sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
622419c4d53f249fb6a46ef75dd656023291ac2d526b2e26bc736d67db9da077 | Python | 4,694 | 174 | #%%
import pymaid
import matplotlib.pyplot as plt
import numpy as np
import seaborn as sns
from scipy.ndimage import gaussian_filter1d
from src.data import load_maggot_graph, load_palette
from src.io import savefig
from src.visualization import adjplot, set_theme
set_theme(font_scale=1.25)
def stashfig(name, **kws):... |
74f213376d1d38b8003688700e04dd54077e0ddbfa7c5bb6b5657d4b050850a5 | Python | 4,696 | 125 | import torch
import torch.nn as nn
import torch.nn.functional as F
from mmcv.cnn import CONV_LAYERS, ConvAWS2d, constant_init
from mmcv.ops.deform_conv import deform_conv2d
@CONV_LAYERS.register_module(name='SAC')
class SAConv2d(ConvAWS2d):
"""SAC (Switchable Atrous Convolution)
This is an implementation of... |
1bf3b3700b62ad5a224cd2b2e81189ff0db6522b94739f66b44f019ac71ddeea | Python | 4,697 | 155 | """
interfaces
Created by: Martin Sicho
On: 26.04.22, 13:12
"""
from abc import ABC, abstractmethod
from drugex.logs import logger
from drugex.molecules.interfaces import MolSupplier
class Vocabulary(ABC):
"""
Definition of the vocabulary interface. All vocabularies contain "words" that are used for encodin... |
4692f6d3f04fa5031f0fb6e977a88097c2f0feeaf0a26fbb9f11b18a692348eb | Python | 4,697 | 127 | # -*- coding: utf-8 -*-
'''
@author: Mahbub Ul Alam (mahbub@dsv.su.se)
@version: 1.0+
@copyright: Copyright (c) Mahbub Ul Alam (mahbub@dsv.su.se)
@license : MIT License
'''
import torch.nn as nn
import torch
from torch.nn.utils.rnn import pack_padded_sequence, pad_packed_sequence
import numpy as np
class RNN_LSTM(nn... |
edd5e53429f160939015ef2ab19d1883d1cef09eb5cfa74b0b123371b166abd6 | Python | 4,698 | 136 | # This script is part of navis (http://www.github.com/schlegelp/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# 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 Foundation, either version 3 of... |
011b80c8eeb4a82adb3c833394f8ba1172b369e90d1bf61112a163f8dc387ff9 | Python | 4,700 | 166 | import statistics
import numpy as np
import os
import json
def load_config():
config_file = os.path.abspath(os.path.join(os.curdir, 'config2.json'))
with open(config_file, 'r', ) as config_file:
config_string = config_file.read()
return json.loads(config_string)
def solve(graph, labels):
"... |
992030763b02d1f406830188c16f6466265c60aa820825cc9bc81cd7e9990900 | Python | 4,700 | 105 | import os
import argparse
import torch
import torch.nn.functional as F
import torch.optim as optim
from network.resEGNN import resEGNN_with_ne
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='Predict model quality and output numpy array format.')
parser.add_argument('--train', type=st... |
3f5150aab51fd883470fbd67063491abb4b20077ff950c61ea727bdac7e0930a | Python | 4,701 | 141 | from typing import Dict, Iterable, List, Tuple
from oaklib.datamodels.vocabulary import IS_A, PART_OF
from oaklib.interfaces.obograph_interface import OboGraphInterface
from oaklib.types import CURIE, PRED_CURIE, SUBSET_CURIE
from oaklib.utilities.semsim.similarity_utils import (
ListPair,
compute_all_pairs,
... |
515ef1adacb953b26e65c4f68933204becae4e5f14af1cee722c3d107b1b797e | Python | 4,701 | 160 | '''
Make a big figure of all selected fits
'''
from brian2 import *
import os
from pylab import *
import matplotlib.pyplot as plt
import yaml
from scipy.signal import butter, sosfilt
from file_management import *
from plotting import *
import pandas as pd
from os.path import join, splitext, split
from fitting import *
... |
52abd8c0ccdfce63d5be3996c5d14c2916487ccda5879560b4d3ede6d5f0b4dd | Python | 4,701 | 127 | # -*- coding: utf-8 -*-
'''
@author: Mahbub Ul Alam (mahbub@dsv.su.se)
@version: 1.0+
@copyright: Copyright (c) Mahbub Ul Alam (mahbub@dsv.su.se)
@license : MIT License
'''
import torch.nn as nn
import torch
from torch.nn.utils.rnn import pack_padded_sequence, pad_packed_sequence
import numpy as np
class RNN_LSTM(nn... |
400bf47e62f7efc8b9ccc177dd7ce0c72258958938f61b4ffe19af241d121b1b | Python | 4,702 | 133 | """
Copyright (c) 2019, National Institute of Informatics
All rights reserved.
