sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
aad53c1b3f9985da8a5478977f006d7799fb2b474e65d235823150627463b9da | Python | 7,520 | 127 | """ Main function for this repo. """
import argparse
import torch,json,os
import time
from misc import pprint,ensure_path,timer
from trainer.pre import PreTrainer
from trainer.adapt import AdaptTrainer
from trainer.self import SelfTrainer
import os.path as osp
# dataset_pool = ['BTNx','ACON_Ab','ACON_Ag','DeepBlue_Ag'... |
7b8b91e5c6c2ffe6382a08015308816d5f0872e70caa69e264a819ea64412800 | Python | 7,523 | 210 | import argparse
import datetime
import json
import os
import time
import tqdm
import numpy as np
import pandas as pd
import torch
import torch.nn.functional as F
from torch.utils.data import DataLoader
from atom3d.datasets import LMDBDataset
from model import CNN3D_SMP
from data import CNN3D_TransformSMP
# Constru... |
799dc7f1b84615c288f12d456f49322e0541b48008ff0b7f2efc982f6daadcc8 | Python | 7,524 | 112 | import numpy as np
import pickle
from writePredictionResults import writePredictionResults
from evaluationCriteria import y2sensitivity, y2confusionMat, printConfusionMat, mathewsCorrelationCoefficient, multiClassMCC
from tester import printMetadata
def getStatistics(params, testFileIDandClassifierIDs_byMethod, y_test... |
fa5c9ae33f1de3dcbb243a3673c94304c2ecbbb6988b4c073159b27fb0ca07bd | Python | 7,524 | 163 | import os
import sys
import stat
from os.path import join as pjoin, exists as pexists, realpath
import numpy as np
import pickle
import networkx as nx
from neuropredict import run_workflow
from pyradigm import MLDataset
from graynet import parcellate
"""#---------------------------------#-----------------------------... |
3552e974cc8384f98a2ea97c50a4ca1b112553d6ed718dc37140c8a24bd50e3d | Python | 7,526 | 133 | """Global constants for the GNN project"""
from sklearn.preprocessing import OneHotEncoder
import numpy as np
from torch.nn.functional import l1_loss, mse_loss, huber_loss
from torch_geometric.nn import SAGEConv, GATv2Conv
from torch.nn import ReLU, Tanh
CORDERO = {'Ac': 2.15, 'Al': 1.21, 'Am': 1.80, 'Sb': 1.39, 'Ar... |
0b84536d6a0a961b148507cc4ce81908ba5004005515fa418a9b0b9d7ae7c4a7 | Python | 7,529 | 145 | import os
import numpy as np
import pandas as pd
import scipy.io as sio
import nibabel as nib
from sklearn.linear_model import Ridge
from os.path import join as pjoin
from nilearn.glm.first_level import make_first_level_design_matrix
from had_utils import save2cifti, roi_mask
# define path
# make sure the dataset_path... |
5f3772372a60adaa88e9f6427e640ed54b2ec2753b926e2843e9da41629ef018 | Python | 7,529 | 172 | import enum
import logging
import threading
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, connect_storage_client, maybe_download_object
from mprl.utility_services.payoff_table import PayoffTable, Pol... |
4c5675e7460fd51726c608ae8f1a6908a2d9eb8211902040e90a9c74da1446fd | Python | 7,531 | 205 | """Interface module to dtaidist package.
Exposes basic interface, excluding multivariate case.
"""
__author__ = ["fkiraly"]
import numpy as np
import pandas as pd
from sktime.alignment.base import BaseAligner
class AlignerDtwDtai(BaseAligner):
"""Aligner interface for dtaidistance time warping alignment.
... |
1817a617e54b5c7f0e8916d31ed66679bd7a525d574d9cde7f76dd195f9b06c8 | Python | 7,534 | 223 | """Tests for get intervals in time series forests."""
import numpy as np
import pytest
from numpy.random import RandomState
from sktime.base._panel.forest._tsf import _get_intervals
from sktime.tests.test_switch import run_test_module_changed
@pytest.mark.skipif(
not run_test_module_changed("sktime.base._panel.... |
cc2e2d6abfd4fcb8f32db226d62cb43efa4a4e27a75f1d23460998ca79ff65ac | Python | 7,534 | 243 | import os
import copy
import time
import math
import random
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import torch
import torch.nn as nn
import torchvision
import warnings
warnings.filterwarnings('ignore')
# hyperparameters
train_batch_size = 4
learning_rate_init = 0.0002
num_cycles ... |
e965c87bc7e9376cac2d2c52ff73c9de5e0a8c8fba3f5f201f9d6db92fd22058 | Python | 7,534 | 179 | # 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 logging
import numpy as np
logger = logging.getLogger(__name__)
logge... |
8f1f07f6dd2098b93ac199fc3bc075f7f131273b8bf61247995d245fb5e36bcb | Python | 7,539 | 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... |
8c9c098efe7a332121b027f93dd7dbfca38fe2605b687902753d77b50ba9e456 | Python | 7,541 | 169 | import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
import networkx as nx
from plotgiiSurf import plotgiiSurf
# plotNetwork3(covMat_yesAD, NetworkDataGeneral.Schaefer400x7.GII, currCoM,LabelNames,cRange,MakerVecYes,panelAll,pSelectCol,colorVec,3)
def plotNetwork3Individual(currFi... |
61194e69768d16efbad1751997fb26eaad8a83c1fc9244c1c7ba4923780511b3 | Python | 7,550 | 274 | from __future__ import annotations
from dataclasses import dataclass
from typing import ClassVar, Callable, Optional, Union, cast
import numpy as np
from pandas import DataFrame
from seaborn._core.groupby import GroupBy
from seaborn._core.scales import Scale
from seaborn._core.typing import Default
default = Default... |
9b98351d2a02233a0277eb209b5be6c39fe21098e98527cf412067cdb7488712 | Python | 7,550 | 209 | # Copyright (c) OpenMMLab. All rights reserved.
