sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
50a683a731d12ca2b7248f9c4c77fa1993ec6af5874f15d5ee78a9fb5f248ad9 | Python | 8,356 | 246 | import tensorflow as tf
import numpy as np
from tensorflow.python.framework import ops
from tensorflow.python.training import moving_averages
def _create_variable(name, shape, initializer):
var = tf.compat.v1.get_variable(name, shape, initializer=initializer)
return var
def variable_with_weight_decay(name,... |
e963dc446914b0b8c15e2de22773c4fe9bb6ffa4e45d10a5fef0e722d1a7b462 | Python | 8,358 | 233 | # Copyright (c) Open-MMLab. All rights reserved.
import io
import os.path as osp
from pathlib import Path
import cv2
import numpy as np
from cv2 import IMREAD_COLOR, IMREAD_GRAYSCALE, IMREAD_UNCHANGED
from mmcv.utils import check_file_exist, is_str, mkdir_or_exist
try:
from turbojpeg import TJCS_RGB, TJPF_BGR, T... |
7e447354208977e301880c2cf6f0daa9c348a37ad61ce1d4fd5161f794b15fbd | Python | 8,360 | 158 | """Environment maps for CARLA's sky light (`world.set_sky_light_map`).
CARLA panorama convention (what the server expects)
---------------------------------------------------
Equirectangular, CARLA world frame (Unreal: X forward, Y right, Z up, left-handed), float32 linear RGB,
shape (H, W, 3), row 0 = zenith:
co... |
6e30d298a1fa548ac016f482d2c3f324a296b835579c654315ce8dd28cbb22f3 | Python | 8,361 | 200 | import os
import time
from datetime import datetime
import cv2
import torch
import numpy as np
import torch.backends.cudnn as cudnn
import torch.nn as nn
import torchvision.transforms.functional as TF
from loguru import logger
from torch.utils import tensorboard
from tqdm import tqdm
from utils.helpers import dir_exist... |
ce77566bdb0d4927ccab7447f72b18793ab7b769870d3b22aca9d06f6aa0d19a | Python | 8,363 | 191 | import os
import sys
import json
import datetime
import pandas as pd
import numpy as np
import math
def check_if_highlighted(s, threshold):
if s == -1:
return "<td style='color:red;'> Prediction Error </td>\n"
elif s == -2:
return "<td> Plan Mis-Match </td>\n"
elif s == -3:
return "... |
0deede0828419ac8cc9fd750b73b846baa4ec74bbcae11162a2e805c97417dfa | Python | 8,364 | 265 | # Copyright 2020 Google Research. 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 applicable law... |
5f87ad1df886f7e8a2712da562e9250a6e684e8ed05772bbca8cb377ba3794ac | Python | 8,364 | 192 | import sys
import os
from multiprocessing import Pool
import math
import argparse
import copy
import itertools
from Logger import Logger
from util import print_table, files_in_dir
from SummaryCreator import SummaryCreator
from ArticleDataSample import ArticleDataSample
from HmmArticle import HmmArticle, HmmArticleConf... |
fc5d3f00b7b041ca3ee89f0fa0ee18fdf082388461c3dccd0d32c4a1341f38af | Python | 8,364 | 191 | # Copyright 2020 Huawei Technologies Co., Ltd
#
# 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 agreed to... |
4d6338451ead30ce530ec03adc557cb0fcc8476b2b77c5daae0fa3d4fadee6da | Python | 8,365 | 233 | __author__ = "Jianfeng Sun"
__version__ = "v1.0"
__copyright__ = "Copyright 2023"
__license__ = "GPL v3.0"
__email__ = "jianfeng.sunmt@gmail.com"
__maintainer__ = "Jianfeng Sun"
from typing import Dict, List
import numpy as np
import pandas as pd
from tmkit.chain.Collate import Collate
from tmkit.db.construct.Networ... |
feb6dc2f50ed8300b9e6fcc71c9efba1ad3798a8cba3caf534ac2304b86c4218 | Python | 8,368 | 197 | '''
collection of chemisorption models.
newns_anderson:
'''
import torch
import numpy as np
class Chemisorption:
def __init__(self, model_name, **kwargs):
# Initialize the class
if model_name == 'gnn':
self.model_num_input = 1
if model_name == 'newns_anderson_semi':
... |
81f36688819c2d1277ad186aebe9bf368182f3db10a62ea998bffd0cf73e8c92 | Python | 8,372 | 170 | #!/usr/bin/env python
#######################################################################
#######################################################################
## Created on June 29th 2018 to annotate merged peaks
#######################################################################
###########################... |
ee19a2711844d5b21736ff588ec59f2f70cd8986540ffa913c14768a9df88b16 | Python | 8,373 | 222 | """
Description:
This script is used to compile the DeepSEA dataset of 919 genomic
features.
