355add143d92a93 | Python | 8,399 | 258 | import os
import re
import sys
import difflib
import inspect
import unittest
import subprocess
from io import BytesIO
from random import shuffle
from pathlib import Path
from collections import defaultdict
import rdflib
from ttlser import CustomTurtleSerializer, SubClassOfTurtleSerializer
from ttlser import CompactTur... |
3a479d3c13c2e3b2118a1f775fac2ff5ed9e3a78aa27cb1db8bec69686b2589b | Python | 8,400 | 229 | #!/usr/bin/env python
import sys
import os
import math
import re
from os.path import isfile, join, isdir
from os import listdir
import csv
from kn_common import pipetools,pipedef
from kn_pipeline_class import CPipeError,CPipeStep
def get_injection_site_location(folder):
allfiles_and_folders = listdir(folder)
... |
4fff36f00cdc2a9a34a2e10468361dab004f4c691e6c56d8fe1eb7b55e3dd546 | Python | 8,403 | 255 | import os
import sys
import time
import math
from datetime import datetime
import random
import logging
from collections import OrderedDict
import numpy as np
import cv2
import torch
from skimage.feature import peak_local_max
from shutil import get_terminal_size
import yaml
try:
from yaml import CLoader as Loader,... |
b92f342fb373d760d1e5ed4a954fd086f52ef91fe8e7e9739a7278ed5b8606ac | Python | 8,408 | 234 | # Copyright 2022 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
7aa2b6afe1f68caa223d56399af1855ec974ebec31bd2f9434335ed930604b34 | Python | 8,410 | 225 | import pandas as pd
import os
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import numpy as np
from sklearn.linear_model import LinearRegression
from sklearn.preprocessing import MinMaxScaler
import CRISPRspec_CRISPRoff_pipeline as pipe
import pickle
def prepare_inputs(config):... |
601116545f58b8d2ecc0446995cc104ae37e5beeec626b4a0a5e732d8525feac | Python | 8,411 | 247 | # Copyright (c) OpenMMLab. All rights reserved.
import pytest
import torch
from torch.nn.modules import AvgPool2d
from torch.nn.modules.batchnorm import _BatchNorm
from mmcls.models.backbones import SEResNet
from mmcls.models.backbones.resnet import ResLayer
from mmcls.models.backbones.seresnet import SEBottleneck, SE... |
f37c0455016f7263ecbf6cd95f51b89ba66382bb20018766e71934259665f64c | Python | 8,412 | 220 | # coding=utf-8
# Copyright (C) 2021. Huawei Technologies Co., Ltd. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# ... |
7e3fc29830b16f729bb0adc5585d63665f82fbcaf5ffd97bed99ac9e20a16919 | Python | 8,413 | 248 | """
Utility methods for datasets.
"""
from __future__ import annotations
import hashlib
import sys
from pathlib import Path
from typing import Any
import numpy as np
import requests
from numpy.typing import ArrayLike
def download_progress_bar(file_url: str, file_dest: str):
"""
Download while outputting a ... |
19246fbabf9c1553ff558a42979b1ca318c893d0d458e630b8d64311aa35d578 | Python | 8,419 | 214 | # Copyright 2019-2021 The AmpliGraph Authors. All Rights Reserved.
#
# This file is Licensed under the Apache License, Version 2.0.
# A copy of the Licence is available in LICENCE, or at:
#
# http://www.apache.org/licenses/LICENSE-2.0
#
import numpy as np
from ..datasets import AmpligraphDatasetAdapter, SQLiteAdapt... |
e7abda27e960d52b111bea9cedf2ef8718ffb129d566ebd035bd315fae6cdc49 | Python | 8,423 | 249 | # copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
"""BoxCoxBiasAdjustedForecaster implementation."""
__author__ = ["sanskarmodi8"]
import pandas as pd
from scipy.special import inv_boxcox
from sktime.forecasting.base import BaseForecaster
from sktime.forecasting.base._delegate import _Delegate... |
8ae631ec38e5ba3dfbb5abfa8db693b89d2906a1527b5a5023c03a01e601d2db | Python | 8,424 | 228 | import os
import numpy as np
import tensorflow as tf
def create_callbacks(
network_name,
tensorboard=False,
**update_parameters,
):
CSVlogger_path = os.path.join(
update_parameters["save_model_path"], "val_result.csv"
)
# if os.path.isfile(self.CSVlogger_path): os.remove(self.CSVlogg... |
b4c3b6491dbb62d6742dc74a524d153afea2b5eec82428ff0e0cd4fdf3478064 | Python | 8,429 | 173 |
import ray
from ray.rllib.agents.trainer import with_common_config, with_base_config
from ray.rllib.models.catalog import MODEL_DEFAULTS
from ray.rllib.utils import try_import_tf
import json
import os
import pandas as pd
import multiprocessing
from itertools import repeat
from mprl.scripts.poker_parallel_algos.utils... |
77a3e631a737b7ec5bc8ef3611c030cbda003b9b2bfc7f0d592749be3c321183 | Python | 8,433 | 244 | # Copyright 2019 DeepMind Technologies Ltd. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... |
61534d9ddfbcc22d05476dd4bab731c69dd66f2bdf77601d3d0170bfe3c21f8d | Python | 8,441 | 239 | # copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
"""Converter utilities between dask and pandas, with multiindex convention.