import torch.nn as nn
import torch.nn.functional as F
from ..builder import LOSSES
from .utils import weight_reduce_loss
def cross_entropy(pred,
label,
weight=None,
reduction='mean',
avg_factor=Non... |
efef512ea44b8d466fef4bfad5fe9591f0889b31c6c32ceb6a20feb2287e5b4c | Python | 7,554 | 171 | """
@file: dataset_loader.py
Created on 22.10.18
@project: crazy_ara_refactor
@author: queensgambit
Please describe what the content of this file is about
"""
import glob
import logging
import numpy as np
import zarr
from DeepCrazyhouse.configs.main_config import main_config
from DeepCrazyhouse.src.domain.util import ... |
fe38c17fc1ca6af65d14f4f3be5c9216a0c85df5925ffac31cd6e7ba4acd6551 | Python | 7,558 | 227 | import numpy as np
import pandas as pd
import tensorflow as tf
from keras.losses import mse
from keras.preprocessing.text import Tokenizer
import sys
import importlib
config_path = ".".join(["models", sys.argv[1]]) + "." if len(sys.argv) >= 2 else ""
config = importlib.import_module(config_path+"config")
attention_set... |
332ea0702e9cadbaf08035302fa75bf52dcbda4e0f953f1cdf939a9b65b41129 | Python | 7,562 | 164 | import subprocess
import sys
import os
from pathlib import Path
import argparse
from nilearn import datasets
from nilearn.regions import connected_regions
from bcblib.tools.general_utils import open_json
from bcblib.tools.nifti_utils import load_nifti
def run_command(command):
"""Run a command in the shell."""
... |
99aedf31d51e0dcd0591a2d6f0a7f17dae445367e944fbdd15adf9490f5df679 | Python | 7,566 | 183 | import os
import sys
import random
import math
import time
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from sklearn.model_selection import train_test_split
from sklearn.metrics import auc, precision_score, classification_report, plot_confusion_matrix, f1_score, confusion_matrix
from sklearn... |
edffa981a11856c1164658264a332a52cf44f1e978634b44130574d33e8ca736 | Python | 7,568 | 174 | # -*- coding: utf-8 -*-
"""
Created on Fri Sep 2 12:57:53 2016
@author: wanglab
"""
from __future__ import division
from tools.utils.io import makedir, listdirfull, makedir, removedir, chunkit, writer, load_kwargs
from tools.utils.directorydeterminer import directorydeterminer
from tools.analysis.network_analysis imp... |
691e7b9c54d7b3e33f0140ab02df7b9530e381cf6e3da99f3c3dc27493b5374a | Python | 7,573 | 260 | # Mocapy: A parallelized Dynamic Bayesian Network toolkit
#
# Copyright (C) 2004 Thomas Hamelryck
#
# This library is free software: you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation, either version 3 of the
# License... |
d22eac89f337d21e6c1c637e32cf7da4e4e332166842bf915d1949b05ffa4699 | Python | 7,573 | 250 | """Time Series Forest (TSF) classifier base class."""
__author__ = [
"TonyBagnall",
"kkoziara",
"luiszugasti",
"kanand77",
"mloning",
"Oleksii Kachaiev",
]
__all__ = [
"BaseTimeSeriesForest",
"_transform",
"_get_intervals",
"_fit_estimator",
]
import math
import numpy as np
fr... |
5d3c88d2feb196fcfc9736d6aa324ec61610cb2d97ce967c6e916557d1b2b3ad | Python | 7,574 | 213 | # SPDX-License-Identifier: LGPL-3.0-or-later
import logging
from collections.abc import (
Iterable,
Sized,
)
import numpy as np
from deepmd.loggers import (
is_node_main_process,
)
log = logging.getLogger(__name__)
def compute_total_numb_batch(
numb_batches: Iterable[int],
sampler_weights: np.n... |
5dd5cff6bc3276dac1cdb2398ba86337b21e487622cb64fabfc3f81196b7d2b6 | Python | 7,574 | 235 | #!/usr/bin/env python
__doc__ = """
Training.
