sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
c357c33fd1c32242d8061799b58ede9dcb56f00598004e78191c6391aa674dd1 | Python | 2,395 | 71 | """ Summary
This script is somewhat the same as the 3_postprocess_data.py script,
with the only exception that the decision whether a paper must be removed
is solely based on the author.
If the 4_seperate_authors.py script found that it is likely that multiple
authors (persons) are associated with the same name, the au... |
9320f8dc3a642db7cdb15b03e9c5f0abeb1d8530cb6d21e4560d4d5ef2654871 | Python | 2,396 | 72 | # 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... |
36189cc2375dc864fae37052b0e9fb80279b591c05e127973d5e04f40c42b6bb | Python | 2,399 | 64 | from os.path import isdir, join
from os import mkdir
from preprocess import PreProcessor
from keras.layers import GRU
from models.RNN import RNN
import itertools
def RNN_args():
""" Get GNN model and hyperparameters """
train_args = dict(layers=3, recurrent_layer=GRU, bidirect=False,
... |
6ba800147f645d8a925359901bfb9fc2a18d15a9571515154d0b3b5119b1914e | Python | 2,399 | 72 | from anndata._core.anndata import AnnData
from pandas.core.frame import DataFrame
import pytest
import pandas as pd
import scanpy as sc
from anndata import AnnData
import numpy as np
from palantir.utils import (
run_density,
run_low_density_variability,
run_density_evaluation,
)
@pytest.fixture
def mock_... |
ce0532dbc55d0a2d0a5901784af5c2467a7d009049d28ac04cae2ac6c70c8625 | Python | 2,399 | 70 | """
run cmd
"""
import os, argparse, subprocess, re
def run_cmd(args):
# input
cmd = args.cmd
projectdir = args.projectdir
# subject
if args.subject:
subjects = args.subject
else:
subjects = [sub.replace("sub-", "") for sub in os.listdir(os.path.join(projectdir, 'data', 'b... |
fc1b7903a93a8793981c243b14cb6f2d3b6566518cd6217e10cca9a00b0d9bda | Python | 2,399 | 75 | # Copyright (c) ONNX Project Contributors
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import numpy as np
from onnx.reference.ops._op import OpRun
def _slice(
data: np.ndarray,
starts: np.ndarray,
ends: np.ndarray,
axes: np.ndarray | None = None,
steps: np.ndarray | ... |
0fd49c14929fd5533d3262b547c6b65117e39e4a4ea6ddf80c79b5fc42954cbe | Python | 2,400 | 70 | # 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 STFT(Base):
@staticmethod
def export() -> None:
signal... |
67eba35084099bffaaa90bfcd3ef3d5dbf484540293fe77be1216b3fe75efef0 | Python | 2,400 | 38 | from sklearn.metrics import precision_score, recall_score, f1_score, confusion_matrix
import numpy as np
# input gold labels and pred labels
# display prec,rec,F1 and confusion matrix
# also return the prec,rec,F1
def get_and_display_results(y_true, y_pred, report_confusion_mat = False):
prec, rec, f1 = pre... |
9aa3f94da1e4d62419a1b52c6a0c214a6a96b9fc5cf2680bf7d9c13b0a822be9 | Python | 2,401 | 70 | # 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... |
dd8bd4766c825eb46da0dc339a3758a8f1397b714507ece06169b99ac21b220a | Python | 2,402 | 59 | # copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
"""Clone plugin for preserving pretrained state in estimators."""