Author: Huy H. Nguyen
-----------------------------------------------------
Script for testing classification of ClassNSeg (the proposed method)
"""
import os
import torch
import numpy as np
import torch.utils.data
import torchvision.datase... |
6cd237fa94d40348c74c5ebb31cb787425fe2ac6bf3700b04cbafc19a7976978 | Python | 4,702 | 123 | # -*- coding: utf-8 -*-
"""Utility functions to download files."""
import os
import hashlib
import zipfile
import tarfile
import requests
from tqdm.auto import tqdm
CHUNKSIZE = 1048576 # 1 MB
RETRIES = 3
def download_file(url, out_path, extract_out_path=None, byte_size=None, sha256sum=None, progress=True, callb... |
dae2c048a875decc90b18dbf60331eb6ea62b1214e654acf371fc022a918367d | Python | 4,702 | 132 | # 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... |
3908226c43385067c43790a5d6a688b849efbc60d3aa742df290323dafa9613d | Python | 4,703 | 124 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
"""Configure Eelbrain"""
from multiprocessing import cpu_count
import os
from matplotlib.colors import to_rgb
SUPPRESS_WARNINGS = True
CONFIG = {
'n_workers': cpu_count(),
'eelbrain': True,
'autorun': None,
'show': True,
'format': 'svg',
... |
68fcec0e0692a770720ac8c7ab56b15d54c8d56940a7ffdbe5ef409071cdfbf5 | Python | 4,703 | 130 | # 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... |
781d17a8fa244a29b5682cf2d1ff1dd3e70de9391ec9c64341cd4effae6fa1b8 | Python | 4,704 | 125 | # This script is part of navis (http://www.github.com/schlegelp/navis).
# but has been adapted from vispy (http://www.vispy.org)
#
# 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 Foundation, ... |
95b4ef8fb4323bd6afafefb0c83532523336e0f43b9a4625ba5bdc61b6019450 | Python | 4,707 | 122 | """IGCV3"""
import torch.nn as nn
from models.baselines.base_model.basic import _ConvBNReLU, InvertedIGCV3
__all__ = ['IGCV3', 'get_igcv3', 'igcv3_1_0', 'igcv3_0_5', 'igcv3_0_75', 'igcv3_0_25']
class IGCV3(nn.Module):
def __init__(self, num_classes=1000, width_mult=1.0, dilated=False, norm_layer=nn.BatchNorm2d,... |
fb5acc8975c53e9d3445a5ff91e46fffa46115d44af6dfad946068969ae8f467 | Python | 4,709 | 164 | #!/usr/bin/env python
# Read a .sam file, output several fasta files containing reads which
# do not overlap in the SAM alignment.
# The SAM file is assumed to be sorted by chr and position.
# AUTHOR: Tom Skelly (thomas.skelly@fnlcr.nih.gov)
import os
import sys
import optparse
import re # regular expression... |
391afa90de7a493ed3ad9b5c597275362f6edf22c024da88059ae988e4effc47 | Python | 4,710 | 143 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import multiprocessing
import tensorflow as tf
from tflib.data.dataset import batch_dataset, Dataset
_N_CPU = multiprocessing.cpu_count()
def disk_image_batch_dataset(img_paths,
... |
7f7561b840c6c73d3808bb409623f5a37461574c3bb6366310c6b6f6a3ebed3c | Python | 4,710 | 122 | #
# Copyright (c) 2018 Institute for Basic Science
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge... |
bea07bb77a0e2197493c312b14857502294e0bbfd2f78d2b0d4f79dd2cbb9106 | Python | 4,710 | 134 | # 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... |
ce6c36b8cb878074634cc86b2d6db1c07477fb03cc0676d6022f1899cef2dc79 | Python | 4,711 | 128 | # -*- coding: utf-8 -*-
'''
@author: Mahbub Ul Alam (mahbub@dsv.su.se)
@version: 1.0+
@copyright: Copyright (c) Mahbub Ul Alam (mahbub@dsv.su.se)
@license : MIT License
'''
import torch.nn as nn
import torch
from torch.nn.utils.rnn import pack_padded_sequence, pad_packed_sequence
import numpy as np
import random
cla... |
eef425c7201e19a3c5d68871a411038d13a222c7a121c1b9e8f9ce786f46a706 | Python | 4,711 | 136 | """
File: cmd_line_arguments.py
Created: 2020/06/08
Last Changed: 2020/06/11
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 Foundation, eit... |
cd7264032db0b0a7f6eff6eedffacdcfdd37ee7beaab0533298ce308348de208 | Python | 4,712 | 130 | # -*- coding: utf-8 -*-
'''
@author: Mahbub Ul Alam (mahbub@dsv.su.se)
@version: 1.0+
@copyright: Copyright (c) Mahbub Ul Alam (mahbub@dsv.su.se)
@license : MIT License
'''
import torch.nn as nn
import torch
from torch.nn.utils.rnn import pack_padded_sequence, pad_packed_sequence
import numpy as np
class RNN_LSTM(nn... |
53f4b8c871e5206fede486b4c4210a0778912b075b5220b5374b607e41ca6585 | Python | 4,715 | 136 | #%%
import os
try:
