sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
98a5a00f178636866b2e59a905a994f76c7a0015ad1d2101009ffbfa75c77f94 | Python | 10,804 | 216 | # This code contains minor adjustments to the original code that is available on https://github.com/mircare/Porter5/blob/master/Porter5.py
import argparse, configparser
import os, sys
import time
## check Python version
if sys.version_info[0] < 3:
print("Python2 detected, please use Python3.")
exit()
### se... |
085743df2746758a7ac0682279dc8906a5f0ab2fa695d138f152aae40f17d2ca | Python | 10,806 | 252 | # 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... |
6d652569182a6fbe35d73477ada0898d9046a8adbd395adf15a3d26c004d93b2 | Python | 10,808 | 283 | #!/usr/bin/env python3
"""
File: plot_pca.py
Created: 2021/06/30
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 Foundation, e... |
d23c230084625833f50cf4ec3f7fe03f208a7ee4d370fa368f8fcb1689554db8 | Python | 10,808 | 177 | '''
behavioral classification for hourly time resampling
I know these loitering distances (5 km) may not be the best - will change in future versions!
successive loitering 5E+03 m: successive mean waypoints are within 5E3m and within the hour window the excursion (from the mean lat/lon) is also less than 5E3m
p... |
6216ac886935a32ef2012c12b2588c3cab101daa2b3c61b2b1057ba903494cc3 | Python | 10,821 | 340 | """pytest tests/test_forward.py."""
import copy
from os.path import dirname, exists, join
import numpy as np
import pytest
import torch
def _get_config_directory():
"""Find the predefined detector config directory."""
try:
# Assume we are running in the source mmdetection repo
repo_dpath = di... |
49fc11e9b51a7174f93cf1c95eac69e39d16845cc23c90674b4d580178c394da | Python | 10,826 | 287 | from typing import List, Tuple, Dict
from math import sqrt
import numpy as np
import torch
from torch import Tensor
import torch.nn as nn
from torch_geometric.nn import MessagePassing
from torch_geometric.utils import k_hop_subgraph as subgraph
from ._base import _BaseExplainer
class GNNPool(nn.Module):
def __i... |
bb1f1b24647be0038ac37d72d02545688d4e6b66818561ac6e102e0fe60285a1 | Python | 10,827 | 290 | import os
import sys
import torch
import argparse
import torch.nn as nn
import torchvision.transforms as transforms
import torchvision.datasets as datasets
import cv2
import numpy as np
import PIL
from PIL import Image
import time
import logging
import argparse
from detnasnet import ShuffleNetV2DetNAS
from utils import... |
f888382603e7d454bf10990dd7e43d63b450a606b5cb2c326873fbcb8805db64 | Python | 10,827 | 282 | """
Unit testing second order matrix vector product.
"""
from __future__ import (division, print_function, unicode_literals)
import numpy as np
import tensorflow as tf
from tensorflow_forward_ad import logger
from tensorflow_forward_ad.fwgrad import forward_gradients
from tensorflow_forward_ad.second_order import (
... |
58ea3ea36ca6927b83baaaac0644315bd5abbb07cf30bc68e500f2586fce9ae8 | Python | 10,830 | 300 | # import cProfile
import os
import time
from concurrent.futures import ProcessPoolExecutor, ThreadPoolExecutor, as_completed
import numpy as np
import pandas as pd
import pyBigWig
TARGET_LENGTH = 1
SAMPLE_FILES = True
N_PROCESSES = 23
N_THREADS = 16
N_CONCURRENT = 30000
DATA_FOLDER = (
"/mnt/datasets/DeepCT/datas... |
d9e94d73bf205a20f6ba254838f561c8483527af5e9a9fdb45c7ea86a6a87bbc | Python | 10,832 | 319 |