from copy import deepcopy
from skbase.base._clone_plugins import BaseCloner, _default_clone
class _PretrainedCloner(BaseCloner):
"""Clone plugin that preserves pretrained sta... |
436428cb60b4ed27034ad31b1c6f5651b6fde72b847b34ed462d674a0bf8e115 | Python | 2,403 | 68 | import unittest
from pathlib import Path
import pytest
from pyontutils.utils import get_working_dir
from pyontutils.config import auth
from pyontutils.integration_test_helper import _TestScriptsBase, Folders, Repo
import neurondm
class TestScripts(Folders, _TestScriptsBase):
""" woo! """
only = tuple()
lasts =... |
114f550824f34d444bbab26f5d91780494b61cfc46ea203a1ef6450034a9df95 | Python | 2,404 | 72 | from flair.data import Sentence
from flair.datasets import ClassificationCorpus
from flair.models import TARSClassifier
from flair.trainers import ModelTrainer
def test_init_tars_and_switch(tasks_base_path):
# test corpus
corpus = ClassificationCorpus(tasks_base_path / "imdb")
# create a TARS classifier
... |
ae7fa106888aea76161d6b9ffe3c9378fc9175fa5be99914ce8c455e9e0fa069 | Python | 2,406 | 58 | import torch.nn.functional as F
import torch.nn as nn
from Sublayers import FeedForward, MultiHeadAttention, Norm
import sys
import importlib
config_path = ".".join(["models", sys.argv[1]]) + "." if len(sys.argv) >= 2 else ""
attention_setting = importlib.import_module(config_path+"attention_setting")
class EncoderLa... |
482eb8626876fe3d1483b7435bed2fb66b4e15229fa1ddb14c9bef243493d335 | Python | 2,410 | 75 | """Implementation of the NetworkX libraries for pyRDTP
"""
import networkx as nx
import matplotlib.pyplot as plt
def generate(mol, voronoi=False):
"""Generate a graph using the given molecule, the connectivity between the
atoms of the molecule is needed in order to create the graph.
Args:
mol (ob... |
f8170018aac2ee0f9c5419565f07f7c0ceff0249c3423bf141a8e893f36c8d0b | Python | 2,410 | 81 | """evaluate_cloud_cover.py"""
"""
Author: Yimin Yang
Last revision date: Jan 18, 2022
Function: Run this to evaluate the trained model
Ref: https://github.com/HansBambel/SmaAt-UNet
"""
import torch
from torch import nn
import numpy as np
import os
import pickle
from tqdm import tqdm
def compute_loss(model, test_dl, ... |
10e4e68347bee1d4a893152f6826f17fd56d0deab2b717c4ff1290ac6993d7c2 | Python | 2,411 | 71 | # 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... |
98ba5fc0914fd27bcfd109590f06c8e4eae3bc9427f5eee7f49d6d32be06b640 | Python | 2,411 | 73 | #!/usr/bin/env python
from __future__ import print_function
import sys,os
import re
import argparse
import logging
import functools
import gzip
import pandas as pd
desc = 'Combine ref genomes in MG sample'
epi = """DESCRIPTION:
Just combining ref genomes selected to be included in the simulated metagenome sample
"""
p... |
42ebbfce74371cf1ae5878ee74483db56601ced9564ef311ed097d4092fe42bd | Python | 2,412 | 90 | # 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... |
04d7f3a1a53e1feea17f974199416d34bc70fd1ba051a326b64ea26fbfd169f0 | Python | 2,413 | 72 | # 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... |
27be99ec3f345dbd0280732fb944236682edc68222ce77f150c3c0342e108abc | Python | 2,413 | 73 | # -*- 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 ... |
b68cf7d07a5172081d2cb2cf85eaeb9a67b53eee0927175b340a24f8cf8a812b | Python | 2,413 | 77 | import copy
import json
import numbers
import os
from datetime import datetime
import numpy as np
import yaml
def ensure_dir(file_path):
directory = os.path.dirname(file_path)
if not os.path.exists(directory):
os.makedirs(directory, exist_ok=True)
def with_base_config(base_config, extra_config):
... |
f6a2432140476d5379eda034800cc589883a3daa4b470cb22d68457430acbc3d | Python | 2,413 | 73 | # -*- 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/.