os.chdir('/Volumes/GoogleDrive/My Drive/python_code/connectome_tools/')
print(os.getcwd())
except:
pass
#%%
import csv
import pandas as pd
import numpy as np
import seaborn as sns
import matplotlib.pyplot as plt
from pymaid_creds import url, name, password, token
import pymaid
rm = pyma... |
c0c645d63636f0ed1d33993ff29addbfbb04964877169183b6b9c6c3c64327ed | Python | 4,715 | 128 | # -*- coding: utf-8 -*-
'''
@author: Mahbub Ul Alam (mahbub@dsv.su.se)
@version: 1.0+
@copyright: Copyright (c) Mahbub Ul Alam (mahbub@dsv.su.se)
@license : MIT License
'''
import torch.nn as nn
import torch
from torch.nn.utils.rnn import pack_padded_sequence, pad_packed_sequence
import numpy as np
import random
cla... |
e181a381c49f1ced58c069fa2517c4a325e8ad64c1970680fbfa946924f5400f | Python | 4,715 | 104 | # 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... |
8f5165fe5ad7f7e2059dfefecb92d188d0e0c8ff09c8ae7fe026f45258bdcad3 | Python | 4,716 | 146 | from anytree import Node
import numpy as np
from anytree import LevelOrderGroupIter, Node
from .traverse import BaseTraverse
def to_transmission_matrix(adj, p, method="uniform", in_weights=None):
if method == "uniform":
not_probs = (
1 - p
) ** adj # probability of none of the synapse... |
914c47ec1f5e4564685449fcf6044971d217cb54248127b1c0e619efdb9e95c0 | Python | 4,717 | 170 | # SCSCSCSCSCSCSCSCSCSC
# CSB Lab | Indian Institute of Science, Bengaluru
# Chinmay K Haritas
# Toggle Triad ODE
# %%
print("\nSpatial GRNs - Toggle Triad in 2D \n")
print("ODE Solver")
# Import Block
import helpers
from tt_vars import *
from helpers import hill, p_i
np, pd, plt, tqdm, time, njit, prange, animator,... |
e8ed5192215ae1a545dbe421e648b925aecb22010b44b93a4360487b5532b825 | Python | 4,717 | 173 | import itertools
import logging
import random
from pathlib import Path
from typing import List, Tuple
import numpy as np
import tifffile as tf
from attrs import define, field, validators
logger = logging.getLogger(__name__)
def path_exists(instance, attribute, value):
if not value.exists():
raise FileNo... |
40bd0ab8087d4f59ea78d3d8ded04e905583953e5206aa4e55d73c12f84a67b6 | Python | 4,720 | 175 | from typing import Tuple
import logging
import cv2
import numpy as np
from attrs import define
from cenfind.core.data import Field
logger = logging.getLogger(__name__)
@define
class Centriole:
"""
Represents a centriole as a 2d point associated with a Field and a channel index.
The parent attributes i... |
70333954c566d5209a5739d4ad31817fa7e4d9e66246ca70782ec699965d6a63 | Python | 4,721 | 133 | #!/usr/bin/env python
# Copyright (c) 2026 Computer Vision Center (CVC) at the Universitat Autonoma de
# Barcelona (UAB).
#
# This work is licensed under the terms of the MIT license.
# For a copy, see <https://opensource.org/licenses/MIT>.
"""Compare two recorder files (gotten from 'show_recorder_file_info') line by... |
4b50d4ea5d5a5436349fcfcc61a2b0a3802e425dfc18f2db2b57edd3a72e8dae | Python | 4,722 | 123 | #!/usr/bin/python
import numpy as np
import os
import Bio
import shutil
from Bio.PDB import *
import sys
import importlib
from IPython.core.debugger import set_trace
# Local includes
from default_config.masif_opts import masif_opts
from triangulation.computeMSMS import computeMSMS
from triangulation.fixmesh import fi... |
9c725cf7c46942793f64412e9be23c04cc0b7a235f5b7cde7b324c5da1fa8999 | Python | 4,722 | 229 | # Code adopted from https://github.com/tomasjakab/keypointgan
hip = 'hip'
thorax = 'thorax'
r_hip = 'r_hip'
r_knee = 'r_knee'
r_ankle = 'r_ankle'
r_ball = 'r_ball'
r_toes = 'r_toes'
l_hip = 'l_hip'
l_knee = 'l_knee'
l_ankle = 'l_ankle'
l_ball = 'l_ball'
l_toes = 'l_toes'
neck_base = 'neck'
head_center = 'head-center'
... |
2379e21849d9a27a367b107f3538180754f34798008611fce584fdf47b9049d2 | Python | 4,723 | 110 | #!/usr/bin/env python
#title :train.py
#description :Network for MR-tod
#author :Zifei Liang
#date :2022/05/22
#usage :Network for Deep learing from MRI to TOD
#python_version :3.6
from Network import Generator
import Utils_model, Utils
from Utils_model import VGG_LOSS
from... |
0ae8f248a6fcb01050d3e27eb0fa37b721e02384877ed27c3c5f0a86cfe46b71 | Python | 4,725 | 158 | """
Code to explore the PDF and CDF of weight distributions.
We use truncated lognormals to define the distribution of excitatory connections.
We scale that by -8 for inhibitory connections.