Converts between:
pd.DataFrames with ordinary (single-level) index or pd.Multiindex, and
dask DataFrame
If pd.DataFrame has ordinary index, converts using dask compute/fr... |
0e4adec4e9facc915776ac2be8fd25d2b7ad24310054d0c5c47274133a3c0b32 | Python | 8,442 | 256 | # Copyright (c) ONNX Project Contributors
#
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import numpy as np
import onnx
from onnx.backend.test.case.base import Base
from onnx.backend.test.case.node import expect
def argmin_use_numpy(data: np.ndarray, axis: int = 0, keepdims: int = 1) -> ... |
b45c630bfaf284acb202a03ead6df116afd7d4593c7dce9e10702204a67c6c0c | Python | 8,442 | 224 | """get_axon_lengths.py - measure lengths of varios axonal compartments from the
morphology files.
This module is part of *vcnmodel*.
Support::
NIH grants:
DC R01 DC015901 (Spirou, Manis, Ellisman),
DC R01 DC004551 (Manis, 2013-2019, Early development)
DC R01 DC019053 (Manis, 2020-2025, Later develop... |
70b950d53db30a8200da23be839064030445c4b814b70fd213a6616655f5dec7 | Python | 8,446 | 257 | # Copyright 2026 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
098af0e63b9830a451a666eaf51fa38782debd19b269adde7340fc044c02b7ad | Python | 8,447 | 192 | import argparse
import torch
import torch.nn.functional as F
import torch.optim as optim
from sklearn.model_selection import train_test_split
import numpy as np
import pandas as pd
import cv2
import adabound
from torch.optim import lr_scheduler
from sklearn.metrics import confusion_matrix
import seaborn as sns
from mat... |
d8e0094f16dec2aa243f7dad8b283ce607bf77a524027669c1899d88a5bcaaaf | Python | 8,451 | 221 | from functools import cached_property
import logging
from typing import List, Tuple
import pandas as pd
import numpy as np
from sklearn.model_selection import train_test_split, RepeatedStratifiedKFold
from sklearn.linear_model import LinearRegression
from sklearn.preprocessing import RobustScaler
from sklearn.feature_... |
38444927c8a2dbd7ac0da498d8beb18b0d5b83b21b479b19a528d74752d98ac9 | Python | 8,459 | 222 | # -*- coding: utf-8 -*-
import os
from tqdm import tqdm
import torch
from torchtext.data import Field
from onmt.inputters.datareader_base import DataReaderBase
# imports of datatype-specific dependencies
try:
import torchaudio
import librosa
import numpy as np
except ImportError:
torchaudio, librosa,... |
5b4435dcae7e69418b9a337dee33db19756cf0b8fe65d310d5a9324f5c8cce96 | Python | 8,460 | 213 | # SPDX-License-Identifier: LGPL-3.0-or-later
import json
import subprocess
import sys
import tempfile
import unittest
from pathlib import (
Path,
)
import h5py
import numpy as np
import pytest
from deepmd.dpmodel.utils.dist_check import (
compute_min_pair_margin_single,
pair_half_thresholds,
)
from deepmd... |
063ec7083fd145303e6b3061b50a5b302ff4f824a39e04417705d84483827500 | Python | 8,466 | 241 | from argparse import Namespace
from typing import Optional, Tuple
import torch
import numpy as np
from .jet_features import plot_jet_p_cartesian, plot_jet_p_polar
from .particle_features import plot_p_cartesian, plot_p_polar
from .jet_images import plot_jet_image
from .utils import (
get_p_polar,
get_p_cartesi... |
0f115f866688e19c03e8d09d2fdec9da2757896e303af6433239a5669c3b4591 | Python | 8,467 | 178 | """
@file: Node.py
Created on 13.10.18
@project: crazy_ara_refactor
@author: queensgambit
Helper class which stores the statistics of all nodes and in the search tree.