Nicholas Turner <nturner@cs.princeton.edu>, 2017-8
"""
import numpy as np
import os
import time
import torch
from torch import autograd
import utils
REQUIRED_PARAMS = ["max_iter","test_intv","test_iter",
"avgs_intv","chkpt_intv","expt_dir",
... |
d6b11099ec7bda229b4628d9742fb16d89c2e90ef9d7f9460944da8cbf37b57f | Python | 7,578 | 224 | # coding=utf-8
# 2021.03 modified (1) notears_linear(def) to Notears(class)
# 2021.03 added (1) logging;
# (2) BaseLearner
# 2021.03 deleted (1) __main__
# Huawei Technologies Co., Ltd.
#
# Copyright (C) 2021. Huawei Technologies Co., Ltd. All rights reserved.
#
# Copyright (c) Xun Zheng (https... |
af3b1b20cb2e8d4a1b0c55d485f149ffbbd3b7224c3f180e21c91c871e2a1657 | Python | 7,579 | 190 | import os
import numpy as np
import torch
from torch.utils.data import Dataset
from torch_geometric.data import Data
from torch_geometric.loader import DataLoader as PyGDataLoader
from torch_geometric.nn import radius_graph
from rdkit import Chem
from dataset.utils import ani1x_iter_data_buckets
ATOM_DICT = {1: 'H', ... |
750cbf61b8f0530758a6e669ee11162e5156e20ee999114b2ee5aa3fd7deaf8f | Python | 7,581 | 196 | import gc
import os
import h5py
import numpy as np
from rdkit import Chem
from openmm.unit import *
import torch
from torch.utils.data import Dataset
from torch_geometric.data import Data
from torch_geometric.loader import DataLoader as PyGDataLoader
from torch_geometric.nn import radius_graph
posScale = 1*bohr/angstr... |
d84fe4e824668330dbc4bffc04cb274b5dbb11c975b9122302d89e9ce817b91d | Python | 7,581 | 204 | #!/usr/bin/env python
"""
This script reads in the orthogroups and generates .rbh files for different
combinationas of species
"""
import pandas as pd
import numpy as np
import os
import shutil
import sys
# Analyze the Orthofinder results
OGTSVPATH="./fasta/OrthoFinder/Results_Jul02/Orthogroups/Orthogroups.tsv"
sp... |
eae576d4936d170b0f70acb1605d890bf1f191cf887eff676e472ff2d0b4a5ae | Python | 7,582 | 172 | # -*- coding: utf-8 -*-
"""
Created on Wed Jun 22 15:50:46 2016
@author: tpisano + bdeverett
Two approaches. Typically find_site is the more robust for general CTB injection detection. detect_inj_site has more parameters and might be better tunable for specific approaches
"""
from __future__ import division
import Si... |
1cc9636baa45d60be17742987664316c14f4a27de92896396bf8e1b433cdd9f3 | Python | 7,585 | 191 | """
conflict_dacke.py
Simulates the cue conflict paradigm from Dacke et al. (2019).
Dacke et al. (2019) test three scenarios, each performs the
same cue manipulation but with the sun at high, medium, and low
elevations. Dacke et al. (2019) use ranges to determine high, medium,
and low, so we take the midpoint of that... |
90b067e6265bdd6c66e9ae890dd9f1d538aa1b6985c0fc60f556d9fac84a574f | Python | 7,588 | 219 | # Copyright (c) OpenMMLab. All rights reserved.
import logging
import tempfile
import warnings
from unittest.mock import MagicMock, patch
import mmcv.runner
import pytest
import torch
import torch.nn as nn
from mmcv.runner import obj_from_dict
from torch.utils.data import DataLoader, Dataset
from mmcls.apis import si... |
fdc48d0597fb877d9fdc6e21e2db6cd4577514a8405a8b80efcb4ecab3f2a3e6 | Python | 7,590 | 190 | # 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... |
1e5422356ac9471d82b69ce3e0ac7f1da9374a0bc2d7cc174293ec902dd66d33 | Python | 7,591 | 225 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Creates across patient plots in Figure 4 from Wang et al. (2023) Temporal
stability of intracranial EEG abnormality maps for localizing epileptogenic
tissue.
Calculates time-varying D_RS from abnormalities before plotting.
Gabrielle M. Schroeder
CNNP Lab, Newcastle... |
ec860e53dcb2e7dc0ae20c2deb7245e3519fa608b61e526de36794b9b598f3fc | Python | 7,596 | 170 | import numpy as np
class ImageMetaData():
"""Container class for metadata about an image. Stores:
- nxyz (np.ndarray): image shape - computed from provided image.
- dxyz (np.ndarray or scalar): image resolution - if dxyz is a scalar, it is upcast to the length of nxyz.
- xyz (np.ndarray): i... |
3dffef1472d13efd422490c6e0dcbd009f0214229542337a38e3e5c68c62bd97 | Python | 7,597 | 144 | """Registration in the job worker of SlicerWeb: what ElastixLib.web_launcher starts there.
This runs in a Python of its own, the worker's, with the same packages as the page and without
the application: nothing of slicer or qt is imported here. The elastix of ITK-Wasm, the
itkwasm-elastix package, is awaited; the work... |
3c628abf2aec53e8cab089a4508681bca500a5ea63a4f8512363b55d2cd99f12 | Python | 7,599 | 210 |
""" make_sound_waveform.py
Generate a sound waveform - with different choices of sound.