# This script is part of navis (http://www.github.com/schlegelp/navis).
# Copyright (C) 2017 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 o... |
69cb24a70dd41b41f071aa9110ce1033639f0af71a26deda9ba5f4081087db38 | Python | 10,835 | 294 | #%%
import sys
sys.path.append('/Users/mwinding/repos/maggot_models')
from pymaid_creds import url, name, password, token
import pymaid
import matplotlib.pyplot as plt
import seaborn as sns
import numpy as np
import pandas as pd
from src.data import load_metagraph
from src.visualization import CLASS_COLOR_DICT, adjp... |
75d48577ee902e60949e10c7c6ae8c676826eb061d4fef8e17643ce4b37fc34b | Python | 10,835 | 365 | #%% Imports and file loading
from pathlib import Path
import glob
import json
from os import listdir
from operator import itemgetter
import pandas as pd
import networkx as nx
import numpy as np
from graspy.plot import gridplot
from src.data import load_networkx
# File locations
base_path = Path("./maggot_models/data/... |
b58f2d06e96c4d82fbe4873e47509686ac699cc24863a0e99755506dfd95adbf | Python | 10,843 | 278 | # 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 numpy as np
import torch
from torch.autograd import Variable
from torch.nn import functional as F
from logging... |
ddd975a54d317aad2c6c54bff93ef9d049d9ddd409be28a20718083e1fb1b088 | Python | 10,843 | 218 | import os
import numpy as np
import pandas as pd
import scipy.stats as stats
import matplotlib.pyplot as plt
from lmfit import Model
from lmfit.models import LinearModel
def rss_fit(mod_y, data_y):
return np.sum(np.square(mod_y - data_y))
def chow_test(data_y1, data_y2, data_c, bestfit1, bestfit2, bestfit_c):
... |
7116a541fd381077082a322a932e8844fbec3ac59410cfb6e76d2690223975ac | Python | 10,847 | 268 | #######
# This code was written by Nino Verwei and Niek van Hilten at Leiden University, The Netherlands (23 August 2022)
# A convolutional neural network (CNN) is trained on MD data (data.txt) of helical peptide sequences with respective relative free energy values as a measure for lipid packing defect sensing
# Th... |
5fec9828c79b6675afc7285680e602419c944b258a43a35176f746bf5279452e | Python | 10,848 | 275 | """
File: main.py
Created: 2020/10/08
Last Changed: 2021/10/28
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, either version 3 ... |
a8f9bf225aa27ece4ab188a3e646cecbf298d3b8ab5ee42240e678fa6005c8ad | Python | 10,850 | 278 | #!/usr/bin/env python3
"""
File: compare_pvalues.py
Created: 2022/04/06
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 Founda... |
768ce55b7eb87a188606a523615702b47e5c6549540f8e5b847652e9e16ebeda | Python | 10,852 | 252 | import logging
import sys
import torch
from mmdet.core import (bbox2roi, bbox_mapping, merge_aug_bboxes,
merge_aug_masks, multiclass_nms)
logger = logging.getLogger(__name__)
if sys.version_info >= (3, 7):
from mmdet.utils.contextmanagers import completed
class BBoxTestMixin(object):
... |
e7eb5af176f2f461a9e2d4a3be8243f9f23cf83a68c57c61dd9c4cfed026f53a | Python | 10,854 | 388 | """
Utility functions for scHumanNet analysis.
This module contains helper functions for loading data, network operations,
and other utilities.
"""
import numpy as np
import pandas as pd
import networkx as nx
from typing import Dict, List, Optional, Tuple, Union
import pickle
import os
def load_humannet_v3(data_pat... |
fff2acbf5aac6460b88cba4df4f884bad357dbc81157dc6e217696a6f4b1eae7 | Python | 10,858 | 252 | #!/usr/bin/python
####################################################################################################
# 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>
#
# Thi... |
69986072c1fece27b5b03cc68f722d07af4d86188886e414dce42a83e59da4f7 | Python | 10,860 | 274 | import tensorflow as tf
import numpy as np
import h5py
class PatchHandler3D():
# constructor
def __init__(self, data_dir, patch_size, res_increase, batch_size, mask_threshold=0.6):
self.patch_size = patch_size
self.res_increase = res_increase
self.batch_size = batch_size
self.ma... |
d22cc412ed80be56fbf028798330c951bfc09a2dc44ca8cc16e16c49a0c4b648 | Python | 10,860 | 298 | import tempfile
import torch
import torch.nn as nn
from torch import optim
from torch.nn.init import kaiming_normal_
from tqdm.auto import tqdm
from drugex import DEFAULT_DEVICE, DEFAULT_GPUS
from drugex.data.fragments import SequenceFragmentEncoder, FragmentCorpusEncoder
from drugex.data.datasets import SmilesFragD... |
9fb1bc7572fee43b1459b9d8bd4f417afc06a7acf638ad3a62b498a8522a5fcc | Python | 10,863 | 310 | ## System
import os
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3' # no debugging from TF
os.environ['TF_CPP_MIN_VLOG_LEVEL'] = '3'
import time
import copy
## sklearn
from sklearn.decomposition import PCA
from sklearn.manifold import TSNE
## Maths
import math
import numpy as np
import pandas as pd
impo... |
126fc4d930c8adfc5ea6c96df4c4a6575377e56acb34cbac42b86cc45f28252a | Python | 10,864 | 199 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'picachooserTemplate.ui'
#
# Created by: PyQt5 UI code generator 5.15.7
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
from PyQt5 import ... |
65177ce9b2d96fdc1aa08c75f0f1710a58e65a8b9cdf95c61be29a830ab81ddd | Python | 10,864 | 277 | # 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... |
f5c9b7982f2ea9fc33b86c53e4237d4224327d9264f8b7752efd966e9f63f5e8 | Python | 10,864 | 258 | import pandas as pd
import boto3
from shapely.geometry import shape, Point, MultiLineString, LineString
import json
EU_COUNTRIES = ["Austria", "Belgium", "Bulgaria", "Croatia", "Cyprus", "Czech Republic", "Denmark", "Estonia",
"Finland", "France", "Germany", "Greece", "Hungary", "Ireland", "Italy... |
860bd0362cac08c15a861dcb50985b358d7e742b3ec9b94b057519390092c03a | Python | 10,872 | 375 | # %% [markdown]
# ##
import os
import time
from pathlib import Path
import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import pymaid
import seaborn as sns
from src.graph import MetaGraph
from src.io import savecsv, savefig
from src.pymaid import start_instance
from src.vi... |
92a00307f4b679cf48094c8e43c0b822300277d8eb68cc6bf3c0f8bb63ff072f | Python | 10,882 | 244 | """
Copyright Dejan Kostyszyn 2019
This method trains the network.
