sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
0bf723688a0cdaa89434938fff0dfcc6bd132233047e7d43dcb01fac37ac8a15 | Python | 4,119 | 146 | import pytest
import torch
from torch.testing import assert_close
from ..data_processors import (
DefaultDataProcessor,
IncrementalDataProcessor,
MGPatchingDataProcessor,
)
from ..normalizers import UnitGaussianNormalizer
from neuralop.tests.test_utils import DummyModel
def test_DefaultDataProcessor_pi... |
49b14733dd25ef93ac7dd3b7cd998b955060b1f6762c0bc72f35af9d2bf8bc24 | Python | 4,120 | 120 | import numpy as np
from graspologic.utils import largest_connected_component
import pandas as pd
def get_paired_inds(meta, check_in=True, pair_key="pair", pair_id_key="pair_id"):
pair_meta = meta.copy()
pair_meta["_inds"] = range(len(pair_meta))
# remove any center neurons
pair_meta = pair_meta[pair_... |
cc3f52d373031333f676880676e0fa2652d3ad69a44ec27069e08d4959af1e6a | Python | 4,120 | 107 | """Tiny stdlib HTTP helpers (JSON + multipart) so worker adapters stay dependency-free."""
from __future__ import annotations
import json
import mimetypes
import os
import secrets
import tempfile
import urllib.error
import urllib.request
from pathlib import Path
from typing import Any, Iterable
class HttpError(Runt... |
dd477b1511d26065d0bcd18036a1abc4fb78087f60a044822e3f82d3a5fd7479 | Python | 4,121 | 126 | import argparse
import logging
import spacy
import json
import multiprocessing
import numpy as np
import time
from tqdm import tqdm
import matplotlib.pyplot as plt
from os.path import join
nlp = spacy.load('en_core_sci_sm', disable=['ner', "tagger"])
def get_ngrams(orig_text):
doc = nlp(orig_text)
if args.lem... |
0901f53169e42700b7608c0de85c13ffe9fb69bd940e41d245374bdcc9dbac3e | Python | 4,122 | 104 | # -*- coding: utf-8 -*-
# Generator classes to dynamically load the data.
# COPYRIGHT: TU Delft, Netherlands. 2021.
import glob
import h5py
import random
import numpy as np
from tensorflow.keras.utils import Sequence
class DataGenerator(Sequence):
"""
Generates data for Keras.
Assumes that the data is stor... |
965e869e91eadfeb79ca67c6085d79882b8b2fb7d6ce546543ea1e77ffc8a443 | Python | 4,122 | 116 | from src.utils.tokenizer import smi_tokenizer, remove_floats
from sklearn.model_selection import train_test_split
from chembl_structure_pipeline import standardizer
from rdkit.Chem import MolStandardize
from rdkit import Chem
import modin.pandas as pd
import os
os.environ["MODIN_CPUS"] = "16"
os.environ["MODI... |
86a71891ee80ce916071c712ca499fa2cab409aeb60283ff1c8bb3cc761beb86 | Python | 4,123 | 109 | # Copyright (c) 2015-present, Facebook, Inc.
# All rights reserved.
import os
import json
from torchvision import datasets, transforms
from torchvision.datasets.folder import ImageFolder, default_loader
from timm.data.constants import IMAGENET_DEFAULT_MEAN, IMAGENET_DEFAULT_STD
from timm.data import create_transform
... |
d57f35ecb6d4ac99ca28597792cd18ec38582f838c82bfaea272180ede761247 | Python | 4,124 | 130 | import torch
from torch import Tensor
from torch.nn import PairwiseDistance as pdist
def make_node_ref(nodes: torch.Tensor):
'''
Makes a node reference to unite node indicies across explanations.
Returns a dictionary keyed on node indices in tensor provided.
Args:
nodes (torch.tensor): Te... |
565909f043309d07271529f1b71e4fb0aa776e6b0e1332ab3d77e07f842e0a46 | Python | 4,125 | 163 | # -*- coding: utf-8 -*-
"""
Created on Tue Jul 20 18:47:06 2021
@author: N.V
"""
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.animation as animation
from matplotlib.animation import FuncAnimation
import os
# note that this must be executed before 'import numba'
os.environ['NUMBA_DISABLE_INTEL_... |
46750d639558d95e34584caf8800a80ec4b6b7b5a9eed21a7d3e3ae8af593f91 | Python | 4,126 | 154 | """Elekta Task Dataset: AE-HMM Pipeline.
In this script we train an Amplitude Envelope Hidden Markov Model (AE-HMM)
on source reconstructed task MEG data.
The examples/toolbox_paper/elekta_task/get_data.py script can be used
to download the training data.