This was taken from model_run2.py, and is a stand-alone version,
and the parameters are taken from model_params.py
It is used by vcnmodel.plotters.plot_runs and
vcnmodel.plotters.plot_sims to show the stimulus waveforms
a... |
5aa1ae163852f48f5ea0e88604e8208b77d860ca364bdd04812f7907b0bec2df | Python | 7,601 | 229 | """
Script to center and crop an MRI based on regions given by the CerebrA atlas.
Distributed under MIT License by Clément POIRET.
"""
import argparse
import tempfile
from pathlib import Path
from shutil import rmtree
import ants
from rich import print
from rich.console import Console
from rich.progress import track
... |
226a57c7b6cd0dc2f6821d596e69a6154bea1df47a7c655fbe62a2fee5fc9598 | Python | 7,603 | 165 | from scripts import configurations as cfg
from scripts import preprocess
from scripts import data_handler as dh
from scripts import cross_validation_tl as cv_tl
from scripts import ensemble_util
from scripts import testing_util
from scripts import hyper_parameter_search as hps
from scripts import postprocess
i... |
b7d177c79552889305fe5a286d5c1fafe44c77075b29d161518f661a34d096a2 | Python | 7,603 | 210 | import csv
import logging
import math
from collections import defaultdict
from pathlib import Path
from typing import Union
import matplotlib.pyplot as plt
import numpy as np
from matplotlib.axes import Axes
# header for 'weights.txt'
WEIGHT_NAME = 1
WEIGHT_NUMBER = 2
WEIGHT_VALUE = 3
log = logging.getLogger("flair"... |
6efc704cf734c74cd33c4a7d81d4d6f5935a73e0ce69109580da7fa3698f882b | Python | 7,608 | 195 | # Copyright (c) OpenMMLab. All rights reserved.
from mmcv.cnn import ConvModule
from torch.nn.modules.batchnorm import _BatchNorm
from ..builder import BACKBONES
from ..utils import InvertedResidual
from .base_backbone import BaseBackbone
@BACKBONES.register_module()
class MobileNetV3(BaseBackbone):
"""MobileNet... |
74d6e23d39bdf29979cab8ea44958b17bc53744042496ba96982cbc98b0d31da | Python | 7,609 | 208 | """Hidden Markov Model with Gaussian emissions.
Please see the original library
(https://github.com/hmmlearn/hmmlearn/blob/main/lib/hmmlearn/hmm.py)
"""
from sktime.detection.hmm_learn import BaseHMMLearn
__author__ = ["miraep8"]
__all__ = ["GaussianHMM"]
class GaussianHMM(BaseHMMLearn):
"""Hidden Markov Model... |
def7bdcde20cab37b27e905d209103d28c561b6b05cb9a23b607f3034cfe642c | Python | 7,609 | 184 | """
Test generating a series of EPSPs in a MSO cell in response to tone pip. This
test demonstrates how a binaural circuit can be constructed.
This script:
1. Creates multiple SGCs (base instance has 3) converging onto two bushy cells.
The 2 bushy cells then converge onto one MSO cell
2. Connects the group of sg... |
a5360e2fea88334e1c9e47b22eee68ff1067a577415ffa83c3fd7d8c1382d41f | Python | 7,610 | 189 | # 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... |
8a8c1f6f75a4f6b044bf8816f55d136915441ca73f8d5c5dd37f836c622f641c | Python | 7,611 | 243 | from argparse import Namespace
import logging
import os
import os.path as osp
from pathlib import Path
from typing import List, Optional, Tuple, Union
import torch
import matplotlib.pyplot as plt
import glob
import numpy as np
def create_model_folder(args: Namespace) -> str:
make_dir(args.save_dir)
return mak... |
8d60b037f00ca48d491b5908cade084ec3bc318f9af338e4bcaaafbfeb866c38 | Python | 7,619 | 243 | # SPDX-License-Identifier: LGPL-3.0-or-later
"""Shared infrastructure for the LAMMPS Python tests.
Model paths, expected values, and scenario-specific assertions stay in their
test modules. This module owns setup that must remain identical across model
formats and backends, so changes to the LAMMPS test system have on... |
25ee135022dbccfc9642520c505fc675541264d85eda201bee5e96c920174476 | Python | 7,620 | 218 | from __future__ import annotations
import functools
import math
from typing import TYPE_CHECKING
import numpy as np
from optuna.pruners import BasePruner
from optuna.study._study_direction import StudyDirection
from optuna.trial._state import TrialState
if TYPE_CHECKING:
from collections.abc import KeysView
... |
f0ab9a11c3316351c9721a320e84ef53f2c182d14cf12f26c9ea9119126d19bc | Python | 7,621 | 232 | #!/usr/bin/env python
__doc__ = """
3D Box class.