"""
from copy import deepcopy
from threading import Lock
import chess
import numpy as np
QSIZE = 100
class Node: # Too many instance attributes (1... |
fbbec0a1542fa7a96251260cbe7b0b32df47720678127e612581505ac19b6282 | Python | 8,467 | 256 | """
Collect data about the speed of one backend (numpy) as we change the number of neurons and the number of components
William Nourse
December 15th 2021
"""
import numpy as np
import time
import pickle
from sns_toolbox.networks import Network
from sns_toolbox.neurons import NonSpikingNeuron, SpikingNeuron
from sns_to... |
d67eb747b2457351c117f7d7528611eb370c4ceae9c82d62509e043bd6cc0e58 | Python | 8,468 | 181 | import sys
import numpy as np
import torch
import time
import pickle
from sns_toolbox.neurons import NonSpikingNeuron
from sns_toolbox.connections import NonSpikingSynapse
from sns_toolbox.networks import Network
# Personal stuff to send an email once data collection is finished
#sys.path.extend(['/home/sns'])
#from ... |
110fbf09c277b4814f1b300cfa41c666349e2b5ff4e8d60dc1280e98b1fbaf0a | Python | 8,469 | 212 | __author__ = ["chrisholder", "jlines", "TonyBagnall"]
import numpy as np
from sktime.dists_kernels._numba_distances.base import (
DistanceAlignmentPathCallable,
DistanceCallable,
NumbaDistance,
)
class _MsmDistance(NumbaDistance):
r"""Move-split-merge (MSM) distance between two time series.
(M... |
fccc2f7dffdc793f243a4ffd18c2319c86045cb79050e3503ae379fe728b927c | Python | 8,470 | 222 | """
@file: FullRoundTripTests.py
Created on 22.08.18
@project: DeepCrazyhouse
@author: queensgambit
Loads the plane representation for the test dataset and iterates through all board positions and moves.
"""
import unittest
from multiprocessing import Pool
from copy import deepcopy
import logging
import chess
import ... |
dedcba436cc84d6c8b5ebb2d95de57133c64813ed203fb34ed56d857992f2cb3 | Python | 8,474 | 222 | """
@file: FullRoundTripTests.py
Created on 22.08.18
@project: DeepCrazyhouse
@author: queensgambit
Loads the plane representation for the test dataset and iterates through all board positions and moves.
"""
import unittest
from multiprocessing import Pool
from copy import deepcopy
import logging
import chess
import ... |
1d35bb43526bdf5a18ecca661fd3fc9efb704768ed3c37d3862ba946be0cb05b | Python | 8,475 | 205 | # Copyright 2019 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
658d7f1ff89e544a10c6db26a9b7637779b81a2f501bed21d6797b918bb2dedd | Python | 8,475 | 256 | # Copyright 2026 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
d057f6aae0fd628c40ac6faba26057284febfe1354f12e2fddd7886a2a75f0ea | Python | 8,475 | 282 | import torch
from torch.nn import Module
from lgn.cg_lib import CGModule
from lgn.g_lib import g_torch, GWeight, GTau, GScalar, GVec
class MixReps(CGModule):
"""
The module to linearly mix a representation.
The input musst have predefined types tau_in and tau_out.
Parameters
----------
tau_in... |
644dc7193f4627c0da4a3c35e65f59ae784e58fb03bb9ff7b2803b8edc2f5490 | Python | 8,476 | 251 | # -*- coding: utf-8 -*-
"""
Module for preprocessing utilities. These are supposed to complement
the preproessing utilities that are available with MNE.
"""
import numpy as np
from math import ceil
from anlffr.utils import logger, verbose
from mne import pick_channels
from mne.filter import filter_data
@verbose
def... |
d3c7606d13400b2aa5623f0704848111676bc33e32bbe70286c2d83a6d872bf8 | Python | 8,476 | 283 | import torch
from torch.nn import Module
from lgn.cg_lib import CGModule
from lgn.g_lib import g_torch, GWeight, GTau, GScalar, GVec
class MixReps(CGModule):
"""
The module to linearly mix a representation.
The input musst have predefined types tau_in and tau_out.