Functions listed in the config are defined in osl_dynamics.co... |
6d7f107458ea1c53b1fb1f1e9f056bdd133b8d1489840bd83a5bad0586d510f8 | Python | 4,126 | 129 | #
# Expansion Hunter Denovo
# Copyright (c) 2017 Illumina, Inc.
#
# Author: Egor Dolzhenko <edolzhenko@illumina.com>,
# Sai Chen <schen6@illumina.com>
# Concept: Michael Eberle <meberle@illumina.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General... |
db371129b61e4320de1f53253514619e329e20193577fe4d1f9b976ea255c21d | Python | 4,127 | 119 | import sys
import os
import hashlib
import struct
import subprocess
import collections
import argparse
import re
dm_single_close_quote = u'\u2019' # unicode
dm_double_close_quote = u'\u201d'
END_TOKENS = ['.', '!', '?', '...', "'", "`", '"', dm_single_close_quote, dm_double_close_quote, ")"] # acceptable ways to end ... |
e289ee59218c041f50fa15eeb24caa438f7e7219ac2cfa141b50c4f563c0eac1 | Python | 4,128 | 146 | """
Set of standardized tests for RACCOON
F. Comitani @2020-2022
"""
import sys
import json
import argparse
import numpy as np
import pandas as pd
from sklearn.datasets import make_blobs
from clustering import *
from classification import *
from update import *
def _create_dataset():
""" Creates a dummy dat... |
e45514a742e3752c392d851c51bf41b41473fc8d7d2871431ca12877f3f9cb86 | Python | 4,128 | 116 | import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
from scipy import stats
import matplotlib.ticker as mtick
def plot_data_vs_fit(xdata, ydata, fit, xlabel, ylabel, title, **kwargs):
# plot data and fit
f = plt.figure(figsize = (7,5))
plt.scatter(xdata, ydata, la... |
d0c6b2bb494b336b3b670b93118df997bc8bf40ca4499a7b1fa156900e8ff789 | Python | 4,133 | 90 | # 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... |
5949cd19fc537ced8db357dc612a18e103206d73c920b65da4867ab284b6ab9e | Python | 4,134 | 146 | import argparse
import glob
import os
import re
import numpy as np
import multiprocessing as mp
import traceback
"""This script is used to condense Bcl-2 family energy tables for a protein-peptide complex into one just for the 20-amino-acid length peptide. This is done by adding all pair energies between the peptide a... |
d1b1bafabfb7fcefb89e7996b811e0a987e179c5d93a3326f00b13cb7ed16854 | Python | 4,134 | 127 | from tctx.analysis import simbatch as sb
from tqdm.auto import tqdm as pbar
from tctx.analysis import amat as am
import numpy as np
import pandas as pd
from matplotlib import pyplot as plt
def extract_batch(
batch_original, sim_gids,
min_participation=None,
rank_method='first', ei_type='all',... |
5915b4515356ff5a5c2a7d91a5ed1a35ab8713e363f9bea16f1f81d3781ca455 | Python | 4,135 | 145 | # Get statistics for a given file (pickle) of SG instance
import os, argparse
import torch
import numpy as np
from graphxai.datasets import load_ShapeGGen
import matplotlib.pyplot as plt
from sklearn.linear_model import LogisticRegression
from sklearn.model_selection import GridSearchCV
from graphxai.gnn_models.node_... |
cf90da4af559771e28bfcbfde724a472ccfdef4b32eb99cf1e8f82b6007dac31 | Python | 4,135 | 128 | from mpi4py import MPI
import glob
import simulator as sm
import os
import numpy as np
import sys
# Note rank 0 is not used for simulations. It causes problems with the subprocess module.
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
nproc = comm.Get_size()
# print('nproc = ', nproc)
sim_name = '/global/home/users/ya... |
fa30ca6095461c09b2ec684119c031229461f749da541cb8a2288dbfda8aecc6 | Python | 4,135 | 125 | import numpy as np
import os
from ..preprocess import permute as perm
from ..utils import path as pth
class Brain:
"""A class containing data that represents a single brain.
Attributes:
connectome (array): Array of the connectome.
reducedConnectome (array): Connectome with extreme components... |
2e5218eba330eceb788ad2a3d59d07e2b4ee8268708c0c5bab763ae18a70e5f9 | Python | 4,136 | 113 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
# Set up custom environment before nearly anything else is imported
# NOTE: this should be the first import (no not reorder)
from maskrcnn_benchmark.utils.env import setup_environment # noqa F401 isort:skip
import argparse
import os
import torch... |
6de23cbfe984d97e2f829ccc7489ea2239421a59d80e36f3f1d0e7a7b0e8e030 | Python | 4,138 | 177 | # Libraries
import pandas as pd
import numpy as np
import pickle
# Path
path = './combined_tidy_v0.0.10.csv'
# Read data ad model
data = pd.read_csv(path, parse_dates=['date'])