Usage:
process_chromatin_profiles.py <features>
<ENCODE-DNase> <ENCODE-TF> <Roadmap>
<output-dir>
process_chromatin_profiles.py -h | --help
Options:
... |
ebc069061efa5bb4716f7623a55938fa10b3981872105e46bb68b82a93c38304 | Python | 8,376 | 210 | # Copyright 2022 Huawei Technologies Co., Ltd
#
# 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 agreed to... |
4c264f9228549fc0d59a8748542bc9bd706576f2c68d0c269d5aa4d7bd645a7e | Python | 8,378 | 209 | import os, tqdm
import ipdb
import argparse, sys; sys.path.append('../..')
import random as rand
import numpy as np
import torch
from metrics import graph_exp_cf_fairness, graph_exp_group_fairness
from graphxai.explainers import *
from graphxai.datasets import load_ShapeGGen
from graphxai.datasets.shape_graph import S... |
9b4d86c51423e4d90a3b207d14dc2d798e420df0c2574f16dc1eff44b16390d1 | Python | 8,379 | 244 | '''
ANN model trained on the PB embeddings
'''
# libraries
import pandas as pd
import numpy as np
from sklearn import preprocessing
import math
import pickle
import tensorflow as tf
from tensorflow.keras.models import Model, load_model
from tensorflow.keras import optimizers, regularizers
from tensorflow.keras.layer... |
cebbf3596c959671ae85d9343fcc69b4e9125c3aa4b6753889505ccddd1157d9 | Python | 8,379 | 251 | # Copyright 2020 Google Research. 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 applicable law... |
904bf9a49500ef00690fdf91737e5dd43b2ab11c38236f658ccfca926e96cc3d | Python | 8,383 | 297 | #!/usr/bin/env python3
"""
Utils functions for phys2cvr.
Attributes
----------
LGR :
Logger
"""
import datetime
import logging
import os
import sys
from pathlib import Path
import numpy as np
LGR = logging.getLogger(__name__)
LGR.setLevel(logging.INFO)
def if_declared_force_type(var, dtype, varname='an input ... |
8c565e8e702d95837e1e142092a196eb833f9858ba7a471cc16be6d359f695f6 | Python | 8,385 | 177 | # Copyright (c) 2016, Konstantinos Kamnitsas
# All rights reserved.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the BSD license. See the accompanying LICENSE file
# or read the terms at https://opensource.org/licenses/BSD-3-Clause.
from __future__ import absolute_im... |
c72c8880de60098692028156d45eaf7701abcb15198941fe8e3c12d6c42903d8 | Python | 8,388 | 254 | # -*- coding: utf-8 -*-
"""
Created on Tue Nov 7 21:51:03 2023
@author: H.Yokoyama
"""
fdir = __file__
from IPython import get_ipython
from copy import deepcopy, copy
get_ipython().magic('reset -sf')
#get_ipython().magic('cls')
import os
current_path = os.path.dirname(__file__)
os.chdir(current_path)
current_p... |
12ed5a945135ced0a590fc9633fe692fd759cc4550b438884b17af752a8988de | Python | 8,389 | 200 | """Targeted point adding attack."""
import os
from tqdm import tqdm
import argparse
import numpy as np
import torch
import torch.backends.cudnn as cudnn
import torch.distributed as dist
from torch.utils.data import DataLoader
from torch.utils.data.distributed import DistributedSampler
from torch.nn.parallel import Di... |
8efc2132db45ee1bb672cc3eff60e356d18bd09c2eee63aa3d7bb3c076cc2bca | Python | 8,390 | 211 | #!/usr/bin/env python3
"""
File: find_opposite_effects.py
Created: 2020/10/22
Last Changed:
Author: M.Vochteloo
Copyright (C) 2020 M.Vochteloo
This program 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... |
c6a22739aa72397dba88bfd22cc2511e0e7e66fcbeb927694e809968675a7990 | Python | 8,390 | 152 | import pandas as pd
import inspect
import os
import numpy as np
import tqdm
import AIS_parameters
import AIS_description
import AIS_geopandas_tagging
import AIS_interp
import datetime
import functions_basic_sak as funsak
fname = os.path.split(inspect.getfile(inspect.currentframe()))[1]
def get_df_old( d... |
15c21bcf43368b5f7907e2dbcceecb35aa7ff5d50b340dc9c5948c6c060d0536 | Python | 8,392 | 242 | """
Some classes to pre-process big connectivity data and speed up the processing.
"""
import numpy as np
import pandas as pd
import numba
import collections
class PresortedGroupBy:
"""using a connections dataframe directly is very costly if you want to do lots of groupby operations
specially for big-ish... |
87c21e4e6471083fbd3abe8b96c8fd0fb46d0bc489622ee182599eba2729a232 | Python | 8,395 | 215 | # Copyright 2021 Huawei Technologies Co., Ltd
#
# 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 agreed to... |
d5d7a2d95bde3120b71dbd38bd531836c2fe506c82c00c8d945ef869717e3ec3 | Python | 8,397 | 161 | import os, sys
import shutil
import matplotlib.pyplot as plt
currentdir = os.path.dirname(os.path.realpath(__file__))
parentdir = os.path.dirname(currentdir)
sys.path.append(parentdir) # PYTHON > 3.3 does not allow relative referencing
import tensorflow as tf
# tf.enable_eager_execution(config=config)
import nump... |
1d0a75aeb9e52cce36dbc43fa29187db9c1961cbcaf20d2915fd329d97b1307b | Python | 8,400 | 209 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
"""Centralized catalog of paths."""
