sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
872df691e9bf8736fa19edef42b1deee92d57b7f392c8a24792d55fb1df005a0 | Python | 4,486 | 135 |
"""
CustomService class definitions
"""
import logging
import time
from builtins import str
import ts
from ts.context import Context, RequestProcessor
from ts.metrics.metrics_store import MetricsStore
from ts.protocol.otf_message_handler import create_predict_response
PREDICTION_METRIC = 'PredictionTime'
logger = ... |
e51cbef47840f7992418368f597b217ea05163e66fbae33c802d9f25c0fdbbed | Python | 4,488 | 101 | """Detect bursts: cycle consistency approach."""
import pandas as pd
from bycycle.utils.checks import check_param_range
from bycycle.burst.utils import check_min_burst_cycles
###################################################################################################
##########################################... |
d2171c0bf09686ede803c9808ae191f791789dc442b5d473f7373bed900c49b6 | Python | 4,489 | 70 | from template_generation_tools import generate_base_class_template, generate_curated_class_template, \
generate_ind_template, merge_class_templates, \
generate_cross_species_template, generate_taxonomies_template, generate_app_specific_template, \
generate_obsolete_ind_template, generate_homologous_to_templ... |
1862ce9ffa6fd4fa1f1cc69bf777ecc8141e04a3ced94cb02925ea107a2e9a84 | Python | 4,492 | 125 | from __future__ import unicode_literals
import sys
import os
import random
from matplotlib.backends import qt_compat
use_pyside = qt_compat.QT_API == qt_compat.QT_API_PYSIDE2
if use_pyside:
from PySide import QtWidgets, QtCore
else:
from PyQt5 import QtWidgets, QtCore
# import matplotlib
# Make sure that we are... |
e44c1c75ab77d3971c889fc398059b295decc289f171d38d0a6b4d3078002022 | Python | 4,493 | 125 | import tensorflow as tf
import numpy as np
import keras
import os
# my scripts
from scripts import training_util
from scripts import configurations as cfg
from scripts import preprocess
from scripts import data_handler as dh
from scripts import fastq_preprocess
from scripts import models_util
from script... |
06a34282411abf31aaf0dc555cb7ca63aef1a3931b48abb1520d54b4191049e7 | Python | 4,496 | 92 | #!/usr/bin/env python
import pandas as pd
def reciprocal_best_hits_blastp_or_diamond_blastp(
x_to_y_blastp_results, y_to_x_blastp_results, outfile):
"""
This function finds reciprocal best blastp hits between two samples.
The input is a blastp results file where x was blasted against y,
and ... |
36ec2f285bfe7ef2d0785bcb0c41ae02f1b67b7b7981855781e05098737d18c3 | Python | 4,496 | 110 | from IPython.core.debugger import set_trace
import numpy as np
import tensorflow as tf
from src.utilities.findiff.findiff_general import solver_arguments
from src.solvers.findiff.findiff_solver import fd_solve
########################################################
"""
Common along with testcase specific arguments... |
d6e5a1b04f77286e0df70896a0c744a24517c5fa11732ce75c392d8c01a1a442 | Python | 4,496 | 155 | # 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... |
336962e0f3e225fdbb74e7376f6c9c09f1dfec0775016c4161cf4ea5215acc93 | Python | 4,498 | 111 | # 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... |
72beef0923a07c924cc42d4a4c752ef88e1161ce1d1671d7ba0ac186596410a3 | Python | 4,498 | 104 | import json
import pytest
from siibra.retrieval.bids import (
find_bids_sidecars,
load_bids_metadata,
parse_bids_filename,
)
from siibra.retrieval.repositories import LocalFileRepository
@pytest.mark.parametrize("name, entities, suffix, extension, datatype", [
("sub-01/anat/sub-01_T1w.nii.gz", {"sub... |
811e15e71af80a32214b30e05bbded315ed18d4f767fe1e52a9e3eff49dc08d5 | Python | 4,499 | 133 | #from __future__ import division
#from __future__ import print_function
#import warnings
#warnings.filterwarnings("ignore")
import time
import argparse
import pdb
import pickle
import os
import shutil
import glob
import pandas as pd
import itertools
import numpy as np
import matplotlib.pyplot as plt
from tools import ... |
ec77f79eb8d1e03007627cfa9347a04283c6a249fec4b496d488a7ff3be96ffb | Python | 4,500 | 125 | import sys
import socket
import struct
import numpy as np
from functools import reduce
from os import listdir
from datetime import datetime
from functools import reduce
from time import sleep
from dataReader import DataReader
from parameterSetup import ParameterSetup
# sends mock signal to online.py by con... |
1092effa50a40aa761db87c4d274067760333db53b69a501c8e7845fe4465846 | Python | 4,502 | 146 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import numpy as np
import random
import sys
from ray.rllib.utils.compression import unpack_if_needed, pack_if_needed
from ray.rllib.utils.window_stat import WindowStat
class CustomValueReplayBuffer(object):... |
8fe18b047b6ddec9349789c695a4e5b5ff68c3055b359054687d0f40c8f7fbf2 | Python | 4,502 | 147 | import math
import numpy as np
from . import blend
from ..geometry import *
class ForwardScanner(object):
"""
Forward scanner.