Parameters
----------
tau_in... |
c270256dd3086bbe794af91f3d11a8c846b856a9fac39a2e9a9e602aced582bf | Python | 8,481 | 232 | from __future__ import annotations
from dataclasses import dataclass
from typing import ClassVar
import numpy as np
import pandas as pd
from pandas import DataFrame
from seaborn._core.groupby import GroupBy
from seaborn._core.scales import Scale
from seaborn._stats.base import Stat
from typing import TYPE_CHECKING
i... |
27c326c281f8940d79e0ddfc2acc96e620b3228448797c371a0c54ff8dbe4235 | Python | 8,482 | 219 | from copy import deepcopy
import numpy as np
import pandas as pd
from cplAE_TE.utils.compute import CCA_extended
from cplAE_TE.utils.load_helpers import get_paths, load_dataset
from cplAE_TE.utils.tree_helpers import get_merged_ordered_classes
from scipy.linalg import sqrtm
from sklearn.decomposition import PCA
from s... |
cc1cb4b71e5ca5313c4f9592a2d44ff8b9c56bca2209ad60ca842fae6858088e | Python | 8,493 | 222 | import anndata as ad
import numpy
import random
import scanpy as sc
import torch
import torch.utils.data as D
from src.constants import *
import pickle
class Dataset(D.Dataset):
def __init__(self, modalities, labels):
super().__init__()
self.modalities = [
torch.tensor(modality, dtype=... |
6cc6f8e2cb1032692da967af672db664a043ae84895572d140a954e851145fa6 | Python | 8,497 | 293 | # Copyright 2026 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
b4800a26e067841c8070e7bdfad385ccaf8b048c03f45e1ee9d316c6610572df | Python | 8,497 | 227 | import argparse
import logging
import os
import time
import datetime
import matplotlib.pyplot as plt
import numpy as np
import seaborn as sns
import pandas as pd
import torch
import torch.nn.functional as F
from torch_geometric.data import DataLoader
from model import GNN_PSR
from data import GNNTransformPSR
from atom... |
e750d91f18d6b49a0e549b831c5976eee750db1018ecae1dfeedb30333932780 | Python | 8,505 | 234 | # Copyright (c) Rahil Gholamipoor
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agree... |
c3554955017fa0253b5c2ff1895f060587dedc35fba9276dcad253330b73396b | Python | 8,506 | 268 | # Copyright 2026 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
29db7b379b80ea8188d483395329377bee6a79fac3a2820a7f18d0064e9d75f2 | Python | 8,507 | 266 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sat Apr 15 18:28:33 2023
Script to plot single problems including lesion and noise plots (Fig. S3, S4)
And gifs of units learning positions - Fig. S2
@author: robert.mok
"""
import os
import sys
import torch
import matplotlib.pyplot as plt
import imageio... |
4ccecd9477822fc98d89951c90ebfb7dc3aae0c090d59875c9992263de9b7e8f | Python | 8,510 | 204 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sun Jun 19 13:51:33 2022
@author: sam
"""
import cv2
import pandas as pd
import numpy as np
import os
from detectron2.config import get_cfg
from detectron2.engine import DefaultPredictor
from detectron2.utils.visualizer import Visualizer, ColorMode
from det... |
f7280cb10c91a19908d4fc43b3964d2c285b8cd0a5dfb9e498fc6ec0fc5be10f | Python | 8,514 | 209 | """Zero-shot anomaly detector built on Tabby-Pretrain.
The predictor is loaded once, frozen, and only used for forward passes: there is
no per-series fitting, so the detector is genuinely zero-shot.
Scoring happens in representation space. The frozen encoder embeds the series
into per-patch latents (no forecasting), ... |
c6c6c543d828c60de1998252bdcb216fa46ce2fce7e1fd9d4766dfc7bfeed578 | Python | 8,523 | 259 | """
An interface for asynchronous vectorized environments.
"""
import multiprocessing as mp
import numpy as np
import ctypes
import gym
from collections import OrderedDict
from rllib.env.vector_env import VectorEnv
_NP_TO_CT = {np.float32: ctypes.c_float,
np.int32: ctypes.c_int32,
np.int8: ... |
b3eb53fd573c75a9f7898762574e178c8ccea388f2092b9db8af38bb87217bef | Python | 8,528 | 220 |
import json
import os
import pytest
from collections import namedtuple
from model_archiver.model_packaging_utils import ModelExportUtils
from model_archiver.manifest_components.engine import EngineType
from model_archiver.manifest_components.manifest import RuntimeType
from model_archiver.model_archiver_error import ... |
525579ff5e678065931ed0e702af3d76c94c017fea0e3a7b08192949378c8206 | Python | 8,534 | 259 | #!/usr/bin/env python
"""CLI for damage_profile: compute overlap statistics between a subject map
and one or more brain atlases.
Usage (custom atlas directory)::
bcb-damage-profile --map lesion.nii.gz --atlas /path/to/atlas --name jhu
Usage (preset atlas)::
bcb-damage-profile --map lesion.nii.gz --preset ro... |