We represent the inhibitory connections with a negative number as a convention to be consistent
with the network simulator (NEST... |
4819179b1d9caf6e1227f12fd19aed7b3387d91320c98be8b105694edc6bee21 | Python | 4,726 | 196 | from pygenn.genn_model import create_custom_weight_update_class, create_custom_postsynaptic_class, create_custom_sparse_connect_init_snippet_class, create_cmlf_class, create_custom_init_var_snippet_class, init_var
import numpy as np
"""
weightupdate model to pass OR activation into ORNs
"""
pass_or = create_custom_we... |
6bb89234bf0579ac47eafa8836e3ef954ebee54ab147a04d01a806cc28d9a99a | Python | 4,726 | 129 | import os
from os.path import join
import numpy as np
import pandas as pd
from sklearn.model_selection import train_test_split
from sklearn.ensemble import RandomForestRegressor
from sklearn.model_selection import ShuffleSplit, GridSearchCV
from sklearn.metrics import (mean_absolute_error, mean_squared_error,
... |
094d7b47ed0caab44b0296509c53e7091d2d3e2c7be6c139d8a14c16e1b2bde0 | Python | 4,727 | 128 | """
File: create_cov_matrices.py
Created: 2020/10/08
Last Changed: 2021/10/21
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 Foundation, eit... |
7f310378bdd70e6c36b3fcee4817e24c10535e07f1d5a328388130563bec0366 | Python | 4,727 | 132 | # 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 ... |
cf0a4f5143bf9915503a44262cbd60684871a0f9d98bb8b7de71cd763e99f6f9 | Python | 4,729 | 159 | import csv
import os
import sys
import math
def reduce_precision(value, prec=2):
return "{:.{}f}".format(round(float(value), prec), prec)
def generate_linear_grid(n=100, a=0, b=1):
h = float(b - a) / n
prec = int(math.log10(n / float(b - a)) + 2)
last_h = b - h
grid = []
for i in range(0, n):
... |
408d3a35c6ba30a0af7256b56973cd07127aa9de0adad841fd74f587d4057e6e | Python | 4,731 | 132 | import math
from mmcv.cnn import build_conv_layer, build_norm_layer
from ..builder import BACKBONES
from ..utils import ResLayer
from .resnet import Bottleneck as _Bottleneck
from .resnet import ResNet
class Bottleneck(_Bottleneck):
expansion = 4
def __init__(self,
inplanes,
... |
9872ffca7289fd6d1fab7577627a5bc394f92d33fe6b15b3d8e800d8079ea8af | Python | 4,731 | 140 | import argparse
import sys
from pathlib import Path
import numpy as np
import torch
from hyperopt import hp, fmin, tpe, Trials, STATUS_OK
from torch.utils.data import DataLoader
from tqdm import tqdm
from functools import partial
import trajectory as tr
from camera_frame import CameraFrameTransformer
from dataloading... |
b06c08cb8ada50ecad300910bdf1fa7c93b38b0a240f68d52528cf37d6ecf22c | Python | 4,731 | 155 | """Serialization with :mod:`pyarrow` (requires pyarrow to be installed)
Usage
-----
A context implements serialization of relevant Eelbrain objects, and can be
re-used indefinitely::
>>> context = pyarrow_context()
>>> s = context.serialize(ds).to_buffer()
>>> ds = context.deserialize(s)
"""
from inspect... |
0729125445bbd047ff5f52b3c1ca270275473988705c06e367e67e6d956f832a | Python | 4,732 | 133 |
import torch
import torch.nn as nn
class MoCo(nn.Module):
"""
Build a MoCo model with a base encoder, a momentum encoder, and two MLPs
https://arxiv.org/abs/1911.05722
"""
def __init__(self, base_encoder, dim=256, mlp_dim=4096, T=1.0):
"""
dim: feature dimension (default: 256)
... |
e9a07eaaf61e9a9c5e4f0019b5eff09182dd300b46723fcaffec997a8ef313b9 | Python | 4,732 | 128 | """Parser for Boomer output"""
import hashlib
import logging
import re
from dataclasses import dataclass, field
from typing import Dict, Iterator, Optional, TextIO
from curies import Converter
from oaklib.datamodels.mapping_cluster_datamodel import MappingCluster, SimpleMapping
from oaklib.datamodels.vocabulary impo... |
68fa644125184e2c953d815463ca3ad0598d851d46ff822d35240e95e56fe74d | Python | 4,738 | 105 | from . import SyncSmokeTest
import carla
import math
# A wheel that jumps is off by far more than this; one that rolls, or holds for
# a frame, is not.
JUMP_TOLERANCE_DEG = 30.0
class VehicleWheelSmokeTest(SyncSmokeTest):
"""Shared setup for the smoke tests that read a vehicle's wheels. Runs on
whatever map... |
a46ea8d2b70e725c5021d9eda4e4a360f1ad1f9bbc1d82b6fa797f60912de75b | Python | 4,741 | 156 | import seaborn as sns
from matplotlib import pyplot as plt
from skfuzzy.cluster import cmeans_predict
import numpy as np
class FuzzySet:
def __call__(self, x):
raise NotImplementedError
def plot(self, canvas, label):
raise NotImplementedError
class TrapezoidFuzzySet(FuzzySet):
def __ini... |
e842d0ec3c361e164f05d6998660b58ade0f67c7f27710e15d2a6f4fc123ff43 | Python | 4,741 | 109 | #!/usr/bin/env python3
"""Draw debug primitives in the CARLA world: points, lines, arrows, boxes, text.