"""
def __init__(self, dataset, scan_spec, **params):
self._init()
self.dataset = dataset
self.scan_spec = dict(scan_spec)
self.params = param... |
13fecb41d9d8554ea8997732d8b3d7b529731894318256b71c3c5e5719c4e9c4 | Python | 4,503 | 124 | # -*- coding: utf-8 -*-
from pyqtgraph.Qt import QtGui, QtCore
from pyqtgraph.pgcollections import OrderedDict
from .TableWidget import TableWidget
from pyqtgraph.python2_3 import asUnicode
import types, traceback
import numpy as np
try:
import metaarray
HAVE_METAARRAY = True
except:
HAVE_METAARRAY = False... |
c3301b93569f8f2b9cb61894e95cc254ea3e860261b6eb67ad3c58f2300b4e3b | Python | 4,503 | 136 | # 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... |
6bdf21ad7d023dac1cdee69e8282137bad6b3e84e1ff02d3f7a2e5673c5a1e4a | Python | 4,504 | 133 | # Copyright (c) OpenMMLab. All rights reserved.
import os
import os.path
import pickle
import numpy as np
import torch.distributed as dist
from mmcv.runner import get_dist_info
from .base_dataset import BaseDataset
from .builder import DATASETS
from .utils import check_integrity, download_and_extract_archive
@DATAS... |
f08851f47d6f888c9a027398f608d43e4248d1dc6d721733ed056e26b5dd037d | Python | 4,504 | 135 | import torch
import torch.nn as nn
import torch.nn.functional as F
import dgl
class GATLayer(nn.Module):
def __init__(self, in_dim, out_dim, e_in_dim, e_out_dim):
super(GATLayer, self).__init__()
self.embed_node = nn.Linear(in_dim, out_dim, bias=False)
self.attn_fc = nn.Linear(2 * out_dim ... |
f3d6e0ac7cfe2fb42fb9e760bcbc53dd5a9f1073f2f50d2f8f4e2f4a429d5c05 | Python | 4,504 | 86 | """
@file: main_config.py
Created on 24.09.18
@project: crazyara
@author: queensgambit
Main Config definition file used for the project.
Adjust the paths accordingly.
"""
# define the default dir where the training data in plane representation is located
# e.g. for supervised learning default_dir = "/data/planes/"
d... |
33d13f482222af51f61a7506d4601a9e18add2411c582d8d2cb8c0d2bf91cb70 | Python | 4,505 | 145 | import numpy as np
from ..external.six.moves import range
from numpy.testing import assert_array_equal
import pytest
from .. import algorithms as algo
@pytest.fixture
def random():
np.random.seed(sum(map(ord, "test_algorithms")))
def test_bootstrap(random):
"""Test that bootstrapping gives the right answe... |
7c741a78dd76e7b85746b19ad3d70f28649140bb3f0c5d9bdbf802d79ee0a956 | Python | 4,506 | 148 | from __future__ import print_function
import numpy as np
from .augment import Augment
from .geometry.box import Box, centered_box
from .geometry.vector import Vec3d
from .perturb import Perturb
__all__ = ['FillBox', 'BlurBox', 'NoiseBox']
class BoxOcclusion(Augment):
"""
Box occlusion.
Args:
p... |
a5ad6ac0ebff68ec51a0280b02227a6902561c966a2cead9bd5e6d33ca171101 | Python | 4,507 | 109 | """Unit tests for the cached volume constructors `from_nifti` and `from_array`.
The space registry and the siibra cache are patched, so no network access is
needed and nothing is written to the user's cache.