"""
import ReadData as rd
import numpy as np
from matplotlib import colors
import torch, os, nrrd, time
from model.UNet import UNet
import matplotlib.pyplot as plt
from options.train_options import TrainOptions
import utils, csv, sys
from os.path impo... |
76c79f165519d27f9ef58e304aa2a07103112127e7a5791bc099f225bdf682c7 | Python | 10,886 | 281 | import torch
import torch.nn as nn
from .resnet_updated import conv3x3
from .resnet_updated import resnetbank50all as resnetbank50
from .globalNet import globalNet
import math
class BasicBlock(nn.Module):
expansion = 1
def __init__(self, inplanes, planes, stride=1, upsample=None, norm_layer=None):
... |
bcec95021243068be456e1bc4c74cd3d5e13c613b6381f7d4eb8216e475c5642 | Python | 10,886 | 258 | from modules.parameters import ParameterSet, ParameterSpace, extract_nestvalid_dict
from modules.input_architect import EncodingLayer, InputNoise
from modules.net_architect import Network
from modules.io import set_storage_locations
from modules.signals import iterate_obj_list
from modules.analysis import characterize_... |
8d754d67271db2a2b53dd63f3def9cae87585bfce6672028d7eb2a2d567b3a6e | Python | 10,890 | 324 | #!/usr/bin/env python3
"""
Phys2bids is a python3 library meant to set physiological files in BIDS
standard.
It was born for Acqknowledge files (BIOPAC), and at the moment it supports
``.acq`` files and ``.txt`` files obtained by labchart (ADInstruments).
It requires python 3.6 or above, as well as the modules:
- `n... |
926265f9ea940a26c3627b59170d05bfdab594a933550a453f5f25fe5666ae1d | Python | 10,895 | 272 | # 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... |
33d25ffe1d81dd46a98b52468fb6d340b1540d162c1bc802873dab43c46547e4 | Python | 10,896 | 224 | import streamlit as st
import pandas as pad
import numpy as np
from joblib import dump, load
from PIL import Image
import sklearn
import tensorflow as tf
from tensorflow import keras
import time
## TO DO #######
## PCA and TSNE representation ##
def main():
""" fonction principale de prédiction d... |
aed835b95eeaa77f97469ec510aa187ba8752424978e0f5c014f504faf0bcbc3 | Python | 10,897 | 294 | #!/usr/bin/env python3
"""
File: plot_cell_fraction_vs_IHC.py
Created: 2022/01/25
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 Softw... |
54355dd7347c8f820f3b8355fa8f3898f3867f0db5cb6892eab33b0c39f6355d | Python | 10,898 | 246 | import os
import errno
import shutil
import numpy as np
from scipy.interpolate import griddata, Rbf, LinearNDInterpolator, NearestNDInterpolator
from skimage.measure import regionprops
from ddmr.layers.b_splines import interpolate_spline
from ddmr.utils.thin_plate_splines import ThinPlateSplines
from tensorflow import ... |
3248a141b038c3db771c2bea32cfea27e34341a370d50bc8d08f372221d8e3f7 | Python | 10,903 | 355 | #%% [markdown]
## Maggot embedding alignment
# > Investigating alignments of the maggot data embeddings
#
# - toc: false
# - badges: false
# - categories: [pedigo, graspologic, maggot]
# - hide: false
# - search_exclude: false
# %%
# collapse
import os
import time
import matplotlib.pyplot as plt
import numpy as np
imp... |
e43d53c080fb41492f940efa5b007118c8ec24ad93d98cd57fb8113dfe54a3ab | Python | 10,906 | 265 | """Base class and socket server for workers.