import os
class DatasetCatalog(object):
DATA_DIR = "datasets"
DATASETS = {
"panoptic_train": {
"img_dir": "coco/train2017",
"target_root": "coco/annotations/panoptic_tra... |
61dae5b40c82549928e8e7141e715857b90d06c89c623cda8a47268200dae7bf | Python | 8,401 | 149 | import os
import graph_nets as gn
import numpy as np
import sonnet as snt
import tensorflow as tf
from GraphBuilder import GraphBuilder
def mila(x, beta=-1):
return x * tf.math.tanh(tf.math.softplus(beta + x))
class IPA(tf.keras.Model):
def __init__(self, cutoff=10.0, l1=0.0, l2=0.0, activation=mila, num_... |
cf9b421b13c2730fa5bf7e760572c068cda31d99ba9a0938fcf2ac98a3f381cf | Python | 8,402 | 209 | """
==========================
AFQ with HCP data
==========================
This example demonstrates how to use the AFQ API to analyze HCP data.
For this example to run properly, you will need to gain access to the HCP data.
This can be done by following this instructions on the webpage
`here <https://wiki.humanconnec... |
bd11876cddae315c9a6d38a3378a5915febc8fe56e3abecdfbb848687de5ff63 | Python | 8,403 | 211 | #!/usr/bin/env python3
"""
File: find_opposite_effects.py
Created: 2020/10/22
Last Changed: 2022/02/10
Author: M.Vochteloo
Copyright (C) 2020 M.Vochteloo
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Fr... |
3af8a21f074190b391b4bdde37f017f62bdad70c7834da1e68ec5148bb7b6650 | Python | 8,410 | 246 | # libraries
import pandas as pd
import numpy as np
from sklearn import preprocessing
import math
import pickle
import tensorflow as tf
from tensorflow.keras.models import Model, load_model
from tensorflow.keras import optimizers, regularizers
from tensorflow.keras.layers import Dense, Dropout, BatchNormalization, Con... |
bb20b2df5296029448be0e499f22c9e0cc5940ebb2168dca772ac3b78de5f986 | Python | 8,411 | 172 | from validate import test
from pathlib import Path
from .heatmap_eval import BaseXAIevaluator
from .heatmap_utlis import postprocess_heatmaps, heatmap_to_binary
import numpy as np
import logging
import pickle, os, glob
import csv
from sklearn.metrics import jaccard_score
from tqdm import tqdm
def tumorsyn_get_test_perf... |
122893bce8b64caf74816b37afe3157f638f0b6b6f8553a1488227ffa420809d | Python | 8,412 | 221 | # Copyright 2021 Huawei Technologies Co., Ltd
#
# 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 a... |
1a9fb4afd3e2e2fef95176a1bb20b520343a41c3dc3e20cbf23eca396988aee7 | Python | 8,414 | 243 | #!/usr/bin/env python3
"""
File: create_decon_upsetplot.py
Created: 2020/11/24
Last Changed:
Author: M.Vochteloo
Copyright (C) 2020 M.Vochteloo
This program 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... |
3898cc9005083f09cf7ed71a736b1ceecc61264da9e711e05edfcaf76f23e5aa | Python | 8,415 | 214 | from __future__ import print_function
# --------------------------------------------------------
# Fast R-CNN
# Copyright (c) 2015 Microsoft
# Licensed under The MIT License [see LICENSE for details]
# Written by Ross Girshick
# --------------------------------------------------------
import datasets
import datasets.i... |
46a5b25c5653caa93b2cdfcb6b546ab1ce93472aedd3320938f14ad4b8cf1ac8 | Python | 8,418 | 200 | import itertools
from scipy import stats
from .motif_counts import *
def intersection1d(lst1, lst2):
return list(set(lst1) & set(lst2))
def get_cnr_stats(g_):
g = g_.to_undirected()
cn_counts = np.zeros(10)
scn_counts = np.zeros(10)
pcn_counts = np.zeros(10)
ccn_counts = np.zeros(10)
... |
28f55cfdc57bb5c917108568f0415cf96ff6f520e646821fff67d08a5d96e5ec | Python | 8,423 | 195 | # Copyright 2022 Huawei Technologies Co., Ltd
#
# 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 agreed to... |
ec019616a0c7f2db1de89075dacaf04ecced80538df06a0877086cae5724b169 | Python | 8,426 | 222 | import sys
import autograd.numpy as anp
from autograd import elementwise_grad, jacobian
from autograd.scipy import stats
from alive_progress import alive_bar
# Lower constraint
def _lower_constraint(lower):
def fun(x):
return lower + anp.exp(x)
return fun
# Interval constraint
def _interval_constraint... |
39c2e2098dc6392e2140f66b7181cf37825600faafa220e4d4197d9796513004 | Python | 8,428 | 184 | import numpy as np
import pandas as pd
import scanpy as sc
# import bbknn
import os
import pickle
import sys
MARKER = "/home/rkawaguc/ipython/BICCN/script/Catactor/analysis/191219_meta/rank_analysis/190214_all_data_three_types/marker_name_list.csv"
def read_markers():
df = pd.read_csv(MARKER)
markers = [x.spl... |
384a41a15c9d6dcfefa3dc47142f3310f7d50a7b41f0f983873b4e4d4b23e491 | Python | 8,434 | 232 | '''
Author: Naiyuan liu
Github: https://github.com/NNNNAI
Date: 2021-11-23 16:55:48
LastEditors: Naiyuan liu
LastEditTime: 2021-11-24 16:58:06
Description:
'''
"""
Copyright (C) 2019 NVIDIA Corporation. All rights reserved.