#
import logging
import os
from ..interfaces imp... |
a0d58a7e4cf314991e22120096af02e337dc33767d5d80ccd0552c0958515570 | Python | 2,414 | 68 | # 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... |
c8ceb58848856e4c56d5a00c87e57a108f602fee7acf4d0f4f4f6e40dcfecb87 | Python | 2,414 | 86 | import numpy as np
from brian2 import *
# import matplotlib.pyplot as plt
import time
import pickle
import brian2cuda
set_device("cuda_standalone", build_on_run=False)
"""
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
NEURON AND SYNAPSE DEFINI... |
af831ec25bd6688e9e355e19cf8e112b105ad112db44126dbe2dfb5bf27f5cae | Python | 2,415 | 67 | from collections import defaultdict
from ilxutils.interlex_sql import IlxSql
from ilxutils.mydifflib import ratio
from ilxutils.tools import open_pickle, create_pickle
import os
import pandas as pd
from pathlib import Path
from sys import exit
sql = IlxSql(db_url=os.environ.get('SCICRUNCH_DB_URL_PRODUCTION'))
data = ... |
a72b7182715657651693baeff133765513d868e95cc7a4264311a53b7dead991 | Python | 2,416 | 81 | import unittest
import rdflib
from neurondm.core import (Config,
LabelMaker,
Phenotype,
NegPhenotype,
Neuron,
LogicalPhenotype,
AND,
... |
1d2ac5bcc081a1ddae49a7808041047faaa8e531f42192585161fe0462e50a39 | Python | 2,420 | 97 | import numpy as np
import cv2
import sys
from time import time
import kcftracker
selectingObject = False
initTracking = False
onTracking = False
ix, iy, cx, cy = -1, -1, -1, -1
w, h = 0, 0
inteval = 1
duration = 0.01
# mouse callback function
def draw_boundingbox(event, x, y, flags, param):
global selectingObject... |
0d7a587cd7ec8cc2594f3ee25d2972f008673a44f9885317d2b7869dc4e73d73 | Python | 2,421 | 66 | # 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... |
d082b4fc3a55ad471a995f4fc37bf13e02d0663eb1682620f823b2b787156438 | Python | 2,422 | 50 |
#=======================================================================================================================
# 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... |
951f40195b368e70727913046183d6def2b00b8d08462e30240fa333da839df0 | Python | 2,424 | 77 | import dolfin as df
import os
# set path to solver
from ffian import flow_model, zero_flow_model
from plotter import Plotter
def run_model(model_v, j_in, Tstop, stim_start, stim_end, stim_protocol):
"""
Arguments:
model_v (str): model version
j_in (float): constant input in input zone (mol/(m... |
dc21eb04c1665f2d34fadc7dd19b3ab57dd8ceee0bd7a7c17932c57a88cee3b7 | Python | 2,424 | 82 | # Copyright 2007 Zachary Pincus
# This file is part of CellTool.
#
# CellTool is free software; you can redistribute it and/or modify
# it under the terms of version 2 of the GNU General Public License as
# published by the Free Software Foundation.
import traceback
import sys
from celltool.utility import warn_tools
i... |
067c6ac323f722515dfe59f736600706cfecc662b1f0f6c145c1be1ba73ba689 | Python | 2,425 | 65 | import joblib
import contextlib
from rdkit import rdBase
class without_rdkit_log: # https://github.com/rdkit/rdkit/issues/2320
"""Context manager to disable RDKit logs. By default all logs are disabled."""
def __init__(
self,
mute_errors: bool = True,
mute_warning: bool = True,
... |
cb3b7df800cfec86e49c29fef5f131125eac345e5543797173233a3d0ca7ee24 | Python | 2,426 | 55 | import face_recognition
import cv2
# This code finds all faces in a list of images using the CNN model.
#
# This demo is for the _special case_ when you need to find faces in LOTS of images very quickly and all the images
# are the exact same size. This is common in video processing applications where you have lots of... |
66a0e1e864062c1db0021c8377c2ae0b03444ac3805801e119cae3b52ad8f46f | Python | 2,427 | 82 | # small RetinaNet
num_classes=3
# model settings
model = dict(
type='RetinaNet',
backbone=dict(
type='ResNet',
depth=50,
num_stages=4,
out_indices=(0, 1, 2, 3),
frozen_stages=1,
norm_cfg=dict(type='BN', requires_grad=True),
norm_eval=True,
style='... |
7ac42637542a03e5724178be92a24ba20b234de3c0d43dc68c5a0a71f4f5bb7c | Python | 2,427 | 81 | import matplotlib as mpl
import seaborn as sns
preset_themes = {}
preset_themes["light_edge"] = {
"axes.spines.right": False,
"axes.spines.top": False,
"axes.spines.left": True,
"axes.spines.bottom": True,
"axes.edgecolor": "lightgrey",
"ytick.color": "grey",
"xtick.color": "grey",
"ax... |
210fe054c012a3d8a83eaf57aff8931a291a0faf6486d2a82a474b24c90456c1 | Python | 2,428 | 55 | #!/usr/bin/env python2
# -*- coding: utf-8 -*-
#
# (C) Copyright 2015 Frankfurt Institute for Advanced Studies
# (C) Copyright 2016 Max-Planck Institute for Brain Research
#
# Author: Philipp Huelsdunk <huelsdunk@fias.uni-frankfurt.de>
#
# Redistribution and use in source and binary forms, with or without
# modificat... |
aa733d37728b1ee5d758f96cee3a280a63a2be994fb9f911f4b1a36379f826be | Python | 2,428 | 89 | """Unit tests for the BaseCatalogue class."""