ebea9bf0dd1215084e2fe6a591441e08da146a529e0af7eb0e05050fbfcb228b | Python | 8,536 | 219 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Created on Mon Dec 10 12:39:16 2018
@author: wanglab
"""
import os, numpy as np, sys, multiprocessing as mp, zipfile
from skimage.external import tifffile
from skimage import filters
import matplotlib.pyplot as plt
import SimpleITK as sitk
#add your clone of the brain... |
27aba55c0f824b4189a1c8edb398ba3139dafbce6328af6296548867bb597e0d | Python | 8,544 | 263 | import os
import sys
import numpy as np
from sklearn.cluster import KMeans
import numpy as np
from sklearn.cluster import KMeans
import glob
from torch_geometric.data import InMemoryDataset, DataLoader
from torch_geometric import data as DATA
import torch
from rdkit import Chem
from rdkit.Chem import MolFromSmiles
imp... |
1cdd9f11a5cb6cadc1d4b11da86450fcad6eb7ce51092623e875f05ee8b6419e | Python | 8,545 | 136 | #create context window and other metadata for a mention identified by NLP (WS or SS) for annotation
#generates annotation files for each annotator and the k random samples for all annotators
#input: brat files of NLP identified cohort, selected by using step14_select_cohort_brat_documents.py under the main project fo... |
e9ecc01a23b5c477fa7cfb56f8ec6b7fc5f4b9d3cbf916a4d7639583faf67e2e | Python | 8,546 | 205 | from typing import cast
import pytest
from flair.data import Sentence
from flair.training_utils import CharEntity, TokenEntity, create_labeled_sentence_from_entity_offsets
@pytest.fixture(params=["resume1.txt"])
def resume(request, resources_path) -> str:
filepath = resources_path / "text_sequences" / request.p... |
026030dfba006efcb96589c788e7315dd96d7bb3a69af4032924b96b29f89f04 | Python | 8,547 | 268 | # Copyright 2026 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
c0f8cd88955b19280a452214b4fb5311be32b724180e78738e6e87f6024bc98c | Python | 8,548 | 185 | import sys
import numpy as np
import torch
import time
import pickle
from sns_toolbox.neurons import NonSpikingNeuron
from sns_toolbox.connections import NonSpikingSynapse
from sns_toolbox.networks import Network
# Personal stuff to send an email once data collection is finished
#sys.path.extend(['/home/sns'])
#from ... |
230aa071ff2c1bcfe22f89a5c3fe0dce2ec759547ec3160b112aa7212d02153c | Python | 8,549 | 239 | # Copyright 2018-2025
# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICE... |
8e64d614e120d838c4fe2cc0bce7b9f9493ee1d611d2047c61790c8873eea7ff | Python | 8,549 | 254 | """
Module containing core functions called by ***_runSFA
03 13 2023
Code by R.W. DiTullio and C Parthiban
"""
import numpy as np
import matplotlib.pyplot as plt
import soundfile as sf
import scipy.ndimage.filters as filt
from tqdm import tqdm
import SFA_Tools.SFA_Sets as s
import SFA_Tools.SFA_eigenspec_fun... |
6687ac8e524555ed508634a2e28f837a10d1dd13789ff1faeb8a0b1036fb1c6a | Python | 8,551 | 185 | import sys
import numpy as np
import torch
import time
import pickle
from sns_toolbox.neurons import NonSpikingNeuron
from sns_toolbox.connections import NonSpikingSynapse
from sns_toolbox.networks import Network
# Personal stuff to send an email once data collection is finished
#sys.path.extend(['/home/sns'])
#from ... |
a90d160a2502ad5f1be028928931cf87b1c4469233f1f039974c49282db1ad07 | Python | 8,551 | 250 | # Copyright 2019 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
bab8d28f1d2a3e7303e9b09beb9752f9eaada0fa747c8cc8c5f3691c47152750 | Python | 8,551 | 230 | # Copyright 2019-2020 The ASReview Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... |
fc1d192c9242942a64752ef7347bc70e4f770d3befa7c0f9e2e33142973a104a | Python | 8,551 | 183 | import sys
import numpy as np
import torch
import time
import pickle
from sns_toolbox.neurons import NonSpikingNeuron
from sns_toolbox.connections import NonSpikingSynapse
from sns_toolbox.networks import Network
# Personal stuff to send an email once data collection is finished
# sys.path.extend(['/home/will'])
# fr... |
975e7ab7010a1eb1ddd2cf37655f0ba085d019332302e8b4b623a5b8c033af1d | Python | 8,553 | 185 | import sys
import numpy as np
import torch
import time
import pickle
from sns_toolbox.neurons import NonSpikingNeuron
from sns_toolbox.connections import NonSpikingSynapse
from sns_toolbox.networks import Network
# Personal stuff to send an email once data collection is finished
sys.path.extend(['/home/will'])
from e... |
cc04bc62dcfc510a0805197dbe979f239c42e3c3f6d28ac55408414905411c2b | Python | 8,553 | 221 | #!/usr/bin/env python
"""AxialTAD inference driver.
Run a trained AxialTAD model on one or more `*_25kb.npy` Hi-C patch files
and emit a single JSON file with per-file probabilities, binary predictions,
and (optionally, when labels are present) precision/recall/F1.