Subclass :class:`Worker`, implement :meth:`Worker.load`, :meth:`Worker.run`
and optionally :meth:`Worker.smoke`, then call :func:`serve` from the
worker's ``__main__``. ``run`` executes in a thread so a blocking inference
loop does not stall the socket; it must poll ``ctx.... |
eb713934ad8b7fb801699ffbcdb38d7ac6d35ee3fdd9144651b298ff7c6eedc0 | Python | 10,914 | 397 | # %% [markdown]
# #
import os
from itertools import chain
import colorcet as cc
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
import pandas as pd
import seaborn as sns
from graspy.cluster import AutoGMMCluster
from graspy.utils import pass_to_ranks
from src.data import load_metagraph
from s... |
4f213064f02c8a34ab4db241fb7fc9d850331f084a9f01d449e2f22de4a284ce | Python | 10,918 | 257 | import shutil
from unittest import TestCase
import os
from os.path import exists
import pandas as pd
import numpy as np
import torch
from torch.utils.data import DataLoader, TensorDataset
from drugex.environment.neural_network import STFullyConnected
from drugex.environment.data import QSARDataset
from drugex.enviro... |
2c9af974bb62f0d6828c44dc1d37d4f62af6b0552e54f129387d69d87d010ee9 | Python | 10,919 | 295 | #!/usr/bin/env python3
#
# 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 u... |
0f9f9333b2530bf317190f5c6b467d2cd1b994b41f9a607d15ab8e673549cc80 | Python | 10,924 | 306 | import torch
import torch.nn.functional as F
from torch import nn, cuda
from torch.autograd import Variable
from torch.nn.modules.batchnorm import _BatchNorm
from torch.nn.parameter import Parameter
class Conv(nn.Module):
def __init__(self, in_ch, out_ch, K=3, S=1, P=1, D=1, activation=nn.ReLU(inplace=True)):
... |
ed19b7e3e803b2dd72de215baa00eb0c891bac7c8c1757ab118f61debb076cd2 | Python | 10,924 | 444 | # %% [markdown]
# ##
import os
import time
import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np
import scipy
import seaborn as sns
from graspy.match import GraphMatch
from graspy.plot import heatmap
from graspy.simulations import sbm
from src.data import load_metagraph
from src.graph import pre... |
a1b5341a0db3d203b6d4857c213f8cd08b1b4281c793b8a45b427c6a9f16a73c | Python | 10,931 | 256 | # 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... |
9e0d26bd5bfa7665b4ee80e675d44fd70ef04bce6303132c03d49fd9ee1bd505 | Python | 10,942 | 175 | #!/usr/bin/env python3
"""
File: check_preprocessing_step.py
Created: 2021/07/08
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 Softwa... |
a3c080b9ba37c3574e22d0b43f6331baa04800a9918d8eb4654265c608f0b61f | Python | 10,942 | 270 | import csv
import os
import sys
from sklearn.cluster import KMeans
import numpy as np
# Court to circuit mapping, which maps from SCDB codebook to the actual Circuit number
# http://scdb.wustl.edu/documentation.php?var=caseOrigin
# http://scdb.wustl.edu/documentation.php?var=caseSource
court_circuit_map = {1: 13,
... |
648f52e496292d87e7e4d20a35aeb03de37bde4b8446086d2c2507242173dced | Python | 10,946 | 327 | """Cancellable implementation of the released RootDetector matcher.
The released tracking package owns descriptor extraction, while this module
owns the deterministic point-matching loop. Version 1 intentionally preserves
the released 2022 algorithm and constants, adding only progress and
cancellation checkpoints.
"""... |
05e051ff515e51cfd28f6811e195ee4a32cfd17213e770d8e647244c0b6b4512 | Python | 10,947 | 311 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
import math
import numpy as np
import torch
from torch import nn
from maskrcnn_benchmark.structures.bounding_box import BoxList
class BufferList(nn.Module):
"""
Similar to nn.ParameterList, but for buffers
"""
def __init__(self... |
e54e6af18a681ea42f9cb8491822b7eb1ff07ce896fe4d731c039f9142fd4406 | Python | 10,947 | 294 | #!/usr/bin/env python