"""
from hashlib import md5
from types import SimpleNamespace
from unittest.mock import Mock, patch
import nu... |
e811b4ae8bffa2e608e2f91a21fd5d12fd18a0d5d484013893cd01e02b99b346 | Python | 4,508 | 118 | import numpy as np
from numba import njit
from hmm_functions import HMMParam, write_HMM_to_file, Simulate_transition
from helper_functions import find_runs
# ---------------------------------------------------------------------------------------------------------------------------------------------------------------... |
2b9af8dd3315a2ab9010919fc3d6ae1e85c8134e33eb0afa80df2dcc90d93b68 | Python | 4,510 | 132 | """
Compare the simulation speed of the different backends
William Nourse
September 9 2021
The correct term is Babes, sir
"""
import numpy as np
import nengo
import time
import pickle
from sns_toolbox.neurons import SpikingNeuron
from sns_toolbox.connections import SpikingSynapse
from sns_toolbox.networks import Netw... |
b090bb1ddac03119ca34b75954a7b55ba8cd87835a03cc2bcb1b7dbcd3f924d4 | Python | 4,510 | 93 | import logging
import time
import grpc
from google.protobuf.empty_pb2 import Empty
from minio import Minio
from mprl.utility_services.cloud_storage import DEFAULT_LOCAL_SAVE_PATH
from mprl.utility_services.payoff_table import PolicySpec
from mprl.utility_services.protobuf.population_server_pb2 import Confirmation, Ev... |
d5aeea4d70c8bd7229eec39bcc79d2350b227c5dbbf77758c99c20a9b1078ad3 | Python | 4,511 | 131 | # Copyright (c) OpenMMLab. All rights reserved.
import argparse
import fcntl
import os
from pathlib import Path
from mmcv import Config, DictAction, track_parallel_progress, track_progress
from mmcls.datasets import PIPELINES, build_dataset
def parse_args():
parser = argparse.ArgumentParser(description='Verify ... |
8865ad567f36fe68590ae027759d454b52a976ac9b549c6db8b3d0309ced99e4 | Python | 4,513 | 124 | import re
import sys
from setuptools import setup
def find_version(filename):
_version_re = re.compile(r"__version__ = '(.*)'")
for line in open(filename):
version_match = _version_re.match(line)
if version_match:
return version_match.group(1)
__version__ = find_version('neurondm... |
e2a99b4fbc43b37bd46cab3babfbbf9dae4529a910351135f332af0856a4ce3c | Python | 4,516 | 206 | # SPDX-License-Identifier: LGPL-3.0-or-later
"""
Public building blocks for the DPA4/SeZM descriptor.
This package re-exports the helper functions, embeddings, equivariant layers,
and quaternion-based Wigner-D utilities used by the DPA4/SeZM descriptor and model.
This package is the dpmodel (array-API) port of
``deep... |
f1fe20c926ce2204654a25c995c5657b9316c2b4d81075ee4db0f8df833a3919 | Python | 4,516 | 119 | from datetime import datetime
from typing import Any, Optional, Union
from flair.trainers.plugins.base import TrainerPlugin
from flair.trainers.plugins.metric_records import MetricName
from flair.training_utils import init_output_file
class LossFilePlugin(TrainerPlugin):
"""Plugin that manages the loss.tsv file ... |
1d6689be4d6f18a02bb4f78a552299fbea51524815df628e33cd6eec353c41f9 | Python | 4,518 | 44 | """
Vector strength for models with SAM tones, different input configurations.
17 Aug 2021 version.
Results are a printout from DataTablesVCN after selecting the data runs.
Run started at: 2022-07-07-11.54.52
WARNING: This table is automatically written by figures.py generate_VS_data_file
and should ... |
993540198b922fafde34414e89094fc5365453ae03a14f6faf1a008ab2f628e2 | Python | 4,518 | 135 | from torch_geometric.data import InMemoryDataset
from torch_geometric.data import Data as DATA
from tqdm import tqdm
import pandas as pd
import numpy as np
import torch
import os
from torch.utils.data import DataLoader, Dataset
import re
class Pre_DTADataset(torch.utils.data.Dataset):
def __init__(s... |
16a08a2ef4848a59d601f0ea137ae890a2619340d4393e7b16ed21f2d65ea269 | Python | 4,521 | 129 | from argparse import Namespace
import json
from pathlib import Path
from pyontutils.core import makeGraph, qname, OntId, OntTerm
from pyontutils.config import auth
from typing import Union, Dict, List
import yaml
from IPython import embed
resources = auth.get_path('resources')
def convert_view_text_to_dict() -> dic... |
f8c7b079cc8b0e020d561af092fa7e477533edb05f3d07fdb2a3a283b269ef80 | Python | 4,522 | 151 | """Tests for transcript pair discovery."""