Licensed under the CC BY-NC-SA 4.0 license (https://creativecommons.org/licenses/by-nc-sa/4.0/... |
6f0b5fc9ffcdd10b7b7979b72a9b73cff216a42d92363894aea83b7540e5ccc5 | Python | 8,434 | 208 | """Configuration objects for CROPro."""
from __future__ import annotations
from dataclasses import asdict, dataclass
from pathlib import Path
from typing import Any, Literal
CropMethod = Literal["center", "random", "stride"]
PatientStatus = Literal["negative", "positive", "unknown"]
SequenceType = Literal["T2W", "bp... |
e46f668240d1be8695ea9998490d75cd4f22ade268847532e3124171ca0d2e43 | Python | 8,434 | 292 | import os
import pickle
import argparse
import warnings
import pandas as pd
from grr.Tools import gagProcess
# PARSE COMMANDLINE ARGUMENTS
parser = argparse.ArgumentParser()
parser.add_argument(
'experiments', type=str, help='Pickled list of Experiment objects'
)
parser.add_argument(
'models',
type=str... |
bcf44cac31e6132c958fa4d6e5345f0d44b5482b12c74a11be3467ee63b8c480 | Python | 8,436 | 234 | import pandas as pd
import numpy as np
import networkx as nx
from networkx.algorithms import bipartite
import itertools
from functools import reduce
from networkx.utils import py_random_state
def grow_bipartite_random(ntarg, p, numspines):
# p : probability of adding a new input edge
G = nx.MultiDiGraph() # mu... |
eda41eacc758a2cd5ea94601af72ce3c6b8ccf42012cc384c0b565bae6290891 | Python | 8,438 | 264 | # coding=utf-8
# Copyright 2020 The Google Research Authors.
#
# 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 applicab... |
9f16bab81dae5618bc5cada9abbbb581986cc4d251dbadf75e8097b0f6d60775 | Python | 8,444 | 241 | import random
import numpy as np
import torch
from torch.utils.data import TensorDataset
def generate_recog_data(T=2000, d=50, R=1, P=0.5, interleave=True, multiRep=False, xDataVals='+-', softLabels=False):
"""Generates "image recognition dataset" sequence of (x,y) tuples.
x[t] is a d-dimensi... |
a5b1d30bd60eef5759aee6459d47c63c96ea908f7150b0d5dc8d166385755618 | Python | 8,444 | 221 | import numpy as np
import os
import matplotlib.pyplot as plt
import matplotlib.animation as animation
from sklearn.manifold import TSNE
from tqdm import tqdm
from scripts import dl_utils
# Sentinel 2 band descriptions
band_descriptions = {
'B1': 'Aerosols, 442nm',
'B2': 'Blue, 492nm',
'B3': 'Green, 559nm',... |
1651e1973844924fbbc5d2ce100dcb6985532ecdf67f02adefff80555f1a3b8f | Python | 8,445 | 199 | #!/usr/bin/env python
import time
from copy import deepcopy
import numpy as np
import torch
from drugex import DEFAULT_DEVICE, DEFAULT_GPUS, utils
from drugex.logs import logger
from drugex.training.explorers.interfaces import Explorer
from drugex.training.generators.utils import unique
from drugex.training.monitors i... |
29eb980b04b9f893245a7d64dc6634d832e5eb319888ff736ca85c81a34e6ccd | Python | 8,447 | 282 | from typing import Any
import numpy as np
from scipy.signal import convolve2d
from skimage.morphology import square
from skimage.feature import peak_local_max
from scipy.ndimage import convolve1d
from dask_image.ndfilters import percentile_filter
import pandas as pd
from math import factorial
import warnings
import log... |
602873a95c4c7707d25f02aa11db96a2500197a773c10252f7ca1ddbb367915f | Python | 8,455 | 357 | # %% [markdown]
# ##
import os
import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from matplotlib.patches import Circle
from mpl_toolkits.axes_grid1 import make_axes_locatable
from mpl_toolkits.mplot3d.art3d import Poly3DCollection
from scipy.integrate... |
15f02111a38ef367ecebceff0011396225c56293068bfc09a8a675fdbbd66397 | Python | 8,458 | 273 | # Auto generated from value_set_configuration.yaml by pythongen.py version: 0.9.0
# Generation date: 2022-11-27T17:19:16
# Schema: value-set-configuration
#
# id: https://w3id.org/linkml/value-set-configuration
# description: A datamodel for configuring value sets and value set expabsions
# license: https://creativecom... |
807b85398436a6c90e67519ec59803f15c10f1391e9b1a1a636d57e4266f1715 | Python | 8,461 | 159 | # Copyright 2021 Huawei Technologies Co., Ltd
#
# 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 agreed to... |
fb1c6a7e0cfb76ca90b7ab4095ca6c39b52ef727c1e68566d6b0670374f4220c | Python | 8,461 | 206 | # Copyright 2022 Huawei Technologies Co., Ltd
#
# 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 agreed to... |
df7496603d9055cdbeb1d24dfafef6fbaf8f250b83e13670d82ef959bd36c30c | Python | 8,462 | 187 | """Structural tests for the skill library and the MCP surface.