__author__ = ["jgyasu"]
import pytest
from sktime.catalogues.base import BaseCatalogue
class DummyCatalogue(BaseCatalogue):
"""Minimal subclass for testing BaseCatalogue behavior."""
def _get(self):
"""Return dummy catalogue contents."""
return... |
be31c9b05213d7ef55fa0611e2a48cda2e3f1f8cf99164f679706ae94aa0a28a | Python | 2,429 | 51 | # 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... |
170958cf67a949b786c22cd863fe189c5c3ed79054c95ea43bd8b4cf882324eb | Python | 2,430 | 63 | # 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... |
37f5a779c0e3867aa399300dd4a59c99478e1f684d18e149846dde48e1436809 | Python | 2,430 | 65 | # 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 numpy as np
import pytest
import pandas as pd
from ampligraph.datasets i... |
1cfde7417f0663b054df827a244a273bdc1cd5e297dbc33a1af47a269830ec10 | Python | 2,431 | 71 | # Copyright (c) OpenMMLab. All rights reserved.
import argparse
import mmcv
from mmcv import Config, DictAction
from mmcls.datasets import build_dataset
def parse_args():
parser = argparse.ArgumentParser(description='Evaluate metric of the '
'results saved in pkl format')
... |
c2bdd90212becf6d67092afa097e306621180356761f40dc7c1278b62583d7dc | Python | 2,431 | 68 | # 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... |
03f10ad0e2e2511ef2217b6d65c376e07f2bba2af7fa79cec5cf85e89e4dd47d | Python | 2,432 | 97 | # Expose base classses
from flair.embeddings.transformer import (
TransformerEmbeddings,
TransformerJitDocumentEmbeddings,
TransformerJitWordEmbeddings,
TransformerOnnxDocumentEmbeddings,
TransformerOnnxWordEmbeddings,
)
from .base import Embeddings, ScalarMix
# Expose document embedding classes
f... |
bf61766f537ac874f8a4be0d193bd92ecd91c92cdf22a2cf480a369cb87346a7 | Python | 2,432 | 65 | import argparse
import biom
import pandas as pd
import numpy as np
import xarray as xr
from q2_differential._model import SingleDESeq2
from birdman.model_util import concatenate_inferences
from birdman import ModelIterator
import time
import logging
import subprocess, os
import tempfile
from multiprocessing import Pool... |
49926264fa82fcc82f5c918dda83b2dc95b67347260d5106ed68b326779c3578 | Python | 2,436 | 78 | # Copyright (c) ONNX Project Contributors
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import json
import os
import onnx.backend.test.case.node
from onnx.backend.test.case.test_case import TestCase
from onnx.backend.test.case.utils import import_recursive
DATA_DIR = os.path.join(
os.... |
233c84fe3ff3fcb34aa20672d0e9cbec041d8f8cedbe0ee11794ed24965896e8 | Python | 2,437 | 78 | # 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... |
40a4a22c2fea53c772363194dd2cef360fb6d70ab1d76c21982d3971cb914995 | Python | 2,437 | 49 | import numpy as np
import pandas as pd
# findPathCoM(pathLUT, AtlasToPathLUT, NetworkDataGeneral['NetworkDataGeneral'][0,0]['Schaefer400x7']['CoM'][0, 0])
def findPathCoM(pathLUT, AtlasToPathLUT, AtlasCoM):
"""Function to find the Center of Mass for Pathology Regions in Atlas
Args:
pathLUT (Dataframe)... |
67f331b1e431612f0c93c11e945b6ddb9bdcb1da956b892fe83c379b48b0ea28 | Python | 2,437 | 73 | import numpy as np
from scipy import ndimage
def create_hypersphere_shape(radius, n_dim=3):
"""
Create an ND binary array with a hyperspherical shape.
Parameters
----------
radius : int
The radius of the hypersphere.
n_dim : int
The number of dimensions. Default is 3.