from pathlib import Path
import pytest
from corset_tools.dist_calc.pairs import read_blast_reciprocal_pairs, read_pairs
from corset_tools.exceptions import InputFormatError
def test_read_pairs_handles_ragged_input(data_dir: Path) -> None:
"""Comments, ragged tabs and ... |
a9e9c5e354580153676c67822ea6c545269dfbdef8fd0f7076f88e4db3c105d7 | Python | 4,523 | 98 | from pyontutils.utils import *
from pyontutils.core import *
from pyontutils.closed_namespaces import *
edge_cases = {
#Definitions
'definition:': 'definition:',
'skos:definition': 'definition:',
'definition': 'definition:',
'NIFRID:birnlexDefinition': 'definition:',
'NIFRID:externallySourcedDe... |
029d80cc07e4c1b424337ce31020968ac5a4007fc26ced762b037b70c52afd52 | Python | 4,524 | 145 | # noqa: INP001
import inspect
import importlib_metadata
# -- Project information -----------------------------------------------------
from sphinx_github_style import get_linkcode_resolve
version = "0.15.1"
release = "0.15.1"
project = "flair"
author = importlib_metadata.metadata(project)["Author"]
copyright = f"202... |
48649cb36254f4daa503bb252b2351ff291e0403374f6905f6e65c973cb732b6 | Python | 4,524 | 132 | # 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... |
0d4685626620f9483eea5f98fe6fcd8914df959a411ad8b8fe1e1cc4697f2c5b | Python | 4,525 | 130 | import unittest
import numpy as np
from numpy.linalg import norm
import os
import pickle
import hbip.predict
import hbip_reproduce as mn
from hbip import preprocess as pp
def base_model_path(name):
return os.path.join("./models", name)
def model_files(name):
return [
os.path.join(base_model_path(na... |
2d52107f89029250d85cca947443598b7c36af85cd4bbf825e4f3d6b6133e309 | Python | 4,525 | 137 | # Copyright 2019 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... |
883e0e0d78c5f0cf60c00c34af531508aa4a3163ffe98647c1346c967bad1ee4 | Python | 4,530 | 197 | # 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... |
d506b0a46d722e3019688789cb8447886fc1611860ffd0c47ce345186eb2f31f | Python | 4,535 | 116 | # Copyright (c) ONNX Project Contributors
#
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import numpy as np
import pytest
from onnx import TensorProto, checker, helper, numpy_helper, version_converter
from onnx.reference import ReferenceEvaluator
CASES = [
("ReduceSum", 13, 12, [2, 2]... |
8559b804ec5ca3fa08431e8ebfb0b09e00816d52ceace9558a2ef7721ebb350a | Python | 4,536 | 101 | from expert.src.model import Model
from tensorflow.keras.callbacks import CSVLogger, ReduceLROnPlateau, EarlyStopping
from expert.src.utils import read_genus_abu, read_labels, load_otlg, zero_weight_unk, parse_otlg, get_dmax
from tensorflow.keras.losses import BinaryCrossentropy
from tensorflow.keras.optimizers imp... |
b86183bf2c1b759aa9e1811bea5ffc63e5e9bef7e263878cb84c4ebda115563e | Python | 4,536 | 88 | # -*- coding: utf-8 -*-
# Written (W) 2008-2012 Christian Widmer
# Written (W) 2008-2010 Cheng Soon Ong
# Written (W) 2012-2014 Daniel Blanchard, dblanchard@ets.org
# Copyright (C) 2008-2012 Max-Planck-Society, 2012-2014 ETS
# This file is part of GridMap.
# GridMap is free software: you can redistribute it and/or m... |
5dd2d105ef9681665d27fbc5b7dafc854f25a70f1693c3a8cfcb214299281367 | Python | 4,537 | 127 | """
4. Running Bycycle on 2D Arrays
===============================
Compute bycycle features for 2D organizations of timeseries.
Bycycle supports computing the features of 2D signals using :class:`~.BycycleGroup`.
Signals may be organized in a different ways, including (n_epochs, n_timepoints) or
(n_channels, n_timep... |
7b9cf2fe3c3994130de635a705ce69f200ee75bc0dc6a91bc5cc01ca2630d95b | Python | 4,537 | 129 | # Copyright (c) ONNX Project Contributors
#
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
from typing import NamedTuple
import ml_dtypes
import numpy as np
from onnx.onnx_pb import TensorProto
class TensorDtypeMap(NamedTuple):
np_dtype: np.dtype
storage_dtype: int
name: str
... |
f6ad2f5629d976265673ffb3a16b7ae8970f3df3638e6a1a1ae168b488b87180 | Python | 4,537 | 137 | # Copyright 2019 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... |
28dc20394a89e653c1b0ec610a3d5072dd558d97b96d0c423c0c0d85957bcf0f | Python | 4,543 | 155 | import sys
import os
import subprocess
import numpy as np
def main():
mot_path = "/MOT"
target_folder_path = "data"
for top_level_folder in ["train", "test"]:
top_level_folder_path = os.path.join(mot_path, top_level_folder)
for trace in os.listdir(top_level_folder_path):
trace... |
76be2215b95b6ab48d38e4e8906458ffa4f82c108d0a82f33b644473236a973c | Python | 4,548 | 129 | # Copyright (c) OpenMMLab. All rights reserved.