Box -- two vectors, forming a box
Modified the code from
https://wiki.python.org/moin/PointsAndRectangles
Kisuk Lee <kisuklee@mit.edu>, 2017
"""
import math
from .vector import Vec3d, minimum, maximum
class Box(object):
"""
A 3D box identified by two vec... |
c0b40d6e78d9e2c828f70cb862d956603f9b584c437a741e4f8dd34f6981320b | Python | 7,628 | 182 | import logging
import os
import threading
import time
from http.server import HTTPServer, SimpleHTTPRequestHandler
from pathlib import Path
from socket import gethostname
import argparse
import yaml
import pandas as pd
import plotly
import plotly.express as px
from grpc import RpcError
from termcolor import colored
f... |
6a0cc607dfe46cd18b3dcc866bf19ea47721d89985a10b7b43ff42444b89c4fa | Python | 7,630 | 245 | # 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
#
# ... |
ecaa8e3e55c4478c94488b26667d9667edbca6f1740be1a84c21eb72c78c56bd | Python | 7,631 | 223 | from typing import Dict, Optional, Tuple
import numpy as np
import pandas as pd
import torch
from scipy.stats import hmean
from sklearn.metrics import classification_report, roc_auc_score
from torch.nn.modules.loss import BCELoss
from torch.optim.adamw import AdamW
from torch.optim.lr_scheduler import OneCycleLR
from ... |
969aacd8db1a0b599492d10f5a651087f802f5567f7c2a334d7c2a0947c9fd14 | Python | 7,634 | 234 | #!/usr/bin/env python
__doc__ = """
3D Box class.
Box -- two vectors, forming a box
Modified the code from
https://wiki.python.org/moin/PointsAndRectangles
Kisuk Lee <kisuklee@mit.edu>, 2017
"""
import math
from .vector import *
__all__ = ['Box', 'centered_box']
class Box(object):
"""
A 3D box identif... |
d00ec4dbcf02df7d013f370192148bf90f99effca73e791e862dd93588c5c9d0 | Python | 7,638 | 181 | import torch
import torch.nn.functional as F
from utils import find_alexnet_layer, find_vgg_layer, find_resnet_layer, find_densenet_layer, find_squeezenet_layer
class GradCAM(object):
"""Calculate GradCAM salinecy map.
A simple example:
# initialize a model, model_dict and gradcam
resnet = ... |
f7ca465904a061c9f2393e0d5e805636e21b05b9af1b3bd767846643da886f6a | Python | 7,644 | 220 | # 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... |
3d160a23d9b8b542d0165776a82ca2e7c2aa7c9027a43942cef9aeab415d4020 | Python | 7,645 | 246 | # Copyright (c) OpenMMLab. All rights reserved.
import pytest
import torch
from torch.nn.modules import GroupNorm
from torch.nn.modules.batchnorm import _BatchNorm
from mmcls.models.backbones import ShuffleNetV1
from mmcls.models.backbones.shufflenet_v1 import ShuffleUnit
def is_block(modules):
"""Check if is Re... |
b9af5839e9637ac96218f45f239b4985e0be83de65ac9053e143b1743928b7b7 | Python | 7,646 | 186 | from typing import Any, Optional
import pytest
import torch
from flair.data import Sentence
from flair.embeddings import Embeddings
from flair.embeddings.base import load_embeddings
class BaseEmbeddingsTest:
embedding_cls: type[Embeddings[Sentence]]
is_token_embedding: bool
is_document_embedding: bool
... |
cc465ff1c5e09a45db4bf2d76c2b49b6a184f7a5a90e384fe8d03565d6bcbc67 | Python | 7,651 | 299 |
"""
OTF Codec
"""
import json
import logging
import struct
import os
from builtins import bytearray
from builtins import bytes
int_size = 4
END_OF_LIST = -1
LOAD_MSG = b'L'
PREDICT_MSG = b'I'
RESPONSE = 3
def retrieve_msg(conn):
"""
Retrieve a message from the socket channel.
:param conn:
:return... |
c11c976c2cfa92bf1ffe9d361c60f0a96064b56afd5bcf669f420711aae3d721 | Python | 7,655 | 257 | '''
Crossover operatons
.. codeauthor:: Nicholas Browning
'''
from __future__ import division
from __future__ import print_function
from __future__ import absolute_import
from builtins import range
from past.utils import old_div
import copy
import numpy as np
from . import Individual
def crossover(settings, individu... |
a0ae5e5c05a6832e2b11fa60ae96947422fd86be4b3d1256fe0f284ff7fa9d45 | Python | 7,656 | 207 | # -*- coding: utf-8 -*-
"""
Created on Thu December 10 11:41:02 2022
@author: Pawan Panwar, Quanpeng Yang, Ashlie Martini
PyL3dMD: Python LAMMPS 3D Molecular Dynamics/Descriptors
Copyright (C) 2022 Pawan Panwar, Quanpeng Yang, Ashlie Martini
This file is part of PyL3dMD.