# Describe.
data.describe().T.to_csv('data.describe.raw.csv')
# ---------------------------------------------------
# Data pre-processing a... |
1f172cb88850390875dbacac98bb6358ea3609d3b77dd9386c73b7d0aee90267 | Python | 4,139 | 125 | from __future__ import print_function
import numpy as np
import argparse
import torch
import pdb
import os
from slideflow.clam.utils import *
from slideflow.clam.utils.eval_utils import initiate_model as initiate_model
from slideflow.clam.models.model_clam import CLAM_MB, CLAM_SB
import csv
def path_to_name(path):
... |
36fbee780f5733ebbb034c11480043f016a438020cddae66a9a22e354682e433 | Python | 4,140 | 114 | 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,
... |
44aa9eaf44f8047bd53c178be37bdc1b23ee854b69452f8fa9f3a9290e839ab8 | Python | 4,140 | 121 | # 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... |
47f05a692d38749a80874e2972bfe0fdec1802644259969a333a6ebe523af2f2 | Python | 4,140 | 128 | import argparse
import os
from glob import glob
import medmnist
import numpy as np
import tensorflow as tf
from medmnist import INFO, Evaluator
from medmnist.info import DEFAULT_ROOT
from PIL import Image
from tqdm import tqdm
def main(data_flag, input_root, output_root, model_dir, run):
if not os.path.isdir(ou... |
8558c00a37a5aa8947646b6e3173c7a330857d49e48c860f7fae7776a9fc1151 | Python | 4,140 | 117 | # Copyright (c) 2017-present, Facebook, Inc.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
#
import os
import argparse
import numpy as np
import torch
from torch.autograd import Variable
from torchvision.utils import mak... |
526f1e2f9f852849a58ef1c09def61d2afcd8a2d6786b253c539a5ddc1f29cd7 | Python | 4,143 | 109 | # 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... |
dad85efd89703cade8ba667dd2daa575a577131cfe375dd0f39a8715bcf9bc1b | Python | 4,144 | 124 | #%%
import os
import sys
try:
os.chdir('/Volumes/GoogleDrive/My Drive/python_code/connectome_tools/')
sys.path.append('/Volumes/GoogleDrive/My Drive/python_code/maggot_models/')
sys.path.append('/Volumes/GoogleDrive/My Drive/python_code/connectome_tools/')
except:
pass
import pandas as pd
import numpy ... |
885409da298688aa8795f5d29b1b698d57130a9e270a0d67344d3f3e9fceba8f | Python | 4,146 | 123 | from __future__ import print_function, absolute_import
import os
import torch
import torch.utils.data as data
from torchvision import transforms
import torchvision.transforms.functional as TF
from dataloader.data_utils import *
def generate_pair_images(root, gap):
images = []
root = os.path.expanduser(root)
... |
b5acd9a1baba2384f1199773e2b895f67300617145e7ea8df03720b7575e0a8a | Python | 4,151 | 99 | # 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... |
d42d25e462d0a31349d9b4f5b2caa20972ff76ba8c5280de2fa0204ac1b78b74 | Python | 4,152 | 139 | import csv
import os
import sys
def feature_to_index(cases, column_nb, offset=0):
feature_set = set()
for case in cases:
if len(case) > column_nb:
feature_set.add(case[column_nb])
l = list(feature_set)
index = {}
i = 0
for f in l:
if f != '':
index[f] = i... |
5da46dbaaaf7a6c2428cab1bbb1e01a92630b92367dfbc7ca1493f1a0d832736 | Python | 4,153 | 88 | import torch
import torch.nn as nn
import torch.nn.functional as F
class Siamese(nn.Module):
def __init__(self):
super(Siamese, self).__init__()
# Using Sequential to create a small model. When `model` is run,
# input will first be passed to `Conv2d(1,20,5)`. The output of
# `Conv... |
f1090d0c4b1b3811cda99a5a50df27f0bb3a9147bf42c649e4d6e3468477ee2d | Python | 4,155 | 179 | # -*- coding: utf-8 -*-
"""
Created on Mon Feb 14 16:15:07 2022
@author: N.V
"""
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.animation as animation
from matplotlib.animation import FuncAnimation
import os
# note that this must be executed before 'import numba'
os.environ['NUMBA_DISABLE_INTEL_... |
a2b45062bc67714c0c27ebcb2bf0a53fa2a5d1b4e2c71f1b78285fc75ac11155 | Python | 4,156 | 138 | import csv
import os
import sys