# Copyright (C) 2011 Genome Research Limited -- See full notice at end
# of module.
# Smith-Waterman aligner with fixed gap penalty. NOTE: This is not
# going to be fast! It's intended for small jobs like finding
# adapters. We need a C version for the heavy lifting.
# To use, create the aligne... |
37419b3fb9dadd61aea8d922aaf9cf8e8dcf6992453cb32c3933eb0eb12d3a24 | Python | 10,953 | 240 | # 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... |
75823ea2572237a14d5dbe096ead51c4725e77de70fca214566e469326092877 | Python | 10,956 | 290 | import os, shutil
import unittest
import numpy as np
import numpy.testing as nptest
import FBEM
import mesh
import mesh.shapes as shapes
from angle_area import is_angle_satisfied, is_area_satisfied
basic_test_folder = 'data/triangulation/test/'
basic_expected_folder = 'data/triangulation/expected/'
rtol = 10 ** - 8
a... |
faa158859709f84f18e0df494c18ed52a387f39159de5194374ac8244b3e54d6 | Python | 10,962 | 312 | ## System
import os
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3' # no debugging from TF
os.environ['TF_CPP_MIN_VLOG_LEVEL'] = '3'
import time
import copy
## sklearn
from sklearn.decomposition import PCA
from sklearn.manifold import TSNE
## Maths
import math
import numpy as np
import pandas as pd
impo... |
adae71300c160a7a0369b4c1540cf6faa2fe379331294e25cee08d7846adf499 | Python | 10,964 | 305 | from abc import ABCMeta
import torch
import torch.nn as nn
from ..utils import constant_init, normal_init
from .conv_module import ConvModule
from .registry import PLUGIN_LAYERS
class _NonLocalNd(nn.Module, metaclass=ABCMeta):
"""Basic Non-local module.
This module is proposed in
"Non-local Neural Netw... |
2f973dede6d2fb56648ac42a363a5a7df5690629583a1e8785858ad9e324bcb5 | Python | 10,966 | 286 | """Patient/case-level train / validation / test splitting for CROPro.
Splitting is always done at the **patient** level (one unit = one patient)
so that all crops from the same patient end up in the same subset. This
prevents data leakage between training, validation, and test sets.
``split_level`` (on :class:`Split... |
8f323682451029a1240d3bd7ab4f91739dc21b5674031ef39a03aa1b63548230 | Python | 10,967 | 265 | import torch
import torch.nn.functional as F
from mmdet.core import bbox_overlaps
from ..builder import HEADS
from .retina_head import RetinaHead
@HEADS.register_module()
class FreeAnchorRetinaHead(RetinaHead):
"""FreeAnchor RetinaHead used in https://arxiv.org/abs/1909.02466.
Args:
num_classes (int... |
7f6f8cf9775d43fe63bc1490e3c7e7bda7da233eea5af9319f3cdbb6387bacf7 | Python | 10,969 | 289 | """
Visualzie using `vedo` (a.k.a. `vtkplotter`) package
- I don't define my own MeshViewer class, because vedo.Mesh class is already very functional
# In jupyter:
# vedo.embedWindow(False)
#embedWindow('2d') # for a static image
"""
import vedo
import FBEM
import numpy as np
def get_colors(num, cmap, endpoint=Tru... |
03276ff0f6f200317d713e1cc77e1fb65a2b0f1e0a8648c0017fa18daa19f0f9 | Python | 10,986 | 325 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Sep 8 16:13:47 2021
@author: Hiroshi 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.chdi... |
91d9e7b9c37db9e31be467373171a79ff888aa815a1f3dbf170717ce423a9084 | Python | 10,989 | 280 | from __future__ import print_function
import numpy as np
import os
import matplotlib.pyplot as plt
import torch
def compute_overlap(a, b):
"""
Parameters
----------
a: (N, 4) ndarray of float
b: (K, 4) ndarray of float
Returns
-------
overlaps: (N, K) ndarray of overlap between boxes... |
b83aaf22e45aa4c48d0df680bb5a15430600ca065249ff33f9ef3d826462a662 | Python | 10,991 | 262 | # Copyright (c) 2021, NVIDIA CORPORATION. All rights reserved.