PyL3dMD is free software: you can redistri... |
f8ef14fa06e0fad1278d5692968c4689d26ebb109af9ae2791e98ebf23c48768 | Python | 7,661 | 212 | import face_recognition
import cv2
from multiprocessing import Process, Manager, cpu_count, set_start_method
import time
import numpy
import threading
import platform
# This is a little bit complicated (but fast) example of running face recognition on live video from your webcam.
# This example is using multiprocess.... |
dd7cd8702cceb3e15bf81c712b89305e6e8047fe00cd0e0b645a1f7c9fb12957 | Python | 7,664 | 209 | from keras.models import load_model
import tensorflow as tf
from keras.callbacks import EarlyStopping, Callback
import warnings
import os
import numpy as np
from keras import backend as K
import keras
class GetBest(Callback):
def __init__(self, filepath=None, monitor='val_loss', save_best=False, verbos... |
4d1bebd8fe1a51eb2b20be2d4f872e83b549cd059faa1a96981838dfec827f2e | Python | 7,665 | 226 | # 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... |
0cd0fdee9632c8dfd66949758059da92c8044c7fb35f540611fea195fc7f452c | Python | 7,666 | 227 | # 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... |
a66f8a977f8bd651d6f5064d2543c0785bbe3af6b52cab6d1fc72ec389d3be04 | Python | 7,666 | 228 | from __future__ import print_function
import re
import os
import sys
import tempfile
import subprocess
import multiprocessing
import multiprocessing.pool
import dxpy
def normalize_timedelta(timedelta):
"""
Given a string like "1w" or "5d", convert it to an integer in seconds.
Integers without a suffix are... |
52ceff5eb9214a8ac2fb0d8d96b132fa25aa81a9241dd94df09350e63c2284bc | Python | 7,671 | 281 | """
Count cluster members contributed by each of two transcriptomes.
When Corset is run over reads from two different transcriptome assemblies, a
cluster that draws all of its members from a single assembly is a warning sign:
the two assemblies' copies of the same gene failed to cross-map and were split
into separate ... |
e028a414c272da566ef37137c0f83fd3709fd9deb5cdbe46fbda7dd8be92b8e6 | Python | 7,671 | 220 | import os
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
from torchvision.transforms import *
import math
from math import log2
class Mish(torch.nn.Module):
def __init__(self):
super(Mish, self).__init__()
def forward(self, x):
retu... |
b7402fdbf95d7074090742f87fa453dbb7c028d5fd04dc2980fd7072d47358a6 | Python | 7,672 | 277 | # 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... |
71b573d2bc49904c227e00e3e03df8d288f3ec6264bfdecee9107ffaf7504417 | Python | 7,674 | 191 | import torch
from flair.data import Token, Sentence, DataPair, Span, DataTriple, Image
from flair.training_utils import identify_dynamic_embeddings
# Helper tensors
dynamic_tensor = torch.tensor([1.0, 2.0], requires_grad=True)
static_tensor = torch.tensor([3.0, 4.0], requires_grad=False)
def test_identify_dynamic_e... |
7d8b3d5da58faae13ff2e2969f51f6725288dd0c3e14cda699fe958ffebbaaa1 | Python | 7,675 | 197 | import math
from utilities.solutionFSHT import Solution
from utilities.fs_utils import transfer_function
from utilities.ht_utils import *
import random # all random should be updated by numpy (faster calculation)
import copy
import numpy as np
class SCA:
def __init__(self, n, function,tf,nfeatures):
... |
345ddddddebfe9c80de82c8f5d8d886e60ba336cb07d2a1d8714f7b9fbf1f240 | Python | 7,677 | 184 |
#=======================================================================================================================
# Copyright (C) 2021 Matvey Safroshkin, Grigory Arutyunov, Patrick Mueller
# Computer Vision Studio
# Friedrich Miescher Laboratory of the Max Planck Society
# Systems Biology of Development, Univer... |
0ed6d90332da5b5c32a31544b7e8533e71020a598dda1e82a1ebd8bdafae5e34 | Python | 7,682 | 184 | """
@file: efficient_scaling.py
Created on 30.04.21
@project: CrazyAra
@author: queensgambit
Grid search for evaluating different depth and channel ratios, as recommended in
EfficientNet by Tan et al. - https://arxiv.org/abs/1905.11946v5
"""
from __future__ import print_function
import os
import sys
sys.path.insert(0... |
bed0053a2c93d6b1156b8613f25a779b0eef5ef805f7bd36fc23f377ebb17571 | Python | 7,689 | 182 | from tensorflow import keras
def cnn_deep(input_shape, output_shape, activation='relu', num_filters=24, first_layer_kernel_size=19, initializer='he_normal'):
l2 = keras.regularizers.l2(1e-6)
# input layer
inputs = keras.layers.Input(shape=input_shape)
# layer 1
nn = keras.layers.Conv... |
fd53cb10f5a7831946d4e7ae506a25f6141426a2b4d0ef5ec0ecab8581252b02 | Python | 7,689 | 200 | import unittest
from pathlib import Path
import rdflib
from pyontutils.core import yield_recursive
from pyontutils.identity_bnode import bnodes, IdentityBNode
from .common import temp_path
class TestIBNode(unittest.TestCase):
def setUp(self):
self.graph1 = rdflib.Graph()
file = Path('ttlser/test/n... |
de1c31ac10dfd033770b65de22a2f058156200e583f9986d41e9dabfbcf87fc2 | Python | 7,694 | 227 | import slideio
import numpy as np
import matplotlib.pyplot as plt
import cv2
import xml.etree.ElementTree as ET
import Switches_Static as st_switches
CNTR_ENH = st_switches.contrast_enhancement
def histogram_equalization(img_in):
channels= cv2.split(img_in)
channels_=[]
clahe = cv2.createCLAHE(clipLimit=C... |
7746a0b4faeb991e8c322b51ea0ad6eba1a97f5b3b8bb443434f347e2a0fbb82 | Python | 7,700 | 203 | # -*- coding: utf-8 -*-
"""
Created on Thu December 10 11:41:02 2022
@author: Pawan Panwar, Quanpeng Yang, Ashlie Martini
PyL3dMD: Python LAMMPS 3D Molecular Dynamics/Descriptors
Copyright (C) 2022 Pawan Panwar, Quanpeng Yang, Ashlie Martini
This file is part of PyL3dMD.