Commands (all take a --life in seconds and an optional --color r,g,b):
point --at X,Y,Z [--size 0.1]
line --from X,Y,Z --to X,Y,Z [--thickness 0.1]
arrow --from X,Y,Z --to X,Y,Z [--thickness 0.1 --a... |
fa26a82fb24ce5be942f0bc8ae1f16a67cf68bafaef03e13d348fcf01a25e015 | Python | 4,741 | 198 | import logging
import os
import shutil
import subprocess
from collections.abc import Generator
from pathlib import Path
from subprocess import TimeoutExpired
_logger = logging.getLogger(__name__)
def _switch_workdir(path: Path | None) -> bool:
"""Check if it makes sense to change directory"""
if path is Non... |
1e8983966efb3dbb25d69f2a839407f934d7bcb7aaf2f4340caa2bdd9a623d40 | Python | 4,742 | 129 | """Fixtures: an API app with a real mock-worker subprocess behind Starlette's TestClient."""
from __future__ import annotations
import sys
import time
from dataclasses import dataclass
from pathlib import Path
import pytest
from starlette.testclient import TestClient
from carla_cosmos.synthetic import make_clip
fro... |
8b4222038a676c6cd3f0db124e293c03c734296955359d78a7f5bf62bfe432a2 | Python | 4,742 | 127 | import pandas as pd
import numpy as np
import networkx as nx
from networkx.algorithms import bipartite
import itertools
def bipartite_random_nsp(ntarg, p, numspines, numinputs):
# p : probability of connecting an edge
G = nx.MultiDiGraph() # multiple edges between two neurons will be counted
list_targ = n... |
d63c3b936f9053f5c603a8c7e2035471ddc5bd142c5bc781fa7d6f4d6896c138 | Python | 4,744 | 120 | # 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... |
ec7ea4ce87e70d353fc937d7368cf1e5fbd97401d8615ea5a000dff4c6f06723 | Python | 4,746 | 113 | # basic imports
import os
import pickle
import numpy as np
import pyqtgraph as qg
# framework imports
from cobel.agents.sfma import SFMAAgent
from cobel.interfaces.gridworld import InterfaceGridworld
from cobel.analysis.rl_monitoring.replay_monitors import OptimalityMonitor
# store experiment directory
cwd = os.getcwd(... |
b111b08f5484f528debfb0a2d65676c8fe2fc393430a9631b8a506c1d051b3e5 | Python | 4,747 | 139 | # 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... |
5560654b5d753c2aa10304cf7d8b7ed096445e72c007f84093dcd3b1bd19fb87 | Python | 4,748 | 175 | import cv2
import torch
from model import U2NET
from torch.autograd import Variable
import numpy as np
from glob import glob
import os
def detect_single_face(face_cascade,img):
# Convert into grayscale
gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
# Detect faces
faces = face_cascade.detectMultiScale(gr... |
f8122590611f40e9e03a54b9f4db38369881742af7ecc06706b07e4e8f4b469d | Python | 4,748 | 139 | # 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... |
21a22a010b10d3e3e2b016d5643afaa1bee48103c1b0681786d02523bfa4cbe0 | Python | 4,750 | 150 | from typing import Tuple, List
import cv2
import numpy as np
import pandas as pd
from attrs import define
from ortools.linear_solver import pywraplp
import logging
from cenfind.core.structures import Centriole, Nucleus
logger = logging.getLogger(__name__)
def flag(is_full: bool) -> Tuple[int, int, int]:
"""
... |
4f5de0424def5c669beef58733ab47eac62146ee27af3a3130007c26877ae53a | Python | 4,751 | 126 | """
Author: Benny
Date: Nov 2019
"""
from data_utils.ModelNetDataLoader import ModelNetDataLoader, load_data, PointSampler, Normalize, RandomNoise, RandomRotate, toTensor
from torchvision import transforms
import argparse
import numpy as np
import os
import torch
import logging
from tqdm import tqdm
import sys
import i... |
631bc3bedf993b5ceee57167535bd954c649aba41ada28b3ce3f86c605cfe7cd | Python | 4,752 | 173 | import random
import re
import torch
import numpy as np
import pandas as pd
from collections import UserList, defaultdict
from rdkit import Chem
REGEX_SML = r'Cl|Br|[#%\)\(\+\-1032547698:=@CBFIHONPS\[\]cionps]'
def normalize_smiles(smi, canonical, isomeric):
normalized = Chem.MolToSmiles(
Chem.MolFromSm... |
e22927d156c75bdafd1350c46c8c8066822208c7f79ae8dce90d072a3c06578d | Python | 4,752 | 132 | #!/usr/bin/env python3
"""
File: export_cf_interaction_to_excel.py
Created: 2022/05/16
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 ... |
1db56b021bc63a4b48fd6692e86bb76730a49fa1564275905f9b82c2dff52d5c | Python | 4,753 | 126 | #!/usr/bin/env python
import os
import cv2
import numpy as np
import os.path as osp
import SimpleITK as sitk
from PIL import Image
def compute_specificity(SEG, GT):
TN = np.sum(np.logical_not(np.logical_or(SEG, GT)))
FP = np.sum(SEG) - np.sum(np.logical_and(SEG, GT))
spec = TN / (TN + FP)
return spec... |
662a5e675a839bee5e5316826dbcc0ff0eaae550792b971a96e93ebf6fce07cf | Python | 4,753 | 149 | import plotly.graph_objs as go
from mne.channels.layout import _find_topomap_coords
from mne.utils.check import _check_sphere
from mne.viz.topomap import _make_head_outlines
import mne
import numpy as np
import RV.constants as c
def get_channel_topography_plot(raw: mne.io.Raw):
"""Generates channel-topography ... |
cd401dfa4212ab9d23fd2ff794e5b012ec46586141c78d389e62e96afbb1e6fd | Python | 4,754 | 102 | import torch
import numpy as np
import torch.nn.functional as F
def spectral_projection_divergence_free(u, domain_size, constraint_modes):
"""Apply spectral projection layer to make a velocity field divergence-free.