def feature_to_index(cases, column_nb, offset=0):
feature_set = set()
for case in cases:
if len(case) > column_nb:
feature_set.add(case[column_nb])
l = list(feature_set)
index = {}
i = 0
for f in l:
if f != '':
index[f] = i... |
93932ab27dfb52e6b57a563db37c8f04a3522f873a0bb8db292a797b02fbde22 | Python | 4,157 | 90 | # 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... |
c99b7b564aa402c64bc93fba6ba4929d4c8ec48ad00e98e8a213bb79b29d3047 | Python | 4,158 | 143 | # 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... |
e55fb316d1b29abf0eb1da3811c3128e9f0ec5085fca5d7ca26b74313abf7aba | Python | 4,158 | 109 | # 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... |
004e94b4dfba590ae8694c38379f861fec36e1c8ed969e1fc32ba6c6c7acce27 | Python | 4,159 | 159 | '''
Figure 7
Statistics of ciliated fits
'''
import pandas as pd
from pylab import *
from matplotlib import gridspec
import seaborn
from file_management import *
from os.path import join
width, height = 3, 5
table = pd.read_csv(join(config['root'], 'Ciliated with PIV', 'tables', 'selection_ciliated.csv'))
box_width ... |
6339adbe2aa91c4c9a6f2e8bacb85aa87a137b3288bb9a2453dc83d7db5e711d | Python | 4,159 | 138 | import csv
import os
import sys
def feature_to_index(cases, column_nb, offset=0):
feature_set = set()
for case in cases:
if len(case) > column_nb:
feature_set.add(case[column_nb])
l = list(feature_set)
index = {}
i = 0
for f in l:
if f != '':
index[f] = i... |
9bc9c717b21a3e4a868843ea953888776a43c899189982f1f41f5487442ba463 | Python | 4,159 | 128 | #!/usr/bin/python
####################################################################################################
# Copyright (c) 2020, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of VessMorphoVis <https://github.com/BlueBrain/VessMorphoVis>
... |
44af93c426ac4ac8a96d0934ff86a7bf4cd9ce32491e8ece27557af2d7fd345f | Python | 4,160 | 105 | import os
import pandas as pd
import torch
import torch.nn as nn
import argparse
from sklearn.model_selection import KFold
from dataset import ViscosityDataset
from model import ViscosityNet
from trainer import Trainer, TrainerConfig
from utils import seed_everything, prepare_training_input
from base import VISCOSITY... |
f705e231811f5e5a23bfa55840c6b1e57513840ca1704d28d6114c523d486345 | Python | 4,160 | 102 | """Regression coverage for singleton-strand accounting (issues #805 and #757)."""
from collections import Counter
import pytest
from MACS3.Signal.FixWidthTrack import FWTrack
@pytest.mark.parametrize("maxnum", [-1, 1, 2])
@pytest.mark.parametrize("reads", [
[],
[(b"chr1", 100, 0)],
[(b"chr1", 100, 1)],... |
f753f3f06f34e50d3fcfb5decb2b0d88ce2b166e044a05eaf2d909b46dda4d08 | Python | 4,160 | 117 | # 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... |
77cef518cb05c1836fc688fae378b25da00aa6df65f18047a8a65e02d03d05be | Python | 4,162 | 85 | 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 as tf
import voxelmorph as vxm
from voxelmorph.tf... |
f3ab91194a7e923aab1edff7288d20f0ad9f596c69e3f54dd1f280f44aad3a4e | Python | 4,163 | 106 | # 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... |
309d6fefab78b319bd9326b5f4d7bdd675e2b29baed97ed7f743cd9d8708915d | Python | 4,165 | 113 | import torch
import torch.nn as nn
import torch.nn.functional as F
import numpy as np
from basic_blocks import (
DownSampling,
EncoderBlock,
DecoderBlock,
Deconvolution,
AttentionBlock,
OutputTransition,
)
from spp_block import Pyramid_Pooling_3D
# NOTE: rsppUnet -> Residual Spatial Pyramid Poo... |
5b2195241958bbfe29fd9a8082ca0c691148bb114f7a2c8437fd748a087e3223 | Python | 4,165 | 123 | # 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... |
e11f5d0eb1d45dc7961e1054f82fe06ef43690fffb16a07277c176a3608b8b81 | Python | 4,165 | 108 | # basic imports
import os
import numpy as np
import pickle
import matplotlib.pyplot as plt
def recover_states(replay: list) -> np.ndarray:
'''
This function extracts the states of replayed experiences.