These guard the invariants a published package must not break: every skill is
discoverable, its frontmatter is complete, its group matches where it lives, its
in-repo links resolve, and its scripts parse. Run with `pytest -q`.
Deliberately no CARLA/UE4 re... |
34d6745d8fdd8b9ed3014584f9e8080f7a8c3f8b2b62ca626007969eb2b3674d | Python | 8,465 | 212 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Variational Animal Motion Embedding 0.1 Toolbox
© K. Luxem & P. Bauer, Department of Cellular Neuroscience
Leibniz Institute for Neurobiology, Magdeburg, Germany
https://github.com/LINCellularNeuroscience/VAME
Licensed under GNU General Public License v3.0
"""
import... |
77dfc293c3d7ee51550ab5b4d2c9020eb62908b0f724f2dc4aebbf1458854aee | Python | 8,466 | 209 | #!/usr/bin/env python3
# Copyright 2017 Chun Chieh Chang
# 2017 Ashish Arora
# 2017 Yiwen Shao
# 2018 Hossein Hadian
# 2018 Desh Raj
""" This script converts images to Kaldi-format feature matrices. The input to
this script is the path to a dat... |
f254eb1272f2f519e00a5dfa1d1d42ef852d161d0f8c918cfa2c627e38d56579 | Python | 8,466 | 166 | r"""
Custom integrators to use with polychrom
----------------------------------------
Here, we develop Brownian integrators capable of integrating the overdamped Langevin equation for a polymer driven by
correlated active forces. The forces can vary in magnitude along the chain, such that each monomer has a different... |
a0310dffb18acc5f3fdb4d0cd138c2e6a5e0832b858e763264d84e10d4eef40a | Python | 8,471 | 195 | # Copyright 2022 Huawei Technologies Co., Ltd
#
# 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 agreed to... |
073efba7d2256c5896ee415ac9ef1b9031e2263a3d818e97c4f85f3e74f0219f | Python | 8,473 | 286 | import re
import math
import pandas as pd
import numpy as np
# _/_/_/ Basic Functions _/_/_/
class CONFIG:
img_out_dir = './'
log_out_fname = img_out_dir + 'plotlog.txt'
summary = {}
category_name = 'ctgry_border'
def set_out_dir(filepath='./'):
CONFIG.img_out_dir = filepath
CONFIG.log_out... |
1ca94d317f860bb4c0f4c426460a8ed5b7b703b8d0fa9be6e6f463c44eafa4ee | Python | 8,477 | 212 | """
Vowel Cooling: Format data for analysis / plotting
Here we do some general housekeeping to get the columns into a common format,
create columns to make the statistics in R more straightforward and bring
together some columns containing redundant information.
We also filter the data for conditions such as correc... |
8e0318b18f26eb536198b666fa3487fa16c95bdc84ac6a876f8064f07079e3ea | Python | 8,477 | 193 | #!/usr/bin/env python3
"""Prove an imported walker really works, on a running CARLA server.
python3 verify_walker.py --id 0053
python3 verify_walker.py --id 0053 --keep # leave it walking
Assets on disk prove nothing, and neither does a factory entry: a walker whose
SkeletalMesh failed to load still LISTS... |
b428bd267e5e9119913039a259a1d7d22ce38671f9af3b4ccd69081d30cc088e | Python | 8,477 | 110 | """Prepare the CC BY Tesla 2018 Model 3 candidate for fidelity review (Blender).
Source: Ameer Studio, Sketchfab 5ef9b845aaf44203b6d04e2c677e444f.
Source retrieved from the public Objaverse collection; attribution retained.
This is a derived asset, not a model authored from scratch.