Parameters
----------
u : torch.Tensor
Input velocity field [batch, 2, he... |
247d68fcc7b2ef33e3861e461ce6e429a01526052055527dae67d483488170f1 | Python | 4,759 | 118 |
import cv2
import numpy as np
from PIL import Image
import math
import numpy as np
# import torch
# from torchvision import transforms
def rotate_image(image, angle, center = None, scale = 1.0):
(h, w) = image.shape[:2]
if center is None:
center = (w / 2, h / 2)
# Perform the rotation
M = cv... |
8041a504b8eca19b3e53ec98663243b57e779521e1f5313d66733cd1286d8dac | Python | 4,759 | 118 | # basic imports
import numpy as np
import pickle
def recover_states(replay: list) -> np.ndarray:
'''
This function extracts the states of replayed experiences.
Parameters
----------
replay : A sequence of replayed experiences.
Returns
----------
sta... |
fad6fad1379734d920f67bbb15d0509087bbcac790d88eca8de8379b0e14ae62 | Python | 4,759 | 105 | """Public API and bounded CLI regressions for disabled llocal (#809)."""
from types import SimpleNamespace
import pytest
from MACS3.Signal.FixWidthTrack import FWTrack
from MACS3.Signal.PairedEndTrack import PETrackI
from MACS3.Signal.PeakDetect import PeakDetect
from test_callpeak_local_windows import inputs
@pyt... |
86ab3e12b62396a0425ac1dd93414c260dc83a6b1ede9b2ed59d03d30b1aed96 | Python | 4,762 | 125 | import os
from os.path import join
import numpy as np
import pandas as pd
from sklearn.model_selection import train_test_split
from sklearn.ensemble import RandomForestRegressor
from sklearn.model_selection import ShuffleSplit, GridSearchCV
from sklearn.metrics import (mean_absolute_error, mean_squared_error,
... |
c571c088c34a280694978f8f0021dcbb3d8d2d2fe0e658ef73c08afc13f00a0f | Python | 4,763 | 131 | """
File: create_auc_per_expl_var_plot.py
Created: 2020-12-17
Last Changed: 2020-12-17
Author(s): H.H.Wiersma
Code to create distribution plot and a mask image used in the research plan
Copyright (C) 2019 H.H.Wiersma
This program is free software: you can redistribute it and/or modify
it under the ter... |
7d3fd3967f4ba6d3e17954cfeb8487ccc74a8898e60197279816b3ced6a3aecc | Python | 4,764 | 156 | from itertools import chain
import pytest
from eelbrain import datasets, plot
from eelbrain.plot import _base
from eelbrain.plot._base import Layout, ImLayout
from eelbrain.testing import skip_on_windows
from eelbrain._wxgui.testing import hide_plots
def assert_layout_ok(*args, **kwargs):
layout = Layout(*args, ... |
8bd846bb0890ccea3ee416ab9ee15b7ff58fcbf465a20b20047e7d3ebb0d39a6 | Python | 4,765 | 153 | import os
import copy
import numpy as np
import pandas as pd
import math
import random
import matplotlib.colors as colors
from sklearn.model_selection import train_test_split
from sklearn.decomposition import PCA
from siVAE.data import data_handler as dh
from siVAE.util import reduce_dimensions
fro... |
bc2ee90f9dfecd981fbfa78ef152db4483b36bc5479f04cebd31209e10324f81 | Python | 4,767 | 127 | import os
import os.path as op
import sys
from abc import ABC, abstractmethod
import numpy as np
import json
from drugex.logs import logger
from drugex.environment.neural_network import STFullyConnected
from sklearn.cross_decomposition import PLSRegression
from sklearn.naive_bayes import GaussianNB
from sklearn.svm i... |
0e61192e94a7e7c6574f01ab062ac4f0bbd2128a7e4a0279a5f910d199eebca5 | Python | 4,769 | 129 | import os
from os.path import join
import numpy as np
import pandas as pd
from sklearn.model_selection import train_test_split
from sklearn.ensemble import RandomForestRegressor
from sklearn.model_selection import ShuffleSplit, GridSearchCV
from sklearn.metrics import (mean_absolute_error, mean_squared_error,
... |
4124aca6fe807d557c9d818927a4df678debf1c77c85f4e4f994f44dd694d160 | Python | 4,771 | 122 | #!/usr/bin/env python3
"""
File: combine_julienbryois2021_files.py
Created: 2022/01/12
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... |
3954c182cc8ed3a1e185c40a8a3d63a9b1b3086baef45b359b97b3a579212182 | Python | 4,772 | 109 | """End-to-end capture against a live CARLA server.