Usage:
python scripts/predict.py \\
--ar... |
22358e7fcb3f35d5d2a8060e8d1caaeff6b93d715ffc4977f9dba63186122717 | Python | 8,558 | 201 | # Copyright 2019 DeepMind Technologies Ltd. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... |
86ee1e8b192da293fbe77a649288fc38723d3d05efabde53444abe8dc5fce0ec | Python | 8,559 | 185 | import sys
import numpy as np
import torch
import time
import pickle
from sns_toolbox.neurons import NonSpikingNeuron
from sns_toolbox.connections import NonSpikingSynapse
from sns_toolbox.networks import Network
# Personal stuff to send an email once data collection is finished
#sys.path.extend(['/home/sns'])
#from ... |
8b9f78eefef60eae7cfe713720469e1150a9c5e8039f43a7a6391883f4621feb | Python | 8,560 | 190 | """
Compare the simulation speed of the different backends
William Nourse
September 9 2021
The correct term is Babes, sir
"""
import numpy as np
import torch
import time
import pickle
from sns_toolbox.neurons import SpikingNeuron
from sns_toolbox.connections import SpikingSynapse
from sns_toolbox.networks import Netw... |
7c6191d4ca14410ff3c58255de9ef9ea7b1f21ddb9e826d98fc7f71f9186755e | Python | 8,567 | 190 | """
Compare the simulation speed of the different backends
William Nourse
September 9 2021
The correct term is Babes, sir
"""
import numpy as np
import torch
import time
import pickle
from sns_toolbox.neurons import SpikingNeuron
from sns_toolbox.connections import SpikingSynapse
from sns_toolbox.networks import Netw... |
adffef8fe7944cf4667a6614f9ad28877619592eff6717fe5cff8cc3dc6e46df | Python | 8,572 | 244 | from typing import Callable, Iterable, Optional, Tuple, Union
import torch
import numpy as np
import matplotlib.pyplot as plt
from utils.utils import make_dir
from .utils import NUM_BINS, PLOT_FONT_SIZE, find_fwhm, get_stats
from scipy import stats
import os.path as osp
import logging
import json
FIGSIZE = (16, 4)
LAB... |
ead1d94bc2e9d12ba2ab0c92e5f9fec74c61fe4ec78f72c96800ac570e1e3308 | Python | 8,572 | 242 | """
This file is for models creation, which consults options
and creates each encoder and decoder accordingly.
"""
import re
import torch
import torch.nn as nn
from torch.nn.init import xavier_uniform_
import onmt.inputters as inputters
import onmt.modules
from onmt.encoders import str2enc
from onmt.decoders import s... |
04163266defb04a4faf6766c56586d17f08e7bae9eb4cfb6863ec839e417fe98 | Python | 8,573 | 242 | """
AQDnet CLI commands implementation
"""
import sys
import os
import glob
import tempfile
import json
import logging
# Add scripts to path for imports
sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..', 'scripts'))
import pandas as pd
import numpy as np
import tensorflow as tf
from tqdm import tqdm
#... |
23a27ea1b3683c14b609f015089f10c7902f24887be8206c211ecdfc8a05fc20 | Python | 8,573 | 247 | # Copyright 2026 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
929560c71fdf54bfe09dc36d3f5337aa37a3ea89e5b51724ea4720d6041649db | Python | 8,573 | 245 | from typing import Callable, Iterable, Optional, Tuple, Union
import torch
import numpy as np
import matplotlib.pyplot as plt
from utils.utils import make_dir
from .utils import NUM_BINS, PLOT_FONT_SIZE, find_fwhm, get_stats
from scipy import stats
import os.path as osp
import logging
import json
FIGSIZE = (16, 4)
LAB... |
28b101e544ae2de83ecf7f3e69974b608391197c010cd5943d3de20224830987 | Python | 8,574 | 266 | # Copyright (c) ONNX Project Contributors
#
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
from typing import TYPE_CHECKING, Any
if TYPE_CHECKING:
from collections.abc import Sequence
import numpy as np
import onnx
from onnx.backend.test.case.base import Base
from onnx.backend.test.cas... |
682e3f108f3c3ee9a9c9b23fde89698c6368dd222866d7975b401bbcfbad2cde | Python | 8,576 | 187 | r"""
This module contains the building blocks for the video prediction models implemented in
https://github.com/Hzzone/Precipitation-Nowcasting (Encoder-Forecaster-based prediction models based on
ConvLSTM/TrajGRU).
"""
from collections import OrderedDict
import torch
import torch.nn as nn
from vp_suite.base import ... |
9bcaec18402ce73c08a7108ef7df7e2b45e2112a96dc8ba223c1122f577dfd44 | Python | 8,577 | 190 | """
Compare the simulation speed of the different backends
William Nourse
September 9 2021
The correct term is Babes, sir
"""
import numpy as np
import torch
import time
import pickle
from sns_toolbox.neurons import SpikingNeuron
from sns_toolbox.connections import SpikingSynapse
from sns_toolbox.networks import Netw... |
b77449ae79ea27342fb64380e69071d7a34e02bc5a61fc832d8afee150c2e55a | Python | 8,577 | 190 | """
Compare the simulation speed of the different backends
William Nourse
September 9 2021
The correct term is Babes, sir
"""
import numpy as np
import torch
import time
import pickle
from sns_toolbox.neurons import SpikingNeuron
from sns_toolbox.connections import SpikingSynapse
from sns_toolbox.networks import Netw... |
eb9056742696f5a9da5b2c47fe29bc5ab11658313f1d971435b20f2f03883d13 | Python | 8,577 | 221 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Apr 9 15:39:25 2021
@author: sam
"""
import argparse
import numpy as np
from tqdm import tqdm
import os.path
import h5py
import buffer_handle
import cv2
import moving_least_squares
from scipy import ndimage
def warp_image(img, p, q, alpha, grid_siz... |
e0f01faae2fae45c9f7b5dfec7b2736dead839408de44ce9713012a7d5ea1361 | Python | 8,582 | 223 | # Copyright 2019-2026 The AmpliGraph Authors. All Rights Reserved.