#
# NVIDIA CORPORATION and its licensors retain all intellectual property
# and proprietary rights in and to this software, related documentation
# and any modifications thereto. Any use, reproduction, disclosure or
# distribution of this software and rel... |
1cbfef645239e2de5cc77fab5b4cac13d417e535d34b1133660a8e602ed93357 | Python | 10,994 | 266 | import torch
import torch.nn as nn
import torch.nn.functional as F
from mmcv.cnn import xavier_init
from mmdet.core import (build_anchor_generator, build_assigner,
build_bbox_coder, build_sampler, multi_apply)
from ..builder import HEADS
from ..losses import smooth_l1_loss
from .anchor_head imp... |
49503d90e733fedd8f3211371d09b1e70e442e580b76138d465fe867f894ecc3 | Python | 11,002 | 248 | import math
import time
import unittest
import numpy as np
from oaklib import get_adapter
from oaklib.datamodels.vocabulary import IS_A, PART_OF
from oaklib.interfaces.embedding_provider_interface import (
CLOSURE_IC_MODEL,
CLOSURE_MODEL,
EmbeddingProviderInterface,
)
from oaklib.utilities.embeddings.clos... |
b017bdf63e9d78d1ce6935901c33f26e7bd93441601eb217831a8712ccb391fa | Python | 11,010 | 204 | #%%
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
from pymaid_creds import url, na... |
75b24919a01cd5dc8e0ae23dcde7392727cf4225653f93542fd56b058ecd98a9 | Python | 11,015 | 287 | import ee
import geemap
from multiprocessing.dummy import Pool as ThreadPool
from tqdm import tqdm
from datetime import datetime
from functools import partial
import json
import os
import numpy as np
import pandas as pd
ee.Initialize()
# Sentinel 2 band descriptions
band_descriptions = {
'B1': 'Aerosols, 442nm',
... |
1b90fcca7cacdbf465bfcecaa11e41ddac48c79728ffedf06df4369e304de8cf | Python | 11,024 | 189 | import os, sys
import shutil
import h5py
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)
... |
4807f917894519f6bc473447686b7acceb3f78c1e78ffe71dd49a89ffa2bf5f9 | Python | 11,025 | 284 | import pytest
from typing import List, Tuple, Union, Optional
from simphox.typing import Shape, Size, Size2, Size3
from simphox.utils import TEST_ZERO, TEST_ONE, Box
from simphox.grid import Grid, YeeGrid
import numpy as np
@pytest.mark.parametrize(
"size, spacing, eps, expected_cell_sizes",
[
((2.5... |
b18b7073fb2175dd91e6aee8285c74bc14654884f07b8452dcc4410db96d4287 | Python | 11,027 | 222 | # 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... |
5d1bf005d9679faf7c3efe5e269d7b92682bf2ab8f5a911f5c92ddaff3f29e9b | Python | 11,030 | 301 | """Contains the SensorServiceDriver class definition.
SensorServiceDriver is an abstract class used by the SensorServiceItemModel to interact with different classes of
sensing devices.
Typical usage example:
class MyCustomDriver(SensorServiceDriver):
...
"""
import enum
from typing import Any... |
5a707c5e556b8eea013c4051ada7b1902fdcb49c48b7515c8f1f88abb96084bb | Python | 11,034 | 212 | # 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.misc.gridworld_tools import make_gridworld
# change directory
cwd = os.getcwd()
# shall the system provide v... |
d1bca822d8380595f3e966a0cbf6e40f36bfe0bd90b9e2e26d97380b7b2c804d | Python | 11,039 | 280 | ####################################################################################################
# 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 ... |
b1933a21c4d0d38b5be1b994848d34df1f6a8a3b8804738975e1dd2aea8b4a2a | Python | 11,045 | 380 | # Import Python SINGLE implementation
from OLM import OLM_Single
# Import hoc interpreter (for SINGLE and FULL)
from neuron import h
import numpy as np
# Import FULL model recording functions
from multicompartment.record import record_V_cai_ica_dend,\
record_V_and_Cai, record_soma
# Import SINGLE model recording fu... |
1ece593dcacacb6d5336cf912fb23b1ab7ec9d9ee30cdd39948bcfacff4871ec | Python | 11,079 | 291 | import random
import tqdm
from torch import nn
import torch
import torch.optim as optim
import copy
import numpy as np
import rulenn.feature_config as fc
from base import BaseModel
import math
import os
import json
class RuleNet(nn.Module):
def __init__(
self, num_variables, num_conjunctions, names, conf... |
c51c278d04fbb6223a5607cd84e224d395cc0436e0948196ce98daf589ea366d | Python | 11,080 | 303 | import functools
from collections import OrderedDict, abc
from inspect import getfullargspec
import numpy as np
import torch
import torch.distributed as dist
import torch.nn as nn
from torch._utils import (_flatten_dense_tensors, _take_tensors,
_unflatten_dense_tensors)
def cast_tensor_type... |
4ff999b7a2398529c1fecf614544392d77a7dfd02639dd8efc64cb634f0e78b7 | Python | 11,081 | 402 | #!/usr/bin/env python
"""
quot/read.py -- image file readers
"""
# ndarrays
import numpy as np
# File paths
import os
# Read config files in TOML format
import toml
# Underlying file readers for each file format
def read_config(path):
"""
Read a config file.