Run with ``CARLA_COSMOS_TEST_PORT=<port> pytest -m integration``. Keeps the
load small (one hero, 8 frames, single camera) because the GPU is shared.
"""
import numpy as np
import pyarrow.parquet as pq
import pytest
pytestmark = pytest.mark.integration
@pytest.fi... |
ab8042535c37a0a22a3af4602eddcf0bdbef0f720ac24ab34d4fc5ec72dbafcf | Python | 4,774 | 109 | # Copyright (c) 2026 Computer Vision Center (CVC) at the Universitat Autonoma de
# Barcelona (UAB).
#
# This work is licensed under the terms of the MIT license.
# For a copy, see <https://opensource.org/licenses/MIT>.
from . import SyncSmokeTest
import carla
import math
import time
class TestVehicleTelemetry(SyncS... |
b7c0cb2c015f6ef32a28d7b4ea55c8e3e66137624bf915b15f1579fccbd3f3fd | Python | 4,775 | 165 | import difflib
import math
import os
from pathlib import Path
from typing import List
from linkml_runtime.utils.yamlutils import YAMLRoot
ROOT = Path(__file__).resolve().parent
INPUT_DIR = ROOT / "input"
OUTPUT_DIR = ROOT / "output"
# When the test suite is parallelised with pytest-xdist, every worker imports
# this... |
000a2251e3e496bc38672d840acc715f8d8c60bcf1b0701baabffd02c6dd4d1b | Python | 4,778 | 166 | # -*- coding: utf-8 -*-
import matplotlib.pyplot as plt
import matplotlib.dates as mdates
import pandas as pd
def plot_test_anomalies(
X_test,
ANOMS,
fig_cols=1,
color="r",
s=10,
alpha=0.4,
fontsize="large",
loc="left",
figsize=(20, 20),
):
n_nodes = X_test.shape[1]
fig_row... |
3906fd8933bfd97615f013fdf16433021a7cbaaca3da63cd248d3df5b3074f1e | Python | 4,778 | 119 | '''
Adapted from kuangliu/pytorch-cifar .
'''
import torch.nn as nn
import torch.nn.functional as F
class BasicBlock(nn.Module):
expansion = 1
def __init__(self, in_planes, planes, stride=1):
super(BasicBlock, self).__init__()
self.conv1 = nn.Conv2d(
in_planes, plan... |
80f246fec05aafcf6c7e4301335ea45bb0e73694fb98b9b102d0979ab78f15a2 | Python | 4,778 | 112 | """Shared helpers: sync mode, traffic population, freezing, cleanup."""
import random, time, carla
def connect():
c = carla.Client("localhost", 2000); c.set_timeout(60)
return c, c.get_world()
def set_sync(world, tm=None, on=True, dt=0.05):
s = world.get_settings(); s.synchronous_mode = on; s.fixed_delta_... |
d4ee1c6de893a25bffb657c82fc2b35cf98c67349e27656ed6ac5b47aef92e9f | Python | 4,778 | 112 | #!/usr/bin/env python3
"""Preview camera rain on a dedicated CARLA server; replaces its current map.
python rain_lens_demo.py --port 4654
Requires pygame and numpy. 1-4 select rain; N switches day/night;
Space toggles automatic cycling; Esc closes and restores world settings.
"""
import argparse
import queue
import ti... |
5bf0c15a65bb92888839011336562651cad48b78d82b68a52ee58b52f82f02c1 | Python | 4,779 | 135 | # Copyright 2021-2022 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... |
aed8867534b97e59f2476bb37569bdfbeef8a7cccd6e45832ca21e601d1da044 | Python | 4,779 | 101 | # SPDX-FileCopyrightText: © 2025 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
#
# SPDX-License-Identifier: MIT
"""``dict_to_camera_spec`` builds every lens model the render engine accepts.
``CameraSpec`` is a oneof over three lens models and NRE serves all three, but this function
used to build ``FthetaCamer... |
fc8801ff52274fa857f058c92cf1755c9546ff8e53aa81cf11555d93febf33bc | Python | 4,783 | 126 | import argparse
from dateutil.relativedelta import relativedelta
import geopandas as gpd
import descarteslabs as dl
from tqdm import tqdm
from scripts import contour_gen, dl_utils
DL_SYSTEM_PARAMS = {
'image': ('us.gcr.io/dl-ci-cd/images/tasks/public/' +
'py3.8:v2020.09.22-5-ga6b4e5fa'),
'cpus... |
0622feb357167a9877da0a619b728a50bad05a66141c623e9c2eedd38b994d01 | Python | 4,784 | 115 | import math
import numpy as np
def get_min_max_size(network_size, scale_list):
conv4_3_scale = scale_list[0]
min_scale = scale_list[1]
max_scale = scale_list[2]
source_num = {'300': 6, '512': 7, '1024': 8}[str(network_size)]
scales = [conv4_3_scale * 0.01]
for i in range(1, source_num + 1):
... |
a81a20e984e40461d72546290bd5eb7d805640ee4ecf58c3b14e797e1b6674ac | Python | 4,784 | 127 | # -*- coding: utf-8 -*-
import queue
from collections import OrderedDict
import pandas as pd
import torch.nn as nn
from utils.model_hook import CModelHook
from utils.summary_tree import CSummaryTree, CSummaryNode
pd.set_option('display.width', 1000)
pd.set_option('display.max_rows', 10000)
def get_parent_node(root... |
271329a7a20ffdbe9e3d1e6c0ea22b70c2d9adf1622753e329f990901fa6d5dc | Python | 4,786 | 159 | ###################################################################
####
#### Version: 1.1.7
#### Date: 6/24/2023
#### Description: This file contains the code for the configuration menu of Neuron EZ. The current config menu contains sections for about, reference, and an option to set debug mode.