#
# This file is Licensed under the Apache License, Version 2.0.
# A copy of the Licence is available in LICENCE, or at:
#
# http://www.apache.org/licenses/LICENSE-2.0
#
import pytest
from ampligraph.datasets.graph_partitioner import AbstractGraphPa... |
c97898ac2c0b44105480acd6b1381b3086431b3fd17f0cee463ae74d2b78cfa4 | Python | 8,589 | 257 | """Tests for the pytorch deep learning adapter."""
import numpy as np
import pytest
from skbase.utils.dependencies import _check_soft_dependencies
from sktime.tests.test_switch import run_test_module_changed
KINDS = ["classifier", "regressor"]
CASES = {
"classifier": {
"criterion": "nllloss",
"c... |
76eb2ae7ccfda37d252fc2108efaab340e46aecd4ab6a2db812e57fd3306987a | Python | 8,593 | 188 | """
Compare the simulation speed of the different backends
William Nourse
September 9 2021
The correct term is Babes, sir
"""
import numpy as np
import torch
import time
import pickle
from sns_toolbox.neurons import SpikingNeuron
from sns_toolbox.connections import SpikingSynapse
from sns_toolbox.networks import Netw... |
0fc108ad4ad242b3ab24a29cac6bc519c1f9e976e43344d2dd6cd9285aa267e9 | Python | 8,597 | 173 | from pathlib import Path
import os
import shutil
from typing import Union, List
import pandas as pd
import numpy as np
import nibabel as nib
from nilearn.image import concat_imgs
from bcblib.tools.spreadsheet_io_utils import import_spreadsheet
import argparse
from bcblib.tools.nifti_utils import is_nifti, file_to_lis... |
69cb06d3dad679e4ee38c71757d3b04857112d0117b0089da68d636a280d53b8 | Python | 8,599 | 177 | import os
from collections import defaultdict
from helper_functions import sortby, Make_folder_if_not_exists, load_fasta, convert_to_bases, clean_files
# ----------------------------------------------------------------------------------------------------------------------------------------------------------------
#... |
085deaf2f918dd16ac405b97c553265d12b123f5872e986b4375011ed6bd7955 | Python | 8,602 | 204 | import argparse
import logging
import os
import time
import datetime
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch_geometric.data import DataLoader as PTGDataLoader
from torch.utils.data import DataLoader
from model ... |
6ebb12e3b16097db520ae6497cc4dcd5bbb411d47b23b406d7a59d2c8f3b7f46 | Python | 8,602 | 209 | # Copyright 2019 DeepMind Technologies Ltd. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... |
257676178be499e3a4529ab83db100ed692a016bd91a4a106c3b85044f2784b9 | Python | 8,605 | 264 | # Copyright 2026 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
785eeef39f0f02025097b4f184bb54f709b3940ed3826a34c7f3be447cded1dc | Python | 8,615 | 238 | import ctypes
import logging
import win32api
#logging.console.setLevel(logging.CRITICAL)
class _WinMonitor(ctypes.Structure):
"""Physical monitor structure from Windows API.
hPhysicalMonitor : handle to physical monitor.