Ret... |
6a5bc99517aae7efa2cca97788a11f9e82e4aa8da5467b4049550f150924eb3b | Python | 2,437 | 89 | """Module exports: data type definitions, checks, validation, fixtures, converters."""
from sktime.datatypes._check import (
check_is_error_msg,
check_is_mtype,
check_is_scitype,
check_raise,
mtype,
scitype,
)
from sktime.datatypes._convert import convert, convert_to
from sktime.datatypes._exam... |
3f67df42894e3dc7061a3aedd575888e56a7b8929c05e6b64acac743264bd12b | Python | 2,438 | 74 | # -*- 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 ... |
3090474870a389dcb9f97db46e35567606e0ead43961779af2c37f14d97d5f6d | Python | 2,439 | 69 | # Copyright (c) OpenMMLab. All rights reserved.
import os.path as osp
import xml.etree.ElementTree as ET
import mmcv
import numpy as np
from .builder import DATASETS
from .multi_label import MultiLabelDataset
@DATASETS.register_module()
class VOC(MultiLabelDataset):
"""`Pascal VOC <http://host.robots.ox.ac.uk/p... |
34a3f2a5daebe07181d5ec8da0b7891e5832db0bb79763376363f678bb0c1377 | Python | 2,439 | 58 | """ Short Summary
This script merges the training and testdata of the Reuters 50/50 dataset. This
is required to try a different train/test split (e.g. 90/10) for comparison with
other works from the literature.
The output is written to dataset-reuters/
"""
import os
import numpy as np
def concatenateFiles(fname):
... |
f516b26777460ddd4a7075ad483b207b72f20c400fd7e9ce776bd7c219728371 | Python | 2,440 | 71 | #!/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/.
#
import argparse
import s... |
55ae283fbae5edd4b645ea584bcca4da7ae9c6e74d5fce135b9b379dfe2291eb | Python | 2,441 | 60 | # 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... |
a5675bf3f70713dfb48b3cd58b78d56a2e66a2f3b37f5fd30ee9aa2e425e3ec3 | Python | 2,443 | 67 | from __future__ import print_function
from os.path import splitext
from parameterSetup import ParameterSetup
import numpy as np
import json
class SDFilter(object):
def __init__(self):
params = ParameterSetup()
pickledDir = params.pickledDir
self.fileIDs_L = []
try:
sd_t... |
6c8f36a22617632f92f7ec18735de0ca89753a376e3bd505f97168ca6790e7cf | Python | 2,445 | 52 | import numpy as np
import os
import sys
from tqdm import tqdm
import torch
from atom3d.util.transforms import prot_graph_transform, mol_graph_transform
from atom3d.datasets import LMDBDataset
from torch_geometric.data import Data, Dataset, DataLoader
import atom3d.util.graph as gr
class GNNTransformLBA(object):
... |
b93ca7bdde55054093aea0b43488ed90700a5af46324e0c59bd987039c69ab6e | Python | 2,445 | 67 | # 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... |
0fa789074551d13297aeda0b3fd05d8b903768524c782b73faa1b378d3987baa | Python | 2,446 | 80 | # SPDX-License-Identifier: LGPL-3.0-or-later
import deepmd.tf2.descriptor as _tf2_descriptor # noqa: F401
import deepmd.tf2.fitting.fitting as _tf2_fitting # noqa: F401
import deepmd.tf2.utils.exclude_mask as _tf2_exclude_mask # noqa: F401
from deepmd.dpmodel.atomic_model.dp_atomic_model import DPAtomicModel as DPAt... |
be83bd1cf9f16891fc40f12d0e2fed2190da01d7778380226a11e67b594f2360 | Python | 2,446 | 76 | import numpy as np
import torch
import pandas as pd
import scipy
def check_species_dict(species_dict):
assert "name" in species_dict, "name is missing from dictionary"
assert "column" in species_dict, "column is missing from dictionary"
def update_weights_focal(true, preds, n_classes, weight):
acc_dict ... |
9144badc7bc2e82e2a269afcd950f63ef0cd145517087273b638d2b815f862cd | Python | 2,447 | 73 | # 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... |
b8b70571001945c7562aacc52dc7a4b20ac1f595cba1eb28039461a4d61f5305 | Python | 2,449 | 66 | # 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... |
8189f68b09b3767efed2784c63a7e22fc4e87103d3d385bb016665aaea5a1f47 | Python | 2,450 | 77 | import timeit