"""
import bpy,bmesh,math,json
from ... |
ab656dc4ccfd07e1e6bf945124c0ef2c97f706e4b29b80b80b8e0cd9f8393008 | Python | 8,481 | 276 | import matplotlib as mpl
import numpy as np
import seaborn as sns
from matplotlib.colors import ListedColormap
from matplotlib.patheffects import Normal, Stroke
from matplotlib.transforms import Bbox
import matplotlib.pyplot as plt
from matplotlib.collections import LineCollection
def shrink_axis(ax, scale=0.7, shift... |
964af97cd0bec25a7385301131c8630e80c36427884cf1abb8d2a8204e1da8e8 | Python | 8,482 | 234 | #!/usr/bin/env python3
"""
File: filter_interaction_eqtls.py
Created: 2020/09/25
Last Changed: 2020/09/29
Author: M.Vochteloo
Copyright (C) 2020 M.Vochteloo
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the ... |
ba405822cadee98801a4e0f475419cceff6088e11eab2089d76c748c99b45552 | Python | 8,484 | 165 | # Copyright 2020 Huawei Technologies Co., Ltd
#
# 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 agreed to... |
e766bfe56a4c1e20a19044c930dcf89016d82bbf49c04c8b2683abb302b4d796 | Python | 8,484 | 234 | #!/usr/bin/env python3
"""
File: filter_interaction_eqtls.py
Created: 2020/09/25
Last Changed: 2022/02/10
Author: M.Vochteloo
Copyright (C) 2020 M.Vochteloo
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the ... |
759f691ab13a19a2697669510f317e8a510e560be1b59e515e4023bbc877f939 | Python | 8,490 | 248 | # Copyright 2021 Huawei Technologies Co., Ltd
#
# 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 agreed to... |
dd85fcfa49aeeccbc589af576b1c33d222577cee8788a48e5d503dc957c7aff0 | Python | 8,494 | 213 | #!/usr/bin/env python3
"""
File: correlate_expression_profiles.py
Created: 2021/10/19
Last Changed:
Author: M.Vochteloo
Copyright (C) 2020 M.Vochteloo
This program 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 ... |
a8daf0f765368b00a0dd0a1cf53c05e4bc37bbbba7f906968ef5f12f609e6129 | Python | 8,496 | 198 | """Public API/CLI regressions for #810 (part of #757)."""
import json
from pathlib import Path
import struct
import subprocess
import sys
import pytest
from conftest import macs3_env, no_core_dumps
from test_Parser_bam_truncation import write_bam
HEADER = (b'BAM\1' + struct.pack('<ii', 0, 1) + struct.pack('<i', 5)... |
82ed6fc74176ba6143d22f3eb80c771e2e23c3abd2caf3ddf7717a1bba853261 | Python | 8,499 | 209 | import os
from os.path import join
import collections
import numpy as np
import pandas as pd
from itertools import chain
from sklearn.model_selection import train_test_split
from sklearn.impute import SimpleImputer, MissingIndicator
from sklearn.pipeline import make_union, Pipeline
from sklearn.ensemble import RandomF... |
4ff0aba62a54c86b99deebcf44f00df8cf1dcbb7d6f0d9688f7ba62eaf32c634 | Python | 8,501 | 323 | """
https://stackoverflow.com/questions/67456368/pytorch-getting-runtimeerror-found-dtype-double-but-expected-float
"""
import pandas as pd
import numpy as np
# Libraries
import torch
import torch.nn as nn
import torch.nn.functional as F
from skorch import NeuralNet
from torch.utils.data import DataLoader
from sk... |
abe462295430cc40da34d81fe11825350efa61451276ea5c917d48f7a0bc339e | Python | 8,501 | 212 | import os
from os.path import join
import collections
import numpy as np
import pandas as pd
from itertools import chain
from sklearn.model_selection import train_test_split
from sklearn.impute import SimpleImputer, MissingIndicator
from sklearn.pipeline import make_union, Pipeline
from sklearn.ensemble import RandomF... |
b3760dc7182bc56e768a29d02299581f1ace37625a351cc0175b2ff7e7272dbf | Python | 8,501 | 220 | import logging
import time
from dataclasses import dataclass
from typing import Any, Dict, Iterable, Iterator, List, Optional
import requests_cache
from oaklib.datamodels import obograph
from oaklib.datamodels.association import Association, NegatedAssociation, PropertyValue
from oaklib.datamodels.search import Searc... |
f31114640d5e5cd53fa43df3a1cdaae92ea24f4505538838fb1efe3856e6e22f | Python | 8,501 | 183 | # basic imports
import os
import numpy as np
import pickle
import pyqtgraph as qg
# framework imports
from cobel.agents.sfma import SFMAAgent
from cobel.interfaces.gridworld import InterfaceGridworld
from cobel.analysis.rl_monitoring.rl_performance_monitors import RewardMonitor, EscapeLatencyMonitor
from cobel.misc.gri... |
64532e272f2a8d8b597942f2f105596c8ab6444c822698fbd81936f2cbb5e9f1 | Python | 8,510 | 348 | # %% [markdown]
# ##
import os
import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from mpl_toolkits.mplot3d.art3d import Poly3DCollection
from scipy.integrate import tplquad
from scipy.stats import gaussian_kde
import pymaid
from src.data import load... |