Parameters
----------
replay : A sequence of replayed experience... |
3369375d8bfb12bd00745620d5a35687fdf3c6e82d8943e4342c566eb6654c60 | Python | 4,166 | 153 | import os
import gzip
from skimage.transform import resize
from skimage.util import montage
import nibabel as nib
import pydicom as pdm
import nilearn as nl
import nilearn.plotting as nlplt
# import h5py
import numpy as np
import pandas as pd
import torch
from torch.utils.data import DataLoader, Dataset
import alb... |
3abbe23247c68fe5f2f35516e2da4db7caf8f95d13be66b2c0086b7ba750df9a | Python | 4,166 | 160 | #%%
import os
import pickle
import time
from pathlib import Path
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
import pandas as pd
import seaborn as sns
from anytree import LevelOrderGroupIter
from scipy.sparse import dia_matrix, diags, load_npz, save_npz
from sklearn.decomposition import Tr... |
708c7020c9c63553c6b4a5fe6bee13b41b392ed119acc69dda6c537374bf56df | Python | 4,168 | 135 | import os
import torch
import torch.utils.data
from PIL import Image
import sys
if sys.version_info[0] == 2:
import xml.etree.cElementTree as ET
else:
import xml.etree.ElementTree as ET
from maskrcnn_benchmark.structures.bounding_box import BoxList
class PascalVOCDataset(torch.utils.data.Dataset):
CL... |
a565f009a32940aac6a6de31d50b6218038afe57147dc59fa83a680366abfc01 | Python | 4,169 | 106 | from __future__ import print_function, division
import numpy as np
from ase.db import connect
from tinnet.regression.regression import Regression
lr = 0.006326505613656666
lamb = 0.1
atom_fea_len = 139
n_conv = 3
h_fea_len = 253
n_h = 1
Esp = -3.343
db = connect('train.db')
images = np.array([r.toatoms()
... |
1168c7799bb1be13460528553989b9bb4134f27e570a5b799177db6c7d56d69a | Python | 4,171 | 118 | import torch.nn as nn
import torch
from math import log2
from kornia.filters import filter2D
class Blur(nn.Module):
def __init__(self):
super().__init__()
f = torch.Tensor([1, 2, 1])
self.register_buffer('f', f)
def forward(self, x):
f = self.f
f = f[None, None, :] * f... |
fb96b07c87461bb6098cb696d6c07485cbe4ab11ec0c357739bb2863538cc81e | Python | 4,175 | 138 | import csv
import os
import sys
def feature_to_index(cases, column_nb, offset=0):
feature_set = set()
for case in cases:
if len(case) > column_nb:
feature_set.add(case[column_nb])
l = list(feature_set)
index = {}
i = 0
for f in l:
if f != '':
index[f] = i... |
67224d0ff88868cc479ad81b1568ba6f1f6db5d6eae53ca0fcaa4aa6abda1aec | Python | 4,176 | 123 | from __future__ import absolute_import
# --------------------------------------------------------
# Fast/er R-CNN
# Licensed under The MIT License [see LICENSE for details]
# Written by Bharath Hariharan
# --------------------------------------------------------
import xml.etree.ElementTree as ET
import os
import nump... |
80aa6624d9f7d2ff68dc73d1370774c173f697cb49b11419910ffa9d0a164208 | Python | 4,182 | 124 | import sys
import torch
import torch.nn.functional as F
import matplotlib.pyplot as plt
from torch_geometric.nn import GCNConv, GINConv
from graphxai.datasets.ba_houses import BAHouses as BAH
#from graphxai.gnn_models.node_classification import train, test
class GCN_1layer(torch.nn.Module):
def __init__(self, hid... |
11908a8a191656210f7ec3ffb4fbed05f0fda5974cdd9905374525f16582904b | Python | 4,183 | 73 | # 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... |
1473b6e731e778d626a826e10e4d4cb2cd5960c9952ce639082722e630856f5a | Python | 4,184 | 116 | #!/usr/bin/env python3
"""
File: replication_plot.py
Created: 2020/06/10
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 Foun... |
5f4403c48525565aeaa49815fcd230205c1906ffb830c9e3a3aef24620bb78a7 | Python | 4,184 | 160 | import numpy as np
from numpy.random import default_rng
from ..utils import get_random_seed
def _input_checks(adjacency, random_seed, effect_size, max_tries):
adjacency = adjacency.copy()
if isinstance(random_seed, np.integer) or random_seed is None:
rng = np.random.default_rng(random_seed)
else:... |
7868015d230b255eeef98437276fe37203cb16070f44e0c22e45ac18e657687e | Python | 4,184 | 92 | __author__ = 'jieqing jiao'
__contact__ = 'jieqing.jiao@gmail.com'
import numpy as np
from niftypad.tac import TAC
from niftypad.kt import dt2tdur
from niftypad.image_process.regions import extract_regional_values
import matplotlib.pyplot as plt
import nibabel as nib
import os
def image_to_parametric(pet_image, dt, ... |
a69a0543439f57c52c9971e1d425860767b83a97b8b77c3333b783b461e1354b | Python | 4,184 | 122 | import random
import numpy as np
import torch
from PIL import Image, ImageFilter
from numpy.random import choice as npc
from torch.utils.data import Dataset
class RoofTrain(Dataset):
def __init__(self, dataset, transform=None):
super(RoofTrain, self).__init__()
np.random.seed(0)
self.data... |
ea8952b63f7afadd131396491c6005efe0a83192716bc76977d8bc6adfe647da | Python | 4,184 | 99 | # Copyright 2023 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... |
1604d71f672538a7648663454e7227fd972808362ed87175fcea4cb11e155363 | Python | 4,186 | 109 | """Shared helpers for the CARLA -> Autoware map tools.