# Note: This example is only tested with Python 3 (not Python 2)
# This is a very simple benchmark to give you an idea of how fast each step of face recognition will run on your system.
# Notice that face detection gets very slow at large image sizes. So you might consider running face detection on a
# ... |
6a960d90277067d701ef8390c41a24d0799f997a7b97a9e23092fc0b75ee2153 | Python | 2,451 | 81 | # 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... |
ab9f283af54760c50261ff72f48d32af43c933e71cf5fac06b501a72e729044c | Python | 2,451 | 79 | import os
import dill
import json
from typing import List
from torch_geometric.data import HeteroData
from molucn.utils.utils import read_list_targets
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import DataStructs
import numpy as np
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem im... |
78f4d584f6ba91096b56667e3503edba6a1ebbd3044669527406daf47712454d | Python | 2,452 | 82 | # -*- coding: utf-8 -*-
# Configuration file for the Sphinx documentation builder.
#
# For the full list of built-in configuration values, see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Project information -----------------------------------------------------
# https://www.... |
cf2013f2af2aebd650234469cf446c63a19da150ec3e1ef9b1c844e798f787fb | Python | 2,452 | 68 | # 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 Greater(Base):
@staticmethod
def export() -> None:
nod... |
f2e8ee389badf8748c03518b9124ae6c6dc8393868f961f69d82048254f855b9 | Python | 2,452 | 77 | # 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... |
6c7c10daf6decc8bd0bd789033f83a2e25cf8f3184c0803f93bb1458eef797de | Python | 2,453 | 89 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Jul 5 15:30:40 2019
@author: reiters
"""
import cv2
import numpy as np
import moving_least_squares
import os.path
import h5py
import matplotlib.pyplot as plt
import pandas as pd
import glob
import time
def norm(data):
with np.errstate(invali... |
9f8df21bcdb26a6e1a4137e0741c402a410d6890598d93c48fb2b96ef55c7879 | Python | 2,453 | 65 | from typing import Union
import time
import pytest
import siibra
from siibra.core.structure import BrainStructure
from siibra.core.space import Space
from siibra.features.image.image import Image
all_image_features = [f for ft in siibra.features.Feature._SUBCLASSES[siibra.features.image.image.Image] for f in ft._get_... |
98090b6b94b8f81e963eaa8619ef19b9f90cf2c275cd605768d5578c7cc5f7ff | Python | 2,454 | 68 | import torch
from torch.utils.data import Dataset
import os
import pickle
import numpy as np
import networkx as nx
import dgl
from collections import Counter
class RetroCenterDatasets(Dataset):
def __init__(self, root, data_split):
self.root = root
self.data_split = data_split
self.data_... |
716567e7295191830d20fbdea54a870a07a103f6908f3423e545e705d108eeb1 | Python | 2,461 | 83 |
import numpy as np
import pandas as pd
import pytest
from numpy.testing import assert_array_equal
from seaborn._core.groupby import GroupBy
from seaborn._stats.order import Perc
class Fixtures:
@pytest.fixture
def df(self, rng):
return pd.DataFrame(dict(x="", y=rng.normal(size=30)))
def get_g... |
a987b36df037840cdc39025cfa22d4579617b99c245369e9eaa50ec3f4284efd | Python | 2,461 | 88 | """NIfTI format conversion and image creation utilities."""
import os
from pathlib import Path
from typing import Optional, Sequence, Tuple, Union
import numpy as np
import nibabel as nib
from bcblib.imaging._types import NiftiLike
from bcblib.imaging.io import load_nifti
# ----------------------------------------... |
f9ba3b5cbb21bb8d8fbc3d67615826c2782016ccbaad115a84ac7ba8bbeafb83 | Python | 2,463 | 86 | from sklearn import cluster
from scipy.spatial import distance
import sklearn.datasets
import matplotlib.pyplot as plt
import numpy as np
def compute_bic(kmeans,X):
"""
FROM: https://stats.stackexchange.com/questions/90769/using-bic-to-estimate-the-number-of-k-in-kmeans?utm_medium=organic&utm_source=goog... |
c1f9377a3ec5bbfcbdbdad3cb0304095d3809d09835a8f20665d0174b73c0e6c | Python | 2,466 | 81 | import numpy as np
import h5py
import os
from mvsec_fcns import *
from joblib import Parallel, delayed
def get_events_flow_mask(idx):
# Events
ts = timestamps[idx]
beg_time = ts - nframes * dt
frame_seq = np.zeros((2, nframes, H, W))
for f in range(nframes):
event_window = events[(event... |
cb17ab2b1fa0db592dc5f5d59b2f5f56ddb66c203fae9d88991b18df080b9b79 | Python | 2,466 | 84 | # 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... |
977bfa227a81051db664582e2b7aecc123802b59b55a439a8fb4851e6206386d | Python | 2,467 | 82 | # Copyright (c) ONNX Project Contributors
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
from onnx.reference.ops.aionnx_preview_training._op_run_training import OpRunTraining
def _apply_momentum(r, t, x, g, v, norm_coefficient, alpha, beta):