import copy
import torch
import torch.nn as nn
from mmcv.runner import OptimizerHook
from mmcv.utils.parrots_wrapper import _BatchNorm
from ..utils import allreduce_grads
from .utils import cast_tensor_type
class Fp16OptimizerHook(OptimizerHook):
"""FP16 optimizer... |
3ec342e8a7df7e42a49a802d0be392a4c7083dc266003e17a731a492389b2b17 | Python | 4,551 | 136 | # 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... |
6ffa99f23913918b6e5691b869d87f364a699f4f78a65556892177ee03fd44db | Python | 4,552 | 121 | # 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... |
dd547a1d1ae973dca0389cecb3a319d530d64f201abcf036c539294fd54b836e | Python | 4,557 | 203 | # Copyright 2019-2021 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... |
7366132ced596dc2ab4b5384aba5e45bb4c7ecae131b8a7c106646166175483d | Python | 4,560 | 129 | # 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... |
816790cc8467e49ad814b716ffe5f97e3ce7ced4bc1ccbece743714293088933 | Python | 4,562 | 129 | import timm
import torch
import torch.nn as nn
from torchvision import models
from utils.func import print_msg, select_out_features
def generate_model(cfg):
model = build_model(cfg)
if cfg.train.checkpoint:
if cfg.dist.distributed:
loc = 'cuda:{}'.format(cfg.dist.gpu)
weights... |
76478263eaed33dcd05ae6846465fe8f031176ade8818f2b627ce320b5e05a14 | Python | 4,564 | 125 | # -*- coding: utf-8 -*-
#
# Copyright © 2013 Charles E. Vejnar
#
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://www.mozilla.org/MPL/2.0/.
#
"""Interface with the `ReadKnead <https://git.s... |
d9855b1c6ab8c3eaf748c0278d30a82bd70b547101dee85986741319603e2fcf | Python | 4,566 | 148 | """
@authors: stanislas chambon / Alexandre Gramfort
goal: edf annotation reader
Modified: Alexander Neergaard Olesen, Stanford University, 2018
"""
import re
import numpy as np
import pandas as pd
import xmltodict
def read_edf_annotations(fname, annotation_format="edf/edf+"):
"""read_edf_annotation... |
c73fb3919662a7deee46b3ca9806b9a428464c57653eafb5913d7e23cda49b2f | Python | 4,567 | 118 | # 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... |
3bc35b691107cea241cca9ce7dd3802cb21778d95ecea9f31f88a98b5e540513 | Python | 4,569 | 158 | # Copyright (c) ONNX Project Contributors
#
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
__all__ = [
"C",
"ONNX_DOMAIN",
"ONNX_ML_DOMAIN",
"AI_ONNX_PREVIEW_DOMAIN",
"AI_ONNX_PREVIEW_TRAINING_DOMAIN",
"has",
"register_schema",
"deregister_schema",
"get_sch... |
bd10141343eabb166780b1b3aecdfd276d6e2582d47c8c2ad66bdc50ede2cd0c | Python | 4,572 | 136 | # SPDX-License-Identifier: LGPL-3.0-or-later
import tempfile
import unittest
from pathlib import (
Path,
)
import h5py
import numpy as np
from deepmd.utils.data_system import (
process_systems,
)
from deepmd.utils.path import (
DPH5Path,
DPPath,
)
class PathTest:
path: DPPath
def test_numpy... |
3384df3fb1784021d45e6806a9bcf8d19a0b60946ea35c97f844f6d3b00b5346 | Python | 4,573 | 122 | """RNG reproducibility, seed-type equivalence, thread safety, and
non-pollution of ``numpy.random`` global state.
These tests pin the behaviour contract that PR #178 established when the
code base moved from the legacy ``numpy.random.seed`` / ``np.random.randint``
(global-state) pattern to per-call ``numpy.random.Gene... |
c51d1952a1a02bfd7b3e5e530f4a88c152460973c381e3b4438f1972b770bcf5 | Python | 4,576 | 158 | #!/usr/bin/env python3 -u
# copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
"""Implements outlier detection from pyOD."""