PyL3dMD is free software: you ... |
d690277725ba35a328fe3e13ec15402771050a2838d1a3ca75457c83906882b3 | Python | 7,702 | 265 | import numpy as np
from .utils import logger, verbose
import time
'''
Module: anlffr.bootstrap
functions to aid random resampling when using anlffr.spectral functions
note: these aren't particularly clever or efficient; but if you're going to
resample, you might as well do it in parallel.
Function Listing
========... |
4d997b26238c5b3825afa77ea7c1ea7bac771d1a931735b25b71e3eaafacde8f | Python | 7,704 | 161 | #!/usr/bin/env python3
# -*- 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/.
#
"""Generate and convert ... |
be1cb0dc8265d78e06e04aca36a47544146dc3b48b23979d8baa99294e76bc02 | Python | 7,705 | 227 | # 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... |
1464483750f2929415a33ce4c150609224933c8852017632118eba9cd4f155b3 | Python | 7,707 | 258 | #!/usr/bin/env python
# coding: utf-8
# In[1]:
import pandas as pd
import matplotlib.pyplot as plt
import numpy as np
import os
import random
import shutil
from sklearn.utils import shuffle
# In[2]:
#read meta data files that stored in csv files from the previous stage.
# random state = 5 will allow you a rea... |
834d92490b68612b8b14408a0a26880ee91db4c38c24f10f6393371579e458c1 | Python | 7,707 | 182 | from typing import Callable, List, Set, Union, Optional, Tuple
import numpy as np
import logging
from .dataset import JetDataset
from .utils import (
checkConvertElements,
checkDownloadZenodoDataset,
getOrderedFeatures,
checkStrToList,
checkListNotEmpty,
)
from .normalisations import NormaliseABC... |
a0b32326536f3a4ee9ea7ad78514393d540a6481cc598c17abb37b701dbed00d | Python | 7,707 | 183 | import argparse
import logging
import os
import sys
import torch
from model import TextSentiment
from torch.utils.data import DataLoader
from torch.utils.data.dataset import random_split
from torchtext.datasets import text_classification
def generate_batch(batch):
r"""
Since the text entries have different le... |
6b4f3771d2448f2be96b9a5fe4b0b444439718443deef1e9c669fbf871187bde | Python | 7,723 | 205 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Apr 19 22:36:46 2022
Plotting correlations between measures. Figures 7 & 8.
@author: nagehan
"""
import scipy
import scipy.stats
import matplotlib.pyplot as plt
import numpy as np
import matplotlib
s = np.array([0.59, 1.44, 1.74, 2.40, 2.32, 2.41, 2.... |
1c3c1890f260e5c783b1a12d24677c446e331300c4e012200bcde3dc9b37f6e4 | Python | 7,726 | 168 | #!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Mon Nov 19 15:42:12 2018
@author: wanglab
"""
import os, sys, shutil
import argparse
from utils.preprocessing.preprocess import get_dims_from_folder, make_indices, make_memmap_from_tiff_list, generate_patch, reconstruct_memmap_array_from_tif_dir
from ut... |
62cdb36916eb954f47f55241d30e71d20928a58ea3b828cc53933780cfb6b7ad | Python | 7,728 | 163 | # 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... |
5f48b9b19c8cd1f70f07edee645fe9465198ed2b56d010b8a6db36377c6401e2 | Python | 7,729 | 227 | # 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... |
4ac001d8039110094a57f7a619aee7b0854a93f3a6271fc103ace9c11a3ae2d0 | Python | 7,734 | 258 | """Reading and writing FASTA files.
Copyright (c) 2022 by
Andrzej Zielezinski (a.zielezinski@gmail.com)
Maciej Michalczyk (mccv99@gmail.com)
https://github.com/aziele/fasta-parser
"""
import bz2 # standard python library
import gzip # standard python library
import io # standard python library
import... |
9b31df0af3e90a5138ff126a1171f94c0844ad8ab08d7fca84ef246a78ed37a8 | Python | 7,744 | 204 | """
This is code to generate stimuli of the desired length
For ophys type sessions, unexpected sequences or violations are included. These are
every 30-90 seconds, and last 2-4 seconds for the visual flow, and 3-6 seconds for the Gabors.
For hab type sessions, no unexpected sequences or violations occur.
Everything ... |
f4058a4599333dde92fe64751e2cff5bc2dd1d553aab694656846bded2331dcb | Python | 7,747 | 258 | """Isolated numba imports for lower_bounding."""