# Add gradient of regularization term.
g... |
729435c6f9314bbcabdc1133f56680f5bb2be16efc09d0145247710e4cfb9cc3 | Python | 2,468 | 72 | # \author Hans J. Johnson
# This file will help store new data
# in a publicly available web location
# for the purpose of allowing larger
# testing data to be separate from
# the source tree.
#
# NOTE: This is not a global solution
# for any developer. Only members
# of the Iowa PINC lab have access
# ... |
86568fe87c6f5f161d1ae0cde5f80f39d76a2209dfba007dddc5243dc7cd7607 | Python | 2,468 | 72 | from pathlib import Path
import numpy as np
from asreview.review.factory import get_reviewer
from asreview.data import ASReviewData
data_fp = Path("tests", "demo_data", "generic_labels.csv")
def test_init_seed():
base_start_idx = None
n_test = 4
seeds = np.random.randint(0, 2**63, 5)
for _ in rang... |
ac6a0f0fb6700292d93066d88e5ca2b88854752b3aef9a28b72afc0eb3009b48 | Python | 2,469 | 57 | #------------------------------------------------------------------------------
# elftools tests
#
# Seva Alekseyev (sevaa@sprynet.com)
# This code is in the public domain
#
# Making sure the two ways of iterating through DIEs (linear and by tree)
# return an identically built tree (parents, children, terminators).
#
#... |
56c44d595de9c944af0768c646655bdb59e1e34f19d99878c1dc8a6c8cd957bc | Python | 2,472 | 62 | # 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... |
98c37d2ecb61681095202f2eda5ecbe3c5b5915cc6edc440cb36894a7458632c | Python | 2,473 | 75 | #!/usr/bin/env python3
import csv
import pickle
from os.path import expanduser
import requests
from pyontutils.utils import chunk_list
try:
breakpoint
except NameError:
from IPython import embed as breakpoint
def main():
with open('nlx_properties', 'rt') as f:
properties = [l.strip() for l in f.r... |
c83728bac245ffbf0c074e052c54c8a154d806fdf3fa866adedfe22879ebb0b4 | Python | 2,473 | 73 | # 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 functools import partial
import tensorflow as tf
def LP_regularizer(tr... |
04194652b1e7cea19630c84b034374ef3e6fda530d8c6757f5976e8033d1429c | Python | 2,474 | 64 | # tifffile/examples/issues125.py
"""Create a fsspec ReferenceFileSystem for a sequence of TIFF files on S3
This Python script uses the tifffile and fsspec libraries to create a
multiscale ReferenceFileSystem JSON file for a sequence of cloud optimized
GeoTIFF (COG) files stored on S3. The tiles of the COG files are u... |
1a86aab7b89ac6b4f0197c33ad8a23b360b969501e94abbda7b26c05e06d37f0 | Python | 2,477 | 49 | # 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... |
08f6eef364dde8dd2ddbc18d0803178e5de94f0b103f19570939447687ced008 | Python | 2,478 | 78 | # In these examples we demonstrate how different templates
import numpy as np
import netplotbrain
import pandas as pd
import matplotlib.pyplot as plt
np.random.seed(2021)