import numpy as np
from skbase.utils.dependencies import _check_soft_dependencies
from sklearn.base import clone
from sktime.detection.base import BaseDetector
__author__ = ... |
1a0105effae3f9e38555cd5cfbebafe23b54dc457529df7136c211fbb6a43b63 | Python | 4,577 | 138 | # -*- coding: utf-8 -*-
#import os
#os.environ["CUDA_VISIBLE_DEVICES"]= "3"
#
# Description :
# Patching training data for QSMnet
#
# Input :
# RDF : the tissue field
# QSM : the COSMOS susceptibility
# x : Serial number of subjects
# y : the orientation of each subject
# z : the number for data augmentation
... |
edbde9fbb286f5326ee1b1486b3c1c21c5ce01941a04355eb51f320f7623f8f9 | Python | 4,581 | 136 | # 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 la... |
ad0df930e6203de1c99451818ed269f19d6460f7949465eff89721d1b3c0f75f | Python | 4,582 | 144 | # 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
class Clip(Base):
@staticmethod
def export() -> None:
node =... |
076083e9c0a123b9d5b83db99f8615645df78e57e392274ce86c70905b25691e | Python | 4,584 | 139 | import fnmatch
import os
import random
from typing import List
import networkx as nx
import numpy as np
import torch
from torch_geometric.data import HeteroData
from torch_geometric.utils import to_networkx
def get_mcs(pairs_list: List[HeteroData]) -> np.ndarray:
MCS = []
for hetero_data in pairs_list:
... |
c8d42bf8a5ed5c671732e655c95f96e04e8d89de3e7cf8f31803df9c76b12994 | Python | 4,584 | 114 | # Generated by the gRPC Python protocol compiler plugin. DO NOT EDIT!
import grpc
import lock_server_pb2 as lock__server__pb2
class LockServerStub(object):
# missing associated documentation comment in .proto file
pass
def __init__(self, channel):
"""Constructor.
Args:
channel: A grpc.Channel.
... |
cdaf3048b05a3a4bbb7b88f4d3f278379338c88640022efbab94cb27d19ecc39 | Python | 4,585 | 93 | # 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.datasets import GraphDataLoader, NoBackend
from ampligraph.data... |
d44b28690aeff872d33178346b955f2eb189b1176cc60d0aeb3c1b3f6f400cca | Python | 4,586 | 156 | """Tests for bcblib.imaging.math."""
import numpy as np
import nibabel as nib
import pytest
from bcblib.imaging.math import (
binarize,
threshold,
dilate,
erode,
apply_mask,
apply_inverse_mask,
add,
subtract,
multiply,
_dilate_array,
_erode_array,
_mask_in_array,
_m... |
5fb1722a07616a8ddecd25906743008c3c65421df4e52fb86b80fadf445a33e7 | Python | 4,588 | 129 | # 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... |
ccb6b821ac22f4414c88e471fb22370c66f542ed0c939519dc8651e7ff9bfa07 | Python | 4,591 | 140 | # 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... |
dbfa4f25ada978c48795dded459e04dd4efcc7e03e6422ba6ad1ecaa70925951 | Python | 4,601 | 138 | #%% [markdown]
# # *C. elegans* connectomes
#%%
import datetime
import time
import networkx as nx
import numpy as np
import pandas as pd
from graspologic.plot import adjplot
from pkg.data import DATA_PATH
from pkg.utils import create_node_data, ensure_connected, select_lateral_nodes
FILENAME = "process_c_elegans"
D... |
c8b025da072e5eb7a91131beebb39f02e36dd5b71712ac8a7745fb87b2bd3f9d | Python | 4,605 | 125 | # Copyright (c) OpenMMLab. All rights reserved.
import torch.utils.checkpoint as cp
from ..builder import BACKBONES
from ..utils.se_layer import SELayer
from .resnet import Bottleneck, ResLayer, ResNet
class SEBottleneck(Bottleneck):
"""SEBottleneck block for SEResNet.
Args:
in_channels (int): The i... |
dfaeaa154fcea6cc8e29f36d33f3a2915242954eeb1979f12f7784660ae4193a | Python | 4,606 | 154 | # -*- coding: utf-8 -*-
"""
Created on Fri Aug 2 17:50:36 2019
@author: daniel
"""
# -*- coding: utf-8 -*-
"""
Created on Thu Dec 15 17:48:41 2016
@author: daniel
"""
from neuron import h
import d1msn as msn
#import iMSN
import spillover_experiment as pe
import pickle
import parameters as p
import matplotlib.pyplo... |
5804ecef8bdfffc72f8e0978d1b27cff0d29bd3027d7ccbd9a781117284707bd | Python | 4,607 | 110 | """
Two iteration weighted average smoothing of each surface measure.
Parameters:
---------
ndl: vertex neighbors from {h}.pial.neighbor.asc file
nb: number of neighbors from {h}.pial.neighbor.asc file
each surface measures from their corresponding text files (SI,H,K,k1,k2,thickness)
Returns:
------
... |
84b36d9785220d090dc573f6890254006b9bd2a7964fc3f727e28ad532c899be | Python | 4,607 | 102 | # 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... |
a2e676d59e1082e0d8111ac020d3c03d89ada32d04278a29a2a6922495a62cdb | Python | 4,607 | 186 | # 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... |
ef9f4e7eca2058a35c7ff0feb832f9f88d2d3db5ba2f5f4f92f838b9e274f135 | Python | 4,607 | 115 | """
Inspect file structure for simulation output
Print a report to the terminal.