args
path : str
returns... |
9e9ca0f3c8586d6fcf3fe918550e8a46b13cfd3224c17da88f95da48d1503948 | Python | 11,081 | 261 | import torch
from mmcv.ops import nms_match
from ..builder import BBOX_SAMPLERS
from ..transforms import bbox2roi
from .base_sampler import BaseSampler
from .sampling_result import SamplingResult
@BBOX_SAMPLERS.register_module()
class ScoreHLRSampler(BaseSampler):
r"""Importance-based Sample Reweighting (ISR_N),... |
db8fbf6426dc2b9cbf00d6dbc3420657782434b752b40c1dde2b25a57ab81e11 | Python | 11,083 | 342 | __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, Union
import numpy as np
import pandas as pd
from sklearn import metrics
from tmkit.contact.Reader import Re... |
41f38abb8f66da6ab6ad90b72fcd68a346fe656e06a5b49194aa751a1f51af8a | Python | 11,085 | 334 | #!/usr/bin/env python
#title :Utils_model.py
#description :Have functions to get optimizer and loss
#author :Deepak Birla
#date :2018/10/30
#usage :imported in other files
#python_version :3.5.4
#Modified by Zifei Liang. 2022/06/06
from keras.layers import Lambda
import ten... |
96653c2d7864a30c5752dc0dc455fa1d2ce206d7c846dd8bd1c7313852e38db0 | Python | 11,086 | 253 | # This file is part of me-features-to-mol-ID-mapping.
#
#
# Copyright © 2021-2022 Blue Brain Project/EPFL
#
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the APACHE-2 License.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANT... |
5e1bbaed9c5c79b9607a59d5e5d08cc152891eda08b795a7c71e1564e4d3d4e0 | Python | 11,090 | 298 | # 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... |
bcf42d1b064096ae0178c4dd2f59dfbb73ac112ad203693373a46118e849ed31 | Python | 11,094 | 315 | # -*- coding: utf-8 -*-
"""
Created on Tue Nov 7 15:10:06 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... |
a2a20ae102fdb30216593ab18462ecea4345c12ec01d4dce84b3d0e7c64f5e95 | Python | 11,097 | 289 | #!/usr/bin/env python3
"""
File: dim_reduction_plot_visualise.py
Created: 2020/12/04
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 S... |
70cea4c5dbd0a96fd77e846fd58149dd7f73eb9895cfbc405ec82e4cafe4b939 | Python | 11,100 | 280 | """
Plot main sound localization figures
For each subject, show:
- Bilateral cooling results as:
- Bubble plots of response counts (normalized for total trial count) for each stimulus and response location, for control and bilateral cooling
- Bar charts of performance (% correct) during contr... |
44da20d469fb7a7f14bcb20f5ddf8ef19452bbc557900d05c7a218df797e2522 | Python | 11,102 | 305 | #!/usr/bin/env python
# coding: utf-8
import math
import numpy as np
from scipy import stats
from scipy.stats import zscore, pearsonr, mannwhitneyu
from random import sample
import matplotlib.pyplot as plt
from common_functions import *
from plotting_functions import *
filename = input("Enter file name containing th... |
090392406c4bb82d6de1fb372fd05a7c2c7a1f263f22c03cf2504dfd7e9ae86b | Python | 11,103 | 285 | #!/usr/bin/env python3
#
# 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 u... |
a778b71ee4b23ea1596b5b9a53da2f25c6252453b360ec984741a39ea33fd10c | Python | 11,103 | 246 | import torch
from torch import nn
import math
from torch.nn.init import xavier_uniform_, zeros_
class AttentionKernelIntegral(torch.nn.Module):
"""Kernel integral transform with attention
Computes \\int_{Omega} k(x, y) * f(y) dy,
where:
K(x, y) = \\sum_{c=1}^d q_c(x) * k_c(y), q(x) = [q_1(x... |
61ee85b4b6a280191b43e94bd3f6c219972f71482bbecc4e16afd08fd93426c4 | Python | 11,109 | 283 | import numpy as np
import time
import os
import matplotlib
import argparse
import csv
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
import torch.backends.cudnn as cudnn
import nibabel as nib
import matplotlib.pyplot as plt
from skimage.metrics import structural_similari... |
110b1d82799bbbe047178cb2f04ca134ff8d89f7d657053ab8d9466381b44f9f | Python | 11,110 | 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... |
a2e040bbb900e229fd7faeb5e2e150ea03eec96070274197fafdf722b0141417 | Python | 11,114 | 289 | """
Lexical Utilities
-----------------
Various utilities for working with lexical aspects of ontologies plus mappings
"""
import logging
import re
from collections import defaultdict
from typing import List, Dict, Optional, Tuple
from linkml_runtime.dumpers import yaml_dumper
from linkml_runtime.loaders import yaml... |
2d6b6e765cb3902d381418caacf4b88940b2238f489c177272ee3c5a1f979414 | Python | 11,118 | 265 | import logging
from dataclasses import dataclass
from typing import Dict, Iterable, Iterator, List, Optional
from oaklib import BasicOntologyInterface
from oaklib.datamodels.obograph import LogicalDefinitionAxiom
from oaklib.datamodels.ontology_metadata import OMOSCHEMA, DefinitionConstraintComponent
from oaklib.datam... |
d8785edc165529d902e3dddc92758fbeb3a7ce913f7ec8361cdf108a1e3e6a43 | Python | 11,118 | 254 | #! /usr/bin/env python3
"""Build the comparison videos for a :mod:`showcase` run.