n = 10 # number of nodes
m = 20 # number of edges
# Different tepmlates have different coordinate systems.
# We generate the same type of data ... |
cddedd63354ceeec3b9c58503dbb3548fb6544901ce346c0bbf9c9bc49830916 | Python | 2,478 | 76 | import random
import pdb
import re
import numpy as np
import torch
from torch.utils.data.dataset import Dataset
class TISDataset(Dataset):
def read_dna_file(self, file_location, class_id):
current_file = open(file_location)
dna_list = []
for line in current_file:
stripped_lin... |
d130b960b669360ab7273ebf06d95587256b90cde6a1ae73ce65fc55de799f78 | Python | 2,478 | 77 | # 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... |
6d2ab8241156be14122f124c4c83c521c22f1c40405c0d21b3155d20653a3889 | Python | 2,480 | 60 | # 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... |
c2a5717e77fd714d54f913d612f73923924fdb41da1d712ed50e82e999c6627f | Python | 2,482 | 76 | # 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 Or(Base):
@staticmethod
def export() -> None:
node = o... |
65b7ca00a5726e6049054d1085ff90adc06d084178dda0d49e2e86c3f1adc4cb | Python | 2,483 | 87 |
"""
Metric class for model server
"""
import time
import socket
from collections import OrderedDict
from builtins import str
from ts.metrics.unit import Units
MetricUnit = Units()
class Metric(object):
"""
Class for generating metrics and printing it to stdout of the worker
"""
def __init__(self... |
b6a6330c465053edc3f5429114504a8d9090b74d4225c89b49503ebf9914a0d7 | Python | 2,483 | 68 | import dolfin as df
from .model_base import ModelBase
class Model(ModelBase):
""" Model setup with input zone in the middle of the domain. """
def __init__(self, model_v, mesh, L, t_PDE, j_in_const, stim_start, stim_end, stim_protocol='constant'):
ModelBase.__init__(self, model_v, mesh, L, t_PDE)
... |
142e8a431eb67ad073e510427e4c201b325b942990944b1a9bc3ffaefbf28a92 | Python | 2,485 | 69 | # 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
#
# ... |
c0a8d597f07025313cdfc241d15109c8b6eea64ed742df15efbaaf1bbd54a04c | Python | 2,488 | 48 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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://w... |
4d5a3670e7b70e61e6fdfb4eb3321c95e807c2ce0a5dfc92101771fe16182347 | Python | 2,489 | 99 | """ProbabilityThresholdEarlyClassifier test code."""
import numpy as np
import pytest
from numpy import testing
from sktime.classification.early_classification import (
ProbabilityThresholdEarlyClassifier,
)
from sktime.classification.interval_based import TimeSeriesForestClassifier
from sktime.datasets import lo... |
447d6ea90921cceaacdf99229d530213260c7031562315e24793ee55699adeaf | Python | 2,490 | 75 | import logging
from typing import Union
import numpy as np
import torch
from torch.utils.data import Dataset
class JetMomentaDataset(Dataset):
"""
PyTorch dataset for GNN autoencoder.
"""
def __init__(
self,
data: Union[torch.Tensor, np.ndarray],
vec_dims: int = 3,
p... |
74f3aca0cbabbcf1b92fef0d004bded7452452635269b6a629f474a83863f521 | Python | 2,490 | 89 | import numpy as np
def make_pulse(stim):
"""
Generate a pulse train for current / voltage command. Returns a tuple.
Parameters
----------
stim : dict
Holds parameters that determine stimulus shape:
* delay : time before first pulse
* Sfreq : frequency of ... |
f782720b9e107b080317a86e23199a12d30e677b0a3178197c3db814e6296ce6 | Python | 2,492 | 64 | import qiime2
import numpy as np
import pandas as pd
import arviz as az
from q2_matchmaker._matching import _matchmaker
from typing import List
from q2_matchmaker._stan import _case_control_data
from q2_matchmaker._stan import _case_control_full
def negative_binomial_case_control(
table: pd.DataFrame,
... |
3f1678f039661542a252604c48f43ae59ca42bd9861c220485d71cf9e25eb7a3 | Python | 2,494 | 84 | import pandas as pd
import numpy as np
import yaml
from types import SimpleNamespace
def generate_data(std_flag):
"""
Generate data for the toy task
Parameters
- std_flag: when the flag is one, data will be standardized
Returns
- (traindata,trainfdata,trainldata): train dataset (his... |
5f1e9ae7f8b929d8df4c0ca918da23e6d3604002fc5aa54c406645d06d8f6d55 | Python | 2,495 | 93 | # 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
#
# ... |
be0b294793e64186ccb35aa94c800185ef3d49a0c9a8d1a36eaba77cd11aabf7 | Python | 2,495 | 65 | # 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... |
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