155f45ac18ca7d082042d8f43c05663ea965c7c7914a25e68828baf61c6dd8f7 | Python | 8,511 | 338 | # %% [markdown]
# #
import os
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from sklearn.manifold import TSNE
from sklearn.model_selection import ParameterGrid
from tqdm import tqdm
from graspy.embed import AdjacencySpectralEmbed, selectSVD, OmnibusEmbed
from graspy.util... |
01f6d6851c90fa2f8f78138f1abae693a55f6d517c20c79dfffbbbcc732a9bda | Python | 8,512 | 337 | import numpy as np
_,ar,_,_,_=np.random.get_state()
seed=1528155142#ar[1] #1669768389 #3519291485 #2147483648 #22506088 #2413843216 #2311804307 #1200295143 #2032192475 Best: 10(1528155142, 3978893405) 2147483648
np.random.seed(seed)
import tensorflow as tf
tf.random.set_seed(seed)
import torch.nn.functional as fn
imp... |
500b59973197b48aca64170a30e7ae5c1aa8ba0cb207e6fdd6f36cf0dab38f22 | Python | 8,513 | 239 | import os
import shutil
import pickle
import torch
import numpy as np
import scipy
from scipy import stats
import pandas as pd
class ContModelScore:
def __init__(self, best_epoch_indx, spearman_corr, pearson_corr):
self.best_epoch_indx = best_epoch_indx
self.spearman_corr = spearman_corr
se... |
e8ba6a698f235b4bb1081a1907dac6c62c57d9822176809c825b9cd3514a1c2c | Python | 8,514 | 230 | import spacy
import os
import glob
import gzip
import pickle
import random
import collections
import tensorflow as tf
import struct
import six
import numbers
import re
from itertools import chain
random.seed(200)
CHUNK_SIZE = 2000
VOCAB_SIZE = 50000
dm_single_close_quote = u'\u2019' # unicode
dm_double_close_quote... |
a528b1a2d67199c64ea9233731e82863916023cb9b9c5690ecb97a96dfcb4b13 | Python | 8,515 | 212 | import os
from os.path import join
import collections
import numpy as np
import pandas as pd
from itertools import chain
from sklearn.model_selection import train_test_split
from sklearn.impute import SimpleImputer, MissingIndicator
from sklearn.pipeline import make_union, Pipeline
from sklearn.ensemble import RandomF... |
af3f2458f0d730375b9666d22bcfa555beade57f3523ede39da28146a962fb39 | Python | 8,515 | 166 | # Copyright 2020-2021 Huawei Technologies Co., Ltd
#
# 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 agre... |
db723f59b02541b5c59e0832caa37ec15d70e16a74903b054c4d20195bab3393 | Python | 8,518 | 264 | import argparse
import yaml
from model.dataloader import TripletData
from model.model import PairModel, TripletModel, TripletGraphModel
import os
import torch.utils.data as Data
import torch
import random
import numpy as np
import pandas as pd
from tqdm import tqdm
def build_dataset(cfg, train=1):
if train == 1:... |
23464d4deaf9a7d28af1b2dd96dd18fbb5b2ffc10913857c614cee96837dfec9 | Python | 8,519 | 189 | import os, sys
currentdir = os.path.dirname(os.path.realpath(__file__))
parentdir = os.path.dirname(currentdir)
sys.path.append(parentdir) # PYTHON > 3.3 does not allow relative referencing
PYCHARM_EXEC = os.getenv('PYCHARM_EXEC') == 'True'
import tensorflow.keras.layers as kl
import tensorflow.keras.backend as K
i... |
d6b5e2ab5154703fa62674b50dbbbaf2e99d0e05fa2abd154699ebc6b2541c7b | Python | 8,524 | 239 | # Copyright 2020-2022 Huawei Technologies Co., Ltd
#
# 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 agre... |
28993acf3681f2e76b59738b2a71bc9a7724077edcdaaf654612e71449bde7dc | Python | 8,525 | 265 | # Copyright 2022 Huawei Technologies Co., Ltd
#
# 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 agreed to... |
fc54eebbf82924d012fc5130742868056734db47b898aa59fd81603e27f38d68 | Python | 8,532 | 213 | """
This file is called by routine which creates mesh from nested dictionaries (convert.py).
"""
import numpy as np
import mesh.orient as orient
import mesh.triangulate2D as tri
from mesh.shapes.Regions2D import RefinementCircle, RefinementMany
def triangulate_sides(width,
coords_upper, coords_l... |
497662414ec112c506388f683cee658dbd734d2233772e49d38c6961bd85da08 | Python | 8,535 | 165 | import os
import sys
import json
import time
import pydicom
import datetime
import pandas as pd
from dicom_scp_class import Retriever_SCP
from dicom_scu_class import Retriever_SCU
def inspect_regs(day):
infofile = "setup_information.json"
f = open(infofile)
info = json.load(f)
f.close()
tx_ct_file... |
c4e6a4e2fada055aeb25d2a3c21c85a8ae51c0d41006b093a9141ab290aee5c0 | Python | 8,539 | 214 | # Copyright 2020-2022 Huawei Technologies Co., Ltd
#
# 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 agre... |
3be1c3bd07028b29794515f32f698bd03851c8c8b48767955472435aa78b970f | Python | 8,541 | 207 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
"""Centralized catalog of paths."""