#### Author: Evan Cobb... |
ec3b64040d33146c66725c623cf73cdf5fc9eacb2d418783c6bc12111682e1f7 | Python | 4,786 | 116 | ####################################################################################################
# Copyright (c) 2019 - 2023, 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 ... |
d2681452dc75e3eb5a45e3d300487396d1976725bfdf5cdb2dc0a4554141d9f6 | Python | 4,787 | 129 | # -*- coding: utf-8 -*-
'''
@author: Mahbub Ul Alam (mahbub@dsv.su.se)
@version: 1.0+
@copyright: Copyright (c) Mahbub Ul Alam (mahbub@dsv.su.se)
@license : MIT License
'''
import torch.nn as nn
import torch
from torch.nn.utils.rnn import pack_padded_sequence, pad_packed_sequence
import numpy as np
import random
cla... |
50eafa3c01824200478886fd080d5b68a53ba1def8620b9b27c3ff2ae74e7901 | Python | 4,788 | 114 | """Phase 3d experiment: latent inhibition as the dual-DAN discriminator.
Compare three agents on the LI paradigm:
1. Pure RPE (Bennett 2021 single-valence on connectome)
2. Pure AIF (Bayesian observer with posterior entropy DAN)
3. Dual-DAN (RPE with eta gated by AIF surprisal)
For each: run two groups (p... |
aa42dd5b04157d5d97c658d935f2179273f31723c916a795b4ea56821541ed87 | Python | 4,788 | 126 | # 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... |
35a2833e9db821f27ce535f1efde395743e3a8c62ca43e255d9445270942ec1a | Python | 4,789 | 137 | import time
import math
# import vis_funcs as vis_funcs
# import utils.vis_funcs as vis_funcs
import numpy as np
import pandas as pd
def timeSince(since):
now = time.time()
s = now - since
m = math.floor(s / 60)
s -= m * 60
return '%dm %ds' % (m, s)
def simple_optimizer(rnn, lr):
for param in ... |
0bdc413af0e1f6b192ec467147d421d49424bb059cc53c3c16f8fff26b143d50 | Python | 4,790 | 132 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
import unetsl.model
import sys
import click
import collections
def patchEndsofUnet(first, second, out="transferred.h5"):
"""
Transfers the weights of the first model to corresponding layers in the
second model. (If inverted the first model is the ta... |
01bbb096812289b0941448b193efc5748d935bd2e35d5464246e780343e6f90e | Python | 4,791 | 151 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
import warnings
import numpy as np
from numpy.testing import assert_allclose, assert_equal
import pytest
import scipy.stats
from eelbrain import datasets
from eelbrain._stats import stats
from eelbrain._stats.permutation import permute_order, rand_rotation_matr... |
5c9ea2172e4b9767e9d1f40588bcc0e7d47b8a720d4d50966ef03288bbf16fb9 | Python | 4,791 | 120 | #!/usr/bin/env python
# rowrateplot - a command line utility to generate spike frequency vs.
# time for groups of neurons. It takes a single filename
# as argument, with a line for each time step containing the simulation
# time, followed by the average spike frequency during that time step for
# each group of ... |
002bd9074962207ff075e4b346f32be3a5125c729d1c0f848e7455136509d050 | Python | 4,793 | 98 | # 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... |
6429ac417af701bd7987578365adc77dc777d51fc3bdcdd40711f79991547eb0 | Python | 4,794 | 132 | # 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... |
647d9191edb7e7a838477c571e2231811c60521f44b285966366227a12d8e110 | Python | 4,794 | 130 | # 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... |
a001a3c05220d2b753f1acbdc48171c4f0e92b10096b2d060d7c64824021fa24 | Python | 4,796 | 146 | import logging
import sys
import warnings
from dataclasses import asdict
import chika
import pandas as pd
from imblearn.metrics import geometric_mean_score
from sklearn.ensemble import ExtraTreesClassifier, RandomForestClassifier
from sklearn.linear_model import LogisticRegression
from sklearn.metrics import cohen_kap... |
228ae887c9f081190f440917a6158648f1a9938f353f644df2d4ae68ce2df8fd | Python | 4,797 | 135 | import torch
from torch.utils.data import Dataset
from mol_tree import MolTree
import numpy as np
from rdkit import Chem
from rdkit.Chem import Descriptors
from rdkit.Chem import AllChem
from torch_geometric.data import Batch
from torch_geometric.data import Data
class MoleculeDataset(Dataset):
def __init__(self... |
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