__author__ = ["chrisholder", "TonyBagnall"]
import math
import numpy as np
from sktime.utils.numba.njit import njit
@njit(cache=True)
def create_shape_on_matrix(
bounding_matrix: np.ndarray,
y_upper_line: np.ndarray,
y_lower_line: np.ndarray | None = No... |
d067e3ca8f33afe8e69bfafe21bd3a07e98ea39f0052653572d98482d46dc0f9 | Python | 7,748 | 175 | """
- For plotting figure 6. Box plot of surface area, sulcal depth, and cortical thickness
"""
def t_sd_box(input_txt, subjects_name, output_folder, max_t, min_t):
import matplotlib.pyplot as plt
import numpy as np
import seaborn as sns
import os
import scipy.stats as stats
path = os... |
a45d50857f57bf467068dac0a9ce4a6503f01c2b2928e72d53a356c0ad26f8a2 | Python | 7,755 | 173 | from itertools import combinations, product
from .combinations import SystemCombination
import numpy as np
def performance_anhilation(system, substitutions, bonds):
accepted = [SystemCombination(system, None, None, None)]
for elem_old, elem_new, numb in substitutions:
comb_lst = [[] for i in range(num... |
12633cee6973f43c892842663cfd3b46445848af6c6431ae2b1f53c5a97784b3 | Python | 7,756 | 211 | """Hidden Markov Model with Gaussian mixture emissions.
Please see the original library
(https://github.com/hmmlearn/hmmlearn/blob/main/lib/hmmlearn/hmm.py)
"""
from sktime.detection.hmm_learn import BaseHMMLearn
__author__ = ["miraep8"]
__all__ = ["GMMHMM"]
class GMMHMM(BaseHMMLearn):
"""Hidden Markov Model w... |
e23e9bf11d45c22c65aaafa1e9a0cb3f7a5a5e027486fef57a65a47f95081757 | Python | 7,760 | 207 | # Copyright 2015 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... |
141cce5b964ec2b6e6133560f72a2d3af0422406b1c86ec8428b7713c8f33f32 | Python | 7,764 | 217 | import torch
import torch.nn as nn
from torch import Tensor
from torch.nn.parameter import Parameter
from spikingjelly.clock_driven import neuron, layer
from .blocks import SeparableSEWResBlock
###############
### SCALING ###
###############
class MultiplyBy(nn.Module):
def __init__(self, scale_value: floa... |
4bc6df1642c01d25e03ab5a352b8068e833c216815f2aeb0ba3035fbc364eae6 | Python | 7,766 | 173 | #------------------------------------------------------------------------------
# elftools tests
#
# Kyle Zeng (zengyhkyle@asu.edu)
# This code is in the public domain
#------------------------------------------------------------------------------
import os
import unittest
from elftools.elf.elffile import ELFFile
from... |
d521707fb8fe9358b6bc18fab8ea9168ffbd7a4e8b5cfc7f3599ade540aa9728 | Python | 7,767 | 187 | """
This script will perform a tree walk through the AWS VGP species directory and
through projects on DNAnexus and compare contents to ensure symlinks are created
for all files.
"""
import boto3
import dxpy
import argparse
import os
VGP_BUCKET = "genomeark"
SHARE_WITH = "org-vgp"
def locate_or_create_dx_drive(drive... |
707f8c7177f1eb6a9d1a8c18c329799fd7d84a16ae3ed4fabb35da66e45aa46f | Python | 7,769 | 227 | """Test suite for lower bounding techniques."""
import numpy as np
import pandas as pd
import pytest
from sktime.dists_kernels._numba_distances.lower_bounding import LowerBounding
from sktime.dists_kernels._numba_distances.tests._utils import (
create_test_distance_numpy,
)
from sktime.tests.test_switch import ru... |
16e20efc80643df025d19ea0e1edcbaeb1a948332428bd42d788eae2b5b05e89 | Python | 7,772 | 261 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sun Jan 30 21:34:56 2022
@author: sam
"""
import h5py
import numpy as np
import matplotlib.pyplot as plt
import glob
from natsort import natsorted
from scipy import stats
import os
import matplotlib.pyplot
import matplotlib.dates
import datetime
import mat... |
04f86881a05b0cd76b7565b806f68c765a3e4e915dc01c0eef026141b698d4a2 | Python | 7,773 | 225 | # Copyright 2018 Google LLC
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... |
b68b19a5132053f018895b3494f975c0f502a2bd780d6c32d014fcf5d93b0ea5 | Python | 7,777 | 214 | """
Model (implemented in Pytorch Lightning) demonstrating how to use augmentations
during training.
"""
import torch
import lightning.pytorch as pl
import numpy as np
class RobustModel(pl.LightningModule):
"""PyTorch Lightning module to specify how augmentation should be applied to a model.
Parameters
... |
482cdcbfd6146bdf3591c92fd6e8fc1678f06d1d688afaf0091a1ad3971c8f1d | Python | 7,780 | 186 | # 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... |
861752552a8d3ede6a397ff3225f75dc5380351599a428171780a23e7bd03c9a | Python | 7,781 | 205 | import io
import logging
import struct
import numpy as np
import pytest
from pyxdf import load_xdf
from pyxdf.pyxdf import StreamData, _parse_numeric_samples, _robust_fit
SRATE = 100
T0 = 1000.123
def _varlen(n):
return b"\x01" + struct.pack("<B", n) if n < 256 else b"\x04" + struct.pack("<I", n)
def _chunk(... |
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