import os
class DatasetCatalog(object):
DATA_DIR = "datasets"
DATASETS = {
"coco_2017_train": {
"img_dir": "coco/train2017",
"ann_file": "coco/annotations/instances_trai... |
9e711fa71163521a3a0acfcff612cd77243fec7bf8f53c9c66f4d984c59730a1 | Python | 8,541 | 180 | #%%
from pymaid_creds import url, name, password, token
from data_settings import pairs_path, data_date_A1_brain
import pymaid
import numpy as np
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
from datetime import date
from contools import Promat, Celltype, Celltype_Analyzer
# allows text t... |
c89a40e63d341141405fb827abf16bf9480da56b20646c2625637519b1d3a01f | Python | 8,542 | 240 | from keras.models import Sequential
from keras.layers import Dense, Conv2D, Flatten, Reshape, Input, Dropout, UpSampling2D, MaxPooling2D, Conv1D
from keras.losses import mse
from tensorflow.keras.optimizers import Adam
from tensorflow.keras import backend as K
import tensorflow as tf
import keras
import tensorfl... |
de928a77d992ba90788b6e8f208705b81676a4e2bb19091625fc46599dd7cdf9 | Python | 8,543 | 213 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
import torch
import torch.nn.functional as F
from torch import nn
class FPN(nn.Module):
"""
Module that adds FPN on top of a list of feature maps.
The feature maps are currently supposed to be in increasing depth
order, and must b... |
0314e8f295ac0624390ec88aaff335bbe1b47336e285ccc83f0e16822c8c2354 | Python | 8,546 | 164 | import argparse
import os
import subprocess
import moxing as mox
_CACHE_DATA_URL = "./cache/data"
_CACHE_TRAIN_URL = "./cache/train"
def _parse_args():
parser = argparse.ArgumentParser('mindspore maskrcnn_mobilenetv1 training')
parser.add_argument('--train_url', type=str, default='obs://neu-base/maskrcnn_1/m... |
2de30661340f4bedcd117377edb66dd8f067b0fb1b86dc164b1b8ff9137b9183 | Python | 8,548 | 244 | """Test queries to the parliament open data API."""
from typing import Callable
from unittest.mock import MagicMock
import pytest
from pytest_mock.plugin import MockerFixture # type: ignore
from fi_parliament_tools.parsing.query import Query
from fi_parliament_tools.parsing.query import SessionQuery
from fi_parliame... |
7b3cfccda075387460cdd45b218bd9df51798d1a12cb341fb5a63e439de1c4c7 | Python | 8,550 | 237 | # This script is used to calculate seasonal cycle for SMAP SM and SMOS TB data
# input files: smap_smos_overlap_3dm.pkl, smos_3dm.pkl
# output files: smap_smos_overlap_3dm_seas_c.pkl, smap_smos_overlap_3dm_seas_c_no_std.pkl, smos_3dm_seas_c.pkl, smos_3dm_seas_c_no_std.pkl, sm_seas_cycle.pkl
import pandas as pd
imp... |
6c8a75dea59469bdb7af394690df00c285296d4defea1983a24a89d26918b851 | Python | 8,555 | 148 | import os, time, json, sys, gc
import numpy as np
import nltk, pandas
import torch
from scipy.sparse import csr_matrix, lil_matrix, save_npz, load_npz
from torch_geometric.data import Data, DataLoader, GraphSAINTRandomWalkSampler, GraphSAINTNodeSampler, GraphSAINTEdgeSampler
from torch_geometric.data.cluster import Clu... |
c10689f5a90fbae4702920c2aa5c61f444c66940046d64ffe8528950f5e26722 | Python | 8,562 | 235 | # Copyright 2022 Huawei Technologies Co., Ltd
#
# 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 a... |
5f285811b22bd3dac7d6668c198c43354f7bbe3849c6f7a1711b89122d0758be | Python | 8,564 | 245 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
import numpy as np
from numpy.testing import assert_array_equal, assert_allclose
import pytest
from scipy import signal
from eelbrain import (
NDVar, Case, Scalar, UTS, datasets,
concatenate, convolve, correlation_coefficient, cross_correlation,
cwt_... |
763e34976e7b2e4d8352b67907bf28e46dfc101197291d515a9674ab409fccd5 | Python | 8,566 | 261 | import abc
import re
from copy import deepcopy
import numpy as np
from .SpikingModel import SpikingModel
from .Filter import constructMedianFilter
from . import Tools
class ThresholdModel(SpikingModel):
"""
Abstract class to define a threshold model.
A threshold model is a model that explicitly describ... |
c87178e55e3f3d1e33158f6b484ac5d16bc1c84f4b3f689a62cffbec81068aab | Python | 8,566 | 193 | # Copyright 2020-2021 Huawei Technologies Co., Ltd
#
# 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 agre... |
f7c5b762c972e10c8844e32c36aed8b5c63bc02a509f7ea9f6d1a550fad738d0 | Python | 8,573 | 208 | ####################################################################################################
# Copyright (c) 2019 - 2021, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of VessMorphoVis <https://github.com/BlueBrain/VessMorphoVis>
#
# This program is free ... |
0f8d5a720f388288b9cacc00c021118d6515ef764be81dfaf6d2d367904aba8c | Python | 8,574 | 192 | """
A randomly sampling batch sequence object
Performs class-balanced sampling across uniformly randomly selected SleepStudy objects.
"""
import logging
import numpy as np
from utime.sequences import BatchSequence
logger = logging.getLogger(__name__)
class BalancedRandomBatchSequence(BatchSequence):
"""
Bat... |
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