Coordinate convention (load-bearing, read this before touching any math):
* CARLA / Unreal is LEFT-handed: x forward/east, y RIGHT (south), z up.
* OpenDRIVE and the Autoware lanelet2/pcd map pair are RIGHT-handed.
CARLA negates y when it imports an OpenDRIVE f... |
3e1747ab7beeec4f2e17af51884e2141e6ad0d6c7241ea7324c5588a56995eb8 | Python | 4,186 | 122 | #!/usr/bin/env python3
"""
@ Lina Teichmann
INPUTS:
call from command line with following inputs:
-bids_dir
OUTPUTS:
Plots the ERFs of the repeat trials.
NOTES:
If it doesn't exist, the script makes a figures folder in the BIDS derivatives folder
"""
import numpy as np
import m... |
4f637c6664bb582dec32f78da1b45733bf0c062d627f5290c620aa5518fe4c4c | Python | 4,187 | 121 | # 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... |
8f01d34b6861a08c359ef75acf4a6e50f4a86787d624d9297c45d1ff7bdba642 | Python | 4,187 | 120 | import os
import shutil
# from libtiff import TIFF
from scipy import misc
import random
import cv2
import numpy as np
# def tif2png(_src_path, _dst_path):
# """
# Usage:
# formatting `tif/tiff` files to `jpg/png` files
# :param _src_path:
# :param _dst_path:
# :return:
# """
# tif ... |
eb0cfb4c79f01c20231c6224a43121e3d1861ae79666cb529793eace1d1c532b | Python | 4,188 | 98 | import os.path
import argparse
parser = argparse.ArgumentParser(description='Make Molgenis Compute samplesheet for NABEC.')
parser.add_argument('samplesheet', help='NABEC samplesheet')
parser.add_argument('cram_dir', help='path to cram file dir for input')
parser.add_argument('fastq_dir', help='path to fastq file dir ... |
6a409e19533c7aac9f3f82e8acfb1a5497e1c4465b6bbb7f1a6a5a637bfea729 | Python | 4,189 | 122 | '''
Author: Naiyuan liu
Github: https://github.com/NNNNAI
Date: 2021-11-23 17:03:58
LastEditors: Naiyuan liu
LastEditTime: 2021-11-24 19:19:52
Description:
'''
import os
import cv2
import glob
import torch
import shutil
import numpy as np
from tqdm import tqdm
from util.reverse2original import reverse2wholeimage
impo... |
08a12f11089296e0963672b0165b077f7a051613503f69491eb3a33e3db97dee | Python | 4,190 | 109 | # This scripts gives an example of hyperparameters search with Sherpa
# input file: smap_smos_overlap_3dm_seas_c_no_std.pkl
# output file: trials' summary
import sklearn as skl
from sklearn import preprocessing
import pandas as pd
import numpy as np
import tensorflow as tf
from tensorflow import keras
from tensorflo... |
e4b19692c7e2a4e519a3055900a5506e1940bb2ba50e6f9c04085ea77c2400cf | Python | 4,190 | 121 | import torch
import numpy as np
from medpy import metric
import torch.nn.functional as F
class AverageMeter(object):
"""Computes and stores the average and current value."""
def __init__(self, name, fmt=":f"):
self.name = name
self.fmt = fmt
self.reset()
self.val = 0
s... |
0862f2be30ca999fcd18a9ebb546f49e99056d9cc73cfc655c78a5418cbdce70 | Python | 4,192 | 116 | """
fragmenters
Created by: Martin Sicho
On: 06.05.22, 12:19
"""
import re
from itertools import combinations
import numpy as np
from rdkit import Chem
from rdkit.Chem import Recap, BRICS
from drugex.logs import logger
from drugex.molecules.converters.interfaces import ConversionException
from drugex.molecules.conve... |
e14dd86126e7407ad8818df771d388ed662d6b7ea90d76b90b453aa55ee7d268 | Python | 4,192 | 130 | from __future__ import division
from collections import OrderedDict
import torch
from mmcv.runner import Runner, DistSamplerSeedHook
from mmcv.parallel import MMDataParallel, MMDistributedDataParallel
from mmdet.core import (DistOptimizerHook, DistEvalmAPHook,
CocoDistEvalRecallHook, CocoDist... |
3d237c016a87cbfcacce27c2094bf062d2a54d86dce52d3c81b972f49023b42d | Python | 4,194 | 187 | # -*- coding: utf-8 -*-
"""
Created on Tue Jul 20 21:08:56 2021
@author: N.V
"""
# -*- coding: utf-8 -*-
"""
Created on Tue Jul 20 18:47:06 2021
@author: N.V
"""
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.animation as animation
from matplotlib.animation import FuncAnimation
import os
# not... |
6b7b51c4c9da1e0a8da5732cb6a2ba226b99e564833470c76f058f26497fbef1 | Python | 4,194 | 145 | #!/usr/bin/env python