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 development)
Copyright 2... |
c08590e55cca92309a36414e4f0bb78395d171cb26c8675f3713a079c303d781 | Python | 4,608 | 125 | # 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... |
7555feba0724285ae6528c02bdd223840ef68129c92b92b339e867c11bde5640 | Python | 4,616 | 180 | import numpy as np
from scipy import interpolate
from scipy.optimize import brentq
def poli2(x, p1, p2):
x1, y1 = p1
x2, y2 = p2
a = -(y1 - y2) / np.power(x1 - x2, 2)
b = -2 * a * x1
c = y2 - a * np.power(x2, 2) - b * x2
return a * np.power(x, 2) + b * x + c
def csigma(x, p1, p2):
x1, ... |
27e612ed47ab46359eda338fef2fea65716e637a8ad6e9ee5934285a3b1138a7 | Python | 4,620 | 141 | """
@file: alpha_vile.py
Created on 30.03.23
@project: CrazyAra
@author: queensgambit
Description of the AlphaVile architecture for the sizes tiny, small, normal and large.
"""
import random
from DeepCrazyhouse.src.domain.neural_net.architectures.pytorch.rise_mobile_v3 import RiseV3
def get_alpha_vile_model(args, m... |
0de0cfbe61c0acbc018b244c64b99d662b81f755fbcb40fd81d17b68915a82cf | Python | 4,621 | 117 | import os
import dotenv as de
import numpy as np
import pandas as pd
import torch
from atom3d.datasets import LMDBDataset
from atom3d.util.voxelize import dotdict, get_center, gen_rot_matrix, get_grid
from torch.utils.data import DataLoader
de.load_dotenv(de.find_dotenv(usecwd=True))
class CNN3D_TransformMSP(obje... |
c999b0963340e252e899a2d853fcb3203b7bcf727bae5a23bda1f9b0864984e1 | Python | 4,622 | 148 | #!/usr/bin/python
"""
Basic test of cnmodel decorator on simple cell
Uses LC_bushy.hoc and XM13 mechanisms.
"""
__author__ = "pbmanis"
import sys
import numpy as np
import timeit
import pyqtgraph as pg
import cnmodel.cells as cells
import cnmodel.decorator as Decorator
from cnmodel.util import pyqtgraphPlotHelpers... |
303dfb32205b0756ffdd417c5bd4d21c498431e26928f23bb823633dfb67910d | Python | 4,623 | 121 | from unittest.mock import patch
import torch
from mmcv.utils import digit_version
from mmcls.datasets import build_dataloader
class TestDataloaderBuilder():
@classmethod
def setup_class(cls):
cls.data = list(range(20))
cls.samples_per_gpu = 5
cls.workers_per_gpu = 1
@patch('mmc... |
a89291d04fc0b08ecc83019468fb8c3469ecc8f5c5efb147b7447c609cf1fd3b | Python | 4,625 | 143 | import pandas as pd
import numpy as np
import matplotlib
#matplotlib.use("Agg")
import seaborn as sns
from matplotlib import pyplot as plt
import sys
colors2 = sns.color_palette("Set1", 12)[6:]
colors = [(0.6, 0.6, 0.6)] * 12
def read_dfs(i, j):
df = pd.read_csv(sys.argv[i], sep="\t", index_col="sample")
... |
ed8dec9e17549e17631e5d96ab983ff024cae7c94d0e9329415aab11ddfa701d | Python | 4,626 | 129 | import os
import copy
import math
import numpy as np
from sklearn.metrics import confusion_matrix
import torch
import torch.nn as nn
import torch.optim as optim
import torch.nn.functional as F
from torch.nn.utils.rnn import pad_sequence
from model import AcrNET
device = torch.device("cuda:0" if torch.cuda.is_availa... |
eaf736da05f8d68ae8c86fa2117e2ac18dbe8b9b5295931c39e9a8867c54552a | Python | 4,628 | 147 | # Copyright 2023 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... |
eff17d1fc8ba31c562d443c5baccc1cc21657119376fa84e96f659137aece242 | Python | 4,630 | 139 | # 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
#
# ... |
fdbc0064cb5105d5380bfd09ace519dfb143197ac1b27b2de788611f8b00a946 | Python | 4,630 | 117 | """
Evaluate models on synthetic data: experiments with the initialization of model weights.
"""
import os
import numpy as np
from six.moves import cPickle
from tensorflow import keras
from gradient_correction import helper, explain, model_zoo, geomath
import tfomics
#-------------------------------------------------... |
c48667274973c33e65cbfd3594dfa82620273485bd54f707389d3cc99e0d46a4 | Python | 4,631 | 142 | # copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
# Ported from skchange (BSD-3-Clause), original authors: johannvk
"""Rank-based change score for multivariate data."""