Reads ``<results>/showcase.json`` (written by ``demos/showcase.py``) and, for
every row that finished, produces
* ``sheet_<row>.mp4`` — ``input | control(s) | output`` side by side, one tile
per stream, each tile labelled;
* ``grid_<r... |
d039e26f29f3cf0202f4a5df5f22adb743a516059be69d3f9fd32b6c68dd6fb7 | Python | 11,119 | 363 | ###############################################################################
# Author: Bernard Hernandez
# Filename:
# Date:
# Description:
#
###############################################################################
# Import scikits preprocessing
from sklearn.preprocessing import MinMaxScaler
from sklearn.pr... |
a1d815d06488875a760c2486f8fbaf56c9eae276e657876b4b83024d0f1b2e2f | Python | 11,124 | 291 | # 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>.
"""Smoke tests for the Traffic Manager control loop: pull-away and cornering
comfort (synchronous, f... |
68c112f8a6c8a97e15e71514bb69f8c093488c3b11ed859528e5d38c1d4acda6 | Python | 11,125 | 308 | """
Written by Nathan Neeteson
Segment images using a trained U-Net and optionally, compare to reference segmentations.
"""
import numpy as np
import torch
from torchvision.transforms import Compose
from torch.utils.data import DataLoader
from models.UNet import UNet
from dataset.SamplePadder import SamplePadder
from... |
a64a33eca4610173f9d95b621440efa6db9c4f0064b615d7ec0bacda0a632a69 | Python | 11,125 | 287 | from argparse import ArgumentParser
import descarteslabs as dl
import json
import numpy as np
import os
from tqdm import tqdm
def deploy_tpa_nn(dlkey, product_id, model_name):
from datetime import datetime
from dateutil.relativedelta import relativedelta
import descarteslabs as dl
import numpy as np
... |
b66a53c395538d4e6c1a69e3c958671e28c87e81aaf40364f94f2991c731ab99 | Python | 11,125 | 349 | # -*- coding: utf-8 -*-
#
# palmari documentation build configuration file, created by
# sphinx-quickstart on Thu Oct 1 00:43:18 2015.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# A... |
326ef4585bf459be07f593d41acff237622e769cf1a373d9bed4f69653d37dc0 | Python | 11,127 | 293 | #!/usr/bin/env python3
"""Export live CARLA traffic-light states keyed by Lanelet2 relation ID.
This process is deliberately a non-ticking CARLA client. It matches each live
traffic-light actor to the generated map's regulatory element by stop-line
center, then atomically writes a small JSON snapshot for the ROS-side ... |
d64ef3591ad89c5abf2976603ca37f4cf1299dbef724ed268d7069baf1c68bee | Python | 11,127 | 300 | import random
import numpy as np
import networkx as nx
from functools import partial
from typing import Optional, Callable, Union
from .shapes import house
from graphxai.utils import khop_subgraph_nx
import matplotlib.pyplot as plt
from graphxai.gnn_models.node_classification.testing import *
def incr_on_unique_house... |
a6e711c41e1c0b007fab5c915795da63f43e3b57c48bbc2d63cccfee7096f499 | Python | 11,128 | 290 | #!/usr/bin/env python3
"""
File: create_decon_upsetplot.py
Created: 2020/11/24
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... |
3157aaa3fb1d39fcbbee05ee357c9aa89a7ea92b079adb360ea7d7bb2ada6107 | Python | 11,131 | 251 | """
File: deconvolution_covariate_comparison.py
Created: 2020/04/15
Last Changed: 2020/06/19
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 ... |
ba0122362b70a44decab014169c35280af2f7b8c19d3659195476c38e928210e | Python | 11,131 | 270 | # 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... |
4b3d6fb0433c97e4eda0833a9f5dda92e024e89e96377a5e159b6f81d25b82a7 | Python | 11,136 | 334 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
For creating simple keras model that takes in a "large" image and
produces a mask from that image.
Saves the result as the original image + mask
.
Input -> (t, c, z, y, x)
Output -> (t, c + 1, z, y, x) with 3 labels mask->not-mask->not-... |
82420c958c00397e2de5ad2f616b33aaf7a25e8af3748f38daf37ab7a614950b | Python | 11,140 | 247 | # 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... |
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