# Classes for managing IsoSeq clusters, including annotation matches.
import os
import sys
import re # for regular expressions
import cPickle as pickle
from tt_log import logger
VERSION = '20150814.01'
logger.debug('version %s loaded' % VERSION)
regexFP = re.compile('f(\... |
b5cac31b0387cc85d4688bebd789d4e58ed45e7b7035ed82a4c3028525fc085d | Python | 4,194 | 104 | # requires: mayavi
# dataset: mne_sample
'''
Example performes a permutation cluster test on source space data and creates
an HTML file describing he output.
'''
import eelbrain as e
# settings
n_samples = 1000
# create an HTML report in which to document results
report = e.Report("MNE Sample Dataset", author="Prof... |
cb5ba8ab35889adcfa7fc9ecd640df8482f0b689f50c0c3f66c0524fac43712c | Python | 4,194 | 109 | # 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... |
999c29de3ee4f19393cbd4a8517683e952caee61aabaddabd2e926cd332b9489 | Python | 4,199 | 89 | import torch
import torch.nn as nn
import torch.nn.functional as F
class ConvBlock(nn.Module):
def __init__(self, in_features, out_features, num, dropout_block, pool=True):
super(ConvBlock, self).__init__()
layers = []
layers.append(nn.Conv3d(in_channels=in_features, out_channels=out_featur... |
12f6070f03f9361d0a4ae168475fc9f98778e314266c894a9049a23bf0a8bbcf | Python | 4,204 | 142 | # Usage createChartJS.py "fileOut...dat"
# Will replace the .dat file with a
# sub-sampled .JS file in a format usable by the Chart.js library
cleanUp = False#True
import csv, re, sys, os
from decimal import Decimal
path = sys.argv[1]
DirName = os.path.dirname(os.path.abspath(path))
FileName = os.path.basename(path)... |
f389a6425ac2fc5b2af3ce5b2e140a3e82ffdd3537127649be217fc83a9b4f5b | Python | 4,204 | 117 | # -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
import tensorflow as tf
from keras.models import Model
from keras.layers import Input, Conv2D, MaxPooling2D, UpSampling2D, Cropping2D, ZeroPadding2D, BatchNormalization, Activation
... |
56a5c8067ac4d7adcea61253889f5bbda478f239166a95170ef17002b1f4415a | Python | 4,209 | 154 | import logging # import first to make sure logging works
from pathlib import Path
import os
# basedir = Path("MCMC_inference_connected")
basedir=Path(".")
results_dir=basedir /"NEWResults_inference_57"
results_dir.mkdir(parents=True, exist_ok=True)
logs=results_dir/ "logs"
logs.mkdir(parents=True, exist_ok=True)... |
a58c96b7e9e6b84da61dff83abef4aabb5598e4a763f98849481d82a9715243b | Python | 4,210 | 117 | from Lif_Parameters import *
from Lif_Equations import eqs_LIF
seed(val)
#####################################
# Initialize the neuronal populations
#####################################
# ------- Layer 0 -------
l0 = NeuronGroup(n_cells, eqs_LIF, method='exponential_euler', threshold='vm>v_th', reset='vm=v_r', refract... |
8edb1462589f878d16dddea5be183d5f5a357f0c38bb40e74e813f1ba978484e | Python | 4,214 | 154 | import logging # import first to make sure logging works
from pathlib import Path
import os
# basedir = Path("MCMC_inference_connected")
basedir=Path(".")