__author__ = ["johannvk"]
import numpy as np
from sktime.detection.base._base_interval_scorer import BaseIntervalScorer
from s... |
44f61f4f6acc78de04de2a5dac46cc9dc53b394692ba6e1c6d2f9bd3219fec8c | Python | 4,632 | 93 | from __future__ import print_function
import numpy as np
from parameterSetup import ParameterSetup
def labels2ID(params, y_seq):
return [params.correctedLabel2depthID[params.labelCorrectionDict[y]] for y in y_seq]
def getEpisodeLengths(params, y_seq):
episodeLengths = [[] for _ in range(len(params.correctedLa... |
4dee0945d1b470d28d2860312fd7f887e660bbd0588b9492de435699c2e9b05e | Python | 4,632 | 118 | # 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... |
97370d1f6cf97363b089e349479c7946962bbd22f961c39a699cacd3dcfa1d47 | Python | 4,639 | 138 | # 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... |
e6ff13eb460c374e656a527026224cc4b03d0e509b2e05050e5e30a671c48165 | Python | 4,639 | 123 | """
@file: validate_train_results_util.py
Created on 03.12.23
@project: CrazyAra
@author: queensgambit
Utility functions for validate_train_results.ipynb
"""
import sys
sys.path.insert(0, '../../../')
import chess
import numpy as np
from copy import deepcopy
import chess.svg
from IPython.display import SVG
import tor... |
70d8afdb417b07b088563a6575d7b1cbdf34fa49e971f00a42affccf97f6c483 | Python | 4,640 | 155 | from __future__ import annotations
from typing import cast
from typing import NamedTuple
from typing import TYPE_CHECKING
import numpy as np
from optuna.logging import get_logger
from optuna.study import Study
from optuna.trial import FrozenTrial
from optuna.trial import TrialState
from optuna.visualization._plotly_... |
54bff25844504b8bbde6dca22d16f27fddf17ea907cc756a81b427ad62b7cf61 | Python | 4,641 | 156 | # copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
"""Output formatting utilities for detection results.
Convert raw detection outputs (change point arrays, segment intervals) to
the ``pd.DataFrame`` format expected by sktime's ``BaseDetector.predict()``.
"""
import numpy as np
import pandas as p... |
87483acdf1e850385e1b69338473aca9377e4e59787ac025a6cdbf7667cea7a8 | Python | 4,641 | 156 | # In Nomine Functions Team
# distributed under license: GPL 3 License http://www.gnu.org/licenses/
import json
import r2pipe
class RadareFunctionAnalyzer:
def __init__(self, filename, use_symbol, depth):
self.r2 = r2pipe.open(filename, flags=['-2'])
self.filename = filename
self.arch, se... |
64cc70ea62bf13f58a79d3aeddd4c01da63217cc85e7ca45689b59de59f4b7fb | Python | 4,642 | 155 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# Copyright © 2023 Charles E. Vejnar
#
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://www.mozilla.org/MPL/2.0/.
#
"""Interface with the `m... |
2d1075a4f010de2d4e90c8d35145a7d4b905f464bf97c09ddc93e3bf369ddd2f | Python | 4,643 | 144 | # 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... |
670a4bd50eed762cd6bc2c39a0c6935c9968246c200f57e00098f080e9a1133e | Python | 4,643 | 170 | #!/usr/bin/env python
__doc__ = """
Miscellaneous Utils
Nicholas Turner <nturner@cs.princeton.edu>, 2017
"""
import importlib
import datetime
import shutil
import types
import os
import re
import torch
from torch.autograd import Variable
import numpy as np
import h5py, tifffile
__all__ = ["timestamp",
... |
403209b896041e7e2351061deb7ff67f10d15518cca94e4cc2cfd6d6b8942555 | Python | 4,644 | 136 | #!/usr/bin/env python
# bax_to_bam 0.0.1
# Generated by dx-app-wizard.
#
# Basic execution pattern: Your app will run on a single machine from
# beginning to end.
#
# See https://wiki.dnanexus.com/Developer-Portal for documentation and
# tutorials on how to modify this file.
#
# DNAnexus Python Bindings (dxpy) document... |
ec5d230989e4e4f593d72349ae1e10a148976cae3a4bd0ad23df26bac49ea2c2 | Python | 4,645 | 140 | # tifffile/numcodecs.py
# Copyright (c) 2021-2022, Christoph Gohlke
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
#... |
f381810ff23fd2eacef7d60941bf150558a8c6ec288af73170ef610076f1a258 | Python | 4,651 | 146 | """
Helper Module containing functions called by SFA_Func
03 13 2023
Code by R.W. DiTullio and C Parthiban
"""
import numpy as np
import scipy as sp
import matplotlib.pyplot as plt
import scipy.stats as stat
from sklearn.decomposition import NMF
#################################################################... |
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