zPhysicalMonitorDescription : Unicode descriptive string. It seems to always
... |
f2b29692073792c48688feafef8ff1736937d7a6a7415acdb316179925fa422b | Python | 8,615 | 264 | # Author : Hari Bharadwaj hari@nmr.mgh.harvard.edu
# License : BSD 3-clause
# Parts of this code were copied from NiTime:
# http://nipy.sourceforge.net/nitime
# Some parts were coped from MNE
import numpy as np
from scipy import fftpack, linalg, interpolate
import warnings
def sum_squared(X):
"""Compute norm of... |
5825525ed8d093ee348b6ca6eaadb6ae1996cce667ca2214102c5b028ec8990f | Python | 8,617 | 249 | # Copyright 2026 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
3da6c28f68b57c32e635863d9169d99d8094fa987e57a4780fd29c816da3ca29 | Python | 8,618 | 219 | __author__ = ["chrisholder", "TonyBagnall"]
from typing import Any
import numpy as np
from sktime.dists_kernels._numba_distances.base import (
DistanceAlignmentPathCallable,
DistanceCallable,
NumbaDistance,
)
class _WdtwDistance(NumbaDistance):
r"""Weighted dynamic time warping (WDTW) distance betw... |
cb4b01c7d588d4f667bfc5b4bd3146d974ec1998b4844a163e61478dd495da9d | Python | 8,619 | 185 | # SAFE TEAM
#
#
# distributed under license: CC BY-NC-SA 4.0 (https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode.txt) #
#
import tensorflow as tf
class NetworkLSTM:
def __init__(self,
features_size,
embedding_size,
max_lv,
T_iterations,... |
61186120697e8f4a447bfdf460b4512c46497162dc92461b375046ebb6449ff9 | Python | 8,620 | 199 | from PyDAQmx import DAQmxCreateTask
from PyDAQmx import DAQmxCreateAIVoltageChan
from PyDAQmx import DAQmxCfgSampClkTiming
from PyDAQmx import DAQmxStartTask
from PyDAQmx import DAQmxReadAnalogF64
from PyDAQmx import DAQmxStopTask
from PyDAQmx import DAQmxClearTask
from PyDAQmx import TaskHandle
from PyDAQmx import DAQ... |
1104685a69352c3aadefc01af0a0207101ebb1ea5822be48c4fdd01f510f34c9 | Python | 8,624 | 194 | from __future__ import print_function
from freqAnalysisTools import band
import sys
import pickle
from os import listdir
from os.path import isfile, join, splitext
import numpy as np
import random
from sklearn import linear_model, svm, ensemble, neural_network
from sklearn.metrics import confusion_matrix
from mpl_toolk... |
7e9b66d744805281288caa02811b2bd4fb9f1f7b0e4c27e2619a1ccbca999d76 | Python | 8,625 | 245 | import os
import numpy as np
import pandas as pd
import logomaker
import matplotlib.pyplot as plt
import math
from keras.models import load_model, Input, Model
from keras.layers import SpatialDropout1D, LSTM, Bidirectional, Flatten, concatenate, Dense, Dropout
import tensorflow as tf
from see_rnn import ge... |
4ef13e2f4a2454854b5cb1a21ec68a1eca7f3d308136e288f32de130b74373ad | Python | 8,626 | 228 | """
Defines:
Functions:
_validate_scalar_to_multi(value, size=3, dtype=float)
_validate_ndarray(array, minimum_ndim=0, required_ndim=None, dtype=None,
forbid_object_dtype=True, broadcast_to_shape=None)
_validate_xyz_resolution(ndim, xyz_resolution)
_compute_axes(shape, x... |
9d57bcc1817d57a77136c979eb1db0dfcdc7a3f97b4f6d9139ed9db4f5e9eebb | Python | 8,626 | 239 | """
Module with handling the parcellation of different cortical atlases.
"""
from pathlib import Path
import nibabel as nib
import numpy as np
from graynet import config_graynet as cfg
from graynet.utils import check_atlas, check_atlas_annot_exist, roi_info
def get_atlas_path(atlas_name=None):
"""Validates th... |
97a0d58481c2026e80f4a7f7fadad663f975ef3573a70a5e7dcb7314b1efb9cb | Python | 8,628 | 222 | def plot_revcorr(p, ax, ax2, respike=False, thr=-20., width=4.0):
d={}
basepath = 'VCN_Cells/VCN_{0:s}/Simulations/AN'.format(p)
h = open(os.path.join(basepath, fn[p]), 'rb')
d[p] = pickle.load(h, )
h.close()
seaborn.set_style('ticks')
syninfo = SC.VCN_Inputs['VCN_{0:s}'.format(p)]
if no... |
76b65a5071e228b925d0ede0af925c475c3340f4e33a51296cf8ce01752f5af0 | Python | 8,629 | 197 | # SAFE TEAM
#
#
# distributed under license: CC BY-NC-SA 4.0 (https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode.txt) #
#
import tensorflow as tf
# structure2vec
# DE-MF : discriminative embedding using Mean Field
class Network:
def __init__(self,
features_size,
embe... |
8fc90a1612778a02c8a359f18b19b467bee772ebea2b7681a20d870e38ae9966 | Python | 8,632 | 158 | # Copyright 2019-2026 The AmpliGraph Authors. All Rights Reserved.
#
# This file is Licensed under the Apache License, Version 2.0.
# A copy of the Licence is available in LICENCE, or at:
#
# http://www.apache.org/licenses/LICENSE-2.0
#
from ampligraph.latent_features import loss_functions
from ampligraph.latent_f... |
321d3e5e593758505956e7b074fa6cf7be6ac9646b0eeb18980c74837923804a | Python | 8,636 | 232 | # Copyright 2022 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... |
e89c41daa5269eacc9090de3f58e5521fbcdd9282863dceec449d34fa740f2c7 | Python | 8,639 | 250 | # Copyright 2026 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
c23734ecad71d7c9a4f503deab353c44b2be6e5789c0f63ebb34305aa17369a7 | Python | 8,641 | 205 | from __future__ import annotations
from copy import copy
from typing import Callable
import numpy as np
from .dataset import JetDataset
from .normalisations import NormaliseABC
from .utils import (
checkConvertElements,
checkDownloadZenodoDataset,
checkListNotEmpty,
checkStrToList,
getOrderedFeat... |
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