results_dir=basedir /"NEWResults_inference_58"
results_dir.mkdir(parents=True, exist_ok=True)
logs=results_dir/ "logs"
logs.mkdir(parents=True, exist_ok=True)... |
b33abd99f704d6819585e73fcc7d0d6221917eceafee57785e8fdbda9d94d82e | Python | 4,215 | 138 | import os.path as op
import random
import numpy as np
import numpy.testing as npt
import pytest
import nibabel as nib
import tempfile
from AFQ.models.csd import fit_csd
from AFQ.models.dti import fit_dti
from AFQ.tractography.tractography import track
from AFQ.utils.testing import make_tracking_data
seeds = np.arra... |
d7174ec69396519479320a57ff0e985d0d6e269bd21db80b5cc9e58fa569d2db | Python | 4,217 | 128 | import os
import pickle
import random
import cv2
import numpy as np
import torch
from torchvision.transforms import functional as F
def get_instance(module, name, config, *args):
return getattr(module, config[name]['type'])(*args, **config[name]['args'])
def seed_torch(seed=42):
random.seed(seed)
os.env... |
fbfe2c302065f8dc33e79677aa7d735b585303bc5d9856aa0397c26030f98383 | Python | 4,218 | 91 | # 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... |
149bdaea7ae623923a42830c111cc385e7b41f81a25d0846294f36dbbc051166 | Python | 4,219 | 130 | import numpy as np
import torch
import torch.nn as nn
class Anchors(nn.Module):
def __init__(self, pyramid_levels=None, strides=None, sizes=None, ratios=None, scales=None):
super(Anchors, self).__init__()
if pyramid_levels is None:
self.pyramid_levels = [3, 4, 5, 6, 7]
if stri... |
74843e9395b3ce4d4eb8432298c3ff0efbf08235ec97e94b53a9446970089e03 | Python | 4,223 | 143 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
import unittest
import glob
import os
import copy
import torch
from maskrcnn_benchmark.modeling.detector import build_detection_model
from maskrcnn_benchmark.structures.image_list import to_image_list
import utils
CONFIG_FILES = [
# bbox
... |
bd770e3ba3ebf5907331ef77f3dd8e2d7cddf63db0f5bbd42b7eeda493b6e31a | Python | 4,223 | 94 | # -*- coding: utf-8 -*-
import numpy as np
from . import mi
from . import utils
from ._base import _EmbeddingCausality, _DirectCausality
class CrossMappingEntropy(_EmbeddingCausality):
def fit(self, data, mi_kwargs=None):
assert data.shape[1] > 1, 'data must have more than 1 column (variable).'
s... |
f07f0e4d648b5dfac212c0f71329c307813c45564dc8228c28583e5dc1524129 | Python | 4,228 | 89 | import os
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
import seaborn as sns
def main():
theme = 'dark'
matplotlib.rcParams['axes.edgecolor'] = '#ff0000'
sns.axes_style("darkgrid")
N = 2999
n_clusters = 14
fixation_end = 1100
s_dm = np.load('s_dm.npy')
s_go = ... |
8a4a274d340125f4ecc7148c59007703165cf3435b9c6d425f49a19ea3fa9f2c | Python | 4,230 | 94 | # 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... |
93151087b88a6915cc4f77840e3f98bf55a097f67934d58bf949d018242c71a0 | Python | 4,230 | 119 | # 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... |
d62bd5134bb5fea0a478ff3728c34686f4f257543bb5d4c37d75d827a28945d2 | Python | 4,231 | 102 | ####################################################################################################
# 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 ... |
78771944ca09aeebada0732acfd7e382138857ae840092064f86ea6e3281a358 | Python | 4,232 | 112 | import numpy as np
from ..simulation.traj_tools import *
from torch_geometric.data import Data
import torch
import numpy as np
from .data_tools import *
EMPTY_FIELD_VALUE = np.nan
class SkeletonTrajData(Data):
def __init__(
self,
raw_positions,
time,
graph_info={},
traj_i... |
8a3cb95a46e673cc6fa449818ff3e63fb79f865569772f663ef4f990b388b587 | Python | 4,233 | 108 | # 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... |
f39702373f5950b61178d6b38d9d6bbf8d7b0f7451e3c8197f649bf22a1d6bb4 | Python | 4,233 | 104 | # 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... |
0cc48381ee8c12f44cbbb17cd851ccfc38539cbc9434b87942298fff01053656 | Python | 4,234 | 141 | import torch.nn as nn
import math
def conv3x3(in_planes, out_planes, stride=1):
"""
3x3 convolution with padding
"""
return nn.Conv2d(in_planes, out_planes, kernel_size=3, stride=stride,
padding=1, bias=False)
class BasicBlock(nn.Module):
expansion = 1
def __init__(... |
4a9178006a10294ab24be4e6e5e5826ab8a2a19046a59c6e94e78bc9f8f269cb | Python | 4,235 | 146 |
if __name__ == '__main__':
# ------------------
# Libraries
# ------------------
# Generic libraries
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
# Basic functions in sklearn
from sklearn import datasets
from sklearn import metrics
from sklear... |
9043e7b7b8b585f635df5a88ff2ee0aa88b4cf889183b95d647f11053b81fd9e | Python | 4,235 | 139 | __author__ = "Jianfeng Sun"
__version__ = "v1.0"
__copyright__ = "Copyright 2023"
__license__ = "GPL v3.0"
__email__ = "jianfeng.sunmt@gmail.com"
__maintainer__ = "Jianfeng Sun"
import pandas as pd
from tmkit.util.Reader import Reader as greader
from tmkit.util.Writer import Writer as gwriter
class Reader:
def ... |
ecdaa1b9e58a66148db7a9856913cf84b60d6ef33e51b4d25e2082afb47c158c | Python | 4,235 | 131 | #%%
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
import connectome_tools.cluster_analysis as clust
import connectome_tools.celltype as ct
import connectome_tools.process_matrix as pm
rm = pymaid.CatmaidIn... |
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